U.S. patent application number 17/344566 was filed with the patent office on 2022-05-12 for compounds that participate in cooperative binding and uses thereof.
The applicant listed for this patent is Revolution Medicines, Inc.. Invention is credited to Neville John ANTHONY, Brian Roger BOWMAN, M. James NICHOLS, Mathew Edward SOWA, Dylan Talbot STILES, Sharon Ann TOWNSON, Gregory Lawrence VERDINE.
Application Number | 20220143202 17/344566 |
Document ID | / |
Family ID | 1000006096194 |
Filed Date | 2022-05-12 |
United States Patent
Application |
20220143202 |
Kind Code |
A1 |
VERDINE; Gregory Lawrence ;
et al. |
May 12, 2022 |
COMPOUNDS THAT PARTICIPATE IN COOPERATIVE BINDING AND USES
THEREOF
Abstract
The invention features compounds (e.g., macrocyclic compounds)
capable of modulating biological processes, for example through
binding to a presenter protein (e.g., a member of the FKBP family,
a member of the cyclophilin family, or PIN1) and a target protein
(e.g., a eukaryotic target protein such as a mammalian target
protein or a fungal target protein or a prokaryotic target protein
such as a bacterial target protein). These compounds bind
endogenous intracellular presenter proteins, such as the FKBPs or
cyclophilins, and the resulting binary complexes selectively bind
and modulate the activity of intracellular target proteins.
Formation of a tripartite complex among the presenter protein, the
compound, and the target protein is driven by both protein-compound
and protein-protein interactions, and both are required for
modulation of the targeted protein's activity. In some embodiments,
the compounds of the invention "re-program" the binding of the
presenter proteins to protein targets that either do not normally
bind to the presenter protein (e.g., do not show detectable binding
in mammalian cells absent the compound). In some embodiments,
provided compounds "re-program" presenter protein binding to
greatly enhance interaction with a particular target with which it
may have some interaction absent the compound. Interactions
achieved through such reprogramming result in an ability to
modulate the activity of these new targets.
Inventors: |
VERDINE; Gregory Lawrence;
(Boston, MA) ; NICHOLS; M. James; (Charlestown,
MA) ; STILES; Dylan Talbot; (Chestnut Hill, MA)
; ANTHONY; Neville John; (Northborough, MA) ;
BOWMAN; Brian Roger; (New Rochelle, NY) ; SOWA;
Mathew Edward; (Watertown, MA) ; TOWNSON; Sharon
Ann; (Somerville, MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Revolution Medicines, Inc. |
Redwood City |
CA |
US |
|
|
Family ID: |
1000006096194 |
Appl. No.: |
17/344566 |
Filed: |
June 10, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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16036141 |
Jul 16, 2018 |
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17344566 |
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14991403 |
Jan 8, 2016 |
10039839 |
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16036141 |
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62101925 |
Jan 9, 2015 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07D 405/06 20130101;
C07K 7/56 20130101; C07D 498/18 20130101; C07K 7/64 20130101; A61K
47/54 20170801; A61K 47/64 20170801; C07K 7/645 20130101; C07D
498/22 20130101; A61K 38/00 20130101 |
International
Class: |
A61K 47/64 20060101
A61K047/64; C07D 498/18 20060101 C07D498/18; C07K 7/64 20060101
C07K007/64; C07K 7/56 20060101 C07K007/56; C07D 405/06 20060101
C07D405/06; C07D 498/22 20060101 C07D498/22; A61K 38/00 20060101
A61K038/00; A61K 47/54 20060101 A61K047/54 |
Claims
1. A macrocyclic compound, or a pharmaceutically acceptable salt
thereof, comprising 14 to 40 ring atoms, said compound comprising:
(a) a mammalian target protein interacting moiety; and (b) a
presenter protein binding moiety; wherein said compound and a
presenter protein form a complex that specifically binds to a
target protein, and each of said compound and said presenter
protein do not substantially bind to said target protein in the
absence of forming said complex; or said compound and a presenter
protein form a complex that binds to a target protein with at least
5-fold greater affinity than the affinity of each of said compound
and said presenter protein to said target protein in the absence of
forming said complex.
2. The compound of claim 1, or a pharmaceutically acceptable salt
thereof, wherein said presenter protein binding moiety comprises
the structure of Formula I: ##STR00041## wherein n is 0 or 1;
X.sup.1 and X.sup.3 are each independently O, S, CR.sup.3R.sup.4,
or NR.sup.5; X.sup.2 is O, S, or NR.sup.5; R.sup.1, R.sup.2,
R.sup.3, and R.sup.4 are each independently hydrogen, hydroxyl,
optionally substituted amino, halogen, thiol, optionally
substituted C.sub.1-C.sub.6 alkyl, optionally substituted
C.sub.2-C.sub.6 alkenyl, optionally substituted C.sub.2-C.sub.6
alkynyl, optionally substituted C.sub.1-C.sub.6 heteroalkyl,
optionally substituted C.sub.2-C.sub.6 heteroalkenyl, optionally
substituted C.sub.2-C.sub.6 heteroalkynyl, optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl, or any two of R.sup.1 R.sup.2,
R.sup.3, or R.sup.4 are taken together with the atom or atoms to
which they are bound to form an optionally substituted carbocyclyl,
optionally substituted heterocyclyl, optionally substituted aryl,
or optionally substituted heteroaryl; each R.sup.5 is,
independently, hydrogen, hydroxyl, optionally substituted
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.6
alkenyl, optionally substituted C.sub.2-C.sub.6 alkynyl, optionally
substituted C.sub.1-C.sub.6 heteroalkyl, optionally substituted
C.sub.2-C.sub.6 heteroalkenyl, optionally substituted
C.sub.2-C.sub.6 heteroalkynyl, optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl, or R.sup.5 and one of R.sup.1,
R.sup.2, R.sup.3, or R.sup.4 are taken together with the atom or
atoms to which they are bound to form an optionally substituted
heterocyclyl or optionally substituted heteroaryl.
3. The compound of claim 2, or a pharmaceutically acceptable salt
thereof, wherein said presenter protein binding moiety comprises
the structure of any one of Formulae II-IV: ##STR00042## wherein o,
and p are independently 0, 1, or 2; q is an integer between 0 and
7; r is an integer between 0 and 4; X.sup.4 and X.sup.5 are each,
independently, absent, CH.sub.2, O, S, SO, SO.sub.2, or NR.sup.11;
each R.sup.6 and R.sup.7 are independently hydrogen, hydroxyl,
optionally substituted amino, halogen, thiol, optionally
substituted C.sub.1-C.sub.6 alkyl, optionally substituted
C.sub.2-C.sub.6 alkenyl, optionally substituted C.sub.2-C.sub.6
alkynyl, optionally substituted C.sub.1-C.sub.6 heteroalkyl,
optionally substituted C.sub.2-C.sub.6 heteroalkenyl, optionally
substituted C.sub.2-C.sub.6 heteroalkynyl, optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, optionally substituted C.sub.2-C.sub.9 heterocyclyl
C.sub.1-C.sub.6 alkyl, or R.sup.6 and R.sup.7 combine with the
carbon atom to which they are bound to form C.dbd.O; each R.sup.8
is, independently, hydroxyl, optionally substituted amino, halogen,
thiol, optionally substituted C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.6 alkenyl, optionally substituted
C.sub.2-C.sub.6 alkynyl, optionally substituted C.sub.1-C.sub.6
heteroalkyl, optionally substituted C.sub.2-C.sub.6 heteroalkenyl,
optionally substituted C.sub.2-C.sub.6 heteroalkynyl, optionally
substituted C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl, or two R.sup.8 combine to form
an optionally substituted C.sub.3-C.sub.10 carbocyclyl, optionally
substituted C.sub.6-C.sub.10 aryl, or optionally substituted
C.sub.2-C.sub.9 heteroaryl; R.sup.9 is optionally substituted
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.6
alkenyl, optionally substituted C.sub.2-C.sub.6 alkynyl, optionally
substituted C.sub.1-C.sub.6 heteroalkyl, optionally substituted
C.sub.2-C.sub.6 heteroalkenyl, optionally substituted
C.sub.2-C.sub.6 heteroalkynyl, optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl; R.sup.10 is optionally
substituted C.sub.1-C.sub.6 alkyl; each R.sup.11 is, independently,
hydroxyl, cyano, optionally substituted amino, halogen, thiol,
optionally substituted C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.6 alkenyl, optionally substituted
C.sub.2-C.sub.6 alkynyl, optionally substituted C.sub.1-C.sub.6
heteroalkyl, optionally substituted C.sub.2-C.sub.6 heteroalkenyl,
optionally substituted C.sub.2-C.sub.6 heteroalkynyl, optionally
substituted C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl; and R.sup.12 and R.sup.13 are
each, independently, hydrogen, optionally substituted
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.6
alkenyl, optionally substituted C.sub.2-C.sub.6 alkynyl, optionally
substituted aryl, C.sub.3-C.sub.7 carbocyclyl, optionally
substituted C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, and
optionally substituted C.sub.3-C.sub.7 carbocyclyl C.sub.1-C.sub.6
alkyl.
4. The compound of claim 3, or a pharmaceutically acceptable salt
thereof, wherein said presenter protein binding moiety comprises
the structure of Formula V: ##STR00043## wherein R.sup.14 is
hydrogen, hydroxyl, optionally substituted C.sub.1-C.sub.6 alkyl,
optionally substituted C.sub.2-C.sub.6 alkenyl, optionally
substituted C.sub.2-C.sub.6 alkynyl, optionally substituted
C.sub.1-C.sub.6 heteroalkyl, optionally substituted C.sub.2-C.sub.6
heteroalkenyl, optionally substituted C.sub.2-C.sub.6
heteroalkynyl, optionally substituted C.sub.3-C.sub.10 carbocyclyl,
optionally substituted C.sub.6-C.sub.10 aryl, optionally
substituted C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.9 heteroaryl, optionally substituted
C.sub.2-C.sub.9 heteroaryl C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.9 heterocyclyl, optionally substituted
C.sub.2-C.sub.9 heterocyclyl C.sub.1-C.sub.6 alkyl.
5. The compound of claim 4, or a pharmaceutically acceptable salt
thereof, wherein said presenter protein binding moiety comprises
the structure of Formula VI or VII: ##STR00044## wherein s and t
are each, independently, an integer from 0 to 7; X.sup.6 and
X.sup.7 are each, independently, O, S, SO, SO.sub.2, or NR.sup.19;
R.sup.15 and R.sup.17 are each, independently, hydrogen hydroxyl,
or optionally substituted C.sub.1-C.sub.6 alkyl; R.sup.16 and
R.sup.18 are each, independently, hydroxyl, optionally substituted
amino, halogen, thiol, optionally substituted C.sub.1-C.sub.6
alkyl, optionally substituted C.sub.2-C.sub.6 alkenyl, optionally
substituted C.sub.2-C.sub.6 alkynyl, optionally substituted
C.sub.1-C.sub.6 heteroalkyl, optionally substituted C.sub.2-C.sub.6
heteroalkenyl, optionally substituted C.sub.2-C.sub.6
heteroalkynyl, optionally substituted C.sub.3-C.sub.10 carbocyclyl,
optionally substituted C.sub.6-C.sub.10 aryl, optionally
substituted C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.9 heteroaryl, optionally substituted
C.sub.2-C.sub.9 heteroaryl C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.9 heterocyclyl, or optionally substituted
C.sub.2-C.sub.9 heterocyclyl C.sub.1-C.sub.6 alkyl; R.sup.19 is
hydrogen, optionally substituted C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.6 alkenyl, optionally substituted
C.sub.2-C.sub.6 alkynyl, optionally substituted C.sub.6-C.sub.10
aryl, C.sub.3-C.sub.7 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, and optionally
substituted C.sub.3-C.sub.7 carbocyclyl C.sub.1-C.sub.6 alkyl; and
Ar is optionally substituted C.sub.6-C.sub.10 aryl or optionally
substituted C.sub.2-C.sub.9 heteroaryl.
6. The compound of claim 1, or a pharmaceutically acceptable salt
thereof, wherein said target interacting moiety comprises the
structure of Formula IX: ##STR00045## wherein u is an integer from
1 to 20; and each Y is, independently, any amino acid, O, NR, S,
S(O) SO.sub.2, or has the structure of any one of Formulae X-XIII:
##STR00046## wherein each R.sup.20 is, independently, hydrogen,
optionally substituted C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.6 alkenyl, optionally substituted
C.sub.2-C.sub.6 alkynyl, optionally substituted aryl,
C.sub.3-C.sub.7 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, and optionally
substituted C.sub.3-C.sub.7 carbocyclyl C.sub.1-C.sub.6 alkyl or
R.sup.19 combines with any R.sup.20, R.sup.21, R.sup.22, R.sup.23,
R.sup.24, R.sup.25, R.sup.26, R.sup.27, R.sup.28, R.sup.29, or
R.sup.30 to form an optionally substituted C.sub.3-C.sub.10
carbocyclyl, optionally substituted C.sub.6-C.sub.10 aryl, or
optionally substituted C.sub.2-C.sub.9 heteroaryl; each R.sup.21
and R.sup.22 is, independently, hydrogen, halogen, optionally
substituted hydroxyl, optionally substituted amino, or R.sup.20 and
R.sup.21 combine to form .dbd.O, optionally substituted
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.6
alkenyl, optionally substituted C.sub.2-C.sub.6 alkynyl, optionally
substituted C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl, or R.sup.21 or R.sup.22
combines with any R.sup.20, R.sup.21, R.sup.22, R.sup.23, R.sup.24,
R.sup.25, R.sup.26, R.sup.27, R.sup.28, R.sup.29, or R.sup.30 to
form an optionally substituted C.sub.3-C.sub.10 carbocyclyl,
optionally substituted C.sub.6-C.sub.10 aryl, or optionally
substituted C.sub.2-C.sub.9 heteroaryl; each R.sup.23 R.sup.24,
R.sup.25 and R.sup.26 is, independently, hydrogen, hydroxyl, or
R.sup.22 and R.sup.23 combine to form .dbd.O, or R.sup.23 R.sup.24
R.sup.25 or R.sup.26 combines with any R.sup.20, R.sup.21,
R.sup.22, R.sup.23, R.sup.24, R.sup.25, R.sup.26, R.sup.27,
R.sup.28, R.sup.29, or R.sup.30 to form an optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, or optionally substituted C.sub.2-C.sub.9
heteroaryl; and each R.sup.27, R.sup.28, R.sup.29, and R.sup.30 is,
independently, hydrogen, halogen, optionally substituted hydroxyl,
optionally substituted amino, optionally substituted
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.6
alkenyl, optionally substituted C.sub.2-C.sub.6 alkynyl, optionally
substituted C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl, or R.sup.27, R.sup.28,
R.sup.29, or R.sup.30 combines with any R.sup.20, R.sup.21,
R.sup.22, R.sup.23, R.sup.24, R.sup.25, R.sup.26, R.sup.27,
R.sup.28, R.sup.29, or R.sup.30 to form an optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, or optionally substituted C.sub.2-C.sub.9
heteroaryl.
7. The compound of claim 1, or a pharmaceutically acceptable salt
thereof, wherein said complex binds to said target protein with at
least 5-fold greater affinity than said complex binds to each of
mTOR and/or calcineurin.
8. The compound of claim 1, or a pharmaceutically acceptable salt
thereof, wherein said complex binds to said target protein with at
least 5-fold greater affinity than the affinity of said compound to
said target when said compound is not bound in a complex with said
presenter protein.
9. The compound of claim 1, or a pharmaceutically acceptable salt
thereof, wherein said complex inhibits the naturally occurring
interaction between said target protein and a ligand that
specifically binds said target protein.
10. The compound of claim 1, or a pharmaceutically acceptable salt
thereof, wherein said presenter protein is a prolyl isomerase.
11. The compound of claim 1, or a pharmaceutically acceptable salt
thereof, wherein said presenter protein is a member of the FKBP
family, a member of the cyclophilin family, or PIN1.
12. The compound of claim 1, or a pharmaceutically acceptable salt
thereof, wherein said mammalian target protein is a GTPase, GTPase
activating protein, Guanine nucleotide-exchange factor, a heat
shock protein, an ion channel, a coiled-coil protein, a kinase, a
phosphatase, a ubiquitin ligase, a transcription factor, a
chromatin modifier/remodeler, or a protein with classical
protein-protein interaction domains and motifs.
13. A presenter protein/compound complex comprising a compound of
claim 1, or a pharmaceutically acceptable salt thereof, and a
presenter protein.
14. A pharmaceutical composition comprising a compound of claim 1,
or a pharmaceutically acceptable salt thereof, and a
pharmaceutically acceptable excipient.
15. A method of modulating a target protein, said method comprising
contacting said target protein with a modulating amount of a
compound of claim 1 or a pharmaceutically acceptable salt
thereof.
16. A method of modulating a target protein, said method comprising
forming a presenter protein/compound complex comprising a compound
of claim 1, or a pharmaceutically acceptable salt thereof, and a
presenter protein in a cell by contacting said cell with an
effective amount of the compound or a pharmaceutically acceptable
salt thereof.
17. A method of modulating a target protein, said method comprising
contacting said target protein with a presenter protein/compound
complex comprising a compound of claim 1, or a pharmaceutically
acceptable salt thereof, and a presenter protein.
18. A method of inhibiting prolyl isomerase activity, said method
comprising contacting a cell expressing said prolyl isomerase with
a compound of claim 1, or a pharmaceutically acceptable salt
thereof, under conditions that permit the formation of a complex
between said compound and said prolyl isomerase, thereby inhibiting
prolyl isomerase activity.
19. A method of forming a presenter protein/compound complex
comprising a compound of claim 1, or a pharmaceutically acceptable
salt thereof, and a presenter protein in a cell, said method
comprising contacting a cell expressing said presenter protein with
the compound, or a pharmaceutically acceptable salt thereof, under
conditions that permit the formation of a complex between said
compound and said presenter protein.
20. A tripartite complex comprising (i) a mammalian target protein
and (ii) a presenter protein/compound complex, said presenter
protein/compound complex comprising a presenter protein and a
macrocyclic compound of claim 1, or a pharmaceutically acceptable
salt thereof.
Description
BACKGROUND
[0001] The vast majority of small molecule drugs act by binding a
functionally important pocket on a target protein, thereby
modulating the activity of that protein. For example, the
cholesterol-lowering drugs statins bind the enzyme active site of
HMG-CoA reductase, thus preventing the enzyme from engaging with
its substrates. The fact that many such drug/target interacting
pairs are known may have misled some into believing that a small
molecule modulator could be discovered for most, if not all,
proteins provided a reasonable amount of time, effort, and
resources. This is far from the case. Current estimates hold that
only about 10% of all human proteins are targetable by small
molecules. The other 90% are currently considered refractory or
intractable toward small molecule drug discovery. Such targets are
commonly referred to as "undruggable." These undruggable targets
include a vast and largely untapped reservoir of medically
important human proteins. Thus, there exists a great deal of
interest in discovering new molecular modalities capable of
modulating the function of such undruggable targets.
SUMMARY
[0002] The present invention features compounds (e.g., macrocyclic
compounds) capable of modulating biological processes, for example
through binding to a presenter protein (e.g., a member of the FKBP
family, a member of the cyclophilin family, or PIN1) and a target
protein. In some embodiments, the target and/or presenter proteins
are intracellular proteins. In some embodiments, the target and/or
presenter proteins are mammalian proteins. In some embodiments,
provided compounds participate in tripartite presenter
protein/compound/target protein complexes inside cells, e.g.,
mammalian cells. In some embodiments, provided compounds may be
useful in the treatment of diseases and disorders such as cancer,
inflammation, or infections.
[0003] In one aspect, the invention features a compound (e.g., a
macrocyclic compound comprising 14 to 40 ring atoms). The compound
includes: (a) a target protein interacting moiety (e.g., a
eukaryotic target protein interacting moiety such as a mammalian
target protein interacting moiety or a fungal target protein
interacting moiety or a prokaryotic target protein interacting
moiety such as a bacterial target protein interacting moiety); and
(b) a presenter protein binding moiety; wherein the compound and a
presenter protein form a complex that specifically binds to a
target protein, and each of the compound and the presenter protein
do not substantially bind to the target protein in the absence of
forming the complex; or the compound and a presenter protein form a
complex that binds to a target protein with at least 5-fold greater
affinity than the affinity of each of the compound and the
presenter protein to the target protein in the absence of forming
said complex; or a pharmaceutically acceptable salt thereof.
[0004] In some embodiments, the compound is a macrocyclic compound.
In certain embodiments, the compound is an acyclic compound.
[0005] In some embodiments, a provided compound includes one or
more linker moieties. In some embodiments, a linker moiety connects
the presenter protein binding moiety (or portion thereof) and the
target protein interacting moiety (or portion thereof).
[0006] In some embodiments, the compound has the structure:
##STR00001##
[0007] wherein A includes a mammalian target protein interacting
moiety;
[0008] B includes a presenter protein binding moiety; and
[0009] L.sup.1 and L.sup.2 are independently selected from a bond
and a linear chain of up to 10 atoms, independently selected from
carbon, nitrogen, oxygen, sulfur or phosphorous atoms, wherein each
atom in the chain is optionally substituted with one or more
substituents independently selected from alkyl, alkenyl, alkynyl,
aryl, heteroaryl, chloro, iodo, bromo, fluoro, hydroxyl, alkoxy,
aryloxy, carboxy, amino, alkylamino, dialkylamino, acylamino,
carboxamido, cyano, oxo, thio, alkylthio, arylthio, acylthio,
alkylsulfonate, arylsulfonate, phosphoryl, and sulfonyl, and
wherein any two atoms in the chain may be taken together with the
substituents bound thereto to form a ring, wherein the ring may be
further substituted and/or fused to one or more optionally
substituted carbocyclic, heterocyclic, aryl, or heteroaryl
rings.
[0010] In some embodiments, the compound has the structure:
##STR00002##
[0011] wherein each of Z.sup.1 and Z.sup.2 are, independently,
hydrogen or hydroxyl.
[0012] In other embodiments, at least one atom of L.sup.1, L.sup.2,
Z.sup.1, and/or Z.sup.2 participates in binding to the presenter
protein and the target protein. In certain embodiments, at least
one atom of L.sup.1, L.sup.2, Z.sup.1, and/or Z.sup.2 does not
participate in binding to the presenter protein or the target
protein.
[0013] In some embodiments, L.sup.1, L.sup.2, Z.sup.1, and/or
Z.sup.2 includes one or more atoms that participates in binding to
the presenter protein and/or to the target protein. In some
embodiments, at least one atom of the one or more of L.sup.1,
L.sup.2, Z.sup.1, and/or Z.sup.2 participates in binding to the
presenter protein and/or the target protein. In certain
embodiments, at least one atom of the one or more of L.sup.1,
L.sup.2, Z.sup.1, and/or Z.sup.2 does not participate in binding to
the presenter protein and/or the target protein.
[0014] In some embodiments, the presenter protein binding moiety
includes 5 to 20 ring atoms (e.g., 5 to 10, 7 to 12, 10 to 15, 12
to 17, or 15 to 20 ring atoms).
[0015] In some embodiments, the compound consists of 14 to 20 ring
atoms (e.g., 14 to 16, 14 to 17, 15 to 18, 16 to 19, or 17 to 20
ring atoms or 14, 15, 16, 17, 18, 19, or 20 ring atoms). In certain
embodiments, the compound consists of 21 to 26 ring atoms (e.g., 21
to 23, 22 to 24, 23 to 25, or 24 to 26 ring atoms or 21, 22, 23,
24, 25, 26 ring atoms). In some embodiments, the compound consists
of 27 to 40 ring atoms (e.g., 27 to 30, 29 to 34, 33 to 38, 37 to
40 ring atoms or 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
39, or 40 ring atoms).
[0016] In some embodiments, the presenter protein binding moiety
includes the structure of Formula I:
##STR00003##
[0017] wherein n is 0 or 1;
[0018] X.sup.1 and X.sup.3 are each independently O, S,
CR.sup.3R.sup.4, or NR.sup.5;
[0019] X.sup.2 is O, S, or NR.sup.5;
[0020] R.sup.1, R.sup.2, R.sup.3, and R.sup.4 are each
independently hydrogen, hydroxyl, optionally substituted amino,
halogen, thiol, optionally substituted C.sub.1-C.sub.6 alkyl,
optionally substituted C.sub.2-C.sub.6 alkenyl, optionally
substituted C.sub.2-C.sub.6 alkynyl, optionally substituted
C.sub.1-C.sub.6 heteroalkyl, optionally substituted C.sub.2-C.sub.6
heteroalkenyl, optionally substituted C.sub.2-C.sub.6
heteroalkynyl, optionally substituted C.sub.3-C.sub.10 carbocyclyl,
optionally substituted C.sub.6-C.sub.10 aryl, optionally
substituted C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.9 heteroaryl, optionally substituted
C.sub.2-C.sub.9 heteroaryl C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.9 heterocyclyl, or optionally substituted
C.sub.2-C.sub.9 heterocyclyl C.sub.1-C.sub.6 alkyl, or any two of
R.sup.1 R.sup.2, R.sup.3, or R.sup.4 are taken together with the
atom or atoms to which they are bound to form an optionally
substituted carbocyclyl, optionally substituted heterocyclyl,
optionally substituted aryl, or optionally substituted heteroaryl;
and
[0021] each R.sup.5 is, independently, hydrogen, hydroxyl,
optionally substituted C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.6 alkenyl, optionally substituted
C.sub.2-C.sub.6 alkynyl, optionally substituted C.sub.1-C.sub.6
heteroalkyl, optionally substituted C.sub.2-C.sub.6 heteroalkenyl,
optionally substituted C.sub.2-C.sub.6 heteroalkynyl, optionally
substituted C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl, or R.sup.5 and one of R.sup.1,
R.sup.2, R.sup.3, or R.sup.4 are taken together with the atom or
atoms to which they are bound to form an optionally substituted
heterocyclyl or optionally substituted heteroaryl.
[0022] In some embodiments, X.sup.1 is connected to L.sup.1 and
X.sup.3 is connected to L.sup.2. In some embodiments, X.sup.1 is
connected to L.sup.2 and X.sup.3 is connected to L.sup.1.
[0023] In some embodiments, the presenter protein binding moiety
includes the structure of Formula Ia:
##STR00004##
[0024] In some embodiments, the presenter protein binding moiety is
or includes the structure of any one of Formulae II-IV:
##STR00005##
[0025] wherein o, and p are independently 0, 1, or 2;
[0026] q is an integer between 0 and 7;
[0027] r is an integer between 0 and 4;
[0028] X.sup.4 and X.sup.5 are each, independently, absent,
CH.sub.2, O, S, SO, SO.sub.2, or NR.sup.13;
[0029] each R.sup.6 and R.sup.7 are independently hydrogen,
hydroxyl, optionally substituted amino, halogen, thiol, optionally
substituted C.sub.1-C.sub.6 alkyl, optionally substituted
C.sub.2-C.sub.6 alkenyl, optionally substituted C.sub.2-C.sub.6
alkynyl, optionally substituted C.sub.1-C.sub.6 heteroalkyl,
optionally substituted C.sub.2-C.sub.6 heteroalkenyl, optionally
substituted C.sub.2-C.sub.6 heteroalkynyl, optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, optionally substituted C.sub.2-C.sub.9 heterocyclyl
C.sub.1-C.sub.6 alkyl, or R.sup.6 and R.sup.7 combine with the
carbon atom to which they are bound to form C.dbd.O or R.sup.6 and
R.sup.7 combine to form an optionally substituted C.sub.3-C.sub.10
carbocyclyl or optionally substituted C.sub.2-C.sub.9
heterocyclyl;
[0030] each R.sup.8 is, independently, hydroxyl, optionally
substituted amino, halogen, thiol, optionally substituted
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.6
alkenyl, optionally substituted C.sub.2-C.sub.6 alkynyl, optionally
substituted C.sub.1-C.sub.6 heteroalkyl, optionally substituted
C.sub.2-C.sub.6 heteroalkenyl, optionally substituted
C.sub.2-C.sub.6 heteroalkynyl, optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl or two R.sup.8 combine to form
an optionally substituted C.sub.3-C.sub.10 carbocyclyl, optionally
substituted C.sub.6-C.sub.10 aryl, or optionally substituted
C.sub.2-C.sub.9 heteroaryl;
[0031] R.sup.9 is optionally substituted C.sub.1-C.sub.6 alkyl,
optionally substituted C.sub.2-C.sub.6 alkenyl, optionally
substituted C.sub.2-C.sub.6 alkynyl, optionally substituted
C.sub.1-C.sub.6 heteroalkyl, optionally substituted C.sub.2-C.sub.6
heteroalkenyl, optionally substituted C.sub.2-C.sub.6
heteroalkynyl, optionally substituted C.sub.3-C.sub.10 carbocyclyl,
optionally substituted C.sub.6-C.sub.10 aryl, optionally
substituted C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.9 heteroaryl, optionally substituted
C.sub.2-C.sub.9 heteroaryl C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.9 heterocyclyl, or optionally substituted
C.sub.2-C.sub.9 heterocyclyl C.sub.1-C.sub.6 alkyl;
[0032] R.sup.10 is optionally substituted C.sub.1-C.sub.6
alkyl;
[0033] each R.sup.11 is, independently, hydroxyl, cyano, optionally
substituted amino, halogen, thiol, optionally substituted
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.6
alkenyl, optionally substituted C.sub.2-C.sub.6 alkynyl, optionally
substituted C.sub.1-C.sub.6 heteroalkyl, optionally substituted
C.sub.2-C.sub.6 heteroalkenyl, optionally substituted
C.sub.2-C.sub.6 heteroalkynyl, optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl or two R.sup.11 combine to form
an optionally substituted C.sub.3-C.sub.10 carbocyclyl, optionally
substituted C.sub.6-C.sub.10 aryl, or optionally substituted
C.sub.2-C.sub.9 heteroaryl; and
[0034] R.sup.12 and R.sup.13 are each, independently, hydrogen,
optionally substituted C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.6 alkenyl, optionally substituted
C.sub.2-C.sub.6 alkynyl, optionally substituted aryl,
C.sub.3-C.sub.7 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, and optionally
substituted C.sub.3--C carbocyclyl C.sub.1-C.sub.6 alkyl.
[0035] In some embodiments, L.sup.1 is connected to the left of the
presenter protein binding moiety and L.sup.2 is connected to the
right of the presenter protein binding moiety. In some embodiments,
L.sup.1 is connected to the right of the presenter protein binding
moiety and L.sup.2 is connected to the left of the presenter
protein binding moiety.
[0036] In some embodiments, the presenter protein binding moiety is
or includes the structure of any one of Formulae IIa-IVa:
##STR00006##
[0037] In some embodiments, the presenter protein binding moiety is
or includes the structure of Formula V:
##STR00007##
[0038] wherein R.sup.14 is hydrogen, hydroxyl, optionally
substituted C.sub.1-C.sub.6 alkyl, optionally substituted
C.sub.2-C.sub.6 alkenyl, optionally substituted C.sub.2-C.sub.6
alkynyl, optionally substituted C.sub.1-C.sub.6 heteroalkyl,
optionally substituted C.sub.2-C.sub.6 heteroalkenyl, optionally
substituted C.sub.2-C.sub.6 heteroalkynyl, optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, optionally substituted C.sub.2-C.sub.9 heterocyclyl
C.sub.1-C.sub.6 alkyl.
[0039] In certain embodiments, the presenter protein binding moiety
is or includes the structure of Formula VI, VII, or VIII:
##STR00008##
[0040] wherein s and t are each, independently, an integer from 0
to 7;
[0041] X.sup.6 and X.sup.7 are each, independently, O, S, SO,
SO.sub.2, or NR.sup.19;
[0042] R.sup.15 and R.sup.17 are each, independently, hydrogen
hydroxyl, or optionally substituted C.sub.1-C.sub.6 alkyl;
[0043] R.sup.16 and R.sup.18 are each, independently, hydroxyl,
optionally substituted amino, halogen, thiol, optionally
substituted C.sub.1-C.sub.6 alkyl, optionally substituted
C.sub.2-C.sub.6 alkenyl, optionally substituted C.sub.2-C.sub.6
alkynyl, optionally substituted C.sub.1-C.sub.6 heteroalkyl,
optionally substituted C.sub.2-C.sub.6 heteroalkenyl, optionally
substituted C.sub.2-C.sub.6 heteroalkynyl, optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl;
[0044] R.sup.19 is optionally substituted C.sub.1-C.sub.6 alkyl,
optionally substituted C.sub.2-C.sub.6 alkenyl, optionally
substituted C.sub.2-C.sub.6 alkynyl, optionally substituted aryl,
C.sub.3-C.sub.7 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, and optionally
substituted C.sub.3-C.sub.7 carbocyclyl C.sub.1-C.sub.6 alkyl;
and
[0045] Ar is optionally substituted C.sub.6-C.sub.10 aryl or
optionally substituted C.sub.2-C.sub.9 heteroaryl.
[0046] In certain embodiments, the presenter protein binding moiety
is or includes the structure:
##STR00009## ##STR00010## ##STR00011##
[0047] In certain embodiments, the presenter protein binding moiety
is or includes the structure:
##STR00012## ##STR00013##
[0048] In some embodiments, presenter protein binding moiety is or
includes the structure:
##STR00014## ##STR00015##
[0049] In some embodiments, presenter protein binding moiety is or
includes the structure:
##STR00016##
[0050] In certain embodiments, the target interacting moiety is or
includes the structure of Formula IX:
##STR00017##
[0051] wherein u is an integer from 1 to 20; and
[0052] each Y is, independently, any amino acid, O, NR.sup.20, S,
S(O), SO.sub.2, or has the structure of any one of Formulae
X-XIII:
##STR00018##
[0053] wherein each R.sup.20 is, independently, hydrogen,
optionally substituted C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.6 alkenyl, optionally substituted
C.sub.2-C.sub.6 alkynyl, optionally substituted aryl,
C.sub.3-C.sub.7 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, and optionally
substituted C.sub.3-C.sub.7 carbocyclyl C.sub.1-C.sub.6 alkyl or
R.sup.20 combines with any R.sup.20, R.sup.21, R.sup.22, R.sup.23,
R.sup.24, R.sup.25, R.sup.26, R.sup.27, R.sup.28, R.sup.29, or
R.sup.30 to form an optionally substituted C.sub.3-C.sub.10
carbocyclyl, optionally substituted C.sub.6-C.sub.10 aryl, or
optionally substituted C.sub.2-C.sub.9 heteroaryl;
[0054] each R.sup.21 and R.sup.22 is, independently, hydrogen,
halogen, optionally substituted hydroxyl, optionally substituted
amino, or R.sup.21 and R.sup.22 combine to form .dbd.O, optionally
substituted C.sub.1-C.sub.6 alkyl, optionally substituted
C.sub.2-C.sub.6 alkenyl, optionally substituted C.sub.2-C.sub.6
alkynyl, optionally substituted C.sub.3-C.sub.10 carbocyclyl,
optionally substituted C.sub.6-C.sub.10 aryl, optionally
substituted C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.9 heteroaryl, optionally substituted
C.sub.2-C.sub.9 heteroaryl C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.9 heterocyclyl, or optionally substituted
C.sub.2-C.sub.9 heterocyclyl C.sub.1-C.sub.6 alkyl, or R.sup.21 or
R.sup.22 combines with any R.sup.20, R.sup.21, R.sup.22, R.sup.23,
R.sup.24, R.sup.25, R.sup.26, R.sup.27, R.sup.28, R.sup.29, or
R.sup.30 to form an optionally substituted C.sub.3-C.sub.10
carbocyclyl, optionally substituted C.sub.6-C.sub.10 aryl, or
optionally substituted C.sub.2-C.sub.9 heteroaryl;
[0055] each R.sup.23, R.sup.24, R.sup.25 or R.sup.26 is,
independently, hydrogen, hydroxyl, or R.sup.23 and R.sup.24 combine
to form .dbd.O, or R.sup.23, R.sup.24, R.sup.25 or R.sup.26
combines with any R.sup.20, R.sup.21, R.sup.22, R.sup.23, R.sup.24,
R.sup.25, R.sup.26, R.sup.27, R.sup.28, R.sup.29, or R.sup.30 to
form an optionally substituted C.sub.3-C.sub.10 carbocyclyl,
optionally substituted C.sub.6-C.sub.10 aryl, or optionally
substituted C.sub.2-C.sub.9 heteroaryl; and
[0056] each R.sup.27, R.sup.28, R.sup.29, and R.sup.30 is,
independently, hydrogen, halogen, optionally substituted hydroxyl,
optionally substituted amino, optionally substituted
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.6
alkenyl, optionally substituted C.sub.2-C.sub.6 alkynyl, optionally
substituted C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl, or R.sup.26, R.sup.27,
R.sup.28, R.sup.29, or R.sup.30 combines with any R.sup.20,
R.sup.21, R.sup.22, R.sup.23, R.sup.24, R.sup.25, R.sup.26,
R.sup.27, R.sup.28, R.sup.29, or R.sup.30 to form an optionally
substituted C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, or optionally substituted C.sub.2-C.sub.9
heteroaryl.
[0057] In certain embodiments, the target interacting moiety is or
includes the structure of Formula IX:
##STR00019##
[0058] In some embodiments, the compound has the structure of any
one of Formulae XIV-XVIII:
##STR00020##
[0059] In some embodiments, the compound does not comprise the
structure:
##STR00021##
[0060] In some embodiments, the target interacting moiety is or
includes the structure:
##STR00022##
[0061] In some embodiments, at least one Y is an N-alkylated amino
acid (e.g., an N-methyl amino acid). In some embodiments, at least
one Y is a D-amino acid. In some embodiments, at least one Y is a
non-natural amino acid. In certain embodiments, at least one Y
includes a depsi-linkage.
[0062] In some embodiments, the compound does not include the
structure:
##STR00023##
[0063] In some embodiments, the portion of the molecule that
comprises each ring atom that participates in binding to the target
protein has a c Log P greater than 2 (e.g., greater than 3, greater
than 4, greater than 5, greater than 6). In certain embodiments,
the portion of the molecule that comprises each ring atom that
participates in binding to the target protein has a polar surface
area less than 350 .ANG..sup.2 (e.g., less than 300 A.sup.2, less
than 250 A.sup.2, less than 200 .ANG..sup.2, less than 150
.ANG..sup.2, less than 125 .ANG..sup.2). In some embodiments, the
portion of the molecule that comprises each ring atom that
participates in binding to the target protein includes at least one
atom of a linker.
[0064] In some embodiments, the compound has a molecular weight
between 400 and 2000 Daltons (e.g., 400 to 600, 500 to 700, 600 to
800, 700 to 900, 800 to 1000, 900 to 1100, 1000 to 1200, 1100 to
1300, 1200 to 1400, 1300 to 1500, 1400 to 1600, 1500 to 1700, 1600
to 1800, 1700 to 1900, or 1800 to 2000 Daltons). In certain
embodiments, the compound has an even number of ring atoms (e.g.,
14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, or 40 ring
atoms). In some embodiments, the compound is cell penetrant. In
some embodiments, the compound is substantially pure (e.g.,
compound is provided in a preparation that is substantially free of
contaminants such as other compounds and/or components of a cell
lysate. In certain embodiments, the compound is isolated. In some
embodiments, the compound is an engineered compound. In some
embodiments, the compound is non-naturally occurring.
