U.S. patent application number 17/159674 was filed with the patent office on 2021-05-20 for tank-binding kinase-1 protacs and associated methods of use.
The applicant listed for this patent is Arvinas Operations, Inc.. Invention is credited to Andrew P. Crew, Hanqing Dong, Yimin Qian, Jing Wang.
Application Number | 20210145832 17/159674 |
Document ID | / |
Family ID | 1000005361037 |
Filed Date | 2021-05-20 |
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United States Patent
Application |
20210145832 |
Kind Code |
A1 |
Crew; Andrew P. ; et
al. |
May 20, 2021 |
TANK-BINDING KINASE-1 PROTACs AND ASSOCIATED METHODS OF USE
Abstract
The present invention relates to bifunctional compounds, which
find utility to degrade and (inhibit) TBK1. In particular, the
present invention is directed to compounds, which contain on one
end an E3 ubiquitin ligase binding moiety which binds to an E3
ubiquitin ligase and on the other end a moiety which binds TBK1
such that TBK1 is placed in proximity to the ubiquitin ligase to
effect degradation (and inhibition) of TBK1. The present invention
exhibits a broad range of pharmacological activities associated
with compounds according to the present invention, consistent with
the degradation/inhibition of TBK1.
Inventors: |
Crew; Andrew P.; (Chester,
CT) ; Wang; Jing; (Milford, CT) ; Dong;
Hanqing; (Madison, CT) ; Qian; Yimin;
(Plainsboro, NJ) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Arvinas Operations, Inc. |
New Haven |
CT |
US |
|
|
Family ID: |
1000005361037 |
Appl. No.: |
17/159674 |
Filed: |
January 27, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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16284790 |
Feb 25, 2019 |
10946017 |
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17159674 |
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15574770 |
Nov 16, 2017 |
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PCT/US2016/036036 |
Jun 6, 2016 |
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16284790 |
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62171299 |
Jun 5, 2015 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07K 5/06034 20130101;
C07D 417/04 20130101; A61K 31/506 20130101; A61K 47/665 20170801;
A61K 2300/00 20130101; C07D 413/04 20130101; A61K 45/06
20130101 |
International
Class: |
A61K 31/506 20060101
A61K031/506; A61K 45/06 20060101 A61K045/06; A61K 47/66 20060101
A61K047/66; C07D 413/04 20060101 C07D413/04; C07D 417/04 20060101
C07D417/04; C07K 5/062 20060101 C07K005/062 |
Claims
1. A method of treating a disease or disorder in a subject, the
method comprising administering a composition comprising a
bifunctional compound and a pharmaceutically acceptable carrier to
a subject in need thereof, wherein the bifunctional compound is
effective in treating or ameliorating at least one symptom of the
disease or disorder and has the chemical structure: TBM-L-ULM,
wherein: TBM is a TBK1 binding moiety; L is a bond or a chemical
linker that covalently couples the TBM and the ULM; and ULM is an
E3 ubiquitin ligase binding moiety.
2. The method of claim 1, wherein the disease or disorder is at
least one of cancer, an inflammatory disease, an autoimmune
disease, septic shock, or a viral infection.
3. The method of claim 1, wherein the TBM structure is represented
by: ##STR00076## wherein R.sub.1 is a group selected from Cl,
CF.sub.3, cyclobutyl, I, F, methyl, ethyl, vinyl, cyclopropyl, or
Br.
4. The method of claim 1, wherein the TBM has the structure:
##STR00077##
5. The method of claim 1, wherein the ULM is a moiety that binds an
E3 ubiquitin ligase selected from the group consisting of Von
Hippel-Lindau (VHL) E3 ubiquitin ligase, IAP, cereblon, and
MDM2.
6. The method of claim 1, wherein the chemical linker (L) is a
group having the structure: -(A').sub.q-, wherein: -(A').sub.q- is
coupled to the ULM and the TBM; and q is an integer greater than or
equal to 0.
7. The method of claim 6, wherein: each A is independently
CR.sup.L1R.sup.L2, O, S, SO, SO.sub.2, NR.sup.L3,
SO.sub.2NR.sup.L3, SONR.sup.L3, CONR.sup.L3, NR.sup.L3CONR.sup.L4,
NR.sup.L3SO.sub.2NR.sup.L4, CO, CR.sup.L1.dbd.CR.sup.L2, C.ident.C,
SiR.sup.L1R.sup.L2, P(O)R.sup.L1, P(O)OR.sup.L1,
NR.sup.L3C(.dbd.NCN)NR.sup.L4, NR.sup.L3C(.dbd.NCN),
NR.sup.L3C(.dbd.CNO.sub.2)NR.sup.L4, C.sub.3-11cycloalkyl
optionally substituted with 1-6 R.sup.L1 and/or R.sup.L2 groups,
C.sub.3-11heteocyclyl optionally substituted with 1-6 R.sup.L1
and/or R.sup.L2 groups, aryl optionally substituted with 1-6
R.sup.L1 and/or R.sup.L2 groups, or heteroaryl optionally
substituted with 1-6 R.sup.L1 and/or R.sup.L2 groups, wherein
R.sup.L1 or R.sup.L2, each independently, can be linked to other A
groups to form cycloalkyl and/or heterocyclyl moiety which can be
further substituted with 1-4 R.sup.L5 groups; and R.sup.L1,
R.sup.L2, R.sup.L3, R.sup.L4 and R.sup.L5 are, each independently,
H, halogen, C.sub.1-8alkyl, OC.sub.1-8alkyl, SC.sub.1-8alkyl,
NHC.sub.1-8alkyl, N(C.sub.1-8alkyl).sub.2, C.sub.3-11cycloalkyl,
aryl, heteroaryl, C.sub.3-11heterocyclyl, OC.sub.3-8cycloalkyl,
SC.sub.3-8cycloalkyl, NHC.sub.3-8cycloalkyl,
N(C.sub.3-8cycloalkyl).sub.2,
N(C.sub.3-8cycloalkyl)(C.sub.1-8alkyl), OH, NH.sub.2, SH,
SO.sub.2C.sub.1-8alkyl, P(O)(OC.sub.1-8alkyl)(C.sub.1-8alkyl),
P(O)(OC.sub.1-8alkyl).sub.2, CC--C.sub.1-8alkyl, CCH,
CH.dbd.CH(C.sub.1-8alkyl),
C(C.sub.1-8alkyl).dbd.CH(C.sub.1-8alkyl),
C(C.sub.1-8alkyl).dbd.C(C.sub.1-8alkyl).sub.2, Si(OH).sub.3,
Si(C.sub.1-8alkyl).sub.3, Si(OH)(C.sub.1-8alkyl).sub.2,
COC.sub.1-8alkyl, CO.sub.2H, halogen, CN, CF.sub.3, CHF.sub.2,
CH.sub.2F, NO.sub.2, SF.sub.5, SO.sub.2NHC.sub.1-8alkyl,
SO.sub.2N(C.sub.1-8alkyl).sub.2, SONHC.sub.1-8alkyl,
SON(C.sub.1-8alkyl).sub.2, CONHC.sub.1-8alkyl,
CON(C.sub.1-8alkyl).sub.2, N(C.sub.1-8alkyl)CONH(C.sub.1-8alkyl),
N(C.sub.1-8alkyl)CON(C.sub.1-8alkyl).sub.2, NHCONH(C.sub.1-8alkyl),
NHCON(C.sub.1-8alkyl).sub.2, NHCONH.sub.2,
N(C.sub.1-8alkyl)SO.sub.2NH(C.sub.1-8alkyl), N(C.sub.1-8alkyl)
SO.sub.2N(C.sub.1-8alkyl).sub.2, NH SO.sub.2NH(C.sub.1-8alkyl), NH
SO.sub.2N(C.sub.1-8alkyl).sub.2, or NH SO.sub.2NH.sub.2.
8. The method of claim 1, wherein the chemical linker (L) is
selected from the group consisting of: ##STR00078## ##STR00079##
##STR00080##
9. The method of claim 1, wherein the ULM has the chemical
structure: ##STR00081## wherein: the dashed line indicates the
attachment of the ULM to the chemical linker group or the TBM;
X.sup.1 and X.sup.2 are each independently a bond, O, NR.sup.Y3,
CR.sup.Y3R.sup.Y4, C.dbd.O, C.dbd.S, SO, or SO.sub.2; R.sup.Y3 and
R.sup.Y4 are each independently: H; or linear or branched C.sub.1-6
alkyl optionally substituted by 1 or more halogen or C.sub.1-6
alkoxyl; R.sup.P is 0, 1, 2, or 3 groups in the pyrrolidine moiety,
wherein each R.sup.P is independently H, halogen, --OH, or
C.sub.1-3alkyl; W.sup.3 is an optionally substituted
-T-N(R.sup.1aR.sup.1b), -T-Aryl, an optionally substituted
-T-Heteroaryl, an optionally substituted -T-Heterocycle, an
optionally substituted --NR.sup.1-T-Aryl, an optionally substituted
--NR.sup.1-T-Heteroaryl, or an optionally substituted
--NR.sup.1-T-Heterocycle, where T is covalently bonded to X.sup.1;
each R.sup.1, R.sup.1a, and R.sup.1b is independently: H; a linear
or branched C.sub.1-6 alkyl group optionally substituted by 1 or
more halogen or --OH; R.sup.Y3C.dbd.O; R.sup.Y3C.dbd.S; R.sup.Y3SO;
R.sup.Y3SO.sub.2; N(R.sup.Y3R.sup.Y4)C.dbd.O;
N(R.sup.Y3R.sup.Y4)C.dbd.S; N(R.sup.Y3R.sup.Y4)SO; or
N(R.sup.Y3R.sup.Y4)SO.sub.2; T is an optionally substituted
--(CH.sub.2).sub.n-- group, wherein each one of the methylene
groups may be optionally substituted with one or two substituents,
selected from: halogen; a linear or branched C.sub.1-C.sub.6 alkyl
group optionally substituted by 1 or more halogen or OH; or the
sidechain of an amino acid, which may be optionally substituted; n
is an integer from 0 to 6; W.sup.4 is ##STR00082## R.sub.14a and
R.sub.14b, is each independently H, haloalkyl, or optionally
substituted alkyl; W.sup.5 is a phenyl or a 5-10 membered
heteroaryl; and R.sub.15 is H, halogen, CN, OH, NO.sub.2, N
R.sub.14aR.sub.14b, OR.sub.14a, CONR.sub.14aR.sub.14b,
NR.sub.14aCOR.sub.14b, SO.sub.2NR.sub.14aR.sub.14b, NR.sub.14a
SO.sub.2R.sub.14b, optionally substituted alkyl, optionally
substituted haloalkyl, optionally substituted haloalkoxy, aryl,
heteroaryl, cycloalkyl, cycloheteroalkyl; or ##STR00083## wherein:
R.sub.17 is H, halogen, optionally substituted C.sub.3-6
cycloalkyl, optionally substituted C.sub.1-6 alkyl, optionally
substituted C.sub.2-6 alkenyl, and C.sub.1-6 haloalkyl; and Xa is S
or O.
10. The method of claim 1, wherein the ULM has the chemical
structure: ##STR00084## ##STR00085## ##STR00086## wherein indicates
the point of attachment to the chemical linker or the TBM.
11. The method of claim 1, wherein the compound has the chemical
structure: ##STR00087##
12. The method of claim 1, wherein the compound has the chemical
structure: ##STR00088##
13. The method of claim 1, wherein the compound is selected from
the group consisting of: ##STR00089## ##STR00090## ##STR00091##
##STR00092## ##STR00093## ##STR00094## ##STR00095## ##STR00096##
and combinations thereof.
14. The method of claim 1, wherein the ULM has a chemical structure
selected the group consisting of: ##STR00097## wherein: W is
independently selected from the group CH.sub.2, CHR, C.dbd.O,
SO.sub.2, NH, and N-alkyl; X is independently selected from the
group absent, O, and S; Y is independently selected from the group
NH, N-alkyl, N-aryl, N-hetaryl, N-cycloalkyl, N-heterocyclyl, O,
and S; Z is independently selected from the group absent, O, and S,
except that both X and Z cannot be absent; G and G' are
independently selected from the group H, alkyl, OH,
CH.sub.2-heterocyclyl optionally substituted with R', and benzyl
optionally substituted with R'; Q1-Q4 represent a N or a C with a
group independently selected from H and R; A is independently
selected from the group H, alkyl, cycloalkyl, Cl, and F; n is an
integer from 1-4; R is: --CONR'R'', --OR', --NR'R'', --SR',
--SO.sub.2R', --SO.sub.2NR'R'', --CR'R''--, --CR'NR'R''--, -aryl,
-hetaryl, -alkyl, -cycloalkyl, -heterocyclyl, --P(O)(OR')R'',
--P(O)R'R'', --OP(O)(OR')R'', --OP(O)R'R'', --Cl, --F, --Br, --I,
--CF.sub.3, --CN, --NR'SO.sub.2NR'R'', --NR'CONR'R'', --CONR'COR'',
--NR'C(.dbd.N--CN)NR'R'', --C(.dbd.N--CN)NR'R'',
--NR'C(.dbd.N--CN)R'', --NR'C(.dbd.C--NO.sub.2)NR'R'',
--SO.sub.2NR'COR'', --NO.sub.2, --CO.sub.2R', --C(C.dbd.N--OR')R'',
--CR'.dbd.CR'R'', --CCR', --S(C.dbd.O)(C.dbd.N--R')R'', --SF.sub.5
and --OCF.sub.3, wherein one R is modified to be covalently joined
to the chemical linker (L) or the TBM: R' and R'' are independently
selected from a bond, H, alkyl, cycloalkyl, aryl, hetaryl, and
heterocyclyl; and represents a bond that may be stereospecific ((R)
or (S)) or non-stereospecific.
15. The method of claim 1, wherein the composition further
comprises at least one additional bioactive agent.
16. The method of claim 15, wherein the bioactive agent is an
anti-cancer agent.
