U.S. patent application number 15/456070 was filed with the patent office on 2018-01-11 for proline-locked stapled peptides and uses thereof.
This patent application is currently assigned to President and Fellows of Harvard College. The applicant listed for this patent is President and Fellows of Harvard College. Invention is credited to Kazuhiro HAYASHI, Gregory L. VERDINE.
Application Number | 20180009847 15/456070 |
Document ID | / |
Family ID | 49382577 |
Filed Date | 2018-01-11 |
United States Patent
Application |
20180009847 |
Kind Code |
A1 |
VERDINE; Gregory L. ; et
al. |
January 11, 2018 |
PROLINE-LOCKED STAPLED PEPTIDES AND USES THEREOF
Abstract
The present invention provides a new type of alpha-helix
nucleating cross-link ("staple") formed by olefin metathesis of a
proline derivative with an alkenyl side chain and another amino
acid derivative with an alkenyl side chain. The proline derivatives
as described herein have been found to be strong nucleators of
alpha-helix formation. The invention also provides moieties for
shielding the free amide N--H's at the N-terminus of an
alpha-helix, thereby further stabilizing the helix. The proline
derivatives, precursors prior to cross-linking, and the
cross-linked peptides are provided as well as methods of using and
preparing these compounds and peptides.
Inventors: |
VERDINE; Gregory L.;
(Boston, MA) ; HAYASHI; Kazuhiro; (Cambridge,
MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
President and Fellows of Harvard College |
Cambridge |
MA |
US |
|
|
Assignee: |
President and Fellows of Harvard
College
Cambridge
MA
|
Family ID: |
49382577 |
Appl. No.: |
15/456070 |
Filed: |
March 10, 2017 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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14431280 |
Mar 25, 2015 |
9617309 |
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PCT/US2013/062004 |
Sep 26, 2013 |
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15456070 |
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61705950 |
Sep 26, 2012 |
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61789157 |
Mar 15, 2013 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07K 7/56 20130101; C07D
207/16 20130101; C07K 1/113 20130101 |
International
Class: |
C07K 7/56 20060101
C07K007/56; C07K 1/113 20060101 C07K001/113; C07D 207/16 20060101
C07D207/16 |
Claims
1. A polypeptide of Formula (P-I): ##STR00078## or a salt or
stereoisomer thereof; wherein: each instance of K and L, is,
independently, a bond or a group consisting of one or more
combinations of substituted or unsubstituted alkylene; substituted
or unsubstituted alkenylene; substituted or unsubstituted
alkynylene; substituted or unsubstituted heteroalkylene;
substituted or unsubstituted heteroalkenylene; substituted or
unsubstituted heteroalkynylene; substituted or unsubstituted
heterocyclene, substituted or unsubstituted carbocyclene,
substituted or unsubstituted arylene; substituted or unsubstituted
heteroarylene; R.sup.a is hydrogen; substituted or unsubstituted
aliphatic; substituted or unsubstituted heteroaliphatic;
substituted or unsubstituted aryl; substituted or unsubstituted
heteroaryl; substituted or unsubstituted acyl; a resin; an amino
protecting group; a label optionally joined by a linker, wherein
the linker is a group consisting of one or more combinations of
substituted or unsubstituted alkylene; substituted or unsubstituted
alkenylene; substituted or unsubstituted alkynylene; substituted or
unsubstituted heteroalkylene; substituted or unsubstituted
heteroalkenylene; substituted or unsubstituted heteroalkynylene;
substituted or unsubstituted carbocyclene; substituted or
unsubstituted heterocyclene; substituted or unsubstituted arylene;
or substituted or unsubstituted heteroarylene; R.sup.b is,
--R.sup.B, --OR.sup.B, --N(R.sup.B).sub.2, or --SR.sup.B, wherein
each instance of R.sup.B is, independently, hydrogen, substituted
or unsubstituted aliphatic; substituted or unsubstituted
heteroaliphatic; substituted or unsubstituted aryl; substituted or
unsubstituted heteroaryl; substituted or unsubstituted acyl; a
resin; a suitable hydroxyl, amino or thiol protecting group; or two
RB groups together form a substituted or unsubstituted 5- to
6-membered heterocyclic or heteroaromatic ring; each instance of
R.sup.C, is, independently, hydrogen; substituted or unsubstituted
aliphatic; substituted or unsubstituted heteroaliphatic;
substituted or unsubstituted aryl; substituted or unsubstituted
heteroaryl; substituted or unsubstituted acyl; substituted or
unsubstituted hydroxyl; substituted or unsubstituted thiol;
substituted or unsubstituted amino; cyano; isocyano; halo; or
nitro; each instance of R.sup.d is, independently, hydrogen;
substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; or an amino protecting group; each instance of
R.sup.e is, independently, hydrogen; substituted or unsubstituted
aliphatic; substituted or unsubstituted heteroaliphatic;
substituted or unsubstituted aryl; substituted or unsubstituted
heteroaryl; substituted or unsubstituted acyl; substituted or
unsubstituted hydroxyl; substituted or unsubstituted thiol;
substituted or unsubstituted amino; cyano; isocyano; halo; or
nitro; each instance of G is, independently, a natural or unnatural
amino acid or a group of the formula: ##STR00079## wherein: n is 1,
2, or 3; and each instance of R.sup.1 and R.sup.2 is independently
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; substituted or unsubstituted hydroxyl;
substituted or unsubstituted thiol; substituted or unsubstituted
amino; or halo, or R.sup.1 and R.sup.2 are joined to form a
carbocyclic or heterocyclic ring; each instance of R.sup.3 and
R.sup.4 is, independently, hydrogen; substituted or unsubstituted
aliphatic; substituted or unsubstituted heteroaliphatic; a hydroxyl
protecting group when attached to an oxygen atom, or an amino
protecting group when attached to a nitrogen atom, or two R.sup.3
groups when attached to a nitrogen atom are joined to form a
heterocyclic ring; each instance of XAA is, independently, a
natural or unnatural amino acid; j is, independently, an integer
between 1 to 10, inclusive; each instance of p is, independently, 1
or 2; each instance of v is, independently, 0 or 1; each instance
of w and z is, independently, an integer between O and 100,
inclusive; each instance of x is, independently, 0, 1, 2, or 3; y
is, independently, 1, 2, 3, or 4; and corresponds to a double or
triple bond.
2. The polypeptide of claim 1 of the formula: ##STR00080## or a
salt or stereoisomer thereof.
3. (canceled)
4. The polynucleotide of claim 1 of the formula: ##STR00081## or a
salt or stereoisomer thereof.
5. (canceled)
6. The polypeptide of claim 1, wherein p is 1.
7. (canceled)
8. The polypeptide of claim 1, wherein each instance of R.sup.e is,
independently, hydrogen, --CH.sub.3, --CH.sub.2OH, --COOH, or
--CH.sub.2COOH.
9. (canceled)
10. The polypeptide of claim 1, wherein R.sup.d is hydrogen.
11. (canceled)
12. The polypeptide of claim 1, wherein each instance of y is,
independently, 2, 3, or 4.
13-15. (canceled)
16. The polypeptide of claim 1, wherein R.sup.a is substituted or
unsubstituted acyl.
17-18. (canceled)
19. The polypeptide of claim 1, wherein R.sup.b is --ORB.
20. The polypeptide of claim 1, wherein each instance of K is,
independently, --CH.sub.2--, --(CH.sub.2).sub.2--, or
--(CH.sub.2).sub.3--.
21. (canceled)
22. The polypeptide of claim 1, wherein each instance of L is,
independently, --CH.sub.2--, --(CH.sub.2).sub.2--, or
--(CH.sub.2).sub.3--.
23. (canceled)
24. The polypeptide of claim 1, wherein x is, independently, 0.
25. The polypeptide of claim 1, wherein corresponds to a double
bond.
26. The polypeptide of claim 1, wherein G is, independently,
serine, arginine, aspartic acid, or glutamic acid.
27. The polypeptide of claim 1, wherein G is: ##STR00082##
28-47. (canceled)
Description
RELATED APPLICATIONS
[0001] The present application claims priority under 35 U.S.C.
.sctn.119(e) to U.S. provisional patent applications, U.S. Ser. No.
61/705,950, filed Sep. 26, 2012, and U.S. Ser. No. 61/789,157,
filed Mar. 15, 2013, each of which is incorporated herein by
reference.
BACKGROUND OF THE INVENTION
[0002] The important biological roles that peptides and
polypeptides play as hormones, enzyme inhibitors, substrates,
neurotransmitters, and neuromediators has led to the widespread use
of peptides and peptide mimetics in medicinal chemistry as
therapeutic agents. The peptide's bioactive conformation, combining
structural elements such as alpha-helices, beta-sheets, turns,
and/or loops, is important as it allows for selective biological
recognition of receptors or enzymes, thereby influencing cell-cell
communication and/or controlling vital cell functions, such as
metabolism, immune defense, and reproduction (Babine et al., Chem.
Rev. (1997) 97:1359). The alpha-helix is one of the major
structural components of peptides. However, alpha-helical peptides
have a propensity for unraveling and forming random coils, which
are, in most cases, biologically less active, or even inactive, and
are highly susceptible to proteolytic degradation.
[0003] Many research groups have developed strategies for the
design and synthesis of more robust peptides as therapeutics. For
example, one strategy has been to incorporate more robust
functionalities into the peptide chain while still maintaining the
peptide's unique conformation and secondary structure (see, for
example, Gante et al., Angew. Chem. Int. Ed. Engl. (1994)
33:1699-1720; Liskamp et al., Redl. Trav. Chim. Pays-Bas (1994)
113:1; Giannis et al., Angew. Chem. Int. Ed. Engl. (1993) 32:1244;
P. D. Bailey, Peptide Chemistry, Wiley, New York, 1990, p. 182; and
references cited therein). Another approach has been to stabilize
the peptide via covalent crosslinks (see, for example, Phelan et
al., J. Am. Chiem. Soc. (1997) 119:455; Leuc et al., Proc. Nat'l.
Acad. Sci. USA (2003) 100:11273; Bracken et al., J. Am. Chem. Soc.
(1994) 116:6432; and Yan et al., Bioorg. Med. Chem. (2004)
14:1403). Crosslinking a polypeptide predisposed to have an
alpha-helical secondary structure can constrain the polypeptide to
its native alpha-helical conformation. The constrained secondary
structure may, for example, increase the peptide's resistance to
proteolytic cleavage, may increase the peptide's hydrophobicity,
may allow for better penetration of the peptide into the target
cell (e.g., through an energy-dependent transport mechanism such as
pinocytosis), and/or may lead to an improvement in the peptide's
biological activity relative to the corresponding uncrosslinked
peptide. Therefore, there remains a need and interest in developing
new crosslinked alpha-helical polypeptides as therapeutic agents as
well as research tools.
SUMMARY OF THE INVENTION
[0004] The present invention provides a new type of alpha-helix
nucleating staple formed using an N-terminal proline derivative
with an alkenyl or alkynyl side chain (e.g., alpha-allylproline).
Although proline is commonly considered to be an alpha-helix
disrupting amino acid, it frequently occurs at the N-terminus of
alpha-helices. Therefore, proline can be considered to be a
helix-nucleating residue. Such a staple using a proline derivative
may be formed with any other amino acid with an alkenyl or alkynyl
side chain using an olefin metathesis reaction. Proline and the
residue preceding it (such as serine, aspartate, and glutamate)
have also been found to be good at cloaking the amide N--H's at the
beginning of an alpha-helix through the formation of hydrogen bonds
and have led to the design of other capping moieties for
alpha-helical peptides as described herein. The proline derivative
for stapling has been found to be a strong nucleator of alpha-helix
formation, and peptides with such a staple may be of use in
targeting various extracellular and intracellular targets as well
as conferring oral bioavailability on peptides.
[0005] In one aspect, the disclosure provides stabilized peptides
(e.g., staples and stitched) and methods for increasing the
stability of peptides. In some embodiments, the disclosure provides
peptides with improved biological properties and methods for
improving the biological properties of peptides. The disclosure
provides peptides with improved capacity to penetrate cell
membranes and/or otherwise get into cells. The disclosure therefore
also provides peptides as therapeutic agents and as deliver aids to
deliver peptide-drug conjugates intracellularly.
[0006] In one aspect, the disclosure provides peptides that are
stabilized by stapling the peptide at the N-terminus of an
alpha-helix through the introduction of a proline-locked staple. It
was surprisingly found that proline could be used to stabilize
peptides. The finding was surprising at least because proline is
commonly considered an .alpha.-helix-disrupting amino acid. In some
embodiments, the proline-locked stapled peptide includes a proline
at position i that is covalently linked to the alpha-carbon of a
second amino acid at position i+3. While alpha-helical peptides are
relatively stable once formed, initiation of alpha helix formation
is challenging because the attendant conformational ordering is
entropically expensive (J. Chem. Phys, 1959, 31, 526-535). As
provided herein, introducing a helix staple, such as a
proline-locked staple at the N-terminus of an alpha-helical peptide
helps with the formation of, and further stabilizes, an
alpha-helix. Once a single turn of the .alpha.-helix is formed, its
downstream propagation can occur spontaneously, provided that
helix-disrupting sequences are not present.
[0007] In one aspect, the disclosure provides peptides with
improved ability to cross cell membranes. An increased ability of
peptides to cross the cell membrane is correlated with an increase
in the capacity of the peptide to acts as a therapeutic. Peptides
often have difficulty crossing (cell) membranes because of the
availability of unpaired hydrogen bonds in the peptide (e.g., in
the peptide backbone). The disclosure provides methods for
minimizing the availability of unpaired hydrogen bonds in a peptide
by binding N-terminal amide protons tightly into hydrogen-bonding
interactions. As disclosed herein, locating an amino acid with a
side chain that can interact with amide protons at the N-terminal
side of an alpha helix minimizes the availability of free amide
protons. The undesired free N-terminal amides are "masked" thereby
minimizing any undesired interactions with other agents (e.g., the
cell membrane or components thereof). In some embodiments, the
amino acid before the proline is an amino acid with a side chain
that can interact with the free amide protons at the beginning of
the helix. For instance, the disclosure provides a modified
arginine with increased ability to mask N-terminal amide protons by
providing additional hydrogen bond acceptor.
[0008] In one aspect, the disclosure provides stabilized peptides
that nucleate .alpha.-helix formation through a proline-locked
staple while also binding N-terminal amide protons tightly through
hydrogen-bonding interactions. As provided herein, the stabilized
peptides with amide proton hydrogen bond acceptors may have a
proline at position i that is covalently coupled to an amino acid
at position i+3, and a modified arginine residue at position i-1
(as described herein) which interacts with the amide protons of the
peptide backbone of the amino acids at position i+1 and i+2. In
certain other embodiments, the i-1 position is occupied by a
natural amino acid such as serine, aspartate, or glutatmate.
[0009] The proline-locked stapled peptides provided herein are
strong nucleators of .alpha.-helix formation, as shown by the high
helicity of peptides bearing the proline-lock feature. In addition,
the peptides provided herein, through masking the N-terminal amide
protons, further enhance the ability of the peptides to cross cell
membranes. Thus, the Pro-locked stapled peptides provided herein
may be used in targeting previously "undruggable" intracellular
therapeutic targets.
[0010] The details of one or more embodiments of the invention are
set forth in the Detailed Description of Certain Embodiments, as
described below. Other features, objects, and advantages of the
invention will be apparent from the Definitions, Examples, Figures.
and Claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[0011] FIG. 1 provides an example of a proline-locked stapled
peptide 4.
[0012] FIG. 2 shows two peptides with partial basic region of
GCN4.
[0013] FIG. 3 shows a LC/MS chromatogram of the olefin-metathesis
reaction between P.sub.R3 and S3.
[0014] FIG. 4 shows the CD spectra of peptides 1 and 2 at
20.degree. C.
[0015] FIG. 5 shows the variable-temperature CD spectra of peptide
2 in 50 mM sodium phosphate solution (pH=8.0).
[0016] FIG. 6 shows an olefin-metathesis resulting in a stapled
peptide.
[0017] FIG. 7 shows a capping strategy for passive membrane
diffusion with a proline-locked stapled peptide.
[0018] FIG. 8 shows a capping strategy for passive membrane
diffusion with asparagine and an asparagine surrogate.
[0019] FIG. 9 shows a GCN4-DNA complex and the basic and
coiled-coil regions of GCNb 4.
[0020] FIG. 10 shows unnatural amino acids used to generate
proline-locked stapled peptides.
[0021] FIG. 11A. and FIG. 11B. show a synthesis scheme for
P.sub.R3.
[0022] FIG. 12 shows a synthesis scheme for PSO3.
[0023] FIG. 13 shows examples of pro line-locked stapled
peptides.
[0024] FIG. 14 shows examples of pro line-locked stapled and
unstapled peptides.
[0025] FIG. 15 shows an example of olefin-metathesis by
Grubbs-catalysis.
[0026] FIG. 16 shows a LC/MS chromatogram of the olefin-metathesis
reaction by Grubbs-catalysis of peptide "4)" (SEQ ID NO:2).
[0027] FIG. 17 shows CD spectra of proline-locked stapled
peptides.
[0028] FIG. 18 shows CD spectra of praline-locked stapled
peptides.
[0029] FIG. 19 shows CD spectra of selected praline-locked stapled
peptides in various solutions.
[0030] FIG. 20 shows CD spectra of selected proline-locked stapled
peptides at various temperatures.
[0031] FIG. 21 shows CD spectra of proline-locked stapled peptides
based on the full-length GCN basic region.
[0032] FIG. 22 shows CD spectra of praline-locked stapled peptides
at various temperatures. "20 Mix" refers to E and Z isomers mixture
of peptide 20.
[0033] FIG. 23 shows the CD spectra of proline-locked stapled
peptides (24 mer).
[0034] FIG. 24 shows the ability of proline-locked stapled peptides
17 and 18 to penetrate cells at the concentration of 0.1 .mu.M.
[0035] FIG. 25 shows the ability of praline-locked stapled peptides
17 and 18 to penetrate cells at the concentration of 1 .mu.M.
[0036] FIG. 26 shows investigation of the endocytosis mechanism of
the peptides. The peptides were labeled with FITC. FIG. 26 A. shows
flow cytometry of peptide 17 and peptide 18. FIG. 26 B. shows flow
cytometry of peptide 18 at different temperatures. FIG. 26 C. shows
CD spectra of peptide 18 at different temperatures. FIG. 26 D.
shows flow cytometry of peptide 18 in the presence of
NaN3.+-.2-deoxy-D-glucose (2-DG). These data indicate that the
internalization of peptide 18 is ATP-dependent.
[0037] FIG. 27 shows analysis of 1 li NMR and NOESY spectra of
peptide 4. The crosspeaks indicate alpha-helix conformation of the
peptides. d.alpha.N(i, i+3) indicates the interaction between an
amide N-li at i position and an alpha proton at i+3 position.
d.alpha.N(1, i+4) indicates the interaction between an amide N-li
at i position and an alpha proton at i+4 position. The coupling
constant below 4 indicates alpha-helix or 310-helix. The coupling
constant below 7 means the existence of a helical structure
including random coil. The residues adopt helical structure at N
and T because dNN(i, i+1) interaction was observed in these
residues. The 13 crosspeaks observed in NOESY spectra of peptide 4
indicate alpha-helix conformation.
[0038] FIG. 28 shows NMR measurements of peptide 4. The coupling
constant between two olefinic protons is 11 liz, which means the
olefin in peptide 4 is of the Z conformation. liigh,NOE value was
observed between two olefinic protons (49, and 77,). These values
indicate the Z-conformation of the olefin in peptide 4.
[0039] FIG. 29 shows CD spectra and NMR of Pro-locked Stapled
peptides (5 mer). FIG. 29 A. shows CD spectra of peptides 21-24.
FIG. 29 B. shows NMR of peptide 22 isomers.
[0040] FIG. 30 shows CD spectra of selected stapled peptides (GCN
14 mer).
[0041] FIG. 31 shows proline stapled peptides against trypsin
proteolysis.
[0042] FIG. 32 shows stability of proline stapled peptides against
trypsin proteolysis.
[0043] FIG. 33A. and FIG. 33B. show CD spectra of exemplified
stapled peptides.
[0044] FIG. 34 shows melting curve of exemplified pro-locked
stapled peptides (i, i+7).
[0045] FIG. 35 shows CD spectra of exemplified stapled
peptides.
[0046] FIG. 36 shows exemplified designed capping molecules.
[0047] FIG. 37A. and FIG. 37B. show CD spectra of exemplified
stapled peptides.
DEFINITIONS
[0048] Definitions of specific functional groups and chemical terms
are described in more detail below. The chemical elements are
identified in accordance with the Periodic Table of the Elements.
CAS version. Handbook of Chemistry and Physics, 75.sup.th Ed.,
inside cover, and specific functional groups are generally defined
as described therein. Additionally, general principles of organic
chemistry, as well as specific functional moieties and reactivity,
are described in Organic Chemistry, Thomas Sorrell, University
Science Books, Sausalito, 1999; Smith and March March's Advanced
Organic Chemistry, 5.sup.th Edition, John Wiley & Sons, Inc.,
New York, 2001; Larock, Comprehensive Organic Transformations, VCH
Publishers, Inc., New York, 1989; and Carruthers, Some Modern
Methods of Organic Synthesis, 3.sup.rd Edition, Cambridge
University Press, Cambridge, 1987.
[0049] Compounds and polypeptides described herein can comprise one
or more asymmetric centers, and thus can exist in various isomeric
forms. e.g., enantiomers and/or diastereomers. For example, the
compounds described herein can be in the form of an individual
enantiomer, diastereomer or geometric isomer, or can be in the form
of a mixture of stereoisomers, including racemic mixtures and
mixtures enriched in one or more stereoisomer. Isomers can be
isolated from mixtures by methods known to those skilled in the
art, including chiral high pressure liquid chromatography (HPLC)
and the formation and crystallization of chiral salts; or preferred
isomers can be prepared by asymmetric syntheses. See, for example.
Jacques et al., Enantiomers. Racemates and Resolutions (Wiley
Interscience. New York, 1981); Wilen et al., Tetrahedron 33:2725
(1977); Eliel, E. L. Stereochemistry of Carbon Compounds
(McGraw-Hill, N.Y., 1962); and Wilen, S. H. Tables of Resolving
Agents and Optical Resolutions p. 268 (E. L. Eliel, Ed., Univ. of
Notre Dame Press, Notre Dame, Ind. 1972). The invention
additionally encompasses compounds and polypeptides described
herein as individual isomers substantially free of other isomers,
and alternatively, as mixtures of various isomers.
[0050] When a range of values is listed, it is intended to
encompass each value and sub-range within the range. For example
"C.sub.1-6 alkyl" is intended to encompass, C.sub.1, C.sub.2,
C.sub.3, C.sub.4, C.sub.5, C.sub.6, C.sub.1-6, C.sub.1-5,
C.sub.1-4, C.sub.1-3, C.sub.1-2, C.sub.2-6, C.sub.2-5, C.sub.2-4,
C.sub.2-3, C.sub.3-6, C.sub.3-5, C.sub.3-4, C.sub.4-6, C.sub.4-5,
and C.sub.5-6 alkyl.
[0051] As used herein, substituent names which end in the suffix
"-ene" refer to a biradical derived from the removal of an
additional hydrogen atom from monoradical group as defined herein.
Thus, for example, the monoradical alkyl, as defined herein, is the
biradical alkylene upon removal of an additional hydrogen atom.
Likewise, alkenyl is alkenylene; alkynyl is alkynylene; heteroalkyl
is heteroalkylene; heteroalkenyl is heteroalkenylene; heteroalkynyl
is heteroalkynylene; carbocyclyl is carbocyclylene; heterocyclyl is
heterocyclylene; aryl is arylene; and heteroaryl is
heteroarylene.
[0052] The term "aliphatic," as used herein, refers to alkyl,
alkenyl, alkynyl, and carbocyclic groups. Likewise, the term
"heteroaliphatic" as used herein, refers to heteroalkyl,
heteroalkenyl, heteroalkynyl, and heterocyclic groups.
[0053] As used herein. "alkyl" refers to a radical of a
straight-chain or branched saturated hydrocarbon group having from
1 to 10 carbon atoms ("C.sub.1-10 alkyl"). In some embodiments, an
alkyl group has 1 to 9 carbon atoms ("C.sub.1-9 alkyl"). In some
embodiments, an alkyl group has 1 to 8 carbon atoms ("C.sub.1-8
alkyl"). In some embodiments, an alkyl group has 1 to 7 carbon
atoms ("C.sub.1-7 alkyl"). In some embodiments, an alkyl group has
1 to 6 carbon atoms ("C.sub.1-6 alkyl"). In some embodiments, an
alkyl group has 1 to 5 carbon atoms ("C.sub.1-5 alkyl"). In some
embodiments, an alkyl group has 1 to 4 carbon atoms ("C.sub.1-4
alkyl"). In some embodiments, an alkyl group has 1 to 3 carbon
atoms ("C.sub.1-3 alkyl"). In some embodiments, an alkyl group has
1 to 2 carbon atoms ("C.sub.1-2 alkyl"). In some embodiments, an
alkyl group has 1 carbon atom ("C.sub.1 alkyl"). In some
embodiments, an alkyl group has 2 to 6 carbon atoms ("C.sub.2-6
alkyl"). Examples of C.sub.1-6 alkyl groups include methyl
(C.sub.1), ethyl (C.sub.2), n-propyl (C.sub.3), isopropyl
(C.sub.3), n-butyl (C.sub.4), tert-butyl (C.sub.4), sec-butyl
(C.sub.4), iso-butyl (C.sub.4), n-pentyl (C.sub.5), 3-pentanyl
(C.sub.5), amyl (C.sub.5), neopentyl (C.sub.5), 3-methyl-2-butanyl
(C.sub.5), tertiary amyl (C.sub.5), and n-hexyl (C.sub.6).
Additional examples of alkyl groups include n-heptyl (C.sub.7),
n-octyl (C.sub.8) and the like. Unless otherwise specified, each
instance of an alkyl group is independently unsubstituted (an
"unsubstituted alkyl") or substituted (a "substituted alkyl") with
one or more substituents. In certain embodiments, the alkyl group
is an unsubstituted C.sub.1-10 alkyl (e.g., --CH.sub.3). In certain
embodiments, the alkyl group is a substituted C.sub.1-10 alkyl.
[0054] As used herein, "haloalkyl" is a substituted alkyl group as
defined herein wherein one or more of the hydrogen atoms are
independently replaced by a halogen, e.g., fluoro, bromo, chloro,
or iodo. "Perhaloalkyl" is a subset of haloalkyl, and refers to an
alkyl group wherein all of the hydrogen atoms are independently
replaced by a halogen, e.g., fluoro, bromo, chloro, or iodo. In
some embodiments, the haloalkyl moiety has 1 to 8 carbon atoms
("C.sub.1-8 haloalkyl"). In some embodiments, the haloalkyl moiety
has 1 to 6 carbon atoms ("C.sub.1-6 haloalkyl"). In some
embodiments, the haloalkyl moiety has 1 to 4 carbon atoms
("C.sub.1-4 haloalkyl"). In some embodiments, the haloalkyl moiety
has 1 to 3 carbon atoms ("C.sub.1-3 haloalkyl"). In some
embodiments, the haloalkyl moiety has 1 to 2 carbon atoms
("C.sub.1-2 haloalkyl"). In some embodiments, all of the haloalkyl
hydrogen atoms are replaced with fluoro to provide a perfluoroalkyl
group. In some embodiments, all of the haloalkyl hydrogen atoms are
replaced with chloro to provide a "perchloroalkyl" group. Examples
of haloalkyl groups include --CF.sub.3, --CF.sub.2CF.sub.3,
--CF.sub.2CF.sub.2CF.sub.3, --CCl.sub.3, --CFCl.sub.2,
--CF.sub.2Cl, and the like.
[0055] As used herein, "heteroalkyl" refers to an alkyl group as
defined herein which further includes at least one heteroatom
(e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen,
or sulfur within (i.e., inserted between adjacent carbon atoms of)
and/or placed at one or more terminal position(s) of the parent
chain. In certain embodiments, a heteroalkyl group refers to a
saturated group having from 1 to 10 carbon atoms and 1, 2, 3, or 4
heteroatoms within the parent chain ("heteroC.sub.1-10 alkyl"). In
some embodiments, a heteroalkyl group is a saturated group having 1
to 9 carbon atoms and 1, 2, 3, or 4 heteroatoms within the parent
chain ("heteroC.sub.1-9 alkyl"). In some embodiments, a heteroalkyl
group is a saturated group having 1 to 8 carbon atoms and 1, 2, 3,
or 4 heteroatoms within the parent chain ("heteroC.sub.1-8 alkyl").
In some embodiments, a heteroalkyl group is a saturated group
having 1 to 7 carbon atoms and 1, 2, 3, or 4 heteroatoms within the
parent chain ("heteroC.sub.1-7 alkyl"). In some embodiments, a
heteroalkyl group is a saturated group having 1 to 6 carbon atoms
and 1, 2, or 3 heteroatoms within the parent chain
("heteroC.sub.1-6 alkyl"). In some embodiments, a heteroalkyl group
is a saturated group having 1 to 5 carbon atoms and 1 or 2
heteroatoms within the parent chain ("heteroC.sub.1-5 alkyl"). In
some embodiments, a heteroalkyl group is a saturated group having 1
to 4 carbon atoms and 1 or 2 heteroatoms within the parent chain
("heteroC.sub.1-4 alkyl"). In some embodiments, a heteroalkyl group
is a saturated group having 1 to 3 carbon atoms and 1 heteroatom
within the parent chain ("heteroC.sub.1-3 alkyl"). In some
embodiments, a heteroalkyl group is a saturated group having 1 to 2
carbon atoms and 1 heteroatom within the parent chain
("heteroC.sub.1-2 alkyl"). In some embodiments, a heteroalkyl group
is a saturated group having 1 carbon atom and 1 heteroatom
("heteroC.sub.1 alkyl"). In some embodiments, a heteroalkyl group
is a saturated group having 2 to 6 carbon atoms and 1 or 2
heteroatoms within the parent chain ("heteroC.sub.2-6 alkyl").
Unless otherwise specified, each instance of a heteroalkyl group is
independently unsubstituted (an "unsubstituted heteroalkyl") or
substituted (a "substituted heteroalkyl") with one or more
substituents. In certain embodiments, the heteroalkyl group is an
unsubstituted heteroC.sub.1-10 alkyl. In certain embodiments, the
heteroalkyl group is a substituted heteroC.sub.1-10 alkyl.
[0056] As used herein. "alkenyl" refers to a radical of a
straight-chain or branched hydrocarbon group having from 2 to 10
carbon atoms and one or more double bonds (e.g., 1, 2, 3, or 4
double bonds) and no triple bonds. In some embodiments, an alkenyl
group has 2 to 9 carbon atoms ("C.sub.2-9 alkenyl"). In some
embodiments, an alkenyl group has 2 to 8 carbon atoms ("C.sub.2-8
alkenyl"). In some embodiments, an alkenyl group has 2 to 7 carbon
atoms ("C.sub.2-7 alkenyl"). In some embodiments, an alkenyl group
has 2 to 6 carbon atoms ("C.sub.2-6 alkenyl"). In some embodiments,
an alkenyl group has 2 to 5 carbon atoms ("C.sub.2-5 alkenyl"). In
some embodiments, an alkenyl group has 2 to 4 carbon atoms
("C.sub.2-4 alkenyl"). In some embodiments, an alkenyl group has 2
to 3 carbon atoms ("C.sub.2-3 alkenyl"). In some embodiments, an
alkenyl group has 2 carbon atoms ("C.sub.2 alkenyl"). The one or
more carbon-carbon double bonds can be internal (such as in
2-butenyl) or terminal (such as in 1-butenyl). Examples of
C.sub.2-4 alkenyl groups include ethenyl (C.sub.2), 1-propenyl
(C.sub.3), 2-propenyl (C.sub.3), 1-butenyl (C.sub.4), 2-butenyl
(C.sub.4), butadienyl (C.sub.4), and the like. Examples of
C.sub.2-6 alkenyl groups include the aforementioned C.sub.2-4
alkenyl groups as well as pentenyl (C.sub.5), pentadienyl
(C.sub.5), hexenyl (C.sub.6), and the like. Additional examples of
alkenyl include heptenyl (C.sub.7), octenyl (C.sub.8), octatrienyl
(C.sub.8), and the like. Unless otherwise specified, each instance
of an alkenyl group is independently unsubstituted (an
"unsubstituted alkenyl") or substituted (a "substituted alkenyl")
with one or more substituents. In certain embodiments, the alkenyl
group is an unsubstituted C.sub.2-10 alkenyl. In certain
embodiments, the alkenyl group is a substituted C.sub.2-10
alkenyl.
[0057] As used herein. "heteroalkenyl" refers to an alkenyl group
as defined herein which further includes at least one heteroatom
(e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen,
or sulfur within (i.e., inserted between adjacent carbon atoms of)
and/or placed at one or more terminal position(s) of the parent
chain. In certain embodiments, a heteroalkenyl group refers to a
group having from 2 to 10 carbon atoms, at least one double bond,
and 1, 2, 3, or 4 heteroatoms within the parent chain
("heteroC.sub.2-10 alkenyl"). In some embodiments, a heteroalkenyl
group has 2 to 9 carbon atoms at least one double bond, and 1, 2,
3, or 4 heteroatoms within the parent chain ("heteroC.sub.2-9
alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 8
carbon atoms, at least one double bond, and 1, 2, 3, or 4
heteroatoms within the parent chain ("heteroC.sub.2-8 alkenyl"). In
some embodiments, a heteroalkenyl group has 2 to 7 carbon atoms, at
least one double bond, and 1, 2, 3, or 4 heteroatoms within the
parent chain ("heteroC.sub.2-7 alkenyl"). In some embodiments, a
heteroalkenyl group has 2 to 6 carbon atoms, at least one double
bond, and 1, 2, or 3 heteroatoms within the parent chain
("heteroC.sub.2-6 alkenyl"). In some embodiments, a heteroalkenyl
group has 2 to 5 carbon atoms, at least one double bond, and 1 or 2
heteroatoms within the parent chain ("heteroC.sub.2-5 alkenyl"). In
some embodiments, a heteroalkenyl group has 2 to 4 carbon atoms, at
least one double bond, and 1 or 2 heteroatoms within the parent
chain ("heteroC.sub.2-4 alkenyl"). In some embodiments, a
heteroalkenyl group has 2 to 3 carbon atoms, at least one double
bond, and 1 heteroatom within the parent chain ("heteroC.sub.2-3
alkenyl"). In some embodiments, a heteroalkenyl group has 2 to 6
carbon atoms, at least one double bond, 1 or 2 heteroatoms within
the parent chain ("heteroC.sub.2-6 alkenyl"). Unless otherwise
specified, each instance of a heteroalkenyl group is independently
unsubstituted (an "unsubstituted heteroalkenyl") or substituted (a
"substituted heteroalkenyl") with one or more substituents. In
certain embodiments, the heteroalkenyl group is an unsubstituted
heteroC.sub.2-10 alkenyl. In certain embodiments, the heteroalkenyl
group is a substituted heteroC.sub.2-10 alkenyl.
[0058] As used herein, "alkynyl" refers to a radical of a
straight-chain or branched hydrocarbon group having from 2 to 10
carbon atoms and one or more triple bonds (e.g., 1, 2, 3, or 4
triple bonds) and optionally one or more double bonds (e.g., 1, 2,
3, or 4 double bonds) ("C.sub.2-10 alkynyl"). An alkynyl group that
has one or more triple bonds and one or more double bonds is also
referred to as an "ene-yene" group. In some embodiments, an alkynyl
group has 2 to 9 carbon atoms ("C.sub.2-9 alkynyl"). In some
embodiments, an alkynyl group has 2 to 8 carbon atoms ("C.sub.2-8
alkynyl"). In some embodiments, an alkynyl group has 2 to 7 carbon
atoms ("C.sub.2-7 alkynyl"). In some embodiments, an alkynyl group
has 2 to 6 carbon atoms ("C.sub.2-6 alkynyl"). In some embodiments,
an alkynyl group has 2 to 5 carbon atoms ("C.sub.2-5 alkynyl"). In
some embodiments, an alkynyl group has 2 to 4 carbon atoms
("C.sub.2-4 alkynyl"). In some embodiments, an alkynyl group has 2
to 3 carbon atoms ("C.sub.2-3 alkynyl"). In some embodiments, an
alkynyl group has 2 carbon atoms ("C.sub.2 alkynyl"). The one or
more carbon-carbon triple bonds can be internal (such as in
2-butynyl) or terminal (such as in 1-butynyl). Examples of
C.sub.2-4 alkynyl groups include, without limitation, ethynyl
(C.sub.2), 1-propynyl (C.sub.3), 2-propynyl (C.sub.3), 1-butynyl
(C.sub.4), 2-butynyl (C.sub.4), and the like. Examples of C.sub.2-6
alkenyl groups include the aforementioned C.sub.2-4 alkynyl groups
as well as pentynyl (C.sub.5), hexynyl (C.sub.6), and the like.
Additional examples of alkynyl include heptynyl (C.sub.7), octynyl
(C.sub.8), and the like. Unless otherwise specified, each instance
of an alkynyl group is independently unsubstituted (an
"unsubstituted alkynyl") or substituted (a "substituted alkynyl")
with one or more substituents. In certain embodiments, the alkynyl
group is an unsubstituted C.sub.2-10 alkynyl. In certain
embodiments, the alkynyl group is a substituted C.sub.2-10
alkynyl.