[0065] In certain embodiments, the complex binds to a target
protein (e.g., (e.g., a eukaryotic target protein such as a
mammalian target protein or a fungal target proteins or a
prokaryotic target protein such as a bacterial target protein) with
at least 5-fold greater (e.g., at least 10-fold greater, at least
20-fold greater, at least 50-fold greater, at least 100-fold
greater) affinity than the complex binds to mTOR and/or
calcineurin. In some embodiments, the complex binds to the target
protein with at least 5-fold greater (e.g., at least 10-fold
greater, at least 20-fold greater, at least 50-fold greater, at
least 100-fold greater) affinity than the affinity of the compound
to the target protein when the compound is not bound in a complex
with the presenter protein. In some embodiments, the complex binds
to the target protein with at least 5-fold greater (e.g., at least
10-fold greater, at least 20-fold greater, at least 50-fold
greater, at least 100-fold greater) affinity than the affinity of
the presenter protein to the target protein when the presenter
protein is not bound in a complex with the compound. In certain
embodiments, the complex inhibits the naturally occurring
interaction between the target protein and a ligand that
specifically binds the target protein.
[0066] In some embodiments, the presenter protein is a prolyl
isomerase (e.g., a member of the FKBP family such as FKBP12,
FKBP12.6, FKBP25, or FKBP52, a member of the cyclophilin family
such as PP1A, CYPB, CYPC, CYP40, CYPE, CYPD, NKTR, SRCyp, CYPH,
CWC27, CYPL1, CYP60, CYPJ, PPIL4, PPIL6, RANBP2, PPWD1, or
PIN1).
[0067] In certain embodiments, the target protein is a eukaryotic
target protein. In some embodiments, the eukaryotic target protein
is a mammalian target protein such as a GTPase, GTPase activating
protein, Guanine nucleotide-exchange factor, a heat shock protein,
an ion channel, a coiled-coil protein, a kinase, a phosphatase, a
ubiquitin ligase, a transcription factor, a chromatin
modifier/remodeler, proteins with classical protein-protein
interaction domains and motifs, or any other protein that
participates in a biological pathway associated with a disease,
disorder or condition. In some embodiments, the eukaryotic target
protein is a fungal target protein. In certain embodiments, the
target protein is a prokaryotic target protein such as a bacterial
target protein.
[0068] In some embodiments, the compound is any one of the
compounds of FIG. 1, or a stereoisomer, or pharmaceutically
acceptable salt thereof:
[0069] In certain embodiments, the compound is any one of the
compounds of FIG. 2, or a stereoisomer, or pharmaceutically
acceptable salt thereof:
[0070] In some aspects, the invention features a presenter
protein/compound complex including any of the compounds of the
invention and a presenter protein.
[0071] In some embodiments of the presenter protein/compound
complex, the presenter protein is a protein encoded by any one of
the genes or a homolog thereof of Table 1. In some embodiments of
the presenter protein/compound complex the presenter protein is a
prolyl isomerase (e.g., a member of the FKBP family such as FKBP12,
FKBP12.6, FKBP25, or FKBP52, a member of the cyclophilin family
such as PP1A, CYPB, CYPC, CYP40, CYPE, CYPD, NKTR, SRCyp, CYPH,
CWC27, CYPL1, CYP60, CYPJ, PPIL4, PPIL6, RANBP2, PPWD1, or
PIN1).
[0072] In some aspects, the invention features a pharmaceutical
composition including any of the compounds or complexes of the
invention and a pharmaceutically acceptable excipient. In some
embodiments, the pharmaceutical composition is in unit dosage
form.
[0073] In some aspects, the invention features a method of
modulating a target protein (e.g., a eukaryotic target protein such
as a mammalian target protein or a fungal target proteins or a
prokaryotic target protein such as a bacterial target protein). In
some embodiments, such a method includes steps of contacting the
target protein with a modulating (e.g., positive or negative
modulation) amount of any of the compounds (e.g., in the presence
of a presenter protein), presenter protein/compound complexes, or
compositions of the invention.
[0074] In some aspects, the invention features a method of
modulating (e.g., positively or negatively modulating) a target
protein (e.g., a eukaryotic target protein such as a mammalian
target protein or a fungal target proteins or a prokaryotic target
protein such as a bacterial target protein). In some embodiments,
such a method includes steps of contacting a cell expressing the
target protein and a presenter protein with an effective amount of
a compound or composition of the invention under conditions wherein
the compound can form a complex with the presenter protein and the
resulting complex can bind to the target protein, thereby
modulating (e.g., positively or negatively modulating) the target
protein.
[0075] In some aspects, the invention features a method of
modulating (e.g., positively or negatively modulating) a target
protein (e.g., a eukaryotic target protein such as a mammalian
target protein or a fungal target proteins or a prokaryotic target
protein such as a bacterial target protein). In some embodiments,
such a method includes steps of contacting the target protein with
a presenter protein/compound complex of the invention, thereby
modulating the target protein.
[0076] In some aspects, the invention features a method of
inhibiting prolyl isomerase activity. In some embodiments, such a
method includes contacting a cell expressing the prolyl isomerase
with a compound or composition of the invention under conditions
that permit the formation of a complex between the compound and the
prolyl isomerase, thereby inhibiting the prolyl isomerase
activity.
[0077] In some aspects, the invention features a method of forming
a presenter protein/compound complex in a cell. In some
embodiments, such a method includes steps of contacting a cell
expressing the presenter protein with a compound or composition of
the invention under conditions that permit the formation of a
complex between the compound and the presenter protein.
[0078] In some aspects, the invention features a method for the
preparation of a compound of the invention. In some embodiments,
such a method includes steps of culturing a bacterial strain of the
genus Streptomyces and isolating the compound from the fermentation
broth. In some embodiments, the bacterial strain is an engineered
strain. In some embodiments, the bacterial strain is engineered in
that it has been modified to produce the compound and/or to secrete
the compound into the broth.
[0079] In some embodiments, the present disclosure provides methods
for preparing a compound as described herein, the method comprising
steps of culturing a bacterial strain of the genus Streptomyces
under conditions in which the strain produces the compound and
releases it into the and isolating the compound from the
fermentation broth.
[0080] In some embodiments, a provided method comprises isolating a
compound as described herein from fermentation broth.
[0081] In some aspects, the invention features a tripartite complex
including (i) a target protein (e.g., a eukaryotic target protein
such as a mammalian target protein or a fungal target proteins or a
prokaryotic target protein such as a bacterial target protein) and
(ii) a presenter protein/compound complex, the presenter
protein/compound complex including a presenter protein and any of
the compounds of the invention.
[0082] In some embodiments of the tripartite complex, the target
protein (e.g., a eukaryotic target protein such as a mammalian
target protein or a fungal target proteins or a prokaryotic target
protein such as a bacterial target protein) does not have a
traditional binding pocket. In some embodiments of the tripartite
complex, the presenter protein/compound complex binds at a flat
surface site on the target protein. In certain embodiments of the
tripartite complex, the compound (e.g., macrocyclic compound) in
the presenter protein/compound complex binds at a hydrophobic
surface site (e.g., a hydrophobic surface site on the target
protein including at least 30%, such as at least 40%, at least 50%,
at least 60%, at least 70%, at least 80%, at least 90%, or at least
95%, hydrophobic residues) on the target protein. In some
embodiments of the tripartite complex, the presenter
protein/compound complex binds to the target protein at a site of a
naturally occurring protein-protein interaction between the target
protein and a protein that specifically binds said target protein.
In some embodiments of the tripartite complex, presenter
protein/compound complex does not bind at an active site of the
target protein. In certain embodiments of the tripartite complex,
presenter protein/compound complex binds at an active site of the
target protein. In some embodiments of the tripartite complex,
target protein is an undruggable target.
[0083] In some embodiments of the tripartite complex, the
structural organization of the compound (e.g., macrocyclic
compound) is substantially unchanged in the tripartite complex
compared to the compound (e.g., macrocyclic compound) in the
presenter protein/compound complex but not in the tripartite
complex.
[0084] In certain embodiments of the tripartite complex, at least
10% (e.g., at least 20%, at least 30%, at least 40%, at least 50%,
at least 60%, at least 70%, at least 80%, at least 90%) of the
total buried surface area of the target protein in the tripartite
complex includes one or more atoms that participate in binding to
the compound (e.g., macrocyclic compound). In some embodiments of
the tripartite complex, at least 10% (e.g., at least 20%, at least
30%, at least 40%, at least 50%, at least 60%, at least 70%, at
least 80%, at least 90%) of the total buried surface area of the
target protein in the tripartite complex includes one or more atoms
that participate in binding to the presenter protein.
[0085] In some embodiments of the tripartite complex, the compound
(e.g., macrocyclic compound) contributes at least 10% (e.g., at
least 20%, at least 30%, at least 40%, at least 50%, at least 60%,
at least 70%, at least 80%, at least 90%) of the total binding free
energy of the tripartite complex. In certain embodiments of the
tripartite complex, the presenter protein contributes at least 10%
(e.g., at least 20%, at least 30%, at least 40%, at least 50%, at
least 60%, at least 70%, at least 80%, at least 90%) of the total
binding free energy of the tripartite complex.
[0086] In some embodiments of the tripartite complex, at least 70%
(e.g., at least 80%, at least 90%, at least 95%) of binding
interactions between one or more atoms of the compound (e.g.,
macrocyclic compound) and one or more atoms of the target protein
(e.g., a eukaryotic target protein such as a mammalian target
protein or a fungal target proteins or a prokaryotic target protein
such as a bacterial target protein) are van der Waals interactions
and/or .pi.-effect interactions.
[0087] In another aspect, the invention features a compound
collection comprising a plurality of compounds (e.g., of
macrocyclic compounds as described herein). In some embodiments,
compound collections include a plurality of compounds that are
variants of one another.
[0088] Chemical Terms Those skilled in the art will appreciate that
certain compounds described herein can exist in one or more
different isomeric (e.g., stereoisomers, geometric isomers,
tautomers) and/or isotopic (e.g., in which one or more atoms has
been substituted with a different isotope of the atom, such as
hydrogen substituted for deuterium) forms. Unless otherwise
indicated or clear from context, a depicted structure can be
understood to represent any such isomeric or isotopic form,
individually or in combination.
[0089] Compounds described herein can be asymmetric (e.g., having
one or more stereocenters). All stereoisomers, such as enantiomers
and diastereomers, are intended unless otherwise indicated.
Compounds of the present disclosure that contain asymmetrically
substituted carbon atoms can be isolated in optically active or
racemic forms. Methods on how to prepare optically active forms
from optically active starting materials are known in the art, such
as by resolution of racemic mixtures or by stereoselective
synthesis. Many geometric isomers of olefins, C.dbd.N double bonds,
and the like can also be present in the compounds described herein,
and all such stable isomers are contemplated in the present
disclosure. Cis and trans geometric isomers of the compounds of the
present disclosure are described and may be isolated as a mixture
of isomers or as separated isomeric forms.
[0090] In some embodiments, one or more compounds depicted herein
may exist in different tautomeric forms. As will be clear from
context, unless explicitly excluded, references to such compounds
encompass all such tautomeric forms. In some embodiments,
tautomeric forms result from the swapping of a single bond with an
adjacent double bond and the concomitant migration of a proton. In
certain embodiments, a tautomeric form may be a prototropic
tautomer, which is an isomeric protonation states having the same
empirical formula and total charge as a reference form. Examples of
moieties with prototropic tautomeric forms are ketone-enol pairs,
amide-imidic acid pairs, lactam-lactim pairs, amide-imidic acid
pairs, enamine-imine pairs, and annular forms where a proton can
occupy two or more positions of a heterocyclic system, such as, 1H-
and 3H-imidazole, 1H-, 2H- and 4H-1,2,4-triazole, 1H- and
2H-isoindole, and 1H- and 2H-pyrazole. In some embodiments,
tautomeric forms can be in equilibrium or sterically locked into
one form by appropriate substitution. In certain embodiments,
tautomeric forms result from acetal interconversion, e.g., the
interconversion illustrated in the scheme below:
##STR00024##
[0091] Those skilled in the art will appreciate that, in some
embodiments, isotopes of compounds described herein may be prepared
and/or utilized in accordance with the present invention.
"Isotopes" refers to atoms having the same atomic number but
different mass numbers resulting from a different number of
neutrons in the nuclei. For example, isotopes of hydrogen include
tritium and deuterium. In some embodiments, an isotopic
substitution (e.g., substitution of hydrogen with deuterium) may
alter the physicochemical properties of the molecules, such as
metabolism and/or the rate of racemization of a chiral center.
[0092] As is known in the art, many chemical entities (in
particular many organic molecules and/or many small molecules) can
adopt a variety of different solid forms such as, for example,
amorphous forms and/or crystalline forms (e.g., polymorphs,
hydrates, solvates, etc). In some embodiments, such entities may be
utilized in any form, including in any solid form. In some
embodiments, such entities are utilized in a particular form, for
example in a particular solid form.
[0093] In some embodiments, compounds described and/or depicted
herein may be provided and/or utilized in salt form.
[0094] In certain embodiments, compounds described and/or depicted
herein may be provided and/or utilized in hydrate or solvate
form.
[0095] At various places in the present specification, substituents
of compounds of the present disclosure are disclosed in groups or
in ranges. It is specifically intended that the present disclosure
include each and every individual subcombination of the members of
such groups and ranges. For example, the term "C.sub.1-6 alkyl" is
specifically intended to individually disclose methyl, ethyl,
C.sub.3 alkyl, C.sub.4 alkyl, C.sub.5 alkyl, and C.sub.8 alkyl.
Furthermore, where a compound includes a plurality of positions at
which substitutes are disclosed in groups or in ranges, unless
otherwise indicated, the present disclosure is intended to cover
individual compounds and groups of compounds (e.g., genera and
subgenera) containing each and every individual subcombination of
members at each position.
[0096] Herein a phrase of the form "optionally substituted X"
(e.g., optionally substituted alkyl) is intended to be equivalent
to "X, wherein X is optionally substituted" (e.g., "alkyl, wherein
said alkyl is optionally substituted"). It is not intended to mean
that the feature "X" (e.g. alkyl) per se is optional.
[0097] The term "alkyl," as used herein, refers to saturated
hydrocarbon groups containing from 1 to 20 (e.g., from 1 to 10 or
from 1 to 6) carbons. In some embodiments, an alkyl group is
unbranched (i.e., is linear); in some embodiments, an alkyl group
is branched. Alkyl groups are exemplified by methyl, ethyl, n- and
iso-propyl, n-, sec-, iso- and tert-butyl, neopentyl, and the like,
and may be optionally substituted with one, two, three, or, in the
case of alkyl groups of two carbons or more, four substituents
independently selected from the group consisting of: (1) C.sub.1-6
alkoxy; (2) C.sub.1-6 alkylsulfinyl; (3) amino, as defined herein
(e.g., unsubstituted amino (i.e., --NH.sub.2) or a substituted
amino (i.e., --N(R.sup.N1).sub.2, where R.sup.N1 is as defined for
amino); (4) C.sub.6-10 aryl-C.sub.1-6 alkoxy; (5) azido; (6) halo;
(7) (C.sub.2-9 heterocyclyl)oxy; (8) hydroxyl, optionally
substituted with an O-protecting group; (9) nitro; (10) oxo (e.g.,
carboxyaldehyde or acyl); (11) C.sub.1-7 spirocyclyl; (12)
thioalkoxy; (13) thiol; (14) --CO.sub.2R.sup.A', optionally
substituted with an O-protecting group and where R.sup.A' is
selected from the group consisting of (a) C.sub.1-20 alkyl (e.g.,
C.sub.1-6 alkyl), (b) C.sub.2-20 alkenyl (e.g., C.sub.2-6 alkenyl),
(c) C.sub.6-10 aryl, (d) hydrogen, (e) C.sub.1-6 alk-C.sub.6-10
aryl, (f) amino-C.sub.1-20 alkyl, (g) polyethylene glycol of
--(CH.sub.2).sub.s2(OCH.sub.2CH.sub.2).sub.s1(CH.sub.2).sub.s3OR',
wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6 or from 1
to 4), each of s2 and s3, independently, is an integer from 0 to 10
(e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1 to 6, or from
1 to 10), and R' is H or C.sub.1-20 alkyl, and (h)
amino-polyethylene glycol of
--NR.sup.N1(CH.sub.2).sub.s2(CH.sub.2CH.sub.2O).sub.s1(CH.sub.2).sub.s3NR-
.sup.N1, wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6
or from 1 to 4), each of s2 and s3, independently, is an integer
from 0 to 10 (e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1
to 6, or from 1 to 10), and each R.sup.N1 is, independently,
hydrogen or optionally substituted C.sub.1-6 alkyl; (15)
--C(O)NR.sup.B'R.sup.C', where each of R.sup.B' and R.sup.C' is,
independently, selected from the group consisting of (a) hydrogen,
(b) C.sub.1-6 alkyl, (c) C.sub.6-10 aryl, and (d) C.sub.1-6
alk-C.sub.6-10 aryl; (16) --SO.sub.2R.sup.D', where R.sup.U is
selected from the group consisting of (a) C.sub.1-6 alkyl, (b)
C.sub.6-10 aryl, (c) C.sub.1-6 alk-C.sub.6-10 aryl, and (d)
hydroxyl; (17) --SO.sub.2NR.sup.E'R.sup.F', where each of R.sup.E'
and R.sup.F' is, independently, selected from the group consisting
of (a) hydrogen, (b) C.sub.1-6 alkyl, (c) C.sub.6-10 aryl and (d)
C.sub.1-6 alk-C.sub.6-10 aryl; (18) --C(O)R.sup.G', where R.sup.G'
is selected from the group consisting of (a) C.sub.1-20 alkyl
(e.g., C.sub.1-6 alkyl), (b) C.sub.2-20 alkenyl (e.g., C.sub.2-6
alkenyl), (c) C.sub.6-10 aryl, (d) hydrogen, (e) C.sub.1-6
alk-C.sub.6-10 aryl, (f) amino-C.sub.1-20 alkyl, (g) polyethylene
glycol of
--(CH.sub.2).sub.s2(OCH.sub.2CH.sub.2).sub.s1(CH.sub.2).sub.s3OR',
wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6 or from 1
to 4), each of s2 and s3, independently, is an integer from 0 to 10
(e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1 to 6, or from
1 to 10), and R' is H or C.sub.1-20 alkyl, and (h)
amino-polyethylene glycol of
--NR.sup.N1(CH.sub.2).sub.s2(CH.sub.2CH.sub.2O).sub.s1(CH.sub.2).sub.s3NR-
.sup.N1, wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6
or from to 4), each of s2 and s3, independently, is an integer from
0 to 10 (e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1 to 6,
or from 1 to 10), and each R.sup.N1 is, independently, hydrogen or
optionally substituted C.sub.1-6 alkyl; (19)
--NR.sup.H'C(O)R.sup.I', wherein R.sup.H' is selected from the
group consisting of (a1) hydrogen and (b1) C.sub.1-6 alkyl, and
R.sup.I' is selected from the group consisting of (a2) C.sub.1-20
alkyl (e.g., C.sub.1-6 alkyl), (b2) C.sub.2-20 alkenyl (e.g.,
C.sub.2-6 alkenyl), (c2) C.sub.6-10 aryl, (d2) hydrogen, (e2)
C.sub.1-6 alk-C.sub.6-10 aryl, (f2) amino-C.sub.1-20 alkyl, (g2)
polyethylene glycol of
--(CH.sub.2).sub.s2(OCH.sub.2CH.sub.2).sub.s1(CH.sub.2).sub.s3OR',
wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6 or from 1
to 4), each of s2 and s3, independently, is an integer from 0 to 10
(e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1 to 6, or from
1 to 10), and R' is H or C.sub.1-20 alkyl, and (h2)
amino-polyethylene glycol of
--NR.sup.N1(CH.sub.2).sub.s2(CH.sub.2CH.sub.2O).sub.s1(CH.sub.2).sub.s3NR-
.sup.N1, wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6
or from 1 to 4), each of s2 and s3, independently, is an integer
from 0 to 10 (e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1
to 6, or from 1 to 10), and each R.sup.N1 is, independently,
hydrogen or optionally substituted C.sub.1-6 alkyl; (20)
--NR.sup.J'C(O)OR.sup.K', wherein R.sup.J' is selected from the
group consisting of (a1) hydrogen and (b1) C.sub.1-6 alkyl, and
R.sup.K' is selected from the group consisting of (a2) C.sub.1-20
alkyl (e.g., C.sub.1-6 alkyl), (b2) C.sub.2-20 alkenyl (e.g.,
C.sub.2-6 alkenyl), (c2) C.sub.6-10 aryl, (d2) hydrogen, (e2)
C.sub.1-6 alk-C.sub.6-10 aryl, (f2) amino-C.sub.1-20 alkyl, (g2)
polyethylene glycol of
--(CH.sub.2).sub.s2(OCH.sub.2CH.sub.2).sub.s1(CH.sub.2).sub.s3OR',
wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6 or from 1
to 4), each of s2 and s3, independently, is an integer from 0 to 10
(e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1 to 6, or from
1 to 10), and R' is H or C.sub.1-20 alkyl, and (h2)
amino-polyethylene glycol of
--NR.sup.N1(CH.sub.2).sub.s2(CH.sub.2CH.sub.2O).sub.s1(CH.sub.2).sub.s3NR-
.sup.N1, wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6
or from 1 to 4), each of s2 and s3, independently, is an integer
from 0 to 10 (e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1
to 6, or from 1 to 10), and each R.sup.N1 is, independently,
hydrogen or optionally substituted C.sub.1-6 alkyl; (21) amidine;
and (22) silyl groups such as trimethylsilyl, t-butyldimethylsilyl,
and tri-isopropylsilyl. In some embodiments, each of these groups
can be further substituted as described herein. For example, the
alkylene group of a C1-alkaryl can be further substituted with an
oxo group to afford the respective aryloyl substituent.
[0098] The term "alkylene" and the prefix "alk-," as used herein,
represent a saturated divalent hydrocarbon group derived from a
straight or branched chain saturated hydrocarbon by the removal of
two hydrogen atoms, and is exemplified by methylene, ethylene,
isopropylene, and the like. The term "C.sub.x-y alkylene" and the
prefix "C.sub.x-y alk-" represent alkylene groups having between x
and y carbons. Exemplary values for x are 1, 2, 3, 4, 5, and 6, and
exemplary values for y are 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16,
18, or 20 (e.g., C.sub.1-6, C.sub.1-10, C.sub.2-20, C.sub.2-6,
C.sub.2-10, or C.sub.2-20 alkylene). In some embodiments, the
alkylene can be further substituted with 1, 2, 3, or 4 substituent
groups as defined herein for an alkyl group.
[0099] The term "alkenyl," as used herein, represents monovalent
straight or branched chain groups of, unless otherwise specified,
from 2 to 20 carbons (e.g., from 2 to 6 or from 2 to 10 carbons)
containing one or more carbon-carbon double bonds and is
exemplified by ethenyl, 1-propenyl, 2-propenyl,
2-methyl-1-propenyl, 1-butenyl, 2-butenyl, and the like. Alkenyls
include both cis and trans isomers. Alkenyl groups may be
optionally substituted with 1, 2, 3, or 4 substituent groups that
are selected, independently, from amino, aryl, cycloalkyl, or
heterocyclyl (e.g., heteroaryl), as defined herein, or any of the
exemplary alkyl substituent groups described herein.
[0100] The term "alkynyl," as used herein, represents monovalent
straight or branched chain groups from 2 to 20 carbon atoms (e.g.,
from 2 to 4, from 2 to 6, or from 2 to 10 carbons) containing a
carbon-carbon triple bond and is exemplified by ethynyl,
1-propynyl, and the like. Alkynyl groups may be optionally
substituted with 1, 2, 3, or 4 substituent groups that are
selected, independently, from aryl, cycloalkyl, or heterocyclyl
(e.g., heteroaryl), as defined herein, or any of the exemplary
alkyl substituent groups described herein.
[0101] The term "amino," as used herein, represents
--N(R.sup.N1).sub.2, wherein each R.sup.N1 is, independently, H,
OH, NO.sub.2, N(R.sup.N2).sub.2, SO.sub.2OR.sup.N2,
SO.sub.2R.sup.N2, SOR.sup.N2, an N-protecting group, alkyl,
alkenyl, alkynyl, alkoxy, aryl, alkaryl, cycloalkyl, alkcycloalkyl,
carboxyalkyl (e.g., optionally substituted with an O-protecting
group, such as optionally substituted arylalkoxycarbonyl groups or
any described herein), sulfoalkyl, acyl (e.g., acetyl,
trifluoroacetyl, or others described herein), alkoxycarbonylalkyl
(e.g., optionally substituted with an O-protecting group, such as
optionally substituted arylalkoxycarbonyl groups or any described
herein), heterocyclyl (e.g., heteroaryl), or alkheterocyclyl (e.g.,
alkheteroaryl), wherein each of these recited R.sup.N1 groups can
be optionally substituted, as defined herein for each group; or two
R.sup.N1 combine to form a heterocyclyl or an N-protecting group,
and wherein each R.sup.N2 is, independently, H, alkyl, or aryl. The
amino groups of the invention can be an unsubstituted amino (i.e.,
--NH.sub.2) or a substituted amino (i.e., --N(R.sup.N1).sub.2). In
a preferred embodiment, amino is --NH.sub.2 or --NHR.sup.N1,
wherein R.sup.N1 is, independently, OH, NO.sub.2, NH.sub.2,
NR.sup.N2.sub.2, SO.sub.2OR.sup.N2, SO.sub.2R.sup.N2, SOR.sup.N2,
alkyl, carboxyalkyl, sulfoalkyl, acyl (e.g., acetyl,
trifluoroacetyl, or others described herein), alkoxycarbonylalkyl
(e.g., t-butoxycarbonylalkyl) or aryl, and each R.sup.N2 can be H,
C.sub.1-20 alkyl (e.g., C.sub.1-6 alkyl), or C.sub.6-10 aryl.
[0102] The term "amino acid," as described herein, refers to a
molecule having a side chain, an amino group, and an acid group
(e.g., a carboxy group of --CO.sub.2H or a sulfo group of
--SO.sub.3H), wherein the amino acid is attached to the parent
molecular group by the side chain, amino group, or acid group
(e.g., the side chain). As used herein, the term "amino acid" in
its broadest sense, refers to any compound and/or substance that
can be incorporated into a polypeptide chain, e.g., through
formation of one or more peptide bonds. In some embodiments, an
amino acid has the general structure H.sub.2N--C(H)(R)--COOH. In
some embodiments, an amino acid is a naturally-occurring amino
acid. In some embodiments, an amino acid is a synthetic amino acid;
in some embodiments, an amino acid is a D-amino acid; in some
embodiments, an amino acid is an L-amino acid. "Standard amino
acid" refers to any of the twenty standard L-amino acids commonly
found in naturally occurring peptides. "Nonstandard amino acid"
refers to any amino acid, other than the standard amino acids,
regardless of whether it is prepared synthetically or obtained from
a natural source. In some embodiments, an amino acid, including a
carboxy- and/or amino-terminal amino acid in a polypeptide, can
contain a structural modification as compared with the general
structure above. For example, in some embodiments, an amino acid
may be modified by methylation, amidation, acetylation, and/or
substitution as compared with the general structure. In some
embodiments, such modification may, for example, alter the
circulating half life of a polypeptide containing the modified
amino acid as compared with one containing an otherwise identical
unmodified amino acid. In some embodiments, such modification does
not significantly alter a relevant activity of a polypeptide
containing the modified amino acid, as compared with one containing
an otherwise identical unmodified amino acid. As will be clear from
context, in some embodiments, the term "amino acid" is used to
refer to a free amino acid; in some embodiments it is used to refer
to an amino acid residue of a polypeptide. In some embodiments, the
amino acid is attached to the parent molecular group by a carbonyl
group, where the side chain or amino group is attached to the
carbonyl group. In some embodiments, the amino acid is an
.alpha.-amino acid. In certain embodiments, the amino acid is a
.beta.-amino acid. In some embodiments, the amino acid is a
.gamma.-amino acid. Exemplary side chains include an optionally
substituted alkyl, aryl, heterocyclyl, alkaryl, alkheterocyclyl,
aminoalkyl, carbamoylalkyl, and carboxyalkyl. Exemplary amino acids
include alanine, arginine, asparagine, aspartic acid, cysteine,
glutamic acid, glutamine, glycine, histidine, hydroxynorvaline,
isoleucine, leucine, lysine, methionine, norvaline, ornithine,
phenylalanine, proline, pyrrolysine, selenocysteine, serine,
taurine, threonine, tryptophan, tyrosine, and valine. Amino acid
groups may be optionally substituted with one, two, three, or, in
the case of amino acid groups of two carbons or more, four
substituents independently selected from the group consisting of:
(1) C.sub.1-6 alkoxy; (2) C.sub.1-6 alkylsulfinyl; (3) amino, as
defined herein (e.g., unsubstituted amino (i.e., --NH.sub.2) or a
substituted amino (i.e., --N(R.sup.N1).sub.2, where R.sup.N1 is as
defined for amino); (4) C.sub.6-10 aryl-C.sub.1-6 alkoxy; (5)
azido; (6) halo; (7) (C.sub.2-9 heterocyclyl)oxy; (8) hydroxyl; (9)
nitro; (10) oxo (e.g., carboxyaldehyde or acyl); (11) C.sub.1-7
spirocyclyl; (12) thioalkoxy; (13) thiol; (14) --CO.sub.2R.sup.A'
where R.sup.A' is selected from the group consisting of (a)
C.sub.1-20 alkyl (e.g., C.sub.1-6 alkyl), (b) C.sub.2-20 alkenyl
(e.g., C.sub.2-6 alkenyl), (c) C.sub.6-10 aryl, (d) hydrogen, (e)
C.sub.1-6 alk-C.sub.6-10 aryl, (f) amino-C.sub.1-20 alkyl, (g)
polyethylene glycol of
--(CH.sub.2).sub.s2(OCH.sub.2CH.sub.2).sub.s1(CH.sub.2).sub.s3OR',
wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6 or from 1
to 4), each of s2 and s3, independently, is an integer from 0 to 10
(e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1 to 6, or from
1 to 10), and R' is H or C.sub.1-20 alkyl, and (h)
amino-polyethylene glycol of
--NR.sup.N1(CH.sub.2).sub.s2(CH.sub.2CH.sub.2O).sub.s1(CH.sub.2).sub.s3NR-
.sup.N1, wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6
or from 1 to 4), each of s2 and s3, independently, is an integer
from 0 to 10 (e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1
to 6, or from 1 to 10), and each R.sup.N1 is, independently,
hydrogen or optionally substituted C.sub.1-6 alkyl; (15)
--C(O)NR.sup.B'R.sup.C', where each of R.sup.B' and R.sup.C' is,
independently, selected from the group consisting of (a) hydrogen,
(b) C.sub.1-6 alkyl, (c) C.sub.6-10 aryl, and (d) C.sub.1-6
alk-C.sub.6-10 aryl; (16) --SO.sub.2R.sup.D', where R.sup.D' is
selected from the group consisting of (a) C.sub.1-6 alkyl, (b)
C.sub.6-10 aryl, (c) C.sub.1-6 alk-C.sub.6-10 aryl, and (d)
hydroxyl; (17) --SO.sub.2NR.sup.E'R.sup.F' where each of R.sup.E'
and R.sup.F' is, independently, selected from the group consisting
of (a) hydrogen, (b) C.sub.1-6 alkyl, (c) C.sub.6-10 aryl and (d)
C.sub.1-6 alk-C.sub.6-10 aryl; (18) --C(O)R.sup.G', where R.sup.G'
is selected from the group consisting of (a) C.sub.1-20 alkyl
(e.g., C.sub.1-6 alkyl), (b) C.sub.2-20 alkenyl (e.g., C.sub.2-6
alkenyl), (c) C.sub.6-10 aryl, (d) hydrogen, (e) C.sub.1-6
alk-C.sub.6-10 aryl, (f) amino-C.sub.1-20 alkyl, (g) polyethylene
glycol of
--(CH.sub.2).sub.s2(OCH.sub.2CH.sub.2).sub.s1(CH.sub.2).sub.s3OR',
wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6 or from 1
to 4), each of s2 and s3, independently, is an integer from 0 to 10
(e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1 to 6, or from
1 to 10), and R' is H or C.sub.1-20 alkyl, and (h)
amino-polyethylene glycol of
--NR.sup.N1(CH.sub.2).sub.s2(CH.sub.2CH.sub.2O).sub.s1(CH.sub.2).sub.s3NR-
.sup.N1, wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6
or from to 4), each of s2 and s3, independently, is an integer from
0 to 10 (e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1 to 6,
or from 1 to 10), and each R.sup.N1 is, independently, hydrogen or
optionally substituted C.sub.1-6 alkyl; (19)
--NR.sup.H'C(O)R.sup.I', wherein R.sup.H' is selected from the
group consisting of (a1) hydrogen and (b1) C.sub.1-6 alkyl, and
R.sup.I' is selected from the group consisting of (a2) C.sub.1-20
alkyl (e.g., C.sub.1-6 alkyl), (b2) C.sub.2-20 alkenyl (e.g.,
C.sub.2-6 alkenyl), (c2) C.sub.6-10 aryl, (d2) hydrogen, (e2)
C.sub.1-6 alk-C.sub.6-10 aryl, (f2) amino-C.sub.1-20 alkyl, (g2)
polyethylene glycol of
--(CH.sub.2).sub.s2(OCH.sub.2CH.sub.2).sub.s1(CH.sub.2).sub.s3OR',
wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6 or from 1
to 4), each of s2 and s3, independently, is an integer from 0 to 10
(e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1 to 6, or from
1 to 10), and R' is H or C.sub.1-20 alkyl, and (h2)
amino-polyethylene glycol of
--NR.sup.N1(CH.sub.2).sub.s2(CH.sub.2CH.sub.2O).sub.s1(CH.sub.2).sub.s3NR-
.sup.N1, wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6
or from 1 to 4), each of s2 and s3, independently, is an integer
from 0 to 10 (e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1
to 6, or from 1 to 10), and each R.sup.N1 is, independently,
hydrogen or optionally substituted C.sub.1-6 alkyl; (20)
--NR.sup.J'C(O)OR.sup.K', wherein R.sup.J' is selected from the
group consisting of (a1) hydrogen and (b1) C.sub.1-6 alkyl, and
R.sup.K' is selected from the group consisting of (a2) C.sub.1-20
alkyl (e.g., C.sub.1-6 alkyl), (b2) C.sub.2-20 alkenyl (e.g.,
C.sub.2-6 alkenyl), (c2) C.sub.6-10 aryl, (d2) hydrogen, (e2)
C.sub.1-6 alk-C.sub.6-10 aryl, (f2) amino-C.sub.1-20 alkyl, (g2)
polyethylene glycol of
--(CH.sub.2).sub.s2(OCH.sub.2CH.sub.2).sub.s1(CH.sub.2).sub.s3OR',
wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6 or from 1
to 4), each of s2 and s3, independently, is an integer from 0 to 10
(e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1 to 6, or from
1 to 10), and R' is H or C.sub.1-20 alkyl, and (h2)
amino-polyethylene glycol of
--NR.sup.N1(CH.sub.2).sub.s2(CH.sub.2CH.sub.2O).sub.s1(CH.sub.2).sub.s3NR-
.sup.N1, wherein s1 is an integer from 1 to 10 (e.g., from 1 to 6
or from 1 to 4), each of s2 and s3, independently, is an integer
from 0 to 10 (e.g., from 0 to 4, from 0 to 6, from 1 to 4, from 1
to 6, or from 1 to 10), and each R.sup.N1 is, independently,
hydrogen or optionally substituted C.sub.1-6 alkyl; and (21)
amidine. In some embodiments, each of these groups can be further
substituted as described herein.
[0103] The term "N-alkylated amino acids" as used herein, refers to
amino acids containing an optionally substituted C.sub.1 to C.sub.6
alkyl on the nitrogen of the amino acid that forms the peptidic
bond. N-alkylated amino acids include, but are not limited to,
N-methyl amino acids, such as N-methyl-alanine, N-methyl-threonine,
N-methyl-phenylalanine, N-methyl-aspartic acid, N-methyl-valine,
N-methyl-leucine, N-methyl-glycine, N-methyl-isoleucine,
N(.alpha.)-methyl-lysine, N(.alpha.)-methyl-asparagine, and
N(.alpha.)-methyl-glutamine.
[0104] The term "aryl," as used herein, represents a mono-,
bicyclic, or multicyclic carbocyclic ring system having one or two
aromatic rings and is exemplified by phenyl, naphthyl,
1,2-dihydronaphthyl, 1,2,3,4-tetrahydronaphthyl, anthracenyl,
phenanthrenyl, fluorenyl, indanyl, indenyl, and the like, and may
be optionally substituted with 1, 2, 3, 4, or 5 substituents
independently selected from the group consisting of: (1) C.sub.1-7
acyl (e.g., carboxyaldehyde); (2) C.sub.1-20 alkyl (e.g., C.sub.1-6
alkyl, C.sub.1-6 alkoxy-C.sub.1-6 alkyl, C1-6
alkylsulfinyl-C.sub.1-6 alkyl, amino-C.sub.1-6 alkyl,
azido-C.sub.1-6 alkyl, (carboxyaldehyde)-C.sub.1-6 alkyl,
halo-C.sub.1-6 alkyl (e.g., perfluoroalkyl), hydroxy-C.sub.1-6
alkyl, nitro-C.sub.1-6 alkyl, or C.sub.1-6 thioalkoxy-C.sub.1-6
alkyl); (3) C.sub.1-20 alkoxy (e.g., C.sub.1-6 alkoxy, such as
perfluoroalkoxy); (4) C.sub.1-6 alkylsulfinyl; (5) C.sub.6-10 aryl;
(6) amino; (7) C.sub.1-6 alk-C.sub.6-10 aryl; (8) azido; (9)
C.sub.3-8 cycloalkyl; (10) C.sub.1-6 alk-C.sub.3-8 cycloalkyl; (11)
halo; (12) C.sub.1-12 heterocyclyl (e.g., C.sub.1-12 heteroaryl);
(13) (C.sub.1-12 heterocyclyl)oxy; (14) hydroxyl; (15) nitro; (16)
C.sub.1-20 thioalkoxy (e.g., C.sub.1-6 thioalkoxy); (17)
--(CH.sub.2).sub.qCO.sub.2R.sup.A', where q is an integer from zero
to four, and R.sup.A' is selected from the group consisting of (a)
C.sub.1-6 alkyl, (b) C.sub.6-10 aryl, (c) hydrogen, and (d)
C.sub.1-6 alk-C.sub.6-10 aryl; (18)
--(CH.sub.2).sub.qCONR.sup.B'R.sup.C', where q is an integer from
zero to four and where R.sup.B' and R.sup.C' are independently
selected from the group consisting of (a) hydrogen, (b) C.sub.1-6
alkyl, (c) C.sub.6-10 aryl, and (d) C.sub.1-6 alk-C.sub.6-10 aryl;
(19) --(CH.sub.2).sub.qSO.sub.2R.sup.D', where q is an integer from
zero to four and where R.sup.D' is selected from the group
consisting of (a) alkyl, (b) C.sub.6-10 aryl, and (c)
alk-C.sub.6-10 aryl; (20)
--(CH.sub.2).sub.qSO.sub.2NR.sup.E'R.sup.F', where q is an integer
from zero to four and where each of R.sup.E' and R.sup.F' is,
independently, selected from the group consisting of (a) hydrogen,
(b) C.sub.1-6 alkyl, (c) C.sub.6-10 aryl, and (d) C.sub.1-6
alk-C.sub.6-10 aryl; (21) thiol; (22) C.sub.6-10 aryloxy; (23)
C.sub.3-8 cycloalkoxy; (24) C.sub.6-10 aryl-C.sub.1-6 alkoxy; (25)
C.sub.1-6 alk-C.sub.1-12 heterocyclyl (e.g., C.sub.1-6
alk-C.sub.1-12 heteroaryl); (26) C.sub.2-20 alkenyl; and (27)
C.sub.2-20 alkynyl. In some embodiments, each of these groups can
be further substituted as described herein. For example, the
alkylene group of a C.sub.1-alkaryl or a C.sub.1-alkheterocyclyl
can be further substituted with an oxo group to afford the
respective aryloyl and (heterocyclyl)oyl substituent group.