17. The method of claim 15, wherein the bioactive agent is at least
one anti-cancer agent selected from selected from the group
consisting of: everolimus, trabectedin, abraxane, TLK 286, AV-299,
DN-101, pazopanib, GSK690693, RTA 744, ON 0910.Na, AZD 6244
(ARRY-142886), AMN-107, TKI-258, GSK461364, AZD 1152, enzastaurin,
vandetanib, ARQ-197, MK-0457, MLN8054, PHA-739358, R-763, AT-9263,
a FLT-3 inhibitor, an androgen receptor inhibitor, a VEGFR
inhibitor, an EGFR TK inhibitor, an aurora kinase inhibitor, a
PIK-1 modulator, a Bcl-2 inhibitor, an HDAC inhbitor, a c-MET
inhibitor, a PARP inhibitor, a Cdk inhibitor, an EGFR TK inhibitor,
an IGFR-TK inhibitor, an anti-HGF antibody, a PI3 kinase
inhibitors, an AKT inhibitor, a JAK/STAT inhibitor, a checkpoint-1
or 2 inhibitor, a focal adhesion kinase inhibitor, a Map kinase
kinase (mek) inhibitor, a VEGF trap antibody, pemetrexed,
erlotinib, dasatanib, nilotinib, decatanib, panitumumab, amrubicin,
oregovomab, Lep-etu, nolatrexed, azd2171, batabulin, ofatumumab,
zanolimumab, edotecarin, tetrandrine, rubitecan, tesmilifene,
oblimersen, ticilimumab, ipilimumab, gossypol, Bio 111, 131-TM-601,
ALT-110, BIO 140, CC 8490, cilengitide, gimatecan, IL13-PE38QQR,
INO 1001, IPdR.sub.1 KRX-0402, lucanthone, LY317615, neuradiab,
vitespan, Rta 744, Sdx 102, talampanel, atrasentan, Xr 311,
romidepsin, ADS-100380, sunitinib, 5-fluorouracil, vorinostat,
etoposide, gemcitabine, doxorubicin, liposomal doxorubicin,
5'-deoxy-5-fluorouridine, vincristine, temozolomide, ZK-304709,
seliciclib; PD0325901, AZD-6244, capecitabine, L-Glutamic acid,
N-[4-[2-(2-amino-4,7-dihydro-4-oxo-1
H--pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl]-, disodium salt,
heptahydrate, camptothecin, PEG-labeled irinotecan, tamoxifen,
toremifene citrate, anastrazole, exemestane, letrozole,
DES(diethylstilbestrol), estradiol, estrogen, conjugated estrogen,
bevacizumab, IMC-1C11, CHIR-258);
3-[5-(methylsulfonylpiperadinemethyl)-indolylj-quinolone,
vatalanib, AG-013736, AVE-0005, the acetate salt of [D-Ser(But)
6,Azgly 10]
(pyro-Glu-His-Trp-Ser-Tyr-D-Ser(But)-Leu-Arg-Pro-Azgly-NH 2 acetate
[C.sub.59H.sub.84N.sub.18Oi.sub.4-(C.sub.2H.sub.4O.sub.2).sub.X
where x=1 to 2.4], goserelin acetate, leuprolide acetate,
triptorelin pamoate, medroxyprogesterone acetate,
hydroxyprogesterone caproate, megestrol acetate, raloxifene,
bicalutamide, flutamide, nilutamide, megestrol acetate, CP-724714;
TAK-165, HKI-272, erlotinib, lapatanib, canertinib, ABX-EGF
antibody, erbitux, EKB-569, PKI-166, GW-572016, Ionafarnib,
BMS-214662, tipifarnib; amifostine, NVP-LAQ824, suberoyl analide
hydroxamic acid, valproic acid, trichostatin A, FK-228, SU11248,
sorafenib, KRN951, aminoglutethimide, arnsacrine, anagrelide,
L-asparaginase, Bacillus Calmette-Guerin (BCG) vaccine, adriamycin,
bleomycin, buserelin, busulfan, carboplatin, carmustine,
chlorambucil, cisplatin, cladribine, clodronate, cyproterone,
cytarabine, dacarbazine, dactinomycin, daunorubicin,
diethylstilbestrol, epirubicin, fludarabine, fludrocortisone,
fluoxymesterone, flutamide, gleevec, gemcitabine, hydroxyurea,
idarubicin, ifosfamide, imatinib, leuprolide, levamisole,
lomustine, mechlorethamine, melphalan, 6-mercaptopurine, mesna,
methotrexate, mitomycin, mitotane, mitoxantrone, nilutamide,
octreotide, oxaliplatin, pamidronate, pentostatin, plicamycin,
porfimer, procarbazine, raltitrexed, rituximab, streptozocin,
teniposide, testosterone, thalidomide, thioguanine, thiotepa,
tretinoin, vindesine, 13-cis-retinoic acid, phenylalanine mustard,
uracil mustard, estramustine, altretamine, floxuridine,
5-deooxyuridine, cytosine arabinoside, 6-mecaptopurine,
deoxycoformycin, calcitriol, valrubicin, mithramycin, vinblastine,
vinorelbine, topotecan, razoxin, marimastat, COL-3, neovastat,
BMS-275291, squalamine, endostatin, SU5416, SU6668, EMD121974,
interleukin-12, IM862, angiostatin, vitaxin, droloxifene,
idoxyfene, spironolactone, finasteride, cimitidine, trastuzumab,
denileukin diftitox,gefitinib, bortezimib, paclitaxel,
cremophor-free paclitaxel, docetaxel, epithilone B, BMS-247550,
BMS-310705, droloxifene, 4-hydroxytamoxifen, pipendoxifene,
ERA-923, arzoxifene, fulvestrant, acolbifene, lasofoxifene,
idoxifene, TSE-424, HMR-3339, ZK186619, topotecan, PTK787/ZK
222584, VX-745, PD 184352, rapamycin,
40-O-(2-hydroxyethyl)-rapamycin, temsirolimus, AP-23573, RAD001,
ABT-578, BC-210, LY294002, LY292223, LY292696, LY293684, LY293646,
wortmannin, ZM336372, L-779,450, PEG-filgrastim, darbepoetin,
erythropoietin, granulocyte colony-stimulating factor,
zolendronate, prednisone, cetuximab, granulocyte macrophage
colony-stimulating factor, histrelin, pegylated interferon alfa-2a,
interferon alfa-2a, pegylated interferon alfa-2b, interferon
alfa-2b, azacitidine, PEG-L-asparaginase, lenalidomide, gemtuzumab,
hydrocortisone, interleukin-11, dexrazoxane, alemtuzumab,
all-transretinoic acid, ketoconazole, interleukin-2, megestrol,
immune globulin, nitrogen mustard, methylprednisolone, ibritgumomab
tiuxetan, androgens, decitabine, hexamethylmelamine, bexarotene,
tositumomab, arsenic trioxide, cortisone, editronate, mitotane,
cyclosporine, liposomal daunorubicin, Edwina-asparaginase,
strontium 89, casopitant, netupitant, an NK-1 receptor antagonist,
palonosetron, aprepitant, diphenhydramine, hydroxyzine,
metoclopramide, lorazepam, alprazolam, haloperidol, droperidol,
dronabinol, dexamethasone, methylprednisolone, prochlorperazine,
granisetron, ondansetron, dolasetron, tropisetron, pegfilgrastim,
erythropoietin, epoetin alfa, darbepoetin alfa and mixtures
thereof.
18. A method of treating a disease or disorder in a subject, the
method comprising administering a composition comprising a
bifunctional compound and a pharmaceutically acceptable carrier to
a subject in need thereof, wherein the bifunctional compound is
effective in treating or ameliorating at least one symptom of the
disease or disorder and has the chemical structure: TBM-L-ULM,
wherein: TBM includes a means for recruiting TBK1; L is a bond or a
chemical linker that covalently couples the TBM and the ULM; and
ULM includes a means for recruiting an E3 ubiquitin ligase.
19. The method of claim 18, wherein the disease or disorder is at
least one of cancer, an inflammatory disease, an autoimmune
disease, septic shock, or a viral infection.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] The present disclosure is a Divisional Application of U.S.
patent application Ser. No. 16/284,790, filed 25 Feb. 2019, titled:
TANK-BINDING KINASE-1 PROTACs AND ASSOCIATED METHODS OF USE, which
is a Continuation Application of U.S. patent application Ser. No.
15/574,770, filed 16 Nov. 2017, titled: TANK-BINDING KINASE-1
PROTACs AND ASSOCIATED METHODS OF USE, which is a National Stage of
PCT/US2016/036036, filed 6 Jun. 2016, titled TANK-BINDING KINASE-1
PROTACs AND ASSOCIATED METHODS OF USE, and which claims priority to
the U.S. Provisional Application No. 62/171,299, filed 5 Jun. 2015,
all of which are incorporated herein by reference in their entirety
for all purposes.
BACKGROUND
1. Field of the Discovery
[0002] The description provides bifunctional compounds and
associated methods of use. The bifunctional compounds are useful as
modulators of targeted ubiquitination, especially with respect to a
variety of polypeptides and other proteins, which are degraded
and/or otherwise inhibited by bifunctional compounds according to
the present invention.
2. Background Information
[0003] The most common therapeutic interventions available to the
prescribing physician are inhibitor-based drugs such that the
active pharmaceutical ingredient mediates the function of the
aberrant protein via direct or allosteric inhibition of the
mechanistic activity of said protein.
[0004] Although inhibition of protein activity is a clinically
validated approach there are significant constraints to its wider
applicability. Firstly, it carries the burden of requiring
protracted target engagement for the mechanism and consequential
function to be effectively abrogated. Many protein-small molecule
interactions are associated with rapid off-rates, resulting in very
low inhibitor occupancy of the protein active site and inadequate
downregulation of downstream signaling.
[0005] Secondly, inability to reach tolerated free-drug
concentrations at or above the in vitro IC.sub.90, either because
of high plasma protein binding, poor pharmacokinetics, or toxicity
can limit the effectiveness of inhibitor drugs.
[0006] Finally, many proteins possess little or no mechanistic
activity, yet execute their biological role by providing a
scaffolding function. As a result, these proteins are less
susceptible to the inhibitor paradigm.
[0007] E3 ubiquitin ligases (of which hundreds are known in humans)
confer substrate specificity for ubiquitination, and therefore, are
more attractive therapeutic targets than general proteasome
inhibitors due to their specificity for certain protein substrates.
The development of ligands of E3 ligases has proven challenging, in
part due to the fact that they must disrupt protein-protein
interactions. However, recent developments have provided specific
ligands which bind to these ligases. For example, since the
discovery of nutlins, the first small molecule E3 ligase
inhibitors, additional compounds have been reported that target E3
ligases but the field remains underdeveloped.
[0008] Technologies that can reduce levels of a target protein in a
manner that requires only transient interactions with the protein
could provide significant therapeutic utility.
SUMMARY
[0009] Proteolysis Targeting Chimeras (PROTACs) (Corson, T. W.;
Aberle, N.; Crews, C. M. ACS Chem. Biol. 2008 3(11) 677-692;
Sakamoto, K. M.; Kim, K. B.; Verma, R.; Ransick, A.; Stein, B.;
Crews, C. M.; Deshaies, R. J. Mol. Cell. Proteomics 2003 2(12)
1350-1358; Sakamoto, K. M.; Kim, K. B.; Kumagai, A.; Mercurio, F.;
Crews, C. M.; Deshaies, R. J. Proc. Natl. Acad. Sci. USA 2001
98(15) 8554-8559) are a class of bifunctional molecules that live
in the "beyond rule of 5" (bRo5) (Barbie, D. A.; Tamayo, P.; Boehm,
J. S.; Kim, S. Y.; Moody, S. E.; Dunn, I. F.; Schinzel, A. C.;
Sandy, P.; Meylan, E.; Scholl, C.; et al. Nature 2009 462 108-112)
space that hijack the endogenous protein homeostasis machinery via
recruitment of an E3 ubiquitin ligase via one component ligand and
associating it with a target protein of interest (PoI) through
another component ligand to mediate ubiquitin transfer to, and
degradation of, the latter via the proteasome (FIG. 1).
[0010] The present disclosure describes compounds, including
compositions comprising the same, which function to recruit
endogenous proteins to an E3 ubiquitin ligase enzyme, e.g., Von
Hippel-Lindau (VHL) E3 ubiquitin ligase, cereblon, IAP (XIAP), and
MDM2, for ubiquitination and subsequent degradation, and methods of
using the same. In particular, the present disclosure provides
bifunctional or proteolysis targeting chimeric (PROTAC) compounds,
which find utility as modulators of targeted ubiquitination and
degradation of TANK-binding kinase 1 (TBK1).
[0011] Thus, in one aspect, the disclosure provides compounds which
function to recruit endogenous proteins, e.g., TBK1 proteins, to E3
Ubiquitin Ligase for ubiquitination and degradation. In certain
embodiments, the compounds have the following general
structure:
TBM-L-ULM (I),
[0012] wherein TBM is an TBK1 binding moiety, ULM is an E3 ligase
binding moiety, e.g., a VHL E3 ligase binding moiety (VLM),
cereblon binding moiety (CLM), XIAP binding moiety, or MDM2 binding
moiety, and L is a bond or a linker moiety which links the TBM and
ULM.
[0013] As such, in certain embodiments, the description provides
compounds having the following general structure:
TBM-L-VLM (II),
[0014] wherein TBM is an TBK1 binding moiety, VLM is a VHL E3
ligase binding moiety and L is a bond or a linker moiety which
links the TBM and VLM.
[0015] It will be understood that the general structures are
exemplary and the respective moieties can be arranged spatially in
any desired order or configuration, e.g., ULM-L-TBM, and VLM-L-TBM
respectively.
[0016] In certain additional embodiments, the compounds comprise a
plurality of E3 ligase binding moieties and/or a plurality of
TBMs.
[0017] In certain embodiments, the description provides a
bifunctional compound having a structure as described herein, a
salt, a polymorph, and a prodrug thereof.
[0018] In another aspect, the description provides compositions
comprising compounds as described herein, and a pharmaceutically
acceptable carrier. In certain embodiments, the compositions are
therapeutic or pharmaceutical compositions comprising an effective
amount of a compound as described herein and a pharmaceutically
acceptable carrier. In certain embodiments, the therapeutic or
pharmaceutical compositions comprise an additional biologically
active agent, e.g., an agent effective for the treatment of
cancer.
[0019] In any of the aspects or embodiments described herein, the
therapeutic compositions comprising compounds described herein can
be in any suitable dosage form, e.g., solid, or liquid, and
configured to be delivered by any suitable route, e.g., oral,
parenteral, intravenous, intraperitoneal, subcutaneous,
intramuscular, etc.
[0020] In another aspect, the disclosure provides methods of
modulating protein ubiquitination and degradation in a subject,
e.g., a cell, a tissue, mammal, or human patient, the method
comprising administering an effective amount of a compound as
described herein or a composition comprising an effective amount of
the same to a subject, wherein the compound or composition
comprising the same is effective in modulating protein
ubiquitination and degradation of the protein in the subject. In
certain embodiments, the protein is TBK1.
[0021] In another aspect, the disclosure provides methods of
modulating TBK1 protein ubiquitination and degradation in a
subject, e.g., a cell, a tissue, mammal, or human patient, the
method comprising administering an effective amount of a compound
as described herein or a composition comprising an effective amount
of the same to a subject, wherein the compound or composition
comprising the same is effective in modulating TBK1 protein
ubiquitination and degradation of the protein in the subject.
[0022] In another aspect, the disclosure provides methods of
treating or ameliorating a symptom of a disease related to TBK1
activity in a subject, e.g., a cell, a tissue, mammal, or human
patient, the method comprising administering an effective amount of
a compound as described herein or a composition comprising an
effective amount of the same to a subject in need thereof, wherein
the compound or composition comprising the same is effective in
treating or ameliorating a symptom of a disease related to TBK1
activity in the subject. In a preferred embodiment, the subject is
a human.
[0023] In another aspect, the disclosure provides methods for
identifying the effects of the degradation of proteins of interest
in a biological system using compounds according to the present
invention.
[0024] In another aspect, the description provides kits comprising
compounds or compositions as described herein. The kit may be
promoted, distributed, or sold as a unit for performing the methods
of the present invention. In addition, the kits of the present
invention may preferably contain instructions which describe a
suitable use. Such kits can be conveniently used, e.g., in clinical
settings, to treat patients.
[0025] Where applicable or not specifically disclaimed, any one of
the embodiments described herein are contemplated to be able to
combine with any other one or more embodiments, even though the
embodiments are described under different aspects of the invention.
As such, the preceding general areas of utility are given by way of
example only and are not intended to be limiting on the scope of
the present disclosure and appended claims. Additional objects and
advantages associated with the compositions, methods, and processes
of the present invention will be appreciated by one of ordinary
skill in the art in light of the instant claims, description, and
examples. For example, the various aspects and embodiments of the
invention may be utilized in numerous combinations, all of which
are expressly contemplated by the present description. These
additional advantages objects and embodiments are expressly
included within the scope of the present invention. The
publications and other materials used herein to illuminate the
background of the invention, and in particular cases, to provide
additional details respecting the practice, are incorporated by
reference.
BRIEF DESCRIPTION OF THE DRAWINGS
[0026] The accompanying drawings, which are incorporated into and
form a part of the specification, illustrate several embodiments of
the present invention and, together with the description, serve to
explain the principles of the invention. The drawings are only for
the purpose of illustrating an embodiment of the invention and are
not to be construed as limiting the invention. Further objects,
features and advantages of the invention will become apparent from
the following detailed description taken in conjunction with the
accompanying figures showing illustrative embodiments of the
invention, in which:
[0027] FIG. 1. Proteolysis Targeting Chimeras (PROTACs) recruit an
E3 ligase to a target protein to facilitate ubiquitin transfer from
the former to the latter;
[0028] FIG. 2. TBK1 ligand 1 and VHL ligand 2 components selected
for inclusion into the TBK1 PROTAC architecture;
[0029] FIG. 3. Snapshot of an aminopyrimidine TBK1 ligand bound to
TBK1 (from 41M0);
[0030] FIG. 4. Snapshot of hydroxyproline VHL ligand chemotype
bound to VHL (from 4W9L);
[0031] FIG. 5. PROTAC 18 is a VHL incompetent epimer of active TBK1
degrader 11;
[0032] FIG. 6. PROTAC 11 but not its VHL-incompetent epimer 18 nor
TBK1 inhibitor 1 effects degradation of TBK1. All 3 display
competent intracellular TBK1/pIRF3 activity;
[0033] FIG. 7. PROTAC 11 mediated degradation of TBK1 is abrogated
in the presence of the proteasome inhibitor carfilzomib;
[0034] FIG. 8A TBK1 degradation in KRAS mutant and wild type cells;
and FIG. 8B Antiproliferative effects of TBK1 degrader 11 on KRAS
mutant and wild type cells; and
[0035] FIG. 9. PROTAC 11 selectively degrades TBK1 over
IKK.epsilon..