[0059] As used herein. "heteroalkynyl" refers to an alkynyl group
as defined herein which further includes at least one heteroatom
(e.g., 1, 2, 3, or 4 heteroatoms) selected from oxygen, nitrogen,
or sulfur within (i.e., inserted between adjacent carbon atoms of)
and/or placed at one or more terminal position(s) of the parent
chain. In certain embodiments, a heteroalkynyl group refers to a
group having from 2 to 10 carbon atoms, at least one triple bond,
and 1, 2, 3, or 4 heteroatoms within the parent chain
("heteroC.sub.2-10 alkynyl"). In some embodiments, a heteroalkynyl
group has 2 to 9 carbon atoms, at least one triple bond, and 1, 2,
3, or 4 heteroatoms within the parent chain ("heteroC.sub.2-9
alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 8
carbon atoms, at least one triple bond, and 1, 2, 3, or 4
heteroatoms within the parent chain ("heteroC.sub.2-8 alkynyl"). In
some embodiments, a heteroalkynyl group has 2 to 7 carbon atoms, at
least one triple bond, and 1, 2, 3, or 4 heteroatoms within the
parent chain ("heteroC.sub.2-7 alkynyl"). In some embodiments, a
heteroalkynyl group has 2 to 6 carbon atoms, at least one triple
bond, and 1, 2, or 3 heteroatoms within the parent chain
("heteroC.sub.2-6 alkynyl"). In some embodiments, a heteroalkynyl
group has 2 to 5 carbon atoms, at least one triple bond, and 1 or 2
heteroatoms within the parent chain ("heteroC.sub.2-5 alkynyl"). In
some embodiments, a heteroalkynyl group has 2 to 4 carbon atoms, at
least one triple bond, and 1 or 2 heteroatoms within the parent
chain ("heteroC.sub.2-4 alkynyl"). In some embodiments, a
heteroalkynyl group has 2 to 3 carbon atoms, at least one triple
bond, and 1 heteroatom within the parent chain ("heteroC.sub.2-3
alkynyl"). In some embodiments, a heteroalkynyl group has 2 to 6
carbon atoms, at least one triple bond, and 1 or 2 heteroatoms
within the parent chain ("heteroC.sub.2-6 alkynyl"). Unless
otherwise specified, each instance of a heteroalkynyl group is
independently unsubstituted (an "unsubstituted heteroalkynyl") or
substituted (a "substituted heteroalkynyl") with one or more
substituents. In certain embodiments, the heteroalkynyl group is an
unsubstituted heteroC.sub.2-10 alkynyl. In certain embodiments, the
heteroalkynyl group is a substituted heteroC.sub.2-10 alkynyl.
[0060] As used herein, "carbocyclyl" or "carbocyclic" refers to a
radical of a non-aromatic cyclic hydrocarbon group having from 3 to
10 ring carbon atoms ("C.sub.3-10 carbocyclyl") and zero
heteroatoms in the non-aromatic ring system. In some embodiments, a
carbocyclyl group has 3 to 8 ring carbon atoms ("C.sub.3-8
carbocyclyl"). In some embodiments, a carbocyclyl group has 3 to 6
ring carbon atoms ("C.sub.3-6 carbocyclyl"). In some embodiments, a
carbocyclyl group has 3 to 6 ring carbon atoms ("C.sub.3-6
carbocyclyl"). In some embodiments, a carbocyclyl group has 5 to 10
ring carbon atoms ("C.sub.5-10 carbocyclyl"). Exemplary C.sub.3-6
carbocyclyl groups include, without limitation, cyclopropyl
(C.sub.3), cyclopropenyl (C.sub.3), cyclobutyl (C.sub.4),
cyclobutenyl (C.sub.4), cyclopentyl (C.sub.5), cyclopentenyl
(C.sub.5), cyclohexyl (C.sub.6), cyclohexenyl (C.sub.6),
cyclohexadienyl (C.sub.6), and the like. Exemplary C.sub.3-8
carbocyclyl groups include, without limitation, the aforementioned
C.sub.3-6 carbocyclyl groups as well as cycloheptyl (C.sub.7),
cycloheptenyl (C.sub.7), cycloheptadienyl (C.sub.7),
cycloheptatrienyl (C.sub.7), cyclooctyl (C.sub.8), cyclooctenyl
(C.sub.8), bicyclo[2.2.1]heptanyl (C.sub.7), bicyclo[2.2.2]octanyl
(C.sub.8), and the like. Exemplary C.sub.3-10 carbocyclyl groups
include, without limitation, the aforementioned C.sub.3-8
carbocyclyl groups as well as cyclononyl (C.sub.9), cyclononenyl
(C.sub.9), cyclodecyl (C.sub.10), cyclodecenyl (C.sub.10),
octahydro-1H-indenyl (C.sub.9), decahydronaphthalenyl (C.sub.10),
spiro[4.5]decanyl (C.sub.10), and the like. As the foregoing
examples illustrate, in certain embodiments, the carbocyclyl group
is either monocyclic ("monocyclic carbocyclyl") or polycyclic
(e.g., containing a fused, bridged or spiro ring system such as a
bicyclic system ("bicyclic carbocyclyl") or tricyclic system
("tricyclic carbocyclyl")) and can be saturated or can contain one
or more carbon-carbon double or triple bonds. "Carbocyclyl" also
includes ring systems wherein the carbocyclyl ring, as defined
above, is fused with one or more aryl or heteroaryl groups wherein
the point of attachment is on the carbocyclyl ring, and in such
instances, the number of carbons continue to designate the number
of carbons in the carbocyclic ring system. Unless otherwise
specified, each instance of a carbocyclyl group is independently
unsubstituted (an "unsubstituted carbocyclyl") or substituted (a
"substituted carbocyclyl") with one or more substituents. In
certain embodiments, the carbocyclyl group is an unsubstituted
C.sub.3-10 carbocyclyl. In certain embodiments, the carbocyclyl
group is a substituted C.sub.3-10 carbocyclyl.
[0061] In some embodiments, "carbocyclyl" is a monocyclic,
saturated carbocyclyl group having from 3 to 10 ring carbon atoms
("C.sub.3-10 cycloalkyl"). In some embodiments, a cycloalkyl group
has 3 to 8 ring carbon atoms ("C.sub.3-8 cycloalkyl"). In some
embodiments, a cycloalkyl group has 3 to 6 ring carbon atoms
("C.sub.3-6 cycloalkyl"). In some embodiments, a cycloalkyl group
has 5 to 6 ring carbon atoms ("C.sub.5-6 cycloalkyl"). In some
embodiments, a cycloalkyl group has 5 to 10 ring carbon atoms
("C.sub.5-10 to cycloalkyl"). Examples of C.sub.3-6 cycloalkyl
groups include cyclopentyl (C.sub.5) and cyclohexyl (C.sub.5).
Examples of C.sub.3-6 cycloalkyl groups include the aforementioned
C.sub.5-6 cycloalkyl groups as well as cyclopropyl (C.sub.3) and
cyclobutyl (C.sub.4). Examples of C.sub.3-8 cycloalkyl groups
include the aforementioned C.sub.3-6 cycloalkyl groups as well as
cycloheptyl (C.sub.7) and cyclooctyl (C.sub.8). Unless otherwise
specified, each instance of a cycloalkyl group is independently
unsubstituted (an "unsubstituted cycloalkyl") or substituted (a
"substituted cycloalkyl") with one or more substituents. In certain
embodiments, the cycloalkyl group is an unsubstituted C.sub.3-10
cycloalkyl. In certain embodiments, the cycloalkyl group is a
substituted C.sub.3-10 cycloalkyl.
[0062] As used herein. "heterocyclyl" or "heterocyclic" refers to a
radical of a 3- to 14-membered non-aromatic ring system having ring
carbon atoms and 1 to 4 ring heteroatoms, wherein each heteroatom
is independently selected from nitrogen, oxygen, and sulfur ("3-14
membered heterocyclyl"). In heterocyclyl groups that contain one or
more nitrogen atoms, the point of attachment can be a carbon or
nitrogen atom, as valency permits. A heterocyclyl group can either
be monocyclic ("monocyclic heterocyclyl") or polycyclic (e.g., a
fused, bridged or spiro ring system such as a bicyclic system
("bicyclic heterocyclyl") or tricyclic system ("tricyclic
heterocyclyl")), and can be saturated or can contain one or more
carbon-carbon double or triple bonds. Heterocyclyl polycyclic ring
systems can include one or more heteroatoms in one or both rings.
"Heterocyclyl" also includes ring systems wherein the heterocyclyl
ring, as defined above, is fused with one or more carbocyclyl
groups wherein the point of attachment is either on the carbocyclyl
or heterocyclyl ring, or ring systems wherein the heterocyclyl
ring, as defined above, is fused with one or more aryl or
heteroaryl groups, wherein the point of attachment is on the
heterocyclyl ring, and in such instances, the number of ring
members continue to designate the number of ring members in the
heterocyclyl ring system. Unless otherwise specified, each instance
of heterocyclyl is independently unsubstituted (an "unsubstituted
heterocyclyl") or substituted (a "substituted heterocyclyl") with
one or more substituents. In certain embodiments, the heterocyclyl
group is an unsubstituted 3-14 membered heterocyclyl. In certain
embodiments, the heterocyclyl group is a substituted 3-14 membered
heterocyclyl.
[0063] In some embodiments, a heterocyclyl group is a 5-10 membered
non-aromatic ring system having ring carbon atoms and 1-4 ring
heteroatoms, wherein each heteroatom is independently selected from
nitrogen, oxygen, and sulfur ("5-10 membered heterocyclyl"). In
some embodiments, a heterocyclyl group is a 5-8 membered
non-aromatic ring system having ring carbon atoms and 1-4 ring
heteroatoms, wherein each heteroatom is independently selected from
nitrogen, oxygen, and sulfur ("5-8 membered heterocyclyl"). In some
embodiments, a heterocyclyl group is a 5-6 membered non-aromatic
ring system having ring carbon atoms and 1-4 ring heteroatoms,
wherein each heteroatom is independently selected from nitrogen,
oxygen, and sulfur ("5-6 membered heterocyclyl"). In some
embodiments, the 5-6 membered heterocyclyl has 1-3 ring heteroatoms
selected from nitrogen, oxygen, and sulfur. In some embodiments,
the 5-6 membered heterocyclyl has 1-2 ring heteroatoms selected
from nitrogen, oxygen, and sulfur. In some embodiments, the 5-6
membered heterocyclyl has 1 ring heteroatom selected from nitrogen,
oxygen, and sulfur.
[0064] Exemplary 3-membered heterocyclyl groups containing 1
heteroatom include, without limitation, azirdinyl, oxiranyl,
thiorenyl. Exemplary 4-membered heterocyclyl groups containing 1
heteroatom include, without limitation, azetidinyl, oxetanyl and
thietanyl. Exemplary 5-membered heterocyclyl groups containing 1
heteroatom include, without limitation, tetrahydrofuranyl,
dihydrofuranyl, tetrahydrothiophenyl, dihydrothiophenyl,
pyrrolidinyl, dihydropyrrolyl and pyrrolyl-2,5-dione. Exemplary
5-membered heterocyclyl groups containing 2 heteroatoms include,
without limitation, dioxolanyl, oxathiolanyl and dithiolanyl.
Exemplary 5-membered heterocyclyl groups containing 3 heteroatoms
include, without limitation, triazolinyl, oxadiazolinyl, and
thiadiazolinyl. Exemplary 6-membered heterocyclyl groups containing
1 heteroatom include, without limitation, piperidinyl,
tetrahydropyranyl, dihydropyridinyl, and thianyl. Exemplary
6-membered heterocyclyl groups containing 2 heteroatoms include,
without limitation, piperazinyl, morpholinyl, dithianyl, dioxanyl.
Exemplary 6-membered heterocyclyl groups containing 2 heteroatoms
include, without limitation, triazinanyl. Exemplary 7-membered
heterocyclyl groups containing 1 heteroatom include, without
limitation, azepanyl, oxepanyl and thiepanyl. Exemplary 8-membered
heterocyclyl groups containing 1 heteroatom include, without
limitation, azocanyl, oxecanyl and thiocanyl. Exemplary bicyclic
heterocyclyl groups include, without limitation, indolinyl,
isoindolinyl, dihydrobenzofuranyl, dihydrobenzothienyl,
tetrahydrobenzothienyl, tetrahydrobenzofuranyl, tetrahydroindolyl,
tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl,
decahydroisoquinolinyl, octahydrochromenyl, octahydroisochromenyl,
decahydronaphthyridinyl, decahydro-1,8-naphthyridinyl,
octahydropyrrolo[3,2-b]pyrrole, indolinyl, phthalimidyl,
naphthalimidyl, chromanyl, chromenyl, 1H-benzo[e][1,4]diazepinyl,
1,4,5,7-tetrahydropyrano[3,4-b]pyrrolyl,
5,6-dihydro-4H-furo[3,2-b]pyrrolyl,
6,7-dihydro-5H-furo[3,2-b]pyranyl,
5,7-dihydro-4H-thieno[2,3-c]pyranyl,
2,3-dihydro-1H-pyrrolo[2,3-b]pyridinyl,
2,3-dihydrofuro[2,3-b]pyridinyl,
4,5,6,7-tetrahydro-1H-pyrrolo-[2,3-b]pyridinyl,
4,5,6,7-tetrahydrofuro[3,2-c]pyridinyl,
4,5,6,7-tetrahydrothieno[3,2-b]pyridinyl,
1,2,3,4-tetrahydro-1,6-naphthyridinyl, and the like.
[0065] As used herein, "aryl" refers to a radical of a monocyclic
or polycyclic (e.g., bicyclic or tricyclic) 4n+2 aromatic ring
system (e.g., having 6, 10, or 14.pi. electrons shared in a cyclic
array) having 6-14 ring carbon atoms and zero heteroatoms provided
in the aromatic ring system ("C.sub.6-14 aryl"). In some
embodiments, an aryl group has 6 ring carbon atoms ("C.sub.6 aryl";
e.g., phenyl). In some embodiments, an aryl group has 10 ring
carbon atoms ("C.sub.10 aryl"; e.g., naphthyl such as 1-naphthyl
and 2-naphthyl). In some embodiments, an aryl group has 14 ring
carbon atoms ("C.sub.14 aryl"; e.g., anthracyl). "Aryl" also
includes ring systems wherein the aryl ring, as defined above, is
fused with one or more carbocyclyl or heterocyclyl groups wherein
the radical or point of attachment is on the aryl ring, and in such
instances, the number of carbon atoms continue to designate the
number of carbon atoms in the aryl ring system. Unless otherwise
specified, each instance of an aryl group is independently
unsubstituted (an "unsubstituted aryl") or substituted (a
"substituted aryl") with one or more substituents. In certain
embodiments, the aryl group is an unsubstituted C.sub.6-14 aryl. In
certain embodiments, the aryl group is a substituted C.sub.6-14
aryl.
[0066] "Aralkyl" is a subset of "alkyl" and refers to an alkyl
group, as defined herein, substituted by an aryl group, as defined
herein, wherein the point of attachment is on the alkyl moiety.
[0067] As used herein, "heteroaryl" refers to a radical of a 5-14
membered monocyclic or polycyclic (e.g., bicyclic or tricyclic)
4n+2 aromatic ring system (e.g., having 6, 10, or 14.pi. electrons
shared in a cyclic array) having ring carbon atoms and 1-4 ring
heteroatoms provided in the aromatic ring system, wherein each
heteroatom is independently selected from nitrogen, oxygen and
sulfur ("5-14 membered heteroaryl"). In heteroaryl groups that
contain one or more nitrogen atoms, the point of attachment can be
a carbon or nitrogen atom, as valency permits. Heteroaryl
polycyclic ring systems can include one or more heteroatoms in one
or both rings. "Heteroaryl" includes ring systems wherein the
heteroaryl ring, as defined above, is fused with one or more
carbocyclyl or heterocyclyl groups wherein the point of attachment
is on the heteroaryl ring, and in such instances, the number of
ring members continue to designate the number of ring members in
the heteroaryl ring system. "Heteroaryl" also includes ring systems
wherein the heteroaryl ring, as defined above, is fused with one or
more aryl groups wherein the point of attachment is either on the
aryl or heteroaryl ring, and in such instances, the number of ring
members designates the number of ring members in the fused
polycyclic (aryl/heteroaryl) ring system. Polycyclic heteroaryl
groups wherein one ring does not contain a heteroatom (e.g.,
indolyl, quinolinyl, carbazolyl, and the like) the point of
attachment can be on either ring, i.e., either the ring bearing a
heteroatom (e.g., 2-indolyl) or the ring that does not contain a
heteroatom (e.g., 5-indolyl).
[0068] In some embodiments, a heteroaryl group is a 5-10 membered
aromatic ring system having ring carbon atoms and 1-4 ring
heteroatoms provided in the aromatic ring system, wherein each
heteroatom is independently selected from nitrogen, oxygen, and
sulfur ("5-10 membered heteroaryl"). In some embodiments, a
heteroaryl group is a 5-8 membered aromatic ring system having ring
carbon atoms and 1-4 ring heteroatoms provided in the aromatic ring
system, wherein each heteroatom is independently selected from
nitrogen, oxygen, and sulfur ("5-8 membered heteroaryl"). In some
embodiments, a heteroaryl group is a 5-6 membered aromatic ring
system having ring carbon atoms and 1-4 ring heteroatoms provided
in the aromatic ring system, wherein each heteroatom is
independently selected from nitrogen, oxygen, and sulfur ("5-6
membered heteroaryl"). In some embodiments, the 5-6 membered
heteroaryl has 1-3 ring heteroatoms selected from nitrogen, oxygen,
and sulfur. In some embodiments, the 5-6 membered heteroaryl has
1-2 ring heteroatoms selected from nitrogen, oxygen, and sulfur. In
some embodiments, the 5-6 membered heteroaryl has 1 ring heteroatom
selected from nitrogen, oxygen, and sulfur. Unless otherwise
specified, each instance of a heteroaryl group is independently
unsubstituted (an "unsubstituted heteroaryl") or substituted (a
"substituted heteroaryl") with one or more substituents. In certain
embodiments, the heteroaryl group is an unsubstituted 5-14 membered
heteroaryl. In certain embodiments, the heteroaryl group is a
substituted 5-14 membered heteroaryl.
[0069] Exemplary 5-membered heteroaryl groups containing 1
heteroatom include, without limitation, pyrrolyl, furanyl and
thiophenyl. Exemplary 5-membered heteroaryl groups containing 2
heteroatoms include, without limitation, imidazolyl, pyrazolyl,
oxazolyl, isoxazolyl, thiazolyl, and isothiazolyl. Exemplary
5-membered heteroaryl groups containing 3 heteroatoms include,
without limitation, triazolyl, oxadiazolyl, and thiadiazolyl.
Exemplary 5-membered heteroaryl groups containing 4 heteroatoms
include, without limitation, tetrazolyl. Exemplary 6-membered
heteroaryl groups containing 1 heteroatom include, without
limitation, pyridinyl. Exemplary 6-membered heteroaryl groups
containing 2 heteroatoms include, without limitation, pyridazinyl,
pyrimidinyl, and pyrazinyl. Exemplary 6-membered heteroaryl groups
containing 3 or 4 heteroatoms include, without limitation,
triazinyl and tetrazinyl, respectively. Exemplary 7-membered
heteroaryl groups containing 1 heteroatom include, without
limitation, azepinyl, oxepinyl, and thiepinyl. Exemplary
5,6-bicyclic heteroaryl groups include, without limitation,
indolyl, isoindolyl, indazolyl, benzotriazolyl, benzothiophenyl,
isobenzothiophenyl, benzofuranyl, benzoisofuranyl, benzimidazolyl,
benzoxazolyl, benzisoxazolyl, benzoxadiazolyl, benzthiazolyl,
benzisothiazolyl, benzthiadiazolyl, indolizinyl, and purinyl.
Exemplary 6,6-bicyclic heteroaryl groups include, without
limitation, naphthyridinyl, pteridinyl, quinolinyl, isoquinolinyl,
cinnolinyl, quinoxalinyl, phthalazinyl, and quinazolinyl. Exemplary
tricyclic heteroaryl groups include, without limitation,
phenanthridinyl, dibenzofuranyl, carbazolyl, acridinyl,
phenothiazinyl, phenoxazinyl and phenazinyl.
[0070] "Heteroaralkyl" is a subset of "alkyl" and refers to an
alkyl group, as defined herein, substituted by a heteroaryl group,
as defined herein, wherein the point of attachment is on the alkyl
moiety.
[0071] As used herein, the term "partially unsaturated" refers to a
group that includes at least one double or triple bond. The term
"partially unsaturated" is intended to encompass rings having
multiple sites of unsaturation, but is not intended to include
aromatic groups (e.g., aryl or heteroaryl moieties) as herein
defined.
[0072] As used herein, the term "saturated" refers to a group that
does not contain a double or triple bond, i.e., contains all single
bonds.
[0073] As understood from the above, alkyl, alkenyl, alkynyl,
heteroalkyl, heteroalkenyl, heteroalkynyl, carbocyclyl,
heterocyclyl, aryl, and heteroaryl groups, as defined herein, are,
in certain embodiments, optionally substituted. Optionally
substituted refers to a group which may be substituted or
unsubstituted (e.g., "substituted" or "unsubstituted" alkyl,
"substituted" or "unsubstituted" alkenyl, "substituted" or
"unsubstituted" alkynyl, "substituted" or "unsubstituted"
heteroalkyl, "substituted" or "unsubstituted" heteroalkenyl,
"substituted" or "unsubstituted" heteroalkynyl, "substituted" or
"unsubstituted" carbocyclyl, "substituted" or "unsubstituted"
heterocyclyl, "substituted" or "unsubstituted" aryl or
"substituted" or "unsubstituted" heteroaryl group). In general, the
term "substituted", whether preceded by the term "optionally" or
not, means that at least one hydrogen present on a group (e.g., a
carbon or nitrogen atom) is replaced with a permissible
substituent, e.g., a substituent which upon substitution results in
a stable compound. e.g., a compound which does not spontaneously
undergo transformation such as by rearrangement, cyclization,
elimination, or other reaction. Unless otherwise indicated, a
"substituted" group has a substituent at one or more substitutable
positions of the group, and when more than one position in any
given structure is substituted, the substituent is either the same
or different at each position. The term "substituted" is
contemplated to include substitution with all permissible
substituents of organic compounds, any of the substituents
described herein that results in the formation of a stable
compound. The present invention contemplates any and all such
combinations in order to arrive at a stable compound. For purposes
of this invention, heteroatoms such as nitrogen may have hydrogen
substituents and/or any suitable substituent as described herein
which satisfy the valencies of the heteroatoms and results in the
formation of a stable moiety.
[0074] Exemplary carbon atom substituents include, but are not
limited to, halogen, --CN, --NO.sub.2, --N.sub.3, --SO.sub.2H,
--SO.sub.3H, --OH, --OR.sup.aa, --ON(R.sup.bb).sub.2,
--N(R.sup.bb).sub.2, --N(R.sup.bb).sub.3.sup.+X.sup.-,
--N(OR.sup.cc)R.sup.bb, --SH, --SR.sup.aa, --SSR.sup.cc,
--C(.dbd.O)R.sup.aa, --CO.sub.2H, --CHO, --C(OR.sup.cc).sub.2,
--CO.sub.2R.sup.aa, --OC(.dbd.O)R.sup.aa, --OCO.sub.2R.sup.aa,
--C(.dbd.O)N(R.sup.bb).sub.2, --OC(.dbd.O)N(R.sup.bb).sub.2,
--NR.sup.bbC(.dbd.O)R.sup.aa, --NR.sup.bbCO.sub.2R.sup.aa,
--NR.sup.bbC(.dbd.O)N(R.sup.bb).sub.2, --C(.dbd.NR.sup.bb)R.sup.aa,
--C(.dbd.NR.sup.bb)OR.sup.aa, --OC(.dbd.NR.sup.bb)R.sup.aa,
--OC(.dbd.NR.sup.bb)OR.sup.aa,
--C(.dbd.NR.sup.bb)N(R.sup.bb).sub.2,
--OC(.dbd.NR.sup.bb)N(R.sup.bb).sub.2,
--NR.sup.bbC(.dbd.NR.sup.bb)N(R.sup.bb).sub.2,
--C(.dbd.O)NR.sup.bbSO.sub.2R.sup.aa, --NR.sup.bbSO.sub.2R.sup.aa,
--SO.sub.2N(R.sup.bb).sub.2, --SO.sub.2R.sup.aa,
--SO.sub.2OR.sup.aa, --OSO.sub.2R.sup.aa, --S(.dbd.O)R.sup.aa,
--OS(.dbd.O)R.sup.aa, --Si(R.sup.aa).sub.3, --OSi(R.sup.aa).sub.3
--C(.dbd.S)N(R.sup.bb).sub.2, --C(.dbd.O)SR.sup.aa,
--C(.dbd.S)SR.sup.aa, --SC(.dbd.S)SR.sup.aa, --SC(.dbd.O)SR.sup.aa,
--OC(.dbd.O)SR.sup.aa, --SC(.dbd.O)OR.sup.aa, --SC(.dbd.O)R.sup.aa,
--P(.dbd.O).sub.2R.sup.aa, --OP(.dbd.O).sub.2R.sup.aa,
--P(.dbd.O)(R.sup.aa).sub.2, --OP(.dbd.O)(R.sup.aa).sub.2,
--OP(.dbd.O)(OR.sup.cc), --P(.dbd.O).sub.2N(R.sup.bb).sub.2,
--OP(.dbd.O).sub.2N(R.sup.bb).sub.2, --P(.dbd.O)(NR.sup.bb).sub.2,
--OP(.dbd.O)(NR.sup.bb).sub.2,
--NR.sup.bbP(.dbd.O)(OR.sup.cc).sub.2,
--NR.sup.bbP(.dbd.O)(NR.sup.bb).sub.2, P(R.sup.cc).sub.2,
--P(R.sup.cc).sub.3, --OP(R.sup.cc).sub.2, --OP(R.sup.cc).sub.3,
--B(R.sup.aa).sub.2, --B(OR.sup.cc).sub.2, --BR.sup.aa(OR.sup.cc),
C.sub.1-10 alkyl, C.sub.1-10 perhaloalkyl, C.sub.2-10 alkenyl,
C.sub.2-10 alkynyl, C.sub.3-14 carbocyclyl, 3-14 membered
heterocyclyl, C.sub.6-14 aryl, and 5-14 membered heteroaryl,
wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl,
aryl, and heteroaryl is independently substituted with 0, 1, 2, 3,
4, or 5 R.sup.dd groups;
[0075] or two geminal hydrogens on a carbon atom are replaced with
the group .dbd.O, .dbd.S, .dbd.NN(R.sup.bb).sub.2,
.dbd.NNR.sup.bbC(.dbd.O)R.sup.aa,
.dbd.NNR.sup.bbC(.dbd.O)OR.sup.aa,
.dbd.NNR.sup.bbS(.dbd.O).sub.2R.sup.aa, .dbd.NR.sup.bb, or
.dbd.NOR.sup.cc;
[0076] each instance of R.sup.aa is, independently, selected from
C.sub.1-10 to alkyl, C.sub.1-10 perhaloalkyl, C.sub.2-10 alkenyl,
C.sub.2-10 alkynyl, C.sub.3-10 carbocyclyl, 3-14 membered
heterocyclyl, C.sub.6-14 aryl, and 5-14 membered heteroaryl, or two
R.sup.aa groups are joined to form a 3-14 membered heterocyclyl or
5-14 membered heteroaryl ring, wherein each alkyl, alkenyl,
alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is
independently substituted with 0, 1, 2, 3, 4, or 5 R.sup.dd
groups;
[0077] each instance of R.sup.bb is, independently, selected from
hydrogen, --OH, --OR.sup.aa, --N(R.sup.cc).sub.2, --CN,
--C(.dbd.O)R.sup.aa, --C(.dbd.O)N(R.sup.cc), --CO.sub.2R.sup.aa,
--SO.sub.2R.sup.aa, --C(.dbd.NR.sup.cc)OR.sup.aa,
--C(.dbd.NR.sup.cc)N(R.sup.cc).sub.2, --SO.sub.2N(R.sup.cc).sub.2,
--SO.sub.2R.sup.cc, --SO.sub.2OR.sup.cc, --SOR.sup.aa,
--C(.dbd.S)N(R.sup.cc).sub.2, --C(.dbd.O)SR.sup.cc,
--C(.dbd.S)SR.sup.cc, --P(.dbd.O).sub.2R.sup.aa,
--P(.dbd.O)(R.sup.aa).sub.2, --P(.dbd.O).sub.2N(R.sup.cc).sub.2,
--P(.dbd.O)(NR.sup.cc).sub.2, C.sub.1-10 alkyl, C.sub.1-10
perhaloalkyl, C.sub.2-10 alkenyl, C.sub.2-10 alkynyl, C.sub.3-10
carbocyclyl, 3-14 membered heterocyclyl, C.sub.6-14 aryl, and 5-14
membered heteroaryl, or two R.sup.bb groups are joined to form a
3-14 membered heterocyclyl or 5-14 membered heteroaryl ring,
wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl,
aryl, and heteroaryl is independently substituted with 0, 1, 2, 3,
4, or 5 R.sup.dd groups;
[0078] each instance of R.sup.cc is, independently, selected from
hydrogen, C.sub.1-10 alkyl, C.sub.1-10 perhaloalkyl, C.sub.2-10
alkenyl. C.sub.2-10 alkynyl, C.sub.3-10 carbocyclyl, 3-14 membered
heterocyclyl, C.sub.6-14 aryl, and 5-14 membered heteroaryl, or two
R.sup.cc groups are joined to form a 3-14 membered heterocyclyl or
5-14 membered heteroaryl ring, wherein each alkyl, alkenyl,
alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is
independently substituted with 0, 1, 2, 3, 4, or 5 R.sup.dd
groups;
[0079] each instance of R.sup.dd is, independently, selected from
halogen, --CN, --NO.sub.2, --N.sub.3, --SO.sub.2H, --SO.sub.3H,
--OH, --OR.sup.ee--, --ON(R.sup.ff).sub.2, --N(R.sup.ff),
--N(R.sup.ff).sub.3.sup.+X.sup.-, --N(OR.sup.ee)R.sup.ff, --SH,
--SR.sup.ee, --SSR.sup.ee, --C(.dbd.O)R.sup.ee, --CO.sub.2H,
--CO.sub.2R.sup.ee, --OC(.dbd.O)R.sup.ee, --OCO.sub.2R.sup.ee,
--C(.dbd.O)N(R.sup.ff).sub.2, --OC(.dbd.O)N(R.sup.ff).sub.2,
--NR.sup.ffC(.dbd.O)R.sup.ee, --NR.sup.ffCO.sub.2R.sup.ee,
--NR.sup.ffC(.dbd.O)N(R.sup.ff), --C(.dbd.NR.sup.ff)OR.sup.ee,
--OC(.dbd.NR.sup.ff)R.sup.ee, --OC(.dbd.NR.sup.ff)OR.sup.ee--,
--C(.dbd.NR.sup.ff)N(R.sup.ff).sub.2,
--OC(.dbd.NR.sup.ff)N(R.sup.ff).sub.2,
--NR.sup.ffC(.dbd.NR.sup.ff)N(R.sup.ff).sub.2,
--NR.sup.ffSO.sub.2R.sup.ee, --SO.sub.2N(R.sup.ff).sub.2,
--SO.sub.2R.sup.ee, --SO.sub.2OR.sup.ee, --OSO.sub.2R.sup.ee,
--S(.dbd.O)R.sup.ee, --Si(R.sup.ee).sub.3, --OSi(R.sup.ee).sub.3,
--C(.dbd.S)N(R.sup.ff).sub.2, --C(.dbd.O)SR.sup.ee,
--C(.dbd.S)SR.sup.ee, --SC(.dbd.S)SR.sup.ee,
--P(.dbd.O).sub.2R.sup.ee, --P(.dbd.O)(R.sup.ee).sub.2,
--OP(.dbd.O)(R.sup.ee).sub.2, --OP(.dbd.O)(OR.sup.ee).sub.2,
C.sub.1-6 alkyl, C.sub.1-6 perhaloalkyl, C.sub.2-6 alkenyl,
C.sub.2-6 alkynyl, C.sub.3-10 carbocyclyl, 3-10 membered
heterocyclyl, C.sub.6-10 aryl, 5-10 membered heteroaryl, wherein
each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and
heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5
R.sup.gg groups, or two geminal R.sup.dd substituents can be joined
to form .dbd.O or .dbd.S;
[0080] each instance of R.sup.ee is independently, selected from
C.sub.1-6 alkyl, C.sub.1-6 perhaloalkyl, C.sub.2-6 alkenyl,
C.sub.2-6 alkynyl, C.sub.3-10 carbocyclyl, C.sub.6-10 aryl, 3-10
membered heterocyclyl, and 3-10 membered heteroaryl, wherein each
alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl, aryl, and
heteroaryl is independently substituted with 0, 1, 2, 3, 4, or 5
R.sup.gg groups;
[0081] each instance of R.sup.ff is, independently, selected from
hydrogen, C.sub.1-6 alkyl, C.sub.1-6 perhaloalkyl, C.sub.2-6
alkenyl, C.sub.2-6 alkynyl, C.sub.3-10 carbocyclyl, 3-10 membered
heterocyclyl, C.sub.6-10 aryl and 5-10 membered heteroaryl, or two
R.sup.ff groups are joined to form a 3-14 membered heterocyclyl or
5-14 membered heteroaryl ring, wherein each alkyl, alkenyl,
alkynyl, carbocyclyl, heterocyclyl, aryl, and heteroaryl is
independently substituted with 0, 1, 2, 3, 4, or 5 R.sup.gg groups;
and
[0082] each instance of R.sup.gg is, independently, halogen, --CN,
--NO.sub.2, --N.sub.3, -SO.sub.2H, --SO.sub.3H, --OH, --OC.sub.1-6
alkyl, --ON(C.sub.1-6 alkyl).sub.2, --N(C.sub.1-6 alkyl).sub.2,
--N(C.sub.1-6 alkyl).sub.3.sup.+X.sup.-, --NH(C.sub.1-6
alkyl).sub.2.sup.+X.sup.-,
--NH.sub.2(C.sub.1-6 alkyl).sup.+X.sup.-, --NH.sub.3.sup.+X.sup.-,
--N(OC.sub.1-6 alkyl)(C.sub.1-6 alkyl), --N(OH)(C.sub.1-6 alkyl),
--NH(OH), --SH, --SC.sub.1-6 alkyl, --SS(C.sub.1-6 alkyl),
--C(.dbd.O)(C.sub.1-6 alkyl), --CO.sub.2H, --CO.sub.2(C.sub.1-6
alkyl), --OC(.dbd.O)(C.sub.1-6 alkyl), --OCO.sub.2(C.sub.1-6
alkyl), --C(.dbd.O)NH.sub.2, --C(.dbd.O)N(C.sub.1-6 alkyl).sub.2,
--OC(.dbd.O)NH(C.sub.1-6 alkyl), --NHC(.dbd.O)(C.sub.1-6 alkyl),
--N(C.sub.1-6 alkyl)C(.dbd.O)(C.sub.1-6 alkyl),
--NHCO.sub.2(C.sub.1-6 alkyl), --NHC(.dbd.O)N(C.sub.1-6
alkyl).sub.2, --NHC(.dbd.O)NH(C.sub.1-6 alkyl),
--NHC(.dbd.O)NH.sub.2, --C(.dbd.NH)O(C.sub.1-6 alkyl),
--OC(.dbd.NH)(C.sub.1-6 alkyl), --OC(.dbd.NH)OC.sub.1-6 alkyl,
--C(.dbd.NH)N(C.sub.1-6 alkyl).sub.2, --C(.dbd.NH)NH(C.sub.1-6
alkyl), --C(.dbd.NH)NH.sub.2, --OC(.dbd.NH)N(C.sub.1-6
alkyl).sub.2, --OC(NH)NH(C.sub.1-6 alkyl), --OC(NH)NH.sub.2,
--NHC(NH)N(C.sub.1-6 alkyl).sub.2, --NHC(.dbd.NH)NH.sub.2,
--NHSO.sub.2(C.sub.1-6 alkyl), --SO.sub.2N(C.sub.1-6 alkyl).sub.2,
--SO.sub.2NH(C.sub.1-6 alkyl), --SO.sub.2NH.sub.2,
--SO.sub.2C.sub.1-6 alkyl, --SO.sub.2OC.sub.1-6 alkyl,
--OSO.sub.2C.sub.1-6 alkyl, --SOC.sub.1-6 alkyl, --Si(C.sub.1-6
alkyl).sub.3, --OSi(C.sub.1-6 alkyl).sub.3 --C(.dbd.S)N(C.sub.1-6
alkyl).sub.2, C(.dbd.S)NH(C.sub.1-6 alkyl), C(.dbd.S)NH.sub.2,
--C(.dbd.O)S(C.sub.1-6 alkyl), --C(.dbd.S)SC.sub.1-6 alkyl,
--SC(.dbd.S)SC.sub.1-6 alkyl, --P(.dbd.O).sub.2(C.sub.1-6 alkyl),
--P(.dbd.O)(C.sub.1-6 alkyl).sub.2, --OP(.dbd.O)(C.sub.1-6
alkyl).sub.2, --OP(.dbd.O)(OC.sub.1-6 alkyl).sub.2, C.sub.1-6
alkyl, C.sub.1-6 perhaloalkyl, C.sub.2-6 alkenyl, C.sub.2-6
alkynyl, C.sub.3-10 carbocyclyl, C.sub.6-10 aryl, 3-10 membered
heterocyclyl, 5-10 membered heteroaryl; or two geminal R.sup.gg
substituents can be joined to form .dbd.O or .dbd.S; wherein X is a
counterion.
[0083] As used herein, the term "hydroxyl" or "hydroxy" refers to
the group --OH. The term "substituted hydroxyl" or "substituted
hydroxyl," by extension, refers to a hydroxyl group wherein the
oxygen atom directly attached to the parent molecule is substituted
with a group other than hydrogen, and includes groups selected from
--OR.sup.aa, --ON(R.sup.aa).sub.2, --OC(.dbd.O)SR.sup.aa,
--OC(.dbd.O)R.sup.aa, --OCO.sub.2R.sup.aa,
--OC(.dbd.O)N(R.sup.bb).sub.2, --OC(.dbd.NR.sup.bb)R.sup.aa,
--OC(.dbd.NR.sup.bb)OR.sup.aa,
--OC(.dbd.NR.sup.bb)N(R.sup.bb).sub.2, --OS(.dbd.O)R.sup.aa,
--OSO.sub.2R.sup.aa, --OSi(R.sup.aa).sub.3, --OP(R.sup.cc).sub.2,
--OP(R.sup.cc).sub.3, --OP(.dbd.O).sub.2R.sup.aa,
--OP(.dbd.O)(R.sup.aa).sub.2, --OP(.dbd.O)(OR.sup.cc).sub.2,
--OP(.dbd.O).sub.2N(R.sup.bb).sub.2, and
--OP(.dbd.O)(NR.sup.bb).sub.2, wherein R.sup.aa, R.sup.bb, and
R.sup.cc are as defined herein.