[0105] The "arylalkyl" group, which as used herein, represents an
aryl group, as defined herein, attached to the parent molecular
group through an alkylene group, as defined herein. Exemplary
unsubstituted arylalkyl groups are from 7 to 30 carbons (e.g., from
7 to 16 or from 7 to 20 carbons, such as C.sub.1-6 alk-C.sub.6-10
aryl, C.sub.1-10 alk-C.sub.6-10 aryl, or C.sub.1-20 alk-C.sub.6-10
aryl). In some embodiments, the alkylene and the aryl each can be
further substituted with 1, 2, 3, or 4 substituent groups as
defined herein for the respective groups. Other groups preceded by
the prefix "alk-" are defined in the same manner, where "alk"
refers to a C.sub.1-6 alkylene, unless otherwise noted, and the
attached chemical structure is as defined herein.
[0106] The term "azido" represents an --N.sub.3 group, which can
also be represented as --N.dbd.N.dbd.N.
[0107] The terms "carbocyclic" and "carbocyclyl," as used herein,
refer to an optionally substituted C.sub.3-12 monocyclic, bicyclic,
or tricyclic non-aromatic ring structure in which the rings are
formed by carbon atoms. Carbocyclic structures include cycloalkyl,
cycloalkenyl, and cycloalkynyl groups.
[0108] The "carbocyclylalkyl" group, which as used herein,
represents a carbocyclic group, as defined herein, attached to the
parent molecular group through an alkylene group, as defined
herein. Exemplary unsubstituted carbocyclylalkyl groups are from 7
to 30 carbons (e.g., from 7 to 16 or from 7 to 20 carbons, such as
C.sub.1-6 alk-C.sub.6-10 carbocyclyl, C.sub.1-10 alk-C.sub.6-10
carbocyclyl, or C.sub.1-20 alk-C.sub.6-10 carbocyclyl). In some
embodiments, the alkylene and the carbocyclyl each can be further
substituted with 1, 2, 3, or 4 substituent groups as defined herein
for the respective groups. Other groups preceded by the prefix
"alk-" are defined in the same manner, where "alk" refers to a
C.sub.1-6 alkylene, unless otherwise noted, and the attached
chemical structure is as defined herein.
[0109] The term "carbonyl," as used herein, represents a C(O)
group, which can also be represented as C.dbd.O.
[0110] The term "carboxy," as used herein, means --CO.sub.2H.
[0111] The term "cyano," as used herein, represents an --CN
group.
[0112] The term "cycloalkyl," as used herein represents a
monovalent saturated or unsaturated non-aromatic cyclic hydrocarbon
group from three to eight carbons, unless otherwise specified, and
is exemplified by cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl,
cycloheptyl, bicycle heptyl, and the like. When the cycloalkyl
group includes one carbon-carbon double bond, the cycloalkyl group
can be referred to as a "cycloalkenyl" group. Exemplary
cycloalkenyl groups include cyclopentenyl, cyclohexenyl, and the
like. The cycloalkyl groups of this invention can be optionally
substituted with: (1) C.sub.1-7 acyl (e.g., carboxyaldehyde); (2)
C.sub.1-20 alkyl (e.g., C.sub.1-6 alkyl, C.sub.1-6 alkoxy-C.sub.1-6
alkyl, C.sub.1-6 alkylsulfinyl-C.sub.1-6 alkyl, amino-C.sub.1-6
alkyl, azido-C.sub.1-6 alkyl, (carboxyaldehyde)-C.sub.1-6 alkyl,
halo-C.sub.1-6 alkyl (e.g., perfluoroalkyl), hydroxy-C.sub.1-6
alkyl, nitro-C.sub.1-6 alkyl, or C.sub.1-6 thioalkoxy-C.sub.1-6
alkyl); (3) C.sub.1-20 alkoxy (e.g., C.sub.1-6 alkoxy, such as
perfluoroalkoxy); (4) C.sub.1-6 alkylsulfinyl; (5) C.sub.6-10 aryl;
(6) amino; (7) C.sub.1-6 alk-C.sub.6-10 aryl; (8) azido; (9)
C.sub.3-8 cycloalkyl; (10) C.sub.1-6 alk-C.sub.3-8 cycloalkyl; (11)
halo; (12) C.sub.1-12 heterocyclyl (e.g., C.sub.1-12 heteroaryl);
(13) (C.sub.1-12 heterocyclyl)oxy; (14) hydroxyl; (15) nitro; (16)
C.sub.1-20 thioalkoxy (e.g., C.sub.1-6 thioalkoxy); (17)
--(CH.sub.2).sub.qCO.sub.2R.sup.A' where q is an integer from zero
to four, and R.sup.A' is selected from the group consisting of (a)
C.sub.1-6 alkyl, (b) C.sub.6-10 aryl, (c) hydrogen, and (d)
C.sub.1-6 alk-C.sub.6-10 aryl; (18)
--(CH.sub.2).sub.qCONR.sup.B'R.sup.C', where q is an integer from
zero to four and where R.sup.B' and R.sup.C' are independently
selected from the group consisting of (a) hydrogen, (b) C.sub.6-10
alkyl, (c) C.sub.6-10 aryl, and (d) C.sub.1-6 alk-C.sub.6-10 aryl;
(19) --(CH.sub.2).sub.qSO.sub.2R.sup.D', where q is an integer from
zero to four and where R.sup.D' is selected from the group
consisting of (a) C.sub.6-10 alkyl, (b) C.sub.6-10 aryl, and (c)
C.sub.1-6 alk-C.sub.6-10 aryl; (20)
--(CH.sub.2).sub.qSO.sub.2NR.sup.E'R.sup.F', where q is an integer
from zero to four and where each of R.sup.E' and R.sup.F' is
independently, selected from the group consisting of (a) hydrogen,
(b) C.sub.6-10 alkyl, (c) C.sub.6-10 aryl, and (d) C.sub.1-6
alk-C.sub.6-10 aryl; (21) thiol; (22) C.sub.6-10 aryloxy; (23)
C.sub.3-8 cycloalkoxy; (24) C.sub.6-10 aryl-C.sub.1-6 alkoxy; (25)
C.sub.1-6 alk-C.sub.1-12 heterocyclyl (e.g., C.sub.1-6
alk-C.sub.1-12 heteroaryl); (26) oxo; (27) C.sub.2-20 alkenyl; and
(28) C.sub.2-20 alkynyl. In some embodiments, each of these groups
can be further substituted as described herein. For example, the
alkylene group of a C.sub.1-alkaryl or a C.sub.1-alkheterocyclyl
can be further substituted with an oxo group to afford the
respective aryloyl and (heterocyclyl)oyl substituent group.
[0113] The "cycloalkylalkyl" group, which as used herein,
represents a cycloalkyl group, as defined herein, attached to the
parent molecular group through an alkylene group, as defined herein
(e.g., an alkylene group of from 1 to 4, from 1 to 6, from 1 to 10,
or form 1 to 20 carbons). In some embodiments, the alkylene and the
cycloalkyl each can be further substituted with 1, 2, 3, or 4
substituent groups as defined herein for the respective group.
[0114] The term "diastereomer," as used herein means stereoisomers
that are not mirror images of one another and are
non-superimposable on one another.
[0115] The term "enantiomer," as used herein, means each individual
optically active form of a compound of the invention, having an
optical purity or enantiomeric excess (as determined by methods
standard in the art) of at least 80% (i.e., at least 90% of one
enantiomer and at most 10% of the other enantiomer), preferably at
least 90% and more preferably at least 98%.
[0116] The term "halo," as used herein, represents a halogen
selected from bromine, chlorine, iodine, or fluorine.
[0117] The term "heteroalkyl," as used herein, refers to an alkyl
group, as defined herein, in which one or two of the constituent
carbon atoms have each been replaced by nitrogen, oxygen, or
sulfur. In some embodiments, the heteroalkyl group can be further
substituted with 1, 2, 3, or 4 substituent groups as described
herein for alkyl groups. The terms "heteroalkenyl" and
heteroalkynyl," as used herein refer to alkenyl and alkynyl groups,
as defined herein, respectively, in which one or two of the
constituent carbon atoms have each been replaced by nitrogen,
oxygen, or sulfur. In some embodiments, the heteroalkenyl and
heteroalkynyl groups can be further substituted with 1, 2, 3, or 4
substituent groups as described herein for alkyl groups.
[0118] The term "heteroaryl," as used herein, represents that
subset of heterocyclyls, as defined herein, which are aromatic:
i.e., they contain 4n+2 pi electrons within the mono- or
multicyclic ring system. Exemplary unsubstituted heteroaryl groups
are of 1 to 12 (e.g., 1 to 11, 1 to 10, 1 to 9, 2 to 12, 2 to 11, 2
to 10, or 2 to 9) carbons. In some embodiment, the heteroaryl is
substituted with 1, 2, 3, or 4 substituents groups as defined for a
heterocyclyl group.
[0119] The term "heteroarylalkyl" refers to a heteroaryl group, as
defined herein, attached to the parent molecular group through an
alkylene group, as defined herein. Exemplary unsubstituted
heteroarylalkyl groups are from 2 to 32 carbons (e.g., from 2 to
22, from 2 to 18, from 2 to 17, from 2 to 16, from 3 to 15, from 2
to 14, from 2 to 13, or from 2 to 12 carbons, such as C.sub.1-6
alk-C.sub.1-12 heteroaryl, C.sub.1-10 alk-C.sub.1-12 heteroaryl, or
C.sub.1-20 alk-C.sub.1-12 heteroaryl). In some embodiments, the
alkylene and the heteroaryl each can be further substituted with 1,
2, 3, or 4 substituent groups as defined herein for the respective
group. Heteroarylalkyl groups are a subset of heterocyclylalkyl
groups.
[0120] The term "heterocyclyl," as used herein represents a 5-, 6-
or 7-membered ring, unless otherwise specified, containing one,
two, three, or four heteroatoms independently selected from the
group consisting of nitrogen, oxygen, and sulfur. The 5-membered
ring has zero to two double bonds, and the 6- and 7-membered rings
have zero to three double bonds. Exemplary unsubstituted
heterocyclyl groups are of 1 to 12 (e.g., 1 to 11, 1 to 10, 1 to 9,
2 to 12, 2 to 11, 2 to 10, or 2 to 9) carbons. The term
"heterocyclyl" also represents a heterocyclic compound having a
bridged multicyclic structure in which one or more carbons and/or
heteroatoms bridges two non-adjacent members of a monocyclic ring,
e.g., a quinuclidinyl group. The term "heterocyclyl" includes
bicyclic, tricyclic, and tetracyclic groups in which any of the
above heterocyclic rings is fused to one, two, or three carbocyclic
rings, e.g., an aryl ring, a cyclohexane ring, a cyclohexene ring,
a cyclopentane ring, a cyclopentene ring, or another monocyclic
heterocyclic ring, such as indolyl, quinolyl, isoquinolyl,
tetrahydroquinolyl, benzofuryl, benzothienyl and the like. Examples
of fused heterocyclyls include tropanes and
1,2,3,5,8,8a-hexahydroindolizine. Heterocyclics include pyrrolyl,
pyrrolinyl, pyrrolidinyl, pyrazolyl, pyrazolinyl, pyrazolidinyl,
imidazolyl, imidazolinyl, imidazolidinyl, pyridyl, piperidinyl,
homopiperidinyl, pyrazinyl, piperazinyl, pyrimidinyl, pyridazinyl,
oxazolyl, oxazolidinyl, isoxazolyl, isoxazolidiniyl, morpholinyl,
thiomorpholinyl, thiazolyl, thiazolidinyl, isothiazolyl,
isothiazolidinyl, indolyl, indazolyl, quinolyl, isoquinolyl,
quinoxalinyl, dihydroquinoxalinyl, quinazolinyl, cinnolinyl,
phthalazinyl, benzimidazolyl, benzothiazolyl, benzoxazolyl,
benzothiadiazolyl, furyl, thienyl, thiazolidinyl, isothiazolyl,
triazolyl, tetrazolyl, oxadiazolyl (e.g., 1,2,3-oxadiazolyl),
purinyl, thiadiazolyl (e.g., 1,2,3-thiadiazolyl),
tetrahydrofuranyl, dihydrofuranyl, tetrahydrothienyl,
dihydrothienyl, dihydroindolyl, dihydroquinolyl,
tetrahydroquinolyl, tetrahydroisoquinolyl, dihydroisoquinolyl,
pyranyl, dihydropyranyl, dithiazolyl, benzofuranyl,
isobenzofuranyl, benzothienyl, and the like, including dihydro and
tetrahydro forms thereof, where one or more double bonds are
reduced and replaced with hydrogens. Still other exemplary
heterocyclyls include: 2,3,4,5-tetrahydro-2-oxo-oxazolyl;
2,3-dihydro-2-oxo-1H-imidazolyl;
2,3,4,5-tetrahydro-5-oxo-1H-pyrazolyl (e.g.,
2,3,4,5-tetrahydro-2-phenyl-5-oxo-1H-pyrazolyl);
2,3,4,5-tetrahydro-2,4-dioxo-1H-imidazolyl (e.g.,
2,3,4,5-tetrahydro-2,4-dioxo-5-methyl-5-phenyl-1H-imidazolyl);
2,3-dihydro-2-thioxo-1,3,4-oxadiazolyl (e.g.,
2,3-dihydro-2-thioxo-5-phenyl-1,3,4-oxadiazolyl);
4,5-dihydro-5-oxo-1H-triazolyl (e.g., 4,5-dihydro-3-methyl-4-amino
5-oxo-1H-triazolyl); 1,2,3,4-tetrahydro-2,4-dioxopyridinyl (e.g.,
1,2,3,4-tetrahydro-2,4-dioxo-3,3-diethylpyridinyl);
2,6-dioxo-piperidinyl (e.g.,
2,6-dioxo-3-ethyl-3-phenylpiperidinyl);
1,6-dihydro-6-oxopyridiminyl; 1,6-dihydro-4-oxopyrimidinyl (e.g.,
2-(methylthio)-1,6-dihydro-4-oxo-5-methylpyrimidin-1-yl);
1,2,3,4-tetrahydro-2,4-dioxopyrimidinyl (e.g.,
1,2,3,4-tetrahydro-2,4-dioxo-3-ethylpyrimidinyl);
1,6-dihydro-6-oxo-pyridazinyl (e.g.,
1,6-dihydro-6-oxo-3-ethylpyridazinyl);
1,6-dihydro-6-oxo-1,2,4-triazinyl (e.g.,
1,6-dihydro-5-isopropyl-6-oxo-1,2,4-triazinyl);
2,3-dihydro-2-oxo-1H-indolyl (e.g.,
3,3-dimethyl-2,3-dihydro-2-oxo-1H-indolyl and
2,3-dihydro-2-oxo-3,3'-spiropropane-1H-indol-1-yl);
1,3-dihydro-1-oxo-2H-iso-indolyl;
1,3-dihydro-1,3-dioxo-2H-iso-indolyl; 1H-benzopyrazolyl (e.g.,
1-(ethoxycarbonyl)-1H-benzopyrazolyl);
2,3-dihydro-2-oxo-1H-benzimidazolyl (e.g.,
3-ethyl-2,3-dihydro-2-oxo-1H-benzimidazolyl);
2,3-dihydro-2-oxo-benzoxazolyl (e.g.,
5-chloro-2,3-dihydro-2-oxo-benzoxazolyl);
2,3-dihydro-2-oxo-benzoxazolyl; 2-oxo-2H-benzopyranyl;
1,4-benzodioxanyl; 1,3-benzodioxanyl;
2,3-dihydro-3-oxo,4H-1,3-benzothiazinyl;
3,4-dihydro-4-oxo-3H-quinazolinyl (e.g.,
2-methyl-3,4-dihydro-4-oxo-3H-quinazolinyl);
1,2,3,4-tetrahydro-2,4-dioxo-3H-quinazolyl (e.g.,
1-ethyl-1,2,3,4-tetrahydro-2,4-dioxo-3H-quinazolyl);
1,2,3,6-tetrahydro-2,6-dioxo-7H-purinyl (e.g.,
1,2,3,6-tetrahydro-1,3-dimethyl-2,6-dioxo-7H-purinyl);
1,2,3,6-tetrahydro-2,6-dioxo-1H-purinyl (e.g.,
1,2,3,6-tetrahydro-3,7-dimethyl-2,6-dioxo-1H-purinyl);
2-oxobenz[c,d]indolyl; 1,1-dioxo-2H-naphth[1,8-c,d]isothiazolyl;
and 1,8-naphthylenedicarboxamido. Additional heterocyclics include
3,3a,4,5,6,6a-hexahydro-pyrrolo[3,4-b]pyrrol-(2H)-yl, and
2,5-diazabicyclo[2.2.1]heptan-2-yl, homopiperazinyl (or
diazepanyl), tetrahydropyranyl, dithiazolyl, benzofuranyl,
benzothienyl, oxepanyl, thiepanyl, azocanyl, oxecanyl, and
thiocanyl. Heterocyclic groups also include groups of the
formula
##STR00025##
where
[0121] E' is selected from the group consisting of --N-- and
--CH--; F' is selected from the group consisting of --N.dbd.CH--,
--NH--CH.sub.2--, --NH--C(O)--, --NH--, --CH.dbd.N--,
--CH.sub.2--NH--, --C(O)--NH--, --CH.dbd.CH--, --CH.sub.2--,
--CH.sub.2CH.sub.2--, --CH.sub.2O--, --OCH.sub.2--, --O--, and
--S--; and G' is selected from the group consisting of --CH-- and
--N--. Any of the heterocyclyl groups mentioned herein may be
optionally substituted with one, two, three, four or five
substituents independently selected from the group consisting of:
(1) C.sub.1-7 acyl (e.g., carboxyaldehyde); (2) C.sub.1-20 alkyl
(e.g., C.sub.1-6 alkyl, C.sub.1-6 alkoxy-C.sub.1-6 alkyl, C.sub.1-6
alkylsulfinyl-C.sub.1-6 alkyl, amino-C.sub.1-6 alkyl,
azido-C.sub.1-6 alkyl, (carboxyaldehyde)-C.sub.1-6 alkyl, halo-C-B
alkyl (e.g., perfluoroalkyl), hydroxy-C.sub.1-6 alkyl,
nitro-C.sub.1-6 alkyl, or C.sub.1-6 thioalkoxy-C.sub.1-6 alkyl);
(3) C.sub.1-20 alkoxy (e.g., C.sub.1-6 alkoxy, such as
perfluoroalkoxy); (4) C.sub.1-6 alkylsulfinyl; (5) C.sub.6-10 aryl;
(6) amino; (7) C.sub.1-6 alk-C.sub.6-10 aryl; (8) azido; (9)
C.sub.3-8 cycloalkyl; (10) C.sub.1-6 alk-C.sub.3-8 cycloalkyl; (11)
halo; (12) C.sub.1-12 heterocyclyl (e.g., C.sub.2-12 heteroaryl);
(13) (C.sub.1-12 heterocyclyl)oxy; (14) hydroxyl; (15) nitro; (16)
C.sub.1-20 thioalkoxy (e.g., C.sub.1-6 thioalkoxy); (17)
--(CH.sub.2).sub.qCO.sub.2R.sup.A', where q is an integer from zero
to four, and R.sup.A' is selected from the group consisting of (a)
C.sub.1-6 alkyl, (b) C.sub.6-10 aryl, (c) hydrogen, and (d)
C.sub.1-6 alk-C.sub.6-10 aryl; (18)
--(CH.sub.2).sub.qCONR.sup.B'R.sup.C', where q is an integer from
zero to four and where R.sup.B' and R.sup.C' are independently
selected from the group consisting of (a) hydrogen, (b) C.sub.1-6
alkyl, (c) C.sub.6-10 aryl, and (d) C.sub.1-6 alk-C.sub.6-10 aryl;
(19) --(CH.sub.2).sub.qSO.sub.2R.sup.D', where q is an integer from
zero to four and where R.sup.D' is selected from the group
consisting of (a) C.sub.1-6 alkyl, (b) C.sub.6-10 aryl, and (c)
C.sub.1-6 alk-C.sub.6-10 aryl; (20)
--(CH.sub.2).sub.qSO.sub.2NR.sup.E'R.sup.F', where q is an integer
from zero to four and where each of R.sup.E' and R.sup.F' is,
independently, selected from the group consisting of (a) hydrogen,
(b) C.sub.1-6 alkyl, (c) C.sub.6-10 aryl, and (d) C.sub.1-6
alk-C.sub.6-10 aryl; (21) thiol; (22) C.sub.6-10 aryloxy; (23)
C.sub.3-8 cycloalkoxy; (24) arylalkoxy; (25) C.sub.1-6
alk-C.sub.1-12 heterocyclyl (e.g., C.sub.1-6 alk-C.sub.1-12
heteroaryl); (26) oxo; (27) (C.sub.1-12 heterocyclyl)imino; (28)
C.sub.2-20 alkenyl; and (29) C.sub.2-20 alkynyl. In some
embodiments, each of these groups can be further substituted as
described herein. For example, the alkylene group of a
C.sub.1-alkaryl or a C.sub.1-alkheterocyclyl can be further
substituted with an oxo group to afford the respective aryloyl and
(heterocyclyl)oyl substituent group.
[0122] The "heterocyclylalkyl" group, which as used herein,
represents a heterocyclyl group, as defined herein, attached to the
parent molecular group through an alkylene group, as defined
herein. Exemplary unsubstituted heterocyclylalkyl groups are from 2
to 32 carbons (e.g., from 2 to 22, from 2 to 18, from 2 to 17, from
2 to 16, from 3 to 15, from 2 to 14, from 2 to 13, or from 2 to 12
carbons, such as C.sub.1-6 alk-C.sub.1-12 heterocyclyl, C.sub.1-10
alk-C.sub.1-12 heterocyclyl, or C.sub.1-20 alk-C.sub.1-12
heterocyclyl). In some embodiments, the alkylene and the
heterocyclyl each can be further substituted with 1, 2, 3, or 4
substituent groups as defined herein for the respective group.
[0123] The term "hydrocarbon," as used herein, represents a group
consisting only of carbon and hydrogen atoms.
[0124] The term "hydroxyl," as used herein, represents an --OH
group. In some embodiments, the hydroxyl group can be substituted
with 1, 2, 3, or 4 substituent groups (e.g., O-protecting groups)
as defined herein for an alkyl.
[0125] The term "isomer," as used herein, means any tautomer,
stereoisomer, enantiomer, or diastereomer of any compound of the
invention. It is recognized that the compounds of the invention can
have one or more chiral centers and/or double bonds and, therefore,
exist as stereoisomers, such as double-bond isomers (i.e.,
geometric E/Z isomers) or diastereomers (e.g., enantiomers (i.e.,
(+) or (-)) or cis/trans isomers). According to the invention, the
chemical structures depicted herein, and therefore the compounds of
the invention, encompass all of the corresponding stereoisomers,
that is, both the stereomerically pure form (e.g., geometrically
pure, enantiomerically pure, or diastereomerically pure) and
enantiomeric and stereoisomeric mixtures, e.g., racemates.
Enantiomeric and stereoisomeric mixtures of compounds of the
invention can typically be resolved into their component
enantiomers or stereoisomers by well-known methods, such as
chiral-phase gas chromatography, chiral-phase high performance
liquid chromatography, crystallizing the compound as a chiral salt
complex, or crystallizing the compound in a chiral solvent.
Enantiomers and stereoisomers can also be obtained from
stereomerically or enantiomerically pure intermediates, reagents,
and catalysts by well-known asymmetric synthetic methods.
[0126] The term "N-protected amino," as used herein, refers to an
amino group, as defined herein, to which is attached one or two
N-protecting groups, as defined herein.
[0127] The term "N-protecting group," as used herein, represents
those groups intended to protect an amino group against undesirable
reactions during synthetic procedures. Commonly used N-protecting
groups are disclosed in Greene, "Protective Groups in Organic
Synthesis," 3.sup.rd Edition (John Wiley & Sons, New York,
1999), which is incorporated herein by reference. N-protecting
groups include acyl, aryloyl, or carbamyl groups such as formyl,
acetyl, propionyl, pivaloyl, t-butylacetyl, 2-chloroacetyl,
2-bromoacetyl, trifluoroacetyl, trichloroacetyl, phthalyl,
o-nitrophenoxyacetyl, .alpha.-chlorobutyryl, benzoyl,
4-chlorobenzoyl, 4-bromobenzoyl, 4-nitrobenzoyl, and chiral
auxiliaries such as protected or unprotected D, L or D, L-amino
acids such as alanine, leucine, phenylalanine, and the like;
sulfonyl-containing groups such as benzenesulfonyl,
p-toluenesulfonyl, and the like; carbamate forming groups such as
benzyloxycarbonyl, p-chlorobenzyloxycarbonyl,
p-methoxybenzyloxycarbonyl, p-nitrobenzyloxycarbonyl,
2-nitrobenzyloxycarbonyl, p-bromobenzyloxycarbonyl,
3,4-dimethoxybenzyloxycarbonyl, 3,5-dimethoxybenzyloxycarbonyl,
2,4-dimethoxybenzyloxycarbonyl, 4-methoxybenzyloxycarbonyl,
2-nitro-4,5-dimethoxybenzyloxycarbonyl,
3,4,5-trimethoxybenzyloxycarbonyl,
1-(p-biphenylyl)-1-methylethoxycarbonyl,
.alpha.,.alpha.-dimethyl-3,5-dimethoxybenzyloxycarbonyl,
benzhydryloxy carbonyl, t-butyloxycarbonyl,
diisopropylmethoxycarbonyl, isopropyloxycarbonyl, ethoxycarbonyl,
methoxycarbonyl, allyloxycarbonyl, 2,2,2-trichloroethoxycarbonyl,
phenoxycarbonyl, 4-nitrophenoxy carbonyl,
fluorenyl-9-methoxycarbonyl, cyclopentyloxycarbonyl,
adamantyloxycarbonyl, cyclohexyloxycarbonyl, phenylthiocarbonyl,
and the like, alkaryl groups such as benzyl, triphenylmethyl,
benzyloxymethyl, and the like and silyl groups, such as
trimethylsilyl, and the like. Preferred N-protecting groups are
formyl, acetyl, benzoyl, pivaloyl, t-butylacetyl, alanyl,
phenylsulfonyl, benzyl, t-butyloxycarbonyl (Boc), and
benzyloxycarbonyl (Cbz).
[0128] The term "nitro," as used herein, represents an --NO.sub.2
group.
[0129] The term "O-protecting group," as used herein, represents
those groups intended to protect an oxygen containing (e.g.,
phenol, hydroxyl, or carbonyl) group against undesirable reactions
during synthetic procedures. Commonly used O-protecting groups are
disclosed in Greene, "Protective Groups in Organic Synthesis,"
3.sup.rd Edition (John Wiley & Sons, New York, 1999), which is
incorporated herein by reference. Exemplary O-protecting groups
include acyl, aryloyl, or carbamyl groups, such as formyl, acetyl,
propionyl, pivaloyl, t-butylacetyl, 2-chloroacetyl, 2-bromoacetyl,
trifluoroacetyl, trichloroacetyl, phthalyl, o-nitrophenoxyacetyl,
.alpha.-chlorobutyryl, benzoyl, 4-chlorobenzoyl, 4-bromobenzoyl,
t-butyldimethylsilyl, tri-iso-propylsilyloxymethyl,
4,4'-dimethoxytrityl, isobutyryl, phenoxyacetyl,
4-isopropylpehenoxyacetyl, dimethylformamidino, and 4-nitrobenzoyl;
alkylcarbonyl groups, such as acyl, acetyl, propionyl, pivaloyl,
and the like; optionally substituted arylcarbonyl groups, such as
benzoyl; silyl groups, such as trimethylsilyl (TMS),
tert-butyldimethylsilyl (TBDMS), tri-iso-propylsilyloxymethyl
(TOM), triisopropylsilyl (TIPS), and the like; ether-forming groups
with the hydroxyl, such methyl, methoxymethyl, tetrahydropyranyl,
benzyl, p-methoxybenzyl, trityl, and the like; alkoxycarbonyls,
such as methoxycarbonyl, ethoxycarbonyl, isopropoxycarbonyl,
n-isopropoxycarbonyl, n-butyloxycarbonyl, isobutyloxycarbonyl,
sec-butyloxycarbonyl, t-butyloxycarbonyl, 2-ethylhexyloxycarbonyl,
cyclohexyloxycarbonyl, methyloxycarbonyl, and the like;
alkoxyalkoxycarbonyl groups, such as methoxymethoxycarbonyl,
ethoxymethoxycarbonyl, 2-methoxyethoxycarbonyl,
2-ethoxyethoxycarbonyl, 2-butoxyethoxycarbonyl,
2-methoxyethoxymethoxycarbonyl, allyloxycarbonyl,
propargyloxycarbonyl, 2-butenoxycarbonyl,
3-methyl-2-butenoxycarbonyl, and the like; haloalkoxycarbonyls,
such as 2-chloroethoxycarbonyl, 2-chloroethoxycarbonyl,
2,2,2-trichloroethoxycarbonyl, and the like; optionally substituted
arylalkoxycarbonyl groups, such as benzyloxycarbonyl,
p-methylbenzyloxycarbonyl, p-methoxybenzyloxycarbonyl,
p-nitrobenzyloxycarbonyl, 2,4-dinitrobenzyloxycarbonyl,
3,5-dimethylbenzyloxycarbonyl, p-chlorobenzyloxycarbonyl,
p-bromobenzyloxy-carbonyl, fluorenylmethyloxycarbonyl, and the
like; and optionally substituted aryloxycarbonyl groups, such as
phenoxycarbonyl, p-nitrophenoxycarbonyl, o-nitrophenoxycarbonyl,
2,4-dinitrophenoxycarbonyl, p-methyl-phenoxycarbonyl,
m-methylphenoxycarbonyl, o-bromophenoxycarbonyl,
3,5-dimethylphenoxycarbonyl, p-chlorophenoxycarbonyl,
2-chloro-4-nitrophenoxy-carbonyl, and the like); substituted alkyl,
aryl, and alkaryl ethers (e.g., trityl; methylthiomethyl;
methoxymethyl; benzyloxymethyl; siloxymethyl;
2,2,2-trichloroethoxymethyl; tetrahydropyranyl; tetrahydrofuranyl;
ethoxyethyl; 1-[2-(trimethylsilyl)ethoxy]ethyl;
2-trimethylsilylethyl; t-butyl ether; p-chlorophenyl,
p-methoxyphenyl, p-nitrophenyl, benzyl, p-methoxybenzyl, and
nitrobenzyl); silyl ethers (e.g., trimethylsilyl; triethylsilyl;
triisopropylsilyl; dimethylisopropylsilyl; t-butyldimethylsilyl;
t-butyldiphenylsilyl; tribenzylsilyl; triphenylsilyl; and
diphenymethylsilyl); carbonates (e.g., methyl, methoxymethyl,
9-fluorenylmethyl; ethyl; 2,2,2-trichloroethyl;
2-(trimethylsilyl)ethyl; vinyl, allyl, nitrophenyl; benzyl;
methoxybenzyl; 3,4-dimethoxybenzyl; and nitrobenzyl);
carbonyl-protecting groups (e.g., acetal and ketal groups, such as
dimethyl acetal, 1,3-dioxolane, and the like; acylal groups; and
dithiane groups, such as 1,3-dithianes, 1,3-dithiolane, and the
like); carboxylic acid-protecting groups (e.g., ester groups, such
as methyl ester, benzyl ester, t-butyl ester, orthoesters, and the
like; and oxazoline groups.
[0130] The term "oxo" as used herein, represents .dbd.O.
[0131] The prefix "perfluoro," as used herein, represents anyl
group, as defined herein, where each hydrogen radical bound to the
alkyl group has been replaced by a fluoride radical. For example,
perfluoroalkyl groups are exemplified by trifluoromethyl,
pentafluoroethyl, and the like.
[0132] The term "protected hydroxyl," as used herein, refers to an
oxygen atom bound to an O-protecting group.
[0133] The term "spirocyclyl," as used herein, represents a
C.sub.2-7 alkylene diradical, both ends of which are bonded to the
same carbon atom of the parent group to form a spirocyclic group,
and also a C.sub.1-6 heteroalkylene diradical, both ends of which
are bonded to the same atom. The heteroalkylene radical forming the
spirocyclyl group can containing one, two, three, or four
heteroatoms independently selected from the group consisting of
nitrogen, oxygen, and sulfur. In some embodiments, the spirocyclyl
group includes one to seven carbons, excluding the carbon atom to
which the diradical is attached. The spirocyclyl groups of the
invention may be optionally substituted with 1, 2, 3, or 4
substituents provided herein as optional substituents for
cycloalkyl and/or heterocyclyl groups.
[0134] The term "stereoisomer," as used herein, refers to all
possible different isomeric as well as conformational forms which a
compound may possess (e.g., a compound of any formula described
herein), in particular all possible stereochemically and
conformationally isomeric forms, all diastereomers, enantiomers
and/or conformers of the basic molecular structure. Some compounds
of the present invention may exist in different tautomeric forms,
all of the latter being included within the scope of the present
invention.
[0135] The term "sulfonyl," as used herein, represents an
--S(O).sub.2-- group.
[0136] The term "thiol," as used herein. represents an --SH
group.
Definitions
[0137] In this application, unless otherwise clear from context,
(i) the term "a" may be understood to mean "at least one"; (ii) the
term "or" may be understood to mean "and/or"; (iii) the terms
"comprising" and "including" may be understood to encompass
itemized components or steps whether presented by themselves or
together with one or more additional components or steps; and (iv)
the terms "about" and "approximately" may be understood to permit
standard variation as would be understood by those of ordinary
skill in the art; and (v) where ranges are provided, endpoints are
included.
[0138] As used herein, the term ".pi.-effect interaction" refers to
attractive, non-covalent interactions between aromatic rings.
[0139] As used herein, the term "active site" refers to the
location on a protein (e.g., an enzyme) where substrate molecules
bind and undergo a chemical reaction. By "does not bind at the
active site" is meant that no atoms of a compound or complex
substantially participate in binding with residues within the
active site (e.g., residues that participate in binding to a
natural substrate molecule).
[0140] As used herein, the term "administration" refers to the
administration of a composition (e.g., a compound, a complex or a
preparation that includes a compound or complex as described
herein) to a subject or system. Administration to an animal subject
(e.g., to a human) may be by any appropriate route. For example, in
some embodiments, administration may be bronchial (including by
bronchial instillation), buccal, enteral, interdermal,
intra-arterial, intradermal, intragastric, intramedullary,
intramuscular, intranasal, intraperitoneal, intrathecal,
intravenous, intraventricular, mucosal, nasal, oral, rectal,
subcutaneous, sublingual, topical, tracheal (including by
intratracheal instillation), transdermal, vaginal and vitreal.
[0141] As is known in the art, "affinity" is a measure of the
tightness with which a particular ligand binds to its partner.
Affinities can be measured in different ways. In some embodiments,
affinity is measured by a quantitative assay. In some such
embodiments, binding partner concentration may be fixed to be in
excess of ligand concentration so as to mimic physiological
conditions. Alternatively or additionally, in some embodiments,
binding partner concentration and/or ligand concentration may be
varied. In some such embodiments, affinity may be compared to a
reference under comparable conditions (e.g., concentrations).
[0142] As used herein, the term "analog" refers to a substance that
shares one or more particular structural features, elements,
components, or moieties with a reference substance. Typically, an
"analog" shows significant structural similarity with the reference
substance, for example sharing a core or consensus structure, but
also differs in certain discrete ways. In some embodiments, an
analog is a substance that can be generated from the reference
substance by chemical manipulation of the reference substance. In
some embodiments, an analog is a substance that can be generated
through performance of a synthetic process substantially similar to
(e.g., sharing a plurality of steps with) one that generates the
reference substance. In some embodiments, an analog is or can be
generated through performance of a synthetic process different from
that used to generate the reference substance.
[0143] As used herein, the term "animal" refers to any member of
the animal kingdom. In some embodiments, "animal" refers to humans,
at any stage of development. In some embodiments, "animal" refers
to non-human animals, at any stage of development. In some
embodiments, the non-human animal is a mammal (e.g., a rodent, a
mouse, a rat, a rabbit, a monkey, a dog, a cat, a sheep, cattle, a
primate, and/or a pig). In some embodiments, animals include, but
are not limited to, mammals, birds, reptiles, amphibians, fish,
and/or worms. In some embodiments, an animal may be a transgenic
animal, genetically-engineered animal, and/or a clone.
[0144] As used herein, the term "antagonist" refers to a compound
that i) inhibits, decreases or reduces the effects of a target
protein (e.g., a eukaryotic target protein such as a mammalian
target protein or a fungal target protein or a prokaryotic target
protein such as a bacterial target protein); and/or ii) inhibits,
decreases, reduces, or delays one or more biological events. An
antagonist may be direct (in which case it exerts its influence
directly upon its target) or indirect (in which case it exerts its
influence by other than binding to its target; e.g., by interacting
with a regulator of the target protein (e.g., a eukaryotic target
protein such as a mammalian target protein or a fungal target
protein or a prokaryotic target protein such as a bacterial target
protein), for example so that level or activity of the target
protein is altered).
[0145] As used herein, the terms "approximately" and "about" are
each intended to encompass normal statistical variation as would be
understood by those of ordinary skill in the art as appropriate to
the relevant context. In certain embodiments, the terms
"approximately" or "about" each refer to a range of values that
fall within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%,
10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or less in either
direction (greater than or less than) of a stated value, unless
otherwise stated or otherwise evident from the context (e.g., where
such number would exceed 100% of a possible value).
[0146] Two events or entities are "associated" with one another, as
that term is used herein, if the presence, level and/or form of one
is correlated with that of the other. For example, a particular
entity (e.g., polypeptide) is considered to be associated with a
particular disease, disorder, or condition, if its presence, level
and/or form correlates with incidence of and/or susceptibility of
the disease, disorder, or condition (e.g., across a relevant
population). In some embodiments, two or more entities are
physically "associated" with one another if they interact, directly
or indirectly, so that they are and remain in physical proximity
with one another. In some embodiments, two or more entities that
are physically associated with one another are covalently linked to
one another; in some embodiments, two or more entities that are
physically associated with one another are not covalently linked to
one another but are non-covalently associated, for example by means
of hydrogen bonds, van der Waals interaction, hydrophobic
interactions, magnetism, and combinations thereof.
[0147] It will be understood that the term "binding" as used
herein, typically refers to association (e.g., non-covalent or
covalent) between or among two or more entities. "Direct" binding
involves physical contact between entities or moieties; indirect
binding involves physical interaction by way of physical contact
with one or more intermediate entities. Binding between two or more
entities can typically be assessed in any of a variety of
contexts--including where interacting entities or moieties are
studied in isolation or in the context of more complex systems
(e.g., while covalently or otherwise associated with a carrier
entity and/or in a biological system or cell).
[0148] The affinity of a molecule X for its partner Y can generally
be represented by the dissociation constant (K.sub.D). Affinity can
be measured by common methods known in the art, including those
described herein. Specific illustrative and exemplary embodiments
for measuring binding affinity are described below. The term
"K.sub.D," as used herein, is intended to refer to the dissociation
equilibrium constant of a particular compound-protein or
complex-protein interaction. Typically, the compounds of the
invention bind to presenter proteins with a dissociation
equilibrium constant (K.sub.D) of less than about 10.sup.-6 M, such
as less than approximately 10.sup.-7 M, 10.sup.-8 M, 10.sup.-9 M,
or 10.sup.-10 M or even lower, e.g., when determined by surface
plasmon resonance (SPR) technology using the presenter protein as
the analyte and the compound as the ligand. The presenter
protein/compound complexes of the invention bind to target proteins
(e.g., a eukaryotic target protein such as a mammalian target
protein or a fungal target protein or a prokaryotic target protein
such as a bacterial target protein) with a dissociation equilibrium
constant (K.sub.D) of less than about 10.sup.-6 M, such as less
than approximately 10.sup.-7 M, 10.sup.-8 M, 10.sup.-9 M, or
10.sup.-10 M or even lower, e.g., when determined by surface
plasmon resonance (SPR) technology using the target protein as the
analyte and the complex as the ligand.