DETAILED DESCRIPTION
[0036] The following is a detailed description provided to aid
those skilled in the art in practicing the present invention. Those
of ordinary skill in the art may make modifications and variations
in the embodiments described herein without departing from the
spirit or scope of the present disclosure. All publications, patent
applications, patents, figures and other references mentioned
herein are expressly incorporated by reference in their
entirety.
[0037] The present description relates to the surprising and
unexpected discovery that an E3 ubiquitin ligase protein can
ubiquitinate a target protein once the E3 ubiquitin ligase protein
and the target protein are brought into proximity by a chimeric
construct (e.g., PROTAC) as described herein, which binds the E3
ubiquitin ligase protein and the target protein. Accordingly, the
present description provides compounds, compositions comprising the
same, and associated methods of use for ubiquitination and
degradation of a chosen target protein, e.g., TBK1 (See FIG.
1).
[0038] The present description is related in certain aspects to
U.S. Patent Publication 2014/0356322A1, which is incorporated
herein by reference in its entirety for all purposes.
[0039] Unless otherwise defined, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention belongs. The
terminology used in the description is for describing particular
embodiments only and is not intended to be limiting of the
invention.
[0040] Where a range of values is provided, it is understood that
each intervening value, to the tenth of the unit of the lower limit
unless the context clearly dictates otherwise (such as in the case
of a group containing a number of carbon atoms in which case each
carbon atom number falling within the range is provided), between
the upper and lower limit of that range and any other stated or
intervening value in that stated range is encompassed within the
invention. The upper and lower limits of these smaller ranges may
independently be included in the smaller ranges is also encompassed
within the invention, subject to any specifically excluded limit in
the stated range. Where the stated range includes one or both of
the limits, ranges excluding either both of those included limits
are also included in the invention.
[0041] The following terms are used to describe the present
invention. In instances where a term is not specifically defined
herein, that term is given an art-recognized meaning by those of
ordinary skill applying that term in context to its use in
describing the present invention.
[0042] The articles "a" and "an" as used herein and in the appended
claims are used herein to refer to one or to more than one (i.e.,
to at least one) of the grammatical object of the article unless
the context clearly indicates otherwise. By way of example, "an
element" means one element or more than one element.
[0043] The phrase "and/or," as used herein in the specification and
in the claims, should be understood to mean "either or both" of the
elements so conjoined, i.e., elements that are conjunctively
present in some cases and disjunctively present in other cases.
Multiple elements listed with "and/or" should be construed in the
same fashion, i.e., "one or more" of the elements so conjoined.
Other elements may optionally be present other than the elements
specifically identified by the "and/or" clause, whether related or
unrelated to those elements specifically identified. Thus, as a
non-limiting example, a reference to "A and/or B", when used in
conjunction with open-ended language such as "comprising" can
refer, in one embodiment, to A only (optionally including elements
other than B); in another embodiment, to B only (optionally
including elements other than A); in yet another embodiment, to
both A and B (optionally including other elements); etc.
[0044] As used herein in the specification and in the claims, "or"
should be understood to have the same meaning as "and/or" as
defined above. For example, when separating items in a list, "or"
or "and/or" shall be interpreted as being inclusive, i.e., the
inclusion of at least one, but also including more than one, of a
number or list of elements, and, optionally, additional unlisted
items. Only terms clearly indicated to the contrary, such as "only
one of" or "exactly one of," or, when used in the claims,
"consisting of," will refer to the inclusion of exactly one element
of a number or list of elements. In general, the term "or" as used
herein shall only be interpreted as indicating exclusive
alternatives (i.e., "one or the other but not both") when preceded
by terms of exclusivity, such as "either," "one of," "only one of,"
or "exactly one of."
[0045] The term "about" and the like, as used herein, in
association with numeric values or ranges, reflects the fact that
there is a certain level of variation that is recognized and
tolerated in the art due to practical and/or theoretical
limitations. For example, minor variation is tolerated due to
inherent variances in the manner in which certain devices operate
and/or measurements are taken. In accordance with the above, the
phrase "about" is normally used to encompass values within the
standard deviation or standard error.
[0046] In the claims, as well as in the specification above, all
transitional phrases such as "comprising," "including," "carrying,"
"having," "containing," "involving," "holding," "composed of," and
the like are to be understood to be open-ended, i.e., to mean
including but not limited to. Only the transitional phrases
"consisting of" and "consisting essentially of" shall be closed or
semi-closed transitional phrases, respectively, as set forth in the
United States Patent Office Manual of Patent Examining Procedures,
Section 2111.03.
[0047] As used herein in the specification and in the claims, the
phrase "at least one," in reference to a list of one or more
elements, should be understood to mean at least one element
selected from anyone or more of the elements in the list of
elements, but not necessarily including at least one of each and
every element specifically listed within the list of elements and
not excluding any combinations of elements in the list of elements.
This definition also allows that elements may optionally be present
other than the elements specifically identified within the list of
elements to which the phrase "at least one" refers, whether related
or unrelated to those elements specifically identified. Thus, as a
nonlimiting example, "at least one of A and B" (or, equivalently,
"at least one of A or B," or, equivalently "at least one of A
and/or B") can refer, in one embodiment, to at least one,
optionally including more than one, A, with no B present (and
optionally including elements other than B); in another embodiment,
to at least one, optionally including more than one, B, with no A
present (and optionally including elements other than A); in yet
another embodiment, to at least one, optionally including more than
one, A, and at least one, optionally including more than one, B
(and optionally including other elements); etc.
[0048] It should also be understood that, in certain methods
described herein that include more than one step or act, the order
of the steps or acts of the method is not necessarily limited to
the order in which the steps or acts of the method are recited
unless the context indicates otherwise.
[0049] The terms "co-administration" and "co-administering" or
"combination therapy" can refer to both concurrent administration
(administration of two or more therapeutic agents at the same time)
and time varied administration (administration of one or more
therapeutic agents at a time different from that of the
administration of an additional therapeutic agent or agents), as
long as the therapeutic agents are present in the patient to some
extent, preferably at effective amounts, at the same time. In
certain preferred aspects, one or more of the present compounds
described herein, are co-administered in combination with at least
one additional bioactive agent, especially including an anticancer
agent. In particularly preferred aspects, the co-administration of
compounds results in synergistic activity and/or therapy, including
anticancer activity.
[0050] The term "effective" can mean, but is in no way limited to,
that amount/dose of the active pharmaceutical ingredient, which,
when used in the context of its intended use, effectuates or is
sufficient to prevent, inhibit the occurrence, ameliorate, delay or
treat (alleviate a symptom to some extent, preferably all) the
symptoms of a condition, disorder or disease state in a subject in
need of such treatment or receiving such treatment. The term
effective subsumes all other effective amount or effective
concentration terms, e.g., "effective amount/dose,"
"pharmaceutically effective amount/dose" or "therapeutically
effective amount/dose," which are otherwise described or used in
the present application.
[0051] The effective amount depends on the type and severity of
disease, the composition used, the route of administration, the
type of mammal being treated, the physical characteristics of the
specific mammal under consideration, concurrent medication, and
other factors which those skilled in the medical arts will
recognize. The exact amount can be ascertainable by one skilled in
the art using known techniques (see, e.g., Lieberman,
Pharmaceutical Dosage Forms (vols. 1-3, 1992); Lloyd, The Art,
Science and Technology of Pharmaceutical Compounding (1999);
Pickar, Dosage Calculations (1999); and Remington: The Science and
Practice of Pharmacy, 20th Edition, 2003, Gennaro, Ed., Lippincott,
Williams & Wilkins).
[0052] The term "pharmacological composition," "therapeutic
composition," "therapeutic formulation" or "pharmaceutically
acceptable formulation" can mean, but is in no way limited to, a
composition or formulation that allows for the effective
distribution of an agent provided by the invention, which is in a
form suitable for administration to the physical location most
suitable for their desired activity, e.g., systemic
administration.
[0053] The term "pharmaceutically acceptable" or "pharmacologically
acceptable" can mean, but is in no way limited to, entities and
compositions that do not produce an adverse, allergic or other
untoward reaction when administered to an animal, or a human, as
appropriate.
[0054] The term "pharmaceutically acceptable carrier" or
"pharmacologically acceptable carrier" can mean, but is in no way
limited to, any and all solvents, dispersion media, coatings,
antibacterial and antifungal agents, isotonic and absorption
delaying agents, and the like, compatible with pharmaceutical
administration. Suitable carriers are described in the most recent
edition of Remington's Pharmaceutical Sciences, a standard
reference text in the field, which is incorporated herein by
reference. Preferred examples of such carriers or diluents include,
but are not limited to, water, saline, finger's solutions, dextrose
solution, and 5% human serum albumin. Liposomes and non-aqueous
vehicles such as fixed oils may also be used. The use of such media
and agents for pharmaceutically active substances is well known in
the art. Except insofar as any conventional media or agent is
incompatible with the active compound, use thereof in the
compositions is contemplated. Supplementary active compounds can
also be incorporated into the compositions.
[0055] The term "systemic administration" refers to a route of
administration that is, e.g., enteral or parenteral, and results in
the systemic distribution of an agent leading to systemic
absorption or accumulation of drugs in the blood stream followed by
distribution throughout the entire body. Suitable forms, in part,
depend upon the use or the route of entry, for example oral,
transdermal, or by injection. Such forms should not prevent the
composition or formulation from reaching a target cell (i.e., a
cell to which the negatively charged polymer is desired to be
delivered to). For example, pharmacological compositions injected
into the blood stream should be soluble. Other factors are known in
the art, and include considerations such as toxicity and forms
which prevent the composition or formulation from exerting its
effect. Administration routes which lead to systemic absorption
include, without limitations: intravenous, subcutaneous,
intraperitoneal, inhalation, oral, intrapulmonary and
intramuscular. The rate of entry of a drug into the circulation has
been shown to be a function of molecular weight or size. The use of
a liposome or other drug carrier comprising the compounds of the
instant invention can potentially localize the drug, for example,
in certain tissue types, such as the tissues of the reticular
endothelial system (RES). A liposome formulation which can
facilitate the association of drug with the surface of cells, such
as, lymphocytes and macrophages is also useful.
[0056] The term "local administration" refers to a route of
administration in which the agent is delivered to a site that is
apposite or proximal, e.g., within about 10 cm, to the site of the
lesion or disease.
[0057] The term "compound", as used herein, unless otherwise
indicated, refers to any specific chemical compound disclosed
herein and includes tautomers, regioisomers, geometric isomers, and
where applicable, stereoisomers, including optical isomers
(enantiomers) and other stereoisomers (diastereomers) thereof, as
well as pharmaceutically acceptable salts and derivatives
(including prodrug forms) thereof where applicable, in context.
Within its use in context, the term compound generally refers to a
single compound, but also may include other compounds such as
stereoisomers, regioisomers and/or optical isomers (including
racemic mixtures) as well as specific enantiomers or
enantiomerically enriched mixtures of disclosed compounds. The term
also refers, in context to prodrug forms of compounds which have
been modified to facilitate the administration and delivery of
compounds to a site of activity. It is noted that in describing the
present compounds, numerous substituents and variables associated
with same, among others, are described.
[0058] It is understood by those of ordinary skill that molecules
which are described herein are stable compounds as generally
described hereunder. When the bond is shown, both a double bond and
single bond are represented within the context of the compound
shown.
[0059] As used herein, "derivatives" can mean compositions formed
from the native compounds either directly, by modification, or by
partial substitution. As used herein, "analogs" can mean
compositions that have a structure similar to, but not identical
to, the native compound.
[0060] The term "Ubiquitin Ligase" refers to a family of proteins
that facilitate the transfer of ubiquitin to a specific substrate
protein, targeting the substrate protein for degradation. For
example, Von Hippel-Lindau E3 Ubiquitin Ligase or VCB E3 Ubiquitin
Ligase is protein that alone or in combination with an E2
ubiquitin-conjugating enzyme causes the attachment of ubiquitin to
a lysine on a target protein, and subsequently targets the specific
protein substrates for degradation by the proteasome. Thus, E3
ubiquitin ligase alone or in complex with an E2 ubiquitin
conjugating enzyme is responsible for the transfer of ubiquitin to
targeted proteins. In general, the ubiquitin ligase is involved in
polyubiquitination such that a second ubiquitin is attached to the
first; a third is attached to the second, and so forth.
Polyubiquitination marks proteins for degradation by the
proteasome. However, there are some ubiquitination events that are
limited to mono-ubiquitination, in which only a single ubiquitin is
added by the ubiquitin ligase to a substrate molecule.
Mono-ubiquitinated proteins are not targeted to the proteasome for
degradation, but may instead be altered in their cellular location
or function, for example, via binding other proteins that have
domains capable of binding ubiquitin. Further complicating matters,
different lysines on ubiquitin can be targeted by an E3 to make
chains. The most common lysine is Lys48 on the ubiquitin chain.
This is the lysine used to make polyubiquitin, which is recognized
by the proteasome.
[0061] The term "subject" is used throughout the specification to
describe a cell, tissue, or animal, preferably a human or a
domesticated animal, to whom treatment, including prophylactic
treatment, with the compositions according to the present invention
is provided. For treatment of those infections, conditions or
disease states which are specific for a specific animal such as a
human patient, the term patient refers to that specific animal,
including a domesticated animal such as a dog or cat or a farm
animal such as a horse, cow, sheep, etc. In general, in the present
invention, the term patient refers to a human patient unless
otherwise stated or implied from the context of the use of the
term.
Compounds
[0062] In one aspect, the present invention provides compounds
useful for regulating protein activity. The composition comprises a
ubiquitin pathway protein binding moiety (preferably for an E3
ubiquitin ligase, alone or in complex with an E2 ubiquitin
conjugating enzyme which is responsible for the transfer of
ubiquitin to targeted proteins) according to a defined chemical
structure and a protein targeting moiety which are linked or
coupled together, preferably through a linker, wherein the
ubiquitin pathway protein binding moiety recognizes an ubiquitin
pathway protein and the targeting moiety recognizes a target
protein (e.g., TBK1).
[0063] In certain embodiments, the disclosure provides compounds
which function to recruit TBK1 proteins to E3 Ubiquitin Ligase for
ubiquintination and degradation. In certain embodiments, the
compounds have the following general structure:
TBM-L-ULM (I),
wherein ULM is an E3 ligase binding moiety, e.g., a moiety that
binds a member selected from the group of Von Hippel-Lindau (VHL)
E3 ubiquitin ligase, cereblon, IAP (XIAP), and MDM2, TBM is a TBK1
binding moiety, which binds to a TBK1 protein and L is a bond or a
chemical linker moiety which links the TBM and ULM.
[0064] Without being bound by any particular theory, it is
hypothesized that due at least in part to the proximity of TBK1 and
the E3 ubiquitin ligase, the TBK1 is ubiquitinated by the ubiquitin
ligase and degraded. In certain embodiments, the TBM is chemically
linked or coupled directly to the ULM group. In certain additional
embodiments, the TBM is chemically linked or coupled to the ULM via
a chemical linker moiety.
[0065] The von Hippel-Lindau (VHL) tumor suppressor. VHL comprises
the substrate recognition subunit/E3 ligase complex VCB, which
includes elongins B and C, and a complex including Cullin-2 and
Rbx1. The primary substrate of VHL is Hypoxia Inducible Factor
1.alpha. (HIF-1.alpha.), a transcription factor that upregulates
genes such as the pro-angiogenic growth factor VEGF and the red
blood cell inducing cytokine erythropoietin in response to low
oxygen levels. We generated the first small molecule ligands of Von
Hippel Lindau (VHL) to the substrate recognition subunit of the E3
ligase, VCB, an important target in cancer, chronic anemia and
ischemia, and obtained crystal structures confirming that the
compound mimics the binding mode of the transcription factor
HIF-1.alpha., the major substrate of VHL.