[0084] As used herein, the term "thiol" or "thio" refers to the
group --SH. The term "substituted thiol" or "substituted thio." by
extension, refers to a thiol group wherein the sulfur atom directly
attached to the parent molecule is substituted with a group other
than hydrogen, and includes groups selected from --SR.sup.aa,
S--SR.sup.cc, --SC(.dbd.S)SR.sup.aa, --SC(.dbd.O)SR,
--SC(.dbd.O)OR.sup.aa, and --SC(.dbd.O)R.sup.aa, wherein R.sup.aa
and R.sup.cc are as defined herein.
[0085] As used herein, the term, "amino" refers to the group
--NH.sub.2. The term "substituted amino," by extension, refers to a
monosubstituted amino, a disubstituted amino, or a trisubstituted
amino, as defined herein.
[0086] As used herein, the term "monosubstituted amino" refers to
an amino group wherein the nitrogen atom directly attached to the
parent molecule is substituted with one hydrogen and one group
other than hydrogen, and includes groups selected from
--NH(R.sup.bb), --NHC(.dbd.O)R.sup.aa, --NHCO.sub.2R.sup.aa,
--NHC(.dbd.O)N(R.sup.bb).sub.2, --NHC(.dbd.NR.sup.bb)N(R.sup.bb),
--NHSO.sub.2R.sup.aa, --NHP(.dbd.O)(OR.sup.cc).sub.2, and
--NHP(.dbd.O)(NR.sup.bb).sub.2, wherein R.sup.aa, R.sup.bb, and
R.sup.cc are as defined herein, and wherein R.sup.bb of the group
--NH(R.sup.bb) is not hydrogen.
[0087] As used herein, the term "disubstituted amino" refers to an
amino group wherein the nitrogen atom directly attached to the
parent molecule is substituted with two groups other than hydrogen,
and includes groups selected from --N(R.sup.bb).sub.2, --NR.sup.bb
C(.dbd.O)R.sup.aa, --NR.sup.bbCO.sub.2R.sup.aa,
--NR.sup.bbC(.dbd.O)N(R.sup.bb).sub.2,
--NR.sup.bbC(.dbd.NR.sup.bb)N(R.sup.bb).sub.2,
--NR.sup.bbSO.sub.2R.sup.aa, --NR.sup.bbP(.dbd.O)(OR.sup.cc).sub.2,
and --NR.sup.bbP(.dbd.O)(NR.sup.bb).sub.2, wherein R.sup.aa,
R.sup.bb, and R.sup.cc are as defined herein, with the proviso that
the nitrogen atom directly attached to the parent molecule is not
substituted with hydrogen.
[0088] As used herein, the term "trisubstituted amino" or a
"quaternary amino salt" or a "quaternary salt" refers to a nitrogen
atom covalently attached to four groups such that the nitrogen is
cationic, wherein the cationic nitrogen atom is further complexed
with an anionic counterion, e.g., such as groups of the Formula
--N(R.sup.bb).sub.3.sup.+X.sup.- and
--N(R.sup.bb).sub.2.sup.+X.sup.-, wherein R.sup.bb and X.sup.- are
as defined herein.
[0089] As used herein, a "counterion" or "anionic counterion" is a
negatively charged group associated with a cationic quaternary
amino group in order to maintain electronic neutrality. Exemplary
counterions include halide ions (e.g., F.sup.+, Cl.sup.-, Br.sup.-,
I.sup.-), NO.sub.3.sup.-, ClO.sub.4.sup.-, OH.sup.-,
H.sub.2PO.sub.4.sup.-, HSO.sub.4.sup.-, sulfonate ions (e.g.,
methansulfonate, trifluoromethanesulfonate, p-toluenesulfonate,
benzenesulfonate, 10-camphor sulfonate, naphthalene-2-sulfonate,
naphthalene-1-sulfonic acid-5-sulfonate, ethan-1-sulfonic
acid-2-sulfonate, and the like), and carboxylate ions (e.g.,
acetate, ethanoate, propanoate, benzoate, glycerate, lactate,
tartrate, glycolate, and the like).
[0090] As used herein, the term "sulfonyl" refers to a group
selected from --SO.sub.2N(R.sup.bb).sub.2, --SO.sub.2R.sup.aa, and
--SO.sub.2OR.sup.aa, wherein R.sup.aa and R.sup.bb are as defined
herein.
[0091] As used herein, the term "sulfinyl" refers to the group
--S(.dbd.O)R.sup.aa, wherein R.sup.aa is as defined herein.
[0092] As used herein, the term "acyl" refers a group wherein the
carbon directly attached to the parent molecule is sp.sup.2
hybridized, and is substituted with an oxygen, nitrogen or sulfur
atom, e.g., a group selected from ketones (--C(.dbd.O)R.sup.aa),
carboxylic acids (--CO.sub.2H), aldehydes (--CHO), esters
(--CO.sub.2R.sup.aa), thioesters (--C(.dbd.O)SR.sup.aa,
--C(.dbd.S)SR.sup.aa), amides (--C(.dbd.O)N(R.sup.bb).sub.2,
--C(.dbd.O)NR.sup.bbSO.sub.2R.sup.aa) thioamides
(--C(.dbd.S)N(R.sup.bb).sub.2), and imines
(--C(.dbd.NR.sup.bb)R.sup.aa--, --C(.dbd.NR.sup.bb)OR.sup.aa),
--C(.dbd.NR.sup.bb)N(R.sup.bb).sub.2), wherein R.sup.aa and
R.sup.bb are as defined herein.
[0093] As used herein, the term "azido" refers to a group of the
formula --N.sub.3.
[0094] As used herein, the term "cyano" refers to a group of the
formula --CN.
[0095] As used herein, the term "isocyano" refers to a group of the
formula --NC.
[0096] As used herein, the term "nitro" refers to a group of the
formula --NO.sub.2.
[0097] As used herein, the term "halo" or "halogen" refers to
fluorine (fluoro, --F), chlorine (chloro, --Cl), bromine (bromo,
--Br), or iodine (iodo, --I).
[0098] As used herein, the term "oxo" refers to a group of the
formula .dbd.O.
[0099] As used herein, the term "thiooxo" refers to a group of the
formula .dbd.S.
[0100] As used herein, the term "imino" refers to a group of the
formula .dbd.N(R.sup.b).
[0101] As used herein, the term "silyl" refers to the group
--Si(R.sup.aa).sub.3, wherein R.sup.aa is as defined herein.
[0102] Nitrogen atoms can be substituted or unsubstituted as
valency permits, and include primary, secondary, tertiary, and
quarternary nitrogen atoms. Exemplary nitrogen atom substitutents
include, but are not limited to, hydrogen, --OH, --OR.sup.aa,
--N(R.sup.cc).sub.2, --CN, --C(.dbd.O)R.sup.aa,
--C(.dbd.O)N(R.sup.cc).sub.2, --CO.sub.2R.sup.aa,
--SO.sub.2R.sup.aa, --C(.dbd.NR.sup.bb)R.sup.aa,
--C(.dbd.NR.sup.cc)OR.sup.aa, --C(.dbd.NR.sup.cc)N(R.sup.cc).sub.2,
--SO.sub.2N(R.sup.cc).sub.2, --SO.sub.2R.sup.cc,
--SO.sub.2OR.sup.cc, --SOR.sup.aa, --C(.dbd.S)N(R.sup.cc).sub.2,
--C(.dbd.O)SR.sup.cc, --C(.dbd.S)SR.sup.cc,
--P(.dbd.O).sub.2R.sup.aa, --P(.dbd.O)(R.sup.aa).sub.2,
--P(.dbd.O).sub.2N(R.sup.cc).sub.2, --P(.dbd.O)(NR.sup.cc).sub.2,
C.sub.1-10 alkyl, C.sub.1-10 perhaloalkyl, C.sub.2-10 alkenyl,
C.sub.2-10 alkynyl, C.sub.3-10 carbocyclyl, 3-14 membered
heterocyclyl, C.sub.6-14 aryl, and 5-14 membered heteroaryl, or two
R.sup.cc groups attached to a nitrogen atom are joined to form a
3-14 membered heterocyclyl or 5-14 membered heteroaryl ring,
wherein each alkyl, alkenyl, alkynyl, carbocyclyl, heterocyclyl,
aryl, and heteroaryl is independently substituted with 0, 1, 2, 3,
4, or 5 R.sup.dd groups, and wherein R.sup.aa, R.sup.bb, R.sup.cc
and R.sup.dd are as defined above.
[0103] In certain embodiments, the substituent present on the
nitrogen atom is an amino protecting group (also referred to herein
as a "nitrogen protecting group"). Amino protecting groups include,
but are not limited to, --OH, --OR.sup.aa, --N(R.sup.cc).sub.2,
--C(.dbd.O)R.sup.aa, --C(.dbd.O)N(R.sup.cc).sub.2,
--CO.sub.2R.sup.aa, --SO.sub.2R.sup.aa,
--C(.dbd.NR.sup.cc)R.sup.aa, --C(.dbd.NR.sup.cc)OR.sup.aa,
--C(.dbd.NR.sup.cc)N(R.sup.cc).sub.2, --SO.sub.2N(R.sup.cc),
--SO.sub.2R.sup.cc, --SO.sub.2OR.sup.cc, --SOR.sup.aa,
--C(.dbd.S)N(R.sup.cc).sub.2, --C(.dbd.O)SR.sup.cc,
--C(.dbd.S)SR.sup.cc, C.sub.1-10 alkyl (e.g., aralkyl,
heteroaralkyl), C.sub.2-10 alkenyl, C.sub.2-10 alkynyl, C.sub.3-10
carbocyclyl, 3-14 membered heterocyclyl, C.sub.6-14 aryl, and 5-14
membered heteroaryl groups, wherein each alkyl, alkenyl, alkynyl,
carbocyclyl, heterocyclyl, aralkyl, aryl, and heteroaryl is
independently substituted with 0, 1, 2, 3, 4, or 5 R.sup.dd groups,
and wherein R.sup.aa, R.sup.bb, R.sup.cc and R.sup.dd are as
defined herein. Amino protecting groups are well known in the art
and include those described in detail in Protecting Groups in
Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3.sup.rd
edition, John Wiley & Sons, 1999, incorporated herein by
reference.
[0104] For example, amino protecting groups such as amide groups
(e.g., --C(.dbd.O)R.sup.aa) include, but are not limited to,
formamide, acetamide, chloroacetamide, trichloroacetamide,
trifluoroacetamide, phenylacetamide, 3-phenylpropanamide,
picolinamide, 3-pyridylcarboxamide, N-benzoylphenylalanyl
derivative, benzamide, p-phenylbenzamide, o-nitophenylacetamide,
o-nitrophenoxyacetamide, acetoacetamide,
(N'-dithiobenzyloxyacylamino)acetamide,
3-(p-hydroxyphenyl)propanamide, 3-(o-nitrophenyl)propanamide,
2-methyl-2-(o-nitrophenoxy)propanamide,
2-methyl-2-(o-phenylazophenoxy)propanamide, 4-chlorobutanamide,
3-methyl-3-nitrobutanamide, o-nitrocinnamide, N-acetylmethionine
derivative, o-nitrobenzamide and o-(benzoyloxymethyl)benzamide.
[0105] Amino protecting groups such as carbamate groups (e.g.,
--C(.dbd.O)OR.sup.aa) include, but are not limited to, methyl
carbamate, ethyl carbamante, 9-fluorenylmethyl carbamate (Fmoc),
9-(2-sulfo)fluorenylmethyl carbamate,
9-(2,7-dibromo)fluorenylmethyl carbamate,
2,7-di-t-butyl-[9-(10,10-dioxo-10,10,10,10-tetrahydrothioxanthyl)]methyl
carbamate (DBD-Tmoc), 4-methoxyphenacyl carbamate (Phenoc),
2,2,2-trichloroethyl carbamate (Troc), 2-trimethylsilylethyl
carbamate (Teoc), 2-phenylethyl carbamate (hZ),
1-(1-adamantyl)-1-methylethyl carbamate (Adpoc),
1,1-dimethyl-2-haloethyl carbamate, 1,1-dimethyl-2,2-dibromoethyl
carbamate (DB-t-BOC), 1,1-dimethyl-2,2,2-trichloroethyl carbamate
(TCBOC), 1-methyl-1-(4-biphenylyl)ethyl carbamate (Bpoc),
1-(3,5-di-t-butylphenyl)-1-methylethyl carbamate (t-Bumeoc), 2-(2'-
and 4'-pyridyl)ethyl carbamate (Pyoc),
2-(N,N-dicyclohexylcarboxamido)ethyl carbamate, t-butyl carbamate
(BOC), 1-adamantyl carbamate (Adoc), vinyl carbamate (Voc), allyl
carbamate (Alloc), 1-isopropylallyl carbamate (Ipaoc), cinnamyl
carbamate (Coc), 4-nitrocinnamyl carbamate (Noc), 8-quinolyl
carbamate, N-hydroxypiperidinyl carbamate, alkyldithio carbamate,
benzyl carbamate (Cbz), p-methoxybenzyl carbamate (Moz),
p-nitobenzyl carbamate, p-bromobenzyl carbamate, p-chlorobenzyl
carbamate, 2,4-dichlorobenzyl carbamate, 4-methylsulfinylbenzyl
carbamate (Msz), 9-anthrylmethyl carbamate, diphenylmethyl
carbamate, 2-methylthioethyl carbamate, 2-methylsulfonylethyl
carbamate, 2-(p-toluenesulfonyl)ethyl carbamate,
[2-(1,3-dithianyl)]methyl carbamate (Dmoc), 4-methylthiophenyl
carbamate (Mtpc), 2,4-dimethylthiophenyl carbamate (Bmpc),
2-phosphonioethyl carbamate (Peoc), 2-triphenylphosphonioisopropyl
carbamate (Ppoc), 1,1-dimethyl-2-cyanoethyl carbamate,
m-chloro-p-acyloxybenzyl carbamate, p-(dihydroxyboryl)benzyl
carbamate, 5-benzisoxazolylmethyl carbamate,
2-(trifluoromethyl)-6-chromonylmethyl carbamate (Tcroc),
m-nitrophenyl carbamate, 3,5-dimethoxybenzyl carbamate,
o-nitrobenzyl carbamate, 3,4-dimethoxy-6-nitrobenzyl carbamate,
phenyl(o-nitrophenyl)methyl carbamate, t-amyl carbamate, S-benzyl
thiocarbamate, p-cyanobenzyl carbamate, cyclobutyl carbamate,
cyclohexyl carbamate, cyclopentyl carbamate, cyclopropylmethyl
carbamate, p-decyloxybenzyl carbamate, 2,2-dimethoxyacylvinyl
carbamate, o-(N,N-dimethylcarboxamido)benzyl carbamate,
1,1-dimethyl-3-(N,N-dimethylcarboxamido)propyl carbamate,
1,1-dimethylpropynyl carbamate, di(2-pyridyl)methyl carbamate,
2-furanylmethyl carbamate, 2-iodoethyl carbamate, isobornyl
carbamate, isobutyl carbamate, isonicotinyl carbamate,
p-(p'-methoxyphenylazo)benzyl carbamate, 1-methylcyclobutyl
carbamate, 1-methylcyclohexyl carbamate,
1-methyl-1-cyclopropylmethyl carbamate,
1-methyl-1-(3,5-dimethoxyphenyl)ethyl carbamate,
1-methyl-1-(p-phenylazophenyl)ethyl carbamate,
1-methyl-1-phenylethyl carbamate, 1-methyl-1-(4-pyridyl)ethyl
carbamate, phenyl carbamate, p-(phenylazo)benzyl carbamate,
2,4,6-tri-t-butylphenyl carbamate, 4-(trimethylammonium)benzyl
carbamate, and 2,4,6-trimethylbenzyl carbamate.
[0106] Amino protecting groups such as sulfonamide groups (e.g.,
--S(.dbd.O).sub.2R.sup.aa) include, but are not limited to,
p-toluenesulfonamide (Ts), benzenesulfonamide,
2,3,6,-trimethyl-4-methoxybenzenesulfonamide (Mtr),
2,4,6-trimethoxybenzenesulfonamide (Mtb),
2,6-dimethyl-4-methoxybenzenesulfonamide (Pme),
2,3,5,6-tetramethyl-4-methoxybenzenesulfonamide (Mte),
4-methoxybenzenesulfonamide (Mbs),
2,4,6-trimethylbenzenesulfonamide (Mts),
2,6-dimethoxy-4-methylbenzenesulfonamide (iMds),
2,2,5,7,8-pentamethylchroman-6-sulfonamide (Pmc),
methanesulfonamide (Ms), .beta.-trimethylsilylethanesulfonamide
(SES), 9-anthracenesulfonamide,
4-(4',8'-dimethoxynaphthylmethyl)benzenesulfonamide (DNMBS),
benzylsulfonamide, trifluoromethylsulfonamide, and
phenacylsulfonamide.
[0107] Other amino protecting groups include, but are not limited
to, phenothiazinyl-(10)-acyl derivative,
N'-p-toluenesulfonylaminoacyl derivative, N'-phenylaminothioacyl
derivative, N-benzoylphenylalanyl derivative, N-acetylmethionine
derivative, 4,5-diphenyl-3-oxazolin-2-one, N-phthalimide,
N-dithiasuccinimide (Dts), N-2,3-diphenylmaleimide,
N-2,5-dimethylpyrrole, N-1,1,4,4-tetramethyldisilylazacyclopentane
adduct (STABASE), 5-substituted
1,3-dimethyl-1,3,5-triazacyclohexan-2-one, 5-substituted
1,3-dibenzyl-1,3,5-triazacyclohexan-2-one, 1-substituted
3,5-dinitro-4-pyridone, N-methylamine, N-allylamine,
N-[2-(trimethylsilyl)ethoxy]methylamine (SEM),
N-3-acetoxypropylamine,
N-(1-isopropyl-4-nitro-2-oxo-3-pyroolin-3-yl)amine, quaternary
ammonium salts, N-benzylamine, N-di(4-methoxyphenyl)methylamine,
N-5-dibenzosuberylamine, N-triphenylmethylamine (Tr),
N-[(4-methoxyphenyl)diphenylmethyl]amine (MMTr),
N-9-phenylfluorenylamine (PhF),
N-2,7-dichloro-9-fluorenylmethyleneamine, N-ferrocenylmethylamino
(Fcm), N-2-picolylamino N'-oxide, N-1,1-dimethylthiomethyleneamine,
N-benzylideneamine, N-p-methoxybenzylideneamine,
N-diphenylmethyleneamine, N-[(2-pyridyl)mesityl]methyleneamine,
N--(N',N'-dimethylaminomethylene)amine, N,N'-isopropylidenediamine,
N-p-nitrobenzylideneamine, N-salicylideneamine,
N-5-chlorosalicylideneamine,
N-(5-chloro-2-hydroxyphenyl)phenylmethyleneamnine,
N-cyclohexylideneamine, N-(5,5-dimethyl-3-oxo-1-cyclohexenyl)amine,
N-borane derivative, N-diphenylborinic acid derivative,
N-[phenyl(pentaacylchromium- or tungsten)acyl]amine, N-copper
chelate, N-zinc chelate, N-nitroamine, N-nitrosoamine, amine
N-oxide, diphenylphosphinamide (Dpp), dimethylthiophosphinamide
(Mpt), diphenylthiophosphinamide (Ppt), dialkyl phosphoramidates,
dibenzyl phosphoramidate, diphenyl phosphoramidate,
benzenesulfenamide, o-nitrobenzenesulfenamide (Nps),
2,4-dinitrobenzenesulfenamide, pentachlorobenzenesulfenamide,
2-nitro-4-methoxybenzenesulfenamide, triphenylmethylsulfenamide,
and 3-nitropyridinesulfenamide (Npys).
[0108] In certain embodiments, the substituent present on an oxygen
atom is a hydroxyl protecting group (also referred to herein as an
"oxygen protecting group"). Hydroxyl protecting groups include, but
are not limited to, --R.sup.aa, --N(R.sup.bb).sub.2,
--C(.dbd.O)SR.sup.aa, --C(.dbd.O)R.sup.aa, --CO.sub.2R.sup.aa,
--C(.dbd.O)N(R.sup.bb).sub.2, --C(.dbd.NR.sup.bb)R.sup.aa,
--C(.dbd.NR.sup.bb)OR.sup.aa, --C(.dbd.NR.sup.bb)N(R.sup.bb).sub.2,
--S(.dbd.O)R.sup.aa, --SO.sub.2R.sup.aa, --Si(R.sup.aa).sub.3,
--P(R.sup.cc).sub.2, --P(R.sup.cc).sub.3,
--P(.dbd.O).sub.2R.sup.aa, --P(.dbd.O)(R.sup.aa).sub.2,
--P(.dbd.O)(OR.sup.cc).sub.2, --P(.dbd.O).sub.2N(R.sup.bb).sub.2,
and --P(.dbd.O)(NR.sup.bb).sub.2, wherein R.sup.aa, R.sup.bb, and
R.sup.cc are as defined herein. Hydroxyl protecting groups are well
known in the art and include those described in detail in
Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M.
Wuts, 3.sup.rd edition, John Wiley & Sons, 1999, incorporated
herein by reference.
[0109] Exemplary hydroxyl protecting groups include, but are not
limited to, methyl, methoxylmethyl (MOM), methylthiomethyl (MTM),
t-butylthiomethyl, (phenyldimethylsilyl)methoxymethyl (SMOM),
benzyloxymethyl (BOM), p-methoxybenzyloxymethyl (PMBM),
(4-methoxyphenoxy)methyl (p-AOM), guaiacolmethyl (GUM),
t-butoxymethyl, 4-pentenyloxymethyl (POM), siloxymethyl,
2-methoxyethoxymethyl (MEM), 2,2,2-trichloroethoxymethyl,
bis(2-chloroethoxy)methyl, 2-(trimethylsilyl)ethoxymethyl (SEMOR),
tetrahydropyranyl (THP), 3-bromotetrahydropyranyl,
tetrahydrothiopyranyl, 1-methoxycyclohexyl,
4-methoxytetrahydropyranyl (MTHP), 4-methoxytetrahydrothiopyranyl,
4-methoxytetrahydrothiopyranyl S,S-dioxide,
1-[(2-chloro-4-methyl)phenyl]-4-methoxypiperidin-4-yl (CTMP),
1,4-dioxan-2-yl, tetrahydrofuranyl, tetrahydrothiofuranyl,
2,3,3a,4,5,6,7,7a-octahydro-7,8,8-trimethyl-4,7-methanobenzofuran-2-yl,
1-ethoxyethyl, 1-(2-chloroethoxy)ethyl, 1-methyl-1-methoxyethyl,
1-methyl-1-benzyloxyethyl, 1-methyl-1-benzyloxy-2-fluoroethyl,
2,2,2-trichloroethyl, 2-trimethylsilylethyl,
2-(phenylselenyl)ethyl, t-butyl, allyl, p-chlorophenyl,
p-methoxyphenyl, 2,4-dinitrophenyl, benzyl (Bn), p-methoxybenzyl,
3,4-dimethoxybenzyl, o-nitrobenzyl, p-nitrobenzyl, p-halobenzyl,
2,6-dichlorobenzyl, p-cyanobenzyl, p-phenylbenzyl, 2-picolyl,
4-picolyl, 3-methyl-2-picolyl N-oxido, diphenylmethyl,
p,p'-dinitrobenzhydryl, 5-dibenzosuberyl, triphenylmethyl,
.alpha.-naphthyldiphenylmethyl, p-methoxyphenyldiphenylmethyl,
di(p-methoxyphenyl)phenylmethyl, tri(4-methoxyphenyl)methyl,
4-(4'-bromophenacyloxyphenyl)diphenylmethyl,
4,4',4''-tris(4,5-dichlorophthalimidophenyl)methyl,
4,4',4''-tris(levulinoyloxyphenyl)methyl,
4,4',4''-tris(benzoyloxyphenyl)methyl,
3-(imidazol-1-yl)bis(4',4''-dimethoxyphenyl)methyl,
1,1-bis(4-methoxyphenyl)-1'-pyrenylmethyl, 9-anthryl,
9-(9-phenyl)xanthenyl, 9-(9-phenyl-10-oxo)anthryl,
1,3-benzodithiolan-2-yl, benzisothiazolyl S,S-dioxido,
trimethylsilyl (TMS), triethylsilyl (TES), triisopropylsilyl
(TIPS), dimethylisopropylsilyl (IPDMS), diethylisopropylsilyl
(DEIPS), dimethylthexylsilyl, 1-butyldimethylsilyl (TBDMS),
t-butyldiphenylsilyl (TBDPS), tribenzylsilyl, tri-p-xylylsilyl,
triphenylsilyl, diphenylmethylsilyl (DPMS),
t-butylhnethoxyphenylsilyl (TBMPS), formate, benzoylformate,
acetate, chloroacetate, dichloroacetate, trichloroacetate,
trifluoroacetate, methoxyacetate, triphenylmethoxyacetate,
phenoxyacetate, p-chlorophenoxyacetate, 3-phenylpropionate,
4-oxopentanoate (levulinate), 4,4-(ethylenedithio)pentanoate
(levulinoyldithioacetal), pivaloate, adamantoate, crotonate,
4-methoxycrotonate, benzoate, p-phenylbenzoate,
2,4,6-trimethylbenzoate (mesitoate), alkyl methyl carbonate,
9-fluorenylmethyl carbonate (Fmoc), alkyl ethyl carbonate, alkyl
2,2,2-trichloroethyl carbonate (Troc), 2-(trimethylsilyl)ethyl
carbonate (TMSEC), 2-(phenylsulfonyl) ethyl carbonate (Psec),
2-(triphenylphosphonio) ethyl carbonate (Peoc), alkyl isobutyl
carbonate, alkyl vinyl carbonate alkyl allyl carbonate, alkyl
p-nitrophenyl carbonate, alkyl benzyl carbonate, alkyl
p-methoxybenzyl carbonate, alkyl 3,4-dimethoxybenzyl carbonate,
alkyl o-nitrobenzyl carbonate, alkyl p-nitrobenzyl carbonate, alkyl
S-benzyl thiocarbonate, 4-ethoxy-1-napththyl carbonate, methyl
dithiocarbonate, 2-iodobenzoate, 4-azidobutyrate,
4-nitro-4-methylpentanoate, o-(dibromomethyl)benzoate,
2-formylbenzenesulfonate, 2-(methylthiomethoxy)ethyl,
4-(methylthiomethoxy)butyrate, 2-(methylthiomethoxymethyl)benzoate,
2,6-dichloro-4-methylphenoxyacetate,
2,6-dichloro-4-(1,1,3,3-tetramethylbutyl)phenoxyacetate,
2,4-bis(1,1-dimethylpropyl)phenoxyacetate, chlorodiphenylacetate,
isobutyrate, monosuccinoate, (E)-2-methyl-2-butenoate,
o-(methoxyacyl)benzoate, .alpha.-naphthoate, nitrate, alkyl
N,N,N',N'-tetramethylphosphorodiamidate, alkyl N-phenylcarbamate,
borate, dimethylphosphinothioyl, alkyl 2,4-dinitrophenylsulfenate,
sulfate, methanesulfonate (mesylate), benzylsulfonate, and tosylate
(Ts).
[0110] A "thiol protecting group" is well known in the art and
include those described in detail in Protecting Groups in Organic
Synthesis, T. W. Greene and P. G. M. Wuts, 3.sup.rd edition, John
Wiley & Sons, 1999, the entirety of which is incorporated
herein by reference. Examples of protected thiol groups further
include, but are not limited to, thioesters, carbonates, sulfonates
allyl thioethers, thioethers, silyl thioethers, alkyl thioethers,
arylalkyl thioethers, and alkyloxyalkyl thioethers. Examples of
ester groups include formates, acetates, proprionates, pentanoates,
crotonates, and benzoates. Specific examples of ester groups
include formate, benzoyl formate, chloroacetate, trifluoroacetate,
methoxyacetate, triphenylmethoxyacetate, p-chlorophenoxyacetate,
3-phenylpropionate, 4-oxopentanoate,
4,4-(ethylenedithio)pentanoate, pivaloate (trimethylacetate),
crotonate, 4-methoxy-crotonate, benzoate, p-benylbenzoate,
2,4,6-trimethylbenzoate. Examples of carbonates include
9-fluorenylmethyl, ethyl, 2,2,2-trichloroethyl,
2-(trimethylsilyl)ethyl, 2-(phenylsulfonyl)ethyl, vinyl, allyl, and
p-nitrobenzyl carbonate. Examples of silyl groups include
trimethylsilyl, triethylsilyl, t-butyldimethylsilyl,
t-butyldiphenylsilyl, triisopropylsilyl ether, and other
trialkylsilyl ethers. Examples of alkyl groups include methyl,
benzyl, p-methoxybenzyl, 3,4-dimethoxybenzyl, trityl, t-butyl, and
allyl ether, or derivatives thereof. Examples of arylalkyl groups
include benzyl, p-methoxybenzyl (MPM), 3,4-dimethoxybenzyl,
O-nitrobenzyl, p-nitrobenzyl, p-halobenzyl, 2,6-dichlorobenzyl,
p-cyanobenzyl, 2- and 4-picolyl ethers.
[0111] The term "amino acid" refers to a molecule containing both
an amino group and a carboxyl group. Amino acids include
alpha-amino acids and beta-amino acids, the structures of which are
depicted below. In certain embodiments, the amino acid is an alpha
amino acid. In certain embodiments, the amino acid is an unnatural
amino acid. In certain embodiments, the amino acid is a natural
amino acid. In certain embodiments, the amino acid is an unnatural
amino acid.
##STR00001##
[0112] Exemplary amino acids include, without limitation, natural
alpha amino acids such as D- and L-isomers of the 20 common
naturally occurring alpha amino acids found in peptides, u peptides
(e.g., A, R, N, C, D, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, V,
as provided in Table 1 depicted below), unnatural alpha-amino acids
(as depicted in Tables 2 and 3 below), natural beta-amino acids
(e.g., beta-alanine), and unnatural beta-amino acids.
[0113] Amino acids used in the construction of peptides of the
present invention may be prepared by organic synthesis, or obtained
by other routes, such as, for example, degradation of or isolation
from a natural source. In certain embodiments of the present
invention, the formula -[X.sub.AA]- or -[G]- corresponds to the
natural and/or unnatural amino acids having the following
formulae:
##STR00002##
wherein R and R' correspond a suitable amino acid side chain, as
defined below and herein, and R.sup.a is as defined below and
herein.
TABLE-US-00001 TABLE 1 Exemplary natural alpha-amino Amino acid
side chains acids R R' L-Alanine (A) --CH.sub.3 --H L-Arginine (R)
--CH.sub.2CH.sub.2CH.sub.2--NHC(.dbd.NH)NH.sub.2 --H L-Asparagine
(N) --CH.sub.2C(.dbd.O)NH.sub.2 --H L-Aspartic acid (D)
--CH.sub.2CO.sub.2H --H L-Cysteine (C) --CH.sub.2SH --H L-Glutamic
acid (E) --CH.sub.2CH.sub.2CO.sub.2H --H L-Glutamine (Q)
--CH.sub.2CH.sub.2C(.dbd.O)NH.sub.2 --H Glycine (G) --H --H
L-Histidine (H) --CH.sub.2-2-(1H-imidazole) --H L-Isoleucine (I)
-sec-butyl --H L-Leucine (L) -iso-butyl --H L-Lysine (K)
--CH.sub.2CH.sub.2CH.sub.2CH.sub.2NH.sub.2 --H L-Methionine (M)
--CH.sub.2CH.sub.2SCH.sub.3 --H L-Phenylalanine (F) --CH.sub.2Ph
--H L-Proline (P) -2-(pyrrolidine) --H L-Serine (S) --CH.sub.2OH
--H L-Threonine (T) --CH.sub.2CH(OH)(CH.sub.3) --H L-Tryptophan (W)
--CH.sub.2-3-(1H-indole) --H L-Tyrosine (Y)
--CH.sub.2-(p-hydroxyphenyl) --H L-Valine (V) -isopropyl --H
TABLE-US-00002 TABLE 2 Exemplary unnatural alpha-amino Amino acid
side chains acids R R' D-Alanine --H --CH.sub.3 D-Arginine --H
--CH.sub.2CH.sub.2CH.sub.2--NHC(.dbd.NH)NH.sub.2 D-Asparagine --H
--CH.sub.2C(.dbd.O)NH.sub.2 D-Aspartic --H --CH.sub.2CO.sub.2H acid
D-Cysteine --H --CH.sub.2SH D-Glutamic --H
--CH.sub.2CH.sub.2CO.sub.2H acid D-Glutamine --H
--CH.sub.2CH.sub.2C(.dbd.O)NH.sub.2 D-Histidine --H
--CH.sub.2-2-(1H-imidazole) D-Isoleucine --H -sec-butyl D-Leucine
--H -iso-butyl D-Lysine --H
--CH.sub.2CH.sub.2CH.sub.2CH.sub.2NH.sub.2 D-Methionine --H
--CH.sub.2CH.sub.2SCH.sub.3 D-Phenyl- --H --CH.sub.2Ph alanine
D-Proline --H -2-(pyrrolidine) D-Serine --H --CH.sub.2OH
D-Threonine --H --CH.sub.2CH(OH)(CH.sub.3) D-Tryptophan --H
--CH.sub.2-3-(1H-indole) D-Tyrosine --H
--CH.sub.2-(p-hydroxyphenyl) D-Valine --H -isopropyl Di-vinyl
--CH.dbd.CH.sub.2 --CH.dbd.CH.sub.2 Exemplary unnatural alpha-amino
acids R and R' are equal to: .alpha.-methyl-Alanine --CH.sub.3
--CH.sub.3 (Aib) .alpha.-methyl-Arginine --CH.sub.3
--CH.sub.2CH.sub.2CH.sub.2--NHC(.dbd.NH)NH.sub.2
.alpha.-methyl-Asparagine --CH.sub.3 --CH.sub.2C(.dbd.O)NH.sub.2
.alpha.-methyl-Aspartic --CH.sub.3 --CH.sub.2CO.sub.2H acid
.alpha.-methyl-Cysteine --CH.sub.3 --CH.sub.2SH
.alpha.-methyl-Glutamic --CH.sub.3 --CH.sub.2CH.sub.2CO.sub.2H acid
.alpha.-methyl-Glutamine --CH.sub.3
--CH.sub.2CH.sub.2C(.dbd.O)NH.sub.2 .alpha.-methyl-Histidine
--CH.sub.3 --CH.sub.2-2-(1H-imidazole) .alpha.-methyl-Isoleucine
--CH.sub.3 -sec-butyl .alpha.-methyl-Leucine --CH.sub.3 -iso-butyl
.alpha.-methyl-Lysine --CH.sub.3
--CH.sub.2CH.sub.2CH.sub.2CH.sub.2NH.sub.2
.alpha.-methyl-Methionine --CH.sub.3 --CH.sub.2CH.sub.2SCH.sub.3
.alpha.-methyl-Phenyl- --CH.sub.3 --CH.sub.2Ph alanine
.alpha.-metlyl-Proline --CH.sub.3 -2-(pyrrolidine)
.alpha.-methyl-Serine --CH.sub.3 --CH.sub.2OH
.alpha.-methyl-Threonine --CH.sub.3 --CH.sub.2CH(OH)(CH.sub.3)
.alpha.-methyl-Tryptophan --CH.sub.3 --CH.sub.2-3-(1H-indole)
.alpha.-methyl-Tyrosine --CH.sub.3 --CH.sub.2-(p-hydroxyphenyl)
.alpha.-methyl-Valine --CH.sub.3 -isopropyl Di-vinyl
--CH.dbd.CH.sub.2 --CH.dbd.CH.sub.2 Norleucine --H
--CH.sub.2CH.sub.2CH.sub.2CH.sub.3
TABLE-US-00003 TABLE 3 Exemplary unnatural Amino acid side chains
alpha-amino acids R and R' is equal to hydrogen or --CH.sub.3, and:
Terminally unsaturated
--(CH.sub.2).sub.g--S--(CH.sub.2).sub.gCH.dbd.CH.sub.2, alpha-amino
acids and --(CH.sub.2).sub.g--O--(CH.sub.2).sub.gCH.dbd.CH.sub.2,
bis alpha-amino acids
--(CH.sub.2).sub.g--NH--(CH.sub.2).sub.gCH.dbd.CH.sub.2, (e.g.,
modified cysteine,
--(CH.sub.2).sub.g--(C.dbd.O)--S--(CH.sub.2).sub.gCH.dbd.CH.sub.2,
modified lysine, modified
--(CH.sub.2).sub.g--(C.dbd.O)--O--(CH.sub.2).sub.gCH.dbd.CH.sub.2,
tryptophan, modified
--(CH.sub.2).sub.g--(C.dbd.O)--NH--(CH.sub.2).sub.gCH.dbd.CH.sub.2,
serine, modified
--CH.sub.2CH.sub.2CH.sub.2CH.sub.2--NH--(CH.sub.2).sub.gCH.dbd.CH.sub.2,
threonine, modified
--(C.sub.6H.sub.5)-p-O--(CH.sub.2).sub.gCH.dbd.CH.sub.2, proline,
modified --CH(CH.sub.3)--O--(CH.sub.2).sub.gCH.dbd.CH.sub.2,
histidine, modified --CH.sub.2CH(--O--CH.dbd.CH.sub.2)(CH.sub.3),
alanine, and the like),
-histidine-N((CH.sub.2).sub.gCH.dbd.CH.sub.2),
-tryptophan-N((CH.sub.2).sub.gCH.dbd.CH.sub.2), and
--(CH.sub.2).sub.g+1(CH.dbd.CH.sub.2), wherein: each instance of g
is, independently, 0 to 10. Exemplary unnatural alpha-amino acids
##STR00003## ##STR00004## ##STR00005## ##STR00006## ##STR00007##
##STR00008## ##STR00009## ##STR00010## ##STR00011## ##STR00012##
##STR00013## ##STR00014##
[0114] There are many known unnatural amino acids any of which may
be included in the peptides of the present invention. See for
example, S. Hunt, The Non-Protein Amino Acids: In Chemistry and
Biochemistry of the Amino Acids, edited by G. C. Barrett, Chapman
and Hall, 1985. Some examples of unnatural amino acids are
4-hydroxyproline, desmosine, gamma-aminobutyric acid,
beta-cyanoalanine, norvaline,
4-(E)-butenyl-4(R)-methyl-N-methyl-L-threonine, N-methyl-L-leucine,
1-amino-cyclopropanecarboxylic acid,
1-amino-2-phenyl-cyclopropanecarboxylic acid,
1-amino-cyclobutanecarboxylic acid, 4-amino-cyclopentenecarboxylic
acid, 3-amino-cyclohexanecarboxylic acid, 4-piperidylacetic acid,
4-amino-1-methylpyrrole-2-carboxylic acid, 2,4-diaminobutyric acid,
2,3-diaminopropionic acid, 2,4-diaminobutyric acid,
2-aminoheptanedioic acid, 4-(aminomethyl)benzoic acid,
4-aminobenzoic acid, ortho-, meta- and para-substituted
phenylalanines (e.g., substituted with --C(.dbd.O)C.sub.6H.sub.5;
--CF.sub.3; --CN; -halo; --NO.sub.2; CH.sub.3), disubstituted
phenylalanines, substituted tyrosines (e.g., further substituted
with --C(.dbd.O)C.sub.6H.sub.5; --CF.sub.3; --CN; -halo;
--NO.sub.2; CH.sub.3), and statine. Additionally, the amino acids
suitable for use in the present invention may be derivatized to
include amino acid residues that are hydroxylated, phosphorylated,
sulfonated, acylated, and glycosylated, to name a few.