[0149] As used herein, the term "binding free energy" refers to the
difference in energy between bound and unbound states of a complex.
Binding free energy may be determined by methods known in the art
including using the equation .DELTA.G=-RTInK using an
experimentally derived dissociation constant, Kd. Binding free
energy can be calculated using a computational algorithm known in
the art, e.g., molecular dynamic simulations, free-energy
perturbations or Monte Carlo protocols, as implemented in
commercial software such as AMBER (Cornell et al. J. Am. Chem. Soc.
1995, 117, 5179) CHARMM (Brooks et al. J. Comp. Chem. 1983, 4,
187), or Desmond (Boowers et al. Proc. ACM/IEEE Conf.
Supercomputing, 2006, SCO6).
[0150] As used herein, the term "buried surface area" refers to the
surface area of a protein or a complex that is not exposed to
solvent. Buried surface area may be determined by methods known in
the art including by calculating inaccessibility to solvent.
Inaccessibility to solvent may be calculated computationally with a
rolling probe of 1.4 A, using a program such as PDBePISA release
version 1.48 (http://www.ebi.ac.uk/pdbe/pisa/).
[0151] As used herein, the term "cell penetrant" refers to
compounds that when added to a cell's environment can enter the
intracellular domain without killing the cell. Whether a compound
is cell penetrant may be determined using any method known in the
art, e.g., the biosensor method described herein
[0152] As used herein, the term "characteristic portion" is used,
in the broadest sense, to refer to a portion of a substance whose
presence (or absence) correlates with presence (or absence) of a
particular feature, attribute, or activity of the substance. In
some embodiments, a characteristic portion of a substance is a
portion that is found in the substance and in related substances
that share the particular feature, attribute or activity, but not
in those that do not share the particular feature, attribute or
activity. In certain embodiments, a characteristic portion shares
at least one functional characteristic with the intact substance.
For example, in some embodiments, a "characteristic portion" of a
protein or polypeptide is one that contains a continuous stretch of
amino acids, or a collection of continuous stretches of amino
acids, that together are characteristic of a protein or
polypeptide. In some embodiments, each such continuous stretch
generally contains at least 2, 5, 10, 15, 20, 50, or more amino
acids. In general, a characteristic portion of a substance (e.g.,
of a protein, antibody, etc.) is one that, in addition to the
sequence and/or structural identity specified above, shares at
least one functional characteristic with the relevant intact
substance. In some embodiments, a characteristic portion may be
biologically active.
[0153] As used herein, the phrase "characteristic sequence element"
refers to a sequence element found in a polymer (e.g., in a
polypeptide or nucleic acid) that represents a characteristic
portion of that polymer. In some embodiments, presence of a
characteristic sequence element correlates with presence or level
of a particular activity or property of the polymer. In some
embodiments, presence (or absence) of a characteristic sequence
element defines a particular polymer as a member (or not a member)
of a particular family or group of such polymers. A characteristic
sequence element typically comprises at least two monomers (e.g.,
amino acids or nucleotides). In some embodiments, a characteristic
sequence element includes at least 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 20, 25, 30, 35, 40, 45, 50, or more monomers (e.g.,
contiguously linked monomers). In some embodiments, a
characteristic sequence element includes at least first and second
stretches of contiguous monomers spaced apart by one or more spacer
regions whose length may or may not vary across polymers that share
the sequence element. In certain embodiments, particular
characteristic sequence elements may be referred to as
"motifs".
[0154] As used herein, the term "c log P" refers to the calculated
partition coefficient of a molecule or portion of a molecule. The
partition coefficient is the ratio of concentrations of a compound
in a mixture of two immiscible phases at equilibrium (e.g., octanol
and water) and measures the hydrophobicity or hydrophilicity of a
compound. A variety of methods are available in the art for
determining c log P For example, in some embodiments, c log P can
be determined using quantitative structure-property relationship
algorithms known in the art (e.g., using fragment based prediction
methods that predict the log P of a compound by determining the sum
of its non-overlapping molecular fragments). Several algorithms for
calculating c log P are known in the art including those used by
molecular editing software such as CHEMDRAW.RTM. Pro, Version
12.0.2.1092 (Cambridgesoft, Cambridge, Mass.) and MARVINSKETCH.RTM.
(ChemAxon, Budapest, Hungary). A compound is considered to have met
a threshold c Log P if it meets the threshold in at least one of
the above methods.
[0155] As used herein, the term "collection" refers to a group of
2, 5, 10, 10.sup.2, 10.sup.3, 10.sup.4, 10.sup.5, 10.sup.6,
10.sup.7, 10.sup.8, 10.sup.9, or more different molecules. In some
embodiments, at least 10% (e.g., at least 20%, at least 30%, at
least 40%, at least 50%, at least 60%, at least 70%, at least 80%,
at least 90%, at least 95%, at least 99% or 100%) of the compounds
in the collection are compounds (e.g., macrocyclic compounds)s
described herein.
[0156] As used herein, the term "combination therapy" refers to
those situations in which a subject is simultaneously exposed to
two or more therapeutic regimens (e.g., two or more compounds such
as macrocyclic compounds). In some embodiments, two or more
compounds may be administered simultaneously; in some embodiments,
such compounds may be administered sequentially; in some
embodiments, such compounds are administered in overlapping dosing
regimens.
[0157] The term "comparable," as used herein, refers to two or more
compounds, entities, situations, sets of conditions, etc that may
not be identical to one another but that are sufficiently similar
to permit comparison therebetween so that conclusions may
reasonably be drawn based on differences or similarities observed.
In some embodiments, comparable sets of conditions, circumstances,
individuals, or populations are characterized by a plurality of
substantially identical features and one or a small number of
varied features. Those of ordinary skill in the art will
understand, in context, what degree of identity is required in any
given circumstance for two or more such compounds, entities,
situations, sets of conditions, etc to be considered comparable.
For example, those of ordinary skill in the art will appreciate
that sets of circumstances, individuals, or populations are
comparable to one another when characterized by a sufficient number
and type of substantially identical features to warrant a
reasonable conclusion that differences in results obtained or
phenomena observed under or with different sets of circumstances,
individuals, or populations are caused by or indicative of the
variation in those features that are varied.
[0158] As used herein, the term "complex" refers to a group of two
or more compounds and/or proteins which are bound together through
a binding interaction (e.g., a non-covalent interaction, such as a
hydrophobic effect interaction, an electrostatic interaction, a van
der Waals interaction, or .pi.-effect interaction). Examples of
complexes are "presenter protein/compound complex" which include a
compound of the invention bound to a presenter protein.
[0159] As used herein, the term "corresponding to" is often used to
designate a structural element or moiety in an compound of interest
that shares a position (e.g., in three-dimensional space or
relative to another element or moiety) with one present in an
appropriate reference compound. For example, in some embodiments,
the term is used to refer to position/identity of a residue in a
polymer, such as an amino acid residue in a polypeptide or a
nucleotide residue in a nucleic acid. Those of ordinary skill will
appreciate that, for purposes of simplicity, residues in such a
polymer are often designated using a canonical numbering system
based on a reference related polymer, so that a residue in a first
polymer "corresponding to" a residue at position 190 in the
reference polymer, for example, need not actually be the 190.sup.th
residue in the first polymer but rather corresponds to the residue
found at the 190.sup.th position in the reference polymer; those of
ordinary skill in the art readily appreciate how to identify
"corresponding" amino acids, including through use of one or more
commercially-available algorithms specifically designed for polymer
sequence comparisons.
[0160] As used herein, the term "designed" refers to a compound (i)
whose structure is or was selected by the hand of man; (ii) that is
produced by a process requiring the hand of man; and/or (iii) that
is distinct from natural substances and other known compounds.
[0161] Many methodologies described herein include a step of
"determining." Those of ordinary skill in the art, reading the
present specification, will appreciate that such "determining" can
utilize or be accomplished through use of any of a variety of
techniques available to those skilled in the art, including for
example specific techniques explicitly referred to herein. In some
embodiments, determining involves manipulation of a physical
sample. In some embodiments, determining involves consideration
and/or manipulation of data or information, for example utilizing a
computer or other processing unit adapted to perform a relevant
analysis. In some embodiments, determining involves receiving
relevant information and/or materials from a source. In some
embodiments, determining involves comparing one or more features of
a sample or entity to a comparable reference.
[0162] As used herein, the term "depsi-linkage" refers to the
replacement of an amide bond with an ester bond.
[0163] As used herein, the term "dosage form" refers to a
physically discrete unit of an active compound (e.g., a therapeutic
or diagnostic agent) for administration to a subject. Each unit
contains a predetermined quantity of active agent. In some
embodiments, such quantity is a unit dosage amount (or a whole
fraction thereof) appropriate for administration in accordance with
a dosing regimen that has been determined to correlate with a
desired or beneficial outcome when administered to a relevant
population (i.e., with a therapeutic dosing regimen). Those of
ordinary skill in the art appreciate that the total amount of a
therapeutic composition or compound administered to a particular
subject is determined by one or more attending physicians and may
involve administration of multiple dosage forms.
[0164] As used herein, the term "dosing regimen" refers to a set of
unit doses (typically more than one) that are administered
individually to a subject, typically separated by periods of time.
In some embodiments, a given therapeutic compound has a recommended
dosing regimen, which may involve one or more doses. In some
embodiments, a dosing regimen comprises a plurality of doses each
of which are separated from one another by a time period of the
same length; in some embodiments, a dosing regimen comprises a
plurality of doses and at least two different time periods
separating individual doses. In some embodiments, all doses within
a dosing regimen are of the same unit dose amount. In some
embodiments, different doses within a dosing regimen are of
different amounts. In some embodiments, a dosing regimen comprises
a first dose in a first dose amount, followed by one or more
additional doses in a second dose amount different from the first
dose amount. In some embodiments, a dosing regimen comprises a
first dose in a first dose amount, followed by one or more
additional doses in a second dose amount same as the first dose
amount In some embodiments, a dosing regimen is correlated with a
desired or beneficial outcome when administered across a relevant
population (i.e., is a therapeutic dosing regimen).
[0165] As used herein, the term "engineered" is used to describe a
compound whose design and/or production involves action of the hand
of man. For example, in some embodiments, an "engineered" compound
is prepared by in vitro chemical synthesis. In some embodiments, an
"engineered" compound is produced by a cell that has been
genetically manipulated relative to a reference wild type cell. In
some embodiments, an "engineered" compound is produced by a cell in
culture. In some embodiments, an "engineered" compound is produced
by a cell in culture conditions specifically modified to enhance
production of the compound. In some embodiments, an "engineered"
compound has a structure designed or selected by in silico
modeling.
[0166] As used herein, the term "flat surface site," as is
understood in the art, refers to a site on a surface of a protein
structure that has a relatively flat character, (e.g., a site that
does not include a well-defined pocket or cavity with an area of
greater than 500 .ANG..sup.2, a volume of greater than 400
.ANG..sup.3, and a depth greater than 13 .ANG.). In some
embodiments, a site may be determined to be flat by utilizing a
commercial algorithim known in the art e.g., a site may be
determined to be flat if it does not include a well-defined pocket
or cavity with an area of greater than 500 .ANG..sup.2, a volume of
greater than 400 .ANG..sup.3, and a depth greater than 13 .ANG. as
determined by CAST (Liang et al. Prot. Sci. 1998, 7:1884) or
Sitemap (Halgren J. Chem. Inf. Model. 2009, 49:377). Those of
ordinary skill in the art are familiar with the concept of flatness
and, moreover are aware of its relationship to "druggability." In
some embodiments, a protein is considered to have a flat surface
site if it is undruggable as defined herein, e.g., is determined to
be undruggable using the program DOGSITESCORER.RTM..
[0167] As used herein, the term "hydrophobic residue" refers to an
amino acid that has a hydropathy index value equal to or greater
than proline. Examples of hydrophobic residues are valine,
isoleucine, leucine, methionine, phenylalanine, tryptophan,
alanine, glycine, and cysteine.
[0168] As used herein, the term "hydrophobic surface site" refers
to site on a surface of a protein structure comprising at least 30%
hydrophobic residues).
[0169] As used herein, the term "identity" refers to the overall
relatedness between polymeric molecules, e.g., between nucleic acid
molecules (e.g., DNA molecules and/or RNA molecules) and/or between
polypeptide molecules. Calculation of the percent identity of two
nucleic acid sequences, for example, can be performed by aligning
the two sequences for optimal comparison purposes (e.g., gaps can
be introduced in one or both of a first and a second nucleic acid
sequences for optimal alignment and non-identical sequences can be
disregarded for comparison purposes). In certain embodiments, the
length of a sequence aligned for comparison purposes is at least
30%, at least 40%, at least 50%, at least 60%, at least 70%, at
least 80%, at least 90%, at least 95%, or substantially 100% of the
length of the reference sequence. The nucleotides at corresponding
nucleotide positions are then compared. When a position in the
first sequence is occupied by the same nucleotide as the
corresponding position in the second sequence, then the molecules
are identical at that position. The percent identity between the
two sequences is a function of the number of identical positions
shared by the sequences, taking into account the number of gaps,
and the length of each gap, which needs to be introduced for
optimal alignment of the two sequences. The comparison of sequences
and determination of percent identity between two sequences can be
accomplished using a mathematical algorithm. For example, the
percent identity between two nucleotide sequences can be determined
using the algorithm of Meyers and Miller (CABIOS, 1989, 4: 11-17),
which has been incorporated into the ALIGN program (version 2.0)
using a PAM120 weight residue table, a gap length penalty of 12 and
a gap penalty of 4. The percent identity between two nucleotide
sequences can, alternatively, be determined using the GAP program
in the GCG software package using an NWSgapdna.CMP matrix.
[0170] As used herein, the term "isolated" refers to a substance
and/or entity that has been (1) separated from at least some of the
components with which it was associated when initially produced
(whether in nature and/or in an experimental setting), and/or (2)
designed, produced, prepared, and/or manufactured by the hand of
man. Isolated substances and/or entities may be separated from
about 10%, about 20%, about 30%, about 40%, about 50%, about 60%,
about 70%, about 80%, about 90%, about 91%, about 92%, about 93%,
about 94%, about 95%, about 96%, about 97%, about 98%, about 99%,
or more than about 99% of the other components with which they were
initially associated. In some embodiments, isolated compounds are
about 80%, about 85%, about 90%, about 91%, about 92%, about 93%,
about 94%, about 95%, about 96%, about 97%, about 98%, about 99%,
or more than about 99% pure. As used herein, a substance is "pure"
if it is substantially free of other components. In some
embodiments, as will be understood by those skilled in the art, a
substance may still be considered "isolated" or even "pure", after
having been combined with certain other components such as, for
example, one or more carriers or excipients (e.g., buffer, solvent,
water, etc.); in such embodiments, percent isolation or purity of
the substance is calculated without including such carriers or
excipients. In some embodiments, isolation involves or requires
disruption of covalent bonds (e.g., to isolate a polypeptide domain
from a longer polypeptide and/or to isolate a nucleotide sequence
element from a longer oligonucleotide or nucleic acid).
[0171] The term "macrocyclic compound," as used herein, refers to a
small molecule compound containing a ring with nine or more ring
atoms. Macrocyclic compounds include macrolides, a group of small
molecules containing a macrocyclic lactone, such as erythromycin,
rapamycin, and FK506. In some embodiments, a macrocyclic compound
is a small molecule in which greater than 25% (e.g., greater than
30%, greater than 35%, greater than 40%, greater than 45%) of the
non-hydrogen atoms in the small molecule are included in a single
or fused ring structure. In some embodiments, the macrocyclic
compound is not a compound described in Benjamin et al. Nat. Rev.
Drug. Discov. 2011, 10(11), 868-880 or Sweeney, Z. K. et al. J.
Med. Chem. 2014, epub ahead of print, the structures of which are
incorporated by reference.
[0172] The term "target protein interacting moiety" as used herein,
refers to a group of ring atoms and the moieties attached thereto
(e.g., atoms within 20 atoms of a ring atom such as, atoms within
15 atoms of a ring atom, atoms within 10 atoms of a ring atom,
atoms within 5 atoms of a ring atom) that, when the compound is in
a complex with a presenter protein, specifically bind to a target
protein (e.g., a eukaryotic target protein such as a mammalian
target protein or a fungal target protein or a prokaryotic target
protein such as a bacterial target protein).
[0173] The term "modulator" is used to refer to an entity whose
presence or level in a system in which an activity of interest is
observed correlates with a change in level and/or nature of that
activity as compared with that observed under otherwise comparable
conditions when the modulator is absent. In some embodiments, a
modulator is an activator, in that activity is increased in its
presence as compared with that observed under otherwise comparable
conditions when the modulator is absent. In some embodiments, a
modulator is an antagonist or inhibitor, in that activity is
reduced in its presence as compared with otherwise comparable
conditions when the modulator is absent. In some embodiments, a
modulator interacts directly with a target entity whose activity is
of interest. In some embodiments, a modulator interacts indirectly
(i.e., directly with an intermediate compound that interacts with
the target entity) with a target entity whose activity is of
interest. In some embodiments, a modulator affects level of a
target entity of interest; alternatively or additionally, in some
embodiments, a modulator affects activity of a target entity of
interest without affecting level of the target entity. In some
embodiments, a modulator affects both level and activity of a
target entity of interest, so that an observed difference in
activity is not entirely explained by or commensurate with an
observed difference in level. In some embodiments, a modulator is
an allosteric modulator such as an allosteric agonist.
[0174] As used herein, an atom that "participates in binding" is
within 4 .ANG. of the entity to which they bind or connects to an
atom that is with 4 .ANG. of the entity to which they bind.
[0175] As used herein, the term "pharmaceutical composition" refers
to an active compound, formulated together with one or more
pharmaceutically acceptable carriers. In some embodiments, active
compound is present in unit dose amount appropriate for
administration in a therapeutic regimen that shows a statistically
significant probability of achieving a predetermined therapeutic
effect when administered to a relevant population. In some
embodiments, pharmaceutical compositions may be specially
formulated for administration in solid or liquid form, including
those adapted for the following: oral administration, for example,
drenches (aqueous or non-aqueous solutions or suspensions),
tablets, e.g., those targeted for buccal, sublingual, and systemic
absorption, boluses, powders, granules, pastes for application to
the tongue; parenteral administration, for example, by
subcutaneous, intramuscular, intravenous or epidural injection as,
for example, a sterile solution or suspension, or sustained-release
formulation; topical application, for example, as a cream,
ointment, or a controlled-release patch or spray applied to the
skin, lungs, or oral cavity; intravaginally or intrarectally, for
example, as a pessary, cream, or foam; sublingually; ocularly;
transdermally; or nasally, pulmonary, and to other mucosal
surfaces.
[0176] A "pharmaceutically acceptable excipient," as used herein,
refers any inactive ingredient (for example, a vehicle capable of
suspending or dissolving the active compound) having the properties
of being nontoxic and non-inflammatory in a subject. Typical
excipients include, for example: antiadherents, antioxidants,
binders, coatings, compression aids, disintegrants, dyes (colors),
emollients, emulsifiers, fillers (diluents), film formers or
coatings, flavors, fragrances, glidants (flow enhancers),
lubricants, preservatives, printing inks, sorbents, suspensing or
dispersing agents, sweeteners, or waters of hydration. Excipients
include, but are not limited to: butylated hydroxytoluene (BHT),
calcium carbonate, calcium phosphate (dibasic), calcium stearate,
croscarmellose, crosslinked polyvinyl pyrrolidone, citric acid,
crospovidone, cysteine, ethylcellulose, gelatin, hydroxypropyl
cellulose, hydroxypropyl methylcellulose, lactose, magnesium
stearate, maltitol, mannitol, methionine, methylcellulose, methyl
paraben, microcrystalline cellulose, polyethylene glycol, polyvinyl
pyrrolidone, povidone, pregelatinized starch, propyl paraben,
retinyl palmitate, shellac, silicon dioxide, sodium carboxymethyl
cellulose, sodium citrate, sodium starch glycolate, sorbitol,
starch (corn), stearic acid, stearic acid, sucrose, talc, titanium
dioxide, vitamin A, vitamin E, vitamin C, and xylitol. Those of
ordinary skill in the art are familiar with a variety of agents and
materials useful as excipients.
[0177] The term "pharmaceutically acceptable salt," as use herein,
refers to those salts of the compounds described here that are,
within the scope of sound medical judgment, suitable for use in
contact with the tissues of humans and animals without undue
toxicity, irritation, allergic response and the like and are
commensurate with a reasonable benefit/risk ratio. Pharmaceutically
acceptable salts are well known in the art. For example,
pharmaceutically acceptable salts are described in: Berge et al.,
J. Pharmaceutical Sciences 66:1-19, 1977 and in Pharmaceutical
Salts: Properties, Selection, and Use, (Eds. P. H. Stahl and C. G.
Wermuth), Wiley-VCH, 2008. The salts can be prepared in situ during
the final isolation and purification of the compounds described
herein or separately by reacting the free base group with a
suitable organic acid.
[0178] The compounds of the invention may have ionizable groups so
as to be capable of preparation as pharmaceutically acceptable
salts. These salts may be acid addition salts involving inorganic
or organic acids or the salts may, in the case of acidic forms of
the compounds of the invention be prepared from inorganic or
organic bases. Frequently, the compounds are prepared or used as
pharmaceutically acceptable salts prepared as addition products of
pharmaceutically acceptable acids or bases. Suitable
pharmaceutically acceptable acids and bases are well-known in the
art, such as hydrochloric, sulphuric, hydrobromic, acetic, lactic,
citric, or tartaric acids for forming acid addition salts, and
potassium hydroxide, sodium hydroxide, ammonium hydroxide,
caffeine, various amines, and the like for forming basic salts.
Methods for preparation of the appropriate salts are
well-established in the art.
[0179] Representative acid addition salts include acetate, adipate,
alginate, ascorbate, aspartate, benzenesulfonate, benzoate,
bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate,
cyclopentanepropionate, digluconate, dodecylsulfate,
ethanesulfonate, fumarate, glucoheptonate, glycerophosphate,
hemisulfate, heptonate, hexanoate, hydrobromide, hydrochloride,
hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate,
laurate, lauryl sulfate, malate, maleate, malonate,
methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate,
oleate, oxalate, palmitate, pamoate, pectinate, persulfate,
3-phenylpropionate, phosphate, picrate, pivalate, propionate,
stearate, succinate, sulfate, tartrate, thiocyanate,
toluenesulfonate, undecanoate, valerate salts and the like.
Representative alkali or alkaline earth metal salts include sodium,
lithium, potassium, calcium, magnesium and the like, as well as
nontoxic ammonium, quaternary ammonium, and amine cations,
including, but not limited to ammonium, tetramethylammonium,
tetraethylammonium, methylamine, dimethylamine, trimethylamine,
triethylamine, ethylamine and the like.
[0180] The term "polar surface area" refers to the surface sum over
all polar atoms of a molecule or portion of a molecule, including
their attached hydrogens. Polar surface area is determined
computationally using a program such as CHEMDRAW.RTM. Pro, Version
12.0.2.1092 (Cambridgesoft, Cambridge, Mass.).
[0181] The term "presenter protein" refers to a protein that binds
to a small molecule to form a complex that binds to and modulates
the activity of a target protein (e.g., a eukaryotic target protein
such as a mammalian target protein or a fungal target protein or a
prokaryotic target protein such as a bacterial target protein). In
some embodiments, the presenter protein is a relatively abundant
protein (e.g., the presenter protein is sufficiently abundant that
participation in a tripartite complex does not substantially impact
the biological role of the presenter protein in a cell and/or
viability or other attributes of the cell). In certain embodiments,
the presenter protein is a protein that has chaperone activity
within a cell. In some embodiments, the presenter protein is a
protein that has multiple natural interaction partners within a
cell. In certain embodiments, the presenter protein is one which is
known to bind a small molecule to form a binary complex that is
known to or suspected of binding to and modulating the biological
activity of a target protein.
[0182] The term "presenter protein binding moiety" refers to a
group of ring atoms and the moieties attached thereto (e.g., atoms
within 20 atoms of a ring atom such as, atoms within 15 atoms of a
ring atom, atoms within 10 atoms of a ring atom, atoms within 5
atoms of a ring atom) that participate in binding to a presenter
protein such that the compound specifically binds to said presenter
protein, for example, with a K.sub.D of less than 10 .mu.M (e.g.,
less than 5 .mu.M, less than 1 .mu.M, less than 500 nM, less than
200 nM, less than 100 nM, less than 75 nM, less than 50 nM, less
than 25 nM, less than 10 nM) or inhibits the peptidyl-prolyl
isomerase activity of the presenter protein, for example, with an
IC.sub.50 of less than 1 .mu.M (e.g., less than 0.5 .mu.M, less
than 0.1 .mu.M, less than 0.05 .mu.M, less than 0.01 .mu.M). It
will be understood that the presenter protein binding moiety does
not necessarily encompass the entirety of atoms in the compound
that interact with the presenter protein. It will also be
understood that one or more atoms of the presenter protein binding
moiety may be within the target protein interaction moiety (e.g.,
eukaryotic target protein interacting moiety such as mammalian
target protein interacting moiety or fungal target protein
interacting moiety or prokaryotic target protein interacting moiety
such as a bacterial target protein interacting moiety).
[0183] The term "pure" means substantially pure or free of unwanted
components (e.g., other compounds and/or other components of a cell
lysate), material defilement, admixture or imperfection.
[0184] The term "reference" is often used herein to describe a
standard or control compound, individual, population, sample,
sequence or value against which a compound, individual, population,
sample, sequence or value of interest is compared. In some
embodiments, a reference compound, individual, population, sample,
sequence or value is tested and/or determined substantially
simultaneously with the testing or determination of the compound,
individual, population, sample, sequence or value of interest. In
some embodiments, a reference compound, individual, population,
sample, sequence or value is a historical reference, optionally
embodied in a tangible medium. Typically, as would be understood by
those skilled in the art, a reference compound, individual,
population, sample, sequence or value is determined or
characterized under conditions comparable to those utilized to
determine or characterize the compound, individual, population,
sample, sequence or value of interest.
[0185] The term "ring atoms" refers to the atoms of a cyclic
compound that comprise the innermost portion of the ring. For
example, using this method FK506 has 21 ring atoms and rapamycin
has 29 ring atoms.
[0186] The term "site of a naturally occurring protein-protein
interaction" refers to a location on the surface of the structure
of a protein that includes atoms which participate in binding
between the protein and another protein in the proteins natural
environment.
[0187] The term "small molecule" means a low molecular weight
organic and/or inorganic compound. In general, a "small molecule"
is a molecule that is less than about 5 kilodaltons (kD) in size.
In some embodiments, a small molecule is less than about 4 kD, 3
kD, about 2 kD, or about 1 kD. In some embodiments, the small
molecule is less than about 800 daltons (D), about 600 D, about 500
D, about 400 D, about 300 D, about 200 D, or about 100 D. In some
embodiments, a small molecule is less than about 2000 g/mol, less
than about 1500 g/mol, less than about 1000 g/mol, less than about
800 g/mol, or less than about 500 g/mol. In some embodiments, a
small molecule is not a polymer. In some embodiments, a small
molecule does not include a polymeric moiety. In some embodiments,
a small molecule is not a protein or polypeptide (e.g., is not an
oligopeptide or peptide). In some embodiments, a small molecule is
not a polynucleotide (e.g., is not an oligonucleotide). In some
embodiments, a small molecule is not a polysaccharide. In some
embodiments, a small molecule does not comprise a polysaccharide
(e.g., is not a glycoprotein, proteoglycan, glycolipid, etc.). In
some embodiments, a small molecule is not a lipid. In some
embodiments, a small molecule is a modulating compound. In some
embodiments, a small molecule is biologically active. In some
embodiments, a small molecule is detectable (e.g., comprises at
least one detectable moiety). In some embodiments, a small molecule
is a therapeutic.
[0188] Those of ordinary skill in the art, reading the present
disclosure, will appreciate that certain small molecule compounds
described herein may be provided and/or utilized in any of a
variety of forms such as, for example, salt forms, protected forms,
pro-drug forms, ester forms, isomeric forms (e.g., optical and/or
structural isomers), isotopic forms, etc. In some embodiments,
reference to a particular compound may relate to a specific form of
that compound. In some embodiments, reference to a particular
compound may relate to that compound in any form. In some
embodiments, where a compound is one that exists or is found in
nature, that compound may be provided and/or utilized in accordance
in the present invention in a form different from that in which it
exists or is found in nature. Those of ordinary skill in the art
will appreciate that a compound preparation including a different
level, amount, or ratio of one or more individual forms than a
reference preparation or source (e.g., a natural source) of the
compound may be considered to be a different form of the compound
as described herein. Thus, in some embodiments, for example, a
preparation of a single stereoisomer of a compound may be
considered to be a different form of the compound than a racemic
mixture of the compound; a particular salt of a compound may be
considered to be a different form from another salt form of the
compound; a preparation containing one conformational isomer ((Z)
or (E)) of a double bond may be considered to be a different form
from one containing the other conformational isomer ((E) or (Z)) of
the double bond; a preparation in which one or more atoms is a
different isotope than is present in a reference preparation may be
considered to be a different form; etc.
[0189] As used herein, the terms "specific binding" or "specific
for" or "specific to" refer to an interaction between a binding
agent and a target entity. As will be understood by those of
ordinary skill, an interaction is considered to be "specific" if it
is favored in the presence of alternative interactions, for
example, binding with a K.sub.D of less than 10 .mu.M (e.g., less
than 5 .mu.M, less than 1 .mu.M, less than 500 nM, less than 200
nM, less than 100 nM, less than 75 nM, less than 50 nM, less than
25 nM, less than 10 nM). In many embodiments, specific interaction
is dependent upon the presence of a particular structural feature
of the target entity (e.g., an epitope, a cleft, a binding site).
It is to be understood that specificity need not be absolute. In
some embodiments, specificity may be evaluated relative to that of
the binding agent for one or more other potential target entities
(e.g., competitors). In some embodiments, specificity is evaluated
relative to that of a reference specific binding agent. In some
embodiments specificity is evaluated relative to that of a
reference non-specific binding agent.
[0190] The term "specific" when used with reference to a compound
having an activity, is understood by those skilled in the art to
mean that the compound discriminates between potential target
entities or states. For example, in some embodiments, a compound is
said to bind "specifically" to its target if it binds
preferentially with that target in the presence of one or more
competing alternative targets. In many embodiments, specific
interaction is dependent upon the presence of a particular
structural feature of the target entity (e.g., an epitope, a cleft,
a binding site). It is to be understood that specificity need not
be absolute. In some embodiments, specificity may be evaluated
relative to that of the binding agent for one or more other
potential target entities (e.g., competitors). In some embodiments,
specificity is evaluated relative to that of a reference specific
binding agent. In some embodiments specificity is evaluated
relative to that of a reference non-specific binding agent. In some
embodiments, the agent or entity does not detectably bind to the
competing alternative target under conditions of binding to its
target entity. In some embodiments, binding agent binds with higher
on-rate, lower off-rate, increased affinity, decreased
dissociation, and/or increased stability to its target entity as
compared with the competing alternative target(s).
[0191] The term "structural organization" refers to the average
three dimensional configuration of the atoms and bonds of molecule.
By "substantially unchanged structural organization" is meant that
the root mean squared deviation (RMSD) of two aligned structures is
less than 1. The RMSD can be calculated, e.g., by using the align
command in PyMOL version 1.7rc1 (Schrodinger LLC). Alternatively,
RMSD can be calculated using the ExecutiveRMS parameter from the
algorithm LigAlign (J. Mol. Graphics and Modelling 2010, 29,
93-101).
[0192] The term "substantially" refers to the qualitative condition
of exhibiting total or near-total extent or degree of a
characteristic or property of interest. One of ordinary skill in
the biological arts will understand that biological and chemical
phenomena rarely, if ever, go to completion and/or proceed to
completeness or achieve or avoid an absolute result. The term
"substantially" is therefore used herein to capture the potential
lack of completeness inherent in many biological and chemical
phenomena.
[0193] The term "does not substantially bind" to a particular
protein as used herein can be exhibited, for example, by a molecule
or portion of a molecule having a K.sub.D for the target of
10.sup.-4 M or greater, alternatively 10.sup.-5 M or greater,
alternatively 10.sup.-6 M or greater, alternatively 10.sup.-7 M or
greater, alternatively 10.sup.-8 M or greater, alternatively
10.sup.-9 M or greater, alternatively 10.sup.-10 M or greater,
alternatively 10.sup.-11 M or greater, alternatively 10.sup.-12 M
or greater, or a K.sub.D in the range of 10.sup.-4 M to 10.sup.-12
M or 10.sup.-6 M to 10.sup.-10 M or 10.sup.-7 M to 10.sup.-9 M.
[0194] The term "substantial structural similarity" refers to
presence of shared structural features such as presence and/or
identity of particular amino acids at particular positions (see
definitions of "shared sequence homology" and "shared sequence
identity"). In some embodiments the term "substantial structural
similarity" refers to presence and/or identity of structural
elements (for example: loops, sheets, helices, H-bond donors,
H-bond acceptors, glycosylation patterns, salt bridges, and
disulfide bonds). In some embodiments, the term "substantial
structural similarity" refers to three dimensional arrangement
and/or orientation of atoms or moieties relative to one another
(for example: distance and/or angles between or among them between
an agent of interest and a reference agent).
[0195] The term "target protein" refers to a protein that is not
mTOR or calcineurin that binds with a small molecule/presenter
protein/compound complex as described herein, but that does not
substantially bind with either the small molecule or the presenter
protein alone. In some embodiments, the small molecule/presenter
protein/compound complex does not substantially bind to mTOR or
calcineurin. In some embodiments, the target protein participates
in a biological pathway associated with a disease, disorder or
condition. In some embodiments, a target protein is a
naturally-occurring protein; in some such embodiments, a target
protein is naturally found in certain mammalian cells (e.g., a
mammalian target protein), fungal cells (e.g., a fungal target
protein), bacterial cells (e.g., a bacterial target protein) or
plant cells (e.g., a plant target protein). In some embodiments, a
target protein is characterized by natural interaction with one or
more natural presenter protein/natural small molecule complexes. In
some embodiments, a target protein is characterized by natural
interactions with a plurality of different natural presenter
protein/natural small molecule complexes; in some such embodiments
some or all of the complexes utilize the same presenter protein
(and different small molecules). In some embodiments, a target
protein does not substantially bind to a complex of cyclosporin,
rapamycin, or FK506 and a presenter protein (e.g., FKBP). Target
proteins can be naturally occurring, e.g., wild type.
Alternatively, the target protein can vary from the wild type
protein but still retain biological function, e.g., as an allelic
variant, a splice mutant or a biologically active fragment.
Exemplary mammalian target proteins are GTPases, GTPase activating
protein, Guanine nucleotide-exchange factor, heat shock proteins,
ion channels, coiled-coil proteins, kinases, phosphatases,
ubiquitin ligases, transcription factors, chromatin
modifier/remodelers, proteins with classical protein-protein
interaction domains and motifs, or any other proteins that
participate in a biological pathway associated with a disease,
disorder or condition.
[0196] The term "target protein interacting moiety" refers to a
group of ring atoms and the moieties attached thereto (e.g., atoms
within 20 atoms of a ring atom such as, atoms within 15 atoms of a
ring atom, atoms within 10 atoms of a ring atom, atoms within 5
atoms of a ring atom) that participate in binding to a target
protein (e.g., a eukaryotic target protein such as a mammalian
target protein or a fungal target protein or a prokaryotic target
protein such as a bacterial target protein) when the compound is in
a complex with a presenter protein. It will be understood that the
target protein interacting moiety does not necessarily encompass
the entirety of atoms in the compound that interact with the target
protein. It will also be understood that one or more atoms of the
presenter protein binding moiety may also be present in the target
protein interacting moiety.
[0197] A "therapeutic regimen" refers to a dosing regimen whose
administration across a relevant population is correlated with a
desired or beneficial therapeutic outcome.
[0198] The term "therapeutically effective amount" means an amount
that is sufficient, when administered to a population suffering
from or susceptible to a disease, disorder, and/or condition in
accordance with a therapeutic dosing regimen, to treat the disease,
disorder, and/or condition. In some embodiments, a therapeutically
effective amount is one that reduces the incidence and/or severity
of, and/or delays onset of, one or more symptoms of the disease,
disorder, and/or condition. Those of ordinary skill in the art will
appreciate that the term "therapeutically effective amount" does
not in fact require successful treatment be achieved in a
particular individual. Rather, a therapeutically effective amount
may be that amount that provides a particular desired
pharmacological response in a significant number of subjects when
administered to patients in need of such treatment. It is
specifically understood that particular subjects may, in fact, be
"refractory" to a "therapeutically effective amount." To give but
one example, a refractory subject may have a low bioavailability
such that clinical efficacy is not obtainable. In some embodiments,
reference to a therapeutically effective amount may be a reference
to an amount as measured in one or more specific tissues (e.g., a
tissue affected by the disease, disorder or condition) or fluids
(e.g., blood, saliva, serum, sweart, tears, urine, etc). Those of
ordinary skill in the art will appreciate that, in some
embodiments, a therapeutically effective amount may be formulated
and/or administered in a single dose. In some embodiments, a
therapeutically effective amount may be formulated and/or
administered in a plurality of doses, for example, as part of a
dosing regimen.
[0199] The term "traditional binding pocket" refers to cavities or
pockets on a protein structure with physiochemical and/or geometric
properties comparable to proteins whose activity has been modulated
by one or more small molecules. In some embodiments, a traditional
binding pocket is a well-defined pocket with a volume greater than
1000 .ANG..sup.3. Those of ordinary skill in the art are familiar
with the concept of a traditional binding pocket and, moreover are
aware of its relationship to "druggability". In certain
embodiments, a protein is considered to not have a traditional
binding pocket if it is undruggable, as defined herein.
[0200] The term "treatment" (also "treat" or "treating"), in its
broadest sense, refers to any administration of a substance (e.g.,
provided compositions) that partially or completely alleviates,
ameliorates, relives, inhibits, delays onset of, reduces severity
of, and/or reduces incidence of one or more symptoms, features,
and/or causes of a particular disease, disorder, and/or condition.
In some embodiments, such treatment may be administered to a
subject who does not exhibit signs of the relevant disease,
disorder and/or condition and/or of a subject who exhibits only
early signs of the disease, disorder, and/or condition.
Alternatively or additionally, in some embodiments, treatment may
be administered to a subject who exhibits one or more established
signs of the relevant disease, disorder and/or condition. In some
embodiments, treatment may be of a subject who has been diagnosed
as suffering from the relevant disease, disorder, and/or condition.
In some embodiments, treatment may be of a subject known to have
one or more susceptibility factors that are statistically
correlated with increased risk of development of the relevant
disease, disorder, and/or condition.
[0201] The term "undruggable target" refers to proteins that are
not members of a protein family which is known to be targeted by
drugs and/or does not possess a binding site that is suitable for
high-affinity binding to a small molecule. Methods for determining
whether a target protein is undruggable are known in the art. For
example, whether a target protein is undruggable may be determined
using an structure-based algorithim, such as those used by the
program DOGSITESCORER.RTM. (Universitat Hamburg, Hamburg, Germany)
that assesses druggability based on parameters computed for binding
pockets on a protein including volume, surface area, lipophilic
surface area, depth, and/or hydrophobic ratio.