[0066] Inhibitors of Apoptosis Protein (IAPs) are guardian
ubiquitin ligases that keep classic pro-apoptotic proteins in
check, and regulates not only caspases and apoptosis, but also
modulates inflammatory signaling and immunity, copper homeostasis,
mitogenic kinase signaling, cell proliferation, as well as cell
invasion and metastasis. IAPs act as a direct caspase inhibitor,
and directly bind to the active site pocket of CASP3 and CASP7 and
obstruct substrate entry. IAPS also inactivate CASP9 by keeping it
in a monomeric, inactive state. IAP acts as an E3 ubiquitin-protein
ligase regulating NF-kappa-B signaling and the target proteins for
its E3 ubiquitin-protein ligase activity include: RIPK1, CASP3,
CASP7, CASP8, CASP9, MAP3K2/MEKK2, DIABLO/SMAC, AIFM1, CCS and
BIRC5/survivin. Ubiquitination of CCS leads to enhancement of its
chaperone activity toward its physiologic target, SOD1, rather than
proteasomal degradation. Ubiquitinion of MAP3K2/MEKK2 and AIFM1
does not lead to proteasomal degradation. IAP plays a role in
copper homeostasis by ubiquitinating COMMD1 and promoting its
proteasomal degradation, and can also function as E3
ubiquitin-protein ligase of the NEDD8 conjugation pathway,
targeting effector caspases for neddylation and inactivation. IAP
regulates the BMP signaling pathway and the SMAD and MAP3K7/TAK1
dependent pathways leading to NF-kappa-B and JNK activation.
[0067] IAPs are an important regulator of innate immune signaling
via regulation of Nodlike receptors (NLRs), and protects cells from
spontaneous formation of the ripoptosome, a large multi-protein
complex that has the capability to kill cancer cells in a
caspase-dependent and caspase-independent manner. Suppresses
ripoptosome formation by ubiquitinating RIPK1 and CASP8. Acts as a
positive regulator of Wnt signaling and ubiquitinates TLE1, TLE2,
TLE3, TLE4 and AES. Ubiquitination of TLE3 results in inhibition of
its interaction with TCF7L2/TCF4 thereby allowing efficient
recruitment and binding of the transcriptional coactivator
beta-catenin to TCF7L2/TCF4 that is required to initiate a
Wnt-specific transcriptional program. Inhibitors of the IAP, which
are useful in making compounds as described herein, are known in
the art.
[0068] Mouse double minute 2 homolog (MDM2) also known as E3
ubiquitin-protein ligase Mdm2 is a protein that in humans is
encoded by the MDM2 gene. Mdm2 is an important negative regulator
of the p53 tumor suppressor. Mdm2 protein functions both as an E3
ubiquitin ligase that recognizes the N-terminal trans-activation
domain (TAD) of the p53 tumor suppressor and an inhibitor of p53
transcriptional activation. Inhibitors of the MDM2-p53 interaction,
which are useful in making compounds as described herein, include
the cis-imidazoline analog nutlin.
[0069] Cereblon is a protein that in humans is encoded by the CRBN
gene. CRBN orthologs are highly conserved from plants to humans,
which underscores its physiological importance. Cereblon forms an
E3 ubiquitin ligase complex with damaged DNA binding protein 1
(DDB1), Cullin-4A (CUL4A), and regulator of cullins 1 (ROC1). This
complex ubiquitinates a number of other proteins. Through a
mechanism which has not been completely elucidated, cereblon
ubquitination of target proteins results in increased levels of
fibroblast growth factor 8 (FGF8) and fibroblast growth factor 10
(FGF10). FGF8 in turn regulates a number of developmental
processes, such as limb and auditory vesicle formation. The net
result is that this ubiquitin ligase complex is important for limb
outgrowth in embryos. In the absence of cereblon, DDB1 forms a
complex with DDB2 that functions as a DNA damage-binding
protein.
[0070] Thalidomide, which has been approved for the treatment of a
number of immunological indications, has also been approved for the
treatment of certain neoplastic diseases, including multiple
myeloma. In addition to multiple myeloma, thalidomide and several
of its analogs are also currently under investigation for use in
treating a variety of other types of cancer. While the precise
mechanism of thalidomide's anti-tumor activity is still emerging,
it is known to inhibit angiogenesis. Recent literature discussing
the biology of the imides includes Lu et al Science 343, 305 (2014)
and Kronke et al Science 343, 301 (2014).
[0071] Significantly, thalidomide and its analogs e.g.
pomolinamiode and lenalinomide, are known to bind cereblon. These
agents bind to cereblon, altering the specificity of the complex to
induce the ubiquitination and degradation of Ikaros (IKZF1) and
Aiolos (IKZF3), transcription factors essential for multiple
myeloma growth. Indeed, higher expression of cereblon has been
linked to an increase in efficacy of imide drugs in the treatment
of multiple myeloma. Therefore, thalidomide and its analogs are
useful cereblon binding moieties for use in making compounds as
described herein.
[0072] In additional embodiments, the description provides
compounds having the following general structure:
TBM-L-VLM (II),
wherein TBM is a TBK1 binding moiety and VLM is a Von Hippel-Lindau
E3 Ubiquitin Ligase binding moiety, and L is a bond or a chemical
linker moiety which links the TBM and VLM. The ULM or VLM group and
TBM group may be covalently linked to the linker group through any
covalent bond which is appropriate and stable to the chemistry of
the linker.
[0073] In certain embodiments, the bifunctional compound further
comprises a chemical linker ("L"). In this example, the structure
of the bifunctional compound can be depicted as:
TBM-L-CLM (II),
[0074] wherein TBM is a TBK1 binding moiety, L is a linker, and CLM
is a cereblon E3 ubiquitin ligase binding moiety.
[0075] It will be understood that the general structures are
exemplary and the respective moieties can be arranged in any
desired order or configuration, e.g., ULM-L-TBM, and VLM-L-TBM
respectively. In certain additional embodiments, the compounds
comprise a plurality of E3 ligase binding moieties and/or a
plurality of TBMs.
[0076] In any of the aspects or embodiments of compounds described
herein, unless indicated otherwise, the compounds are intended to
encompass pharmaceutically acceptable salts, enantiomers,
stereoisomers, solvates or polymorphs thereof.
[0077] Exemplary ULMs
[0078] In certain embodiments of the compounds as described herein,
the ULM comprises a chemical structure selected from the group
ULM-a:
##STR00001##
wherein: [0079] a dashed line indicates the attachment of at least
one TBM, another ULM or VLM (i.e., ULM' or VLM'), or a chemical
linker moiety coupling at least one TBM, a ULM' or VLM' to the
other end of the linker; [0080] X.sup.1, X.sup.2 are each
independently a bond, O, NR.sup.Y3, CR.sup.Y3R.sup.Y4, C.dbd.O,
C.dbd.S, SO, SO.sub.2; [0081] R.sup.Y3, R.sup.Y4 are each
independently H, C.sub.1-6 alkyl (linear, branched, optionally
substituted by 1 or more halo, C.sub.1-6 alkoxyl); [0082]
optionally substituted by 1-3 R.sup.P groups in the pyrrolidine
moiety, wherein each R.sup.P is independently H, halo, --OH,
C.sub.1-3alkyl; [0083] W.sup.3 is an optionally substituted
-T-N(R.sup.1aR.sup.1b), -T-Aryl, an optionally substituted
-T-Heteroaryl, an optionally substituted -T-Heterocycle, an
optionally substituted --NR.sup.1-T-Aryl, an optionally substituted
--NR.sup.1-T-Heteroaryl or an optionally substituted
--NR.sup.1-T-Heterocycle, where T is covalently bonded to X.sup.1;
[0084] each R.sup.1, R.sup.1a, R.sup.1b is independently H, a C1-C6
alkyl group (linear, branched, optionally substituted by 1 or more
halo, --OH), R.sup.Y3C.dbd.O, R.sup.Y3C.dbd.S, R.sup.Y3SO,
R.sup.Y3SO.sub.2, N(R.sup.Y3R.sup.Y4)C.dbd.O,
N(R.sup.Y3R.sup.Y4)C.dbd.S, N(R.sup.Y3R.sup.Y4)SO,
N(R.sup.Y3R.sup.Y4)SO.sub.2; [0085] T is an optionally substituted
--(CH.sub.2).sub.n-- group, wherein each one of the methylene
groups may be optionally substituted with one or two substituents,
preferably selected from halogen, a C1-C6 alkyl group (linear,
branched, optionally substituted by 1 or more halogen, --OH) or the
sidechain of an amino acid as otherwise described herein,
preferably methyl, which may be optionally substituted; and n is 0
to 6, often 0, 1, 2, or 3, preferably 0.
[0086] Alternatively, T may also be a --(CH.sub.2O).sub.n-- group,
a --(OCH.sub.2).sub.n-- group, a --(CH.sub.2CH.sub.2O).sub.n-group,
a --(OCH.sub.2CH.sub.2).sub.n-- group, each of which groups is
optionally substituted; and
[0087] W.sup.4 is an optionally substituted --NR.sup.1-T-Aryl, an
optionally substituted --NR.sup.1-T-Heteroaryl group or an
optionally substituted --NR.sup.1-T-Heterocycle, where where
--NR.sup.1 is covalently bonded to X.sup.2; R.sup.1 is H or
CH.sub.3, preferably H, and T is an optionally substituted
--(CH.sub.2).sub.n-- group, wherein each one of the methylene
groups may be optionally substituted with one or two substituents,
preferably selected from halogen, an amino acid sidechain as
otherwise described herein or a C1-C6 alkyl group (linear,
branched, optionally substituted by 1 or more halo, --OH),
preferably one or two methyl groups, which may be optionally
substituted; and n is 0 to 6, often 0, 1, 2 or 3, preferably 0 or
1.
[0088] Alternatively, T may also be a --(CH.sub.2O).sub.n-- group,
a --(OCH.sub.2).sub.n-- group, a --(CH.sub.2CH.sub.2O).sub.n--
group, a --(OCH.sub.2CH.sub.2).sub.n-- group, all of which groups
are optionally substituted.
[0089] In any of the embodiments described herein, W.sup.3 and/or
W.sup.4 can be attached to a linker moiety as described herein.
[0090] In certain embodiments, aryl groups for W.sup.3 include
optionally substituted phenyl or naphthyl groups, preferably phenyl
groups, wherein the phenyl or naphthyl group is optionally
substituted with a linker group to which is attached a TBM group
(including a ULM' group) and/or a halogen (preferably F or Cl), an
amine, monoalkyl- or dialkyl amine (preferably, dimethylamine), an
amido group (preferably a --(CH.sub.2).sub.m--NR.sub.1C(O)R.sub.2
group where m, R.sub.1 and R.sub.2 are the same as for R.sup.1), a
halogen (often F or Cl), OH, CH.sub.3, CF.sub.3, OMe, OCF.sub.3,
NO.sub.2, CN or a S(O).sub.2R.sub.S group (R.sub.S is a a
C.sub.1-C.sub.6 alkyl group, an optionally substituted aryl,
heteroaryl or heterocycle group or a
--(CH.sub.2).sub.mNR.sub.1R.sub.2 group), each of which may be
substituted in ortho-, meta- and/or para-positions of the phenyl
ring, preferably para-), or an Aryl (preferably phenyl), heteroaryl
or heterocycle. Preferably said substituent phenyl group is an
optionally substituted phenyl group (i.e., the substituent phenyl
group itself is preferably substituted with at least one of F, Cl,
OH, SH, COOH, CH.sub.3, CF.sub.3, OMe, OCF.sub.3, NO.sub.2, CN or a
linker group to which is attached a TBM group (including a ULM'
group), wherein the substitution occurs in ortho-, meta- and/or
para-positions of the phenyl ring, preferably para-, a naphthyl
group, which may be optionally substituted including as described
above, an optionally substituted heteroaryl (preferably an
optionally substituted isoxazole including a methylsubstituted
isoxazole, an optionally substituted oxazole including a
methylsubstituted oxazole, an optionally substituted thiazole
including a methyl substituted thiazole, an optionally substituted
pyrrole including a methylsubstituted pyrrole, an optionally
substituted imidazole including a methylimidazole, a
benzylimidazole or methoxybenzylimidazole, an oximidazole or
methyloximidazole, an optionally substituted diazole group,
including a methyldiazole group, an optionally substituted triazole
group, including a methylsubstituted triazole group, a pyridine
group, including a halo- (preferably, F) or
methylsubstitutedpyridine group or an oxapyridine group (where the
pyridine group is linked to the phenyl group by an oxygen) or an
optionally substituted heterocycle (tetrahydrofuran,
tetrahydrothiophene, pyrrolidine, piperidine, morpholine,
piperazine, tetrahydroquinoline, oxane or thiane. Each of the aryl,
heteroaryl or heterocyclic groups may be optionally substituted
with a linker group to which is attached a TBM group (including a
ULM' group).
[0091] In certain embodiments, heteroaryl groups for W.sup.3
include an optionally substituted quinoline (which may be attached
to the pharmacophore or substituted on any carbon atom within the
quinoline ring), an optionally substituted indole (including
dihydroindole), an optionally substituted indolizine, an optionally
substituted azaindolizine (2, 3 or 4-azaindolizine) an optionally
substituted benzimidazole, benzodiazole, benzoxofuran, an
optionally substituted imidazole, an optionally substituted
isoxazole, an optionally substituted oxazole (preferably methyl
substituted), an optionally substituted diazole, an optionally
substituted triazole, a tetrazole, an optionally substituted
benzofuran, an optionally substituted thiophene, an optionally
substituted thiazole (preferably methyl and/or thiol substituted),
an optionally substituted isothiazole, an optionally substituted
triazole (preferably a 1,2,3-triazole substituted with a methyl
group, a triisopropylsilyl group, an optionally substituted
--(CH.sub.2).sub.mO--C.sub.1-C.sub.6 alkyl group or an optionally
substituted --(CH.sub.2).sub.mC(O)--O--C.sub.1-C.sub.6 alkyl
group), an optionally substituted pyridine (2-, 3, or 4-pyridine)
or a group according to the chemical structure:
##STR00002##
wherein: [0092] S.sup.c is CHR.sup.SS, NR.sup.URE, or O; [0093]
R.sup.HET is H, CN, NO.sub.2, halo (preferably Cl or F), optionally
substituted C.sub.1-C.sub.6 alkyl (preferably substituted with one
or two hydroxyl groups or up to three halo groups (e.g. CF.sub.3),
optionally substituted O(C.sub.1-C.sub.6 alkyl) (preferably
substituted with one or two hydroxyl groups or up to three halo
groups) or an optionally substituted acetylenic group
--C.ident.C--R.sub.a where R.sub.a is H or a C.sub.1-C.sub.6 alkyl
group (preferably C.sub.1-C.sub.3 alkyl); [0094] R.sup.SS is H, CN,
NO.sub.2, halo (preferably F or Cl), optionally substituted
C.sub.1-C.sub.6 alkyl (preferably substituted with one or two
hydroxyl groups or up to three halo groups), optionally substituted
O--(C.sub.1-C.sub.6 alkyl) (preferably substituted with one or two
hydroxyl groups or up to three halo groups) or an optionally
substituted --C(O)(C.sub.1-C.sub.6 alkyl) (preferably substituted
with one or two hydroxyl groups or up to three halo groups); [0095]
R.sup.URE is H, a C.sub.1-C.sub.6 alkyl (preferably H or
C.sub.1-C.sub.3 alkyl) or a --C(O)(C.sub.1-C.sub.6 alkyl), each of
which groups is optionally substituted with one or two hydroxyl
groups or up to three halogen, preferably fluorine groups, or an
optionally substituted heterocycle, for example piperidine,
morpholine, pyrrolidine, tetrahydrofuran, tetrahydrothiophene,
piperidine, piperazine, each of which is optionally substituted;
and [0096] Y.sup.C is N or C--R.sup.YC, where R.sup.YC is H, OH,
CN, NO.sub.2, halo (preferably Cl or F), optionally substituted
C.sub.1-C.sub.6 alkyl (preferably substituted with one or two
hydroxyl groups or up to three halo groups (e.g. CF.sub.3),
optionally substituted O(C.sub.1-C.sub.6 alkyl) (preferably
substituted with one or two hydroxyl groups or up to three halo
groups) or an optionally substituted acetylenic group
--C.ident.C--R.sub.a where R.sub.a is H or a C.sub.1-C.sub.6 alkyl
group (preferably C.sub.1-C.sub.3 alkyl). Each of said heteroaryl
groups may be optionally substituted with a linker group to which
is attached a TBM group (including a ULM' group).