[0115] The term "amino acid side chain" refers to a group attached
to the alpha- or beta-carbon of an amino acid. A "suitable amino
acid side chain" includes, but is not limited to, any of the
suitable amino acid side chains as defined above, and as provided
in Tables 1 to 3.
[0116] For example, suitable amino acid side chains include methyl
(as the alpha-amino acid side chain for alanine is methyl),
4-hydroxyphenylmethyl (as the alpha-amino acid side chain for
tyrosine is 4-hydroxyphenylmethyl) and thiomethyl (as the
alpha-amino acid side chain for cysteine is thiomethyl), etc. A
"terminally unsaturated amino acid side chain" refers to an amino
acid side chain bearing a terminal unsaturated moiety, such as a
substituted or unsubstituted, double bond (e.g., olefinic) or a
triple bond (e.g., acetylenic), that participates in crosslinking
reaction with other terminal unsaturated moieties in the
polypeptide chain. In certain embodiments, a "terminally
unsaturated amino acid side chain" is a terminal olefinic amino
acid side chain. In certain embodiments, a "terminally unsaturated
amino acid side chain" is a terminal acetylenic amino acid side
chain. In certain embodiments, the terminal moiety of a "terminally
unsaturated amino acid side chain" is not further substituted.
Terminally unsaturated amino acid side chains include, but are not
limited to, side chains as depicted in Table 3.
[0117] A "peptide" or "polypeptide" comprises a polymer of amino
acid residues linked together by peptide (amide) bonds. The
term(s), as used herein, refers to proteins, polypeptides, and
peptide of any size, structure, or function. Typically, a peptide
or polypeptide will be at least three amino acids long. A peptide
or polypeptide may refer to an individual protein or a collection
of proteins. Inventive proteins preferably contain only natural
amino acids, although non-natural amino acids (i.e., compounds that
do not occur in nature but that can be incorporated into a
polypeptide chain) and/or amino acid analogs as are known in the
art may alternatively be employed. One or more of the amino acids
in a peptide or polypeptide may be modified, for example, by the
addition of a chemical entity such as a carbohydrate group, a
hydroxyl group, a phosphate group, a farnesyl group, an isofarnesyl
group, a fatty acid group, a linker for conjugation,
functionalization, or other modification. A peptide or polypeptide
may also be a single molecule or may be a multi-molecular complex,
such as a protein. A peptide or polypeptide may be just a fragment
of a naturally occurring protein or peptide. A peptide or
polypeptide may be naturally occurring, recombinant, or synthetic,
or any combination thereof.
[0118] As used herein "dipeptide" refers to two covalently linked
amino acids.
[0119] As used herein, the term "salt" or "pharmaceutically
acceptable salt" refers to those salts which are, within the scope
of sound medical judgment, suitable for use in contact with the
tissues of humans and lower 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, Berge et al.,
describes pharmaceutically acceptable salts in detail in J.
Pharmaceutical Sciences (1977) 66:1-19. Pharmaceutically acceptable
salts of the compounds of this invention include those derived from
suitable inorganic and organic acids and bases. Examples of
pharmaceutically acceptable, nontoxic acid addition salts are salts
of an amino group formed with inorganic acids such as hydrochloric
acid, hydrobromic acid, phosphoric acid, sulfuric acid and
perchloric acid or with organic acids such as acetic acid, oxalic
acid, maleic acid, tartaric acid, citric acid, succinic acid or
malonic acid or by using other methods used in the art such as ion
exchange. Other pharmaceutically acceptable salts include adipate,
alginate, ascorbate, aspartate, benzenesulfonate, benzoate,
bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate,
cyclopentanepropionate, digluconate, dodecylsulfate,
ethanesulfonate, formate, fumarate, glucoheptonate,
glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate,
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,
p-toluenesulfonate, undecanoate, valerate salts, and the like.
Salts derived from appropriate bases include alkali metal, alkaline
earth metal, ammonium and N.sup.+(C.sub.1-4alkyl).sub.4 salts.
Representative alkali or alkaline earth metal salts include sodium,
lithium, potassium, calcium, magnesium, and the like. Further
pharmaceutically acceptable salts include, when appropriate,
quaternary salts, e.g., cationic trisubstituted amino groups, e.g.,
as defined herein.
[0120] The following definitions are more general terms used
throughout the present application.
[0121] The term "subject," as used herein, refers to any animal. In
certain embodiments, the subject is a mammal. In certain
embodiments, the term "subject", as used herein, refers to a human
(e.g., a man, a woman, or a child).
[0122] The terms "administer," "administering," or
"administration," as used herein refers to implanting, absorbing,
ingesting, injecting, or inhaling, the inventive polypeptide or
compound.
[0123] The terms "treat" or "treating," as used herein, refers to
partially or completely alleviating, inhibiting, ameliorating,
and/or relieving the disease or condition from which the subject is
suffering.
[0124] The terms "effective amount" and "therapeutically effective
amount," as used herein, refer to the amount or concentration of a
biologically active agent conjugated to a stitched or stapled
polypeptide as described herein, or amount or concentration of a
stitched or stapled polypeptide as described herein, that, when
administered to a subject, is effective to at least partially treat
a condition from which the subject is suffering.
[0125] As used herein, when two entities are "conjugated" to one
another they are linked by a direct or indirect covalent or
non-covalent interaction. In certain embodiments, the association
is covalent. In other embodiments, the association is non-covalent.
Non-covalent interactions include hydrogen bonding, van der Waals
interactions, hydrophobic interactions, magnetic interactions, and
electrostatic interactions. An indirect covalent interaction is
when two entities are covalently connected, optionally through a
linker group.
[0126] As used herein, a "biologically active agent" or
"therapeutically active agent" refers to any substance used as a
medicine for treatment, prevention, delay, reduction or
amelioration of a disease, condition, or disorder, and refers to a
substance that is useful for therapy, including prophylactic and
therapeutic treatment. A biologically active agent also includes a
compound that increases the effect or effectiveness of another
compound, for example, by enhancing potency or reducing adverse
effects of the other compound.
[0127] In certain embodiments, a biologically active agent is an
anti-cancer agent, antibiotic, anti-viral agent, anti-HIV agent,
anti-parasite agent, anti-protozoal agent, anesthetic,
anticoagulant, inhibitor of an enzyme, steroidal agent, steroidal
or non-steroidal anti-inflammatory agent, antihistamine,
immunosuppressant agent, anti-neoplastic agent, antigen, vaccine,
antibody, decongestant, sedative, opioid, analgesic, anti-pyretic,
birth control agent, hormone, prostaglandin, progestational agent,
anti-glaucoma agent, ophthalmic agent, anti-cholinergic, analgesic,
anti-depressant, anti-psychotic, neurotoxin, hypnotic,
tranquilizer, anti-convulsant, muscle relaxant, anti-Parkinson
agent, anti-spasmodic, muscle contractant, channel blocker, miotic
agent, anti-secretory agent, anti-thrombotic agent, anticoagulant,
anti-cholinergic, .beta.-adrenergic blocking agent, diuretic,
cardiovascular active agent, vasoactive agent, vasodilating agent,
anti-hypertensive agent, angiogenic agent, modulators of
cell-extracellular matrix interactions (e.g. cell growth inhibitors
and anti-adhesion molecules), or inhibitors/intercalators of DNA.
RNA, protein-protein interactions, protein-receptor interactions,
etc.
[0128] Exemplary biologically active agents include, but are not
limited to, small organic molecules such as drug compounds,
peptides, proteins, carbohydrates, monosaccharides,
oligosaccharides, polysaccharides, nucleoproteins, mucoproteins,
lipoproteins, synthetic polypeptides or proteins, small molecules
linked to proteins, glycoproteins, steroids, nucleic acids, DNAs,
RNAs, nucleotides, nucleosides, oligonucleotides, antisense
oligonucleotides, lipids, hormones, vitamins, and cells. In certain
embodiments, the biologically active agent is a cell. Exemplary
cells include immune system cells (e.g., mast, lymphocyte, plasma
cell, macrophage, dendritic cell, neutrophils, eosinophils),
connective tissue cells (e.g., blood cells, erythrocytes,
leucocytes, megakarocytes, fibroblasts, osteoclasts), stem cells
(e.g., embryonic stem cells, adult stem cells), bone cells, glial
cells, pancreatic cells, kidney cells, nerve cells, skin cells,
liver cells, muscle cells, adipocytes, Schwann cells, Langerhans
cells, as well as (micro)-tissues such as the Islets of
Langerhans.
[0129] In certain embodiments, the biologically active agent is a
small organic molecule. In certain embodiments, a small organic
molecule is non-peptidic. In certain embodiments, a small organic
molecule is non-oligomeric. In certain embodiments, a small organic
molecule is a natural product or a natural product-like compound
having a partial structure (e.g., a substructure) based on the full
structure of a natural product. Exemplary natural products include
steroids, penicillins, prostaglandins, venoms, toxins, morphine,
paclitaxel (Taxol), morphine, cocaine, digitalis, quinine,
tubocurarine, nicotine, muscarine, artemisinin, cephalosporins,
tetracyclines, aminoglycosides, rifamycins, chloramphenicol,
asperlicin, lovastatin, ciclosporin, curacin A, eleutherobin,
discodermolide, bryostatins, dolostatins, cephalostatins,
antibiotic peptides, epibatidine, .alpha.-bungarotoxin,
tetrodotoxin, teprotide, and neurotoxins from Clostridium
botulinum. In certain embodiments, a small organic molecule is a
drug approved by the Food and Drugs Administration as provided in
the Code of Federal Regulations (CFR).
[0130] As used herein, a "label" refers to a moiety that has at
least one element, isotope, or functional group incorporated into
the moiety which enables detection of the inventive polypeptide to
which the label is attached. Labels can be directly attached (ie.
via a bond) or can be attached by a linker (e.g., such as, for
example, a cyclic or acyclic, branched or unbranched, substituted
or unsubstituted alkylene; cyclic or acyclic, branched or
unbranched, substituted or unsubstituted alkenylene; cyclic or
acyclic, branched or unbranched, substituted or unsubstituted
alkynylene; cyclic or acyclic, branched or unbranched, substituted
or unsubstituted heteroalkylene; cyclic or acyclic, branched or
unbranched, substituted or unsubstituted heteroalkenylene; cyclic
or acyclic, branched or unbranched, substituted or unsubstituted
heteroalkynylene; substituted or unsubstituted arylene; substituted
or unsubstituted heteroarylene; or substituted or unsubstituted
acylene, or any combination thereof, which can make up a linker).
It will be appreciated that the label may be attached to the
inventive polypeptide at any position that does not interfere with
the biological activity or characteristic of the inventive
polypeptide that is being detected.
[0131] In general, a label can fall into any one (or more) of five
classes; a) a label which contains isotopic moieties, which may be
radioactive or heavy isotopes, including, but not limited to,
.sup.2H, .sup.3H, .sup.13C, .sup.14C, .sup.15N, .sup.31P, .sup.32P,
.sup.35S, .sup.67Ga, .sup.99mTc (Tc-99m). .sup.111In, .sup.123I,
.sup.125I, .sup.169Yb, and .sup.186Re; b) a label which contains an
immune moiety, which may be antibodies or antigens, which may be
bound to enzymes (e.g., such as horseradish peroxidase); c) a label
which is a colored, luminescent, phosphorescent, or fluorescent
moieties (e.g., such as the fluorescent label FITC); d) a label
which has one or more photoaffinity moieties; and e) a label which
has a ligand moiety with one or more known binding partners (such
as biotin-streptavidin. FK506-FKBP, etc.). Any of these type of
labels as described above may also be referred to as "diagnostic
agents" as defined herein.
[0132] In certain embodiments, such as in the identification of a
biological target, label comprises a radioactive isotope,
preferably an isotope which emits detectable particles, such as
.beta. particles. In certain embodiments, the label comprises one
or more photoaftinity moieties for the direct elucidation of
intermolecular interactions in biological systems. A variety of
known photophores can be employed, most relying on photoconversion
of diazo compounds, azides, or diazirines to nitrenes or carbenes
(see. Bayley, H., Photogenerated Reagents in Biochemistry and
Molecular Biology (1983), Elsevier, Amsterdam, the entire contents
of which are incorporated herein by reference). In certain
embodiments of the invention, the photoaffinity labels employed are
o-, m- and p-azidobenzoyls, substituted with one or more halogen
moieties, including, but not limited to
4-azido-2,3,5,6-tetrafluorobenzoic acid.
[0133] In certain embodiments, the label comprises one or more
fluorescent moieties. In certain embodiments, the label is the
fluorescent label FITC. In certain embodiments, the label comprises
a ligand moiety with one or more known binding partners. In certain
embodiments, the label comprises the ligand moiety biotin.
[0134] As used herein, a "diagnostic agent" refers to imaging
agents. Exemplary imaging agents include, but are not limited to,
those used in positron emissions tomography (PET), computer
assisted tomography (CAT), single photon emission computerized
tomography, x-ray, fluoroscopy, and magnetic resonance imaging
(MRI); anti-emetics; and contrast agents. Exemplary diagnostic
agents include but are not limited to, fluorescent moieties,
luminescent moieties, magnetic moieties; gadolinium chelates (e.g.,
gadolinium chelates with DTPA, DTPA-BMA, DOTA and HP-DO3A), iron
chelates, magnesium chelates, manganese chelates, copper chelates,
chromium chelates, iodine-based materials useful for CAT and x-ray
imaging, and radionuclides. Suitable radionuclides include, but are
not limited to, .sup.123I. .sup.125I, .sup.130I, .sup.131I,
.sup.133I, .sup.135I, .sup.47Sc, .sup.72As, .sup.72Se, .sup.90Y,
.sup.88Y, .sup.97Ru, .sup.100Pd, .sup.101mRh, .sup.119Sb,
.sup.128Ba, .sup.197Hg, .sup.211At, .sup.212Bi, .sup.212Pb,
.sup.109Pd, .sup.111In, .sup.67Ga, .sup.68Ga, .sup.67Cu, .sup.75Br,
.sup.77Br, .sup.99mTc, .sup.14C, .sup.13N, .sup.15O, .sup.32P,
.sup.33P, and .sup.18F. Fluorescent and luminescent moieties
include, but are not limited to, a variety of different organic or
inorganic small molecules commonly referred to as "dyes," "labels,"
or "indicators." Examples include, but are not limited to,
fluorescein, rhodamine, acridine dyes, Alexa dyes, cyanine dyes,
etc. Fluorescent and luminescent moieties may include a variety of
naturally occurring proteins and derivatives thereof, e.g.,
genetically engineered variants. For example, fluorescent proteins
include green fluorescent protein (GFP), enhanced GFP, red, blue,
yellow, cyan, and sapphire fluorescent proteins, reef coral
fluorescent protein, etc. Luminescent proteins include luciferase,
aequorin and derivatives thereof. Numerous fluorescent and
luminescent dyes and proteins are known in the art (see, e.g., U.S.
Patent Publication 2004/0067503; Valeur, B., "Molecular
Fluorescence: Principles and Applications," John Wiley and Sons,
2002; and Handbook of Fluorescent Probes and Research Products,
Molecular Probes, 9.sup.th edition, 2002).
Detailed Description of Certain Embodiments of the Invention
[0135] In one aspect, the disclosure provides stabilized stapled
peptides with a proline derivative for stapling at the N-terminus
of the helix and methods for increasing the stability of peptides
using a proline-derivative for stapling. In some embodiments, the
disclosure provides peptides with increased alpha-helicity and
methods for increasing the alpha-helicity of peptides. In some
embodiments, the disclosure provides stapled peptides with a
proline derivative at the N-terminus of the alpha-helix and methods
for providing such stapled peptides. In some embodiments, the
disclosure provides proline-locked stapled peptides and methods for
providing proline-locked stapled peptides.
[0136] In one aspect, the disclosure provides peptides that are
stabilized by stapling the peptide at the N-terminus of an
alpha-helix through the introduction of a proline-containing staple
or a proline-locked staple. It was surprisingly found that proline
could be used to stabilize peptides. The finding was surprising at
least because proline is commonly considered an
.alpha.-helix-disrupting amino acid. In some embodiments, the
proline-locked stapled peptide includes a proline at position i
that is covalently connected with the alpha-carbon of a second
amino acid at position i+3. While alpha-helical peptides are
relatively stable once formed, initiation of alpha helix formation
is challenging because the attendant conformational ordering is
entropically expensive (J. Chem. Phys. 1959, 31, 526-535). As
provided herein, introducing a helix staple, such as a proline
staple or a proline-locked staple at the N-terminus of an alpha
helical peptide helps with the formation of, and further
stabilizes, an alpha-helix. Once a single turn of the .alpha.-helix
is formed, its downstream propagation can occur spontaneously,
provided that helix-disruption sequences are not present.
[0137] In one aspect, the disclosure provides a peptide stapling
system having helix-nucleating ability. In some embodiments, the
peptide stapling system is a peptide with a proline-derivative at
the N-terminus of the staple. In some embodiments, the peptide
stapling system is a proline-locked stapled peptide or "Pro-lock".
It should be appreciated that the peptide stabilized by a
proline-lock may be a peptide that is mostly in alpha-helical
conformation, or the peptide may be part of a larger protein that
includes one or more alpha-helical regions. In some embodiments,
the Pro-locked staple is located in the N-terminal region of a
peptide. In some embodiments, the proline of the Pro-locked staple
is located at the N-terminal position of the helix. In some
embodiments, the Pro-locked staple comprises a covalent bind
between a proline at position i and a second amino acid at position
i+3 in a peptide. It should be appreciated that homo-proline and
other unnatural cyclic amino acids, as described further herein,
can be used instead of proline in the proline locks. To facilitate
to covalent bond of the proline-lock, the proline comprises an
additional functional group that can undergo a reaction to for a
covalent bond. In some embodiments, the functional group is a
double bond (e.g., a vinyl group). In some embodiments, the
functional group is located at the alpha-carbon on the proline. In
some embodiments, the functional group is located on any position
on the proline ring.
[0138] In some embodiments, the amino acid at position i+3 is
serine, alanine, glycine, aspartic acid or glutamic acid. To
facilitate the formation of the covalent bond of the proline-lock
the amino acid at position i+3 may include an additional functional
group that can undergo a reaction to form a covalent bond. In some
embodiments, the additional functional group that can undergo a
reaction to form a covalent bond is located at the alpha carbon of
the second amino acid. In some embodiments, the group that can
undergo a reaction to form a covalent bond is part of the natural
side chain of the amino acid.
[0139] In some embodiments, the proline locked staple includes a
covalent binding between a proline at position i and an amino acid
located at position i+3. In some embodiments, the helix-nucleating
"staple" is formed between an N-terminal .alpha.-allylproline
(e.g., P.sub.R3) and an .alpha.-methyl, .alpha.-allylglycine
(S.sub.3) at positions i and i+3 in a peptide. In some embodiments,
the helix-nucleating "staple" is formed between
(R)--N-(Acetyl)-2-(2'-propenyl)proline ("P.sub.R3") or
(R)--N-[(9H-Fluoren-9-ylmethoxy)carbonyl]-2-(2'-propenyl)proline
and
(S)--N-[(9H-Fluoren-9-ylmethoxy)carbonyl]-2-(2'-propylenyl)alanine
at positions i and i+3 in a peptide.
[0140] The unnatural amino acids of the proline-lock can be
introduced into the peptide through peptide synthesis techniques as
described herein. In some embodiments, the amino acid sequence
including the proline lock is synthesized or prepared separately
and the amino acid sequence is coupled to a peptide to be
stabilized. Thus, in some embodiments, the disclosure provides a
method of increasing the stability and/or helicity of peptide that
include a step of coupling the peptide to an amino acid sequence
comprising a proline-locked staple.
[0141] The proline-locked peptides comprising the covalent bond may
be synthesized according to any of the methods disclosed herein. In
some embodiments, a crosslink between the proline with the
functional group and the amino acid at position i+3 is formed by
Grubb's catalyst. In some embodiments, a crosslink between the
proline with the functional group and the amino acid at position
i+3 is formed by ruthenium-mediated olefin metathesis. In some
embodiment, the Pro-locked stapled peptides are synthesized using
(R)--N-(Acetyl)-2-(2'-propenyl)proline and
(S)--N-[(9H-Fluoren-9-ylmethoxy)carbonyl]-2-(2'-propylenyl)alanine
as amino acid building blocks at position i and i+3, respectively,
allowing for the generation of a proline-locked stapled peptide. In
some embodiments, the peptides are subjected to ruthenium-mediated
olefin metathesis, resulting in formation of an exclusively cis
olefinic crosslink.
[0142] In some embodiments, the peptides provided herein comprise
stabilizing elements in addition to the proline-locked staple. In
some embodiments, the peptides comprise multiple pro-locked
staples. In some embodiments, the peptides comprise a Pro-locked
staples and a staple other than a Pro-locked staple. Peptide
staples other than Pro-locked staples are provided for instance in
WO2008/121767. In general, it has been shown that the pharmacologic
properties of .alpha.-helical peptides can be greatly improved
through the use of a hydrocarbon "staple" that enforces the
.alpha.-helical conformation of peptides (See e.g., Science, 2004,
305, 1466-1470). In some embodiments, the proline-locked staple and
a second staple connect at amino acid i+3 or overlap in amino acid
sequence. Thus, for instance, in addition to a proline-locked amino
staple between i and i+3, a peptide may have a second staple that
starts at position i+3 (e.g., between i+3 and i+7), or a second
staple that starts at position i+1 or i+2, and thus "overlaps" with
the proline-locked staple. Compared to stapled peptides disclosed
previously, the Pro-locked stapled peptides disclosed herein have
the extra advantage that they can be used even when a crosslink
cannot be introduced into any position of an .alpha.-helix other
than at its N-terminus.
[0143] In some embodiments, the peptides comprising the
proline-locked staples may have additional stabilizing elements. In
some embodiments, the peptides have an amino acid composition
allowing for helix stabilizing salt bridges. In some embodiments,
the peptides have been modified to covalently connect the salt
bridges. In some embodiments, the peptides have functional groups
that stabilize the helix dipole.
[0144] In one aspect, the disclosure provides peptides with an
improved ability to cross cell membranes. An increased ability of
peptides to cross the cell membrane is correlated with an increase
in the capacity of the peptide to acts as a therapeutic. Peptides
often have difficulty crossing (cell) membranes because of the
availability of unpaired hydrogen bonds in the peptide (e.g., in
the peptide backbone). The disclosure provides methods for
minimizing the availability of unpaired hydrogen bonds in a peptide
by binding N-terminal amide protons tightly into hydrogen-bonding
interactions. As disclosed herein, locating an amino acid with a
side chain that can interact with amide protons at the N-terminal
side of an alpha helix minimizes the availability of unwanted amide
protons. The undesired free N-terminal amide proteins are "masked"
thereby minimizing any undesired interactions with other agents
(e.g., the cell membrane or components thereof). In some
embodiments, the amino acid with the side chain that can interact
with amide protons is modified to increase the available hydrogen
binders. For instance, the disclosure provides a modified arginine
with increased ability to mask N-terminal amide protons by
providing additional hydrogen-bonding interaction partners.
[0145] In one aspect, the disclosure provides methods and
compositions for improving pharmacological properties of peptides.
In some embodiments, the disclosure provides peptides with improved
capacity for passive cell penetration (e.g., by improved capacity
for passive cell membrane traversal). In some embodiments, the
disclosure provides methods for improving the passive cell
penetration of peptides. In some embodiments, the disclosure
provides peptides with minimized unwanted N-terminal amide N--H
proton interactions. In some embodiments, the disclosure provides
methods for generating peptides with minimized unwanted amide N--H
proton interactions. Decreasing the availability of freely
available hydrogen bonds in N--H protons will minimize the
interactions the peptide will have with third parties (e.g., a
membrane or membrane components) allowing for better traversal of
the membrane. In some embodiments, the disclosure provides peptides
with improved passive cell penetration and minimized amide N--H
proton interactions. In some embodiments, the disclosure provides
methods for improving the passive cell penetration of peptides by
minimizing amide N--H proton interactions. In some embodiments, the
peptides with improved passive cell penetration are proline-locked
staple peptides. In some embodiments, the peptides with improved
passive cell penetration have minimized amide N--H bond
interactions by "cloaking" or "masking" the amide N--H's. In some
embodiments, the peptides with minimized amide N--H interactions
have minimized the interactions of amide N--H's located at the
N-terminus of the peptide. In some embodiments, the peptides with
improved passive cell penetration are proline-locked staple
peptides with minimized amide N--H bond interactions. In some
embodiments, the amide N--H interactions are minimized by
introducing an amino acid with a negatively charged side chain
and/or electron donor on its side chain on the N-terminal side of
the polypeptide. In some embodiments, the amide N--H interactions
are minimized by introducing an amino acid with a negatively
charged side chain and/or electron donor on its side chain on the
N-terminal side of a helix within the polypeptide. In some
embodiments, the amino acid allowing for the minimization of N--H
proton interactions is serine, threonine, aspartic acid, glutamic
acid or asparagine. In some embodiments, the amino acid is has been
modified to increase the number of electron donating groups on the
side chain. In some embodiments, the amino acid is a modified
asparagine as disclosed herein (also called "asparagine
surrogate").
[0146] In one aspect, the disclosure provides stabilized peptides
that nucleate .alpha.-helix formation through a proline-locked
staple while also binding N-terminal amide protons tightly through
hydrogen-bonding interactions. As provided herein, the stabilized
peptides with amide proton binding can have a proline at position i
that is covalently coupled to an amino acid at position i+3, and a
modified arginine at position i-1 which interacts with the amide
protons of the peptide backbone of the amino acids at position i+1
and i+2
[0147] Promotion of .alpha.-helix stability and masking of
N-terminal N--H's improve the biophysical and pharmacological
properties of a peptide, including oral bioavailability, binding
affinity for a receptor, resistance to proteolytic degradation,
cell-penetration, and reduction in the rate of renal clearance. The
proline-locked stapled peptides provided herein are strong
nucleators of .alpha.-helix formation, as shown by the
exceptionally high helicity of peptides bearing the proline-lock.
In addition, the peptides provided herein, through masking the
N-terminal amide protons, further enhance the ability of the
peptides to cross cell membranes. Thus, the Pro-locked stapled
peptides provided herein can be used in targeting previously
"undruggable" intracellular therapeutic targets.
Polypeptides and Precursors
[0148] Various stapled and stitched polypeptides are described
herein which include proline-locked staple. "Peptide stapling" is a
term coined from a synthetic methodology wherein two
olefin-containing sidechains present in a polypeptide chain are
covalently joined (e.g., "stapled together") using a ring-closing
metathesis (RCM) reaction to form a cross-linked ring (see, the
cover art for J. Org. Chem. (2001) vol. 66, issue 16 describing
metathesis-based crosslinking of alpha-helical peptides; Blackwell
et al.; Angew Chem. Int. Ed. (1994) 37:3281). However, the term
"peptide stapling." as used herein, encompasses the joining of two
double bond-containing sidechains, two triple bond-containing
sidechains, or one double bond-containing and one triple
bond-containing side chain, which may be present in a polypeptide
chain, using any number of reaction conditions and/or catalysts to
facilitate such a reaction, to provide a singly "stapled"
polypeptide. Additionally, the term "peptide stitching," as used
herein, refers to multiple and tandem "stapling" events in a single
polypeptide chain to provide a "stitched" (or multiply stapled)
polypeptide.
[0149] The stapling or stitching contemplated herein involves
contact of a precursor "unstapled" or "unstitched" polypeptide with
a ring closing metathesis (RCM) catalyst to provide a stapled or
stitched polypeptide. One of ordinary skill in the art will realize
that a variety of RCM catalysts can be utilized. In certain
embodiments, the RCM catalyst is a tungsten (W), molybdenum (Mo),
or ruthenium (Ru) catalyst. In certain embodiments, the RCM
catalyst is a ruthenuim catalyst. Exemplary RCM catalysts
employable by the above synthetic method may be described in Grubbs
et al., Acc. Chem. Res. 1995, 28, 446-452; U.S. Pat. No. 5,811,515;
Schrock et al., Organometallics (1982) 1 1645; Gallivan et al.,
Tetrahedron Letters (2005) 46:2577-2580; Furstner et al., J. Am.
Chem. Soc. (1999) 121:9453; and Chem. Eur. J. (2001) 7:5299; the
entire contents of each of which are incorporated herein by
reference.
[0150] Thus, in one aspect, provided is a precursor polypeptide of
Formula (P-I):
##STR00015##
or a salt or stereoisomer thereof; wherein:
[0151] each instance of K and L, is, independently, a bond or a
group consisting of one or more combinations of substituted or
unsubstituted alkylene; substituted or unsubstituted alkenylene;
substituted or unsubstituted alkynylene; substituted or
unsubstituted heteroalkylene; substituted or unsubstituted
heteroalkenylene; substituted or unsubstituted heteroalkynylene;
substituted or unsubstituted heterocyclene, substituted or
unsubstituted carbocyclene, substituted or unsubstituted arylene;
substituted or unsubstituted heteroarylene;
[0152] R.sup.a is hydrogen; substituted or unsubstituted aliphatic;
substituted or unsubstituted heteroaliphatic; substituted or
unsubstituted aryl; substituted or unsubstituted heteroaryl;
substituted or unsubstituted acyl; a resin; an amino protecting
group; a label optionally joined by a linker, wherein the linker is
a group consisting of one or more combinations of substituted or
unsubstituted alkylene; substituted or unsubstituted alkenylene;
substituted or unsubstituted alkynylene; substituted or
unsubstituted heteroalkylene; substituted or unsubstituted
heteroalkenylene; substituted or unsubstituted heteroalkynylene;
substituted or unsubstituted carbocyclene; substituted or
unsubstituted heterocyclene; substituted or unsubstituted arylene;
or substituted or unsubstituted heteroarylene:
[0153] R.sup.b is, --R.sup.B, --OR.sup.B, --N(R.sup.B).sub.2, or
--SR.sup.B, wherein each instance of R.sup.B is, independently,
hydrogen, substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; a resin; a suitable hydroxyl, amino or thiol
protecting group; or two R.sup.B groups together form a substituted
or unsubstituted 5 to 6 membered heterocyclic or heteroaromatic
ring;
[0154] each instance of R.sup.c, is, independently, hydrogen;
substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; substituted or unsubstituted hydroxyl;
substituted or unsubstituted thiol; substituted or unsubstituted
amino; cyano; isocyano; halo; or nitro;
[0155] each instance of R.sup.d is, independently, hydrogen;
substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; or an amino protecting group;
[0156] each instance of R.sup.e is, independently, hydrogen;
substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; substituted or unsubstituted hydroxyl;
substituted or unsubstituted thiol; substituted or unsubstituted
amino; cyano; isocyano; halo; or nitro;
[0157] each instance of G is, independently, a natural or unnatural
amino acid or a group of the formula:
##STR00016##
wherein:
[0158] n is 1, 2, or 3; and
[0159] each instance of R.sup.1 and R.sup.2 is independently
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; substituted or unsubstituted hydroxyl;
substituted or unsubstituted thiol; substituted or unsubstituted
amino; or halo, or R.sup.1 and R.sup.2 are joined to form a
carbocyclic or heterocyclic ring;
[0160] each instance of R.sup.3 and R.sup.4 is, independently,
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; a hydroxyl protecting group when
attached to an oxygen atom, or an amino protecting group when
attached to a nitrogen atom, or two R.sup.3 groups when attached to
a nitrogen atom are joined to form a heterocyclic ring;
[0161] each instance of R.sup.q is independently halogen, --CN,
--NO.sub.2, --N.sub.3, optionally substituted alkyl, optionally
substituted alkenyl, optionally substituted alkynyl, optionally
substituted carbocyclyl, optionally substituted phenyl, optionally
substituted heterocyclyl, optionally substituted heteroaryl,
optionally substituted alkoxy, an optionally substituted amino
group, or optionally substituted acyl;
[0162] q1 is 0, 1, 2, 3, or 4;
[0163] each instance of X.sub.AA is, independently, a natural or
unnatural amino acid:
[0164] j is, independently, an integer between 1 to 10,
inclusive;
[0165] each instance of p is, independently, 1 or 2;
[0166] each instance of v is, independently, 0 or 1;
[0167] each instance of w and z is, independently, an integer
between 0 and 100, inclusive;
[0168] each instance of x is, independently, 0, 1, 2, or 3;
[0169] y is, independently, an integer of 1 to 8, inclusive;
and
[0170] corresponds to a double or triple bond.
[0171] In certain embodiments, the corresponds to a double bond. In
certain embodiments, the corresponds to a triple bond.
[0172] In certain embodiments, the polypeptide of Formula (P-I) is
of the formula:
##STR00017##
or a salt or stereoisomer thereof.
[0173] In certain embodiments, the polypeptide of Formula (P-I) is
any one of the formula:
##STR00018##
or a salt or stereoisomer thereof.
[0174] In certain embodiments, the polypeptide of Formula (P-I) is
any one of the formula:
##STR00019##
or a salt or stereoisomer thereof.
[0175] In certain embodiments, the polypeptide of Formula (P-I) is
of the formula:
##STR00020##
or a salt stereoisomer thereof.
[0176] In certain embodiments, the polypeptide of Formula (P-I) is
any one of the formulae:
##STR00021## ##STR00022##
or a salt or stereoisomer thereof.
[0177] In certain embodiments, the polypeptide of Formula (P-I) is
any one of the formulae:
##STR00023## ##STR00024##
or a salt or stereoisomer thereof.
[0178] In certain embodiments, the precursor polypeptide of Formula
(P-I), upon contact with a ring closing metathesis catalyst,
generates a stapled polypeptide of Formula (I):
##STR00025##
or a salt or stereoisomer thereof; wherein:
[0179] each instance of K and L, is, independently, a bond or a
group consisting of one or more combinations of substituted or
unsubstituted alkylene; substituted or unsubstituted alkenylene;
substituted or unsubstituted alkynylene; substituted or
unsubstituted heteroalkylene; substituted or unsubstituted
heteroalkenylene; substituted or unsubstituted heteroalkynylene;
substituted or unsubstituted heterocyclene, substituted or
unsubstituted carbocyclene, substituted or unsubstituted arylene;
substituted or unsubstituted heteroarylene;
[0180] R.sup.a is hydrogen; substituted or unsubstituted aliphatic;
substituted or unsubstituted heteroaliphatic; substituted or
unsubstituted aryl; substituted or unsubstituted heteroaryl;
substituted or unsubstituted acyl; a resin; an amino protecting
group; a label optionally joined by a linker, wherein the linker is
a group consisting of one or more combinations of substituted or
unsubstituted alkylene; substituted or unsubstituted alkenylene;
substituted or unsubstituted alkynylene; substituted or
unsubstituted heteroalkylene; substituted or unsubstituted
heteroalkenylene; substituted or unsubstituted carbocyclene;
substituted or unsubstituted heterocyclene; substituted or
unsubstituted arylene; or substituted or unsubstituted
heteroarylene;
[0181] R.sup.b is, --R.sup.B, --OR.sup.B, --N(R.sup.B).sub.2, or
--SR.sup.B, wherein each instance of R.sup.B is, independently,
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; a resin; a suitable hydroxyl, amino or thiol
protecting group; or two R.sup.B groups together form a substituted
or unsubstituted 5- to 6-membered heterocyclic or heteroaromatic
ring;
[0182] each instance of R.sup.KL is, independently, hydrogen;
substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; substituted or unsubstituted hydroxyl;
substituted or unsubstituted thiol; substituted or unsubstituted
amino; azido; cyano; isocyano; halo; or nitro;
[0183] each instance of R.sup.d is, independently, hydrogen;
substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; or R.sup.d is an amino protecting group;
[0184] each instance of R.sup.e is, independently, a suitable amino
acid side chain; hydrogen; substituted or unsubstituted aliphatic;
substituted or unsubstituted heteroaliphatic; substituted or
unsubstituted aryl; substituted or unsubstituted heteroaryl;
substituted or unsubstituted acyl; substituted or unsubstituted
hydroxyl; substituted or unsubstituted thiol; substituted or
unsubstituted amino; cyano; isocyano; halo; or nitro:
[0185] each instance of G is, independently, a natural or unnatural
amino acid or a group of the formula:
##STR00026##
wherein:
[0186] n is 1, 2, or 3; and
[0187] each instance of R.sup.1 and R.sup.2 is independently
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl:
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; substituted or unsubstituted hydroxyl;
substituted or unsubstituted thiol; substituted or unsubstituted
amino; or halo, or R.sup.1 and R.sup.2 are joined to form a
carbocyclic or heterocyclic ring;
[0188] each instance of R.sup.3 and R.sup.4 is, independently,
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; a hydroxyl protecting group when
attached to an oxygen atom, or an amino protecting group when
attached to a nitrogen atom, or two R.sup.3 groups when attached to
a nitrogen atom are joined to form a heterocyclic ring;
[0189] each instance of R.sup.q is independently halogen, --CN,
--NO.sub.2, --N.sub.3, optionally substituted alkyl, optionally
substituted alkenyl, optionally substituted alkynyl, optionally
substituted carbocyclyl, optionally substituted phenyl, optionally
substituted heterocyclyl, optionally substituted heteroaryl,
optionally substituted alkoxy, an optionally substituted amino
group, or optionally substituted acyl;
[0190] q1 is 0, 1, 2, 3, or 4:
[0191] each instance of X.sub.AA is, independently, a natural or
unnatural amino acid;
[0192] j is, independently, an integer between 1 to 10,
inclusive;
[0193] p is, independently, 1 or 2;
[0194] each instance of q is independently, 0, 1, or 2;
[0195] v is, independently, 0 or 1;
[0196] each instance of w and z is, independently, an integer
between 0 and 100;
[0197] y is, independently, an integer of 1 to 8, inclusive;
and
[0198] corresponds to a single, double or triple bond.