[0202] As used herein, the term "van der Waals interaction" refers
to the attractive or repulsive forces between atoms that are not
due to covalent bonds, electrostatic interactions, or hydrogen
bonding.
[0203] The term "variant" refers to an entity that shows
significant structural identity with a reference entity but differs
structurally from the reference entity in the presence or level of
one or more chemical moieties as compared with the reference
entity. In many embodiments, a variant also differs functionally
from its reference entity. In general, whether a particular entity
is properly considered to be a "variant" of a reference entity is
based on its degree of structural identity with the reference
entity. As will be appreciated by those skilled in the art, any
biological or chemical reference entity has certain characteristic
structural elements. A variant, by definition, is a distinct
chemical entity that shares one or more such characteristic
structural elements. To give but a few examples, a small molecule
may have a characteristic core structural element (e.g., a
macrocycle core) and/or one or more characteristic pendent moieties
so that a variant of the small molecule is one that shares the core
structural element and the characteristic pendent moieties but
differs in other pendent moieties and/or in types of bonds present
(single vs double, E vs Z, etc) within the core, a polypeptide may
have a characteristic sequence element comprised of a plurality of
amino acids having designated positions relative to one another in
linear or three-dimensional space and/or contributing to a
particular biological function, a nucleic acid may have a
characteristic sequence element comprised of a plurality of
nucleotide residues having designated positions relative to on
another in linear or three-dimensional space. For example, a
variant polypeptide may differ from a reference polypeptide as a
result of one or more differences in amino acid sequence and/or one
or more differences in chemical moieties (e.g., carbohydrates,
lipids, etc) covalently attached to the polypeptide backbone. In
some embodiments, a variant polypeptide shows an overall sequence
identity with a reference polypeptide that is at least 85%, 86%,
87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, or 99%.
Alternatively or additionally, in some embodiments, a variant
polypeptide does not share at least one characteristic sequence
element with a reference polypeptide. In some embodiments, the
reference polypeptide has one or more biological activities. In
some embodiments, a variant polypeptide shares one or more of the
biological activities of the reference polypeptide. In some
embodiments, a variant polypeptide lacks one or more of the
biological activities of the reference polypeptide. In some
embodiments, a variant polypeptide shows a reduced level of one or
more biological activities as compared with the reference
polypeptide. In many embodiments, a polypeptide of interest is
considered to be a "variant" of a parent or reference polypeptide
if the polypeptide of interest has an amino acid sequence that is
identical to that of the parent but for a small number of sequence
alterations at particular positions. Typically, fewer than 20%,
15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% of the residues in the
variant are substituted as compared with the parent. In some
embodiments, a variant has 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1
substituted residue as compared with a parent. Often, a variant has
a very small number (e.g., fewer than 5, 4, 3, 2, or 1) number of
substituted functional residues (i.e., residues that participate in
a particular biological activity). Furthermore, a variant typically
has not more than 5, 4, 3, 2, or 1 additions or deletions, and
often has no additions or deletions, as compared with the parent.
Moreover, any additions or deletions are typically fewer than about
25, about 20, about 19, about 18, about 17, about 16, about 15,
about 14, about 13, about 10, about 9, about 8, about 7, about 6,
and commonly are fewer than about 5, about 4, about 3, or about 2
residues. In some embodiments, the parent or reference polypeptide
is one found in nature. As will be understood by those of ordinary
skill in the art, a plurality of variants of a particular
polypeptide of interest may commonly be found in nature.
[0204] The term "wild-type" refers to an entity having a structure
and/or activity as found in nature in a "normal" (as contrasted
with mutant, diseased, altered, etc) state or context. Those of
ordinary skill in the art will appreciate that wild-type genes and
polypeptides often exist in multiple different forms (e.g.,
alleles).
BRIEF DESCRIPTION OF THE DRAWINGS
[0205] FIG. 1 is a table of exemplary compounds of the
invention.
[0206] FIG. 2 is a table of exemplary compounds of the
invention.
DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS
[0207] Small molecules are limited in their targeting ability
because their interactions with the target are driven by adhesive
forces, the strength of which is roughly proportional to contact
surface area. Because of their small size, the only way for a small
molecule to build up enough intermolecular contact surface area to
effectively interact with a target protein is to be literally
engulfed by that protein. Indeed, a large body of both experimental
and computational data supports the view that only those proteins
having a hydrophobic "pocket" on their surface are capable of
binding small molecules. In those cases, binding is enabled by
engulfment.
[0208] Nature has evolved a strategy that allows a small molecule
to interact with target proteins at sites other than hydrophobic
pockets. This strategy is exemplified by naturally occurring
immunosuppressive drugs cyclosporine A, rapamycin, and FK506. The
biological activity of these drugs involves the formation of a
high-affinity complex of the small molecule with a small presenting
protein. The composite surface of the small molecule and the
presenting protein engages the target. Thus, for example, the
binary complex formed between cyclosporin A and cyclophilin A
targets calcineurin with high affinity and specificity, but neither
cyclosporin A or cyclophilin A alone binds calcineurin with
measurable affinity.
[0209] Many important therapeutic targets exert their function by
complexation with other proteins. The protein/protein interaction
surfaces in many of these systems contain an inner core of
hydrophobic side chains surrounded by a wide ring of polar
residues. The hydrophobic residues contribute nearly all of the
energetically favorable contacts, and hence this cluster has been
designated as a "hotspot" for engagement in protein-protein
interactions. Importantly, in the aforementioned complexes of
naturally occurring small molecules with small presenting proteins,
the small molecule provides a cluster of hydrophobic functionality
akin to a hotspot, and the protein provides the ring of mostly
polar residues. In other words, presented small molecule systems
mimic the surface architecture employed widely in natural
protein/protein interaction systems.
[0210] Nature has demonstrated the ability to reprogram the target
specificity of presented small molecules--portable hotspots-through
evolutionary diversification. In the best characterized example,
the complex formed between FK506 binding protein (FKBP) and FK506
targets calcineurin. However, FKBP can also form a complex with the
related molecule rapamycin, and that complex interacts with a
completely different target, TorC1. To date, no methodology has
been developed to reprogram the binding and modulating ability of
presenter protein/ligand interfaces so that they can interact with
and modulate other target proteins that have previously been
considered undruggable.
[0211] In addition, it is well established that some drug
candidates fail because they modulate the activity of both the
intended target and other non-intended proteins as well. The
problem is particularly daunting when the drug binding site of the
target protein is similar to binding sites in non-target proteins.
The insulin like growth factor receptor (IGF-1R), whose ATP binding
pocket is structurally similar to the binding pocket of the
non-target insulin receptor (IR), is one such example. Small
molecule development candidates that were designed to target IGF-1R
typically have the unacceptable side effect of also modulating the
insulin receptor. However, structural dissimilarities do exist
between these two proteins in the regions surrounding the ATP
binding pocket. Despite such knowledge, no methodology exists to
date to take advantage of those differences and develop drugs that
are specific to IGF-1R over IR.
[0212] The present invention features compounds (e.g., macrocyclic
compounds) capable of modulating biological processes, for example
through binding to a presenter protein (e.g., a member of the FKBP
family, a member of the cyclophilin family, or PIN1) and a target
protein. In some embodiments, the target and/or presenter proteins
are intracellular proteins. In some embodiments, the target and/or
presenter proteins are mammalian proteins. In some embodiments,
provided compounds participate in tripartite presenter
protein/compound/target protein complexes inside cells, e.g.,
mammalian cells. In some embodiments, provided compounds may be
useful in the treatment of diseases and disorders such as cancer,
inflammation, or infections.
Compounds
[0213] The invention features compounds (e.g., macrocyclic
compounds) capable of modulating biological processes, for example
through binding to a presenter protein (e.g., a member of the FKBP
family, a member of the cyclophilin family, or PIN1) and a target
protein (e.g., a eukaryotic target protein such as a mammalian
target protein or a fungal target protein or a prokaryotic target
protein such as a bacterial target protein). In brief, these
compounds bind endogenous intracellular presenter proteins, such as
the FKBPs and the resulting binary complexes selectively bind and
modulate the activity of intracellular target proteins. Without
wishing to be bound by any particular theory, we proposed that
formation of a tripartite complex among the presenter protein, the
compound, and the target protein is driven by both protein-compound
and protein-protein interactions, and both are required for
modulation (e.g., positive or negative modulation) of the targeted
protein's activity. In some embodiments, the compounds of the
invention "re-program" the binding of the presenter proteins to
protein targets that either do not normally bind to the presenter
protein or have binding that is greatly enhanced in the presence of
the compound thereby resulting in the ability to modulate (e.g.,
positively or negatively modulate) the activity of these new
targets.
[0214] As described herein, compounds of the invention include a
presenter protein binding moiety and a target protein interacting
moiety. In some embodiments, the presenter protein binding moiety
and target protein interacting moiety are separate portions of the
ring structure, e.g., they do not overlap. In some embodiments, the
presenter protein binding moiety and target protein interacting
moiety are connected to one another by linkers on one or both
sides.
[0215] In some embodiments, compounds of the invention do not
substantially bind to the target protein in the absence of forming
a complex, as described herein. In some embodiments, a complex of a
compound of the invention and a presenter protein binds to the
target protein with at least 5-fold (at least 10-fold, at least
20-fold, at least 30-fold, at least 40-fold, at least 50-fold, at
least 100-fold) greater affinity than the affinity of the compound
to the target protein in the absence of forming a complex, as
described herein. In certain embodiments, compounds of the
invention do not substantially modulate the activity of the target
protein in the absence forming a complex with a presenter protein.
For example, in some embodiments, the compounds of the invention
inhibit the activity of the target protein with an IC.sub.50 of
greater than 10 .mu.M (e.g., greater than 20 .mu.M, greater than 50
.mu.M, greater than 100 .mu.M, greater than 500 .mu.M).
Alternatively, compounds of the invention enhance the activity of
the target protein with an AC.sub.50 of greater than 10 .mu.M
(e.g., greater than 20 .mu.M, greater than 50 .mu.M, greater than
100 .mu.M, greater than 500 .mu.M). In certain embodiments, a
complex of the compound and a presenter protein is at least 5-fold
active (i.e., has a 5-fold lower IC.sub.50 or AC.sub.50) than the
compound alone.
[0216] Compounds (e.g., macrocyclic compounds) of the invention
generally bind strongly to the presenter protein. For example, in
some embodiments, the compounds (e.g., macrocyclic compounds) of
the invention bind to the presenter protein with a K.sub.D of less
than 10 .mu.M (e.g., less than 5 .mu.M, less than 1 .mu.M, less
than 500 nM, less than 200 nM, less than 100 nM, less than 75 nM,
less than 50 nM, less than 25 nM, less than 10 nM) or inhibit the
peptidyl-prolyl isomerase activity of the presenter protein, for
example, with an IC.sub.50 of less than 1 .mu.M (e.g., less than
0.5 .mu.M, less than 0.1 .mu.M, less than 0.05 .mu.M, less than
0.01 .mu.M).
[0217] In some embodiments, the invention includes compounds having
a structure according to formulae XIV to XVIII as described
herein:
##STR00026##
[0218] In certain embodiments, a compound has the structure of any
of the compounds in FIG. 1 or FIG. 2.
[0219] In some embodiments, a compound is a natural compound (e.g.,
synthesized by an genetically unmodified bacterial strain). In some
embodiments, a compound is a variant of a natural compound (e.g., a
semi-synthetic compound). In some embodiments, a variant shares
ring size with the reference natural compound. In some embodiments,
a variant differs from the reference natural compound only by
identity of one or more substituents (e.g., for at least one
position, the variant has a different substitutent or set of
substituents than is found at the corresponding position in an
appropriate reference compound).
[0220] In some embodiments, compounds of the invention (e.g.,
macrocyclic compounds of the invention) include 12 to 40 ring atoms
(e.g., 12 to 20 ring atoms, 14 to 20 ring atoms, 17 to 25 ring
atom, 21 to 26 ring atoms, 20 to 30 ring atoms, 25 to 35 ring
atoms, 30 to 40 ring atoms). In some embodiments, such compounds
include 19 ring atoms. In some embodiments, such compounds have an
even number of ring atoms. In certain embodiments, at least 25%
(e.g., at least 30%, at least 35%, at least 40%, at least 45%) of
the atoms in the compound are included in a single or fused ring
system.
[0221] In some embodiments, compounds of the invention include a
ring (e.g., a macrocycle) whose ring atoms are selected from the
group consisting of carbon atoms, hydrogen atoms, nitrogen atoms,
oxygen atoms, sulfur atoms, phosphorous atoms, silicon atoms and
combinations thereof; in some embodiments all ring atoms in the
compound are selected from this group. In some embodiments,
compounds of the invention include a ring (e.g., a macrocycle)
whose ring atoms are selected only from the group consisting carbon
atoms, hydrogen atoms, nitrogen atoms, oxygen atoms and
combinations thereof; in some embodiments, all ring atoms in the
compound are selected only from the group consisting carbon atoms,
hydrogen atoms, nitrogen atoms, oxygen atoms and combinations
thereof.
[0222] In certain embodiments, ring linkage in provided compounds
(e.g., macrocyclic compounds) of the invention includes a ketone,
an ester, an amide, an ether, a thioester, a urea, an amidine, or a
hydrocarbon.
[0223] In some embodiments, a provided compound is non-peptidal. In
certain embodiments, a provided compound includes one or more amino
acid residues. In some embodiments, a provided compound includes
only amino acid residues.
[0224] In some embodiments, the molecular weight of compounds of
the invention is between 400 and 2000 daltons (e.g., 400 to 600
daltons, 500 to 700 daltons, 600 to 800 daltons, 700 to 900
daltons, 800 to 1000 daltons, 900 to 1100 daltons, 1000 to 1200
daltons, 1100 to 1300 daltons, 1200 to 1400 daltons, 1300 to 1500
daltons, 1400 to 1600 daltons, 1500 to 1700 daltons, 1600 to 1800
daltons, 1700 to 1900 daltons, 1800 to 2000 daltons, 400 to 1000
daltons, 1000-2000 daltons). In some embodiments, the molecular
weight of compounds of the invention is less than 2000 daltons
(e.g., less than 500 daltons, less than 600 daltons, less than 700
daltons, less than 800 daltons, less than 900 daltons, less than
1000 daltons, less than 1100 daltons, less than 1200 daltons, less
than 1300 daltons, less than 1400 daltons, less than 1500 daltons,
less than 1600 daltons, less than 1700 daltons, less than 1800
daltons, less than 1900 daltons).
[0225] In certain embodiments, molecule provided compound is
hydrophobic. For example, in some embodiments, compounds have a c
Log P of equal to or greater than 2 (e.g., equal to or greater than
2.5, equal to or greater than 3.0, equal to or greater than 3.5,
equal to or greater than 4, equal to or greater than 4.5, equal to
or greater than 5, equal to or greater than 5.5, equal to or
greater than 6, equal to or greater than 6.5, equal to or greater
than 7). Alternatively, in some embodiments, compounds have a c Log
P of between 2 and 7 (e.g., between 2 and 4, between 3.5 and 4.5,
between 4 and 5, between 4.5 and 5.5, between 5 and 6, between 5.5
and 6.5, between 6 and 7, between 4 and 7, between 4 and 6, between
4 and 5.5). A provided compound may also be characterized as
hydrophobic by having low solubility in water. For example, in some
embodiments, compounds have a solubility of greater than 1 .mu.M in
water (e.g., greater than 1 .mu.M, greater than 2 .mu.M, greater
than 5 .mu.M, greater than 10 .mu.M, greater than 20 .mu.M, greater
than 30 .mu.M, greater than 40 .mu.M, greater than 50 .mu.M,
greater than 75 .mu.M, greater than 100 .mu.M). Alternatively, in
some embodiments, compounds have a solubility in water of between
1-100 .mu.M (e.g., 1-10 .mu.M, 5-10 .mu.M, 5-20 .mu.M, 10-50 .mu.M,
5-50 .mu.M, 20-100 .mu.M).
[0226] In some embodiments, compounds of the invention are cell
penetrant (e.g., they are able to enter the intracellular domain of
a cell without killing the cell and/or are capable of entering the
intercellular domain when contacted with extracellular
environs).
[0227] Compounds of the invention may or may not be naturally
occurring. In some embodiments, compounds of the invention are not
naturally occurring. In certain embodiments, compounds of the
invention are engineered. An engineered compound is a compound
whose design and/or production involves action of the hand of man
(e.g., a compound prepared by chemical synthesis, a compound
prepared by a cell that has been genetically manipulated relative
to a reference wild type cell, a compound produced by a cell in
culture conditions modified to enhance production of the
compound).
[0228] In certain embodiments, a provided compound (e.g.,
macrocyclic compound) is not a compound described in in Benjamin et
al. Nat. Rev. Drug. Discov. 2011, 10(11), 868-880 or Sweeney, Z. K.
et al. J. Med. Chem. 2014, epub ahead of print, the structures of
which are incorporated by reference and/or a compound having the
structure:
[0229] Presenter Protein Binding Moiety
[0230] Compounds of the invention include a presenter protein
binding moiety. This moiety includes the group of ring atoms (e.g.,
5 to 20 ring atoms, 5 to 10 ring atoms, 10 to 20 ring atoms) and
the moieties attached thereto (e.g., atoms within 20 atoms of a
ring atom such as, atoms within 15 atoms of a ring atom, atoms
within 10 atoms of a ring atom, atoms within 5 atoms of a ring
atom) that participate in binding to a presenter protein such that
a provided compound specifically binds to said presenter protein,
for example, with a K.sub.D of less than 10 .mu.M (e.g., less than
5 .mu.M, less than 1 .mu.M, less than 500 nM, less than 200 nM,
less than 100 nM, less than 75 nM, less than 50 nM, less than 25
nM, less than 10 nM) or inhibits the peptidyl-prolyl isomerase
activity of the presenter protein, for example, with an IC.sub.50
of less than 1 .mu.M (e.g., less than 0.5 .mu.M, less than 0.1
.mu.M, less than 0.05 .mu.M, less than 0.01 .mu.M). In some
embodiments, the presenter protein binding moiety does not
encompass the entirety of atoms in a provided compound that
interact with the presenter protein. In some embodiments, one or
more atoms of the presenter protein binding moiety may be within
the target protein interaction moiety (e.g., eukaryotic target
protein interacting moiety such as a mammalian target protein
interacting moiety or a fungal target protein interacting moiety or
prokaryotic target protein interacting moiety such as a bacterial
target protein interacting moiety). In certain embodiments, one or
more atoms of the presenter protein binding moiety do not interact
with the presenter protein.
[0231] In some embodiments, a presenter protein binding moiety
includes a N-acyl proline moiety, a N-acyl-pipecolic acid moiety, a
N-acyl 3-morpholino-carboxylic acid moiety, and/or a N-acyl
piperzic acid moiety (e.g., with acylation on either nitrogen atom.
In certain embodiments, a presenter protein binding moiety includes
a N-acyl-pipecolic acid moiety. In some embodiments, a presenter
protein binding moiety includes a N-acyl proline moiety. In certain
embodiments, a presenter protein binding moiety includes a N-acyl
3-morpholino-carboxylic acid moiety. In some embodiments, a
presenter protein binding moiety includes a N-acyl piperic acid
moiety.
[0232] In some embodiments, at least one atom of a presenter
protein binding moiety participates in binding with one or more
(e.g., two, three, four, five, six, seven, eight, nine, ten,
eleven, twelve, thirteen, fourteen, or fifteen) of Tyr 27, Phe 37,
Asp 38, Arg 41, Phe 47, Gln 54, Glu 55, Val 56, Ile 57, Trp 60, Ala
82, Try 83, His 88, Ile 92, and/or Phe 100 of FKBP12. In some
embodiments, at least one at of a presenter protein binding moiety
participates in binding with at least one (e.g., two, three, or
four) of Arg 41, Gln 54, Glu 55, and/or Ala 82 of FKBP12.
[0233] In some embodiments, a presenter protein binding moiety has
a structure according to Formula I-VIII:
##STR00027##
[0234] In some embodiments, a presenter protein binding moiety has
a structure according to Formula Ia-IVa:
##STR00028##
[0235] In some embodiments, a presenter protein binding moiety
includes or consists of the structure:
##STR00029## ##STR00030## ##STR00031##
or a stereoisomer thereof.
[0236] In certain embodiments, the presenter protein binding moiety
is or includes the structure:
##STR00032## ##STR00033##
[0237] Target Protein Interacting Moiety
[0238] Compounds of the invention include a target protein
interacting moiety (e.g., a eukaryotic target protein interacting
moiety such as a mammalian target protein interacting moiety or a
fungal target protein interacting moiety or a prokaryotic target
protein interacting moiety such as a bacterial target protein
interacting moiety). This moiety includes the group of ring atoms
(e.g., 5 to 20 ring atoms, 5 to 10 ring atoms, 10 to 20 ring atoms)
and the moieties attached thereto (e.g., atoms within 20 atoms of a
ring atom such as, atoms within 15 atoms of a ring atom, atoms
within 10 atoms of a ring atom, atoms within 5 atoms of a ring
atom) that when the compound is in a complex with a presenter
protein, specifically bind to a target protein. In some
embodiments, a target protein interacting moiety comprises a
plurality of the atoms in the compound that interact with the
target protein. In some embodiments, one or more atoms of a target
protein interacting moiety may be within the presenter protein
binding moiety. In certain embodiments, one or more atoms of a
target protein interacting moiety do not interact with the target
protein.
[0239] A target protein can bind to a ring atom in a target protein
interacting moiety. Alternatively, a target protein can bind to two
or more ring atoms in a target protein interacting moiety. In
another alternative, a target protein bind can to a substituent
attached to one or more ring atoms in a target protein interacting
moiety. In another alternative, a target protein can bind to a ring
atom in a target protein interacting moiety and to a substituent
attached to one or more ring atoms in a target protein interacting
moiety. In another alternative, a target protein binds to a group
that mimics a natural ligand of a target protein and wherein the
group that mimics a natural ligand of a target protein is attached
to a target protein interacting moiety. In yet another alternative,
a target protein binds to a presenter protein and the affinity of a
target protein for a presenter protein in the binary complex is
increased relative to the affinity of a target protein for a
presenter protein in the absence of the complex. Binding in these
examples is typically through, but not limited to non-covalent
interactions of a target protein to a target protein interacting
moiety.
[0240] In some embodiments, a target protein interacting moiety is
hydrophobic. For example, in some embodiments, a target protein
interacting moiety has a c Log P of equal to or greater than 2
(e.g., equal to or greater than 2.5, equal to or greater than 3,
equal to or greater than 3.5, equal to or greater than 4, equal to
or greater than 4.5, equal to or greater than 5, equal to or
greater than 5.5, equal to or greater than 6, equal to or greater
than 6.5, equal to or greater than 7). Alternatively, in some
embodiments, a target protein interacting moiety has a c Log P of
between 2 and 7 (e.g., between 2 and 4, between 2.5 and 4.5,
between 3 and 5, between 3.5 and 5.5, between 4 and 6, between 4.5
and 6.5, between 5 and 7, between 3 and 6, between 3 and 5, between
3 and 5.5). A target protein interacting moiety may also be
characterized as hydrophobic by having low polar surface area. For
example, in some embodiments, a target protein interacting moiety
has a polar surface area of less than 350 .ANG..sup.2 (e.g., less
than 300 .ANG..sup.2, less than 250 .ANG..sup.2, less than 200
.ANG..sup.2, less than 150 .ANG..sup.2, less than 125
.ANG..sup.2).
[0241] In some embodiments, a target protein interacting moiety
comprises one or more hydrophobic pendant groups (e.g., one or more
methyl, ethyl, isopropyl, phenyl, benzyl, and/or phenethyl groups).
In some embodiments, the pendant groups comprise fewer than 30
total atoms (e.g., fewer than 25 total atoms, fewer than 20 total
atoms, fewer than 15 total atoms, fewer than 10 total atoms.)
Alternatively, in some embodiments, the pendant groups comprise
between 10 and 30 total atoms (e.g., 10 to 20 total atoms, 15 to 25
total atoms, 20 to 30 total atoms). In certain embodiments the
pendant groups have a molecular weight less than 200 daltons (e.g.,
less than 150 daltons, less than 100 daltons, less than 75 daltons,
less than 50 daltons). Alternatively, in some embodiments, the
pendant groups have a molecular weight between 50 to 200 daltons
(e.g., 50 to 100 daltons, 75 to 150 daltons, 100 to 200
daltons).
[0242] In some embodiments, a target protein interacting moiety is
hydrocarbon based (e.g., the moiety comprises mostly carbon-carbon
bonds). In some embodiments, a target protein interacting moiety is
hydrocarbon based and includes a linear bivalent C.sub.4-C.sub.30
(e.g., C.sub.6-C.sub.20, C.sub.6-C.sub.15) aliphatic group
consisting predominantly of carbon and hydrogen, optionally
including one or more double bonds. In some embodiments, the
bivalent aliphatic group can also be substituted with a group that
mimics a natural ligand that binds to a target protein. Examples
include phosphotyrosine mimics and ATP mimetics.
[0243] In some embodiments, a target protein interacting moiety is
peptide based (e.g., the moiety comprises peptide bonds). In some
embodiments, a target protein interacting moiety is peptide based
and includes one or more (e.g., two, three, four, five, six, seven,
or eight) alanine residues, one or more (e.g., two, three, four,
five, six, seven, or eight) valine residues, one or more isoleucine
(e.g., two, three, four, five, six, seven, or eight) residues, one
or more leucine (e.g., two, three, four, five, six, seven, or
eight) residues, one or more methionine (e.g., two, three, four,
five, six, seven, or eight) residues, one or more phenylalanine
(e.g., two, three, four, five, six, seven, or eight) residues, one
or more (e.g., two, three, four, five, six, seven, or eight)
tyrosine residues, one or more (e.g., two, three, four, five, six,
seven, or eight) tryptophan residues, one or more (e.g., two,
three, four, five, six, seven, or eight) glycine residues, and/or
one or more (e.g., two, three, four, five, six, seven, or eight)
proline residues. In some embodiments, a target protein interacting
moiety is peptide based an includes one or more (e.g., two, three,
four, five, six, seven, or eight) arginine residues or one or more
(e.g., two, three, four, five, six, seven, or eight) lysine
residues. In some embodiments, a target protein interacting moiety
is peptide based and includes one or more (e.g., two, three, four,
five, six, seven, or eight) non-natural amino acids, one or more
(e.g., two, three, four, five, six, seven, or eight) D-amino acids,
and/or one or more (e.g., two, three, four, five, six, seven, or
eight) N-alkylated amino acids. In some embodiments, a target
protein interacting moiety is peptide based and includes
predominantly D-amino acids (e.g., at least 50% of the amino acids
are D-amino acids, at least 75% of the amino acids are D-amino
acids, 100% of the amino acids are D-amino acids). In certain
embodiments, a target protein interacting moiety is peptide based
and includes predominantly N-alkylated amino acids (e.g., at least
50% of the amino acids are N-alkylated amino acids, at least 75% of
the amino acids are N-alkylated amino acids, 100% of the amino
acids are N-alkylated amino acids). In certain embodiments, a
target protein interacting moiety is peptide based and includes one
or more (e.g., two, three, four, five, six, seven, or eight)
depsi-linkages.
[0244] In some embodiments, a target protein interacting moiety
(e.g., a eukaryotic target protein interacting moiety such as a
mammalian target protein interacting moiety or a fungal target
protein interacting moiety or a prokaryotic target protein
interacting moiety such as a bacterial target protein interacting
moiety) has a structure according to Formula IX:
##STR00034##
[0245] wherein u is an integer from 1 to 20; and
[0246] each Y is, independently, any amino acid, O, NR.sup.20, S,
S(O), SO.sub.2, or has the structure of any one of Formulae
X-XIII:
##STR00035##
[0247] wherein each R.sup.20 is, independently, hydrogen,
optionally substituted C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.6 alkenyl, optionally substituted
C.sub.2-C.sub.6 alkynyl, optionally substituted aryl,
C.sub.3-C.sub.7 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, and optionally
substituted C.sub.3-C.sub.7 carbocyclyl C.sub.1-C.sub.6 alkyl or
R.sup.19 combines with any R.sup.20, R.sup.21, R.sup.22, R.sup.23,
R.sup.24, R.sup.25, R.sup.26, R.sup.27, R.sup.28, R.sup.29, or
R.sup.30 to form an optionally substituted C.sub.3-C.sub.10
carbocyclyl, optionally substituted C.sub.6-C.sub.10 aryl, or
optionally substituted C.sub.2-C.sub.9 heteroaryl;
[0248] each R.sup.21 and R.sup.22 is, independently, hydrogen,
halogen, optionally substituted hydroxyl, optionally substituted
amino, or R.sup.20 and R.sup.21 combine to form .dbd.O, optionally
substituted C.sub.1-C.sub.6 alkyl, optionally substituted
C.sub.2-C.sub.6 alkenyl, optionally substituted C.sub.2-C.sub.6
alkynyl, optionally substituted C.sub.3-C.sub.10 carbocyclyl,
optionally substituted C.sub.6-C.sub.10 aryl, optionally
substituted C.sub.6-C.sub.10 aryl C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.9 heteroaryl, optionally substituted
C.sub.2-C.sub.9 heteroaryl C.sub.1-C.sub.6 alkyl, optionally
substituted C.sub.2-C.sub.9 heterocyclyl, or optionally substituted
C.sub.2-C.sub.9 heterocyclyl C.sub.1-C.sub.6 alkyl, or R.sup.21 or
R.sup.22 combines with any R.sup.20, R.sup.21, R.sup.22, R.sup.23,
R.sup.24, R.sup.25, R.sup.26, R.sup.27, R.sup.28, R.sup.29, or
R.sup.30 to form an optionally substituted C.sub.3-C.sub.10
carbocyclyl, optionally substituted C.sub.6-C.sub.10 aryl, or
optionally substituted C.sub.2-C.sub.9 heteroaryl;
[0249] each R.sup.23, R.sup.24, R.sup.25 and R.sup.26 is,
independently, hydrogen, hydroxyl, or R.sup.23 and R.sup.24 combine
to form .dbd.O, or R.sup.23, R.sup.24, R.sup.25 or R.sup.26
combines with any R.sup.20, R.sup.21, R.sup.22, R.sup.23, R.sup.24,
R.sup.25, R.sup.26, R.sup.27, R.sup.28, R.sup.29, or R.sup.30 to
form an optionally substituted C.sub.3-C.sub.10 carbocyclyl,
optionally substituted C.sub.6-C.sub.10 aryl, or optionally
substituted C.sub.2-C.sub.9 heteroaryl; and
[0250] each R.sup.27, R.sup.28, R.sup.29, and R.sup.30 is,
independently, hydrogen, optionally substituted C.sub.1-C.sub.6
alkyl, optionally substituted C.sub.2-C.sub.6 alkenyl, optionally
substituted C.sub.2-C.sub.6 alkynyl, optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, optionally substituted C.sub.6-C.sub.10 aryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heteroaryl, optionally substituted C.sub.2-C.sub.9 heteroaryl
C.sub.1-C.sub.6 alkyl, optionally substituted C.sub.2-C.sub.9
heterocyclyl, or optionally substituted C.sub.2-C.sub.9
heterocyclyl C.sub.1-C.sub.6 alkyl, or R.sup.27, R.sup.28,
R.sup.29, or R.sup.30 combines with any R.sup.20, R.sup.21,
R.sup.22, R.sup.23, R.sup.24, R.sup.25, R.sup.26, R.sup.27,
R.sup.28, R.sup.29, or R.sup.30 to form an optionally substituted
C.sub.3-C.sub.10 carbocyclyl, optionally substituted
C.sub.6-C.sub.10 aryl, or optionally substituted C.sub.2-C.sub.9
heteroaryl.
[0251] In some embodiments, a target protein interacting moiety has
a structure according to Formula IXa:
##STR00036##
[0252] In certain embodiments, a target protein interacting moiety
(e.g., a eukaryotic target protein interacting moiety such as a
mammalian target protein interacting moiety or a fungal target
protein interacting moiety or a prokaryotic target protein
interacting moiety such as a bacterial target protein interacting
moiety) does not include the structure:
##STR00037##
[0253] Linkers
[0254] The compounds of the invention include a linker (e.g., two
linkers connecting the presenter protein binding moiety and target
protein interacting moiety (e.g., a eukaryotic target protein
interacting moiety such as a mammalian target protein interacting
moiety or a fungal target protein interacting moiety or a
prokaryotic target protein interacting moiety such as a bacterial
target protein interacting moiety)). The linker component of the
invention is, at its simplest, a bond, but may also provide a
linear, cyclic, or branched molecular skeleton having pendant
groups covalently linking two moieties.
[0255] In some embodiments, at least one atom of a linker
participates in binding to the presenter protein and/or the target
protein. In certain embodiments, at least one atom of a linker does
not participate in binding to the presenter protein and/or the
target protein.
[0256] Thus, linking of the two moieties is achieved by covalent
means, involving bond formation with one or more functional groups
located on either moiety. Examples of chemically reactive
functional groups which may be employed for this purpose include,
without limitation, amino, hydroxyl, sulfhydryl, carboxyl,
carbonyl, carbohydrate groups, vicinal diols, thioethers,
2-aminoalcohols, 2-aminothiols, guanidinyl, imidazolyl, and
phenolic groups.
[0257] The covalent linking of the two moieties may be effected
using a linker that contains reactive moieties capable of reaction
with such functional groups present in either moiety. For example,
an amine group of a moiety may react with a carboxyl group of the
linker, or an activated derivative thereof, resulting in the
formation of an amide linking the two.
[0258] Examples of moieties capable of reaction with sulfhydryl
groups include .alpha.-haloacetyl compounds of the type
XCH.sub.2CO-- (where X=Br, Cl, or I), which show particular
reactivity for sulfhydryl groups, but which can also be used to
modify imidazolyl, thioether, phenol, and amino groups as described
by Gurd, Methods Enzymol. 11:532 (1967). N-Maleimide derivatives
are also considered selective towards sulfhydryl groups, but may
additionally be useful in coupling to amino groups under certain
conditions. Reagents such as 2-iminothiolane (Traut et al.,
Biochemistry 12:3266 (1973)), which introduce a thiol group through
conversion of an amino group, may be considered as sulfhydryl
reagents if linking occurs through the formation of disulfide
bridges.
[0259] Examples of reactive moieties capable of reaction with amino
groups include, for example, alkylating and acylating agents.
Representative alkylating agents include:
[0260] (i) .alpha.-haloacetyl compounds, which show specificity
towards amino groups in the absence of reactive thiol groups and
are of the type XCH.sub.2CO-- (where X=Br, Cl, or I), for example,
as described by Wong Biochemistry 24:5337 (1979);
[0261] (ii) N-maleimide derivatives, which may react with amino
groups either through a Michael type reaction or through acylation
by addition to the ring carbonyl group, for example, as described
by Smyth et al., J. Am. Chem. Soc. 82:4600 (1960) and Biochem. J.
91:589 (1964);
[0262] (iii) aryl halides such as reactive nitrohaloaromatic
compounds;
[0263] (iv) alkyl halides, as described, for example, by McKenzie
et al., J. Protein Chem. 7:581 (1988);
[0264] (v) aldehydes and ketones capable of Schiff's base formation
with amino groups, the adducts formed usually being stabilized
through reduction to give a stable amine;
[0265] (vi) epoxide derivatives such as epichlorohydrin and
bisoxiranes, which may react with amino, sulfhydryl, or phenolic
hydroxyl groups;
[0266] (vii) chlorine-containing derivatives of s-triazines, which
are very reactive towards nucleophiles such as amino, sufhydryl,
and hydroxyl groups;
[0267] (viii) aziridines based on s-triazine compounds detailed
above, e.g., as described by Ross, J. Adv. Cancer Res. 2:1 (1954),
which react with nucleophiles such as amino groups by ring
opening;
[0268] (ix) squaric acid diethyl esters as described by Tietze,
Chem. Ber. 124:1215 (1991); and
[0269] (x) .alpha.-haloalkyl ethers, which are more reactive
alkylating agents than normal alkyl halides because of the
activation caused by the ether oxygen atom, as described by
Benneche et al., Eur. J. Med. Chem. 28:463 (1993).
[0270] Representative amino-reactive acylating agents include:
[0271] (i) isocyanates and isothiocyanates, particularly aromatic
derivatives, which form stable urea and thiourea derivatives
respectively;
[0272] (ii) sulfonyl chlorides, which have been described by Herzig
et al., Biopolymers 2:349 (1964);
[0273] (iii) acid halides;
[0274] (iv) active esters such as nitrophenylesters or
N-hydroxysuccinimidyl esters;
[0275] (v) acid anhydrides such as mixed, symmetrical, or
N-carboxyanhydrides;
[0276] (vi) other useful reagents for amide bond formation, for
example, as described by M. Bodansky, Principles of Peptide
Synthesis, Springer-Verlag, 1984;
[0277] (vii) acylazides, e.g., wherein the azide group is generated
from a preformed hydrazide derivative using sodium nitrite, as
described by Wetz et al., Anal. Biochem. 58:347 (1974);
[0278] (viii) imidoesters, which form stable amidines on reaction
with amino groups, for example, as described by Hunter and Ludwig,
J. Am. Chem. Soc. 84:3491 (1962); and
[0279] (ix) haloheteroaryl groups such as halopyridine or
halopyrimidine.
[0280] Aldehydes and ketones may be reacted with amines to form
Schiff's bases, which may advantageously be stabilized through
reductive amination. Alkoxylamino moieties readily react with
ketones and aldehydes to produce stable alkoxamines, for example,
as described by Webb et al., in Bioconjugate Chem. 1:96 (1990).
[0281] Examples of reactive moieties capable of reaction with
carboxyl groups include diazo compounds such as diazoacetate esters
and diazoacetamides, which react with high specificity to generate
ester groups, for example, as described by Herriot, Adv. Protein
Chem. 3:169 (1947). Carboxyl modifying reagents such as
carbodiimides, which react through O-acylurea formation followed by
amide bond formation, may also be employed.
[0282] It will be appreciated that functional groups in either
moiety may, if desired, be converted to other functional groups
prior to reaction, for example, to confer additional reactivity or
selectivity. Examples of methods useful for this purpose include
conversion of amines to carboxyls using reagents such as
dicarboxylic anhydrides; conversion of amines to thiols using
reagents such as N-acetylhomocysteine thiolactone,
S-acetylmercaptosuccinic anhydride, 2-iminothiolane, or
thiol-containing succinimidyl derivatives; conversion of thiols to
carboxyls using reagents such as .alpha.-haloacetates; conversion
of thiols to amines using reagents such as ethylenimine or
2-bromoethylamine; conversion of carboxyls to amines using reagents
such as carbodiimides followed by diamines; and conversion of
alcohols to thiols using reagents such as tosyl chloride followed
by transesterification with thioacetate and hydrolysis to the thiol
with sodium acetate.
[0283] So-called zero-length linkers, involving direct covalent
joining of a reactive chemical group of one moiety with a reactive
chemical group of the other without introducing additional linking
material may, if desired, be used in accordance with the
invention.
[0284] More commonly, however, the linker will include two or more
reactive moieties, as described above, connected by a spacer
element. The presence of such a spacer permits bifunctional linkers
to react with specific functional groups within either moiety,
resulting in a covalent linkage between the two. The reactive
moieties in a linker may be the same (homobifunctional linker) or
different (heterobifunctional linker, or, where several dissimilar
reactive moieties are present, heteromultifunctional linker),
providing a diversity of potential reagents that may bring about
covalent attachment between the two moieties.