[0097] In additional embodiments, heterocycle groups for W.sup.3
include tetrahydroquinoline, piperidine, piperazine, pyrrollidine,
morpholine, tetrahydrofuran, tetrahydrothiophene, oxane and thiane,
each of which groups may be optionally substituted or a group
according to the chemical structure:
##STR00003##
wherein: [0098] R.sup.PRO is H, optionally substituted
C.sub.1-C.sub.6 alkyl or an optionally substituted aryl (phenyl or
napthyl), heteroaryl or heterocyclic group selected from the group
consisting of oxazole, isoxazole, thiazole, isothiazole, imidazole,
diazole, oximidazole, pyrrole, pyrollidine, furan, dihydrofuran,
tetrahydrofuran, thiene, dihydrothiene, tetrahydrothiene, pyridine,
piperidine, piperazine, morpholine, quinoline, (each preferably
substituted with a C.sub.1-C.sub.3 alkyl group, preferably methyl
or a halo group, preferably F or Cl), benzofuran, indole,
indolizine, azaindolizine; [0099] R.sup.PRO1 and R.sup.PRO2 are
each independently H, an optionally substituted C.sub.1-C.sub.3
alkyl group or together form a keto group, and each n is 0, 1, 2,
3, 4, 5, or 6 (preferably 0 or 1), wherein each of said Heterocycle
groups may be optionally substituted with a linker group to which
is attached a TBM group (including a ULM' group) or a
pharmaceutically acceptable salt, stereoisomer, solvate or
polymorph thereof.
[0100] In certain embodiments, W.sup.3 substituents for use in the
present invention also include specifically (and without limitation
to the specific compound disclosed) the W.sup.3 substituents which
are found in the identified compounds disclosed herein (which
includes the specific compounds which are disclosed in the present
specification, and the figures which are attached hereto). Each of
these W.sup.3 substituents may be used in conjunction with any
number of W.sup.4 substituents, which are also disclosed
herein.
[0101] In certain embodiments, Aryl groups for W.sup.4 include
optionally substituted phenyl or naphthyl groups, preferably phenyl
groups, wherein the phenyl group is optionally substituted with a
linker group to which is attached an TBMTBM group (including a ULM'
group), a halogen (preferably F or Cl), an amine, monoalkyl- or
dialkyl amine (preferably, dimethylamine), F, Cl, OH, COOH,
C.sub.1-C.sub.6 alkyl, preferably CH.sub.3, CF.sub.3, OMe,
OCF.sub.3, NO.sub.2, or CN group (each of which may be substituted
in ortho-, meta- and/or para-positions of the phenyl ring,
preferably para-), an optionally substituted phenyl group (the
phenyl group itself is preferably substituted with a linker group
attached to a TBM group, including a ULM' group), and/or at least
one of F, Cl, OH, COOH, CH.sub.3, CF.sub.3, OMe, OCF.sub.3,
NO.sub.2, or CN group (in ortho-, meta- and/or para-positions of
the phenyl ring, preferably para-), a naphthyl group, which may be
optionally substituted, an optionally substituted heteroaryl,
preferably an optionally substituted isoxazole including a
methylsubstituted isoxazole, an optionally substituted oxazole
including a methylsubstituted oxazole, an optionally substituted
thiazole including a methyl substituted thiazole, an optionally
substituted isothiazole including a methyl substituted isothiazole,
an optionally substituted pyrrole including a methylsubstituted
pyrrole, an optionally substituted imidazole including a
methylimidazole, an optionally substituted benzimidazole or
methoxybenzylimidazole, an optionally substituted oximidazole or
methyloximidazole, an optionally substituted diazole group,
including a methyldiazole group, an optionally substituted triazole
group, including a methylsubstituted triazole group, an optionally
substituted pyridine group, including a halo-(preferably, F) or
methylsubstitutedpyridine group or an oxapyridine group (where the
pyridine group is linked to the phenyl group by an oxygen), an
optionally substituted furan, an optionally substituted benzofuran,
an optionally substituted dihydrobenzofuran, an optionally
substituted indole, indolizine or azaindolizine (2, 3, or
4-azaindolizine), an optionally substituted quinoline, an
optionally substituted group according to the chemical
structure:
##STR00004##
wherein: [0102] S.sup.c is CHR.sup.SS, NR.sup.URE, or O; [0103]
R.sup.HET is H, CN, NO.sub.2, halo (preferably Cl or F), optionally
substituted C.sub.1-C.sub.6 alkyl (preferably substituted with one
or two hydroxyl groups or up to three halo groups (e.g. CF.sub.3),
optionally substituted O(C.sub.1-C.sub.6 alkyl) (preferably
substituted with one or two hydroxyl groups or up to three halo
groups) or an optionally substituted acetylenic group
--C.ident.C--R.sub.a where R.sub.a is H or a C.sub.1-C.sub.6 alkyl
group (preferably C.sub.1-C.sub.3 alkyl); [0104] R.sup.SS is H, CN,
NO.sub.2, halo (preferably F or Cl), optionally substituted
C.sub.1-C.sub.6 alkyl (preferably substituted with one or two
hydroxyl groups or up to three halo groups), optionally substituted
O--(C.sub.1-C.sub.6 alkyl) (preferably substituted with one or two
hydroxyl groups or up to three halo groups) or an optionally
substituted --C(O)(C.sub.1-C.sub.6 alkyl) (preferably substituted
with one or two hydroxyl groups or up to three halo groups); [0105]
R.sup.URE is H, a C.sub.1-C.sub.6 alkyl (preferably H or
C.sub.1-C.sub.3 alkyl) or a --C(O)(C.sub.1-C.sub.6 alkyl) each of
which groups is optionally substituted with one or two hydroxyl
groups or up to three halogen, preferably fluorine groups, or an
optionally substituted phenyl group, an optionally substituted
heteroaryl, or an optionally substituted heterocycle, preferably
for example piperidine, morpholine, pyrrolidine, tetrahydrofuran);
[0106] .sup.PRO is H, optionally substituted C.sub.1-C.sub.6 alkyl
or an optionally substituted aryl (phenyl or napthyl), heteroaryl
or heterocyclic group selected from the group consisting of
oxazole, isoxazole, thiazole, isothiazole, imidazole, diazole,
oximidazole, pyrrole, pyrollidine, furan, dihydrofuran,
tetrahydrofuran, thiene, dihydrothiene, tetrahydrothiene, pyridine,
piperidine, piperazine, morpholine, quinoline, (each preferably
substituted with a C.sub.1-C.sub.3 alkyl group, preferably methyl
or a halo group, preferably F or Cl), benzofuran, indole,
indolizine, azaindolizine; [0107] R.sup.PRO1 and R.sup.PRO2 are
each independently H, an optionally substituted C.sub.1-C.sub.3
alkyl group or together form a keto group; and [0108] each n is
independently 0, 1, 2, 3, 4, 5, or 6 (preferably 0 or 1), or an
optionally substituted heterocycle, preferably tetrahydrofuran,
tetrahydrothiene, piperidine, piperazine or morpholine (each of
which groups when substituted, are preferably substituted with a
methyl or halo (F, Br, Cl), each of which groups may be optionally
substituted with a linker group to which is attached a TBM group
(including a ULM' group).
[0109] In certain preferred aspects,
##STR00005##
where R.sup.PRO and n are the same as above.
[0110] In certain embodiments, heteroaryl groups for W.sup.4
include an optionally substituted quinoline (which may be attached
to the pharmacophore or substituted on any carbon atom within the
quinoline ring), an optionally substituted indole, an optionally
substituted indolizine, an optionally substituted azaindolizine, an
optionally substituted benzofuran, including an optionally
substituted benzofuran, an optionally substituted isoxazole, an
optionally substituted thiazole, an optionally substituted
isothiazole, an optionally substituted thiophene, an optionally
substituted pyridine (2-, 3, or 4-pyridine), an optionally
substituted imidazole, an optionally substituted pyrrole, an
optionally substituted diazole, an optionally substituted triazole,
a tetrazole, an optionally substituted oximidazole, or a group
according to the chemical structure:
##STR00006##
wherein: [0111] S.sup.c is CHR.sup.SS, NR.sup.URE, or O; [0112]
.sup.HET is H, CN, NO.sub.2, halo (preferably Cl or F), optionally
substituted C.sub.1-C.sub.6 alkyl (preferably substituted with one
or two hydroxyl groups or up to three halo groups (e.g. CF.sub.3),
optionally substituted O(C.sub.1-C.sub.6 alkyl) (preferably
substituted with one or two hydroxyl groups or up to three halo
groups) or an optionally substituted acetylenic group
--C.ident.C--R.sub.a where R.sub.a is H or a C.sub.1-C.sub.6 alkyl
group (preferably C.sub.1-C.sub.3 alkyl); [0113] R.sup.SS is H, CN,
NO.sub.2, halo (preferably F or Cl), optionally substituted
C.sub.1-C.sub.6 alkyl (preferably substituted with one or two
hydroxyl groups or up to three halo groups), optionally substituted
O--(C.sub.1-C.sub.6 alkyl) (preferably substituted with one or two
hydroxyl groups or up to three halo groups) or an optionally
substituted --C(O)(C.sub.1-C.sub.6 alkyl) (preferably substituted
with one or two hydroxyl groups or up to three halo groups); [0114]
R.sup.URE is H, a C.sub.1-C.sub.6 alkyl (preferably H or
C.sub.1-C.sub.3 alkyl) or a --C(O)(C.sub.1-C.sub.6 alkyl), each of
which groups is optionally substituted with one or two hydroxyl
groups or up to three halogen, preferably fluorine groups, or an
optionally substituted heterocycle, for example piperidine,
morpholine, pyrrolidine, tetrahydrofuran, tetrahydrothiophene,
piperidine, piperazine, each of which is optionally substituted,
and [0115] Y.sup.C is N or C--R.sup.YC, where R.sup.YC is H, OH,
CN, NO.sub.2, halo (preferably Cl or F), optionally substituted
C.sub.1-C.sub.6 alkyl (preferably substituted with one or two
hydroxyl groups or up to three halo groups (e.g. CF.sub.3),
optionally substituted O(C.sub.1-C.sub.6 alkyl) (preferably
substituted with one or two hydroxyl groups or up to three halo
groups) or an optionally substituted acetylenic group
--C.ident.C--R.sub.a where R.sub.a is H or a C.sub.1-C.sub.6 alkyl
group (preferably C.sub.1-C.sub.3 alkyl), each of which groups may
be optionally substituted with a linker group to which is attached
a TBM group (including a ULM' group).
[0116] In certain embodiments, heterocycle groups for W.sup.4
include tetrahydrofuran, tetrahydrothiene, tetrahydroquinoline,
piperidine, piperazine, pyrrollidine, morpholine, oxane or thiane,
each of which groups may be optionally substituted, or a group
according to the chemical structure:
##STR00007##
preferably, a
##STR00008##
wherein: [0117] R.sup.PRO is H, optionally substituted
C.sub.1-C.sub.6 alkyl or an optionally substituted aryl, heteroaryl
or heterocyclic group; [0118] R.sup.PRO1 and R.sup.PRO2 are each
independently H, an optionally substituted C.sub.1-C.sub.3 alkyl
group or together form a keto group and [0119] each n is
independently 0, 1, 2, 3, 4, 5, or 6 (often 0 or 1), each of which
groups may be optionally substituted with a linker group to which
is attached a TBM group (including a ULM' group) In additional
embodiments, W.sup.4 substituents for use in the present invention
also include specifically (and without limitation to the specific
compound disclosed) the W.sup.4 substituents which are found in the
identified compounds disclosed herein (which includes the specific
compounds which are disclosed in the present specification, and the
figures which are attached hereto). Each of these W.sup.4
substituents may be used in conjunction with any number of W.sup.3
substituents which are also disclosed herein.
[0120] In certain additional embodiments, ULM-a, is optionally
substituted by 1-3 R.sup.P groups in the pyrrolidine moiety. Each
R.sup.P is independently H, halo, --OH, C.sub.1-3alkyl.
[0121] In any of the embodiments described herein, the W.sup.3,
W.sup.4 can independently be covalently coupled to a linker which
is attached one or more TBM groups.
[0122] In certain embodiments, ULM is a group (derivatized or
configured to be linked or coupled to an TBM via a linker (as
indicated by the dashed line) according to the chemical
structure:
##STR00009##
wherein: [0123] W.sup.3 is optionally substituted aryl, optionally
substituted heteroaryl, or
[0123] ##STR00010## [0124] each R.sub.9 and R.sub.10 is
independently hydrogen, optionally substituted alkyl, optionally
substituted cycloalkyl, optionally substituted hydroxyalkyl,
optionally substituted heteroaryl, or haloalkyl; or R.sub.9,
R.sub.10, and the carbon atom to which they are attached form an
optionally substituted cycloalkyl; [0125] R.sub.11 is optionally
substituted heterocyclic, optionally substituted alkoxy, optionally
substituted heteroaryl, optionally substituted aryl,
[0125] ##STR00011## [0126] R.sub.12 is H or optionally substituted
alkyl; [0127] R.sub.13 is H, optionally substituted alkyl,
optionally substituted alkylcarbonyl, optionally substituted
(cycloalkyl)alkylcarbonyl, optionally substituted aralkylcarbonyl,
optionally substituted arylcarbonyl, optionally substituted
(heterocyclyl)carbonyl, or optionally substituted aralkyl; [0128]
R.sub.14a, R.sub.14b, is each independently H, haloalkyl, or
optionally substituted alkyl; [0129] W.sup.5 is a phenyl or a 5-10
membered heteroaryl, [0130] R.sub.15 is H, halogen, CN, OH,
NO.sub.2, N R.sub.14aR.sub.14b, OR.sub.14a, CONR.sub.14aR.sub.14b,
NR.sub.14aCOR.sub.14b, SO.sub.2NR.sub.14aR.sub.14b,
NR.sub.14aSO.sub.2R.sub.14b, optionally substituted alkyl,
optionally substituted haloalkyl, optionally substituted
haloalkoxy; aryl, heteroaryl, cycloalkyl, cycloheteroalkyl; [0131]
each R.sub.16 is independently halo, optionally substituted alkyl,
optionally substituted haloalkyl, hydroxy, or optionally
substituted haloalkoxy; [0132] o is 0, 1, 2, 3, or 4; [0133] each
R.sub.18 is independently halo, optionally substituted alkoxy,
cyano, optionally substituted alkyl, haloalkyl, haloalkoxy or a
linker; and [0134] p is 0, 1, 2, 3, or 4.
[0135] In certain embodiments, R.sub.15 is
##STR00012##
wherein R.sub.17 is H, halo, optionally substituted
C.sub.3-6cycloalkyl, optionally substituted C.sub.1-6alkyl,
optionally substituted C.sub.1-6alkenyl, and C.sub.1-6haloalkyl;
and Xa is S or 0.
[0136] In certain embodiments, R.sub.17 is selected from the group
methyl, ethyl, isopropyl, and cyclopropyl.
[0137] In certain additional embodiments, R.sub.15 is selected from
the group consisting of:
##STR00013##
[0138] In certain embodiments, R.sub.11 is selected from the group
consisting of:
##STR00014## ##STR00015##
[0139] In certain embodiments, the ULM (derivatized or configured
to be linked or coupled to an TBM via a linker (as indicated by the
dashed line)) has the structure:
##STR00016##
wherein: [0140] R.sub.14a is independently H, haloalkyl, methyl, or
optionally substituted alkyl; [0141] R.sub.15 is
##STR00017##
[0141] wherein R.sub.17 is H, halo, optionally substituted
C.sub.3-6cycloalkyl, optionally substituted C.sub.1-6alkyl,
optionally substituted C.sub.1-6alkenyl, and C.sub.1-6haloalky
[0142] R.sub.17 is methyl, ethyl, isopropyl, or cyclopropyl; [0143]
R.sub.9 is H; [0144] R.sub.10 is isopropyl, tert-butyl, sec-butyl,
cyclopentyl, or cyclohexyl; [0145] R.sub.11 is
[0145] ##STR00018## [0146] R.sub.12 is H [0147] R.sub.13 is H,
optionally substituted alkyl, optionally substituted alkylcarbonyl,
optionally substituted (cycloalkyl)alkylcarbonyl, optionally
substituted aralkylcarbonyl, optionally substituted arylcarbonyl,
optionally substituted (heterocyclyl)carbonyl, or optionally
substituted aralkyl; and
[0148] In certain embodiments, the ULM or VLM is selected from the
group consisting of:
##STR00019## ##STR00020## ##STR00021##
attached to the linker moiety at the position indicated.