[0199] In certain embodiments, the corresponds to a double bond. In
certain embodiments, the corresponds to a triple bond.
[0200] In certain embodiments, the polypeptide of Formula (I) is of
the formula:
##STR00027##
or a salt or stereoisomer thereof.
[0201] In certain embodiments, the polypeptide of Formula (I) is
any one of the formulae:
##STR00028##
or a salt thereof.
[0202] In certain embodiments, the polypeptide of Formula (I) is
any one of the formulae:
##STR00029##
or a salt thereof.
[0203] In certain embodiments, the polypeptide of Formula (I) is of
the formulae:
##STR00030##
or a salt or stereoisomer thereof.
[0204] In certain embodiments, the polypeptide of Formula (I) is
any one of the formula:
##STR00031## ##STR00032##
or a salt thereof.
[0205] In certain embodiments, the polypeptide of Formula (I) is
any one of the formula:
##STR00033## ##STR00034##
or a salt thereof.
[0206] In another aspect, provided is a precursor polypeptide of
Formula (P-II):
##STR00035##
or a salt or stereoisomer thereof; wherein:
[0207] each instance of K, L.sub.1, L.sub.2, and M is
independently, a bond or a up consisting one or more combinations
of substituted or unsubstituted alkylene; substituted or
unsubstituted alkenylene; substituted or unsubstituted alkynylene;
substituted or unsubstituted heteroalkylene; substituted or
unsubstituted heteroalkenylene; substituted or unsubstituted
heteroalkynylene; substituted or unsubstituted heterocyclene,
substituted or unsubstituted carbocyclene; substituted or
unsubstituted arylene; and substituted or unsubstituted
heteroarylene;
[0208] R.sup.a is hydrogen, substituted or unsubstituted aliphatic;
substituted or unsubstituted heteroaliphatic; substituted or
unsubstituted aryl; substituted or unsubstituted heteroaryl;
substituted or unsubstituted acyl; a resin; an amino protecting
group; a label optionally joined by a linker, wherein the linker is
a group consisting of one or more combinations of substituted or
unsubstituted alkylene; substituted or unsubstituted alkenylene;
substituted or unsubstituted alkynylene; substituted or
unsubstituted heteroalkylene; substituted or unsubstituted
heteroalkenylene; substituted or unsubstituted carbocyclene;
substituted or unsubstituted heterocyclene; substituted or
unsubstituted arylene; or substituted or unsubstituted
heteroarylene;
[0209] R.sup.b is, --R.sup.B, --OR.sup.B, --N(R.sup.B).sub.2, or
--SR.sup.B, wherein each instance of R.sup.B is, independently,
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; a resin; a suitable hydroxyl, amino or thiol
protecting group; or two R.sup.B groups together form a substituted
or unsubstituted 5- to 6-membered heterocyclic or heteroaromatic
ring;
[0210] each instance of R.sup.c, is, independently, hydrogen;
substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; substituted or unsubstituted hydroxyl;
substituted or unsubstituted thiol; substituted or unsubstituted
amino; cyano; isocyano; halo; or nitro;
[0211] each instance of R.sup.d is, independently, hydrogen;
substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; or R.sup.d is an amino protecting group;
[0212] each instance of R.sup.e is, independently, a suitable amino
acid side chain; hydrogen; substituted or unsubstituted aliphatic;
substituted or unsubstituted heteroaliphatic; substituted or
unsubstituted aryl; substituted or unsubstituted heteroaryl;
substituted or unsubstituted acyl; substituted or unsubstituted
hydroxyl; substituted or unsubstituted thiol; substituted or
unsubstituted amino; cyano; isocyano; halo; or nitro;
[0213] each instance of G is, independently, a natural or unnatural
amino acid or a group of the formula:
##STR00036##
wherein:
[0214] n is 1, 2, or 3; and
[0215] each instance of R.sup.1 and R.sup.2 is independently
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; substituted or unsubstituted hydroxyl;
substituted or unsubstituted thiol; substituted or unsubstituted
amino; or halo, or R.sup.1 and R.sup.2 are joined to form a
carbocyclic or heterocyclic ring:
[0216] each instance of R.sup.3 and R.sup.4 is, independently,
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; a hydroxyl protecting group when
attached to an oxygen atom, or an amino protecting group when
attached to a nitrogen atom, or two R.sup.3 groups when attached to
a nitrogen atom are joined to form a heterocyclic ring;
[0217] each instance of R.sup.q is independently halogen, --CN,
--NO.sub.2, --N.sub.3, optionally substituted alkyl, optionally
substituted alkenyl, optionally substituted alkynyl, optionally
substituted carbocyclyl, optionally substituted phenyl, optionally
substituted heterocyclyl, optionally substituted heteroaryl,
optionally substituted alkoxy, an optionally substituted amino
group, or optionally substituted acyl:
[0218] q1 is 0, 1, 2, 3, or 4;
[0219] each instance of X.sub.AA is, independently, a natural or
unnatural amino acid;
[0220] j is, independently, an integer between 1 to 10,
inclusive;
[0221] p is, independently, 1 or 2;
[0222] v is, independently, 0 or 1;
[0223] s is 0, 1, or 2;
[0224] each instance of t, w and z is, independently, an integer
between 0 and 100, inclusive;
[0225] each instance of x is, independently, 0, 1, 2, or 3;
[0226] y is, independently, 1, 2, 3, or 4; and
[0227] corresponds to a double or triple bond.
[0228] In certain embodiments, the corresponds to a double bond. In
certain embodiments, the corresponds to a triple bond.
[0229] In certain embodiments, the polypeptide of Formula (P-II) is
of the formula:
##STR00037##
or a salt or stereoisomer thereof.
[0230] In certain embodiments, the polypeptide of Formula (P-II) is
any one of the formula:
##STR00038##
or salt or stereoisomer thereof.
[0231] In certain embodiments, the polypeptide of Formula (P-II) is
any one of the formula:
##STR00039##
or salt or stereoisomer thereof.
[0232] In certain embodiments, the polypeptide of Formula (P-II) is
of the formula:
##STR00040##
or a salt or stereoisomer thereof.
[0233] In certain embodiments, the polypeptide of Formula (II) is
any one of the formula:
##STR00041##
or a salt or stereoisomer thereof.
[0234] In certain embodiments, the polypeptide of Formula (II) is
any one of the formula:
##STR00042##
or a salt or stereoisomer thereof.
[0235] Furthermore, in certain embodiments, the precursor
polypeptide of Formula (P-II) upon contact with a ring closing
methathesis catalyst, generates a stitched polypeptide of Formula
(II):
##STR00043##
or a salt or stereoisomer thereof. wherein:
[0236] each instance of K, M, L.sub.1, and L.sub.2, is
independently, a bond or a group consisting of one or more
combinations of substituted or unsubstituted alkylene; substituted
or unsubstituted alkenylene; substituted or unsubstituted
alkynylene; substituted or unsubstituted heteroalkylene;
substituted or unsubstituted heteroalkenylene; substituted or
unsubstituted heteroalkynylene; substituted or unsubstituted
heterocyclene, substituted or unsubstituted carbocyclene,
substituted or unsubstituted arylene; substituted or unsubstituted
heteroarylene;
[0237] R.sup.a is hydrogen; substituted or unsubstituted aliphatic;
substituted or unsubstituted heteroaliphatic; substituted or
unsubstituted aryl; substituted or unsubstituted heteroaryl;
substituted or unsubstituted acyl; a resin; an amino protecting
group; a label optionally joined by a linker, wherein the linker is
a group consisting of one or more combinations of substituted or
unsubstituted alkylene; substituted or unsubstituted alkenylene;
substituted or unsubstituted alkynylene; substituted or
unsubstituted heteroalkylene; substituted or unsubstituted
heteroalkenylene; substituted or unsubstituted carbocyclene;
substituted or unsubstituted heterocyclene; substituted or
unsubstituted arylene; or substituted or unsubstituted
heteroarylene;
[0238] R.sup.b is, --R.sup.B, --OR.sup.B, --N(R.sup.B).sub.2, or
--SR.sup.B, wherein each instance of R.sup.B is, independently,
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; a resin; a suitable hydroxyl, amino or thiol
protecting group; or two R.sup.B groups together form a substituted
or unsubstituted 5- to 6-membered heterocyclic or heteroaromatic
ring;
[0239] each instance of R.sup.c, is, independently, hydrogen;
substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; substituted or unsubstituted hydroxyl;
substituted or unsubstituted thiol; substituted or unsubstituted
amino; cyano; isocyano; halo; or nitro;
[0240] each instance of R.sup.d is, independently, hydrogen;
substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; or R.sup.d is an amino protecting group;
[0241] each instance of R.sup.e is, independently, a suitable amino
acid side chain; hydrogen; substituted or unsubstituted aliphatic;
substituted or unsubstituted heteroaliphatic; substituted or
unsubstituted aryl; substituted or unsubstituted heteroaryl;
substituted or unsubstituted acyl; substituted or unsubstituted
hydroxyl; substituted or unsubstituted thiol; substituted or
unsubstituted amino; cyano; isocyano; halo; or nitro;
[0242] each instance of R.sup.KL, R.sup.LL, and R.sup.LM, is,
independently, hydrogen; substituted or unsubstituted aliphatic;
substituted or unsubstituted heteroaliphatic; substituted or
unsubstituted aryl; substituted or unsubstituted heteroaryl;
substituted or unsubstituted acyl; substituted or unsubstituted
hydroxyl; substituted or unsubstituted thiol; substituted or
unsubstituted amino; azido; cyano; isocyano; halo; nitro;
[0243] each instance of G is, independently, a natural or unnatural
amino acid or a group of the formula:
##STR00044##
wherein:
[0244] n is 1, 2, or 3; and
[0245] each instance of R.sup.1 and R.sup.2 is independently
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; substituted or unsubstituted hydroxyl;
substituted or unsubstituted thiol; substituted or unsubstituted
amino; or halo, or R.sup.1 and R.sup.2 are joined to form a
carbocyclic or heterocyclic ring;
[0246] each instance of R.sup.3 and R.sup.4 is, independently,
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; a hydroxyl protecting group when
attached to an oxygen atom, or an amino protecting group when
attached to a nitrogen atom, or two R.sup.3 groups when attached to
a nitrogen atom are joined to form a heterocyclic ring;
[0247] each instance of R.sup.q is independently halogen, --CN,
--NO.sub.2, --N.sub.3, optionally substituted alkyl, optionally
substituted alkenyl, optionally substituted alkynyl, optionally
substituted carbocyclyl, optionally substituted phenyl, optionally
substituted heterocyclyl, optionally substituted heteroaryl,
optionally substituted alkoxy, an optionally substituted amino
group, or optionally substituted acyl;
[0248] q1 is 0, 1, 2, 3, or 4;
[0249] each instance of X.sub.AA, is, independently, a natural or
unnatural amino acid;
[0250] j is, independently, an integer between 1 to 10,
inclusive;
[0251] p is, independently, 1 or 2;
[0252] each instance of q is independently, 0, 1 or 2;
[0253] v is, independently, an integer between 0 to 1;
[0254] s is 0, 1, or 2;
[0255] each instance of t, w and z is, independently, an integer
between 0 and 100;
[0256] y is, independently, an integer of 1 to 8, inclusive;
and
[0257] corresponds to a single, double or triple bond.
[0258] In certain embodiments, the corresponds to a double bond. In
certain embodiments, the corresponds to a triple bond.
[0259] In certain embodiments, the polypeptide of Formula (II) is
of the formula:
##STR00045##
or a salt or stereoisomer thereof.
[0260] In certain embodiments, the polypeptide of Formula (II) is
any one of the formula:
##STR00046##
or a salt or stereoisomer thereof.
[0261] In certain embodiments, the polypeptide of Formula (II) is
any one of the formula:
##STR00047##
or a salt or stereoisomer thereof.
[0262] In certain embodiments, the polypeptide of Formula (II) is
of the formula:
##STR00048##
or a salt or stereoisomer thereof.
[0263] In certain embodiments, the polypeptide of Formula (II) is
any one of the formula:
##STR00049##
or a salt or stereoisomer thereof.
[0264] In certain embodiments, the polypeptide of Formula (II) is
any one of the formula
##STR00050##
or a salt or stereoisomer thereof.
[0265] In yet another aspect, provided are compounds useful in the
preparation of the precursor polypeptides which include, but are
not limited to, compounds of Formula (III):
##STR00051##
or salts or stereoisomers thereof; wherein:
[0266] p is 1 or 2;
[0267] K is a bond or a group consisting of one or more
combinations of substituted or unsubstituted alkylene; substituted
or unsubstituted alkenylene; substituted or unsubstituted
alkynylene; substituted or unsubstituted heteroalkylene;
substituted or unsubstituted heteroalkenylene; substituted or
unsubstituted heteroalkynylene; substituted or unsubstituted
heterocyclene, substituted or unsubstituted carbocyclene,
substituted or unsubstituted arylene; substituted or unsubstituted
heteroarylene;
[0268] R.sup.a is hydrogen, substituted or unsubstituted aliphatic;
substituted or unsubstituted heteroaliphatic; substituted or
unsubstituted aryl; substituted or unsubstituted heteroaryl;
substituted or unsubstituted acyl; a resin; an amino protecting
group; or a label optionally joined by a linker, wherein the linker
is a group consisting of one or more combinations of substituted or
unsubstituted alkylene; substituted or unsubstituted alkenylene;
substituted or unsubstituted alkynylene; substituted or
unsubstituted heteroalkylene; substituted or unsubstituted
heteroalkenylene; substituted or unsubstituted carbocyclene;
substituted or unsubstituted heterocyclene; substituted or
unsubstituted arylene; or substituted or unsubstituted
heteroarylene;
[0269] R.sup.b is, --R.sup.B, --OR.sup.B, --N(R.sup.B).sub.2, or
--SR.sup.B, wherein each instance of R.sup.B is, independently,
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; a resin; a suitable hydroxyl, amino or thiol
protecting group; or two R.sup.B groups together form a substituted
or unsubstituted 5- to 6-membered heterocyclic or heteroaromatic
ring;
[0270] each instance of R.sup.c, is, independently, hydrogen;
substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; substituted or unsubstituted hydroxyl;
substituted or unsubstituted thiol; substituted or unsubstituted
amino; cyano; isocyano; halo; or nitro;
[0271] x is 0, 1, 2, or 3; and
[0272] corresponds to a single, double or triple bond.
[0273] In certain embodiments, the corresponds to a double bond. In
certain embodiments, the corresponds to a triple bond.
[0274] In certain embodiments, the compound of Formula (III) is of
the formula:
##STR00052##
or salt or stereoisomer thereof.
[0275] In certain embodiments, the compound of Formula (III) is any
one of the formula:
##STR00053##
or salt thereof.
[0276] In certain embodiments, the compound of Formula (III) is any
one of the formula:
##STR00054##
or salt thereof.
[0277] In certain embodiments, the compound of Formula (III) is of
the formula:
##STR00055##
or salt or stereoisomer thereof.
[0278] In certain embodiments, the compound of Formula (III) is any
one of the formula:
##STR00056##
or salt thereof.
[0279] In certain embodiments, the compound of Formula (III) is any
one of the formula:
##STR00057##
or salt thereof. Groups K, L, L.sub.1, L.sub.2, and M
[0280] As generally defined above, each instance of K, L, L.sub.1,
L.sub.2, and M is, independently, a bond or a group consisting of
one or more combinations of substituted or unsubstituted alkylene;
substituted or unsubstituted alkenylene; substituted or
unsubstituted alkynylene; substituted or unsubstituted
heteroalkylene; substituted or unsubstituted heteroalkenylene;
substituted or unsubstituted heteroalkynylene; substituted or
unsubstituted heterocyclene, substituted or unsubstituted
carbocyclene, substituted or unsubstituted arylene; substituted or
unsubstituted heteroarylene.
[0281] As used herein, reference to a group consisting of "one or
more combinations" refers to a group comparing 1, 2, 3, 4 or more
combinations of the recited divinyl moieties. For example, the
group may consist of an alkylene attached to a heteroalkylene,
which may be further optionally attached to another alkylene. As
used herein "at least one instance" refers to 1, 2, 3, or 4
instances of the recited moiety.
[0282] In certain embodiments, K is a bond.
[0283] In certain embodiments, K is a group consisting of one or
more combinations of substituted or unsubstituted alkylene;
substituted or unsubstituted alkenylene; substituted or
unsubstituted alkynylene; substituted or unsubstituted
heteroalkylene; substituted or unsubstituted heteroalkenylene;
substituted or unsubstituted heteroalkynylene; substituted or
unsubstituted heterocyclene, substituted or unsubstituted
carbocyclene, substituted or unsubstituted arylene; substituted or
unsubstituted heteroarylene.
[0284] In certain embodiments, K is a group which comprises at
least one instance of substituted or unsubstituted alkylene, e.g.,
substituted or unsubstituted C.sub.1-6 alkylene, substituted or
unsubstituted C.sub.1-2alkylene, substituted or unsubstituted
C.sub.2-3alkylene, substituted or unsubstituted C.sub.3-4alkylene,
substituted or unsubstituted C.sub.4-5alkylene, or substituted or
unsubstituted C.sub.5-6alkylene. Exemplary alkylene groups include
unsubstituted alkylene groups such as methylene --CH.sub.2--,
ethylene --(CH.sub.2).sub.2--, n-propylene --(CH.sub.2).sub.3--,
n-butylene --(CH.sub.2).sub.4--, n-pentylene --(CH.sub.2).sub.5--,
and n-hexylene --(CH.sub.2).sub.6--. In certain embodiments, K is
--CH.sub.2--. In certain embodiments, K is --(CH.sub.2).sub.2--. In
certain embodiments, K is --(CH.sub.2).sub.3--.
[0285] In certain embodiments, K is a group which comprises at
least one instance of substituted or unsubstituted alkenylene,
e.g., substituted or unsubstituted C.sub.2-6alkenylene, substituted
or unsubstituted C.sub.2-3alkenylene, substituted or unsubstituted
C.sub.3-4alkenylene, substituted or unsubstituted
C.sub.4-5alkenylene, or substituted or unsubstituted
C.sub.5-6alkenylene.
[0286] In certain embodiments, K is a group which comprises at
least one instance of substituted or unsubstituted alkynylene,
e.g., substituted or unsubstituted C.sub.2-6alkynylene, substituted
or unsubstituted C.sub.2-3alkynylene, substituted or unsubstituted
C.sub.3-4alkynylene, substituted or unsubstituted
C.sub.4-5alkynylene, or substituted or unsubstituted
C.sub.5-6alkynylene.
[0287] In certain embodiments, K is a group which comprises at
least one instance of substituted or unsubstituted heteroalkylene.
e.g., substituted or unsubstituted heteroC.sub.1-6alkylene,
substituted or unsubstituted heteroC.sub.1-2alkylene, substituted
or unsubstituted heteroC.sub.2-3alkylene, substituted or
unsubstituted heteroC.sub.3-4alkylene, substituted or unsubstituted
heteroC.sub.4-5alkylene, or substituted or unsubstituted
heteroC.sub.5-6alkylene. Exemplary heteroalkylene groups include
unsubstituted alkylene groups such as
--(CH.sub.2).sub.2--O(CH.sub.2).sub.2--, --OCH.sub.2--,
--O(CH.sub.2).sub.2--, --O(CH.sub.2).sub.3--,
--O(CH.sub.2).sub.4--, --O(CH.sub.2).sub.5--, and
--O(CH.sub.2).sub.6--. In certain embodiments, K is --CH.sub.2O--,
wherein O is linked to the heterocyclyl with nitrogen and CH.sub.2
is linked to "." In certain embodiments, K is
--(CH.sub.2).sub.2O--, wherein O is linked to the heterocyclyl with
nitrogen and CH.sub.2 is linked to "." In certain embodiments, K is
--(CH.sub.2).sub.3O--, wherein O is linked to the heterocyclyl with
nitrogen and CH.sub.2 is linked to "."
[0288] In certain embodiments. K is a group which comprises at
least one instance of substituted or unsubstituted
heteroalkenylene. e.g., substituted or unsubstituted
heteroC.sub.2-6alkenylene, substituted or unsubstituted
heteroC.sub.2-3alkenylene, substituted or unsubstituted
heteroC.sub.3-4alkenylene, substituted or unsubstituted
heteroC.sub.4-5alkenylene, or substituted or unsubstituted
heteroC.sub.5-6alkenylene.
[0289] In certain embodiments, K is a group which comprises at
least one instance of substituted or unsubstituted
heteroalkynylene, e.g., substituted or unsubstituted
heteroC.sub.2-6 alkynylene, substituted or unsubstituted
heteroC.sub.2-3alkynylene, substituted or unsubstituted
heteroC.sub.3-4 alkynylene, substituted or unsubstituted
heteroC.sub.4-5alkynylene, or substituted or unsubstituted
heteroC.sub.5-6alkynylene.
[0290] In certain embodiments, K is a group which comprises at
least one instance of substituted or unsubstituted carbocyclylene,
e.g., substituted or unsubstituted C.sub.3-6carbocyclylene,
substituted or unsubstituted C.sub.3-4 carbocyclylene, substituted
or unsubstituted C.sub.4-5 carbocyclylene, or substituted or
unsubstituted C.sub.5-6 carbocyclylene.
[0291] In certain embodiments, K is a group which comprises at
least one instance of substituted or unsubstituted heterocyclylene,
e.g., substituted or unsubstituted C.sub.3-6 heterocyclylene,
substituted or unsubstituted C.sub.3-4 heterocyclylene, substituted
or unsubstituted C.sub.4-5 heterocyclylene, or substituted or
unsubstituted C.sub.5-6 heterocyclylene.
[0292] In certain embodiments. K is a group which comprises at
least one instance of substituted or unsubstituted arylene, e.g.,
substituted or unsubstituted phenylene.
[0293] In certain embodiments, K is a group which comprises at
least one instance of substituted or unsubstituted heteroarylene,
e.g., substituted or unsubstituted 5- to 6-membered
heteroarylene.
[0294] In certain embodiments, L is a bond.
[0295] In certain embodiments, L is a group consisting of one or
more combinations of substituted or unsubstituted alkylene;
substituted or unsubstituted alkenylene; substituted or
unsubstituted alkynylene; substituted or unsubstituted
heteroalkylene; substituted or unsubstituted heteroalkenylene;
substituted or unsubstituted heteroalkynylene; substituted or
unsubstituted heterocyclene, substituted or unsubstituted
carbocyclene, substituted or unsubstituted arylene; substituted or
unsubstituted heteroarylene.
[0296] In certain embodiments, L is a group which comprises at
least one instance of substituted or unsubstituted alkylene, e.g.,
substituted or unsubstituted C.sub.1-6alkylene, substituted or
unsubstituted C.sub.1-2alkylene, substituted or unsubstituted
C.sub.2-3alkylene, substituted or unsubstituted C.sub.3-4alkylene,
substituted or unsubstituted C.sub.4-5alkylene, or substituted or
unsubstituted C.sub.5-6alkylene. Exemplary alkylene groups include
unsubstituted alkylene groups such as methylene --CH.sub.2--,
ethylene --(CH.sub.2).sub.2--, n-propylene --(CH.sub.2).sub.3--,
n-butylene --(CH.sub.2).sub.4--, n-pentylene --(CH.sub.2).sub.5--,
and n-hexylene --(CH.sub.2).sub.6--. In certain embodiments, L is
--CH.sub.2--. In certain embodiments. L is --(CH.sub.2).sub.2--. In
certain embodiments, L is --(CH.sub.2).sub.3--. In certain
embodiments. L is --(CH.sub.2).sub.4--. In certain embodiments, L
is --(CH.sub.2).sub.5--. In certain embodiments, L is
--(CH.sub.2).sub.6--.
[0297] In certain embodiments, L is a group which comprises at
least one instance of substituted or unsubstituted alkenylene,
e.g., substituted or unsubstituted C.sub.2-6alkenylene, substituted
or unsubstituted C.sub.2-3alkenylene, substituted or unsubstituted
C.sub.3-4alkenylene, substituted or unsubstituted
C.sub.4-5alkenylene, or substituted or unsubstituted
C.sub.5-6alkenylene.
[0298] In certain embodiments, L is a group which comprises at
least one instance of substituted or unsubstituted alkynylene,
e.g., substituted or unsubstituted C.sub.2-6alkynylene, substituted
or unsubstituted C.sub.2-3alkynylene, substituted or unsubstituted
C.sub.3-4alkynylene, substituted or unsubstituted
C.sub.4-5alkynylene, or substituted or unsubstituted
C.sub.5-6alkynylene.
[0299] In certain embodiments, L is a group which comprises at
least one instance of substituted or unsubstituted heteroalkylene,
e.g., substituted or unsubstituted heteroC.sub.1-6alkylene,
substituted or unsubstituted heteroC.sub.1-2alkylene, substituted
or unsubstituted heteroC.sub.2-3alkylene, substituted or
unsubstituted heteroC.sub.3-4alkylene, substituted or unsubstituted
heteroC.sub.4-5alkylene, or substituted or unsubstituted
heteroC.sub.5-6alkylene. Exemplary heteroalkylene groups include
unsubstituted alkylene groups such as
--(CH.sub.2).sub.2--O(CH.sub.2).sub.2--, --OCH.sub.2--,
--O(CH.sub.2).sub.2--, --O(CH.sub.2).sub.3--,
--O(CH.sub.2).sub.4--, --O(CH.sub.2).sub.5--, and
--O(CH.sub.2).sub.6--.
[0300] In certain embodiments, L is a group which comprises at
least one instance of substituted or unsubstituted
heteroalkenylene, e.g., substituted or unsubstituted
heteroC.sub.2-6alkenylene, substituted or unsubstituted
heteroC.sub.2-3alkenylene, substituted or unsubstituted
heteroC.sub.3-4alkenylene, substituted or unsubstituted
heteroC.sub.4-5alkenylene, or substituted or unsubstituted
heteroC.sub.5-6 alkenylene.
[0301] In certain embodiments, L is a group which comprises at
least one instance of substituted or unsubstituted
heteroalkynylene, e.g., substituted or unsubstituted
heteroC.sub.2-6alkynylene, substituted or unsubstituted
heteroC.sub.2-3alkynylene, substituted or unsubstituted
heteroC.sub.3-4alkynylene, substituted or unsubstituted
heteroC.sub.4-5alkynylene, or substituted or unsubstituted
heteroC.sub.5-6alkynylene.
[0302] In certain embodiments, L is a group which comprises at
least one instance of substituted or unsubstituted carbocyclylene,
e.g., substituted or unsubstituted C.sub.3-6carbocyclylene,
substituted or unsubstituted C.sub.3-4carbocyclylene, substituted
or unsubstituted C.sub.4-5 carbocyclylene, or substituted or
unsubstituted C.sub.5-6 carbocyclylene.
[0303] In certain embodiments, L is a group which comprises at
least one instance of substituted or unsubstituted heterocyclylene,
e.g., substituted or unsubstituted C.sub.3-6 heterocyclylene,
substituted or unsubstituted C.sub.3-4 heterocyclylene, substituted
or unsubstituted C.sub.4-5 heterocyclylene, or substituted or
unsubstituted C.sub.5-6 heterocyclylene.
[0304] In certain embodiments, L is a group which comprises at
least one instance of substituted or unsubstituted arylene. e.g.,
substituted or unsubstituted phenylene.
[0305] In certain embodiments, L is a group which comprises at
least one instance of substituted or unsubstituted heteroarylene,
e.g., substituted or unsubstituted 5- to 6-membered
heteroarylene.
[0306] In certain embodiments, L.sub.1 is a bond.
[0307] In certain embodiments. L.sub.1 is a group consisting of one
or more combinations of substituted or unsubstituted alkylene;
substituted or unsubstituted alkenylene; substituted or
unsubstituted alkynylene; substituted or unsubstituted
heteroalkylene; substituted or unsubstituted heteroalkenylene;
substituted or unsubstituted heteroalkynylene; substituted or
unsubstituted heterocyclene, substituted or unsubstituted
carbocyclene, substituted or unsubstituted arylene; substituted or
unsubstituted heteroarylene.
[0308] In certain embodiments, L.sub.1 is a group which comprises
at least one instance of substituted or unsubstituted alkylene,
e.g., substituted or unsubstituted C.sub.1-6alkylene, substituted
or unsubstituted C.sub.1-2alkylene, substituted or unsubstituted
C.sub.2-3alkylene, substituted or unsubstituted C.sub.3-5alkylene,
substituted or unsubstituted C.sub.4-5alkylene, or substituted or
unsubstituted C.sub.5-6alkylene. Exemplary alkylene groups include
unsubstituted alkylene groups such as methylene --CH.sub.2--,
ethylene --(CH.sub.2).sub.2--, n-propylene --(CH.sub.2).sub.3--,
n-butylene --(CH.sub.2).sub.4--, n-pentylene --(CH.sub.2).sub.5--,
and n-hexylene --(CH.sub.2).sub.6--. In certain embodiments,
L.sub.1 is --CH.sub.2--. In certain embodiments, L.sub.1 is
--(CH.sub.2).sub.2--. In certain embodiments, L.sub.1 is
--(CH.sub.2).sub.3--. In certain embodiments, L.sub.1 is
--(CH.sub.2).sub.4--. In certain embodiments, L.sub.1 is
--(CH.sub.2).sub.5--. In certain embodiments, L.sub.1 is
--(CH.sub.2).sub.6--.
[0309] In certain embodiments, L.sub.1 is a group which comprises
at least one instance of substituted or unsubstituted alkenylene,
e.g., substituted or unsubstituted C.sub.2-6alkenylene, substituted
or unsubstituted C.sub.2-3alkenylene, substituted or unsubstituted
C.sub.3-4alkenylene, substituted or unsubstituted
C.sub.4-5alkenylene, or substituted or unsubstituted
C.sub.5-6alkenylene.
[0310] In certain embodiments. L.sub.1 is a group which comprises
at least one instance of substituted or unsubstituted alkynylene,
e.g., substituted or unsubstituted C.sub.2-6alkynylene, substituted
or unsubstituted C.sub.2-3alkynylene, substituted or unsubstituted
C.sub.3-4alkynylene, substituted or unsubstituted
C.sub.4-5alkynylene, or substituted or unsubstituted
C.sub.5-6alkynylene.
[0311] In certain embodiments, L.sub.1 is a group which comprises
at least one instance of substituted or unsubstituted
heteroalkylene, e.g., substituted or unsubstituted
heteroC.sub.1-6alkylene, substituted or unsubstituted
heteroC.sub.1-2alkylene, substituted or unsubstituted
heteroC.sub.2-3alkylene, substituted or unsubstituted
heteroC.sub.3-4alkylene, substituted or unsubstituted
heteroC.sub.4-5alkylene, or substituted or unsubstituted
heteroC.sub.5 alkylene. Exemplary heteroalkylene groups include
unsubstituted alkylene groups such as
--(CH.sub.2).sub.2--O(CH.sub.2).sub.2--. --OCH.sub.2--,
--O(CH.sub.2).sub.2--, --O(CH.sub.2).sub.3--.
--O(CH.sub.2).sub.4--, --O(CH.sub.2).sub.5--, and
--O(CH.sub.2).sub.6--.
[0312] In certain embodiments, L.sub.1 is a group which comprises
at least one instance of substituted or unsubstituted
heteroalkenylene, e.g., substituted or unsubstituted
heteroC.sub.2-6alkenylene, substituted or unsubstituted
heteroC.sub.2-3alkenylene, substituted or unsubstituted
heteroC.sub.3-4alkenylene, substituted or unsubstituted
heteroC.sub.4-5alkenylene, or substituted or unsubstituted
heteroC.sub.5-6alkenylene.
[0313] In certain embodiments, L.sub.1 is a group which comprises
at least one instance of substituted or unsubstituted
heteroalkynylene, e.g., substituted or unsubstituted
heteroC.sub.2-6alkynylene, substituted or unsubstituted
heteroC.sub.2-3alkynylene, substituted or unsubstituted
heteroC.sub.3-4alkynylene, substituted or unsubstituted
heteroC.sub.4-5alkynylene, or substituted or unsubstituted
heteroC.sub.5-6alkynylene.
[0314] In certain embodiments, L.sub.1 is a group which comprises
at least one instance of substituted or unsubstituted
carbocyclylene, e.g., substituted or unsubstituted
C.sub.3-6carbocyclylene, substituted or unsubstituted
C.sub.3-4carbocyclylene, substituted or unsubstituted C.sub.4-5
carbocyclylene, or substituted or unsubstituted C.sub.5-6
carbocyclylene.
[0315] In certain embodiments, L.sub.1 is a group which comprises
at least one instance of substituted or unsubstituted
heterocyclylene, e.g., substituted or unsubstituted C.sub.3-6
heterocyclylene, substituted or unsubstituted C.sub.3-4
heterocyclylene, substituted or unsubstituted C.sub.4-5
heterocyclylene, or substituted or unsubstituted C.sub.5-6
heterocyclylene.
[0316] In certain embodiments, L.sub.1 is a group which comprises
at least one instance of substituted or unsubstituted arylene,
e.g., substituted or unsubstituted phenylene.
[0317] In certain embodiments, L.sub.1 is a group which comprises
at least one instance of substituted or unsubstituted
heteroarylene, e.g., substituted or unsubstituted 5- to 6-membered
heteroarylene.
[0318] In certain embodiments, L.sub.2 is a bond.
[0319] In certain embodiments, L.sub.2 is a group consisting of one
or more combinations of substituted or unsubstituted alkylene;
substituted or unsubstituted alkenylene; substituted or
unsubstituted alkynylene; substituted or unsubstituted
heteroalkylene; substituted or unsubstituted heteroalkenylene;
substituted or unsubstituted heteroalkynylene; substituted or
unsubstituted heterocyclene, substituted or unsubstituted
carbocyclene, substituted or unsubstituted arylene; substituted or
unsubstituted heteroarylene.
[0320] In certain embodiments, L.sub.2 is a group which comprises
at least one instance of substituted or unsubstituted alkylene,
e.g., substituted or unsubstituted C.sub.1-6alkylene, substituted
or unsubstituted C.sub.1-2alkylene, substituted or unsubstituted
C.sub.2-3alkylene, substituted or unsubstituted C.sub.3-4alkylene,
substituted or unsubstituted C.sub.4-5alkylene, or substituted or
unsubstituted C.sub.5-6alkylene. Exemplary alkylene groups include
unsubstituted alkylene groups such as methylene --CH.sub.2--,
ethylene --(CH.sub.2).sub.2--, n-propylene --(CH.sub.2).sub.3--,
n-butylene --(CH.sub.2).sub.4--, n-pentylene --(CH.sub.2).sub.5--,
and n-hexylene --(CH.sub.2).sub.6--. In certain embodiments,
L.sub.2 is --CH.sub.2--. In certain embodiments, L.sub.2 is
--(CH.sub.2).sub.2--. In certain embodiments, L.sub.2 is
--(CH.sub.2).sub.3--. In certain embodiments, L.sub.2 is
--(CH.sub.2).sub.4--. In certain embodiments, L.sub.2 is
--(CH.sub.2).sub.5--. In certain embodiments, L.sub.2 is
--(CH.sub.2).sub.6--.
[0321] In certain embodiments, L.sub.2 is a group which comprises
at least one instance of substituted or unsubstituted alkenylene,
e.g., substituted or unsubstituted C.sub.2-6alkenylene, substituted
or unsubstituted C.sub.2-3alkenylene, substituted or unsubstituted
C.sub.3-4alkenylene, substituted or unsubstituted
C.sub.4-5alkenylene, or substituted or unsubstituted
C.sub.5-6alkenylene.
[0322] In certain embodiments, L.sub.2 is a group which comprises
at least one instance of substituted or unsubstituted alkynylene,
e.g., substituted or unsubstituted C.sub.2-6alkynylene, substituted
or unsubstituted C.sub.2-3alkynylene, substituted or unsubstituted
C.sub.3-4alkynylene, substituted or unsubstituted
C.sub.4-5alkynylene, or substituted or unsubstituted
C.sub.5-6alkynylene.
[0323] In certain embodiments, L.sub.2 is a group which comprises
at least one instance of substituted or unsubstituted
heteroalkylene, e.g., substituted or unsubstituted
heteroC.sub.1-6alkylene, substituted or unsubstituted
heteroC.sub.1-2alkylene, substituted or unsubstituted
heteroC.sub.2-3alkylene, substituted or unsubstituted
heteroC.sub.3-4alkylene, substituted or unsubstituted
heteroC.sub.4-5alkylene, or substituted or unsubstituted
heteroC.sub.5-6alkylene. Exemplary heteroalkylene groups include
unsubstituted alkylene groups such as
--(CH.sub.2).sub.2--O(CH.sub.2).sub.2--, --OCH.sub.2--,
--O(CH.sub.2).sub.2--, --O(CH.sub.2).sub.3--,
--O(CH.sub.2).sub.4--, --O(CH.sub.2).sub.5--, and
--O(CH.sub.2).sub.6--.
[0324] In certain embodiments. L.sub.2 is a group which comprises
at least one instance of substituted or unsubstituted
heteroalkenylene, e.g., substituted or unsubstituted
heteroC.sub.2-6alkenylene, substituted or unsubstituted
heteroC.sub.2-3alkenylene, substituted or unsubstituted
heteroC.sub.3-4alkenylene, substituted or unsubstituted
heteroC.sub.4-5alkenylene, or substituted or unsubstituted
heteroC.sub.5-6alkenylene.