[0285] Spacer elements in the linker typically consist of linear or
branched chains and may include a C.sub.1-10 alkyl, C.sub.2-10
alkenyl, C.sub.2-10 alkynyl, C.sub.2-6 heterocyclyl, C.sub.6-12
aryl, C.sub.7-14 alkaryl, C.sub.3-10 alkheterocyclyl,
C.sub.2-C.sub.100 polyethylene glycol, or C.sub.1-10
heteroalkyl.
[0286] In some instances, the linker is described by Formula V.
[0287] Examples of homobifunctional linkers useful in the
preparation of conjugates of the invention include, without
limitation, diamines and diols selected from ethylenediamine,
propylenediamine and hexamethylenediamine, ethylene glycol,
diethylene glycol, propylene glycol, 1,4-butanediol,
1,6-hexanediol, cyclohexanediol, and polycaprolactone diol.
[0288] In some embodiments, the linker is a bond or a linear chain
of up to 10 atoms, independently selected from carbon, nitrogen,
oxygen, sulfur or phosphorous atoms, wherein each atom in the chain
is optionally substituted with one or more substituents
independently selected from alkyl, alkenyl, alkynyl, aryl,
heteroaryl, chloro, iodo, bromo, fluoro, hydroxyl, alkoxy, aryloxy,
carboxy, amino, alkylamino, dialkylamino, acylamino, carboxamido,
cyano, oxo, thio, alkylthio, arylthio, acylthio, alkylsulfonate,
arylsulfonate, phosphoryl, and sulfonyl, and wherein any two atoms
in the chain may be taken together with the substituents bound
thereto to form a ring, wherein the ring may be further substituted
and/or fused to one or more optionally substituted carbocyclic,
heterocyclic, aryl, or heteroaryl rings.
[0289] In some embodiments, the linker has the structure of Formula
XIX:
A.sup.1-(B.sup.1).sub.a-(C.sup.1).sub.b-(B.sup.2).sub.c-(D)-(B.sup.3).su-
b.d-(C.sup.2).sub.e-(B.sup.4).sub.t-A.sup.2 Formula XIX
[0290] where A.sup.1 is a bond between the linker and presenter
protein binding moiety; A.sup.2 is a bond between the mammalian
target interacting moiety and the linker; B.sup.1, B.sup.2,
B.sup.3, and B.sup.4 each, independently, is selected from
optionally substituted C.sub.1-C.sub.2 alkyl, optionally
substituted C.sub.1-C.sub.3 heteroalkyl, O, S, and NR.sup.N; RN is
hydrogen, optionally substituted C.sub.1-4 alkyl, optionally
substituted C.sub.3-4 alkenyl, optionally substituted C.sub.2-4
alkynyl, optionally substituted C.sub.2-6 heterocyclyl, optionally
substituted C.sub.6-12 aryl, or optionally substituted C.sub.1-7
heteroalkyl; C.sup.1 and C.sup.2 are each, independently, selected
from carbonyl, thiocarbonyl, sulphonyl, or phosphoryl; a, b, c, d,
e, and f are each, independently, 0 or 1; and D is optionally
substituted C.sub.1-10 alkyl, optionally substituted C.sub.2-10
alkenyl, optionally substituted C.sub.2-10 alkynyl, optionally
substituted C.sub.2-6 heterocyclyl, optionally substituted
C.sub.8-12 aryl, optionally substituted C.sub.2-C.sub.10
polyethylene glycol, or optionally substituted C.sub.1-10
heteroalkyl, or a chemical bond linking
A.sup.1-(B.sup.1).sub.a-(C.sup.1).sub.b-(B.sup.2).sub.c- to
-(B.sup.3).sub.d-(C.sup.2).sub.e-(B.sup.4).sub.f-A.sup.2.
[0291] Compound Characteristics
[0292] Pharmacokinetic Parameters
[0293] Preliminary exposure characteristics of the compounds can be
evaluated using, e.g., an in vivo Rat Early Pharmacokinetic (EPK)
study design to show bioavailability. For example, Male
Sprague-Dawley rats can be dosed via oral (PO) gavage in a
particular formulation. Blood samples can then be collected from
the animals at 6 timepoints out to 4 hours post-dose.
Pharmacokinetic analysis can then performed on the LC-MS/MS
measured concentrations for each timepoint of each compound.
[0294] Cell Permeability
[0295] In some embodiments, the compound is cell penetrant. To
determine permeability of a compound any method known in the art
may be employed such as a Biosensor assay as described herein.
Proteins
[0296] Presenter Proteins
[0297] Presenter proteins can bind a small molecule to form a
complex, which can bind to and modulate the activity of a target
protein (e.g., a eukaryotic target protein such as a mammalian
target protein or a fungal target protein or a prokaryotic target
protein such as a bacterial target protein). In some embodiments,
the presenter protein is a mammalian presenter protein (e.g., a
human presenter protein). In some embodiments, the presenter
protein is a fungal presenter protein. In certain embodiments, the
presenter protein is a bacterial presenter protein. In some
embodiments, the presenter protein is a plant presenter protein. In
some embodiments, the presenter protein is a relatively abundant
protein (e.g., the presenter protein is sufficiently abundant that
participation in a tripartite complex does not materially
negatively impact the biological role of the presenter protein in a
cell and/or viability or other attributes of the cell). In some
embodiments, the presenter protein is more abundant than the target
protein. In certain embodiments, the presenter protein is a protein
that has chaperone activity within a cell. In some embodiments, the
presenter protein has multiple natural interaction partners within
a cell. In certain embodiments, the presenter protein is one which
is known to bind a small molecule to form a binary complex that is
known to or suspected of binding to and modulating the biological
activity of a target protein. Immunophilins are a class of
presenter proteins which are known to have these functions and
include FKBPs and cyclophilins. In some embodiments, a reference
presenter protein exhibits peptidyl prolyl isomerase activity; in
some embodiments, a presenter protein shows comparable activity to
the reference presenter protein. In certain embodiments, the
presenter protein is a member of the FKBP family (e.g., FKBP12,
FKBP12.6, FKBP13, FKBP19, FKBP22, FKBP23, FKBP25, FKBP36, FKBP38,
FKBP51, FKBP52, FKBP60, FKBP65, and FKBP133), a member of the
cyclophilin family (e.g., PP1A, CYPB, CYPC, CYP40, CYPE, CYPD,
NKTR, SRCyp, CYPH, CWC27, CYPL1, CYP60, CYPJ, PPIL4, PPIL6, RANBP2,
PPWD1, PPIAL4A, PPIAL4B, PPIAL4C, PPIAL4D, or PPIAL4G), or PIN1.
The "FKBP family" is a family of proteins that have prolyl
isomerase activity and function as protein folding chaperones for
proteins containing proline residues. Genes that encode proteins in
this family include AIP, AIPL1, FKBP1A, FKBP1B, FKBP2, FKBP3,
FKBP4, FKBP5, FKBP6, FKBP7, FKBP8, FKBP9, FKBP9L, FKBP10, FKBP11,
FKBP14, FKBP15, and LOC541473.
[0298] The "cyclophilin family" is a family of proteins that bind
to cyclosporine. Genes that encode proteins in this family include
PPIA, PPIB, PPIC, PPID, PPIE, PPIF, PPIG, PPIH, SDCCAG-10, PPIL1,
PPIL2, PPIL3, PPIL4, P270, PPWD1, and COAS-2. Exemplary
cyclophilins include PP1A, CYPB, CYPC, CYP40, CYPE, CYPD, NKTR,
SRCyp, CYPH, CWC27, CYPL1, CYP60, CYPJ, PPIL4, PPIL6, RANBP2,
PPWD1, PPIAL4A, PPIAL4B, PPIAL4C, PPIAL4D, and PPIAL4G.
[0299] In some embodiments, a presenter protein is a chaperone
protein such as GRP78/BiP, GRP94, GRP170, calnexin, calreticulin,
HSP47, ERp29, Protein disulfide isomerase (PDI), and ERp57.
[0300] In some embodiments, a presenter protein is an allelic
variant or splice variant of a FKBP or cyclophilindisclosed
herein.
[0301] In some embodiments, a presenter protein is a polypeptide
whose amino acid sequence i) shows significant identity with that
of a reference presenter protein; ii) includes a portion that shows
significant identity with a corresponding portion of a reference
presenter protein; and/or iii) includes at least one characteristic
sequence found in presenter protein. In many embodiments, identity
is considered "significant" for the purposes of defining an
presenter protein if it is above 80%, 81%, 82%, 83%, 84%, 85%, 86%,
87%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or
higher. In some embodiments, the portion showing significant
identity has a length of at least 5, 6, 7, 8, 9, 10, 11, 12, 13,
14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,
31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
48, 49, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 110, 120, 130,
140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 300,
350, 450, 500, 550, 600 amino acids or more.
[0302] Representative presenter proteins are encoded by the genes
or homologs thereof listed in Table 1; in some embodiments, a
reference presenter protein is encoded by a gene set forth in Table
1. Also, those of ordinary skill in the art, referring to Table 3,
can readily identify sequences that are characteristic of presenter
proteins generally, and/or of particular subsets of presenter
proteins.
TABLE-US-00001 TABLE 1 Genes that Encode Selected Presenter
Proteins Uniprot Accession Gene Name Number AIP O00170 AIPL1 Q9NZN9
FKBP1A P62942 FKBP1B P68106 FKBP2 P26885 FKBP3 Q00688 FKBP4 Q02790
FKBP5 Q13451 FKBP6 O75344 FKBP7 Q9Y680 FKBP8 Q14318 FKBP9 O95302
FKBP9L Q75LS8 FKBP10 Q96AY3 FKBP11 Q9NYL4 FKBP14 Q9NWM8 FKBP15
Q5T1M5 LOC541473 -- PPIA Q567Q0 PPIB P23284 PPIC P45877 PPID Q08752
PPIE Q9UNP9 PPIG Q13427 PPIH O43447 PPIL1 Q9Y3C6 PPIL2 Q13356 PPIL3
Q9H2H8 PPIL4 Q8WUA2 PPIL5 Q32Q17 PPIL6 Q8IXY8 PPWD1 Q96BP3
[0303] Target Proteins
[0304] A target protein (e.g., a eukaryotic target protein such as
a mammalian target protein or a fungal target protein or a
prokaryotic target protein such as a bacterial target protein) is a
protein which mediates a disease condition or a symptom of a
disease condition. As such, a desirable therapeutic effect can be
achieved by modulating (inhibiting or increasing) its activity.
Target proteins useful in the complexes and methods of the
invention include those which do not naturally associate with a
presenter protein, e.g., those which have an affinity for a
presenter protein in the absence of a binary complex with a
compound of the invention of greater than 1 .mu.M, preferably
greater than 5 .mu.M, and more preferably greater than 10 .mu.M.
Alternatively, target proteins which do not naturally associate
with a presenter protein are those which have an affinity for a
compound of the invention in the absence of a binary complex
greater than 1 .mu.M, preferably greater than 5 .mu.M, and more
preferably greater than 10 .mu.M. In another alternative, target
proteins which do not naturally associate with a presenter protein
are those which have an affinity for a binary complex of
cyclosporine, rapamycin, or FK506 and a presenter protein (e.g.,
FKBP) of greater than 1 .mu.M, preferably greater than 5 .mu.M, and
more preferably greater than 10 .mu.M. In yet another alternative,
target proteins which do not naturally associate with a presenter
protein are those which are other than calcineurin or mTOR. The
selection of suitable target proteins for the complexes and methods
of the invention may depend on the presenter protein. For example,
target proteins that have low affinity for a cyclophilin may have
high affinity for an FKBP and would not be used together with the
latter.
[0305] Target proteins can be naturally occurring, e.g., wild type.
Alternatively, a target protein can vary from the wild type protein
but still retain biological function, e.g., as an allelic variant,
a splice mutant or a biologically active fragment.
[0306] In some embodiments, a target protein is a transmembrane
protein. In some embodiments, a target protein has a coiled coil
structure. In certain embodiments, a target protein is one protein
of a dimeric complex.
[0307] In some embodiments, a target protein of the invention
includes one or more surface sites (e.g., a flat surface site)
characterized in that, in the absence of forming a presenter
protein/compound complex, small molecules typically demonstrate low
or undetectable binding to the site(s). In some embodiments, a
target protein includes one or more surface sites (e.g., a flat
surface site) to which, in the absence of forming a presenter
protein/compound complex, a particular small molecule (e.g., the
compound) shows low or undetectable binding (e.g., binding at least
2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 100 fold or more lower
than that observed with a presenter protein/compound complex
involving the same compound). In some embodiments, a target protein
has a surface characterized by one or more sites (and, in some
embodiments, an entire surface) that lack(s) any a traditional
binding pocket, for example, a cavity or pocket on the protein
structure with physiochemical and/or geometric properties
comparable to proteins whose activity has been modulated by one or
more small molecules. In certain embodiments, a target protein has
a traditional binding pocket and a site for a protein-protein
interaction. In some embodiments, a target protein is an
undruggable target, for example, a target protein is not a member
of a protein family which is known to be targeted by drugs and/or
does not possess a binding site that is expected (e.g., according
to art-accepted understanding, as discussed herein) to be suitable
for binding to a small molecule.
[0308] In some embodiments, the target protein is a GTPase such as
DIRAS1, DIRAS2, DIRAS3, ERAS, GEM, HRAS, KRAS, MRAS, NKIRAS1,
NKIRAS2, NRAS, RALA, RALB, RAP1A, RAP1B, RAP2A, RAP2B, RAP2C,
RASD1, RASD2, RASL10A, RASL10B, RASL11A, RASL11B, RASL12, REM1,
REM2, RERG, RERGL, RRAD, RRAS, RRAS2, RHOA, RHOB, RHOBTB1, RHOBTB2,
RHOBTB3, RHOC, RHOD, RHOF, RHOG, RHOH, RHOJ, RHOQ, RHOU, RHOV,
RND1, RND2, RND3, RAC1, RAC2, RAC3, CDC42, RAB1A, RAB1B, RAB2,
RAB3A, RAB3B, RAB3C, RAB3D, RAB4A, RAB4B, RAB5A, RAB5B, RAB5C,
RAB6A, RAB6B, RAB6C, RAB7A, RAB7B, RAB7L1, RAB8A, RAB8B, RAB9,
RAB9B, RABL2A, RABL2B, RABL4, RAB10, RAB11A, RAB11B, RAB12, RAB13,
RAB14, RAB15, RAB17, RAB18, RAB19, RAB20, RAB21, RAB22A, RAB23,
RAB24, RAB25, RAB26, RAB27A, RAB27B, RAB28, RAB2B, RAB30, RAB31,
RAB32, RAB33A, RAB33B, RAB34, RAB35, RAB36, RAB37, RAB38, RAB39,
RAB39B, RAB40A, RAB40AL, RAB40B, RAB40C, RAB41, RAB42, RAB43,
RAP1A, RAP1B, RAP2A, RAP2B, RAP2C, ARF1, ARF3, ARF4, ARF5, ARF6,
ARL1, ARL2, ARL3, ARL4, ARL5, ARL5C, ARL6, ARL7, ARL8, ARL9,
ARL10A, ARL10B, ARL10C, ARL11, ARL13A, ARL13B, ARL14, ARL15, ARL16,
ARL17, TRIM23, ARL4D, ARFRP1, ARL13B, RAN, RHEB, RHEBL1, RRAD, GEM,
REM, REM2, RIT1, RIT2, RHOT1, or RHOT2. In some embodiments, the
target protein is a GTPas activating protein such as NF1, IQGAP1,
PLEXIN-B1, RASAL1, RASAL2, ARHGAP5, ARHGAP8, ARHGAP12, ARHGAP22,
ARHGAP25, BCR, DLC1, DLC2, DLC3, GRAF, RALBP1, RAP1GAP, SIPA1,
TSC2, AGAP2, ASAP1, or ASAP3. In some embodiments, the target
protein is a Guanine nucleotide-exchange factor such as CNRASGEF,
RASGEF1A, RASGRF2, RASGRP1, RASGRP4, SOS1, RALGDS, RGL1, RGL2, RGR,
ARHGEF10, ASEF/ARHGEF4, ASEF2, DBS, ECT2, GEF-H1, LARG, NET1,
OBSCURIN, P-REX1, P-REX2, PDZ-RHOGEF, TEM4, TIAM1, TRIO, VAV1,
VAV2, VAV3, DOCK1, DOCK2, DOCK3, DOCK4, DOCK8, DOCK10, C3G,
BIG2/ARFGEF2, EFA6, FBX8, or GEP100. In certain embodiments, the
target protein is a protein with a protein-protein interaction
domain such as ARM; BAR; BEACH; BH; BIR; BRCT; BROMO; BTB; C1; C2;
CARD; CC; CALM; CH; CHROMO; CUE; DEATH; DED; DEP; DH; EF-hand; EH;
ENTH; EVH1; F-box; FERM; FF; FH2; FHA; FYVE; GAT; GEL; GLUE; GRAM;
GRIP; GYF; HEAT; HECT; IQ; LRR; MBT; MH1; MH2; MIU; NZF; PAS; PB1;
PDZ; PH; POLO-Box; PTB; PUF; PWWP; PX; RGS; RING; SAM; SC; SH2;
SH3; SOCS; SPRY; START; SWIRM; TIR; TPR; TRAF; SNARE; TUBBY; TUDOR;
UBA; UEV; UIM; VHL; VHS; WD40; WW; SH2; SH3; TRAF; Bromodomain; or
TPR. In some embodiments, the target protein is a heat shock
protein such as Hsp20, Hsp27, Hsp70, Hsp84, alpha B crystalline,
TRAP-1, hsf1, or Hsp90. In certain embodiments, the target protein
is an ion channel such as Cav2.2, Cav3.2, IKACh, Kv1.5, TRPA1,
NAv1.7, Nav1.8, Nav1.9, P2X3, or P2X4. In some embodiments, the
target protein is a coiled-coil protein such as geminin, SPAG4,
VAV1, MAD1, ROCK1, RNF31, NEDP1, HCCM, EEA1, Vimentin, ATF4, Nemo,
SNAP25, Syntaxin 1a, FYCO1, or CEP250. In certain embodiments, the
target protein is a kinase such as ABL, ALK, AXL, BTK, EGFR, FMS,
FAK, FGFR1, 2, 3, 4, FLT3, HER2/ErbB2, HER3/ErbB3, HER4/ErbB4,
IGF1R, INSR, JAK1, JAK2, JAK3, KIT, MET, PDGFRA, PDGFRB, RET RON,
ROR1, ROR2, ROS, SRC, SYK, TIE1, TIE2, TRKA, TRKB, KDR, AKT1, AKT2,
AKT3, PDK1, PKC, RHO, ROCK1, RSK1, RKS2, RKS3, ATM, ATR, CDK1,
CDK2, CDK3, CDK4, CDK5, CDK6, CDK7, CDK8, CDK9, CDK10, ERK1, ERK2,
ERK3, ERK4, GSK3A, GSK3B, JNK1, JNK2, JNK3, AurA, ARuB, PLK1, PLK2,
PLK3, PLK4, IKK, KIN1, cRaf, PKN3, c-Src, Fak, PyK2, or AMPK. In
some embodiments, the target protein is a phosphatase such as WIP1,
SHP2, SHP1, PRL-3, PTP1B, or STEP. In certain embodiments the
target protein is a ubiquitin ligase such as BMI-1, MDM2, NEDD4-1,
Beta-TRCP, SKP2, E6AP, or APC/C. In some embodiments, the target
protein is a chromatin modifier/remodeler such as a chromatin
modifier/remodeler encoded by the gene BRG1, BRM, ATRX, PRDM3,
ASH1L, CBP, KAT6A, KAT6B, MLL, NSD1, SETD2, EP300, KAT2A, or
CREBBP. In some embodiments, the target protein is a transcription
factor such as a transcription factor encoded by the gene EHF,
ELF1, ELF3, ELF4, ELF5, ELK1, ELK3, ELK4, ERF, ERG, ETS1, ETV1,
ETV2, ETV3, ETV4, ETV5, ETV6, FEV, FLI1, GAVPA, SPDEF, SP11, SPIC,
SPIB, E2F1, E2F2, E2F3, E2F4, E2F7, E2F8, ARNTL, BHLHA15, BHLHB2,
BHLBHB3, BHLHE22, BHLHE23, BHLHE41, CLOCK, FIGLA, HAS5, HES7, HEY1,
HEY2, ID4, MAX, MESP1, MLX, MLXIPL, MNT, MSC, MYF6, NEUROD2,
NEUROG2, NHLH1, OLIG1, OLIG2, OLIG3, SREBF2, TCF3, TCF4, TFAP4,
TFE3, TFEB, TFEC, USF1, ARF4, ATF7, BATF3, CEBPB, CEBPD, CEBPG,
CREB3, CREB3L1, DBP, HLF, JDP2, MAFF, MAFG, MAFK, NRL, NFE2, NFIL3,
TEF, XBP1, PROX1, TEAD1, TEAD3, TEAD4, ONECUT3, ALX3, ALX4, ARX,
BARHL2, BARX, BSX, CART1, CDX1, CDX2, DLX1, DLX2, DLX3, DLX4, DLX5,
DLX6, DMBX1, DPRX, DRGX, DUXA, EMX1, EMX2, EN1, EN2, ESX1, EVX1,
EVX2, GBX1, GBX2, GSC, GSC2, GSX1, GSX2, HESX1, HMX1, HMX2, HMX3,
HNF1A, HNF1B, HOMEZ, HOXA1, HOXA10, HOXA13, HOXA2, HOXAB13, HOXB2,
HOXB3, HOXB5, HOXC10, HOXC11, HOXC12, HOXC13, HOXD11, HOXD12,
HOXD13, HOXD8, IRX2, IRX5, ISL2, ISX, LBX2, LHX2, LHX6, LHX9,
LMX1A, LMX1B, MEIS1, MEIS2, MEIS3, MEOX1, MEOX2, MIXL1, MNX1, MSX1,
MSX2, NKX2-3, NKX2-8, NKX3-1, NKX3-2, NKX6-1, NKX6-2, NOTO,
ONECUT1, ONECUT2, OTX1, OTX2, PDX1, PHOX2A, PHOX2B, PITX1, PITX3,
PKNOX1, PROP1, PRRX1, PRRX2, RAX, RAXL1, RHOXF1, SHOX, SHOX2,
TGIF1, TGIF2, TGIF2LX, UNCX, VAX1, VAX2, VENTX, VSX1, VSX2, CUX1,
CUX2, POU F1, POU2F1, POU2F2, POU2F3, POU3F1, POU3F2, POU3F3,
POU3F4, POU4F1, POU4F2, POU4F3, POU5F1P1, POU6F2, RFX2, RFX3, RFX4,
RFX5, TFAP2A, TFAP2B, TFAP2C, GRHL1, TFCP2, NFIA, NFIB, NFIX, GCM1,
GCM2, HSF1, HSF2, HSF4, HSFY2, EBF1, IRF3, IRF4, IRF5, IRF7, IRF8,
IRF9, MEF2A, MEF2B, MEF2D, SRF, NRF1, CPEB1, GMEB2, MYBL1, MYBL2,
SMAD3, CENPB, PAX1, PAX2, PAX9, PAX3, PAX4, PAX5, PAX6, PAX7,
BCL6B, EGR1, EGR2, EGR3, EGR4, GLIS1, GLIS2, GLI2, GLIS3, HIC2,
HINFP1, KLF13, KLF14, KLF16, MTF1, PRDM1, PRDM4, SCRT1, SCRT2,
SNAI2, SP1, SP3, SP4, SP8, YY1, YY2, ZBED1, ZBTB7A, ZBTB7B, ZBTB7C,
ZIC1, ZIC3, ZIC4, ZNF143, ZNF232, ZNF238, ZNF282, ZNF306, ZNF410,
ZNF435, ZBTB49, ZNF524, ZNF713, ZNF740, ZNF75A, ZNF784, ZSCAN4,
CTCF, LEF1, SOX10, SOX14, SOX15, SOX18, SOX2, SOX21, SOX4, SOX7,
SOX8, SOX9, SRY, TCF7L1, FOXO3, FOXB1, FOXC1, FOXC2, FOXD2, FOXD3,
FOXG1, FOXI1, FOXJ2, FOXJ3, FOXK1, FOXL1, FOXO1, FOXO4, FOXO6,
FOXP3, EOMES, MGA, NFAT5, NFATC1, NFKB1, NFKB2, TP63, RUNX2, RUNX3,
T, TBR1, TBX1, TBX15, TBX19, TBX2, TBX20, TBX21, TBX4, TBX5, AR,
ESR1, ESRRA, ESRRB, ESRRG, HNF4A, NR2C2, NR2E1, NR2F1, NR2F6,
NR3C1, NR3C2, NR4A2, RARA, RARB, RARG, RORA, RXRA, RXRB, RXRG,
THRA, THRB, VDR, GATA3, GATA4, or GATA5; or C-myc, Max, Stat3,
androgen receptor, C-Jun, C-Fox, N-Myc, L-Myc, MITF, Hif-1alpha,
Hif-2alpha, Bcl6, E2F1, NF-kappaB, Stat5, or ER(coact). In certain
embodiments, the target protein is TrkA, P2Y14, mPEGS, ASK1, ALK,
Bcl-2, BCL-XL, mSIN1, RORyt, IL17RA, eIF4E, TLR7 R, PCSK9, IgE R,
CD40, CD40L, Shn-3, TNFR1, TNFR2, IL31RA, OSMR, IL12beta1,2, Tau,
FASN, KCTD 6, KCTD 9, Raptor, Rictor, RALGAPA, RALGAPB, Annexin
family members, BCOR, NCOR, beta catenin, AAC 11, PLD1, PLD2,
Frizzled7, RaLP, MLL-1, Myb, Ezh2, RhoGD12, EGFR, CTLA4R, GCGC
(coact), Adiponectin R.sup.2, GPR 81, IMPDH2, IL-4R, IL-13R, IL-1R,
IL2-R, IL-6R, IL-22R, TNF-R, TLR4, Nrlp3, or OTR.
Complexes
[0309] Presenter Protein/Compound Complexes
[0310] In naturally occurring protein-protein interactions, the
binding event is driven largely by hydrophobic residues on flat
surface sites of the two proteins, in contrast to many small
molecule-protein interactions which are driven by interactions
between the small molecule in a cavity or pocket on the protein.
The hydrophobic residues on the flat surface site form hydrophobic
hot spots on the two interacting proteins wherein most of the
binding interactions between the two proteins are van der Waals
interactions. Small molecules may be used as portable hotspots for
proteins which are lacking one (e.g., presenter proteins) through
the formation of complexes (e.g., a presenter protein/compound
complex) to participate in pseudo protein-protein interactions
(e.g., forming a tripartite complex with a target protein).
[0311] Many mammalian proteins are able to bind to any of a
plurality of different partners; in some cases, such alternative
binding interactions contribute to biological activity of the
proteins. Many of these proteins adapt the inherent variability of
the hot spot protein regions to present the same residues in
different structural contexts. More specifically, the
protein-protein interactions can be mediated by a class of natural
products produced by a select group of fungal and bacterial
species. These molecules exhibit both a common structural
organization and resultant functionality that provides the ability
to modulate protein-protein interaction. These molecules contain a
presenter protein binding moiety that is highly conserved and a
target protein interacting moiety that exhibits a high degree of
variability among the different natural products. The presenter
protein binding moiety confers specificity for the presenter
protein and allows the molecule to bind to the presenter protein to
form a binary complex; the mammalian target protein interacting
moiety confers specificity for the target protein and allows the
binary complex to bind to the target protein, typically modulating
(e.g., positively or negatively modulating) its activity.
[0312] These natural products are presented by presenter proteins,
such as FKBPs and cyclophilins and act as diffusible,
cell-penetrant, orally bio-available adaptors for protein-protein
interactions. Examples include well known and clinically relevant
molecules such as Rapamycin (Sirolimus), FK506 (Tacrolimus), and
Cyclosporin. In brief, these molecules bind endogenous
intracellular presenter proteins, the FKBPs e.g. rapamycin and
FK506 or cyclophilins e.g. diluents, and the resulting binary
complexes of presenter protein-bound molecules selectively bind and
inhibit the activity of intracellular target proteins. Formation of
a tripartite complex between the presenter protein, the molecule,
and the target protein is driven by both protein-molecule and
protein-protein interactions and both are required for inhibition
of the target protein. In the example of the FKBP-rapamycin
complex, the intracellular target is the serine-threonine kinase
mTOR, whereas for FKBP-FK506 complex, the intracellular target is
the phosphatase calcineurin. Of particular interest in the
preceding two examples, FKBP12 is utilized as a partner
presentation protein by both the rapamycin and FK506 presentation
ligands. Moreover, the sub-structure components of rapamycin and
FK506 responsible for binding to FKBP12 are closely related
structurally, i.e. the so-called "Conserved Region," but it is the
dramatic structural differences between rapamycin and FK506 in the
non FKBP12-binding regions, i.e. the "Variable Region," that
results in the specific targeting of two distinct intracellular
proteins, mTOR and calcineurin, respectively. In this fashion, the
Variable Regions of rapamycin and FK506 are serving as contributors
to the binding energy necessary for enabling presenter
protein-target protein interaction.
[0313] In some embodiments, a presenter protein/compound complexes
of the invention bind to a target protein with at least 5-fold
(e.g., at least 10-fold, at least 20-fold, at least 30-fold, at
least 40-fold, at least 50-fold, at least 100-fold) greater
affinity than the complex binds to each of mTOR and/or
calcineurin.
[0314] In some embodiments, a presenter protein/compound complexes
of the invention bind to a target protein with at least 5-fold
(e.g., at least 10-fold, at least 20-fold, at least 30-fold, at
least 40-fold, at least 50-fold, at least 100-fold) greater
affinity than the affinity of the compound to a target protein when
the compound is not bound in a complex with a presenter
protein.
[0315] In certain embodiments, a presenter protein/compound
complexes of the invention bind to a target protein with at least
5-fold (e.g., at least 10-fold, at least 20-fold, at least 30-fold,
at least 40-fold, at least 50-fold, at least 100-fold) greater
affinity than the affinity of the presenter protein to a target
protein when the presenter protein is not bound in a complex with a
compound.
[0316] In some embodiments, a presenter protein/compound complexes
of the invention inhibit a naturally occurring interaction between
a target protein and a ligand, such as a protein or a small
molecule that specifically binds to the target protein.
[0317] In certain embodiments, when the presenter protein is a
prolyl isomerase, the prolyl isomerase activity is inhibited by
formation of the presenter protein/compound complex. In some
embodiments of the presenter protein/compound complexes of the
invention, the compound specifically binds to said presenter
protein with a K.sub.D of less than 10 .mu.M (e.g., less than 5
.mu.M, less than 1 .mu.M, less than 500 nM, less than 200 nM, less
than 100 nM, less than 75 nM, less than 50 nM, less than 25 nM,
less than 10 nM) or inhibits the peptidyl-prolyl isomerase activity
of the presenter protein, for example, with an IC.sub.50 of less
than 1 .mu.M (e.g., less than 0.5 .mu.M, less than 0.1 .mu.M, less
than 0.05 .mu.M, less than 0.01 .mu.M).
[0318] Tripartite Complexes
[0319] The vast majority of small molecule drugs act by binding a
functionally important site on a target protein, thereby modulating
(e.g., positively or negatively modulating) the activity of that
protein. For example, the cholesterol-lowering drugs statins bind
the enzyme active site of HMG-CoA reductase, thus preventing the
enzyme from engaging with its substrates. The fact that many such
drug/target interacting pairs are known may have misled some into
believing that a small molecule modulator could be discovered for
most, if not all, proteins provided a reasonable amount of time,
effort, and resources. This is far from the case. Current estimates
hold that only about 10% of all human proteins are targetable by
small molecules. The other 90% are currently considered refractory
or intractable toward small molecule drug discovery. Such targets
are commonly referred to as "undruggable." These undruggable
targets include a vast and largely untapped reservoir of medically
important human proteins. Thus, there exists a great deal of
interest in discovering new molecular modalities capable of
modulating the function of such undruggable targets.
[0320] The present invention encompasses the recognition that small
molecules are typically limited in their targeting ability because
their interactions with the target are driven by adhesive forces,
the strength of which is roughly proportional to contact surface
area. Because of their small size, the only way for a small
molecule to build up enough intermolecular contact surface area to
effectively interact with a target protein is to be literally
engulfed by that protein. Indeed, a large body of both experimental
and computational data supports the view that only those proteins
having a hydrophobic "pocket" on their surface are capable of
binding small molecules. In those cases, binding is enabled by
engulfment. Not a single example exists of a small molecule binding
with high-affinity to a protein outside of a hydrophobic
pocket.
[0321] Nature has evolved a strategy that allows a small molecule
to interact with target proteins at sites other than hydrophobic
pockets. This strategy is exemplified by the naturally occurring
immunosuppressive drugs cyclosporine A, rapamycin, and FK506. The
activity of these drugs involves the formation of a high-affinity
complex of the small molecule with a small presenting protein. The
composite surface of the small molecule and the presenting protein
then engages the target. Thus, for example, the binary complex
formed between cyclosporine A and cyclophilin A targets calcineurin
with high affinity and specificity, but neither cyclosporine A or
cyclophilin A alone binds calcineurin with measurable affinity.
[0322] Many important therapeutic targets exert their function by
complexation with other proteins. The protein/protein interaction
surfaces in many of these systems contain an inner core of
hydrophobic side chains surrounded by a wide ring of polar
residues. The hydrophobic residues contribute nearly all of the
energetically favorable contacts, and hence this cluster has been
designated as a "hotspot" for engagement in protein-protein
interactions. Importantly, in the aforementioned complexes of
naturally occurring small molecules with small presenting proteins,
the small molecule provides a cluster of hydrophobic functionality
akin to a hotspot, and the protein provides the ring of mostly
polar residues. In other words, presented small molecule systems
mimic the surface architecture employed widely in natural
protein/protein interaction systems.
[0323] Compounds (e.g., macrocyclic compounds) of the invention are
capable of modulating biological processes, for example through
binding to a presenter protein (e.g., a member of the FKBP family,
a member of the cyclophilin family, or PIN1) to form a presenter
protein/compound complex as described above which binds to a target
protein to form a tripartite complex. The formation of these
tripartite complexes allow for modulation of proteins that do not
have traditional binding pockets and/or are considered undruggable.
The presenter protein/compound complexes are able to modulate
biological processes through cooperative binding between the
compound and the presenter protein. Both the compound and presenter
protein have low affinity for the target protein alone, but the
presenter protein/compound complex has high affinity for the target
protein. Cooperative binding can be determined by measurement of
the buried surface area of the target protein that includes atoms
from the compound and/or presenter protein and/or by measurement of
the free binding energy contribution of the compound and/or
presenter protein. Binding is considered cooperative if at least
one atom from each of the compound and presenter protein
participates in binding with the target protein.
[0324] The binding of a presenter protein/compound complex and a
target protein is achieved through formation of a combined binding
site including residues from both the presenter protein and
compound that allow for increased affinity that would not be
possible with either the presenter protein or compound alone. For
example at least 20% (e.g., at least 25%, at least 30%, at least
35%, at least 40%, at least 45%, at least 50%) of the total buried
surface area of the target protein in the tripartite complex
includes one or more atoms that participate in binding to the
compound and/or at least 20% (e.g., at least 25%, at least 30%, at
least 35%, at least 40%, at least 45%, at least 50%) of the total
buried surface area of the target protein in the tripartite complex
includes one or more atoms that participate in binding to the
presenter protein. Alternatively, the compound contributes at least
10% (e.g., at least 20%, at least 25%, at least 30%, at least 35%,
at least 40%, at least 45%, at least 50%, at least 60%, at least
70%, at least 80%, at least 90%) of the total binding free energy
of the tripartite complex and/or the presenter protein contributes
at least 10% (e.g., at least 20% at least 25%, at least 30%, at
least 35%, at least 40%, at least 45%, at least 50%, at least 60%,
at least 70%, at least 80%, at least 90%) of the total binding free
energy of the tripartite complex.
[0325] In some embodiments, a presenter protein/compound complex
binds at a flat surface site on a target protein. In some
embodiments, a compound (e.g., macrocyclic compound) in a presenter
protein/compound complex binds at a hydrophobic surface site on a
target protein, e.g., a site that includes at least 50% hydrophobic
residues. In some embodiments, at least 70% of the binding
interactions between one or more of the atoms of a compound and one
or more atoms of a target protein are van der Waals and/or
.pi.-effect interactions. In certain embodiments, a presenter
protein/compound complex binds to a target protein at a site of a
naturally occurring protein-protein interaction between a target
protein and a protein that specifically binds the target protein.
In some embodiments, a presenter protein/compound complex does not
bind at an active site of a target protein. In some embodiments, a
presenter protein/compound complex binds at an active site of a
target protein.
[0326] A characteristic of compounds of the invention that form
tripartite complexes with a presenter protein and a target protein
is a lack of major structural reorganization in the presenter
protein/compound complex compared to the tripartite complex. This
lack of major structural reorganization results in a low entropic
cost to reorganize into a configuration favorable for the formation
of the tripartite complex once the presenter protein/compound
complex has been formed. For example, threshold quantification of
RMSD can be measured using the align command in PyMOL version
1.7rc1 (Schrodinger LLC). Alternatively, RMSD can be calculated
using the ExecutiveRMS parameter from the algorithm LigAlign (J.
Mol. Graphics and Modelling 2010, 29, 93-101). In some embodiments,
the structural organization of the compound (i.e., the average
three dimensional configuration of the atoms and bonds of the
molecule) is substantially unchanged in the tripartite complex
compared to the compound when in the presenter protein/compound
complex before binding to the target protein. For example, the root
mean squared deviation (RMSD) of the two aligned structures is less
than 1.
Utility and Administration
[0327] Compounds and presenter protein/compound complexes described
herein are useful in the methods of the invention and, while not
bound by theory, are believed to exert their desirable effects
through their ability to modulate (e.g., positively or negatively
modulate) the activity of a target protein (e.g., a eukaryotic
target protein such as a mammalian target protein or a fungal
target protein or a prokaryotic target protein such as a bacterial
target protein), through interaction with presenter proteins and
the target protein.
Kits
[0328] In some embodiments, the present invention relates to a kit
for conveniently and effectively carrying out the methods in
accordance with the present invention. In general, the
pharmaceutical pack or kit comprises one or more containers filled
with one or more of the ingredients of the pharmaceutical
compositions of the invention. Such kits are especially suited for
the delivery of solid oral forms such as tablets or capsules. Such
a kit preferably includes a number of unit dosages, and may also
include a card having the dosages oriented in the order of their
intended use. If desired, for instance if the subject suffers from
Alzheimer's disease, a memory aid can be provided, for example in
the form of numbers, letters, or other markings or with a calendar
insert, designating the days in the treatment schedule in which the
dosages can be administered. Alternatively, placebo dosages, or
calcium dietary supplements, either in a form similar to or
distinct from the dosages of the pharmaceutical compositions, can
be included to provide a kit in which a dosage is taken every day.
Optionally associated with such container(s) can be a notice in the
form prescribed by a governmental agency regulating the
manufacture, use or sale of pharmaceutical products, which notice
reflects approval by the agency of manufacture, use or sale for
human administration.
Pharmaceutical Compositions
[0329] For use as treatment of human and animal subjects, the
compounds of the invention can be formulated as pharmaceutical or
veterinary compositions. Depending on the subject to be treated,
the mode of administration, and the type of treatment
desired--e.g., prevention, prophylaxis, or therapy--the compounds
are formulated in ways consonant with these parameters. A summary
of such techniques is found in Remington: The Science and Practice
of Pharmacy, 21.sup.st Edition, Lippincott Williams & Wilkins,
(2005); and Encyclopedia of Pharmaceutical Technology, eds. J.
Swarbrick and J. C. Boylan, 1988-1999, Marcel Dekker, New York,
each of which is incorporated herein by reference.
[0330] Compounds described herein may be present in amounts
totaling 1-95% by weight of the total weight of the composition.