[0149] In one aspect the description provides compounds useful for
binding and/or inhibiting cereblon. In certain embodiments, the
compound is selected from the group consisting of chemical
structures:
##STR00022##
wherein: [0150] W is independently selected from the group
CH.sub.2, CHR, C.dbd.O, SO.sub.2, NH, and N-alkyl; [0151] X is
independently selected from the group, S and H.sub.2; [0152] Y is
independently selected from the group NH, N-alkyl, N-aryl,
N-hetaryl, N-cycloalkyl, N-heterocyclyl, O, and S; [0153] Z is
independently selected from the group, and S or H.sub.2 except that
both X and Z cannot be H.sub.2; [0154] G and G' are independently
selected from the group H, alkyl, OH, CH.sub.2-heterocyclyl
optionally substituted with R', and benzyl optionally substituted
with R'; Q1-Q4 represent a carbon C substituted with a group
independently selected from R', N or N-oxide; [0155] A is
independently selected from the group alkyl, cycloalkyl, Cl and F;
[0156] R comprises, but is not limited to: --CONR'R'', --OR',
--NR'R'', --SR', --SO.sub.2R', --SO.sub.2NR'R'', --CR'R''--,
--CR'NR'R''--, -aryl, -hetaryl, -alkyl, -cycloalkyl, -heterocyclyl,
--P(O)(OR')R'', --P(O)R'R'', --OP(O)(OR')R'', --OP(O)R'R'', --Cl,
--F, --Br, --I, --CF.sub.3, --CN, --NR'SO.sub.2NR'R'',
--NR'CONR'R'', --CONR'COR'', --NR'C(.dbd.N--CN)NR'R'',
--C(.dbd.N--CN)NR'R'', --NR'C(.dbd.N--CN)R'',
--NR'C(.dbd.C--NO.sub.2)NR'R'', --SO.sub.2NR'COR'', --NO.sub.2,
--CO.sub.2R', --C(C.dbd.N--OR')R'', --CR'.dbd.CR'R'', --CCR',
--S(C.dbd.O)(C.dbd.N--R')R'', --SF.sub.5 and --OCF.sub.3 [0157] R'
and R'' are independently selected from a bond, H, alkyl,
cycloalkyl, aryl, hetaryl, heterocyclyl [0158] n is an integer from
1-4; [0159] represents a bond that may be stereospecific ((R) or
(S)) or non-stereospecific; and [0160] R.sub.n comprises 1-4
independent functional groups or atoms.
[0161] In any of the compounds described herein, the CLM comprises
a chemical structure selected from the group:
##STR00023##
wherein: [0162] W is independently selected from the group
CH.sub.2, CHR, C.dbd.O, SO.sub.2, NH, and N-alkyl; [0163] X is
independently selected from the group O, S and H2; [0164] Y is
independently selected from the group NH, N-alkyl, N-aryl,
N-hetaryl, N-cycloalkyl, N-heterocyclyl, O, and S; [0165] Z is
independently selected from the group O, and S or H2 except that
both X and Z cannot be H2; [0166] G and G' are independently
selected from the group H, alkyl, OH, CH.sub.2-heterocyclyl
optionally substituted with R', and benzyl optionally substituted
with R'; [0167] Q1-Q4 represent a carbon C substituted with a group
independently selected from R', N or N-oxide; [0168] A is
independently selected from the group alkyl, cycloalkyl, Cl and F;
[0169] R comprises, but is not limited to: --CONR'R'', --OR',
--NR'R'', --SR', --SO.sub.2R', --SO.sub.2NR'R'', --CR'R''--,
--CR'NR'R''--, -aryl, -hetaryl, -alkyl, -cycloalkyl, -heterocyclyl,
--P(O)(OR')R'', --P(O)R'R'', --OP(O)(OR')R'', --OP(O)R'R'', --Cl,
--F, --Br, --I, --CF3, --CN, --NR'SO.sub.2NR'R'', --NR'CONR'R'',
--CONR'COR'', --NR'C(.dbd.N--CN)NR'R'', --C(.dbd.N--CN)NR'R'',
--NR'C(.dbd.N--CN)R'', --NR'C(.dbd.C--NO.sub.2)NR'R'',
--SO.sub.2NR'COR'', --NO.sub.2, --CO2R', --C(C.dbd.N--OR')R'',
--CR'.dbd.CR'R'', --CCR', --S(C.dbd.O)(C.dbd.N--R')R'', --SF5 and
--OCF3 [0170] R' and R'' are independently selected from a bond, H,
alkyl, cycloalkyl, aryl, hetaryl, heterocyclyl [0171] n is an
integer from 1-4; [0172] represents a bond that may be
stereospecific ((R) or (S)) or non-stereospecific; and [0173] Rn
comprises 1-4 independent functional groups or atoms, and
optionally, one of which is modified to be covalently joined to a
PTM, a chemical linker group (L), a ULM, CLM (or CLM') or
combination thereof.
Exemplary Linkers
[0174] In certain embodiments, the compounds as described herein
include one or more TBM chemically linked or coupled to one or more
ULMs or VLMs via a chemical linker (L). In certain embodiments, the
linker group L is a group comprises one or more covalently
connected structural units of A (e.g. -A.sub.1 . . . A.sub.q-),
wherein A.sub.1 is coupled to an TBM moiety, and q is an integer
greater than or equal to 0. In certain embodiments, q is an integer
greater than or equal to 1.
[0175] In certain embodiments, e. g., where q is greater than 2,
A.sub.q is a group which is connected to a ULM or VLM moiety, and
A.sub.1 and A.sub.q are connected via structural units of A (number
of such structural units of A: q-2).
[0176] In certain embodiments, e. g., where q is 2, A.sub.q is a
group which is connected to A.sub.1 and to a ULM or VLM moiety.
[0177] In certain embodiments, e. g., where q is 1, the structure
of the linker group L is -A.sub.1-, and A.sub.1 is a group which is
connected to a ULM or VLM moiety and an TBM moiety.
[0178] In additional embodiments, q is an integer from 1 to 100, 1
to 90, 1 to 80, 1 to 70, 1 to 60, 1 to 50, 1 to 40, 1 to 30, 1 to
20, or 1 to 10.
[0179] In certain embodiments, A.sub.1 to A.sub.q are, each
independently, a bond, CR.sup.L1R.sup.L2, O, S, SO, SO.sub.2,
NR.sup.L3, SO.sub.2NR.sup.L3, SONR.sup.L3, CONR.sup.L3,
NR.sup.L3CONR.sup.L4, NR.sup.L3SO.sub.2NR.sup.L4, CO,
CR.sup.L1.dbd.CR.sup.L2, C.ident.C, SiR.sup.L1R.sup.L2,
P(O)R.sup.L1, P(O)OR.sup.L1, NR.sup.L3C(.dbd.NCN)NR.sup.L4,
NR.sup.L3C(.dbd.NCN), NR.sup.L3C(.dbd.CNO.sub.2)NR.sup.L4,
C.sub.3-11cycloalkyl optionally substituted with 0-6 R.sup.L1
and/or R.sup.L2 groups, C.sub.3-11heteocyclyl optionally
substituted with 0-6 R.sup.L1 and/or R.sup.L2 groups, aryl
optionally substituted with 0-6 R.sup.L1 and/or R.sup.L2 groups,
heteroaryl optionally substituted with 0-6 R.sup.L1 and/or R.sup.L2
groups, wherein R.sup.L1 or R.sup.L.sub.2, each independently, can
be linked to other A groups to form cycloalkyl and/or heterocyclyl
moeity which can be further substituted with 0-4 R.sup.L1
groups;
[0180] wherein R.sup.L1, R.sup.L2, R.sup.L3, R.sup.L4 and R.sup.L5
are, each independently, H, halo, C.sub.1-8alkyl, OC.sub.1-8alkyl,
SC.sub.1-8alkyl, NHC.sub.1-8alkyl, N(C.sub.1-8alkyl).sub.2,
C.sub.3-11cycloalkyl, aryl, heteroaryl, C.sub.3-11heterocyclyl,
OC.sub.1-8cycloalkyl, SC.sub.1-8cycloalkyl, NHC.sub.1-8cycloalkyl,
N(C.sub.1-8cycloalkyl).sub.2,
N(C.sub.1-8cycloalkyl)(C.sub.1-8alkyl), OH, NH.sub.2, SH,
SO.sub.2C.sub.1-8alkyl, P(O)(OC.sub.1-8alkyl)(C.sub.1-8alkyl),
P(O)(OC.sub.1-8alkyl).sub.2, CC--C.sub.1-8alkyl, CCH,
CH.dbd.CH(C.sub.1-8alkyl),
C(C.sub.1-8alkyl).dbd.CH(C.sub.1-8alkyl),
C(C.sub.1-8alkyl).dbd.C(C.sub.1-8alkyl).sub.2, Si(OH).sub.3,
Si(C.sub.1-8alkyl).sub.3, Si(OH)(C.sub.1-8alkyl).sub.2,
COC.sub.1-8alkyl, CO.sub.2H, halogen, CN, CF.sub.3, CHF.sub.2,
CH.sub.2F, NO.sub.2, SF.sub.5, SO.sub.2NHC.sub.1-8alkyl,
SO.sub.2N(C.sub.1-8alkyl).sub.2, SON(C.sub.1-8alkyl,
SON(C.sub.1-8alkyl).sub.2, CONHC.sub.1-8alkyl,
CON(C.sub.1-8alkyl).sub.2, N(C.sub.1-8alkyl)CONH(C.sub.1-8alkyl),
N(C.sub.1-8alkyl)CON(C.sub.1-8alkyl).sub.2, NHCONH(C.sub.1-8alkyl),
NHCON(C.sub.1-8alkyl).sub.2, NHCONH.sub.2,
N(C.sub.1-8alkyl)SO.sub.2NH(C.sub.1-8alkyl), N(C.sub.1-8alkyl)
SO.sub.2N(C.sub.1-8alkyl).sub.2, NH SO.sub.2NH(C.sub.1-8alkyl), NH
SO.sub.2N(C.sub.1-8alkyl).sub.2, NH SO.sub.2NH.sub.2.
[0181] In certain embodiments, the linker (L) is selected from the
group consisting of):
##STR00024## ##STR00025##
[0182] In additional embodiments, the linker group is optionally
substituted (poly)ethyleneglycol having between 1 and about 100
ethylene glycol units, between about 1 and about 50 ethylene glycol
units, between 1 and about 25 ethylene glycol units, between about
1 and 10 ethylene glycol units, between 1 and about 8 ethylene
glycol units and 1 and 6 ethylene glycol units, between 2 and 4
ethylene glycol units, or optionally substituted alkyl groups
interdispersed with optionally substituted, O, N, S, P or Si atoms.
In certain embodiments, the linker is substituted with an aryl,
phenyl, benzyl, alkyl, alkylene, or heterocycle group. In certain
embodiments, the linker may be asymmetric or symmetrical.
[0183] In another embodiment, the present invention provides a
library of compounds. The library comprises more than one compound
wherein each compound has a formula of TBM-L-ULM, wherein ULM is a
ubiquitin pathway protein binding moiety (preferably, an E3
ubiquitin ligase moiety as otherwise disclosed herein), e.g., a
VLM, and TBM is an TBK1 protein binding moiety, wherein TBM is
coupled (preferably, through a linker moiety) to ULM, and wherein
the ubiquitin pathway protein binding moiety recognizes an
ubiquitin pathway protein, in particular, an E3 ubiquitin
ligase.
[0184] The present description includes, where applicable, the
compositions comprising the pharmaceutically acceptable salts, in
particular, acid or base addition salts of compounds of the present
invention.
[0185] The term "pharmaceutically acceptable salt" is used
throughout the specification to describe, where applicable, a salt
form of one or more of the compounds described herein which are
presented to increase the solubility of the compound in the gastic
juices of the patient's gastrointestinal tract in order to promote
dissolution and the bioavailability of the compounds.
Pharmaceutically acceptable salts include those derived from
pharmaceutically acceptable inorganic or organic bases and acids,
where applicable. Suitable salts include those derived from alkali
metals such as potassium and sodium, alkaline earth metals such as
calcium, magnesium and ammonium salts, among numerous other acids
and bases well known in the pharmaceutical art. Sodium and
potassium salts are particularly preferred as neutralization salts
of the phosphates according to the present invention.
[0186] The acids which are used to prepare the pharmaceutically
acceptable acid addition salts of the aforementioned base compounds
useful in this invention are those which form non-toxic acid
addition salts, i.e., salts containing pharmacologically acceptable
anions, such as the hydrochloride, hydrobromide, hydroiodide,
nitrate, sulfate, bisulfate, phosphate, acid phosphate, acetate,
lactate, citrate, acid citrate, tartrate, bitartrate, succinate,
maleate, fumarate, gluconate, saccharate, benzoate,
methanesulfonate, ethanesulfonate, benzenesulfonate,
p-toluenesulfonate and pamoate [i.e.,
1,1'-methylene-bis-(2-hydroxy-3 naphthoate)]salts, among numerous
others.
[0187] Pharmaceutically acceptable base addition salts may also be
used to produce pharmaceutically acceptable salt forms of the
compounds or derivatives according to the present invention. The
chemical bases that may be used as reagents to prepare
pharmaceutically acceptable base salts of the present compounds
that are acidic in nature are those that form non-toxic base salts
with such compounds. Such non-toxic base salts include, but are not
limited to those derived from such pharmacologically acceptable
cations such as alkali metal cations (eg., potassium and sodium)
and alkaline earth metal cations (eg, calcium, zinc and magnesium),
ammonium or water-soluble amine addition salts such as
N-methylglucamine-(meglumine), and the lower alkanolammonium and
other base salts of pharmaceutically acceptable organic amines,
among others.
Compositions
[0188] In another aspect, the description provides compositions
comprising compounds as described herein, including salts thereof,
and a pharmaceutically acceptable carrier. In certain embodiments,
the compositions are therapeutic or pharmaceutical compositions
comprising an effective amount of a compound as described herein
and a pharmaceutally acceptable carrier.
[0189] The amount of compound in a pharmaceutical composition of
the instant invention that may be combined with the carrier
materials to produce a single dosage form will vary depending upon
the host and disease treated, the particular mode of
administration. Generally, an amount between 0.1 mg/kg and 1000
mg/kg body weight/day of active ingredients is administered
dependent upon potency of the agent. Toxicity and therapeutic
efficacy of such compounds can be determined by standard
pharmaceutical procedures in cell cultures or experimental animals,
e.g., for determining the LD50 (the dose lethal to 50% of the
population) and the ED50 (the dose therapeutically effective in 50%
of the population). The dose ratio between toxic and therapeutic
effects is the therapeutic index and it can be expressed as the
ratio LD50/ED50. Compounds that exhibit large therapeutic indices
are preferred. While compounds that exhibit toxic side effects may
be used, care should be taken to design a delivery system that
targets such compounds to the site of affected tissue in order to
minimize potential damage to uninfected cells and, thereby, reduce
side effects. The data obtained from the cell culture assays and
animal studies can be used in formulating a range of dosage for use
in humans. The dosage of such compounds lies preferably within a
range of circulating concentrations that include the ED50 with
little or no toxicity. The dosage may vary within this range
depending upon the dosage form employed and the route of
administration utilized. For any compound used in the method of the
invention, the therapeutically effective dose can be estimated
initially from cell culture assays. A dose may be formulated in
animal models to achieve a circulating plasma concentration range
that includes the IC50 (i.e., the concentration of the test
compound which achieves a half-maximal inhibition of symptoms) as
determined in cell culture. Such information can be used to more
accurately determine useful doses in humans. Levels in plasma may
be measured, for example, by high performance liquid
chromatography.
[0190] The compositions of the present invention may be formulated
in a conventional manner using one or more pharmaceutically
acceptable carriers and may also be administered in
controlled-release formulations. Pharmaceutically acceptable
carriers that may be used in these pharmaceutical compositions
include, but are not limited to, ion exchangers, alumina, aluminum
stearate, lecithin, serum proteins, such as human serum albumin,
buffer substances such as phosphates, glycine, sorbic acid,
potassium sorbate, partial glyceride mixtures of saturated
vegetable fatty acids, water, salts or electrolytes, such as
prolamine sulfate, disodium hydrogen phosphate, potassium hydrogen
phosphate, sodium chloride, zinc salts, colloidal silica, magnesium
trisilicate, polyvinyl pyrrolidone, cellulose-based substances,
polyethylene glycol, sodium carboxymethylcellulose, polyacrylates,
waxes, polyethylene-polyoxypropylene-block polymers, polyethylene
glycol and wool fat.