[0325] In certain embodiments, L.sub.2 is a group which comprises
at least one instance of substituted or unsubstituted
heteroalkynylene, e.g., substituted or unsubstituted
heteroC.sub.2-6alkynylene, substituted or unsubstituted
heteroC.sub.2-3alkynylene, substituted or unsubstituted
heteroC.sub.3-4alkynylene, substituted or unsubstituted
heteroC.sub.4-5alkynylene, or substituted or unsubstituted
heteroC.sub.5-6alkynylene.
[0326] In certain embodiments, L.sub.2 is a group which comprises
at least one instance of substituted or unsubstituted
carbocyclylene. e.g., substituted or unsubstituted
C.sub.3-6carbocyclylene, substituted or unsubstituted
C.sub.3-4carbocyclylene, substituted or unsubstituted C.sub.4-5
carbocyclylene, or substituted or unsubstituted C.sub.5-6
carbocyclylene.
[0327] In certain embodiments, L.sub.2 is a group which comprises
at least one instance of substituted or unsubstituted
heterocyclylene, e.g., substituted or unsubstituted C.sub.3-6
heterocyclylene, substituted or unsubstituted C.sub.3-4
heterocyclylene, substituted or unsubstituted C.sub.4-5
heterocyclylene, or substituted or unsubstituted C.sub.5-6
heterocyclylene.
[0328] In certain embodiments, L.sub.2 is a group which comprises
at least one instance of substituted or unsubstituted arylene,
e.g., substituted or unsubstituted phenylene.
[0329] In certain embodiments, L.sub.2 is a group which comprises
at least one instance of substituted or unsubstituted
heteroarylene, e.g., substituted or unsubstituted 5- to 6-membered
heteroarylene.
[0330] In certain embodiments, M is a bond.
[0331] In certain embodiments, M is a group consisting of one or
more combinations of substituted or unsubstituted alkylene;
substituted or unsubstituted alkenylene; substituted or
unsubstituted alkynylene; substituted or unsubstituted
heteroalkylene; substituted or unsubstituted heteroalkenylene;
substituted or unsubstituted heteroalkynylene; substituted or
unsubstituted heterocyclene, substituted or unsubstituted
carbocyclene, substituted or unsubstituted arylene; substituted or
unsubstituted heteroarylene.
[0332] In certain embodiments, M is a group which comprises at
least one instance of substituted or unsubstituted alkylene, e.g.,
substituted or unsubstituted C.sub.1-6alkylene, substituted or
unsubstituted C.sub.1-2alkylene, substituted or unsubstituted
C.sub.2-3alkylene, substituted or unsubstituted C.sub.3-4 alkylene,
substituted or unsubstituted C.sub.4-5alkylene, or substituted or
unsubstituted C.sub.5-6alkylene. Exemplary alkylene groups include
unsubstituted alkylene groups such as methylene --CH.sub.2--,
ethylene --(CH.sub.2).sub.2--, n-propylene --(CH.sub.2).sub.3--,
n-butylene --(CH.sub.2).sub.4--, n-pentylene --(CH.sub.2).sub.5--,
and n-hexylene --(CH.sub.2).sub.6--. In certain embodiments, M is
--CH.sub.2--. In certain embodiments, M is --(CH.sub.2).sub.2--. In
certain embodiments, M is --(CH.sub.2).sub.3--. In certain
embodiments, M is --(CH.sub.2).sub.4--. In certain embodiments, M
is --(CH.sub.2).sub.5--. In certain embodiments, M is
--(CH.sub.2).sub.6--.
[0333] In certain embodiments, M is a group which comprises at
least one instance of substituted or unsubstituted alkenylene,
e.g., substituted or unsubstituted C.sub.2-6alkenylene, substituted
or unsubstituted C.sub.2-3alkenylene, substituted or unsubstituted
C.sub.3-4alkenylene, substituted or unsubstituted
C.sub.4-5alkenylene, or substituted or unsubstituted
C.sub.5-6alkenylene.
[0334] In certain embodiments, M is a group which comprises at
least one instance of substituted or unsubstituted alkynylene.
e.g., substituted or unsubstituted C.sub.2-6alkynylene, substituted
or unsubstituted C.sub.2-3alkynylene, substituted or unsubstituted
C.sub.3-4alkynylene, substituted or unsubstituted
C.sub.4-5alkynylene, or substituted or unsubstituted
C.sub.5-6alkynylene.
[0335] In certain embodiments, M is a group which comprises at
least one instance of substituted or unsubstituted heteroalkylene,
e.g., substituted or unsubstituted heteroC.sub.1-6alkylene,
substituted or unsubstituted heteroC.sub.1-2alkylene, substituted
or unsubstituted heteroC.sub.2-3alkylene, substituted or
unsubstituted heteroC.sub.3-4alkylene, substituted or unsubstituted
heteroC.sub.4-5alkylene, or substituted or unsubstituted
heteroC.sub.5-6alkylene. Exemplary heteroalkylene groups include
unsubstituted alkylene groups such as
--(CH.sub.2).sub.2--O(CH.sub.2).sub.2--, --OCH.sub.2--.
--O(CH.sub.2).sub.2--, --O(CH.sub.2).sub.3--,
--O(CH.sub.2).sub.4--, --O(CH.sub.2).sub.5--, and
--O(CH.sub.2).sub.6--.
[0336] In certain embodiments. M is a group which comprises at
least one instance of substituted or unsubstituted
heteroalkenylene, e.g., substituted or unsubstituted
heteroC.sub.2-6alkenylene, substituted or unsubstituted
heteroC.sub.2-3alkenylene, substituted or unsubstituted
heteroC.sub.3-4alkenylene, substituted or unsubstituted
heteroC.sub.4-5alkenylene, or substituted or unsubstituted
heteroC.sub.5-6alkenylene.
[0337] In certain embodiments, M is a group which comprises at
least one instance of substituted or unsubstituted
heteroalkynylene, e.g., substituted or unsubstituted
heteroC.sub.2-6alkynylene, substituted or unsubstituted
heteroC.sub.2-3alkynylene, substituted or unsubstituted
heteroC.sub.3-4alkynylene, substituted or unsubstituted
heteroC.sub.4-5alkynylene, or substituted or unsubstituted
heteroC.sub.5-6alkynylene.
[0338] In certain embodiments, M is a group which comprises at
least one instance of substituted or unsubstituted carbocyclylene.
e.g., substituted or unsubstituted C.sub.3-6carbocyclylene,
substituted or unsubstituted C.sub.3-4carbocyclylene, substituted
or unsubstituted C.sub.4-5 carbocyclylene, or substituted or
unsubstituted C.sub.5-6 carbocyclylene.
[0339] In certain embodiments, M is a group which comprises at
least one instance of substituted or unsubstituted heterocyclylene,
e.g., substituted or unsubstituted C.sub.3-6 heterocyclylene,
substituted or unsubstituted C.sub.3-4 heterocyclylene, substituted
or unsubstituted C.sub.4-5 heterocyclylene, or substituted or
unsubstituted C.sub.5-6 heterocyclylene.
[0340] In certain embodiments, M is a group which comprises at
least one instance of substituted or unsubstituted arylene, e.g.,
substituted or unsubstituted phenylene.
[0341] In certain embodiments, M is a group which comprises at
least one instance of substituted or unsubstituted heteroarylene,
e.g., substituted or unsubstituted 5- to 6-membered
heteroarylene.
Groups R.sup.a and R.sup.b
[0342] As generally defined above, R.sup.a is hydrogen; substituted
or unsubstituted aliphatic; substituted or unsubstituted
heteroaliphatic; substituted or unsubstituted aryl; substituted or
unsubstituted heteroaryl; substituted or unsubstituted acyl; a
resin; an amino protecting group; a label optionally joined by a
linker, wherein the linker is a group consisting of one or more
combinations of substituted or unsubstituted alkylene; substituted
or unsubstituted alkenylene; substituted or unsubstituted
alkynylene; substituted or unsubstituted heteroalkylene;
substituted or unsubstituted heteroalkenylene; substituted or
unsubstituted heteroalkynylene; substituted or unsubstituted
carbocyclene; substituted or unsubstituted heterocyclene;
substituted or unsubstituted arylene; or substituted or
unsubstituted heteroarylene.
[0343] In certain embodiments, R.sup.a is hydrogen.
[0344] In certain embodiments, R.sup.a is substituted or
unsubstituted aliphatic; i.e., substituted or unsubstituted alkyl,
alkenyl, alkynyl, or carbocyclyl.
[0345] In certain embodiments, R.sup.a is substituted or
unsubstituted alkyl, e.g., substituted or unsubstituted
C.sub.1-6alkyl, substituted or unsubstituted C.sub.1-2alkyl,
substituted or unsubstituted C.sub.2-3alkyl, substituted or
unsubstituted C.sub.3-4alkyl, substituted or unsubstituted
C.sub.4-5alkyl, or substituted or unsubstituted C.sub.5-6alkyl.
Exemplary R.sup.a C.sub.1-6alkyl groups include, but are not
limited to, substituted or unsubstituted methyl (C.sub.1), ethyl
(C.sub.2), n-propyl (C.sub.3), isopropyl (C.sub.3), n-butyl
(C.sub.4), tert-butyl (C.sub.4), sec-butyl (C.sub.4), iso-butyl
(C.sub.4), n-pentyl (C.sub.5), 3-pentanyl (C.sub.5), amyl
(C.sub.5), neopentyl (C.sub.5), 3-methyl-2-butanyl (C.sub.5),
tertiary amyl (C.sub.5), and n-hexyl (C.sub.6).
[0346] In certain embodiments, R.sup.a is substituted or
unsubstituted heteroaliphatic; i.e., substituted or unsubstituted
heteroalkyl, heteroalkenyl, heteroalkynyl, or heterocyclyl.
[0347] In certain embodiments, R.sup.a is substituted or
unsubstituted aryl;
[0348] In certain embodiments, R.sup.a is substituted or
unsubstituted heteroaryl.
[0349] In certain embodiments, R.sup.a is substituted or
unsubstituted acyl, e.g., acetyl --C(.dbd.O)CH.sub.3.
[0350] In certain embodiments, R.sup.a is a resin.
[0351] In certain embodiments, R.sup.a is an amino protecting
group.
[0352] In certain embodiments, R.sup.a is a label optionally joined
by a linker.
Group R.sup.b
[0353] As generally defined above, R.sup.b is, --R.sup.B,
--OR.sup.B, --N(R.sup.B).sub.2, or --SR.sup.B, wherein each
instance of R.sup.B is, independently, hydrogen, substituted or
unsubstituted aliphatic substituted or unsubstituted
heteroaliphatic; substituted or unsubstituted aryl; substituted or
unsubstituted heteroaryl; substituted or unsubstituted acyl; a
resin; a suitable hydroxyl, amino or thiol protecting group; or two
R.sup.B groups together form a substituted or unsubstituted 5- to
6-membered heterocyclic or heteroaromatic ring.
[0354] In certain embodiments, R.sup.b is --R.sup.B, e.g., R.sup.b
is hydrogen, substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl. In certain embodiments,
R.sup.b is substituted or unsubstituted aliphatic, e.g.,
substituted or unsubstituted alkyl, alkenyl, alkynyl, or
carbocycyl.
[0355] In certain embodiments, R.sup.b is --OR.sup.B, e.g.,
--OH.
[0356] In certain embodiments, R.sup.b is --N(R.sup.H)h, e.g.,
--NH(C.dbd.O)CH.sub.3.
[0357] In certain embodiments, R.sup.b is --SR.sup.B, e.g.,
--SiH.
Group Rc and Variable x
[0358] As generally defined above, each instance of R.sup.c, is,
independently, hydrogen; substituted or unsubstituted aliphatic;
substituted or unsubstituted heteroaliphatic; substituted or
unsubstituted aryl; substituted or unsubstituted heteroaryl;
substituted or unsubstituted acyl; substituted or unsubstituted
hydroxyl; substituted or unsubstituted thiol; substituted or
unsubstituted amino; cyano; isocyano; halo; or nitro, and each
instance of x is, independently, 0, 1, 2, or 3.
[0359] In certain embodiments, each instance of x is 0 and R.sup.c
is thus absent. In certain embodiments at least one instance of x
is 1, and thus at least one instance of R.sup.c is a non-hydrogen
substituent.
Groups R.sup.KL, R.sup.LL, and R.sup.LM and Variable q
[0360] As generally defined above, each instance of R.sup.KL,
R.sup.LL, and R.sup.LM, is, independently, hydrogen; substituted or
unsubstituted aliphatic; substituted or unsubstituted
heteroaliphatic; substituted or unsubstituted aryl; substituted or
unsubstituted heteroaryl; substituted or unsubstituted acyl;
substituted or unsubstituted hydroxyl; substituted or unsubstituted
thiol; substituted or unsubstituted amino; azido; cyano; isocyano;
halo; nitro; and each instance of q is, independently 0, 1, or
2.
[0361] In certain embodiments, each instance of q is 0 and
R.sup.KL, R.sup.LL, and R.sup.LM, are thus absent. In certain
embodiments at least one instance of q is 1, and thus at least one
instance of R.sup.KL, R.sup.LL, and R.sup.LM, is a non-hydrogen
substituent.
Group R.sup.d
[0362] As generally defined above, each instance of R.sup.d is,
independently, hydrogen; substituted or unsubstituted aliphatic;
substituted or unsubstituted heteroaliphatic; substituted or
unsubstituted aryl; substituted or unsubstituted heteroaryl;
substituted or unsubstituted acyl; or an amino protecting
group.
[0363] In certain embodiments, each instance of R.sup.d is hydrogen
or substituted or unsubstituted aliphatic, e.g., substituted or
unsubstituted alkyl, alkenyl, alkynyl, or carbocycyl. In certain
embodiments, each instance of R.sup.d is hydrogen or substituted or
unsubstituted alkyl, e.g., --CH.sub.3.
Group R.sup.e
[0364] As generally defined above, each instance of R.sup.e is,
independently, hydrogen; substituted or unsubstituted aliphatic;
substituted or unsubstituted heteroaliphatic; substituted or
unsubstituted aryl; substituted or unsubstituted heteroaryl;
substituted or unsubstituted acyl; substituted or unsubstituted
hydroxyl; substituted or unsubstituted thiol; substituted or
unsubstituted amino; cyano; isocyano; halo; or nitro.
[0365] In certain embodiments, each instance of R.sup.e is hydrogen
or substituted or unsubstituted aliphatic, e.g., substituted or
unsubstituted alkyl, alkenyl, alkynyl, or carbocycyl. In certain
embodiments, each instance of R.sup.e is hydrogen or substituted or
unsubstituted, e.g., --CH.sub.3, --CH.sub.2OH, --COOH, or
--CH.sub.2COOH. In certain embodiments, R.sup.e is --CH.sub.3.
Group G and Variable v
[0366] As generally defined above, each instance of G is,
independently, a natural or unnatural amino acid or a group of the
formula:
##STR00058##
wherein:
[0367] n is 1, 2, or 3; and
[0368] each instance of R.sup.1 and R.sup.2 is independently
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; substituted or unsubstituted aryl;
substituted or unsubstituted heteroaryl; substituted or
unsubstituted acyl; substituted or unsubstituted hydroxyl;
substituted or unsubstituted thiol; substituted or unsubstituted
amino; or halo, or R.sup.1 and R.sup.2 are joined to form a
carbocyclic or heterocyclic ring;
[0369] each instance of R.sup.3 and R.sup.4 is, independently,
hydrogen; substituted or unsubstituted aliphatic; substituted or
unsubstituted heteroaliphatic; a hydroxyl protecting group when
attached to an oxygen atom, or an amino protecting group when
attached to a nitrogen atom, or two R.sup.3 groups when attached to
a nitrogen atom are joined to form a heterocyclic ring;
[0370] each instance of R.sup.4 is independently halogen, --CN,
--NO.sub.2, --N.sub.3, optionally substituted alkyl, optionally
substituted alkenyl, optionally substituted alkynyl, optionally
substituted carbocyclyl, optionally substituted phenyl, optionally
substituted heterocyclyl, optionally substituted heteroaryl,
optionally substituted alkoxy, an optionally substituted amino
group, or optionally substituted acyl;
[0371] q1 is 0, 1, 2, 3, or 4; and
[0372] each instance of v is, independently, 0 or 1.
[0373] In certain embodiments, v is 0 and G in that particular
instance is absent.
[0374] However, in certain embodiments, v is 1.
[0375] In certain embodiments, G is independently, serine,
arginine, aspartic acid, or glutamic acid. In certain embodiments,
G is serine. In certain embodiments, G is arginine. In certain
embodiments, G is aspartic acid. In certain embodiments, G is
glutamic acid.
[0376] In certain embodiments, G is a group of formula:
##STR00059##
[0377] In certain embodiments, G is a group of formula:
##STR00060##
[0378] In certain embodiments, G is a group of formula:
##STR00061##
[0379] In certain embodiments, G is a group of formula:
##STR00062##
[0380] In certain embodiments, G is a group of formula:
##STR00063##
[0381] In certain embodiments, G is a group of formula:
##STR00064##
[0382] In certain embodiments, G is a group of formula:
##STR00065##
[0383] In certain embodiments, G is a group of formula:
##STR00066##
[0384] In certain embodiments, n is 1. In certain embodiments, n is
2. In certain embodiments, n is 3.
[0385] In certain embodiments, at least one instance of R.sup.1 is
hydrogen.
[0386] In certain embodiments, at least one instance of R.sup.1 is
substituted or unsubstituted aliphatic, e.g., substituted or
unsubstituted alkyl, alkenyl, alkynyl, or carbocyclyl. In certain
embodiments, at least one instance of R.sup.1 is substituted or
unsubstituted alkyl. e.g., --CH.sub.3.
[0387] In certain embodiments, at least one instance of R.sup.2 is
hydrogen.
[0388] In certain embodiments, at least one instance of R.sup.2 is
substituted or unsubstituted aliphatic, e.g., substituted or
unsubstituted alkyl, alkenyl, alkynyl, or carbocyclyl. In certain
embodiments, at least one instance of R.sup.2 is substituted or
unsubstituted alkyl, e.g., --CH.sub.3.
[0389] In certain embodiments, at least one instance of R.sup.1 is
hydrogen and at least one instance of R.sup.2 is hydrogen.
[0390] In certain embodiments, at least one instance of R.sup.1 is
hydrogen and at least one instance of R.sup.2 is substituted or
unsubstituted alkyl, e.g., --CH.sub.3.
[0391] In certain embodiments, at least one instance of R.sup.1 and
R.sup.2 is substituted or unsubstituted alkyl. e.g., substituted or
unsubstituted C.sub.1-6alkyl, substituted or unsubstituted
C.sub.1-2alkyl, substituted or unsubstituted C.sub.2-3alkyl,
substituted or unsubstituted C.sub.3-4alkyl, substituted or
unsubstituted C.sub.4-5alkyl, or substituted or unsubstituted
C.sub.5-6alkyl. Exemplary C.sub.1-6alkyl groups include, but are
not limited to, substituted or unsubstituted methyl (C.sub.1),
ethyl (C.sub.2), n-propyl (C.sub.3), isopropyl (C.sub.3), n-butyl
(C.sub.4), tert-butyl (C.sub.4), sec-butyl (C.sub.4), iso-butyl
(C.sub.4), n-pentyl (C.sub.5), 3-pentanyl (C.sub.5), amyl
(C.sub.5), neopentyl (C.sub.5), 3-methyl-2-butanyl (C.sub.5),
tertiary amyl (C.sub.5), and n-hexyl (C.sub.6).
[0392] In certain embodiments, at least one instance of R.sup.3 is
hydrogen or substituted or unsubstituted aliphatic, e.g.,
substituted or unsubstituted alkyl, alkenyl, alkynyl, or
carbocyclyl. In certain embodiments, at least one instance of
R.sup.3 is substituted or unsubstituted alkyl, e.g., substituted or
unsubstituted C.sub.1-6alkyl, substituted or unsubstituted
C.sub.1-2alkyl, substituted or unsubstituted C.sub.2-3alkyl,
substituted or unsubstituted C.sub.3-4alkyl, substituted or
unsubstituted C.sub.4-5alkyl, or substituted or unsubstituted
C.sub.5-6alkyl. Exemplary C.sub.1-6alkyl groups include, but are
not limited to, substituted or unsubstituted methyl (C.sub.1),
ethyl (C.sub.2), n-propyl (C.sub.3), isopropyl (C.sub.3), n-butyl
(C.sub.4), tert-butyl (C.sub.4), sec-butyl (C.sub.4), iso-butyl
(C.sub.4), n-pentyl (C.sub.5), 3-pentanyl (C.sub.5), amyl
(C.sub.5), neopentyl (C.sub.5), 3-methyl-2-butanyl (C.sub.5),
tertiary amyl (C.sub.5), and n-hexyl (C.sub.6).
[0393] In certain embodiments, two instance of R.sup.3 when
attached to the same nitrogen atom are joined to form a
heterocyclic ring.
[0394] In certain embodiments, R.sup.4 is hydrogen or substituted
or unsubstituted aliphatic, e.g., substituted or unsubstituted
alkyl, alkenyl, alkynyl, or carbocyclyl. In certain embodiments,
R.sup.4 is substituted or unsubstituted alkyl, e.g., substituted or
unsubstituted C.sub.1-6alkyl, substituted or unsubstituted
C.sub.1-2alkyl, substituted or unsubstituted C.sub.2-3alkyl,
substituted or unsubstituted C.sub.3-4alkyl, substituted or
unsubstituted C.sub.4-5alkyl, or substituted or unsubstituted
C.sub.5-6alkyl. Exemplary C.sub.1-6alkyl groups include, but are
not limited to, substituted or unsubstituted methyl (C.sub.1),
ethyl (C.sub.2), n-propyl (C.sub.3), isopropyl (C.sub.3), n-butyl
(C.sub.4), tert-butyl (C.sub.4), sec-butyl (C.sub.4), iso-butyl
(C.sub.4), n-pentyl (C.sub.5), 3-pentanyl (C.sub.5), amyl
(C.sub.5), neopentyl (C.sub.5), 3-methyl-2-butanyl (C.sub.5),
tertiary amyl (C.sub.5), and n-hexyl (C.sub.6).
[0395] In certain embodiments, q1 is 0. In certain embodiments, q1
is 1. In certain embodiments, q1 is 2. In certain embodiments, q1
is 3. In certain embodiments, q1 is 4.
[0396] In certain embodiments, R.sup.q is halogen, --CN,
--NO.sub.2, --N.sub.3, or optionally substituted alkyl.
[0397] In certain embodiments,
##STR00067##
in Formula (P-I), (I), (P-II), and (II) is one of the following
formulae:
##STR00068##
Group XAA and Variables j, y, p, w, z, s and t
[0398] As generally defined above, each instance of X.sub.AA is,
independently, a natural or unnatural amino acid. Various natural
and unnatural amino acids are generally described herein, and
encompass alpha and beta amino acids moieties joined via peptide
bonds.
[0399] As generally defined above, and each instance of t, w and z
is, independently, an integer between 0 and 100, inclusive.
[0400] In certain embodiments z is an integer of 1 to 10,
inclusive. In certain embodiments z is an integer of 2 to 10,
inclusive. In certain embodiments, z is 1. In certain embodiments,
z is 2. In certain embodiments, z is 3. In certain embodiments, z
is 4. In certain embodiments, z is 5. In certain embodiments, z is
6. In certain embodiments, z is 7. In certain embodiments, z is 9.
In certain embodiments, z is 10.
[0401] In certain embodiments w is 0, 1, or 2 and z is an integer
between 0 and 100, inclusive. In certain embodiments w is 0, 1, or
2 and z is an integer between 0 and 75, inclusive. In certain
embodiments w is 0, 1, or 2 and z is an integer between 0 and 50,
inclusive. In certain embodiments w is 0, 1, or 2 and z is an
integer between 0 and 25, inclusive. In certain embodiments w is 0,
1, or 2 and z is an integer between 0 and 10, inclusive. In certain
embodiments w is 0, 1, or 2 and z is an integer between 0 and 5,
inclusive.
[0402] In certain embodiments w is 0.
[0403] In certain embodiments w is 0, 1, or 2 and t is an integer
between 0 and 100, inclusive. In certain embodiments w is 0, 1, or
2 and t is an integer between 0 and 75, inclusive. In certain
embodiments w is 0, 1, or 2 and t is an integer between 0 and 50,
inclusive. In certain embodiments w is 0, 1, or 2 and t is an
integer between 0 and 25, inclusive. In certain embodiments w is 0,
1, or 2 and t is an integer between 0 and 10, inclusive. In certain
embodiments w is 0, 1, or 2 and t is an integer between 0 and 5,
inclusive.
[0404] As generally defined above, y is independently, an integer
of 1 to 8, inclusive. In certain embodiments, y is independently,
an integer of 1 to 7, inclusive. In certain embodiments, y is
independently, an integer of 1 to 6, inclusive. In certain
embodiments, y is independently, an integer of 1 to 5, inclusive.
In certain embodiments, y is independently, 1, 2, 3, or 4. In
certain embodiments, y is 1. In certain embodiments, y is 2. In
certain embodiments, y is 3. In certain embodiments, y is 4. In
certain embodiments, y is 5. In certain embodiments, y is 6. In
certain embodiments, y is 7. In certain embodiments, y is 8.
[0405] As generally defined above, j is, independently, an integer
between 1 to 10, inclusive, e.g., j is 1, 2, 3, 4, 5, 6, 7, 8, 9,
or 10. In certain embodiments, j is 1. In certain embodiments, j is
2.
[0406] As generally defined above, each instance of p is,
independently, 1 or 2. In certain embodiments, p is 1. In certain
embodiments, p is 2.
[0407] In certain embodiments, j is 1 and p is 1. In certain
embodiments, j is 1 and p is 2.
[0408] In certain embodiments, j is 1, p is 1, and y is 1. In
certain embodiments, j is 1, p is 1, and y is 2. In certain
embodiments, j is 1, p is 1, and y is 3. In certain embodiments, j
is 1, p is 1, and y is 4.
[0409] In certain embodiments, j is 1, p is 2, and y is 1. In
certain embodiments, j is 1, p is 2, and y is 2. In certain
embodiments, j is 1, p is 2, and y is 3. In certain embodiments, j
is 1, p is 2, and y is 4.
[0410] As generally defined above, s is 0, 1, or 2. In certain
embodiments, s is 0. In certain embodiments, s is 1. In certain
embodiments, s is 2.
[0411] In certain embodiments, j is 1, p is 1, and s is 0 or 1. In
certain embodiments, j is 1, p is 2, and s is 0 or 1.
[0412] In certain embodiments, j is 1, p is 1, s is 0 or 1, and y
is 1. In certain embodiments, j is 1, p is 1, s is 0 or 1, and y is
2. In certain embodiments, j is 1, p is 1, s is 0 or 1, and y is 3.
In certain embodiments, j is 1, p is 1, s is 0 or 1, and y is
4.
[0413] In certain embodiments, j is 1, p is 2, s is 0 or 1, and y
is 1. In certain embodiments, j is 1, p is 2, s is 0 or 1, and y is
2. In certain embodiments, j is 1, p is 2, s is 0 or 1, and y is 3.
In certain embodiments, j is 1, p is 2, s is 0 or 1, and y is
4.
[0414] The variables y and z indicate how many amino acids, defined
by the variable [X.sub.AA], there are between amino acids
containing terminally unsaturated amino acid side chain(s), as
provided in polypeptides of Formulae (P-I), (P-II), (I) and (II).
For example, as depicted below for a polypeptide of Formula (P-II),
wherein s is 0; i represents one site of an
alpha,alpha-disubstituted (terminally unsaturated amino acid side
chain) amino acid, variable y provides information as to the
position of the amino acid containing a terminally unsaturated side
chain on the N-terminal side of i, such as the positions i-3, i-4,
i-6, and i-7, and z provides information as to the position of the
amino acid containing a terminally unsaturated side chain on the
C-terminal side of i, such as the positions i+3, i+4, i+6, and i+7.
Table 4 correlates these specific locations of i relative to the
variables y and z for formula (P-II-a).
##STR00069##
TABLE-US-00004 TABLE 4 i - 7 i - 6 i - 4 i - 3 i i + 3 i + 4 i + 6
i + 7 y 6 5 3 2 z 2 3 5 6
[0415] In certain embodiments, each instance of y and z are,
independently, 2, 3, 5, or 6.
[0416] In certain embodiments, both y and z are 2. In certain
embodiments, both y and z are 3. In certain embodiments, both y and
z are 5. In certain embodiments, both y and z are 6.
[0417] In certain embodiments, y is 2 and z is 3. In certain
embodiments, y is 2 and z is 5. In certain embodiments, y is 2 and
z is 6.
[0418] In certain embodiments, y is 3 and z is 2. In certain
embodiments, y is 3 and z is 5. In certain embodiments, y is 3 and
z is 6.
[0419] In certain embodiments, y is 5 and z is 2. In certain
embodiments, y is 5 and z is 3. In certain embodiments, y is 5 and
z is 6.
[0420] In certain embodiments, y is 6 and z is 2. In certain
embodiments, y is 6 and z is 3. In certain embodiments, y is 6 and
z is 5.
Additional Embodiments
[0421] Various combinations of the above embodiments are
contemplated herein.
[0422] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2OH; j is 1; p is 1; v is 0; x is 0; y is 2; and
corresponds to a double bond.
[0423] For example, in certain embodiments of Formula (P-I) and
(I), K and L are independently --CH.sub.2CH.sub.2-- or
--OCH.sub.2--; R.sup.d is --H; R.sup.e is --CH.sub.2OH; j is 1; p
is 1; v is 0; x is 0; y is 2; and, corresponds to a double
bond.
[0424] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2CH.sub.2CH.sub.2--; R.sup.d is --H;
R.sup.e is --CH.sub.2OH; j is 1; p is 1; v is 0; x is 0; y is 2;
and, corresponds to a double bond.
[0425] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2 CH.sub.2OH; j is 1; p is 1; v is 0; x is 0; y is 2; and,
corresponds to a double bond.
[0426] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is --H; j is
1; p is 1; v is 0; x is 0; y is 2; and, corresponds to a double
bond.
[0427] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.3; j is 1; p is 1; v is 0; x is 0; y is 2; and,
corresponds to a double bond. In certain embodiments of Formula
(P-I) and (I), K is --CH.sub.2--; L is --(CH.sub.2).sub.2--;
R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p is 1; v is 0; x is
0; y is 2; and, corresponds to a double bond. In certain
embodiments of Formula (P-I) and (I), K is --CH.sub.2--; L is
--(CH.sub.2).sub.3--; R.sup.d is --H; R.sup.e is -CH.sub.3; j is 1;
p is 1; v is 0; x is 0; y is 2; and, corresponds to a double
bond.
[0428] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.3; j is 1; p is 1; v is 0; x is 0; y is 3; and,
corresponds to a double bond. In certain embodiments of Formula
(P-I) and (I), K is --CH.sub.2--; L is --(CH.sub.2).sub.2--;
R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p is 1; v is 0; x is
0; y is 3; and, corresponds to a double bond. In certain
embodiments of Formula (P-I) and (I), K is --CH.sub.2--; L is
--(CH.sub.2).sub.3--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; v is 0; x is 0; y is 3; and, corresponds to a double
bond.
[0429] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.3; j is 1; p is 1; v is 0; x is 0; y is 5; and,
corresponds to a double bond. In certain embodiments of Formula
(P-I) and (I), K is --CH.sub.2--; L is --(CH.sub.2).sub.2--;
R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p is 1; v is 0; x is
0; y is 5; and, corresponds to a double bond. In certain
embodiments of Formula (P-I) and (I), K is --CH.sub.2--; L is
--(CH.sub.2).sub.3--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; v is 0; x is 0; y is 5; and, corresponds to a double
bond.
[0430] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.3; j is 1; p is 1; v is 0; x is 0; y is 6; and,
corresponds to a double bond. In certain embodiments of Formula
(P-I) and (I), K is --CH.sub.2--; L is --(CH.sub.2).sub.2--;
R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p is 1; v is 0; x is
0; y is 6; and, corresponds to a double bond. In certain
embodiments of Formula (P-I) and (I), K is --CH.sub.2--; L is
--(CH.sub.2).sub.3--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; v is 0; x is 0; y is 6; and, corresponds to a double
bond.
[0431] For example, in certain embodiments of Formula (P-I) and
(I), K is --CH.sub.2O--, wherein O is linked to the heterocyclyl
with nitrogen and CH.sub.2 is linked to "," and L is --CH.sub.2--;
R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p is 1; v is 0; x is
0; y is 2; and, corresponds to a double bond. In certain
embodiments of Formula (P-I) and (I), K is --CH.sub.2O--, wherein O
is linked to the heterocyclyl with nitrogen and CH.sub.2 is linked
to "," and L is --(CH.sub.2).sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.3; j is 1; p is 1; v is 0; x is 0; y is 2; and,
corresponds to a double bond. In certain embodiments of Formula
(P-I) and (I), K is --CH.sub.2O--, wherein O is linked to the
heterocyclyl with nitrogen and CH.sub.2 is linked to "," and L is
--(CH.sub.2).sub.3--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; v is 0; x is 0; y is 2; and, corresponds to a double
bond.
[0432] For example, in certain embodiments of Formula (P-I) and
(I), K is --CH.sub.2O--, wherein O is linked to the heterocyclyl
with nitrogen and CH.sub.2 is linked to "," and L is --CH.sub.2--;
R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p is 1; v is 0; x is
0; y is 3; and, corresponds to a double bond. In certain
embodiments of Formula (P-I) and (I), K is --CH.sub.2O--, wherein O
is linked to the heterocyclyl with nitrogen and CH.sub.2 is linked
to "," and L is --(CH.sub.2).sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.3; j is 1; p is 1; v is 0; x is 0; y is 3; and,
corresponds to a double bond. In certain embodiments of Formula
(P-I) and (I), K is --CH.sub.2O--, wherein O is linked to the
heterocyclyl with nitrogen and CH.sub.2 is linked to "," and L is
--(CH.sub.2).sub.3--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; v is 0; x is 0; y is 3; and, corresponds to a double
bond.
[0433] For example, in certain embodiments of Formula (P-I) and
(I), K is --CH.sub.2O--, wherein O is linked to the heterocyclyl
with nitrogen and CH.sub.2 is linked to "," and L is --CH.sub.2--;
R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p is 1; v is 0; x is
0; y is 5; and, corresponds to a double bond. In certain
embodiments of Formula (P-I) and (I), K is --CH.sub.2O--, wherein O
is linked to the heterocyclyl with nitrogen and CH.sub.2 is linked
to "," and L is --(CH.sub.2).sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.3; j is 1; p is 1; v is 0; x is 0; y is 5; and,
corresponds to a double bond. In certain embodiments of Formula
(P-I) and (I), K is --CH.sub.2O--, wherein O is linked to the
heterocyclyl with nitrogen and CH.sub.2 is linked to "," and L is
--(CH.sub.2).sub.3--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; v is 0; x is 0; y is 5; and, corresponds to a double
bond.
[0434] For example, in certain embodiments of Formula (P-I) and
(I), K is --CH.sub.2O--, wherein O is linked to the heterocyclyl
with nitrogen and CH.sub.2 is linked to "," and L is --CH.sub.2--;
R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p is 1; v is 0; x is
0; y is 6; and, corresponds to a double bond. In certain
embodiments of Formula (P-I) and (I), K is --CH.sub.2O--, wherein O
is linked to the heterocyclyl with nitrogen and CH.sub.2 is linked
to "," and L is --(CH.sub.2).sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.3; j is 1; p is 1; v is 0; x is 0; y is 6; and,
corresponds to a double bond. In certain embodiments of Formula
(P-I) and (I), K is --CH.sub.2O--, wherein O is linked to the
heterocyclyl with nitrogen and CH.sub.2 is linked to "," and L is
--(CH.sub.2).sub.3--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; v is 0; x is 0; y is 6; and, corresponds to a double
bond.
[0435] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.3COOH; j is 1; p is 1; v is 0; x is 0; y is 2; and,
corresponds to a double bond.
[0436] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2 CH.sub.2COOH; j is 1; p is 1; v is 0; x is 0; y is 2;
and, corresponds to a double bond.
[0437] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2OH; j is 1; p is 2; x is 0; v is 0; y is 2; and,
corresponds to a double bond.
[0438] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2OH; j is 1; p is 1; v is 0; x is 2; y is 2; and,
corresponds to a double bond.
[0439] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2OH; j is 1; p is 1; v is 1; x is 0; y is 2; [G] is
serine; and, corresponds to a double bond.
[0440] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2OH; j is 1; p is 1; v is 1; x is 0; y is 2; [G] is
threonine; and, corresponds to a double bond.
[0441] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2OH; j is 1; p is 1; v is 1; x is 0; y is 2; [G] is
aspartic acid; and, corresponds to a double bond.
[0442] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2OH; j is 1; p is 1; v is 1; x is 0; y is 2; [G] is
glutamic acid; and, corresponds to a double bond.
[0443] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2OH; j is 1; p is 1; v is 1; x is 0; y is 2; [G] is
asparagine; and, corresponds to a double bond.
[0444] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2OH; j is 1; p is 1; v is 1; x is 0; y is 2; [G] is;
##STR00070##
and, corresponds to a double bond.
[0445] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2OH; j is 1; p is 1; q is 0; v is 0; y is 2; and,
corresponds to a double bond.
[0446] For example, in certain embodiments of Formula (P-I) and
(I), K and L are --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.2OH; j is 1; p is 1; q is 0; v is 1; y is 2; [G] is;
##STR00071##
and, corresponds to a double bond.
[0447] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z
is 2; and, corresponds to a double bond. In certain embodiments of
Formula (P-II) and (II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--;
M is --CH.sub.2--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p
is 1; s is 0; v is 0; x is 0; y is 2; z is 2; and, corresponds to a
double bond. In certain embodiments of Formula (P-II) and (II),
L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.2--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 2; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.3--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 2; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.4--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 2; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.5--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 2; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.6--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2, z is 2; and, corresponds
to a double bond.