The composition may be provided in a dosage form that is suitable
for intraarticular, oral, parenteral (e.g., intravenous,
intramuscular), rectal, cutaneous, subcutaneous, topical,
transdermal, sublingual, nasal, vaginal, intravesicular,
intraurethral, intrathecal, epidural, aural, or ocular
administration, or by injection, inhalation, or direct contact with
the nasal, genitourinary, reproductive or oral mucosa. Thus, the
pharmaceutical composition may be in the form of, e.g., tablets,
capsules, pills, powders, granulates, suspensions, emulsions,
solutions, gels including hydrogels, pastes, ointments, creams,
plasters, drenches, osmotic delivery devices, suppositories,
enemas, injectables, implants, sprays, preparations suitable for
iontophoretic delivery, or aerosols. The compositions may be
formulated according to conventional pharmaceutical practice.
[0331] In general, for use in treatment, compounds described herein
may be used alone, or in combination with one or more other active
agents. An example of other pharmaceuticals to combine with the
compounds described herein would include pharmaceuticals for the
treatment of the same indication. Another example of a potential
pharmaceutical to combine with compounds described herein would
include pharmaceuticals for the treatment of different yet
associated or related symptoms or indications. Depending on the
mode of administration, compounds will be formulated into suitable
compositions to permit facile delivery. Each compound of a
combination therapy may be formulated in a variety of ways that are
known in the art. For example, the first and second agents of the
combination therapy may be formulated together or separately.
Desirably, the first and second agents are formulated together for
the simultaneous or near simultaneous administration of the
agents.
[0332] Compounds of the invention may be prepared and used as
pharmaceutical compositions comprising an effective amount of a
compound described herein and a pharmaceutically acceptable carrier
or excipient, as is well known in the art. In some embodiments, a
composition includes at least two different pharmaceutically
acceptable excipients or carriers.
[0333] Formulations may be prepared in a manner suitable for
systemic administration or topical or local administration.
Systemic formulations include those designed for injection (e.g.,
intramuscular, intravenous or subcutaneous injection) or may be
prepared for transdermal, transmucosal, or oral administration. A
formulation will generally include a diluents as well as, in some
cases, adjuvants, buffers, preservatives and the like. Compounds
can be administered also in liposomal compositions or as
microemulsions.
[0334] For injection, formulations can be prepared in conventional
forms as liquid solutions or suspensions or as solid forms suitable
for solution or suspension in liquid prior to injection or as
emulsions. Suitable excipients include, for example, water, saline,
dextrose, glycerol and the like. Such compositions may also contain
amounts of nontoxic auxiliary substances such as wetting or
emulsifying agents, pH buffering agents and the like, such as, for
example, sodium acetate, sorbitan monolaurate, and so forth.
[0335] Various sustained release systems for drugs have also been
devised. See, for example, U.S. Pat. No. 5,624,677, which is herein
incorporated by reference.
[0336] Systemic administration may also include relatively
noninvasive methods such as the use of suppositories, transdermal
patches, transmucosal delivery and intranasal administration. Oral
administration is also suitable for compounds of the invention.
Suitable forms include syrups, capsules, and tablets, as is
understood in the art.
[0337] Each compound of a combination therapy, as described herein,
may be formulated in a variety of ways that are known in the art.
For example, the first and second agents of the combination therapy
may be formulated together or separately.
[0338] The individually or separately formulated agents can be
packaged together as a kit. Non-limiting examples include, but are
not limited to, kits that contain, e.g., two pills, a pill and a
powder, a suppository and a liquid in a vial, two topical creams,
etc. The kit can include optional components that aid in the
administration of the unit dose to subjects, such as vials for
reconstituting powder forms, syringes for injection, customized IV
delivery systems, inhalers, etc. Additionally, the unit dose kit
can contain instructions for preparation and administration of the
compositions. The kit may be manufactured as a single use unit dose
for one subject, multiple uses for a particular subject (at a
constant dose or in which the individual compounds may vary in
potency as therapy progresses); or the kit may contain multiple
doses suitable for administration to multiple subjects ("bulk
packaging"). The kit components may be assembled in cartons,
blister packs, bottles, tubes, and the like.
[0339] Formulations for oral use include tablets containing the
active ingredient(s) in a mixture with non-toxic pharmaceutically
acceptable excipients. These excipients may be, for example, inert
diluents or fillers (e.g., sucrose, sorbitol, sugar, mannitol,
microcrystalline cellulose, starches including potato starch,
calcium carbonate, sodium chloride, lactose, calcium phosphate,
calcium sulfate, or sodium phosphate); granulating and
disintegrating agents (e.g., cellulose derivatives including
microcrystalline cellulose, starches including potato starch,
croscarmellose sodium, alginates, or alginic acid); binding agents
(e.g., sucrose, glucose, sorbitol, acacia, alginic acid, sodium
alginate, gelatin, starch, pregelatinized starch, microcrystalline
cellulose, magnesium aluminum silicate, carboxymethylcellulose
sodium, methylcellulose, hydroxypropyl methylcellulose,
ethylcellulose, polyvinylpyrrolidone, or polyethylene glycol); and
lubricating agents, glidants, and antiadhesives (e.g., magnesium
stearate, zinc stearate, stearic acid, silicas, hydrogenated
vegetable oils, or talc). Other pharmaceutically acceptable
excipients can be colorants, flavoring agents, plasticizers,
humectants, buffering agents, and the like.
[0340] Two or more compounds may be mixed together in a tablet,
capsule, or other vehicle, or may be partitioned. In one example,
the first compound is contained on the inside of the tablet, and
the second compound is on the outside, such that a substantial
portion of the second compound is released prior to the release of
the first compound.
[0341] Formulations for oral use may also be provided as chewable
tablets, or as hard gelatin capsules wherein the active ingredient
is mixed with an inert solid diluents (e.g., potato starch,
lactose, microcrystalline cellulose, calcium carbonate, calcium
phosphate or kaolin), or as soft gelatin capsules wherein the
active ingredient is mixed with water or an oil medium, for
example, peanut oil, liquid paraffin, or olive oil. Powders,
granulates, and pellets may be prepared using the ingredients
mentioned above under tablets and capsules in a conventional manner
using, e.g., a mixer, a fluid bed apparatus or a spray drying
equipment.
[0342] Dissolution or diffusion controlled release can be achieved
by appropriate coating of a tablet, capsule, pellet, or granulate
formulation of compounds, or by incorporating the compound into an
appropriate matrix. A controlled release coating may include one or
more of the coating substances mentioned above and/or, e.g.,
shellac, beeswax, glycowax, castor wax, carnauba wax, stearyl
alcohol, glyceryl monostearate, glyceryl distearate, glycerol
palmitostearate, ethylcellulose, acrylic resins, dl-polylactic
acid, cellulose acetate butyrate, polyvinyl chloride, polyvinyl
acetate, vinyl pyrrolidone, polyethylene, polymethacrylate,
methylmethacrylate, 2-hydroxymethacrylate, methacrylate hydrogels,
1,3 butylene glycol, ethylene glycol methacrylate, and/or
polyethylene glycols. In a controlled release matrix formulation,
the matrix material may also include, e.g., hydrated
methylcellulose, carnauba wax and stearyl alcohol, carbopol 934,
silicone, glyceryl tristearate, methyl acrylate-methyl
methacrylate, polyvinyl chloride, polyethylene, and/or halogenated
fluorocarbon.
[0343] The liquid forms in which the compounds and compositions of
the present invention can be incorporated for administration orally
include aqueous solutions, suitably flavored syrups, aqueous or oil
suspensions, and flavored emulsions with edible oils such as
cottonseed oil, sesame oil, coconut oil, or peanut oil, as well as
elixirs and similar pharmaceutical vehicles.
[0344] Generally, when administered to a human, the oral dosage of
any of the compounds of the combination of the invention will
depend on the nature of the compound, and can readily be determined
by one skilled in the art. Typically, such dosage is normally about
0.001 mg to 2000 mg per day, desirably about 1 mg to 1000 mg per
day, and more desirably about 5 mg to 500 mg per day. Dosages up to
200 mg per day may be necessary.
[0345] Administration of each drug in a combination therapy, as
described herein, can, independently, be one to four times daily
for one day to one year, and may even be for the life of the
subject. Chronic, long-term administration may be indicated.
[0346] The following Examples are intended to illustrate the
synthesis of a representative number of compounds and the use of
these compounds for the induction of chemotaxis and antifungal
activity. Accordingly, the Examples are intended to illustrate but
not to limit the invention. Additional compounds not specifically
exemplified may be synthesized using conventional methods in
combination with the methods described herein.
EXAMPLES
Example 1. General Fermentation and Isolation Protocols
[0347] Compounds synthesized by bacterial strains may be fermented
and isolated using the following general protocol:
[0348] General Fermentation Protocol
[0349] Strains: Bacterial strains such as Streptomyces malaysiensis
DSM41697, other producing species or genetically modified
derivatives producing FKBP ligands (Example: F1, F2, F3 or
structurally similar compounds and their analogs) were propagated
aseptically on a solid medium (Example: ISP4).
[0350] Working cell bank: Spores or mycelia derived from the
cultures grown on a solid medium plate at 30.degree. C. for 3-14 d
were used to inoculate a liquid culture (Example: 40 ml ATCC172
liquid medium in an 250 ml Erlenmeyer flask). The culture was
incubated with shaking at 30.degree. C. for 2-3 d. The resulting
cell suspension was mixed with sterile 50% glycerol giving a
mixture containing a final concentration of 15-25% glycerol.
Aliquots (about 1 ml) of glycerol-mycelia mixture were stored at
-80.degree. C. in sterile cryovials until further use.
[0351] Primary seed culture: Primary seed cultures (Example: 40 mL
ATCC172 medium in a 250 mL Erlenmeyer flask) were inoculated with 1
mL working cell bank suspension. Cultures were incubated on a
shaker with a 2-inch throw at 200-220 rpm for 2-3 d at 30.degree.
C.
[0352] Secondary seed culture: Secondary seed cultures (Example:
100-200 mL ATCC172 in an 500 mL Erlenmeyer flask) were inoculated
with the primary seed cultures (5% v/v) and incubated as described
above with various incubation periods of time (Example: 18-48
h).
[0353] Production fermentation in flasks: Production fermentation
was done in a 1.8 L Fernbach or Erlenmeyer flask containing 0.5 L
production medium supporting biosynthesis of these compounds
(Example: Medium 8430 or its derivatives). The culture was
inoculated with a seed culture prepared as described above at 2-5%
(v/v), and incubated as described above conditions for 3-7 d.
[0354] Production fermentation in bioreactors: Production
fermentation was done in a bioreactor (7.5 L capacity, New
Brunswick Scientific, NJ, USA) controlled by a BioFlo 300 module.
The bioreactor containing 5 L of sterilized medium (Example: 8430
and its derivatives) was inoculated with a seed culture (2-5%, v/v)
and incubated for 3-7 d with or without controlled parameters such
as dissolved oxygen amounts (Example: 10-50%), propeller speed
(Example 200-500 rpm), pH (Example: pH 4.5-7.0), temperature
(Example: 25-35.degree. C.), and nutrient feeding when
appropriate.
TABLE-US-00002 ISP4 (per liter) Soluble Starch 10.0 g Dipotassium
Phosphate 1.0 g Magnesium Sulfate USP 1.0 g Sodium Chloride 1.0 g
Ammonium Sulfate 2.0 g Calcium Carbonate 2.0 g Ferrous Sulfate 1.0
mg Manganous Chloride 1.0 mg Zinc Sulfate 1.0 mg Agar 20.0 g
TABLE-US-00003 TABLE 2 ATCC #172 media (per liter) Yeast extract 5
g Difco Soluble Starch 20 g Dextrose 10 g NZ Amine A 5 g Calcium
Carbonate 3 g
[0355] Add distilled water to 1000 mL, no pH adjustment.
TABLE-US-00004 [0355] TABLE 3 8430 Medium Component Amount
Pharmamedia or Proflo 10 g powder (ADM) D-Mannitol 20 g Yeast
extract 1.0 g KH.sub.2PO.sub.4 0.10 g MES buffer, hemi-Na+ salt
20.67 g (adjust media to (100 mM final) pH 6.5 final with 5N NaOH)
MgSO.sub.4.cndot.7H.sub.2O (Anh.) 0.05 g/L
CaCl.sub.2.cndot.2H.sub.2O 0.02 g/L R2 trace elements solution* 2
mL
[0356] Add distilled water to 1000 mL. [0357] Proflo oil containing
dominantly oleate and palmitate was added (4 mL/L) as an antifoam
agent.
TABLE-US-00005 [0357] TABLE 4 * R2 trace element solution. Amount
Element (mg/L) ZnSO.sub.4.cndot.7H.sub.2O 40
FeCl.sub.3.cndot.6H.sub.2O 200 CuCl.sub.2.cndot.2H.sub.2O 10
MnCl.sub.2.cndot.2H.sub.2O 10
Na.sub.2B.sub.4O.sub.7.cndot.10H.sub.2O 10
(NH.sub.4).sub.6Mo.sub.7O.sub.24.cndot.4H.sub.2O 10
[0358] General Isolation Protocol
[0359] Fermentation broth of a strain producing specific compounds
was separated to supernatant and microbial pellets by
centrifugation. Target compounds in the supernatant can be
extracted either with partition extraction using water-immiscible
solvents such as dichloromethane (DCM), ethyl acetate (EtOAc), etc
or with solid phase extraction by mixing with non-polar resins such
as HP20, HP20ss, etc. The target compounds in the pellets can be
extracted repeatedly (4.times.) using ethyl EtOAc-methanol (9:1,
v/v). The microbial extracts are pooled in preparation for
concentrating in vacuo. To this extract can be added the material
eluted from the HP20 beads (using organic solvents such as methanol
(MeOH), DCM, acetonitrile, isopropanol (IPA), etc) and/or the
organic phase of the liquid/liquid extraction of the original
supernatant.
[0360] The combined extracts are filtered through Celite and dried
in vacuo yielding a primary crude and this material is weighed. The
primary crude is dissolved in minimal 100% MeOH or a mixture of DCM
and tetrahydrofuran (THF). To this a binding medium such as silica
gel powder is added to the flask and re-dried in vacuo for
normal-phase silica gel column chromatography. The ratio of crude
to silica gel in the column bed is preferably ca. 1:5 (wt/wt). The
crude material can be fractionated over a RediSep.RTM. Normal-phase
Silica Flash Column using step gradients, linear gradients or
isocratic elution conditions. Elution solvents can include hexane,
heptane, ethyl acetate, ethanol, acetone, isopropanol, or other
organic solvents, or combination. Fractions with enriched target
compound(s) are pooled and dried for further purification after
LC/MS analysis and/or Thin Layer Chromatography (TLC) analysis.
[0361] Further purification could be achieved via normal-phase or
specific prep-HPLC columns such as Waters Spherisorb CN, Waters
Prep Silica, or Kromacil 60-5DIOL. Elution solvents can also
include hexane, heptane, ethyl acetate, ethanol, acetone,
isopropanol, or other organic solvents, or combination. Fractions
with enriched or pure target compound(s) are pooled and dried for
further workup after LC/MS analysis and/or Thin Layer
Chromatography (TLC) analysis.
[0362] Additional purification could be achieved various
reverse-phase prep-HPLC depending on the complexity of the enriched
material and target compounds' properties such as polarity,
solubility, etc. Reverse-phase Prep-HPLC columns employed for
separation include Waters Sunfire Prep C18 OBD, Waters Xbridge Prep
C18 OBD, Kromacil C4, Thermo Acclaim Polar Advantage 2, and
Phenomenex Luna C18. Common solvent systems are a mixture of water
and acetonitrile or methanol without or with 0.1% formic acid or
0.01% trifluoroacetic acid modifiers or 25 mM ammonium formate
buffer. The elution mode can be either linear gradient or
isocratic. Fractions with pure target compound(s) are pooled and
dried for further workup after LC/MS analysis and/or Thin Layer
Chromatography (TLC) analysis.
[0363] Fractions containing pure compounds are subjected to workup
and drying process to obtain pure solid material. Certain target
compounds can be extracted with ethyl acetate or dichloromethane
from aqueous matrix after reverse-phase column chromatographic
purification. Solvent removal and drying techniques include
rotavap, speedvac, and lyophilization. Purity and chemical
structure of purified target compounds are determined by LC-MS(/MS)
and NMR techniques.
Example 2. Isolation of F2 and F3
[0364] 10 L fermentation broth of Streptomyces malaysiensis (NRRL
B-24313; ATCC BAA-13; DSM 41697; JCM 10672; KCTC 9934; NBRC 16446;
CGMCC 4.1900; IFO 16448) producing F1 (target mass 595), F2 (target
mass 609) and Compound 3 (target mass 623) was separated by
centrifugation. F1 and F2 are present in both the clarified broth
and microbial pellets. Target compounds in the supernatant were
extracted once with EtOAc at a ratio of volume (1:1, v/v). The
pellets were extracted 3 times with 1.5 L of EtOAc-MeOH (9:1, v/v)
stirring with an overhead stirrer for 1 h-1.5 h for each
extraction. The organic extracts were filtered through Celite. The
combined filtrates were evaporated at 35.degree. C. until dryness
to afford ca. 30 g of crude extract. The residue was then dissolved
in 90 mL of DCM-THF (80:20, v/v), and to this 60 g of silica gel
were added and dried in vacuo at 35.degree. C. The dried
residue/silica mixture was loaded onto a 120 g RediSep silica gold
cartridge. Compounds were eluted with 100% heptane to heptane-EtOAc
(6:4, v/v) with a linear gradient over 30 min at 85 mL/min and
collected with 50 mL per fraction on a Teledyne ISCO Combiflash Rf
instrument.
[0365] By TLC, F2 enriched fractions were eluted at 20% to 30%
EtOAc in heptane. The pooled fraction was then concentrated at
35.degree. C. to provide 900 mg of enriched F2 material which was
further re-purified on a silica gel cartridge. Ca. 1 mL of DCM was
used to dissolve the fraction and 1.8 g of silica gel was added.
The dried mixture was loaded onto a 80 g RediSep silica gold
cartridge. Compounds were eluted with 100% heptane to heptane-EtOAc
(6:4, v/v) with a linear gradient over 30 min at 60 mL/min and
collected with 50 mL per fraction. By TLC, pure fractions 25-28
were combined for solvent removal in vacuo at 35.degree. C. to
obtain 300 mg of pure F2 (beta-form) for structure elucidation and
biological tests.
[0366] F2: .sup.1H NMR (500 MHz, Benzene-d.sub.6) .delta. 7.20-7.13
(m, 4H), 7.0-7.05 (m, 1H), 5.82 (s, 1H), 5.79-5.69 (m, 2H), 5.51
(m, 1H), 5.46-5.35 (m, 3H), 4.60 (d, J=12 Hz, 1H), 3.98-3.90 (m,
1H), 3.63 (dqd, J=13, 6.5, 3.0 Hz, 1H), 3.22 (d, J=3.6 Hz, 1H),
3.07 (td, J=12, 2.8 Hz, 1H), 3.00 (t, J=9.9 Hz, 1H), 2.93 (dd,
J=13, 4.4 Hz, 1H), 2.63-2.54 (m, 3H), 2.20 (d, J=13 Hz, 1H),
2.11-2.03 (m, 1H), 1.99-1.86 (m, 2H), 1.79-1.71 (m, 1H), 1.68-1.60
(m, 1H), 1.51-1.47 (m, 1H), 1.45 (d, J=6.6 Hz, 3H), 1.37 (m, 4H),
1.31 (m, 1H), 1.30 (d, J=6.6 Hz, 3H), 1.29-1.22 (m, 2H), 1.16-1.08
(m, 1H), 1.04-0.94 (m, 1H), 0.82 (t, J=7.4 Hz, 3H), 0.69 (d, J=6.7
Hz, 3H). .sup.13C NMR (125 MHz, Benzene-d.sub.6) .delta. 209.9,
169.7, 167.5, 141.3, 132.2, 129.6, 129.4, 128.7, 128.0, 127.7,
126.4, 98.2, 79.7, 75.5, 71.1, 51.9, 46.9, 44.2, 44.0, 40.4, 36.2,
35.3, 35.3, 35.2, 34.0, 33.3, 25.4, 25.3, 22.5, 21.1, 17.4, 17.1,
11.6, 9.7. HR-MS [M+Na]*: calc [C36H51NO7+Na].sup.+ 632.3563, obs
632.3569.
[0367] By TLC and LC-MS analysis, Compound 3 enriched fractions
were eluted at 30% to 40% EtOAc in heptane. The pooled fraction was
then concentrated at 35.degree. C. to provide 500 mg of enriched
Compound 3 material which was further re-purified by reverse-phase
prep-HPLC on a Thermo Polar Advantage II column (5 .mu.m,
250.times.21.2 mm). Prep-HPLC conditions included 70% acetonitrile
in water plus 0.1% formic acid, isocratic elution mode at 15
mL/min, 254 nm. The enriched Compound 3 sample was dissolved in 10
mL methanol for repeatable 10 injections. Target Compound 3 peak at
23.5 minute was collected. After extraction with EtOAc from
prep-HPLC pooled fractions and organic solvent removal in vacuo,
250 mg of pure Compound 3 were obtained. Its chemical structure was
subsequently determined by various LC-MS and NMR techniques.
[0368] F3: .sup.1H NMR (500 MHz, Benzene-d6, 1:1 mixture of
rotamers) .delta. 7.30 (m, 1H), 7.20-7.10 (m, 6H), 7.10-7.06 (m,
3H), 7.00 (m, 2H), 5.65-5.55 (m, 2H), 5.45 (m, 1H), 5.25-5.15 (m,
2H), 4.98 (dd, J=15, 7.3 Hz, 1H), 4.89 (dd, J=8.9, 5.0 Hz, 1H),
4.67 (dd, J=15, 8.8 Hz, 1H), 4.45 (m, 2H), 4.20 (m, 1H), 4.13 (m,
1H), 3.87 (m, 1H), 3.57 (m, 2H), 3.35-3.05 (m, 3H), 2.72 (m, 2H),
2.65-2.50 (m, 2H), 2.50-2.30 (m, 6H), 2.08 (m, 1H), 1.93 (m, 1H),
1.80-0.90 (m, 50H) [1.71 (d, J=6.8 Hz, 3H), 1.54 (d, J=6.8 Hz,
3H)], 1.24 (d, J=6.5 Hz, 3H), 1.18 (d, J=6.6 Hz, 3H), 1.08 (d,
J=6.8 Hz, 3H), 1.01 (m, J=6.7 Hz, 3H)], 0.73 (t, J=7.5 Hz, 3H),
0.69 (t, J=7.5 Hz, 3H). .sup.13C NMR (125 MHz, Benzene-d.sub.6)
.delta. 201.5, 199.9, 197.8, 191.6, 170.4, 169.5, 166.8, 166.6,
145.4, 144.8, 140.6, 140.5, 133.9, 131.3, 129.7, 129.4, 129.3,
128.8, 128.8, 128.4, 128.3, 126.6, 126.5, 126.0, 100.0, 99.3, 80.6,
78.2, 73.1, 72.4, 71.7, 70.6, 57.1, 52.6, 51.9, 51.1, 45.8, 45.4,
44.2, 42.5, 42.2, 39.8, 35.8, 35.7, 35.6, 34.1, 33.6, 33.4, 29.9,
29.9, 29.3, 28.2, 27.4, 27.1, 25.1, 25.1, 22.3, 22.2, 21.3, 21.2,
16.6, 16.2, 14.6, 13.7, 11.2, 11.1, 10.6, 9.5. HR-MS [M+H].sup.+:
calc [C.sub.36H.sub.49NO.sub.8+H].sup.+ 624.3536, obs 624.3547.
Example 3. Isolation of F22
[0369] 10 L of fermentation broth produced from a recombinant
strain S1806 were centrifuged to obtain the pellets and
supernatant. The pellets were extracted 3 times with 1.5 L of
EtOAc-MeOH (9:1, v/v). The organic solvents were combined and
concentrated in vacuo to obtain 1.8 g of crude extract. To this, 2
mL of Heptane-THF (4:1, v/v) was added to dissolve and 2 g of
Celite were then added to obtain the dried mixture after removal of
solvents on a rotavapor at 30.degree. C. The dried residue/celite
mixture was loaded onto a 40 g RediSep silica gold cartridge for
column chromatography. Compounds were fractionated with a linear
gradient elution from 100% n-heptane to 40% EtOAc in heptane (v/v)
over 25 min at 20 mL/min collected with 50 mL per fraction. F22
(target mass 607) was primarily enriched in Fraction 14 identified
by LC-MS analysis. Fraction 14 was then dried in vacuo at
30.degree. C. to afford 17.8 mg solid material which was further
purified by prep-HPLC on a Thermo Polar Advantage II column (5
.mu.m, 250.times.21.2 mm). Prep-HPLC conditions included 90%
acetonitrile in water plus 0.1% formic acid, isocratic elution mode
at 15 mL/min, 254 nm. The sample was dissolved in 1.78 mL methanol
for repeatable 5 injections. Target F22 peak at 11.5 minute was
collected. After solvent removal in vacuo, 3.64 mg of pure F22 was
obtained. Its chemical structure was subsequently determined by
various LC-MS/MS and NMR techniques.
Example 4. Synthesis of Selected Compounds
Instrumentation:
[0370] Purification was performed on HPLC preparative using Agilent
SD-1 system.
[0371] Electrospray LC/MS analysis was performed using an Agilent
1260 Infinity system equipped with an Agilent 1260 series LC pump.
The methods used were:
Analytical HPLC Method 1:
[0372] Agilent Zorbax Extend C-18 reverse phase column
(2.1.times.50 mm), 1.8 .mu.m:
Solvent A: Water+0.1% Formic Acid
Solvent B: Acetonitrile+0.1% Formic Acid
[0373] Flow rate: 0.5 mL/min Injection volume: 5 .mu.L Column
temperature: 40.degree. C.
Gradient:
TABLE-US-00006 [0374] Time, min % A % B 0 95 5 3 30 70 10 0 100 13
0 100 14 95 5 16 95 5
Analytical HPLC Method 2:
ThermoScientific Acclaim, Polar Advantage II, 4.6.times.150 mm, 5
.mu.m
Solvent A: Water+0.1% Formic Acid
Solvent B: Acetonitrile+0.1% Formic Acid
[0375] Flow rate: 0.8 mL/min Injection volume: 5 .mu.L Column
temperature: 40.degree. C.
Isocratic:
TABLE-US-00007 [0376] Time, min % A % B 0 20 80 6 20 80 7 5 95 9 5
95 10 20 80 12 20 80
[0377] Electrospray UHPLC/MS was performed using an Agilent 1290
Infinity system equipped with an Agilent 1290 series LC pump. The
columns used were the same.
Analytical UHPLC Method 1:
[0378] Agilent Zorbax Extend C-18 reverse phase column
(2.1.times.50 mm), 1.8 .mu.m:
Solvent A: Water+0.1% Formic Acid
Solvent B: Acetonitrile+0.1% Formic Acid
[0379] Flow rate: 0.5 mL/min Injection volume: 5 .mu.L Column
temperature: 40.degree. C.
Gradient:
TABLE-US-00008 [0380] Time, min % A % B 0 95.24 4.76 5.21 30.19
69.81 9.66 9.04 90.96 10.5 0 100 11.5 0 100 12 95.24 4.76 13 95.24
4.76
[0381] Purification Method A: Performed using an ACCLAIM Polar
Advantage II (21.2.times.250 mm) column. Flow rate 17 mL/min,
isocratic 70% B. Solvent A was 0.1% aqueous formic acid, solvent B
was 100% acetonitrile containing 0.1% formic acid.
Synthesis of F11
Synthesis of
(2S)-1-((4R,7S)-7-((2R,3S,4R,11S,12R)-12-benzyl-3,11-dihydroxy-4-methylte-
tradecan-2-yl)-2-hydroxy-4-methyl-3-oxooxepane-2-carbonyl)piperidine-2-car-
boxylic acid C-11 lactone. F11
##STR00038##
[0383] To a mixture of
(2S)-1-((4R,7S)-7-((2R,3S,4R,6E,9E,11R,12R)-12-benzyl-3,11-dihydroxy-4-me-
thyltetradeca-6,9-dien-2-yl)-2-hydroxy-4-methyl-3-oxooxepane-2-carbonyl)pi-
peridine-2-carboxylic acid C-11 lactone (5 mg, 8.2 umol) and 10%
palladium on carbon (2 mg) and a stirrer bead under nitrogen was
added ethyl acetate (1 mL). The flask was charged with hydrogen and
stirred vigorously for 1.5 hr. The atmosphere of hydrogen was
replaced with nitrogen and the reaction filtered through celite.
The celite pad was washed with more ethyl acetate and the solvent
evaporated in vacuo. The residue was purified by chromatography on
silica gel, gradient elution ethyl acetate: hexanes 40:60 to 100:0
to afford the title compound.
[0384] 1H NMR (CDCl3, 500 MHz): .delta. 7.28 (m, 2H), 7.19 (m, 1H),
7.13 (d, J=6.98 Hz, 2H), 5.65 (s, 1H), 5.26 (d, J=4.92 Hz, 1H),
5.11 (m, 1H), 4.67 (d, J=13.02 Hz, 1H), 4.02 (dd, J=10.67, 1.13 Hz,
1H), 3.35 (m, 1H), 3.23-3.10 (m, 2H), 2.72 (dd, J=13.85, 5.50 Hz,
1H), 2.50 (dd, J=13.93, 9.25 Hz, 1H), 2.39 (m, 1H), 1.95-1.73 (m,
5H), 1.71-1.15 (m, 25H), 1.03 (d, J=6.71 Hz, 3H), 0.85 (t, J=7.42
Hz, 3H), 0.79 (d, J=6.82 Hz, 3H) ppm.
[0385] 13C NMR (CDCl3, 500 MHz): .delta. 210.5, 170.3, 167.4,
140.5, 129.0, 128.3, 126.0, 97.8, 79.1, 76.9, 71.1, 52.0, 45.9,
43.9, 43.5, 39.9, 36.3, 35.1, 33.1, 32.3, 31.9, 29.1, 27.9, 27.1,
25.8, 25.1, 23.4, 22.1, 21.1, 20.0, 17.0, 16.6, 11.5, 8.9 ppm.
[0386] MS (ESI): calculated for (C36H55NO7+H)+ 614.4057, found
614.4066.
Synthesis of F24
Synthesis of
(S)-1-(2-((2R,3R,6S)-6-((2R,3R,4S,6E,9E,11R,12R)-12-benzyl-3,11-dihydroxy-
-4-methyl-5-oxotetradeca-6,9-dien-2-yl)-2-hydroxy-3-methyltetrahydro-2H-py-
ran-2-yl)-2-oxoacetyl)piperidine-2-carboxylic acid C-11 lactone
##STR00039##
[0388] To a solution of F3 (24.2 mg, 36.7 .mu.mol) in ethyl acetate
(1 mL) under nitrogen was added 10% Pd/C (12 mg, 50% w/w). The
flask was charged with hydrogen and the suspension was stirred at
room temperature for 30 min. The hydrogen was replaced with
nitrogen and the reaction mixture was then filtered through celite.
The filtrate was concentrated under vacuum to give 24 mg of crude
product, of which, a portion was purified using Method A to afford
the tetrahydro WDB-003 as a white solid (11 mg, 47.8%). TLC: (50/50
heptane/ethyl acetate) Rf=0.45.
[0389] .sup.1H NMR (400 MHz, C.sub.6D6, 1:0.3 mixture of rotamers,
asterisk (*) denotes peaks associated with the minor isomer)
.delta. 7.25-7.0 (m, 5H), 6.18* (s, 1H), 5.33-5.28 (m, 2H), 5.11*
(d, J=12 Hz, 1H), 4.92* (m, 1H), 4.45* (d, J=12 Hz, 1H), 4.24 (m,
1H), 4.06* (td, J=8 Hz, 1H), 3.40 (dd, J=4 Hz, 1H), 3.88 (t, J=8
Hz, 1H), 3.65 (d, J=12 Hz, 1H), 3.30 (td, J=12 Hz, 1H), 3.02* (td,
J=12, 4 Hz, 1H), 2.84* (m, 1H), 2.74 (dd, 16, 8 Hz, 1H), 2.65 (q, 8
Hz, 1H), 2.61-2.48 (m, 2H), 2.38-2.09 (m, 5H), 1.73-1.54 (m, 6H),
1.47-1.02 (m, 28H), 0.90 (m, 4H), 0.80 (t, J=8 Hz, 3H), 0.73* (t,
J=8 Hz, 3H) ppm.
[0390] .sup.13C NMR (400 MHz, C.sub.6D.sub.6) .delta.: 212.59,
197.51, 170.64, 166.70, 140.93, 129.39, 128.77, 128.17, 127.94,
126.43, 99.30, 76.54, 72.64, 71.61, 52.46, 51.24, 46.46, 45.30,
41.62, 40.82, 36.20, 35.31, 32.09, 29.96, 29.47, 27.67, 26.17,
25.71, 24.92, 22.57, 21.78, 21.59, 16.59, 13.68, 11.49, 10.37 ppm.
MS (ESI): calculated for (C36H53NO8+Na)*650.37, found 650.3.
Synthesis of F25
Synthesis of (2S)-1-((4R,7S)-7-((2R,3R,4S,11
S,12R)-12-benzyl-3,11-dihydroxy-4-methyl-5-oxotetradecan-2-yl)-2-hydroxy--
4-methyl-3-oxooxepane-2-carbonyl)piperidine-2-carboxylic acid C-11
lactone
##STR00040##
[0392] tert-Butyldimethylsilyl trifluoromethanesulfonate (6.9
.mu.L, 30.1 .mu.mol) was added by syringe to an ice-cooled solution
of
(S)-1-(2-((2R,3R,6S)-6-((2R,3R,4S,6E,9E,11R,12R)-12-benzyl-3,11-dihydroxy-
-4-methyl-5-oxotetradeca-6,9-dien-2-yl)-2-hydroxy-3-methyltetrahydro-2H-py-
ran-2-yl)-2-oxoacetyl)piperidine-2-carboxylic acid C-11 lactone-F24
(18.8 mg, 30.1 .mu.L) and triethylamine (4.0 .mu.L, 30.1 .mu.L) in
dichloromethane (2 mL) under nitrogen. The resulting solution was
stirred at 0.degree. C. for 15 min and was then allowed to warm to
room temperature for 2 h. The reaction was cooled to 0.degree. C.
and a second portion of triethylamine (4.0 .mu.L, 30.1 .mu.L) and
tert-butyldimethylsilyl trifluoromethanesulfonate (6.9 .mu.L, 30.1
.mu.mol) was added. The reaction was again allowed to warm to room
temperature and stirred under nitrogen 16 h. Dichloromethane (10
mL) and 0.5 M aqueous sodium bicarbonate solution (10 mL) were
added and the organic layer was separated and washed with 5% brine
solution (10 mL), dried over anhydrous sodium sulfate, filtered,
and the filtrate concentrated in vacuo. The crude product was
purified using method A to afford the starting material as a white
solid (2.52 mg) and the title compound (4.51 mg) as a white
solid.
[0393] .sup.1H NMR (400 MHz, C.sub.6D.sub.6) .delta. 7.26-7.16 (m,
4H), 7.07 (tt, J=6.4, 2 Hz, 1H), 5.58 (s, 1H), 5.39 (d, J=4.8 Hz,
1H), 5.17 (m, 1H), 4.67 (d, J=12.4 Hz, 1H), 4.29 (d, J=10.8 Hz,
1H), 3.42 (m, 1H), 3.06 (td, J=11.2, 2.8 Hz, 1H), 2.92 (t, J=10 Hz,
1H), 2.85 (m, 1H), 2.75 (s, 1H), 2.66 (dd, J=14, 5.6 Hz, 1H), 2.52
(dd, J=14, 9.2 Hz, 1H), 2.35 (m, 1H), 2.28 (m, 1H), 1.84 (m, 2H),
1.68-1.59 (m, 2H), 1.46-1.06 (m, 23H), 0.88 (m, 4H), 0.82 (t, 3H,
J=7.2 Hz) ppm.
[0394] .sup.13C NMR (400 MHz, C.sub.6D.sub.6) .delta.: 226.15,
210.53, 209.8, 179.03, 167.59, 140.84, 129.40, 128.77, 128.18,
127.9, 126.45, 98.16, 79.21, 76.85, 70.48, 52.20, 46.07, 44.46,
43.88, 42.76, 36.67, 35.30, 35.14, 32.88, 30.53, 27.94, 25.49,
25.32, 24.57, 22.39, 21.36, 20.72, 16.98, 15.16, 11.68, 9.08
ppm.
[0395] MS (ESI): calculated for (C.sub.36H.sub.53NO.sub.8+Na).sup.+
650.37, found 650.3.
Example 5. Synthesis of Cyclosporine Analogs
[0396] General Protocol
[0397] Over 2,000 analogs of cyclosporine have been made using
solution-phase peptide synthesis, for example according to the
method of Li et al. J. Org. Chem 2000(65), 2951. In the amino acid
sequence of cyclosporine:
cyclo-(D-Ala.sup.8-MeLeu.sup.9-MeLeu.sup.10-MeVal.sup.11-MeLeu.sup.1-Nva.-
sup.2-Sar.sup.3-MeLeu.sup.4-Val.sup.5-MeLeu.sup.6-Ala.sup.7), the
polypeptide stretch from D-Ala.sup.8 to Sar.sup.3 can be considered
the "constant" region responsible for the majority of binding with
cyclophilin A. Therefore cyclosporine analogues that preserve
cyclophilin binding can be made by synthesis of a tetrapeptide
surrogate for the MeLeu.sup.4-Val.sup.5-MeLeu.sup.6-Ala.sup.7
fragment, then elongation and cyclization.
[0398] In a specific example for the synthesis of
cyclo-(D-Ala.sup.8-MeLeu.sup.9-MeLeu.sup.10-MeVal.sup.11-MeLeu.sup.1-Nva.-
sup.2-Sar.sup.3-Gly.sup.4-Gly.sup.5-Gly.sup.6-Gly.sup.7),
Fmoc-Gly-OH and Ala-OBzl are coupled in the presence of
2,6-lutidine and BDMP
(5-(1H-benzotriazol-1-yloxy)-3,4-dihydro-1-methyl 2H-pyrrolium
hexachloroantimonate) to yield Fmoc-Gly-Gly-OBzl. Removal of the
Fmoc group with diethylamine followed by coupling with Fmoc-Gly-OH
(promoted by BDMP) yields Fmoc-Gly-Gly-Gly-OBzl. Another iteration
of Fmoc removal and Fmoc-Gly-OH coupling yields
Fmoc-Gly-Gly-Gly-Gly-OBzl. This suitably protected tetrapeptide can
be elaborated to the cyclosporine analog
cyclo-(D-Ala.sup.8-MeLeu.sup.9-MeLeu.sup.10-MeVal.sup.11-MeLeu.sup.1-Nva.-
sup.2-Sar.sup.3-Gly.sup.4-Gly.sup.5-Gly.sup.6-Gly.sup.7) in
accordance with the methods provided by Li et al.
Example 6. Synthesis of Cyclic Peptide Compounds of the
Invention
[0399] General Protocol
[0400] The general method described by Ishizawa et al. J. Am. Chem.
Soc. 2013(135), 5433 can be used. A synthetic constant region is
prepared wherein the ends terminate in a carboxylic acid, and a
(2-chloroacetamido)-acylated amine (in either orientation).
Subsequently, a peptidic variable region is prepared using standard
Fmoc solid phase peptide synthesis (SPPS), starting from
Fmoc-Gly-Wang resin. A cysteine residue is incorporated at an
internal position so as to effect later macrocyclization. The
linear polypeptide is coupled with the synthetic constant region,
then cleaved from the resin using trifluoroacetic acid. To promote
macrocyclization, the peptide is treated with triethylamine in
DMSO.