[0191] The active compound is included in the pharmaceutically
acceptable carrier or diluent in an amount sufficient to deliver to
a patient a therapeutically effective amount for the desired
indication, without causing serious toxic effects in the patient
treated. A preferred dose of the active compound for all of the
herein-mentioned conditions is in the range from about 10 ng/kg to
300 mg/kg, preferably 0.1 to 100 mg/kg per day, more generally 0.5
to about 25 mg per kilogram body weight of the recipient/patient
per day. A typical topical dosage will range from 0.01-5% wt/wt in
a suitable carrier.
[0192] The compound is conveniently administered in any suitable
unit dosage form, including but not limited to one containing less
than 1 mg, 1 mg to 3000 mg, preferably 5 to 500 mg of active
ingredient per unit dosage form. An oral dosage of about 25-250 mg
is often convenient.
[0193] The active ingredient is preferably administered to achieve
peak plasma concentrations of the active compound of about
0.00001-30 mM, preferably about 0.1-30 .mu.M. This may be achieved,
for example, by the intravenous injection of a solution or
formulation of the active ingredient, optionally in saline, or an
aqueous medium or administered as a bolus of the active ingredient.
Oral administration is also appropriate to generate effective
plasma concentrations of active agent.
[0194] The concentration of active compound in the drug composition
will depend on absorption, distribution, inactivation, and
excretion rates of the drug as well as other factors known to those
of skill in the art. It is to be noted that dosage values will also
vary with the severity of the condition to be alleviated. It is to
be further understood that for any particular subject, specific
dosage regimens should be adjusted over time according to the
individual need and the professional judgment of the person
administering or supervising the administration of the
compositions, and that the concentration ranges set forth herein
are exemplary only and are not intended to limit the scope or
practice of the claimed composition. The active ingredient may be
administered at once, or may be divided into a number of smaller
doses to be administered at varying intervals of time.
[0195] If administered intravenously, preferred carriers are
physiological saline or phosphate buffered saline (PBS).
[0196] In one embodiment, the active compounds are prepared with
carriers that will protect the compound against rapid elimination
from the body, such as a controlled release formulation, including
implants and microencapsulated delivery systems. Biodegradable,
biocompatible polymers can be used, such as ethylene vinyl acetate,
polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and
polylactic acid. Methods for preparation of such formulations will
be apparent to those skilled in the art.
[0197] Liposomal suspensions may also be pharmaceutically
acceptable carriers. These may be prepared according to methods
known to those skilled in the art, for example, as described in
U.S. Pat. No. 4,522,811 (which is incorporated herein by reference
in its entirety). For example, liposome formulations may be
prepared by dissolving appropriate lipid(s) (such as stearoyl
phosphatidyl ethanolamine, stearoyl phosphatidyl choline,
arachadoyl phosphatidyl choline, and cholesterol) in an inorganic
solvent that is then evaporated, leaving behind a thin film of
dried lipid on the surface of the container. An aqueous solution of
the active compound are then introduced into the container. The
container is then swirled by hand to free lipid material from the
sides of the container and to disperse lipid aggregates, thereby
forming the liposomal suspension.
Modes of Administration
[0198] In any of the aspects or embodiments described herein, the
therapeutic compositions comprising compounds described herein can
be in any suitable dosage form configured to be delivered by any
suitable route. For example, the compounds can be administered by
any appropriate route, for example, orally, parenterally,
intravenously, intradermally, subcutaneously, or topically,
including transdermally, in liquid, cream, gel, or solid form,
rectally, nasally, buccally, vaginally or via an implanted
reservoir or by aerosol form.
[0199] The term "parenteral" as used herein includes subcutaneous,
intravenous, intramuscular, intra-articular, intra-synovial,
intrasternal, intrathecal, intrahepatic, intralesional and
intracranial injection or infusion techniques. Preferably, the
compositions are administered orally, intraperitoneally or
intravenously.
[0200] The compounds as described herein may be administered in
single or divided doses by the oral, parenteral or topical routes.
Administration of the active compound may range from continuous
(intravenous drip) to several oral administrations per day (for
example, Q.I.D.) and may include oral, topical, parenteral,
intramuscular, intravenous, sub-cutaneous, transdermal (which may
include a penetration enhancement agent), buccal, sublingual and
suppository administration, among other routes of administration.
Enteric coated oral tablets may also be used to enhance
bioavailability of the compounds from an oral route of
administration. The most effective dosage form will depend upon the
pharmacokinetics of the particular agent chosen as well as the
severity of disease in the patient.
[0201] Administration of compounds as sprays, mists, or aerosols
for intra-nasal, intra-tracheal or pulmonary administration may
also be used. Compounds as described herein may be administered in
immediate release, intermediate release or sustained or controlled
release forms. Sustained or controlled release forms are preferably
administered orally, but also in suppository and transdermal or
other topical forms. Intramuscular injections in liposomal form may
also be used to control or sustain the release of compound at an
injection site.
[0202] Sterile injectable forms of the compositions as described
herein may be aqueous or oleaginous suspension. These suspensions
may be formulated according to techniques known in the art using
suitable dispersing or wetting agents and suspending agents. The
sterile injectable preparation may also be a sterile injectable
solution or suspension in a non-toxic 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 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
may be employed including synthetic mono- or di-glycerides. Fatty
acids, such as oleic acid and its glyceride derivatives are useful
in the preparation of injectables, as are natural
pharmaceutically-acceptable oils, such as olive oil or castor oil,
especially in their polyoxyethylated versions. These oil solutions
or suspensions may also contain a long-chain alcohol diluent or
dispersant, such as Ph. Helv or similar alcohol.
[0203] The pharmaceutical compositions as described herein may be
orally administered in any orally acceptable dosage form including,
but not limited to, capsules, tablets, aqueous suspensions or
solutions. In the case of tablets for oral use, carriers which are
commonly used include lactose and corn starch. Lubricating agents,
such as magnesium stearate, are also typically added. For oral
administration in a capsule form, useful diluents include lactose
and dried corn starch. When aqueous suspensions are required for
oral use, the active ingredient is combined with emulsifying and
suspending agents. If desired, certain sweetening, flavoring or
coloring agents may also be added. Oral compositions will generally
include an inert diluent or an edible carrier. They may be enclosed
in gelatin capsules or compressed into tablets. For the purpose of
oral therapeutic administration, the active compound or its prodrug
derivative can be incorporated with excipients and used in the form
of tablets, troches, or capsules. Pharmaceutically compatible
binding agents, and/or adjuvant materials are included as part of
the composition.
[0204] The tablets, pills, capsules, troches and the like can
contain any of the following ingredients, or compounds of a similar
nature: a binder such as microcrystalline cellulose, gum tragacanth
or gelatin; an excipient such as starch or lactose, a dispersing
agent such as alginic acid, Primogel, or corn starch; a lubricant
such as magnesium stearate or Sterotes; a glidant such as colloidal
silicon dioxide; a sweetening agent such as sucrose or saccharin;
or a flavoring agent such as peppermint, methyl salicylate, or
orange flavoring. When the dosage unit form is a capsule, it can
contain, in addition to material of the above type, a liquid
carrier such as a fatty oil. In addition, dosage unit forms can
contain various other materials which modify the physical form of
the dosage unit, for example, coatings of sugar, shellac, or
enteric agents.
[0205] The active compound or pharmaceutically acceptable salt
thereof can be administered as a component of an elixir,
suspension, syrup, wafer, chewing gum or the like. A syrup may
contain, in addition to the active compounds, sucrose as a
sweetening agent and certain preservatives, dyes and colorings and
flavors.
[0206] Alternatively, the pharmaceutical compositions as described
herein may be administered in the form of suppositories for rectal
administration. These can be prepared by mixing the agent with a
suitable non-irritating excipient, which is solid at room
temperature but liquid at rectal temperature and therefore will
melt in the rectum to release the drug. Such materials include
cocoa butter, beeswax and polyethylene glycols.
[0207] The pharmaceutical compositions of this invention may also
be administered topically. Suitable topical formulations are
readily prepared for each of these areas or organs. Topical
application for the lower intestinal tract can be effected in a
rectal suppository formulation (see above) or in a suitable enema
formulation. Topically-acceptable transdermal patches may also be
used. For topical applications, the pharmaceutical compositions may
be formulated in a suitable ointment containing the active
component suspended or dissolved in one or more carriers. Carriers
for topical administration of the compounds of this invention
include, but are not limited to, mineral oil, liquid petrolatum,
white petrolatum, propylene glycol, polyoxyethylene,
polyoxypropylene compound, emulsifying wax and water. In certain
preferred aspects of the invention, the compounds may be coated
onto a stent which is to be surgically implanted into a patient in
order to inhibit or reduce the likelihood of occlusion occurring in
the stent in the patient.
[0208] Alternatively, the pharmaceutical compositions can be
formulated in a suitable lotion or cream containing the active
components suspended or dissolved in one or more pharmaceutically
acceptable carriers. Suitable carriers include, but are not limited
to, mineral oil, sorbitan monostearate, polysorbate 60, cetyl
esters wax, cetearyl alcohol, 2-octyldodecanol, benzyl alcohol and
water.
[0209] For ophthalmic use, the pharmaceutical compositions may be
formulated as micronized suspensions in isotonic, pH adjusted
sterile saline, or, preferably, as solutions in isotonic, pH
adjusted sterile saline, either with our without a preservative
such as benzylalkonium chloride. Alternatively, for ophthalmic
uses, the pharmaceutical compositions may be formulated in an
ointment such as petrolatum.
[0210] The pharmaceutical compositions of this invention may also
be administered by nasal aerosol or inhalation. Such compositions
are prepared according to techniques well-known in the art of
pharmaceutical formulation and may be prepared as solutions in
saline, employing benzyl alcohol or other suitable preservatives,
absorption promoters to enhance bioavailability, fluorocarbons,
and/or other conventional solubilizing or dispersing agents.
[0211] Solutions or suspensions used for parenteral, intradermal,
subcutaneous, or topical application can include the following
components: a sterile diluent such as water for injection, saline
solution, fixed oils, polyethylene glycols, glycerine, propylene
glycol or other synthetic solvents; antibacterial agents such as
benzyl alcohol or methyl parabens; antioxidants such as ascorbic
acid or sodium bisulfite; chelating agents such as
ethylenediaminetetraacetic acid; buffers such as acetates, citrates
or phosphates and agents for the adjustment of tonicity such as
sodium chloride or dextrose. The parental preparation can be
enclosed in ampoules, disposable syringes or multiple dose vials
made of glass or plastic.
[0212] It should also be understood that a specific dosage and
treatment regimen for any particular patient will depend upon a
variety of factors, including the activity of the specific compound
employed, the age, body weight, general health, sex, diet, time of
administration, rate of excretion, drug combination, and the
judgment of the treating physician and the severity of the
particular disease or condition being treated.
[0213] A patient or subject in need of therapy using compounds as
described herein can be treated by administering to the patient
(subject) an effective amount of the compound including
pharmaceutically acceptable salts, solvates or polymorphs, thereof
optionally in a pharmaceutically acceptable carrier or diluent,
either alone, or in combination with other known agents.
Co-Administration
[0214] Disease states of conditions which may be treated using
compounds or compositions according to the present description
include, but not limited to, for example, cancer (e.g., prostate
cancer), and Kennedy's disease. In certain embodiments, the
therapeutic or pharmaceutical compositions comprise an effective
amount of an additional biologically or bioactive active agent,
e.g., an agent effective for the treatment of cancer, that is
co-administered.
[0215] The term "coadministration" or "combination therapy" shall
mean that at least two compounds or compositions are administered
to the patient at the same time, such that effective amounts or
concentrations of each of the two or more compounds may be found in
the patient at a given point in time. Although compounds according
to the present invention may be co-administered to a patient at the
same time, the term embraces both administration of two or more
agents at the same time or at different times, provided that
effective concentrations of all coadministered compounds or
compositions are found in the subject at a given time. In certain
preferred aspects of the present invention, one or more of the
present compounds described above, are coadministered in
combination with at least one additional bioactive agent,
especially including an anticancer agent. In particularly preferred
aspects of the invention, the co-administration of compounds
results in synergistic therapeutic, including anticancer
therapy.
[0216] In another aspect, the description provides a composition
comprising an effective amount of two or more of the PROTAC
compounds as described herein, and a pharmaceutically acceptable
carrier. In certain embodiments, the composition further comprises
an effective or synergistic amount of another bioactive agent that
is not a PROTAC compound.
[0217] Pharmaceutical compositions comprising combinations of an
effective amount of at least one bifunctional compound according to
the present invention, and one or more of the compounds otherwise
described herein, all in effective amounts, in combination with a
pharmaceutically effective amount of a carrier, additive or
excipient, represents a further aspect of the present
invention.
[0218] The term "bioactive agent" is used to describe an agent,
other than the PROTAC compounds described herein, which is used in
combination with the present compounds as an agent with biological
activity to assist in effecting an intended therapy, inhibition
and/or prevention/prophylaxis for which the present compounds are
used. Preferred bioactive agents for use herein include those
agents which have pharmacological activity similar to that for
which the present compounds are used or administered and include
for example, anti-cancer agents.