[0448] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z
is 3; and, corresponds to a double bond. In certain embodiments of
Formula (P-II) and (II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--;
M is --CH.sub.2--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p
is 1; s is 0; v is 0; x is 0; y is 2; z is 3; and, corresponds to a
double bond. In certain embodiments of Formula (P-II) and (II),
L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.2--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 3; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.3--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 3; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.4--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 3; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.5--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 3; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.6--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 3; and, corresponds
to a double bond.
[0449] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z
is 6; and, corresponds to a double bond. In certain embodiments of
Formula (P-II) and (II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--;
M is --CH.sub.2--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p
is 1; s is 0; v is 0; x is 0; y is 2; z is 6; and, corresponds to a
double bond. In certain embodiments of Formula (P-II) and (II),
L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.2--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 6; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.3--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 6; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.4--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 2; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.5--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 6; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; M is
--(CH.sub.2).sub.6--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 6; and, corresponds
to a double bond.
[0450] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2, K, and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0 v is 0; x is 0; y is 2; z is
2; and, corresponds to a double bond. In certain embodiments of
Formula (P-II) and (II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--;
K is --CH.sub.2--; M is --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.3; j is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 2;
and, corresponds to a double bond. In certain embodiments of
Formula (P-II) and (II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--;
K is --CH.sub.2--; M is --(CH.sub.2).sub.2--; R.sup.d is --H;
R.sup.e is --CH.sub.3; j is 1; p is 1; s is 0; v is 0; x is 0; y is
2; z is 2; and, corresponds to a double bond. In certain
embodiments of Formula (P-II) and (II), L.sub.1, L.sub.2 are
--(CH.sub.2).sub.3--; K is --CH.sub.2--; M is --(CH.sub.2).sub.3--;
R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p is 1; s is 0; v is
0; x is 0; y is 2; z is 2; and, corresponds to a double bond. In
certain embodiments of Formula (P-II) and (II), L.sub.1, L.sub.2
are --(CH.sub.2).sub.3--; K is --CH.sub.2--; M is
--(CH.sub.2).sub.4--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 2; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; K is --CH.sub.2--;
M is --(CH.sub.2).sub.5--; R.sup.d is --H; R.sup.e is --CH.sub.3; j
is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 2; and,
corresponds to a double bond. In certain embodiments of Formula
(P-II) and (II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; K is
--CH.sub.2--; M is --(CH.sub.2).sub.6--; R.sup.d is --H; R.sup.e is
CH.sub.3; j is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 2;
and, corresponds to a double bond.
[0451] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2, K, and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z
is 3; and, corresponds to a double bond. In certain embodiments of
Formula (P-II) and (II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--;
K is --CH.sub.2--; M is --CH.sub.2--; R.sup.d is --H; R.sup.e is
CH.sub.3; j is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 3;
and, corresponds to a double bond. In certain embodiments of
Formula (P-II) and (II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--;
K is --CH.sub.2--; M is --(CH.sub.2).sub.2--; R.sup.d is --H;
R.sup.e is CH.sub.3; j is 1; p is 1; s is 0; v is 0; x is 0; y is
2; z is 3; and, corresponds to a double bond. In certain
embodiments of Formula (P-II) and (II), L.sub.1, L.sub.2 are
--(CH.sub.2).sub.3--; K is --CH.sub.2--; M is --(CH.sub.2).sub.3--;
R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p is 1; s is 0; v is
0; x is 0; y is 2; z is 3; and, corresponds to a double bond. In
certain embodiments of Formula (P-II) and (II), L.sub.1, L.sub.2
are --(CH.sub.2).sub.3--; K is --CH.sub.2--; M is
--(CH.sub.2).sub.4--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0 v is 0; x is 0; y is 2; z is 3; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; K is --CH.sub.2--;
M is --(CH.sub.2)--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1;
p is 1; s is 0; v is 0; x is 0; y is 2; z is 3; and, corresponds to
a double bond. In certain embodiments of Formula (P-II) and (II),
L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; K is --CH.sub.2--; M is
--(CH.sub.2).sub.6--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 3; and, corresponds
to a double bond.
[0452] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2, K, and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z
is 6; and, corresponds to a double bond. In certain embodiments of
Formula (P-II) and (II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--;
K is --CH.sub.2--; M is --CH.sub.2--; R.sup.d is --H; R.sup.e is
--CH.sub.3; j is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 6;
and, corresponds to a double bond. In certain embodiments of
Formula (P-II) and (II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--;
K is --CH.sub.2--; M is --(CH.sub.2).sub.2--; R.sup.d is --H;
R.sup.e is --CH.sub.3; j is 1; p is 1; s is 0; v is 0; x is 0; y is
2; z is 6; and, corresponds to a double bond. In certain
embodiments of Formula (P-II) and (II), L.sub.1, L.sub.2 are
--(CH.sub.2).sub.3--; K is --CH.sub.2--; M is (CH.sub.2).sub.3--;
R.sup.d is --H; R.sup.e is --CH.sub.3; j is 1; p is 1; s is 0; v is
0; x is 0; y is 2; z is 6; and, corresponds to a double bond. In
certain embodiments of Formula (P-II) and (II), L.sub.1, L.sub.2
are --(CH.sub.2).sub.3--; K is --CH.sub.2--; M is
--(CH.sub.2).sub.4--; R.sup.d is --H; R.sup.e is --CH.sub.3; j is
1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 2; and, corresponds
to a double bond. In certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; K is --CH.sub.2--;
M is --(CH.sub.2).sub.5--; R.sup.d is --H; R.sup.e is --CH.sub.3; j
is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 6; and,
corresponds to a double bond. In certain embodiments of Formula
(P-II) and (II), L.sub.1, L.sub.2 are --(CH.sub.2).sub.3--; K is
--CH.sub.2--; M is --(CH.sub.2)--; R.sup.d is --H; R.sup.e is
--CH.sub.3; j is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z is 6;
and, corresponds to a double bond.
[0453] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2 CH.sub.2--; R.sup.d is
--H; R.sup.e is --H; j is 1; p is 1; s is 0; v is 0; x is 0; y is
2; z is 2; and, corresponds to a double bond.
[0454] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2 CH.sub.2 CH.sub.2--;
R.sup.d is --H; R.sup.e is --H; j is 1; p is 1; s is 0; v is 0; x
is 0; y is 2; z is 2; and, corresponds to a double bond.
[0455] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --CH.sub.3; j is 1; p is 1; s is 0; v is 0; x is 0; y is
2; z is 2; and, corresponds to a double bond.
[0456] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --CH.sub.2CH.sub.3; j is 1; p is 1; s is 0; v is 0; x is
0; y is 2; z is 2; and, corresponds to a double bond.
[0457] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 2; s is 0; v is 0; x is 0; y is 2; z
is 2; and, corresponds to a double bond.
[0458] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 1; v is 0; x is 0; y is 2; z
is 2; and, corresponds to a double bond.
[0459] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 0; x is 2; y is 2; z
is 2; and, corresponds to a double bond.
[0460] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 0; x is 0; y is 2; z
is 3; and, corresponds to a double bond.
[0461] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1 is s 1; s is 0; v is 0; x is 0; y is 2; z is
4; and, corresponds to a double bond.
[0462] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0, v is 0; x is 0; y is 2; z
is 5; and, corresponds to a double bond.
[0463] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 1; x is 0; y is 2; z
is 2; [G] is serine; and, corresponds to a double bond.
[0464] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 1; x is 0; y is 2; z
is 2; [G] is threonine; and, corresponds to a double bond.
[0465] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 1; x is 0; y is 2; z
is 2; [G] is aspartic acid; and, corresponds to a double bond.
[0466] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 1; x is 0; y is 2; z
is 2; [G] is glutamic acid; and, corresponds to a double bond.
[0467] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 1; x is 0; y is 2; z
is 2; [G] is asparagine; and, corresponds to a double bond.
[0468] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; s is 0; v is 1; x is 0; y is 2; z
is 2; [G] is
##STR00072##
and, corresponds to a double bond.
[0469] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; q is 0; s is 0; v is 0; y is 2; z
is 2; and, corresponds to a double bond.
[0470] For example, in certain embodiments of Formula (P-II) and
(II), L.sub.1, L.sub.2 and M are --CH.sub.2--; R.sup.d is --H;
R.sup.e is --H; j is 1; p is 1; q is 0; s is 0; v is 1; y is 2; z
is 2; [G] is
##STR00073##
and, corresponds to a double bond.
[0471] In any of the above embodiments, wherein [G] is a group of
formula:
##STR00074##
in certain embodiments, w is 0, and R.sup.a is
--C(CH.sub.3).sub.3.
[0472] In any of the above embodiments, wherein [G] is a group of
any one of the following formulae:
##STR00075##
[0473] In any of the above embodiments, wherein
##STR00076##
is of any one of the following formulae:
##STR00077##
Methods of Use
[0474] The present disclosure provides methods of treating a
disease, disorder, or condition comprising administering to a
subject diagnosed with or having susceptibility to the disease,
disorder, or condition, a therapeutically effective amount of a
stitched or stapled polypeptide as described herein, or
pharmaceutically acceptable salt or stereoisomer thereof. Exemplary
diseases, disorders, or conditions which may be treated by
administration of a stitched or stapled polypeptide as described
herein comprise proliferative, neurological, immunological,
endocrinologic, cardiovascular, hematologic, and inflammatory
diseases, disorders, or conditions, and conditions characterized by
premature or unwanted cell death.
[0475] As used herein a proliferative disease, condition, or
disorder includes, but is not limited to, cancer, hematopoietic
neoplastic disorders, proliferative breast disease, proliferative
disorders of the lung, proliferative disorders of the colon,
proliferative disorders of the liver, and proliferative disorders
of the ovary.
[0476] Examples of cancers treatable by the methods disclosed
herein include carcinoma, sarcoma, or metastatic disorders, breast
cancer, ovarian cancer, colon cancer, lung cancer, fibrosarcoma,
myosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma,
chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma,
lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's
tumor, leiomyosarcoma, rhabdomyosarcoma, gastric cancer, esophageal
cancer, rectal cancer, pancreatic cancer, ovarian cancer, prostate
cancer, uterine cancer, cancer of the head and neck, skin cancer,
brain cancer, squamnous cell carcinoma, sebaceous gland carcinoma,
papillary carcinoma, papillary adenocarcinoma, cystadenocarcinoma,
medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma,
hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal
carcinoma. Wilm's tumor, cervical cancer, testicular cancer, small
cell lung carcinoma, non-small cell lung carcinoma, bladder
carcinoma, epithelial carcinoma, glioma, astrocytoma,
medulloblastoma, craniopharyngioma, ependymoma, pinealoma,
hemangioblastoma, acoustic neuroma, oligodendroglioma, meningioma,
melanoma, neuroblastoma, retinoblastoma, leukemia, lymphoma, or
Kaposi sarcoma.
[0477] Examples of hematopoietic neoplastic disorders treatable by
the above method includes diseases involving
hyperplastic/neoplastic cells of hematopoietic origin, e.g.,
arising from myeloid, lymphoid or erythroid lineages, or precursor
cells thereof. In certain embodiments, the diseases arise from
poorly differentiated acute leukemias, e.g., erythroblastic
leukemia and acute megakaryoblastic leukemia. Additional exemplary
myeloid disorders include, but are not limited to, acute promyeloid
leukemia (APML), acute myelogenous leukemia (AML) and chronic
myelogenous leukemia (CML) (reviewed in Vaickus, L. (1991) Crit
Rev. in Oncol./Hemotol. 11:267-97); lymphoid malignancies include,
but are not limited to acute lymphoblastic leukemia (ALL) which
includes B-lineage ALL and T-lineage ALL, chronic lymphocytic
leukemia (CLL), prolymphocytic leukemia (PLL), hairy cell leukemia
(HLL) and Waldenstrom's macroglobulinemia (WM). Additional forms of
malignant lymphomas include, but are not limited to non-Hodgkin
lymphoma and variants thereof, peripheral T cell lymphomas, adult T
cell leukemia/lymphoma (ATL), cutaneous T-cell lymphoma (CTCL),
large granular lymphocytic leukemia (LGF), Hodgkin's disease and
Reed-Stemberg disease.
[0478] Examples of proliferative breast disease treatable by the
methods disclosed herein include epithelial hyperplasia, sclerosing
adenosis, and small duct papillomas; tumors, e.g., stromal tumors
such as fibroadenoma, phyllodes tumor, and sarcomas, and epithelial
tumors such as large duct papilloma; carcinoma of the breast
including in situ (noninvasive) carcinoma that includes ductal
carcinoma in situ (including Paget's disease) and lobular carcinoma
in situ, and invasive (infiltrating) carcinoma including, but not
limited to, invasive ductal carcinoma, invasive lobular carcinoma,
medullary carcinoma, colloid (mucinous) carcinoma, tubular
carcinoma, and invasive papillary carcinoma, and miscellaneous
malignant neoplasms. Disorders in the male breast include, but are
not limited to, gynecomastia and carcinoma.
[0479] Examples of proliferative disorders of the lung treatable by
the methods disclosed herein include, but are not limited to,
bronchogenic carcinoma, including paraneoplastic syndromes,
bronchioloalveolar carcinoma, neuroendocrine tumors, such as
bronchial carcinoid, miscellaneous tumors, and metastatic tumors;
pathologies of the pleura, including inflammatory pleural
effusions, noninflammatory pleural effusions, pneumothorax, and
pleural tumors, including solitary fibrous tumors (pleural fibroma)
and malignant mesothelioma.
[0480] Examples of proliferative disorders of the colon treatable
by the methods disclosed herein include, but are not limited to,
non-neoplastic polyps, adenomas, familial syndromes, colorectal
carcinogenesis, colorectal carcinoma, and carcinoid tumors.
[0481] Examples of proliferative disorders of the liver treatable
by the methods disclosed herein include, but are not limited to,
nodular hyperplasias, adenomas, and malignant tumors, including
primary carcinoma of the liver and metastatic tumors.
[0482] Examples of proliferative disorders of the ovary treatable
by the methods disclosed herein include, but are not limited to,
ovarian tumors such as, tumors of coelomic epithelium, serous
tumors, mucinous tumors, endometeriod tumors, clear cell
adenocarcinoma, cystadenofibroma, brenner tumor, surface epithelial
tumors; germ cell tumors such as mature (benign) teratomas,
monodermal teratomas, immature malignant teratomas, dysgerminoma,
endodermal sinus tumor, choriocarcinoma; sex cord-stomal tumors
such as, granulosa-theca cell tumors, thecomafibromas,
androblastomas, hill cell tumors, and gonadoblastoma; and
metastatic tumors such as Krukenberg tumors.
[0483] The polypeptides described herein can also be used to treat,
prevent or diagnose conditions characterised by overactive cell
death or cellular death due to physiologic insult etc. Some
examples of conditions characterized by premature or unwanted cell
death are or alternatively unwanted or excessive cellular
proliferation include, but are not limited to
hypocellular/hypoplastic, acellular/aplastic, or
hypercellular/hyperplastic conditions. Some examples include
hematologic disorders including but not limited to fanconi anemia,
aplastic anemia, thalaessemia, congenital neutropenia,
myelodysplasia. The polypeptides disclosed herein can be used to
decrease apoptosis and can be used to treat disorders associated
with an undesirable level of cell death. Thus, the anti-apoptotic
of the peptides disclosed herein can be used to treat disorders
such as those that lead to cell death associated with viral
infection, e.g., associated with infection with human
immunodeficiency virus (HIV).
[0484] The peptides disclosed herein can be used to treat disorders
associated with undesirable cell death. A wide variety of
neurological diseases are characterized by the gradual loss of
specific sets of neurons, and the anti-apoptotic peptides can be
used in the treatment of these disorders. Such disorders include
Alzheimer's disease. Parkinson's disease, amyotrophic lateral
sclerosis (ALS) retinitis pigmentosa, spinal muscular atrophy, and
various forms of cerebellar degeneration. The cell loss in these
diseases does not induce an inflammatory response, and apoptosis
appears to be the mechanism of cell death. In addition, a number of
hematologic diseases are associated with a decreased production of
blood cells. These disorders include anemia associated with chronic
disease, aplastic anemia, chronic neutropenia, and the
myelodysplastic syndromes. Disorders of blood cell production, such
as myelodysplastic syndrome and some forms of aplastic anemia, are
associated with increased apoptotic cell death within the bone
marrow. These disorders could result from the activation of genes
that promote apoptosis, acquired deficiencies in stromal cells or
hematopoietic survival factors, or the direct effects of toxins and
mediators of immune responses. Two common disorders associated with
cell death are myocardial infarctions and stroke. In both
disorders, cells within the central area of ischemia, which is
produced in the event of acute loss of blood flow, appear to die
rapidly as a result of necrosis. However, outside the central
ischemic zone, cells die over a more protracted time period and
morphologically appear to die by apoptosis.
[0485] Some examples of neurologic disorders that can be treated
with the polypeptides described herein include but are not limited
to Alzheimer's Disease, Down's Syndrome, Dutch Type Hereditary
Cerebral Hemorrhage Amyloidosis, Reactive Amyloidosis. Familial
Amyloid Nephropathy with Urticaria and Deafness, Muckle-Wells
Syndrome, Idiopathic Myeloma; Macroglobulinemia-Associated Myeloma,
Familial Amyloid Polyneuropathy, Familial Amyloid Cardiomyopathy,
Isolated Cardiac Amyloid, Systemic Senile Amyloidosis, Adult Onset
Diabetes. Insulinoma, Isolated Atrial Amyloid. Medullary Carcinoma
of the Thyroid, Familial Amyloidosis, Hereditary Cerebral
Hemorrhage with Amyloidosis, Familial Amyloidotic Polyneuropathy,
Scrapie, Creutzfeldt-Jacob Disease, Gerstmann Straussler-Scheinker
Syndrome, Bovine Spongiform Encephalitis, a Prion-mediated disease,
Huntington's Disease, Pick's Disease, Amyotrophic Lateral
Schlerosis (ALS), Parkinson's Disease, and Lewy Body Disease.
[0486] Some examples of endocrinologic disorders that can be
treated with the polypeptides described herein include, but are not
limited to, diabetes, hypothyroidism, hypopituitarism,
hypoparathyroidism, hypogonadism, fertility disorders, etc.
[0487] Some examples of immunologic disorders that can be treated
with the polypeptides described herein include, but are not limited
to, organ transplant rejection, arthritis, lupus, IBD, Crohn's
disease, asthma, multiple sclerosis, diabetes, Graft versus host
diseases, autoimmune diseases, psoriasis, rheumatoid arthritis,
etc.
[0488] Examples of cardiovascular disorders that can be treated or
prevented with the polypeptides described herein include, but are
not limited to, atherosclerosis, myocardial infarction, stroke,
thrombosis, aneurism, heart failure, ischemnic heart disease,
angina pectoris, sudden cardiac death, hypertensive heart disease;
non-coronary vessel disease, such as arteriolosclerosis, small
vessel disease, nephropathy, hypertriglyceridemia,
hypercholesterolernia, hyperlipidemia, xanthomatosis, asthma,
hypertension, emphysema and chronic pulmonary disease; or a
cardiovascular condition associated with interventional procedures
("procedural vascular trauma"), such as restenosis following
angioplasty, placement of a shunt, stent, synthetic or natural
excision grafts, indwelling catheter, valve or other implantable
devices.
[0489] The stapled and stitched polypeptides provides herein can
treat the above-described diseases, disorders, or conditions, for
instance, by disrupting native protein-protein, protein-ligand,
and/or protein-receptor interactions. For example, many
biologically important protein/protein interactions, such as
p53/MDM2 and Bcl-X1/Bak, are mediated by one protein donating a
helix into a cleft of its helix-accepting partner. The interaction
of p53 and MDM2 and mutations in the p53 gene have been identified
in virtually half of all reported cancer cases (see, Shair Chem.
& Biol. 1997, 4, 791, the entire contents of which are
incorporated herein by reference). As stresses are imposed on a
cell, p53 is believed to orchestrate a response that leads to
either cell-cycle arrest and DNA repair, or programmed cell death.
As well as mutations in the p53 gene that alter the function of the
p53 protein directly, p53 can be altered by changes in MDM2. The
MDM2 protein has been shown to bind to p53 and disrupt
transcriptional activation by associating with the transactivation
domain of p53. For example, an 11 amino-acid peptide derived from
the transactivation domain of p53 forms an amphipathic alpha-helix
of 2.5 turns that inserts into the MDM2 crevice.
[0490] Thus, in certain embodiments, a stitched or stapled
polypeptide as described herein is an alpha helical polypeptide
that is capable of binding tightly to a helix acceptor and
disrupting native protein/protein interactions. These structures
may then be screened using high throughput techniques to identify
optimal small molecule peptides. In certain embodiments, a stitched
or stapled polypeptide as described herein is an alpha helical p53
polypeptide capable of binding to the Xenopus MDM2 protein. The
novel structures that disrupt the MDM2 interaction might be useful
for many applications, including, but not limited to, control of
soft tissue sarcomas (which overexpresses MDM2 in the presence of
wild type p53). These cancers may be held in check with small
molecules that could intercept MDM2, thereby preventing suppression
of p53. Additionally, small molecules disrupters of MDM2-p53
interactions could be used as adjuvant therapy to help control and
modulate the extent of the p53 dependent apoptosis response in
conventional chemotherapy.
[0491] In certain embodiments, polypeptides disclosed herein are
homologous to a known alpha helical peptide. In certain
embodiments, the inventive polypeptide is at least 80%, 85%, 90%,
or 95% homologous to a known alpha helical peptide.
[0492] In addition, polypeptides disclosed herein may be useful in
the area of materials science. For example, molecules such as
lipids and other polymeric molecules may be attached to the
terminal peptide moieties and thus generate potentially important
biomaterials.
[0493] In addition to the above-mentioned uses, polypeptides
disclosed herein may be used for studies in bioinorganic chemistry
or in catalysis, either as a ligand for a transition metal capable
of mimicking an important biological environment, or by acting in
concert with a particular transition metal catalyst to effect a
desired chemical reaction.
Pharmaceutical Compositions
[0494] The present disclosure provides pharmaceutical compositions
comprising a stitched or stapled polypeptide as described herein
and, optionally, a pharmaceutically acceptable excipient. Such
pharmaceutical compositions may optionally comprise one or more
additional biologically-active substances. In accordance with some
embodiments, a method of administering a pharmaceutical composition
to a subject in need thereof is provided. In some embodiments,
pharmaceutical compositions are administered to humans. For the
purposes of the present disclosure, the phrase "active ingredient"
generally refers to a stitched or stapled polypeptide as described
herein.
[0495] Although the descriptions of pharmaceutical compositions
provided herein are principally directed to pharmaceutical
compositions which are suitable for administration to humans, it
will be understood by the skilled artisan that such compositions
are generally suitable for administration to animals of all sorts.
Modification of pharmaceutical compositions suitable for
administration to humans in order to render the compositions
suitable for administration to various animals is well understood,
and the ordinarily skilled veterinary pharmacologist can design
and/or perform such modification with merely ordinary, if any,
experimentation. Subjects to which administration of the
pharmaceutical compositions as described herein is contemplated
include, but are not limited to, humans and/or other primates;
mammals, including commercially relevant mammals such as cattle,
pigs, horses, sheep, cats, and/or dogs; and/or birds, including
commercially relevant birds such as chickens, ducks, geese, and/or
turkeys.
[0496] The formulations of the pharmaceutical compositions
described herein may be prepared by any method known or hereafter
developed in the art of pharmacology. In general, such preparatory
methods include the step of bringing the active ingredient into
association with a carrier and/or one or more other accessory
ingredients, and then, if necessary and/or desirable, shaping
and/or packaging the product into a desired single- or multi-dose
unit.
[0497] A pharmaceutical composition may be prepared, packaged,
and/or sold in bulk, as a single unit dose, and/or as a plurality
of single unit doses. As used herein, a "unit dose" is discrete
amount of the pharmaceutical composition comprising a predetermined
amount of the active ingredient. The amount of the active
ingredient is generally equal to the dosage of the active
ingredient which would be administered to a subject and/or a
convenient fraction of such a dosage such as, for example, one-half
or one-third of such a dosage.
[0498] The relative amounts of the active ingredient, the
pharmaceutically acceptable carrier, and/or any additional
ingredients in a pharmaceutical composition of the disclosure will
vary, depending upon the identity, size, and/or condition of the
subject treated and further depending upon the route by which the
composition is to be administered. By way of example, the
composition may comprise between 0.1% and 100% (w/w) active
ingredient.
[0499] Pharmaceutical formulations may additionally comprise a
pharmaceutically acceptable excipient, which, as used herein,
includes any and all solvents, dispersion media, diluents, or other
liquid vehicles, dispersion or suspension aids, surface active
agents, isotonic agents, thickening or emulsifying agents,
preservatives, solid binders, lubricants and the like, as suited to
the particular dosage form desired. Remington's The Science and
Practice of Pharmacy, 21 Edition, A. R. Gennaro, (Lippincott,
Williams & Wilkins, Baltimore. Md., 2006) discloses various
carriers used in formulating pharmaceutical compositions and known
techniques for the preparation thereof. Except insofar as any
conventional carrier medium is incompatible with a substance or its
derivatives, such as by producing any undesirable biological effect
or otherwise interacting in a deleterious manner with any other
component(s) of the pharmaceutical composition, its use is
contemplated to be within the scope of this disclosure.
[0500] In some embodiments, the pharmaceutically acceptable
excipient is at least 95%, 96%, 97%, 98%, 99%, or 100% pure. In
some embodiments, the excipient is approved for use in humans and
for veterinary use. In some embodiments, the excipient is approved
by United States Food and Drug Administration. In some embodiments,
the excipient is pharmaceutical grade. In some embodiments, the
excipient meets the standards of the United States Pharmacopoeia
(USP), the European Pharmacopoeia (EP), the British Pharmacopoeia,
and/or the International Pharmacopoeia.
[0501] Pharmaceutically acceptable excipients used in the
manufacture of pharmaceutical compositions include, but are not
limited to, inert diluents, dispersing and/or granulating agents,
surface active agents and/or emulsifiers, disintegrating agents,
binding agents, preservatives, buffering agents, lubricating
agents, and/or oils. Such excipients may optionally be included in
the inventive formulations. Excipients such as cocoa butter and
suppository waxes, coloring agents, coating agents, sweetening,
flavoring, and perfuming agents can be present in the composition,
according to the judgment of the formulator.
[0502] Exemplary diluents include, but are not limited to, calcium
carbonate, sodium carbonate, calcium phosphate, dicalcium
phosphate, calcium sulfate, calcium hydrogen phosphate, sodium
phosphate lactose, sucrose, cellulose, microcrystalline cellulose,
kaolin, mannitol, sorbitol, inositol, sodium chloride, dry starch,
cornstarch, powdered sugar, etc., and combinations thereof
[0503] Exemplary granulating and/or dispersing agents include, but
are not limited to, potato starch, corn starch, tapioca starch,
sodium starch glycolate, clays, alginic acid, guar gum, citrus
pulp, agar, bentonite, cellulose and wood products, natural sponge,
cation-exchange resins, calcium carbonate, silicates, sodium
carbonate, cross-linked poly(vinyl-pyrrolidone) (crospovidone),
sodium carboxymethyl starch (sodium starch glycolate),
carboxymethyl cellulose, cross-linked sodium carboxymethyl
cellulose (croscarmellose), methylcellulose, pregelatinized starch
(starch 1500), microcrystalline starch, water insoluble starch,
calcium carboxymethyl cellulose, magnesium aluminum silicate
(Veegum), sodium lauryl sulfate, quaternary ammonium compounds,
etc., and combinations thereof.
[0504] Exemplary surface active agents and/or emulsifiers include,
but are not limited to, natural emulsifiers (e.g. acacia, agar,
alginic acid, sodium alginate, tragacanth, chondrux, cholesterol,
xanthan, pectin, gelatin, egg yolk, casein, wool fat, cholesterol,
wax, and lecithin), colloidal clays (e.g. bentonite [aluminum
silicate] and Veegum [magnesium aluminum silicate]), long chain
amino acid derivatives, high molecular weight alcohols (e.g.
stearyl alcohol, cetyl alcohol, oleyl alcohol, triacetin
monostearate, ethylene glycol distearate, glyceryl monostearate,
and propylene glycol monostearate, polyvinyl alcohol), carbomers
(e.g. carboxy polymethylene, polyacrylic acid, acrylic acid
polymer, and carboxyvinyl polymer), carrageenan, cellulosic
derivatives (e.g. carboxymethylcellulose sodium, powdered
cellulose, hydroxymethyl cellulose, hydroxypropyl cellulose,
hydroxypropyl methylcellulose, methylcellulose), sorbitan fatty
acid esters (e.g. polyoxyethylene sorbitan monolaurate [Tween 20],
polyoxyethylene sorbitan [Tween 60], polyoxyethylene sorbitan
monooleate [Tween 80], sorbitan monopalmitate [Span 40], sorbitan
monostearate [Span 60], sorbitan tristearate [Span 65], glyceryl
monooleate, sorbitan monooleate [Span 80]), polyoxyethylene esters
(e.g. polyoxyethylene monostearate [Myrj 45], polyoxyethylene
hydrogenated castor oil, polyethoxylated castor oil,
polyoxymethylene stearate, and Solutol), sucrose fatty acid esters,
polyethylene glycol fatty acid esters (e.g. Cremophor),
polyoxyethylene ethers, (e.g. polyoxyethylene lauryl ether [Brij
30]), poly(vinyl-pyrrolidone), diethylene glycol monolaurate,
triethanolamine oleate, sodium oleate, potassium oleate, ethyl
oleate, oleic acid, ethyl laurate, sodium lauryl sulfate, Pluronic
F 68, Poloxamer 188, cetrimonium bromide, cetylpyridinium chloride,
benzalkonium chloride, docusate sodium, etc. and/or combinations
thereof.
[0505] Exemplary binding agents include, but are not limited to,
starch (e.g. cornstarch and starch paste); gelatin; sugars (e.g.
sucrose, glucose, dextrose, dextrin, molasses, lactose, lactitol,
mannitol); natural and synthetic gums (e.g. acacia, sodium
alginate, extract of Irish moss, panwar gum, ghatti gum, mucilage
of isapol husks, carboxymethylcellulose, methylcellulose,
ethylcellulose, hydroxyethylcellulose, hydroxypropyl cellulose,
hydroxypropyl methylcellulose, microcrystalline cellulose,
cellulose acetate, poly(vinyl-pyrrolidone), magnesium aluminum
silicate (Veegum), and larch arabogalactan); alginates;
polyethylene oxide; polyethylene glycol; inorganic calcium salts;
silicic acid; polymethacrylates; waxes; water; alcohol; etc.; and
combinations thereof.
[0506] Exemplary preservatives may include antioxidants, chelating
agents, antimicrobial preservatives, antifungal preservatives,
alcohol preservatives, acidic preservatives, and other
preservatives. Exemplary antioxidants include, but are not limited
to, alpha tocopherol, ascorbic acid, acorbyl palmitate, butylated
hydroxyanisole, butylated hydroxytoluene, monothioglycerol,
potassium metabisulfite, propionic acid, propyl gallate, sodium
ascorbate, sodium bisulfite, sodium metabisulfite, and sodium
sulfite. Exemplary chelating agents include
ethylenediaminetetraacetic acid (EDTA), citric acid monohydrate,
disodium edetate, dipotassium edetate, edetic acid, fumaric acid,
malic acid, phosphoric acid, sodium edetate, tartaric acid, and
trisodium edetate. Exemplary antimicrobial preservatives include,
but are not limited to, benzalkonium chloride, benzethonium
chloride, benzyl alcohol, bronopol, cetrimide, cetylpyridinium
chloride, chlorhexidine, chlorobutanol, chlorocresol,
chloroxylenol, cresol, ethyl alcohol, glycerin, hexetidine,
imidurea, phenol, phenoxyethanol, phenylethyl alcohol,
phenylmercuric nitrate, propylene glycol, and thimerosal. Exemplary
antifungal preservatives include, but are not limited to, butyl
paraben, methyl paraben, ethyl paraben, propyl paraben, benzoic
acid, hydroxybenzoic acid, potassium benzoate, potassium sorbate,
sodium benzoate, sodium propionate, and sorbic acid. Exemplary
alcohol preservatives include, but are not limited to, ethanol,
polyethylene glycol, phenol, phenolic compounds, bisphenol,
chlorobutanol, hydroxybenzoate, and phenylethyl alcohol. Exemplary
acidic preservatives include, but are not limited to, vitamin A,
vitamin C, vitamin E, beta-carotene, citric acid, acetic acid,
dehydroacetic acid, ascorbic acid, sorbic acid, and phytic acid.
Other preservatives include, but are not limited to, tocopherol,
tocopherol acetate, deteroxime mesylate, cetrimide, butylated
hydroxyanisol (BHA), butylated hydroxytoluened (BHT),
ethylenediamine, sodium lauryl sulfate (SLS), sodium lauryl ether
sulfate (SLES), sodium bisulfite, sodium metabisulfite, potassium
sulfite, potassium metabisulfite, Glydant Plus, Phenonip,
methylparaben, Germall 115, Germaben II, Neolone, Kathon, and
Euxyl. In certain embodiments, the preservative is an anti-oxidant.
In other embodiments, the preservative is a chelating agent.
[0507] Exemplary buffering agents include, but are not limited to,
citrate buffer solutions, acetate buffer solutions, phosphate
buffer solutions, ammonium chloride, calcium carbonate, calcium
chloride, calcium citrate, calcium glubionate, calcium gluceptate,
calcium gluconate, D-gluconic acid, calcium glycerophosphate,
calcium lactate, propanoic acid, calcium levulinate, pentanoic
acid, dibasic calcium phosphate, phosphoric acid, tribasic calcium
phosphate, calcium hydroxide phosphate, potassium acetate,
potassium chloride, potassium gluconate, potassium mixtures,
dibasic potassium phosphate, monobasic potassium phosphate,
potassium phosphate mixtures, sodium acetate, sodium bicarbonate,
sodium chloride, sodium citrate, sodium lactate, dibasic sodium
phosphate, monobasic sodium phosphate, sodium phosphate mixtures,
tromethamine, magnesium hydroxide, aluminum hydroxide, alginic
acid, pyrogen-free water, isotonic saline, Ringer's solution, ethyl
alcohol, etc., and combinations thereof.
[0508] Exemplary lubricating agents include, but are not limited
to, magnesium stearate, calcium stearate, stearic acid, silica,
talc, malt, glyceryl behanate, hydrogenated vegetable oils,
polyethylene glycol, sodium benzoate, sodium acetate, sodium
chloride, leucine, magnesium lauryl sulfate, sodium lauryl sulfate,
etc., and combinations thereof.
[0509] Exemplary oils include, but are not limited to, almond,
apricot kernel, avocado, babassu, bergamot, black current seed,
borage, cade, camomile, canola, caraway, carnauba, castor,
cinnamon, cocoa butter, coconut, cod liver, coffee, corn, cotton
seed, emu, eucalyptus, evening primrose, fish, flaxseed, geraniol,
gourd, grape seed, hazel nut, hyssop, isopropyl myristate, jojoba,
kukui nut, lavandin, lavender, lemon, litsea cubeba, macademia nut,
mallow, mango seed, meadowfoam seed, mink, nutmeg, olive, orange,
orange roughy, palm, palm kernel, peach kernel, peanut, poppy seed,
pumpkin seed, rapeseed, rice bran, rosemary, safflower, sandalwood,
sasquana, savoury, sea buckthorn, sesame, shea butter, silicone,
soybean, sunflower, tea tree, thistle, tsubaki, vetiver, walnut,
and wheat germ oils. Exemplary oils include, but are not limited
to, butyl stearate, caprylic triglyceride, capric triglyceride,
cyclomethicone, diethyl sebacate, dimethicone 360, isopropyl
myristate, mineral oil, octyldodecanol, oleyl alcohol, silicone
oil, and combinations thereof.
[0510] Liquid dosage forms for oral and parenteral administration
include, but are not limited to, pharmaceutically acceptable
emulsions, microemulsions, solutions, suspensions, syrups and
elixirs. In addition to the active ingredients, the liquid dosage
forms may comprise inert diluents commonly used in the art such as,
for example, water or other solvents, solubilizing agents and
emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl
carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate,
propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in
particular, cottonseed, groundnut, corn, germ, olive, castor, and
sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene
glycols and fatty acid esters of sorbitan, and mixtures thereof.
Besides inert diluents, the oral compositions can include adjuvants
such as wetting agents, emulsifying and suspending agents,
sweetening, flavoring, and perfuming agents. In certain embodiments
for parenteral administration, the polypeptides of the disclosure
are mixed with solubilizing agents such as Cremophor, alcohols,
oils, modified oils, glycols, polysorbates, cyclodextrins,
polymers, and combinations thereof.
[0511] Injectable preparations, for example, sterile injectable
aqueous or oleaginous suspensions may be formulated according to
the known art using suitable dispersing or wetting agents and
suspending agents. The sterile injectable preparation may be a
sterile injectable solution, suspension or emulsion in a nontoxic
parenterally acceptable diluent or solvent, for example, as a
solution in 1,3-butanediol. Among the acceptable vehicles and
solvents that may be employed are water, Ringer's solution, U.S.P.
and isotonic sodium chloride solution. In addition, sterile, fixed
oils are conventionally employed as a solvent or suspending medium.
For this purpose any bland fixed oil can be employed including
synthetic mono- or diglycerides. In addition, fatty acids such as
oleic acid are used in the preparation of injectables.
[0512] The injectable formulations can be sterilized, for example,
by filtration through a bacterial-retaining filter, or by
incorporating sterilizing agents in the form of sterile solid
compositions which can be dissolved or dispersed in sterile water
or other sterile injectable medium prior to use.
[0513] In order to prolong the effect of a drug, it is often
desirable to slow the absorption of the drug from subcutaneous or
intramuscular injection. This may be accomplished by the use of a
liquid suspension of crystalline or amorphous material with poor
water solubility. The rate of absorption of the drug then depends
upon its rate of dissolution which, in turn, may depend upon
crystal size and crystalline form. Alternatively, delayed
absorption of a parenterally administered drug form is accomplished
by dissolving or suspending the drug in an oil vehicle.
[0514] Compositions for rectal or vaginal administration are
typically suppositories which can be prepared by mixing the
polypeptides of the disclosure with suitable non-irritating
excipients or carriers such as cocoa butter, polyethylene glycol or
a suppository wax which are solid at ambient temperature but liquid
at body temperature and therefore melt in the rectum or vaginal
cavity and release the active ingredient.