Example 7. Binding of Compounds to Cyclophilin A
[0401] The binding of compounds of the invention to Cyclophilin A
can be determined using the following protocol.
[0402] General Protocol
[0403] This protocol utilizes Perkin Elmers AlphaLISA technology
platform to detect cyclosporine analogues by measuring the
inhibition of binding of biotinylated Cyclosporin A to FLAG tagged
Cyclophilin A.
[0404] Reagents: 10.times.TBST Buffer (Boston BioProducts IBB-181),
Biotinylated Cyclosporin A (in-house), FLAG tagged Cyclophilin A
(in-house); anti-FLAG Donor beads (PerkinElmer AS103) and
Streptavidin Acceptor beads (PerkinElmer AL025); Compounds in DMSO
(in-house), Cyclosporin A (LC Labs Cat #C-6000).
[0405] Equipment: Biotek Synergy2, Janus MTD Head pipettor,
Eppendorf Repeat Pipettor
[0406] Supplies: White 96-well Corning 1/2h area plates (Cat
#3642), 96-well polypropylene full skirt (180 ul) PCR plates,
96-well Viaflow P20 tips for Janus MTD Head pipettor.
[0407] Experimental Protocol/Description of Assay: Add 20 uL of 6
nM Biotinylated CsA working stock to each well of the 96-well
plate. Add 1 uL of test compound (100% DMSO) to each well of the
plate using the Janus MTD head and P20 tips (except control wells).
Add 1 uL of DMSO to negative control wells and 1 uL of 500 uM
Cyclosporin A solution to positive control wells. In the dark, add
20 uL of combined Donor/Acceptor beads to each well. Incubate in
the dark for 30 minutes at room temperature. In the dark, add 10 uL
of 25 nM Flag tagged CypA working stock to each well. Incubate in
the dark for 60 minutes at room temperature. Protect plate from
light until reading on Biotek Synergy2 Plate Reader; Alphalisa
96-well protocol (680 excitation/615 emission).
[0408] Results: The binding affinity of 104 cyclosporine analogs
for cyclophilin A was determined as shown in Table 5.
TABLE-US-00009 TABLE 5 Cyclophilin A Binding of Cyclosporine
Analogs IC50 value % inhibition of of CsA % CsA binding to binding
to # signal Cyclophilin A Cyclophilin A C1 0.56 99.44 <2 uM C2
5.25 94.75 <2 uM C3 13.43 86.57 <2 uM C4 4.12 95.88 <2 uM
C5 9.09 90.91 <2 uM C6 7.29 92.71 <2 uM C7 2.65 97.35 <2
uM C8 9.44 90.56 <2 uM C9 0.11 99.89 <2 uM C10 0.56 99.44
<2 uM C11 6.27 93.73 <2 uM C12 3.22 96.78 <2 uM C13 2.70
97.30 <2 uM C14 9.36 90.64 <2 uM C15 2.93 97.07 <2 uM C16
2.56 97.44 <2 uM C17 17.17 82.83 <2 uM C18 2.12 97.88 <2
uM C19 16.79 83.21 <2 uM C20 2.77 97.23 <2 uM C21 31.08 68.92
<2 uM C22 5.97 94.03 <2 uM C23 1.28 98.72 <2 uM C24 6.65
93.35 <2 uM C25 0.37 99.63 <2 uM C26 3.92 96.08 <2 uM C27
5.27 94.73 <2 uM C28 1.06 98.94 <2 uM C29 1.23 98.77 <2 uM
C30 0.06 99.94 <2 uM C31 -0.03 100.03 <2 uM C32 0.14 99.86
<2 uM C33 -0.08 100.08 <2 uM C34 -0.01 100.01 <2 uM C35
0.89 99.11 <2 uM C36 2.08 97.92 <2 uM C37 1.56 98.44 <2 uM
C38 1.57 98.43 <2 uM C39 3.78 96.22 <2 uM C40 0.40 99.60
<2 uM C41 0.73 99.27 <2 uM C42 1.26 98.74 <2 uM C43 0.29
99.71 <2 uM C44 -0.07 100.07 <2 uM C45 -0.03 100.03 <2 uM
C46 1.04 98.96 <2 uM C47 4.29 95.71 <2 uM C48 15.72 84.28
<2 uM C49 19.41 80.59 <2 uM C50 6.06 93.94 <2 uM C51 3.38
96.62 <2 uM C52 7.40 92.60 <2 uM C53 -0.01 100.01 <2 uM
C54 0.90 99.10 <2 uM C55 32.88 67.12 <2 uM C56 2.44 97.56
<2 uM C57 0.15 99.85 <2 uM C58 3.28 96.72 <2 uM C59 11.76
88.24 <2 uM C60 52.68 47.32 <2 uM C61 14.38 85.62 <2 uM
C62 27.12 72.88 <2 uM C63 4.64 95.36 <2 uM C64 28.50 71.50
<2 uM C65 0.27 99.73 <2 uM C66 10.95 89.05 <2 uM C67 40.86
59.14 <2 uM C68 20.46 79.54 <2 uM C69 0.03 99.97 <2 uM C70
0.05 99.95 <2 uM C71 -0.05 100.05 <2 uM C72 2.78 97.22 <2
uM C73 0.01 99.99 <2 uM C74 4.92 95.08 <2 uM C75 3.88 96.12
<2 uM C76 5.09 94.91 <2 uM C77 0.44 99.56 <2 uM C78 1.42
98.58 <2 uM C79 3.24 96.76 <2 uM C80 3.35 96.65 <2 uM C81
0.76 99.24 <2 uM C82 0.77 99.23 <2 uM C83 0.65 99.35 <2 uM
C84 6.81 93.19 <2 uM C85 0.87 99.13 <2 uM C86 17.23 82.77
<2 uM C87 4.53 95.47 <2 uM C88 5.94 94.06 <2 uM C89 3.10
96.90 <2 uM C90 6.46 93.54 <2 uM C91 5.17 94.83 <2 uM C92
9.00 91.00 <2 uM C93 1.28 98.72 <2 uM C94 3.71 96.29 <2 uM
C95 6.90 93.10 <2 uM C96 5.00 95.00 <2 uM C97 6.42 93.58
<2 uM C98 4.70 95.30 <2 uM C99 2.59 97.41 <2 uM C100 4.28
95.72 <2 uM C101 0.15 99.85 <2 uM C102 0.70 99.30 <2 uM
C103 13.65 86.35 <2 uM C104 0.99 99.01 <2 uM
Example 8. Binding of Compounds to FKBP12
[0409] The binding of compounds of the invention to FKBP12 can be
determined using the following protocol.
[0410] General Protocol
[0411] This protocol utilizes Perkin Elmers AlphaLISA technology
platform to detect FKBP binders by measuring the inhibition of
binding of biotinylated FK506 to FLAG tagged FKBP12.
[0412] Reagents: 10.times.TBST Buffer (Boston BioProducts IBB-181),
Biotinylated FK506 (in-house), FLAG tagged FKBP (in-house);
anti-FLAG Donor beads (PerkinElmer AS103) and Streptavidin Acceptor
beads (PerkinElmer AL125); Compounds in DMSO (in-house), FK506.
[0413] Equipment: Biotek Synergy2, Janus MTD Head pipettor,
Eppendorf Repeat Pipettor Supplies: White 96-well Corning 1/2 area
plates (Cat #3642), 96-well polypropylene full skirt (180 ul) PCR
plates, 96-well Viaflow P20 tips for Janus MTD Head pipettor.
[0414] Experimental Protocol/Description of Assay: Add 20 uL of
12.5 nM FKBP-FLAG working stock to each well of the 96-well plate.
Add 1 uL of test compound (100% DMSO) to each well of the plate
using the Janus MTD head and P20 tips (except control wells). Add 1
uL of DMSO to negative control wells and 1 uL of 50 uM FK506
solution to positive control wells. In the dark, add 20 uL of
combined Donor/Acceptor beads to each well. Incubate in the dark
for 30 minutes at room temperature. In the dark, add 10 uL of 5 nM
biotinylated FK506 working stock to each well. Incubate in the dark
for 60 minutes at room temperature. Protect plate from light until
reading on Biotek Synergy2 Plate Reader; Alphalisa 96-well protocol
(680 excitation/615 emission).
[0415] Results: The FKBP12 binding for selected compounds was
determined as shown in Table 6.
TABLE-US-00010 TABLE 6 FKBP12 Binding Binding affinity to FKBP12 #
(by displacement of FK506) F1 355 nM F2 1.5 nM F3 0.34 nM F4 4.8 nM
F5 18.8 nM F6 60 nM F7 26 nM F8 10.6 F9 0.3 nM F10 21.1 nM F11 0.51
nM F12 36.3 nM F13 33.6 nM F14 1800 nM F15 1930 nM F16 67.5 nM F17
0.26 nM F18 229 nM F19 0.22 nM F20 0.95 nM F21 1.1 nM F22 785 nM
F23 4690 nM F24 0.21 nM
Example 9. SPR Protocol to Measure Binding of a Compound to
FKBP12
[0416] This protocol utilizes Surface Plasmon Resonance (SPR) as a
method to determine kinetics (K.sub.D, K.sub.a, K.sub.d) for the
binding of compound (analyte) to immobilized FKBP12 (ligand).
[0417] Reagents: Compound in 100% DMSO (in-house), 10.times.HBS-P+
buffer (GE Healthcare BR-1006-71), Assay buffer (1.times.HBS-P+
buffer, 1% DMSO), 12.times.HIS tagged FKBP12 (in-house).
[0418] Equipment: BIACORE.TM. X100 (GE Healthcare)
[0419] Supplies: NTA Sensor chip (GE Healthcare BR-1000-34)
[0420] Experimental Protocol: Experiments are performed at
25.degree. C. Stock solution of 12.times.HIS tagged FKBP12 is
diluted to 100 nM in assay buffer (1% DMSO final). Approximately
500-600 RU of FKBP12 is immobilized on one of two flow cells of an
activated NTA chip. The second flow cell is not activated as a
reference for non-specific interaction of the analyte to the sensor
chip. Various concentrations of compound (1 nM-1 .mu.M range),
serially diluted into the same assay buffer (1% DMSO final), are
injected onto the FKBP12 surface and reference surface at a flow
rate of 10 .mu.l/min. The surface is regenerated between analyte
injections with 350 mM EDTA.
[0421] Data Fitting: The BiaEvaluation software program is used for
data fitting. All data is reference subtracted against both the
reference flow cell and a buffer injection. For kinetic analyses,
data is locally fit to a 1:1 interaction model.
TABLE-US-00011 TABLE 7 FKBP12 Binding Data SPR affinity to #
FKBP12: K.sub.D F1 71.5 nM F2 12.6 nM F3 1.3 nM F4 23.1 nM F5 7 nM
F6 141.2 nM F7 120 nM F8 66 nM F9 0.23 nM F10 17.2 nM F11 21.5 nM
F12 21.2 nM F13 105.7 nM F16 290 nM F17 0.2 nM
Example 10. Determination of Binding of F2 and F11 to FKBP12 by
SPR
[0422] This protocol utilizes Surface Plasmon Resonance (SPR) as a
method to determine kinetics (K.sub.D, K.sub.a, K.sub.d) for the
binding of F2 and F11 (analyte) to immobilized FKBP12 (ligand).
[0423] Reagents: F2 and F11 in 100% DMSO (in-house),
10.times.HBS-P+ buffer (GE Healthcare BR-1006-71), Assay buffer
(1.times.HBS-P+ buffer, 1% DMSO), 12.times.HIS tagged FKBP12
(in-house).
[0424] Equipment: BIACORE.TM. X100 (GE Healthcare)
[0425] Supplies: NTA Sensor chip (GE Healthcare BR-1000-34)
[0426] Experimental Protocol: Experiments are performed at
25.degree. C. Stock solution of 12.times.HIS tagged FKBP12 is
diluted to 100 nM in assay buffer (1% DMSO final). Approximately
500-600 RU of FKBP12 is immobilized on one of two flow cells of an
activated NTA chip. The second flow cell is not activated as a
reference for non-specific interaction of the analyte to the sensor
chip. Various concentrations of F2 or F11 (1 nM-1 .mu.M range),
serially diluted into the same assay buffer (1% DMSO final), are
injected onto the FKBP12 surface and reference surface at a flow
rate of 10 .mu.l/min. The surface is regenerated between analyte
injections with 350 mM EDTA.
[0427] Data Fitting: The BiaEvaluation software program is used for
data fitting. All data is reference subtracted against both the
reference flow cell and a buffer injection. For kinetic analyses,
data is locally fit to a 1:1 interaction model.
[0428] Results: The values for binding of F2 to FKBP 12 are:
K.sub.a (1/Ms): 4.50.times.10.sup.4; K.sub.d (1/s):
5.94.times.10.sup.-4; and K.sub.D: 13.2 nM.
[0429] The values for binding of F11 to FKBP12 are: K.sub.a (1/Ms):
5.67.times.10.sup.5; K.sub.d (1/s): 8.8.times.10.sup.-3; and
K.sub.D: 15.6 nM.
Example 11. Determination of Cell Permeability of Compounds
[0430] Cell permeability of compounds can be determined using the
following protocol.
[0431] General Protocol
[0432] This protocol utilizes a modified FKBP or cyclophilin
destabilizing mutant to determine the bioactivity of FKBP binding
compounds or cyclophilin binding compounds in whole cell assay.
[0433] Reagents: DMEM, DMEM without Phenol Red, 10% FBS, 1.times.
Sodium Pyruvate, 1.times. Glutamax. Add 125 ul of media with
compound per well.
[0434] Equipment: Biotek Synergy2, Janus MTD Head pipettor,
Eppendorf Repeat Pipettor
[0435] Supplies: White 96-well Corning 1/2 area plates (Cat #3642),
96-well polypropylene full skirt (180 ul) PCR plates, 96-well
Viaflow P20 tips for Janus MTD Head pipettor.
[0436] Experimental Protocol/Description of Assay: Plate
HeLa-FKBP12 cells (for FKBP binding compounds) or HeLa-CyclophilinA
cells (for cyclophilin binding compounds) and seed overnight at 5
k/well (approximately .about.18 hrs.). Using a multi-channel pipet,
take out the old media and add .about.125 ul of new media with
compounds. Compounds are diluted using DMEM without Phenol Red, 10%
FBS, 1.times. Sodium Pyruvate, 1.times. Glutamax. Add 125 ul of
media with compound per well. Cells are treated with compounds at
concentration: 30, 10, 3.33, 1.11, 0.37, 0.12, 0.04 and 0.013 uM.
Time points are taken at 72 hrs and plate read using plate reader
with excitation/emission: 575/620.
[0437] Calculation: Cell binding/permeability is calculated in
fold-change (Total RFU of treated samples/total RFU of DMSO treated
samples or total RFU above background (Total RFU minus total RFU of
DMSO treated samples).
[0438] Results: Cell permeability data was gathered for selected
compounds as shown in Table 8.
TABLE-US-00012 TABLE 8 Biosensor Permeability Biosensor
Permeability # IC50 value C33 <3 uM C34 <3 uM C35 >3 uM
C36 <3 uM C37 >3 uM C38 <3 uM C39 <3 uM C40 <3 uM
C41 >3 uM C42 >3 uM C43 <3 uM C44 <3 uM F2 <1 uM F4
<1 uM F6 <1 uM F9 <1 uM F10 >1 uM F12 >1 uM F13
>1 uM F14 >1 uM F16 >1 uM F17 <1 uM F18 <1 uM F19
<1 uM F20 <1 uM F21 <1 uM F22 >1 uM F23 >1 uM
Example 12. Binding of a Presenter Protein/Compound Complex to a
Target Protein
[0439] The binding of a presenter protein/compound complex of the
invention to a target protein can be determined using the following
protocol.
[0440] General Protocol for Cyclophilin a Complexes
[0441] This protocol utilizes Perkin Elmers AlphaLISA technology
platform to detect cyclosporine analogues by measuring the binding
of 6.times.HIS tagged target protein+FLAG tagged Cyclophilin A and
cyclosporine compound.
[0442] Reagents: 10.times.TBST Buffer (Boston BioProducts IBB-181),
MgCl.sub.2 (Sigman), 6.times.HIS tagged target protein (in-house),
FLAG tagged Cyclophilin A (in-house); anti-FLAG Donor beads
(PerkinElmer AS103) and Streptavidin Acceptor beads (PerkinElmer
AL125); Compounds in DMSO (in-house), Cyclosporin A (LC Labs Cat
#C-6000).
[0443] Equipment: Biotek Synergy2, Janus MTD Head pipettor,
Eppendorf Repeat Pipettor.
[0444] Supplies: White 96-well Corning 1/2 area plates (Cat #3642),
96-well polypropylene full skirt (180 ul) PCR plates, 96-well
Viaflow P20 tips for Janus MTD Head pipettor.
[0445] Experimental Protocol/Description of Assay: Add 20 uL of 250
nM 6.times.HIS tagged target protein working stock to each well of
the 96-well plate. Add 1 uL of test compound (100% DMSO) to each
well of the plate using the Janus MTD head and P20 tips (except
control wells). Add 1 uL of DMSO to control wells. In the dark, add
20 uL of combined Donor/Acceptor beads to each well. Incubate in
the dark for 30 minutes at room temperature. In the dark, add 10 uL
of 10 uM Flag tagged CypA working stock to each well. Incubate in
the dark for 60 minutes at room temperature. Protect plate from
light until reading on Biotek Synergy2 Plate Reader; Alphalisa
96-well protocol (680 excitation/615 emission).
[0446] General Protocol for FKBP12 Complexes
[0447] This protocol utilizes Perkin Elmers AlphaLISA technology
platform to detect compounds by measuring the binding of
6.times.HIS tagged target protein+FLAG tagged FKBP12 and FKBP
binding compound.
[0448] Reagents: 10.times.TBST Buffer (Boston BioProducts IBB-181),
MgCl.sub.2 (Sigman), 6.times.HIS tagged target protein (in-house),
FLAG tagged FKBP12 (in-house); anti-FLAG Donor beads (PerkinElmer
AS103) and Streptavidin Acceptor beads (PerkinElmer AL125);
Compounds in DMSO (in-house), FK506.
[0449] Equipment: Biotek Synergy2, Janus MTD Head pipettor,
Eppendorf Repeat Pipettor.
[0450] Supplies: White 96-well Corning 1/2 area plates (Cat #3642),
96-well polypropylene full skirt (180 ul) PCR plates, 96-well
Viaflow P20 tips for Janus MTD Head pipettor.
[0451] Experimental Protocol/Description of Assay: Add 20 uL of 250
nM 6.times.HIS tagged target protein working stock to each well of
the 96-well plate. Add 1 uL of test compound (100% DMSO) to each
well of the plate using the Janus MTD head and P20 tips (except
control wells). Add 1 uL of DMSO to control wells. In the dark, add
20 uL of combined Donor/Acceptor beads to each well. Incubate in
the dark for 30 minutes at room temperature. In the dark, add 10 uL
of 10 uM Flag tagged FKBP12 working stock to each well. Incubate in
the dark for 60 minutes at room temperature. Protect plate from
light until reading on Biotek Synergy2 Plate Reader; Alphalisa
96-well protocol (680 excitation/615 emission).
Example 13. Determination of Binding of Presenter Protein/Compound
Complexes to Target Proteins by SPR
[0452] This protocol utilizes Surface Plasmon Resonance (SPR) as a
method to determine kinetics (K.sub.D, K.sub.a, K.sub.d) for the
binding of mammalian target protein (analyte) to immobilized
FKBP12-compound binary complex (ligand).
[0453] Reagents: Compound in 100% DMSO (in-house), 10.times.HBS-P+
buffer (GE Healthcare BR-1006-71), Assay buffer (1.times.HBS-P+
buffer, 1% DMSO, 1 .mu.M F2), 12.times.HIS tagged FKBP12
(in-house), mammalian target protein (in-house).
[0454] Equipment: BIACORE.TM. X100 (GE Healthcare)
[0455] Supplies: NTA Sensor chip (GE Healthcare BR-1000-34)
[0456] Experimental Protocol: Experiments are performed at
25.degree. C. Stock solution of 12.times.HIS tagged FKBP12 is
diluted to 100 nM in assay buffer containing 1 .mu.M compound (1%
DMSO final). Approximately 200-400 RU of FKBP12 is immobilized on
one of two flow cells of an activated NTA chip. The second flow
cell is not activated as a reference for non-specific interaction
of the analyte to the sensor chip. Various concentrations of target
protein (1 nM-1 .mu.M range), serially diluted into the same assay
buffer containing 1 .mu.M compound (1% DMSO final), are injected
onto the FKBP12 surface and reference surface at a flow rate of 10
.mu.l/min. The surface is regenerated between analyte injections
with 350 mM EDTA.
[0457] Data Fitting: The BiaEvaluation software program is used for
data fitting. All data is reference subtracted against both the
reference flow cell and a buffer injection. For kinetic analyses,
data is locally fit to a 1:1 interaction model.
Example 14. Determination of Binding of FKBP12/F2 Complex to CEP250
by SPR
[0458] This protocol utilizes Surface Plasmon Resonance (SPR) as a
method to determine kinetics (K.sub.D, K.sub.a, K.sub.d) for the
binding of CEP250 (analyte) to immobilized FKBP12-F2 binary complex
(ligand).
[0459] Reagents: F2 in 100% DMSO (in-house), 10.times.HBS-P+ buffer
(GE Healthcare BR-1006-71), Assay buffer (1.times.HBS-P+ buffer, 1%
DMSO, 1 M F2), 12.times.HIS tagged FKBP12 (in-house),
CEP250.sub.29.2 (residues 1982-2231) and CEP250.sub.11.4 (residues
2134-2231) (in-house).
[0460] Equipment: BIACORE.TM. X100 (GE Healthcare)
[0461] Supplies: NTA Sensor chip (GE Healthcare BR-1000-34)
[0462] Experimental Protocol: Experiments are performed at
25.degree. C. Stock solution of 12.times.HIS tagged FKBP12 is
diluted to 100 nM in assay buffer containing 1 .mu.M F2 (1% DMSO
final). Approximately 200-400 RU of FKBP12 is immobilized on one of
two flow cells of an activated NTA chip. The second flow cell is
not activated as a reference for non-specific interaction of the
analyte to the sensor chip. Various concentrations of CEP250 (1
nM-1 .mu.M range), serially diluted into the same assay buffer
containing 1 .mu.M F2 (1% DMSO final), are injected onto the FKBP12
surface and reference surface at a flow rate of 10 .mu.l/min. The
surface is regenerated between analyte injections with 350 mM
EDTA.
[0463] Data Fitting: The BiaEvaluation software program is used for
data fitting. All data is reference subtracted against both the
reference flow cell and a buffer injection. For kinetic analyses,
data is locally fit to a 1:1 interaction model.
[0464] Results: The k values for the binding of the FKBP12/F2
complex to CEP250.sub.11.4 and CEP250.sub.29.2 are: K.sub.a (1/Ms):
5.71.times.10.sup.5; K.sub.d (1/s): 3.09.times.10.sup.-3; and
K.sub.D: 5.4 nM and K.sub.a (1/Ms): 3.11.times.10.sup.5; K.sub.d
(1/s): 9.25.times.10.sup.-5; and K.sub.D: 0.29 nM,
respectively.
Example 15. Determination of Binding of Presenter Protein/Compound
Complexes to Target Proteins by ITC
[0465] General Protocol
[0466] This protocol utilizes Isothermal Titration Calorimetry
(ITC) to directly measure the heat change associated with binding
of presenter protein (e.g. FKBP, cyclophilin)-compound binary
complexes to target proteins. Measurement of the heat change allows
accurate determination of association constants (K.sub.a), reaction
stoichiometry (N), and the change in binding enthalpy
(.DELTA.H).
[0467] Reagents: Compounds in 100% DMSO (in-house), Protein Buffer
(10 mM HEPES, pH 7.5, 75 mM NaCl, 0.5 mM TCEP), assay buffer
(protein buffer+1% DMSO), presenter protein (e.g. FKBP,
cyclophilin) (in-house), target protein (in-house).
[0468] Equipment: MicroCal.TM. ITC200 (GE Healthcare)
[0469] Experimental Protocol: presenter protein (e.g. FKBP,
cyclophilin) stock solution is diluted to 10 .mu.M in assay buffer
(1% DMSO final). Compound is added to presenter protein to 20 .mu.M
(1% DMSO final), and binary complex is filled into the reaction
cell of the ITC device after 5-10 min pre-incubation time. Target
protein stocks are diluted to 50 .mu.M in assay buffer and
supplemented with 20 .mu.M compound (1% DMSO final) before being
filled into the injection syringe. A control experiment in the
absence of compound is also run to determine the heat associated
with operational artifacts and the dilution of titrant as it is
injected from the syringe into the reaction cell. Data collection
and analysis are as described for binding of FKBP12-F2 and
FKBP12-F11 binary complexes to CEP250.
Example 16. Determination of Binding of FKBP12/F2 and FKBP12/F2
Complexes to CEP250 by ITC
[0470] This protocol utilizes Isothermal Titration Calorimetry
(ITC) to directly measure the heat change associated with binding
of FKBP12-F2 and FKBP12-F11 binary complexes to CEP250. Measurement
of the heat change allows accurate determination of association
constants (K.sub.a), reaction stoichiometry (N), and the change in
binding enthalpy (.DELTA.H).
[0471] Reagents: F2 and F11 in 100% DMSO (in-house), Protein Buffer
(10 mM HEPES, pH 7.5, 75 mM NaCl, 0.5 mM TCEP), assay buffer
(protein buffer+1% DMSO), FKBP12 (in-house), CEP250.sub.29.4
(residues 1982-2231) and CEP250.sub.11.4 (residues 2134-2231)
(in-house).
[0472] Equipment: MicroCal.TM. ITC200 (GE Healthcare)
[0473] Experimental Protocol: FKBP12 stock solution is diluted to
10 .mu.M in assay buffer (1% DMSO final). Compound is added to
FKBP12 to 20 .mu.M (1% DMSO final), and binary complex is filled
into the reaction cell of the ITC device after 5-10 min
pre-incubation time. CEP250 protein stocks are diluted to 50 .mu.M
in assay buffer and supplemented with 20 .mu.M compound (1% DMSO
final) before being filled into the injection syringe. A control
experiment in the absence of compound is also run to determine the
heat associated with operational artifacts and the dilution of
titrant as it is injected from the syringe into the reaction cell.
More detailed experimental parameters are shown in Tables 11 and
12, below:
TABLE-US-00013 TABLE 9 ITC Experimental Parameters Experimental
device: MicroCal .TM. iT.sub.200 (GE Healthcare) sample cell volume
[.mu.l] 270 injector volume [.mu.l] 40 Experimental parameters
Total # of Injections 19 Cell Temperature [.degree. C.] 25
Reference Power [.mu.Cal/s] 5 Initial Delay [s] 200 Stirring Speed
[rpm] 750 Injection parameters Volume [.mu.l] 2 Duration [s] 4
Spacing [s] 170-200 Filter Period [s] 5 Feedback Mode/Gain high
TABLE-US-00014 TABLE 10 Protein and Ligand Concentrations for ITC
Final protein and ligand concentrations DMSO assay cell content
syringe content ligand conc. [%] FKBP12, 10 .mu.M CEP250.sub.29.4,
50 .mu.M none 1.0 FKBP12, 10 .mu.M CEP250.sub.11.4, 50 .mu.M none
1.0 FKBP12, 10 .mu.M CEP250.sub.29.4, 118 .mu.M F2, 20 .mu.M 1.0
FKBP12, 10 .mu.M CEP250.sub.29.4, 118 .mu.M F11, 20 .mu.M 1.0
FKBP12, 10 .mu.M CEP250.sub.11.4, 68 .mu.M F2, 20 .mu.M 1.0 FKBP12,
10 .mu.M CEP250.sub.11.4, 68 .mu.M F11, 20 .mu.M 1.0
[0474] Data Fitting: Data were fitted with the Origin ITC200
software according to the following procedure: [0475] 1) Read raw
data [0476] 2) In "mRawITC": adjust integration peaks and baseline,
integrate all peaks [0477] 3) In "Delta H"--data control: remove
bad data (injection #1 and other artifacts), subtract straight line
(background subtraction) [0478] 4) In "Delta H"--model fitting:
select one set of sites model, perform fitting with
Levenberg-Marquardt algorithm until Chi Square is not reduced
further, finish with "done" (parameters N, K.sub.a and .DELTA.H are
calculated based on fitting)
[0479] ITC measurements for the binding of FKBP12-F2 and FKBP12-F11
binary complexes to CEP250 are summarized in Table 11 below.
TABLE-US-00015 TABLE 11 ITC Measurements .DELTA.H -T*.DELTA.S
.DELTA.G cell syringe T Kd [kJ*mol - [kJ*mol - [kJ*mol - Experiment
content content ligand [K] N [.mu.M]* mol - 1]** mol - 1]*** mol -
1]**** 3 FKBP12, CEP25029.4, none 298 ND ND ND ND ND 10 .mu.M 118
.mu.M 4 FKBP12, CEP25011.4, none 298 ND ND ND ND ND 10 .mu.M 68
.mu.M 5 FKBP12, CEP25029.4, F2, 298 0.50 0.19 -52.21 13.80 -38.41
10 .mu.M 118 .mu.M 20 .mu.M 6 FKBP12, CEP25029.4, F11, 298 0.57
0.36 -58.48 21.73 -36.74 10 .mu.M 118 .mu.M 20 .mu.M 7 FKBP12,
CEP25011.4, F2, 298 0.56 0.07 -49.37 8.62 -40.75 10 .mu.M 68 .mu.M
20 .mu.M 8 FKBP12, CEP25011.4, F11, 298 0.54 0.08 -47.78 7.41
-40.36 10 .mu.M 68 .mu.M 20 .mu.M *Kd (calculated from K.sub.a =
1/K.sub.d) **.DELTA.H ***T*.DELTA.S (calculated from equation
(-T.DELTA.S = .DELTA.G - .DELTA.H) ****.DELTA.G = -RT ln K.sub.a =
RT ln K.sub.d
[0480] Results: Overall, the data for FKBP12-F2 and FKBP12-F11
binary complexes binding to CEP250.sub.11.4 and CEP250.sub.29.4
show similar interaction parameters. K.sub.d values were similar
for all combinations. All interactions show an almost identical
thermodynamic profile in which binding is characterized by a purely
enthalpic binding mode (-T*.DELTA.S term is positive and does not
contribute to the Gibbs free energy). Binding stoichiometries for
all interactions were N=0.5-0.6 and support a 1:2 binding ratio for
1 CEP250 homodimer binding to 2 FKBP12 molecules, as evidenced in
the crystal structure of CEP250.sub.11.4/F2/FKBP12.
Example 17. Crystallographic Structural Determination of Tertiary
Complexes
[0481] General Protocol
[0482] This protocol describes the crystallization and structure
determination method for structures of specific
FKBP12-compound-target protein ternary complexes.
[0483] Reagents: Compound in 100% DMSO (in-house), FKBP12
(in-house), and mammalian target protein (in-house).
[0484] Equipment: Superdex 200 (GE Healthcare)
[0485] Experimental Protocol: A 3:1 molar excess of compound is
added to FKBP12 in 12.5 mM HEPES pH 7.4, 75 mM NaCl buffer, and
incubated overnight at 4.degree. C. A 3:1 molar excess of
FKBP12-compound binary complex is added to target protein and
incubated at 4.degree. C. overnight to complete ternary complex
formation. Pure ternary complex is isolated by gel filtration
purification on a Superdex 200 column in 12.5 mM HEPES pH 7.4, 75
mM NaCl. Purified complex (at 10.sup.-20 mg/ml) is subjected to
crystallization at 22.degree. C. using sitting drop vapor diffusion
using various buffers, surfactants and salt solutions. For data
collection, crystals are transferred to a solution containing
mother liquor supplemented with 20-25% glycerol, and then frozen in
liquid nitrogen. Diffraction datasets are collected at the Advanced
Photon Source (APS) and processed with the HKL program. Molecular
replacement solutions are obtained using the program PHASER in the
CCP4 suite, using the published structure of FKBP12 (PDB-ID 1FKD)
as a search model. Subsequent model building and refinement are
performed according to standard protocols with the software
packages CCP4 and COOT.
Example 18. Crystallographic Structural Determination of Tertiary
Complexes of FKBP12/F2 and FKBP12/F11 Complexes with CEP250
[0486] This protocol describes the crystallization and structure
determination method for structures of FKBP12-Compound 2-CEP250 and
FKBP12-F11-CEP250 ternary complexes.
[0487] Reagents: F2 and F11 in 100% DMSO (in-house), FKBP12
(in-house), and CEP250.sub.11.4 (residues 2134-2231)
(in-house).
[0488] Equipment: Superdex 200 (GE Healthcare)
[0489] Experimental Protocol: A 3:1 molar excess of F2 or F11 is
added to FKBP12 in 12.5 mM HEPES pH 7.4, 75 mM NaCl buffer, and
incubated overnight at 4.degree. C. A 3:1 molar excess of FKBP12-F2
or FKBP12-F11 binary complex is added to CEP250.sub.11.4 and
incubated at 4.degree. C. overnight to complete ternary complex
formation. Pure ternary complex is isolated by gel filtration
purification on a Superdex 200 column in 12.5 mM HEPES pH 7.4, 75
mM NaCl. Purified complex (at 10.sup.-20 mg/ml) is subjected to
crystallization at 22.degree. C. using sitting drop vapor
diffusion. FKBP12-F2-CEP250 crystals grow in a well solution
containing 0.2 M sodium malonate, 0.1 M HEPES 7.0, 21% PEG 3350.
FKBP12-F11-CEP250 crystals grow in a well solution containing 0.1 M
Tris pH 8.5, 0.2 M trimethylamine N-oxide, 22-24% PEG2000 MME. For
data collection crystals are transferred to a solution containing
mother liquor supplemented with 20-25% glycerol, and then frozen in
liquid nitrogen. Diffraction datasets are collected at the Advanced
Photon Source (APS) and processed with the HKL program. Molecular
replacement solutions are obtained using the program PHASER in the
CCP4 suite, using the published structure of FKBP12 (PDB-ID 1FKD)
as a search model. Subsequent model building and refinement are
performed according to standard protocols with the software
packages CCP4 and COOT.
[0490] Results: Overall structure of FKBP12-F2-CEP250: In the
structure of FKBP12 with CEP250 in complex with F2, two FKBP12
monomers are bound to a homodimer of CEP250. The two CEP250
monomers form a coiled-coil structure. There are four hetero dimers
on the asymmetric unit with basically the same overall
conformation. The model comprises residues Met1 to Glu108 of FKBP12
and Asp2142 to His2228 of CEP250. The electron density shows an
unambiguous binding mode for the ligand F2, including the
orientation and conformation of the ligand.
[0491] The CEP250 residues involved in binding F2 are L2190, Q2191,
V2193, A2194, M2195, F2196, L2197, and Q2198. The CEP250 residues
involved in binding to FKBP12 are A2185, S2186, S2189, Q2191,
M2195, Q2198, V2201, L2202, R2204, D2205, S2206, Q2208, Q2209, and
Q2212.
[0492] The total buried surface area of the ternary complex is 1759
.ANG..sup.2. The total buried surface area of CEP250 is 865
.ANG..sup.2 of which 663 .ANG..sup.2 is contributed by FKBP12 and
232 .ANG..sup.2 is contributed by F2.
[0493] 100% of the binding interactions in the ternary complex
between F2 and CEP250 are van der Waals or pi-pi interactions. By
comparison, 100% of the binding interactions between rapamycin and
mTOR are van der Waals or pi-pi interactions, and 89% of the
binding interactions between FK506 and calcineurin are van der
Waals or pi-pi interactions while 11% are hydrogen bonds (two
H-bonds from C13 and C15 OMe to Trp 352 N-H).
[0494] Overall structure of FKBP12-F11-CEP250: In the structure of
FKBP12 with CEP250 in complex with F11, one FKBP12 monomer is bound
to a homodimer of CEP250. The two CEP250 monomers form a
coiled-coil structure. The crystals contain a heterotrimer (one
FKBP12 and two CEP250) in the asymmetric unit. The model comprises
residues Met1 to Glu108 of FKBP12 and Ser2143 to His2228 of CEP250.
One short loop region of FKBP12 (18-19) is not fully defined by
electron density and is not included in the model. The electron
density shows an unambiguous binding mode for the ligand F11,
including the orientation and conformation of the ligand.
[0495] The CEP250 residues involved in binding F2 are L2190, Q2191,
V2193, A2194, M2195, F2196, L2197, and Q2198. The CEP250 residues
involved in binding to FKBP12 are Q2182, A2185, S2186, S2189,
Q2191, M2195, Q2198, V2201, L2202, R2204, D2205, S2206, Q2208,
Q2209, and Q2212.
[0496] The total buried surface area of the ternary complex is 1648
.ANG..sup.2. The total buried surface area of CEP250 is 831
.ANG..sup.2 of which 590 .ANG..sup.2 is contributed by FKBP12 and
241 .ANG..sup.2 is contributed by F2.
Statistics of the Final Structures are Listed in Table 12 and 13
Below.
TABLE-US-00016 [0497] TABLE 12 FKBP12-F2-CEP250 Ligand F2
Resolution [.ANG.] 136.05-2.20 Number of reflections (working/test)
50564/2723 R.sub.cryst [%] 20.8 R.sub.free[%].sup.2 25.6 Total
number of atoms: Protein 6146 Water 226 Ligan 176 PEG 273 Magnesium
1 Maltose 7 Deviation from ideal geometry: .sup.3 Bond lengths
[.ANG.] 0.007 Bond angles [.degree.] 1.17 Bonded B's
[.ANG..sup.2].sup.4 5.4 Ramachandran plot: .sup.5 Most favoured
regions [%] 94.6 Additional allowed regions [%] 4.8 Generously
allowed regions[%] 0.6 Disallowed region [%] 0.0 .sup.1Values as
defined in REFMAC5, without sigma cut-off .sup.2Test-set contains
2.4% of measured reflections .sup.3Root mean square deviations from
geometric target values .sup.4Calculated with MOLEMAN
.sup.5Calculated with PROCHECK
TABLE-US-00017 TABLE 13 FKBP12-F11-CEP250 Ligand F11 Resolution
[.ANG.] 72.84-2.10 Number of reflections (working/test) 16398/877
R.sub.cryst [%] 24.2 R.sub.free[%].sup.2 29.9 Total number of
atoms: Protein 2224 Water 31 Ligand 44 PEG 14 Deviation from ideal
geometry: .sup.3 Bond lengths [.ANG.] 0.008 Bond angles [.degree.]
1.07 Bonded B's [.ANG..sup.2].sup.4 3.0 Ramachandran plot: .sup.5
Most favoured regions [%] 93.5 Additional allowed regions [%] 4.9
Generously allowed regions [%] 1.6 Disallowed region [%] 0.0
.sup.1Values as defined in REFMAC5, without sigma cut-off
.sup.2Test-set contains 5.1% of measured reflections .sup.3Root
mean square deviations from geometric target values
.sup.4Calculated with MOLEMAN .sup.5Calculated with PROCHECK
[0498] While the invention has been described in connection with
specific embodiments thereof, it will be understood that it is
capable of further modifications and this application is intended
to cover any variations, uses, or adaptations of the invention
following, in general, the principles of the invention and
including such departures from the present disclosure come within
known or customary practice within the art to which the invention
pertains and may be applied to the essential features hereinbefore
set forth.
[0499] All publications, patents and patent applications are herein
incorporated by reference in their entirety to the same extent as
if each individual publication, patent or patent application was
specifically and individually indicated to be incorporated by
reference in its entirety.
* * * * *
References