[0515] Solid dosage forms for oral administration include capsules,
tablets, pills, powders, and granules. In such solid dosage forms,
the active ingredient is mixed with at least one inert,
pharmaceutically acceptable excipient or carrier such as sodium
citrate or dicalcium phosphate and/or a) fillers or extenders such
as starches, lactose, sucrose, glucose, mannitol, and silicic acid,
b) binders such as, for example, carboxymethylcellulose, alginates,
gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants
such as glycerol, d) disintegrating agents such as agar, calcium
carbonate, potato or tapioca starch, alginic acid, certain
silicates, and sodium carbonate, e) solution retarding agents such
as paraffin, f) absorption accelerators such as quaternary ammonium
compounds, g) wetting agents such as, for example, cetyl alcohol
and glycerol monostearate, h) absorbents such as kaolin and
bentonite clay, and i) lubricants such as talc, calcium stearate,
magnesium stearate, solid polyethylene glycols, sodium lauryl
sulfate, and mixtures thereof. In the case of capsules, tablets and
pills, the dosage form may comprise buffering agents.
[0516] Solid compositions of a similar type may be employed as
fillers in soft and hard-filled gelatin capsules using such
excipients as lactose or milk sugar as well as high molecular
weight polyethylene glycols and the like. The solid dosage forms of
tablets, dragees, capsules, pills, and granules can be prepared
with coatings and shells such as enteric coatings and other
coatings well known in the pharmaceutical formulating art. They may
optionally comprise opacifying agents and can be of a composition
that they release the active ingredient(s) only, or preferentially,
in a certain part of the intestinal tract, optionally, in a delayed
manner. Examples of embedding compositions which can be used
include polymeric substances and waxes. Solid compositions of a
similar type may be employed as fillers in soft and hard-filled
gelatin capsules using such excipients as lactose or milk sugar as
well as high molecular weight polethylene glycols and the like.
[0517] The active ingredients can be in micro-encapsulated form
with one or more excipients as noted above. The solid dosage forms
of tablets, dragees, capsules, pills, and granules can be prepared
with coatings and shells such as enteric coatings, release
controlling coatings and other coatings well known in the
pharmaceutical formulating art. In such solid dosage forms the
active ingredient may be admixed with at least one inert diluent
such as sucrose, lactose or starch. Such dosage forms may comprise,
as is normal practice, additional substances other than inert
diluents, e.g., tableting lubricants and other tableting aids such
a magnesium stearate and microcrystalline cellulose. In the case of
capsules, tablets and pills, the dosage forms may comprise
buffering agents. They may optionally comprise opacifying agents
and can be of a composition that they release the active
ingredient(s) only, or preferentially, in a certain part of the
intestinal tract, optionally, in a delayed manner. Examples of
embedding compositions which can be used include polymeric
substances and waxes.
[0518] Dosage forms for topical and/or transdermal administration
of a polypeptide of the disclosure may include ointments, pastes,
creams, lotions, gels, powders, solutions, sprays, inhalants and/or
patches. Generally, the active component is admixed under sterile
conditions with a pharmaceutically acceptable carrier and/or any
needed preservatives and/or buffers as may be required.
Additionally, the present disclosure contemplates the use of
transdermal patches, which often have the added advantage of
providing controlled delivery of an active ingredient to the body.
Such dosage forms may be prepared, for example, by dissolving
and/or dispensing the active ingredient in the proper medium.
Alternatively or additionally, the rate may be controlled by either
providing a rate controlling membrane and/or by dispersing the
active ingredient in a polymer matrix and/or gel.
[0519] Suitable devices for use in delivering intradermal
pharmaceutical compositions described herein include short needle
devices such as those described in U.S. Pat. Nos. 4,886,499;
5,190,521; 5,328,483; 5,527,288; 4,270,537; 5,015,235; 5,141,496;
and 5,417,662. Intradermal compositions may be administered by
devices which limit the effective penetration length of a needle
into the skin, such as those described in PCT publication WO
99/34850 and functional equivalents thereof. Jet injection devices
which deliver liquid vaccines to the dermis via a liquid jet
injector and/or via a needle which pierces the stratum corneum and
produces a jet which reaches the dermis are suitable. Jet injection
devices are described, for example, in U.S. Pat. Nos. 5,480,381;
5,599,302; 5,334,144; 5,993,412; 5,649,912; 5,569,189; 5,704,911;
5,383,851; 5,893,397; 5,466,220; 5,339,163; 5,312,335; 5,503,627;
5,064,413; 5,520,639; 4,596,556; 4,790,824; 4,941,880; 4,940,460;
and PCT publications WO 97/37705 and WO 97/13537. Ballistic
powder/particle delivery devices which use compressed gas to
accelerate vaccine in powder form through the outer layers of the
skin to the dermis are suitable. Alternatively or additionally,
conventional syringes may be used in the classical mantoux method
of intradermal administration.
[0520] Formulations suitable for topical administration include,
but are not limited to, liquid and/or semi liquid preparations such
as liniments, lotions, oil in water and/or water in oil emulsions
such as creams, ointments and/or pastes, and/or solutions and/or
suspensions. Topically-administrable formulations may, for example,
comprise from about 1% to about 10% (w/w) active ingredient,
although the concentration of the active ingredient may be as high
as the solubility limit of the active ingredient in the solvent.
Formulations for topical administration may further comprise one or
more of the additional ingredients described herein.
[0521] A pharmaceutical composition of the disclosure may be
prepared, packaged, and/or sold in a formulation suitable for
pulmonary administration via the buccal cavity. Such a formulation
may comprise dry particles which comprise the active ingredient and
which have a diameter in the range from about 0.5 to about 7
nanometers or from about 1 to about 6 nanometers. Such compositions
are conveniently in the form of dry powders for administration
using a device comprising a dry powder reservoir to which a stream
of propellant may be directed to disperse the powder and/or using a
self-propelling solvent/powder dispensing container such as a
device comprising the active ingredient dissolved and/or suspended
in a low-boiling propellant in a sealed container. Such powders
comprise particles wherein at least 98% of the particles by weight
have a diameter greater than 0.5 nanometers and at least 95% of the
particles by number have a diameter less than 7 nanometers.
Alternatively, at least 95% of the particles by weight have a
diameter greater than 1 nanometer and at least 90% of the particles
by number have a diameter less than 6 nanometers. Dry powder
compositions may include a solid fine powder diluent such as sugar
and are conveniently provided in a unit dose form.
[0522] Low boiling propellants generally include liquid propellants
having a boiling point of below 65.degree. F. at atmospheric
pressure. Generally the propellant may constitute 50 to 99.9% (w/w)
of the composition, and the active ingredient may constitute 0.1 to
20% (w/w) of the composition. The propellant may further comprise
additional ingredients such as a liquid non-ionic and/or solid
anionic surfactant and/or a solid diluent (which may have a
particle size of the same order as particles comprising the active
ingredient).
[0523] Pharmaceutical compositions as described herein formulated
for pulmonary delivery may provide the active ingredient in the
form of droplets of a solution and/or suspension. Such formulations
may be prepared, packaged, and/or sold as aqueous and/or dilute
alcoholic solutions and/or suspensions, optionally sterile,
comprising the active ingredient, and may conveniently be
administered using any nebulization and/or atomization device. Such
formulations may further comprise one or more additional
ingredients including, but not limited to, a flavoring agent such
as saccharin sodium, a volatile oil, a buffering agent, a surface
active agent, and/or a preservative such as methylhydroxybenzoate.
The droplets provided by this route of administration may have an
average diameter in the range from about 0.1 to about 200
nanometers.
[0524] The formulations described herein as being useful for
pulmonary delivery are useful for intranasal delivery of a
pharmaceutical composition of the disclosure. Another formulation
suitable for intranasal administration is a coarse powder
comprising the active ingredient and having an average particle
from about 0.2 to 500 micrometers. Such a formulation is
administered in the manner in which snuff is taken, i.e. by rapid
inhalation through the nasal passage from a container of the powder
held close to the nares.
[0525] Formulations suitable for nasal administration may, for
example, comprise from about as little as 0.1% (w/w) and as much as
100% (w/w) of the active ingredient, and may comprise one or more
of the additional ingredients described herein. A pharmaceutical
composition of the disclosure may be prepared, packaged, and/or
sold in a formulation suitable for buccal administration. Such
formulations may, for example, be in the form of tablets and/or
lozenges made using conventional methods, and may, for example, 0.1
to 20% (w/w) active ingredient, the balance comprising an orally
dissolvable and/or degradable composition and, optionally, one or
more of the additional ingredients described herein. Alternately,
formulations suitable for buccal administration may comprise a
powder and/or an aerosolized and/or atomized solution and/or
suspension comprising the active ingredient. Such powdered,
aerosolized, and/or aerosolized formulations, when dispersed, may
have an average particle and/or droplet size in the range from
about 0.1 to about 200 nanometers, and may further comprise one or
more of the additional ingredients described herein.
[0526] A pharmaceutical composition may be prepared, packaged,
and/or sold in a formulation suitable for ophthalmic
administration. Such formulations may, for example, be in the form
of eye drops including, for example, a 0.1/1.0% (w/w) solution
and/or suspension of the active ingredient in an aqueous or oily
liquid carrier. Such drops may further comprise buffering agents,
salts, and/or one or more other of the additional ingredients
described herein. Other opthalmically-administrable formulations
which are useful include those which comprise the active ingredient
in microcrystalline form and/or in a liposomal preparation. Ear
drops and/or eye drops are contemplated as being within the scope
of this disclosure.
[0527] General considerations in the formulation and/or manufacture
of pharmaceutical agents may be found, for example, in Remington:
The Science and Practice of Pharmacy 21.sup.st ed., Lippincott
Williams & Wilkins, 2005.
Administration
[0528] In some embodiments, a therapeutically effective amount of a
pharmaceutical composition as described herein is delivered to a
patient and/or organism prior to, simultaneously with, and/or after
diagnosis with a disease, disorder, and/or condition. In some
embodiments, a therapeutic amount of a pharmaceutical composition
as described herein is delivered to a patient and/or organism prior
to, simultaneously with, and/or after onset of symptoms of a
disease, disorder, and/or condition. In some embodiments, the
amount of the stitched or stapled polypeptide as described herein
is sufficient to treat, alleviate, ameliorate, relieve, delay onset
of, inhibit progression of, reduce severity of, and/or reduce
incidence of one or more symptoms or features of the disease,
disorder, and/or condition.
[0529] The compositions, as disclosed herein, may be administered
using any amount and any route of administration effective for
treatment. The exact amount required will vary from subject to
subject, depending on the species, age, and general condition of
the subject, the severity of the infection, the particular
composition, its mode of administration, its mode of activity, and
the like. The pharmaceutical compositions as described herein are
typically formulated in dosage unit form for ease of administration
and uniformity of dosage. It will be understood, however, that the
total daily usage of the pharmaceutical compositions as described
herein will be decided by the attending physician within the scope
of sound medical judgment. The specific therapeutically effective
dose level for any particular subject or organism will depend upon
a variety of factors including the disorder being treated and the
severity of the disorder; the activity of the specific active
ingredient employed; the specific composition employed; the age,
body weight, general health, sex and diet of the subject; the time
of administration, route of administration, and rate of excretion
of the specific active ingredient employed; the duration of the
treatment; drugs used in combination or coincidental with the
specific active ingredient employed; and like factors well known in
the medical arts.
[0530] The pharmaceutical compositions as described herein may be
administered by any route. In some embodiments, the pharmaceutical
compositions as described herein are administered variety of
routes, including oral, intravenous, intramuscular, intra-arterial,
intramedullary, intrathecal, subcutaneous, intraventricular,
transdermal, interdermal, rectal, intravaginal, intraperitoneal,
topical (as by powders, ointments, creams, and/or drops), mucosal,
nasal, bucal, enteral, sublingual; by intratracheal instillation,
bronchial instillation, and/or inhalation and/or as an oral spray,
nasal spray, and/or aerosol. Specifically contemplated routes are
systemic intravenous injection, regional administration via blood
and/or lymph supply, and/or direct administration to an affected
site. In general the most appropriate route of administration will
depend upon a variety of factors including the nature of the agent
(e.g., its stability in the environment of the gastrointestinal
tract), the condition of the subject (e.g., whether the subject is
able to tolerate oral administration), etc. At present the oral
and/or nasal spray and/or aerosol route is most commonly used to
deliver therapeutic agents directly to the lungs and/or respiratory
system. However, the disclosure embraces the delivery of the
pharmaceutical compositions as described herein by any appropriate
route taking into consideration likely advances in the sciences of
drug delivery.
[0531] In certain embodiments, pharmaceutical compositions
comprising the peptides disclosed herein may be administered at
dosage levels sufficient to deliver from about 0.001 mg/kg to about
100 mg/kg, from about 0.01 mg/kg to about 50 mg/kg, from about 0.1
mg/kg to about 40 mg/kg, from about 0.5 mg/kg to about 30 mg/kg,
from about 0.01 mg/kg to about 10 mg/kg, from about 0.1 mg/kg to
about 10 mg/kg, or from about 1 mg/kg to about 25 mg/kg, of subject
body weight per day, one or more times a day, to obtain the desired
therapeutic effect. The desired dosage may be delivered three times
a day, two times a day, once a day, every other day, every third
day, every week, every two weeks, every three weeks, or every four
weeks. In certain embodiments, the desired dosage may be delivered
using multiple administrations (e.g., two, three, four, five, six,
seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, or
more administrations).
[0532] In some embodiments, the disclosure encompasses "therapeutic
cocktails" comprising the polypeptides disclosed herein. In some
embodiments, the polypeptide comprises a single species which can
bind to multiple targets. In some embodiments, the polypeptides
disclosed herein comprise different targeting moiety species, and
all of the different targeting moiety species can bind to the same
target. In some embodiments, different polypeptides comprise
different targeting moiety species, and all of the different
targeting moiety species can bind to different targets. In some
embodiments, such different targets may be associated with the same
cell type. In some embodiments, such different targets may be
associated with different cell types.
[0533] It will be appreciated that the polypeptides and
pharmaceutical compositions as described herein can be employed in
combination therapies. The particular combination of therapies
(therapeutics or procedures) to employ in a combination regimen
will take into account compatibility of the desired therapeutics
and/or procedures and the desired therapeutic effect to be
achieved. It will be appreciated that the therapies employed may
achieve a desired effect for the same purpose (for example,
stitched or stapled polypeptide as described herein may be useful
for detecting tumors and may be administered concurrently with
another agent useful for detecting tumors), or they may achieve
different effects (e.g., control of any adverse effects).
[0534] Pharmaceutical compositions as described herein may be
administered either alone or in combination with one or more other
therapeutic agents. By "in combination with," it is not intended to
imply that the agents must be administered at the same time and/or
formulated for delivery together, although these methods of
delivery are within the scope of the disclosure. The compositions
can be administered concurrently with, prior to, or subsequent to,
one or more other desired therapeutics or medical procedures. In
general, each agent will be administered at a dose and/or on a time
schedule determined for that agent. Additionally, the disclosure
encompasses the delivery of the a pharmaceutical composition as
described herein in combination with agents that may improve their
bioavailability, reduce and/or modify their metabolism, inhibit
their excretion, and/or modify their distribution within the
body.
[0535] The particular combination of therapies (therapeutics and/or
procedures) to employ in a combination regimen will take into
account compatibility of the desired therapeutics and/or procedures
and/or the desired therapeutic effect to be achieved. It will be
appreciated that the therapies employed may achieve a desired
effect for the same disorder (for example, a stitched or stapled
polypeptide as described herein may be administered concurrently
with another biologically active agent used to treat the same
disorder), and/or they may achieve different effects (e.g., control
of any adverse effects). In some embodiments, polypeptides of the
disclosure are administered with a second biologically active agent
that is approved by the U.S. Food and Drug Administration.
[0536] In will further be appreciated that biologically active
agents utilized in this combination may be administered together in
a single composition or administered separately in different
compositions.
[0537] In general, it is expected that biologically active agents
utilized in combination be utilized at levels that do not exceed
the levels at which they are utilized individually. In some
embodiments, the levels utilized in combination will be lower than
those utilized individually.
[0538] In some embodiments, a pharmaceutical composition as
described herein may be administered in combination with any
biologically active agent or therapeutic regimen that is useful to
treat, alleviate, ameliorate, relieve, delay onset of, inhibit
progression of, reduce severity of, and/or reduce incidence of one
or more symptoms or features of cancer. For example, pharmaceutical
compositions may be administered in combination with traditional
cancer therapies including, but not limited to, surgery,
chemotherapy, radiation therapy, hormonal therapy, immunotherapy,
complementary or alternative therapy, and any combination of these
therapies.
[0539] In some embodiments, pharmaceutical compositions are
administered in combination with surgery to remove a tumor. Because
complete removal of a tumor with minimal or no damage to the rest
of a patient's body is typically the goal of cancer treatment,
surgery is often performed to physically remove part or all of a
tumor. If surgery is unable to completely remove a tumor,
additional therapies (e.g. chemotherapy, radiation therapy,
hormonal therapy, immunotherapy, complementary or alternative
therapy) may be employed.
[0540] In some embodiments, pharmaceutical compositions are
administered in combination with radiation therapy. Radiation
therapy (also known as radiotherapy, X-ray therapy, or irradiation)
is the use of ionizing radiation to kill cancer cells and shrink
tumors. Radiation therapy may be used to treat almost any type of
solid tumor, including cancers of the brain, breast, cervix,
larynx, lung, pancreas, prostate, skin, stomach, uterus, or soft
tissue sarcomas. Radiation can be used to treat leukemia and
lymphoma. Radiation therapy can be administered externally via
external beam radiotherapy (EBRT) or internally via brachytherapy.
Typically, the effects of radiation therapy are localized and
confined to the region being treated. Radiation therapy injures or
destroys tumor cells in an area being treated (e.g. a target organ,
tissue, and/or cell) by damaging their genetic material, preventing
tumor cells from growing and dividing. In general, radiation
therapy attempts to damage as many tumor cells as possible while
limiting harm to nearby healthy tissue. Hence, it is often
administered in multiple doses, allowing healthy tissue to recover
between fractions.
[0541] In some embodiments, pharmaceutical compositions are
administered in combination with immunotherapy. Immunotherapy is
the use of immune mechanisms against tumors which can be used in
various forms of cancer, such as breast cancer (e.g.
trastuzumab/Herceptin.RTM.), leukemia (e.g. gemtuzumab
ozogamicin/Mylotarg.RTM.), and non-Hodgkin's lymphoma (e.g.
rituximab/Rituxan.RTM.). In some embodiments, immunotherapy agents
are monoclonal antibodies directed against proteins that are
characteristic to the cells of the cancer in question. In some
embodiments, immunotherapy agents are cytokines that modulate the
immune system's response. In some embodiments, immunotherapy agents
may be vaccines.
[0542] In some embodiments, vaccines can be administered to prevent
and/or delay the onset of cancer. In some embodiments, cancer
vaccines prevent and/or delay the onset of cancer by preventing
infection by oncogenic infectious agents. In some embodiments,
cancer vaccines prevent and/or delay the onset of cancer by
mounting an immune response against cancer-specific epitopes. To
give but one example of a cancer vaccine, an experimental vaccine
for HPV types 16 and 18 was shown to be 100% successful at
preventing infection with these types of HPV and, thus, are able to
prevent the majority of cervical cancer cases (Harper et al., 2004.
Lancet, 364:1757).
[0543] In some embodiments, pharmaceutical compositions are
administered in combination with complementary and alternative
medicine treatments. Some exemplary complementary measures include,
but are not limited to, botanical medicine (e.g. use of mistletoe
extract combined with traditional chemotherapy for the treatment of
solid tumors); acupuncture for managing chemotherapy-associated
nausea and vomiting and in controlling pain associated with
surgery; prayer, psychological approaches (e.g. "imaging" or
meditation) to aid in pain relief or improve mood. Some exemplary
alternative measures include, but are not limited to, diet and
other lifestyle changes (e.g. plant-based diet, the grape diet, and
the cabbage diet).
[0544] In some embodiments, pharmaceutical compositions are
administered in combination with any of the traditional cancer
treatments described herein, which are often associated with
unpleasant, uncomfortable, and/or dangerous side effects. For
example, chronic pain often results from continued tissue damage
due to the cancer itself or due to the treatment (i.e., surgery,
radiation, chemotherapy). Alternatively or additionally, such
therapies are often associated with hair loss, nausea, vomiting,
diarrhea, constipation, anemia, malnutrition, depression of immune
system, infection, sepsis, hemorrhage, secondary neoplasms,
cardiotoxicity, hepatotoxicity, nephrotoxicity, ototoxicity, etc.
Thus, pharmaceutical compositions which are administered in
combination with any of the traditional cancer treatments described
herein may be also be administered in combination with any
therapeutic agent or therapeutic regimen that is useful to treat,
alleviate, ameliorate, relieve, delay onset of, inhibit progression
of, reduce severity of, and/or reduce incidence of one or more side
effects of cancer treatment. To give but a few examples, pain can
be treated with opioids and/or analgesics (e.g. morphine,
oxycodone, antiemetics, etc.); nausea and vomiting can be treated
with 5-HT.sub.3 inhibitors (e.g. dolasetron/Anzemet.RTM.,
granisetron/Kytril.RTM., ondansetron/Zofran.RTM.,
palonsetron/Aloxi.RTM.) and/or substance P inhibitors (e.g.
aprepitant/Emend.RTM.); immunosuppression can be treated with a
blood transfusion; infection and/or sepsis can be treated with
antibiotics (e.g. penicillins, tetracyclines, cephalosporins,
sulfonamides, aminoglycosides, etc.); and so forth.
[0545] In some embodiments, pharmaceutical compositions may be
administered and/or inventive diagnostic methods may be performed
in combination with any therapeutic agent or therapeutic regimen
that is useful to diagnose one or more symptoms or features of
cancer (e.g. detect the presence of and/or locate a tumor). In some
embodiments, the stitched or stapled polypeptide as described
herein may be used in combination with one or more other diagnostic
agents. To give but one example, polypeptides used to detect tumors
may be administered in combination with other agents useful in the
detection of tumors. For example, the stitched or stapled
polypeptide as described hereins may be administered in combination
with traditional tissue biopsy followed by immunohistochemical
staining and serological tests (e.g. prostate serum antigen test).
Alternatively or additionally, the stitched or stapled polypeptide
as described hereins may be administered in combination with a
contrasting agent for use in computed tomography (CT) scans and/or
MRI.
Kits
[0546] The disclosure provides a variety of kits comprising one or
more of the polypeptides disclosed herein. For example, the
disclosure provides a kit comprising a stitched or stapled
polypeptide as described herein and instructions for use. A kit may
comprise multiple different polypeptides. A kit may comprise any of
a number of additional components or reagents in any combination.
All of the various combinations are not set forth explicitly but
each combination is included in the scope of the disclosure
[0547] According to certain embodiments of the disclosure, a kit
may include, for example, (i) one or more polypeptides and one or
more particular biologically active agents to be delivered; (ii)
instructions for administering the polypeptide to a subject in need
thereof.
[0548] Kits typically include instructions which may, for example,
comprise protocols and/or describe conditions for production of the
polypeptides, administration of the polypeptides to a subject in
need thereof, design of the polypeptides, etc. Kits will generally
include one or more vessels or containers so that some or all of
the individual components and reagents may be separately housed.
Kits may also include a means for enclosing individual containers
in relatively close confinement for commercial sale, e.g., a
plastic box, in which instructions, packaging materials such as
styrofoam, etc., may be enclosed. An identifier, e.g., a bar code,
radio frequency identification (ID) tag, etc., may be present in or
on the kit or in or one or more of the vessels or containers
included in the kit. An identifier can be used, e.g., to uniquely
identify the kit for purposes of quality control, inventory
control, tracking, movement between workstations, etc.
EXAMPLES
[0549] These and other aspects of the present invention will be
further appreciated upon consideration of the following Examples,
which are intended to illustrate certain particular embodiments of
the invention but are not intended to limit its scope, as defined
by the claims.
Example 1: Pro-Locked Stapled Peptides
Materials and Methods
[0550] (R)--N-(Acetyl)-2-(2'-propenyl)proline ("P.sub.R3"), a novel
compound, was synthesized via modification of a reported synthetic
route, followed by acetylation (Synlett, 1999, 1, 33-36;
Tetrahedron, 2005, 61, 10018-10035). A scheme for the synthesis of
P.sub.R3 is shown in FIG. 11.
(R)--N-[(9H-Fluoren-9-ylmethoxy)carbonyl]-2-(2'-propenyl)proline
could be used instead of (R)--N-(Acetyl)-2-(2'-propenyl)proline
("P.sub.R3").
[0551] The compound P.sub.SO3 (See FIG. 10) allows for the
synthesis of linkers originating from a position other than the
alpha-carbon. A scheme for the synthesis of P.sub.SO3 is shown in
FIG. 12. The scheme includes the steps of methyl-esterification,
Fmoc protection, introduction of an allyl group and depotrection of
a Fmoc group.
[0552] The compound P.sub.S3 was synthesized from D-proline
following the synthetic scheme for preparation of the compound
P.sub.SO3.
[0553] The compound P.sub.S5 was synthesized following the
synthetic scheme for preparation of the compound P.sub.R3 by
replacing allyl bromide with 1-iodo-5-pentene.
[0554]
(S)--N-[(9H-Fluoren-9-ylmethoxy)carbonyl]-2-(2'-propylenyl)alanine
was purchased from Okeanos Tech Co.
[0555] The GCN4 basic region was used as a test system to
investigate the properties of the Pro-locked peptides, because the
GCN4 basic region has a canonical nucleating (N-cap) sequence
(N-DPAAL-C) at the N-terminus of its DNA-recognition .alpha.-helix.
(See FIG. 9)
Generation of Pro-Locked Stapled Peptides
[0556] The peptides shown in FIG. 2 were synthesized manually,
using solid phase conditions, rink amide MBHA resin (100-200
meshes) (Novabiochem), and Fmoc main-chain protecting group
chemistry.
[0557] A crosslink was produced through an olefin-metathesis
reaction between P.sub.R3 and S.sub.3 (See FIG. 15). The
olefin-metathesis reaction between P.sub.R3 and S.sub.3 by Grubbs
1st generation catalyst proceeded completely after 16 h and a
single product was observed in LC/MS (FIG. 3 and FIG. 16). The
geometry of the generated olefin group in peptide 2 was determined
to be Z-isomer by NMR measurement (the coupling constant between
two olefinic protons is 11.0 Hz).
[0558] FIG. 10 provides additional amino acids and amino acid
derivatives that were used in the generation of the Pro-locked
stapled peptides described herein.
[0559] FIGS. 13 and 14 provide additional Pro-locked stapled
peptides generated according to the methods provided herein.
Non-cross-linked control peptides are provided in FIG. 14.
Helicity and Stability of Pro-Locked Peptides
[0560] The conformation of peptide 1 and 2 was investigated by CD
measurements (FIG. 4). The data show that peptide 1 adopts a
random-coil and peptide 2 adopts an .alpha.-helix conformation at
20.degree. C. The % helicity of peptide 2 is 67% at 20.degree. C.
The peptide having S.sub.5 rather than S.sub.3 still adopts an
.alpha.-helix conformation at 20.degree. C., but the % helicity is
reduced to 44%.
[0561] The conformation of additional pro-locked peptides as
determined by CD measurements is provided in FIG. 17 and FIG. 18.
(Peptide 1 of FIG. 2 corresponds to Peptide "1)" of FIG. 17, while
Peptide 2 of FIG. 2 corresponds to Peptide "4)" of FIG. 17).
[0562] The stability of the Pro-locked peptide 2 was investigated
by variable temperature CD measurement, and it was found that the
.alpha.-helix conformation was completely maintained in the range
from 20.degree. C. to 90.degree. C. in 50 mM sodium phosphate
buffer (pH 8.0), alone (FIG. 5) and with 100 mM NaCl, 1 M NaCl, and
10% TFE. These observations indicate that the proline stapled
peptides adopt an .alpha.-helix conformation with extraordinary
stability.
[0563] The stability of additional pro-locked peptides as
determined by CD measurements is provided in FIGS. 19-23.
Example 2: Caps for Cloaking Exposed N--H Groups in Peptides
[0564] FIG. 7, FIG. 8, and FIG. 36 provide examples of peptide caps
for cloaking exposed amide N--H groups.
Example 3: Improving Passive Membrane Diffusion of Peptides
[0565] Cells were grown on chamber slides. FITC-labeled peptides 17
and 18 were added to the cell media at 0.1 microM concentration,
and the cells were incubated with the peptide containing cell
media. After incubation, the cells were washed and fixed. Cells
were stained with DAPI, while the presence of peptide was evaluated
using a confocal microscope at a wavelength appropriate for
FITC.
[0566] FIG. 24 shows cell penetration of Pro-locked stapled peptide
18. Significant cell penetration of a FITC-labeled Pro-locked
stapled peptide 18 was shown at 0.1 microM concentration. In
contrast, non-locked WT peptide 17 showed no penetration.
Example 4: Trypsin Digestion
[0567] Peptides (10 nmole) were dissolved in 120 .mu.l digestion
buffer (0.1 M NH.sub.4HCO.sub.3, pH=8) and incubated with trypsin
agatose for 0, 10, 20, 30, 45, 60, and 90 min. The reactions were
quenched by centrifugation. The remaining substrate in the isolated
supernatant was quantified by LC/MS-based peak detection at 220
nm.
OTHER EMBODIMENTS
[0568] In the claims articles such as "a," "an," and "the" may mean
one or more than one unless indicated to the contrary or otherwise
evident from the context. Claims or descriptions that include "or"
between one or more members of a group are considered satisfied if
one, more than one, or all of the group members are present in,
employed in, or otherwise relevant to a given product or process
unless indicated to the contrary or otherwise evident from the
context. The invention includes embodiments in which exactly one
member of the group is present in, employed in, or otherwise
relevant to a given product or process. The invention includes
embodiments in which more than one, or all of the group members are
present in, employed in, or otherwise relevant to a given product
or process.
[0569] Furthermore, the invention encompasses all variations,
combinations, and permutations in which one or more limitations,
elements, clauses, and descriptive terms from one or more of the
listed claims is introduced into another claim. For example, any
claim that is dependent on another claim can be modified to include
one or more limitations found in any other claim that is dependent
on the same base claim. Where elements are presented as lists,
e.g., in Markush group format, each subgroup of the elements is
also disclosed, and any element(s) can be removed from the group.
It should it be understood that, in general, where the invention,
or aspects of the invention, is/are referred to as comprising
particular elements and/or features, certain embodiments of the
invention or aspects of the invention consist, or consist
essentially of, such elements and/or features. For purposes of
simplicity, those embodiments have not been specifically set forth
in haec verba herein. It is also noted that the terms "comprising"
and "containing" are intended to be open and permits the inclusion
of additional elements or steps. Where ranges are given, endpoints
are included. Furthermore, unless otherwise indicated or otherwise
evident from the context and understanding of one of ordinary skill
in the art, values that are expressed as ranges can assume any
specific value or sub-range within the stated ranges in different
embodiments of the invention, to the tenth of the unit of the lower
limit of the range, unless the context clearly dictates
otherwise.
[0570] This application refers to various issued patents, published
patent applications, journal articles, and other publications, all
of which are incorporated herein by reference. If there is a
conflict between any of the incorporated references and the instant
specification, the specification shall control. In addition, any
particular embodiment of the present invention that falls within
the prior art may be explicitly excluded from any one or more of
the claims. Because such embodiments are deemed to be known to one
of ordinary skill in the art, they may be excluded even if the
exclusion is not set forth explicitly herein. Any particular
embodiment of the invention can be excluded from any claim, for any
reason, whether or not related to the existence of prior art.
[0571] Those skilled in the art will recognize or be able to
ascertain using no more than routine experimentation many
equivalents to the specific embodiments described herein. The scope
of the present embodiments described herein is not intended to be
limited to the above Description, but rather is as set forth in the
appended claims. Those of ordinary skill in the art will appreciate
that various changes and modifications to this description may be
made without departing from the spirit or scope of the present
invention, as defined in the following claims.
Sequence CWU 1
1
38114PRTArtificial SequenceSynthetic polypeptide 1Pro Ala Ala Leu
Lys Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 214PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Ser 2Xaa Ala Ala Xaa Lys
Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 326PRTArtificial
SequenceSynthetic polypeptide 3Met Lys Asp Pro Ala Ala Leu Lys Arg
Ala Arg Asn Thr Glu Ala Ala 1 5 10 15 Arg Arg Ser Arg Ala Arg Lys
Leu Gln Arg 20 25 432PRTArtificial SequenceSynthetic polypeptide
4Met Lys Gln Leu Glu Asp Lys Val Glu Glu Leu Leu Ser Lys Asn Tyr 1
5 10 15 His Leu Glu Asn Glu Val Ala Arg Leu Lys Lys Leu Val Gly Glu
Arg 20 25 30 514PRTArtificial SequenceSynthetic
polypeptidemisc_feature(1)..(1)Xaa is a modified Pro 5Xaa Ala Ala
Leu Lys Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 614PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Pro 6Xaa Ala Ala Leu Lys Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10
714PRTArtificial SequenceSynthetic
polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Arg 7Xaa Ala Ala Xaa Lys
Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 814PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Ser 8Xaa Ala Ala Xaa Lys
Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 914PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Arg 9Xaa Ala Ala Xaa Lys
Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 1014PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Pro 10Xaa Ala Ala Leu Lys Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5
10 1114PRTArtificial SequenceSynthetic
polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Ser 11Xaa Ala Ala Xaa Lys
Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 1214PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Arg 12Xaa Ala Ala Xaa Lys
Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 1314PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Ser 13Xaa Ala Ala Xaa Lys
Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 1414PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Argmisc_feature(4)..(4)Xaa is a modified Ser 14Xaa Ala Ala Xaa Lys
Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 158PRTArtificial
SequenceSynthetic polypeptide 15Pro Ala Ala Ala Ala Ala Ala Trp 1 5
168PRTArtificial SequenceSynthetic
polypeptidemisc_feature(1)..(1)Xaa is a modified Pro 16Xaa Ala Ala
Ala Ala Ala Ala Trp 1 5 178PRTArtificial SequenceSynthetic
polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Ser 17Xaa Ala Ala Xaa Ala
Ala Ala Trp 1 5 188PRTArtificial SequenceSynthetic
polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Ser 18Xaa Ala Ala Xaa Ala
Ala Ala Trp 1 5 1914PRTArtificial SequenceSynthetic
polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Ser 19Xaa Ala Ala Xaa Lys
Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 2014PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Ser 20Xaa Ala Ala Xaa Lys
Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 2114PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Argmisc_feature(4)..(4)Xaa is a modified Ser 21Xaa Ala Ala Xaa Lys
Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 2224PRTArtificial
SequenceSynthetic polypeptide 22Pro Ala Ala Leu Lys Arg Ala Arg Asn
Thr Glu Ala Ala Arg Arg Ser 1 5 10 15 Arg Ala Arg Lys Leu Gln Arg
Trp 20 2324PRTArtificial SequenceSynthetic
polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Ser 23Xaa Ala Ala Xaa Lys
Arg Ala Arg Asn Thr Glu Ala Ala Arg Arg Ser 1 5 10 15 Arg Ala Arg
Lys Leu Gln Arg Trp 20 245PRTArtificial SequenceSynthetic
polypeptide 24Pro Ala Ala Leu Trp 1 5 255PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Ser 25Xaa Ala Ala Xaa Trp
1 5 2614PRTArtificial SequenceSynthetic
polypeptidemisc_feature(1)..(1)Xaa is a modified
Sermisc_feature(5)..(5)Xaa is a modified Ser 26Xaa Ala Ala Leu Xaa
Arg Ala Arg Asn Thr Glu Ala Ala Trp 1 5 10 276PRTArtificial
SequenceSynthetic polypeptide 27Asn Thr Glu Ala Ala Trp 1 5
286PRTArtificial SequenceSynthetic
polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified Ser 28Xaa Ala Ala Xaa Lys
Arg 1 5 2914PRTArtificial SequenceSynthetic
polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(7)..(7)Xaa is a modified Ser 29Xaa Ala Ala Leu Lys
Arg Xaa Arg Asn Thr Glu Ala Ala Trp 1 5 10 3014PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(7)..(7)Xaa is a modified Arg 30Xaa Ala Ala Leu Lys
Arg Xaa Arg Asn Thr Glu Ala Ala Trp 1 5 10 3114PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(8)..(8)Xaa is a modified Ser 31Xaa Ala Ala Leu Lys
Arg Ala Xaa Asn Thr Glu Ala Ala Trp 1 5 10 3214PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(8)..(8)Xaa is a modified Arg 32Xaa Ala Ala Leu Lys
Arg Ala Xaa Asn Thr Glu Ala Ala Trp 1 5 10 3314PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Argmisc_feature(8)..(8)Xaa is a modified Ser 33Xaa Ala Ala Leu Lys
Arg Ala Xaa Asn Thr Glu Ala Ala Trp 1 5 10 3414PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(8)..(8)Xaa is a modified Ser 34Xaa Ala Ala Leu Lys
Arg Ala Xaa Asn Thr Glu Ala Ala Trp 1 5 10 3514PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is synthetic amino
acidmisc_feature(7)..(7)Xaa is a modified Ser 35Xaa Ala Ala Xaa Lys
Arg Xaa Arg Asn Thr Glu Ala Ala Trp 1 5 10 3614PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is synthetic amino
acidmisc_feature(8)..(8)Xaa is a modified Arg 36Xaa Ala Ala Xaa Lys
Arg Ala Xaa Asn Thr Glu Ala Ala Trp 1 5 10 3714PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is synthetic amino
acidmisc_feature(11)..(11)Xaa is a modified Ser 37Xaa Ala Ala Xaa
Lys Arg Ala Arg Asn Thr Xaa Ala Ala Trp 1 5 10 3814PRTArtificial
SequenceSynthetic polypeptidemisc_feature(1)..(1)Xaa is a modified
Promisc_feature(4)..(4)Xaa is a modified
Sermisc_feature(12)..(12)Xaa is a modified Arg 38Xaa Ala Ala Xaa
Lys Arg Ala Arg Asn Thr Glu Xaa Ala Trp 1 5 10
* * * * *