[0219] The term "additional anti-cancer agent" is used to describe
an anti-cancer agent, which may be combined with PROTAC compounds
according to the present description to treat cancer. These agents
include, for example, everolimus, trabectedin, abraxane, TLK 286,
AV-299, DN-101, pazopanib, GSK690693, RTA 744, ON 0910.Na, AZD 6244
(ARRY-142886), AMN-107, TKI-258, GSK461364, AZD 1152, enzastaurin,
vandetanib, ARQ-197, MK-0457, MLN8054, PHA-739358, R-763, AT-9263,
a FLT-3 inhibitor, an androgen receptor inhibitor, a VEGFR
inhibitor, an EGFR TK inhibitor, an aurora kinase inhibitor, a
PIK-1 modulator, a Bcl-2 inhibitor, an HDAC inhbitor, a c-MET
inhibitor, a PARP inhibitor, a Cdk inhibitor, an EGFR TK inhibitor,
an IGFR-TK inhibitor, an anti-HGF antibody, a PI3 kinase
inhibitors, an AKT inhibitor, a JAK/STAT inhibitor, a checkpoint-1
or 2 inhibitor, a focal adhesion kinase inhibitor, a Map kinase
kinase (mek) inhibitor, a VEGF trap antibody, pemetrexed,
erlotinib, dasatanib, nilotinib, decatanib, panitumumab, amrubicin,
oregovomab, Lep-etu, nolatrexed, azd2171, batabulin, ofatumumab,
zanolimumab, edotecarin, tetrandrine, rubitecan, tesmilifene,
oblimersen, ticilimumab, ipilimumab, gossypol, Bio 111,
131-I-TM-601, ALT-110, BIO 140, CC 8490, cilengitide, gimatecan,
IL13-PE38QQR, INO 1001, IPdR.sub.1 KRX-0402, lucanthone, LY317615,
neuradiab, vitespan, Rta 744, Sdx 102, talampanel, atrasentan, Xr
311, romidepsin, ADS-100380, sunitinib, 5-fluorouracil, vorinostat,
etoposide, gemcitabine, doxorubicin, liposomal doxorubicin,
5'-deoxy-5-fluorouridine, vincristine, temozolomide, ZK-304709,
seliciclib; PD0325901, AZD-6244, capecitabine, L-Glutamic acid,
N-[4-[2-(2-amino-4,7-dihydro-4-oxo-1
H--pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl]-, disodium salt,
heptahydrate, camptothecin, PEG-labeled irinotecan, tamoxifen,
toremifene citrate, anastrazole, exemestane, letrozole,
DES(diethylstilbestrol), estradiol, estrogen, conjugated estrogen,
bevacizumab, IMC-1C11, CHIR-258);
3-[5-(methylsulfonylpiperadinemethyl)-indolylj-quinolone,
vatalanib, AG-013736, AVE-0005, the acetate salt of [D-Ser(But) 6,
Azgly 10] (pyro-Glu-His-Trp-Ser-Tyr-D-Ser(But)-Leu-Arg-Pro-Azgly-NH
2 acetate
[C.sub.9H.sub.84N.sub.18Oi.sub.4-(C.sub.2H.sub.4O.sub.2).sub.x
where x=1 to 2.4], goserelin acetate, leuprolide acetate,
triptorelin pamoate, medroxyprogesterone acetate,
hydroxyprogesterone caproate, megestrol acetate, raloxifene,
bicalutamide, flutamide, nilutamide, megestrol acetate, CP-724714;
TAK-165, HKI-272, erlotinib, lapatanib, canertinib, ABX-EGF
antibody, erbitux, EKB-569, PKI-166, GW-572016, Ionafarnib,
BMS-214662, tipifarnib; amifostine, NVP-LAQ824, suberoyl analide
hydroxamic acid, valproic acid, trichostatin A, FK-228, SU11248,
sorafenib, KRN951, aminoglutethimide, arnsacrine, anagrelide,
L-asparaginase, Bacillus Calmette-Guerin (BCG) vaccine, adriamycin,
bleomycin, buserelin, busulfan, carboplatin, carmustine,
chlorambucil, cisplatin, cladribine, clodronate, cyproterone,
cytarabine, dacarbazine, dactinomycin, daunorubicin,
diethylstilbestrol, epirubicin, fludarabine, fludrocortisone,
fluoxymesterone, flutamide, gleevec, gemcitabine, hydroxyurea,
idarubicin, ifosfamide, imatinib, leuprolide, levamisole,
lomustine, mechlorethamine, melphalan, 6-mercaptopurine, mesna,
methotrexate, mitomycin, mitotane, mitoxantrone, nilutamide,
octreotide, oxaliplatin, pamidronate, pentostatin, plicamycin,
porfimer, procarbazine, raltitrexed, rituximab, streptozocin,
teniposide, testosterone, thalidomide, thioguanine, thiotepa,
tretinoin, vindesine, 13-cis-retinoic acid, phenylalanine mustard,
uracil mustard, estramustine, altretamine, floxuridine,
5-deooxyuridine, cytosine arabinoside, 6-mecaptopurine,
deoxycoformycin, calcitriol, valrubicin, mithramycin, vinblastine,
vinorelbine, topotecan, razoxin, marimastat, COL-3, neovastat,
BMS-275291 squalamine, endostatin, SU5416, SU6668, EMD121974,
interleukin-12, IM862, angiostatin, vitaxin, droloxifene,
idoxyfene, spironolactone, finasteride, cimitidine, trastuzumab,
denileukin diftitox,gefitinib, bortezimib, paclitaxel,
cremophor-free paclitaxel, docetaxel, epithilone B, BMS-247550,
BMS-310705, droloxifene, 4-hydroxytamoxifen, pipendoxifene,
ERA-923, arzoxifene, fulvestrant, acolbifene, lasofoxifene,
idoxifene, TSE-424, HMR-3339, ZK186619, topotecan, PTK787/ZK
222584, VX-745, PD 184352, rapamycin,
40-O-(2-hydroxyethyl)-rapamycin, temsirolimus, AP-23573, RAD001,
ABT-578, BC-210, LY294002, LY292223, LY292696, LY293684, LY293646,
wortmannin, ZM336372, L-779,450, PEG-filgrastim, darbepoetin,
erythropoietin, granulocyte colony-stimulating factor,
zolendronate, prednisone, cetuximab, granulocyte macrophage
colony-stimulating factor, histrelin, pegylated interferon alfa-2a,
interferon alfa-2a, pegylated interferon alfa-2b, interferon
alfa-2b, azacitidine, PEG-L-asparaginase, lenalidomide, gemtuzumab,
hydrocortisone, interleukin-11, dexrazoxane, alemtuzumab,
all-transretinoic acid, ketoconazole, interleukin-2, megestrol,
immune globulin, nitrogen mustard, methylprednisolone, ibritgumomab
tiuxetan, androgens, decitabine, hexamethylmelamine, bexarotene,
tositumomab, arsenic trioxide, cortisone, editronate, mitotane,
cyclosporine, liposomal daunorubicin, Edwina-asparaginase,
strontium 89, casopitant, netupitant, an NK-1 receptor antagonist,
palonosetron, aprepitant, diphenhydramine, hydroxyzine,
metoclopramide, lorazepam, alprazolam, haloperidol, droperidol,
dronabinol, dexamethasone, methylprednisolone, prochlorperazine,
granisetron, ondansetron, dolasetron, tropisetron, pegfilgrastim,
erythropoietin, epoetin alfa, darbepoetin alfa and mixtures
thereof.
Methods of Treatment
[0220] In another aspect, the disclosure provides methods of
modulating protein ubiquitination and degradation in a subject,
e.g., a cell, a tissue, mammal, or human patient, the method
comprising administering an effective amount of a compound as
described herein or a composition comprising an effective amount of
the same to a subject, wherein the compound or composition
comprising the same is effective in modulating protein
ubquitination and degration of the protein in the subject. In
certain embodiments, the protein is TBK1.
[0221] In certain embodiments, the description provides a method
for regulating protein activity of TBK1 in a patient in need
comprising administering to said patient an amount of a compound as
described herein to a patient.
[0222] In still additional embodiments, the description provides a
method of treating a disease state or condition in a patient
wherein dysregulated protein activity is responsible for said
disease state or condition, said method comprising administering to
said patient an effective amount of a compound as described herein
to said patient in order to regulate said protein activity in said
patient. In certain embodiments, the protein is TBK1.
[0223] The terms "treat", "treating", and "treatment", etc., as
used herein, refer to any action providing a benefit to a patient
for which the present compounds may be administered, including the
treatment of any disease state or condition which is modulated
through the protein to which the present compounds bind. Disease
states or conditions, including cancer, which may be treated using
compounds according to the present invention are set forth
hereinabove.
[0224] In another aspect, the disclosure provides methods of
modulating AR protein ubiquitination and degradation in a subject,
e.g., a cell, a tissue, mammal, or human patient, the method
comprising administering an effective amount of a compound as
described herein or a composition comprising an effective amount of
the same to a subject, wherein the compound or composition
comprising the same is effective in modulating AR protein
ubquitination and degration of the protein in the subject.
[0225] In another aspect, the disclosure provides methods of
treating or ameliorating a symptom of a disease related to TBK1
activity in a subject, e.g., a cell, a tissue, mammal, or human
patient, the method comprising administering an effective amount of
a compound as described herein or a composition comprising an
effective amount of the same to a subject in need thereof, wherein
the compound or composition comprising the same is effective in
treating or ameliorating a symptom of a disease related to TBK1
activity in the subject.
[0226] In certain embodiments, the disease or disorder is asthma,
multiple sclerosis, cancer, prostate cancer, Kenney's disease,
ciliopathies, cleft palate, diabetes, heart disease, hypertension,
inflammatory bowel disease, mental retardation, mood disorder,
obesity, refractive error, infertility, Angelman syndrome, Canavan
disease, Coeliac disease, Charcot-Marie-Tooth disease, Cystic
fibrosis, Duchenne muscular dystrophy, Haemochromatosis,
Haemophilia, Klinefelter's syndrome, Neurofibromatosis,
Phenylketonuria, Polycystic kidney disease, (PKD1) or 4 (PKD2)
Prader-Willi syndrome, Sickle-cell disease, Tay-Sachs disease,
Turner syndrome. In an embodiment, said cancer is squamous-cell
carcinoma, basal cell carcinoma, adenocarcinoma, hepatocellular
carcinomas, and renal cell carcinomas, cancer of the bladder,
bowel, breast, cervix, colon, esophagus, head, kidney, liver, lung,
neck, ovary, pancreas, prostate, and stomach; leukemias; benign and
malignant lymphomas, particularly Burkitt's lymphoma and
Non-Hodgkin's lymphoma; benign and malignant melanomas;
myeloproliferative diseases; sarcomas, including Ewing's sarcoma,
hemangiosarcoma, Kaposi's sarcoma, liposarcoma, myosarcomas,
peripheral neuroepithelioma, synovial sarcoma, gliomas,
astrocytomas, oligodendrogliomas, ependymomas, gliobastomas,
neuroblastomas, ganglioneuromas, gangliogliomas, medulloblastomas,
pineal cell tumors, meningiomas, meningeal sarcomas, neurofibromas,
and Schwannomas; bowel cancer, breast cancer, prostate cancer,
cervical cancer, uterine cancer, lung cancer, ovarian cancer,
testicular cancer, thyroid cancer, astrocytoma, esophageal cancer,
pancreatic cancer, stomach cancer, liver cancer, colon cancer,
melanoma; carcinosarcoma, Hodgkin's disease, Wilms' tumor or
teratocarcinomas. In certain embodiments, the disease to be treated
is cancer, e.g., prostate cancer, or Kennedy's Disease. In a
preferred embodiment, the subject is a human.
[0227] In another aspect, the disclosure provides methods of
treating or ameliorating a symptom of a disease related to TBK1
activity in a subject, e.g., a cell, a tissue, mammal, or human
patient, the method comprising administering an effective amount of
a compound as described herein or a composition comprising an
effective amount of the same and an effective or synergistic amount
of another bioactive agent to a subject in need thereof, wherein
the composition comprising the same is effective in treating or
ameliorating a symptom of a disease related to TBK1 activity in the
subject. In certain embodiments, the disease to be treated is
cancer, e.g., prostate cancer, or Kennedy's Disease. In a preferred
embodiment, the subject is a human. In certain additional
embodiments, the additional bioactive agent is an anti-cancer
agent.
[0228] In alternative aspects, the present invention relates to a
method for treating a disease state by degrading a protein or
polypeptide through which a disease state or condition is modulated
comprising administering to said patient or subject an effective
amount of at least one compound as described hereinabove,
optionally in combination with an additional bioactive agent. The
method according to the present invention may be used to treat a
large number of disease states or conditions including cancer, by
virtue of the administration of effective amounts of at least one
compound described herein.
[0229] In another aspect, the disclosure provides methods for
identifying the effects of the degradation of proteins of interest
in a biological system using compounds according to the present
invention.
Kits
[0230] In another aspect, the description provides kits comprising
compounds or compositions as described herein. The kit may be
promoted, distributed, or sold as a unit for performing the methods
of the present invention. In addition, the kits of the present
invention may preferably contain instructions which describe a
suitable use. Such kits can be conveniently used, e.g., in clinical
settings, to treat patients exhibiting symptoms of, e.g., cancer or
Kennedy's Disease.
Exemplary TBK1 Binding Moieties (TBMs)
[0231] TANK-binding kinase 1 (TBK1) is a serine/threonine kinase
and a noncanonical member of the IKK family implicated in antiviral
immune response as well as tumor genesis and development and is
therefore a target that has attracted considerable attention with
regards to the identification of agents that could diminish its
activity. Of particular note are the various reports regarding the
criticality of TBK1 signaling in KRAS mutant tumors, determined
using RNAi.
[0232] We embarked on a campaign to assess whether TBK1 was
degradable by our technology and if so, whether they replicated the
KRAS synthetic lethality reported with TBK1 RNAi.
[0233] For the design of the TBK1 PROTACs we selected the classic
kinase aminopyridine chemotype 1 as the ligand for TBK1 (K.sub.d
1.3 nM), and our 4-hydroxyproline derivative 2 as the recruitment
ligand for the Von Hippel-Lindau (VHL) E3 ligase (IC.sub.50 500 nM
FP assay) (FIG. 2).
[0234] The PROTAC molecule architecture requires that these ligands
be separated by a connector component (FIG. 2). FIGS. 3 and 4 show
snapshots of the crystal structures of the general VHL and TBK1
ligand chemotypes (PDB codes: 4W9L and 41M0) and suggest points on
these ligands where such a connector could be attached that would
allow ready egress from the protein in question without obvious
detrimental effects on ligand binding. For the TBK1 ligand we
selected the para-position of the pyrimidine 2-aminophenyl moiety;
for the VHL ligand we selected the acetamide moiety as the
tethering position.
[0235] Not knowing a priori what distance the TBK1 and VHL ligands
would have to be positioned in the PROTAC to effectively associate
their respective proteins, we undertook a systematic survey of
connector length using flexible and therefore accommodating alkyl
ether chemistries (Table 1).
TABLE-US-00001 TABLE 1 Effect of connector length on degradation
activity # Con- nector DC.sub.50 D.sub.max PSA Cmpd Connector atoms
(nM) (%) (.ANG..sup.2) 1 NA -- >1000 ND 79 2 NA -- NA NA 112 3
##STR00026## 7 >1000 ND 200 4 ##STR00027## 8 >1000 ND 209 5
##STR00028## 9 >1000 ND 200 6 ##STR00029## 10 >1000 ND 209 7
##STR00030## 11 >1000 ND 219 8 ##STR00031## 12 88 79 209 9
##STR00032## 13 71 86 219 10 ##STR00033## 14 103 92 228 11
##STR00034## 15 32 96 219 12 ##STR00035## 16 95 90 209 13
##STR00036## 17 29 96 237 14 ##STR00037## 18 6 96 228 15
##STR00038## 19 25 96 228 16 ##STR00039## 20 34 96 246 17
##STR00040## 21 3 96 237 NA: not applicable. ND: not determined.
DC.sub.50: concentration at which 50% degradation is observed.
D.sub.max: maximal degradation observed. Data represent the mean of
.gtoreq.2 determinations. ##STR00041##
[0236] From this initial library, potent, sub-micromolar TBK1-VHL
PROTAC degraders were identified (PROTACs 8-17). The gross SAR
clearly indicates a dependence on a minimum connector length with
connectors of <12 atoms (ca. 13A in fully extended form)
demonstrating no appreciable degradation activity. Longer
connectors appear generally well tolerated despite their higher PSA
and possible cell penetrance burden, and the SAR, to the extent it
was explored, indicates no obvious maximum tolerated length. These
observations are consistent with the concept that the bifunctional
PROTAC species mediates the association of the TBK1 and VHL
proteins to form a ternary complex, but that a minimum PROTAC
length is required to allow the proteins to come together without
incurring steric conflicts. It was hypothesized that the very
flexible nature of the connector chemistry allows the longer
connectors to orient themselves as necessary to allow the two
proteins to associate and for ubiquitin to transfer to TBK1. The
extent to which the flexibility of each individual connector allows
it to organize spatially in order to properly orient the VHL-TBK1
interaction likely governs the efficiency of such transfer and
therefore contributes to the subtle degradation SAR seen across
PROTACs 8-17, along with differences in cell permeation.
[0237] To confirm the mechanistic dependence on VHL for TBK1
degradation, we prepared PROTAC 18, an epimer of active PROTAC 11,
which by nature of the reversed (S) stereochemistry at the proline
4-position, has no appreciable binding to VHL (FP IC.sub.50>5
uM) but is identical in all other respects (FIG. 5).
[0238] PROTAC 18 showed no significant degradation of TBK1 (FIG.
6), confirming VHL's role in the degradation of TBK1 by PROTAC 11.
It was confirmed that PROTAC 18 was not significantly compromised
in terms of its TBK1 binding (Kd 5.9 nM), and also assessed the
effect on 11 and 18 on the TBK1 downstream marker pIRF3. Both
agents as well as the parent TBK1 ligand 1 displayed competent
intracellular TBK1 binding as indicated by the inhibition of
pIRF3.
[0239] The involvement of the proteasome in the VHL-mediated
degradation of TBK1 by PROTAC 11 was assessed by addition of the
proteasome inhibitor carfilzomib (Kyprolis.RTM.) to the assay
conditions. Pre-treatment with carfilzomib markedly reduced the
extent of TBK1 degradation by PROTAC 11 indicating that the 26S
proteasome was indeed implicated in the degradation of TBK1 (FIG.
7). Also, the addition of excess VHL ligand 2 to the assay to
compete with PROTAC 11 for VHL, also abrogated TBK1's
degradation.
[0240] With mechanistically specific tool degrader 11 in hand, the
impact of TBK1 binding on degradation potency and efficacy was
evaluated. In order to minimize the impact of any cell permeation
or conformational differences on observed degrader potency, only
the 5-position of the pyrimidine TBK1 ligand component was modified
and only using functionalities that did not substantially alter the
219 .ANG..sup.2 polar surface area of the set (Table 2).
TABLE-US-00002 TABLE 2 Effect of TBK1 affinity on degradation
activity ##STR00042## Cmpd R.sub.1 TBK1 K.sub.d (nM) DC.sub.50 (nM)
D.sub.max (%) 19 H 725 .+-. 85 >1000 ND 20 Cl 10.4 .+-. 0.6 10
96 21 CF.sub.3 13 29 96 22 cBu 1035 .+-. 165 544 70 23 I 4 .+-. 0.4
3 96 24 F 103.5 .+-. 6.5 282 74 25 Me 270 .+-. 40 92 89 26 Et 275
.+-. 35 121 77 27 Vinyl 130 .+-. 10 48 96 28 cPr 245 .+-. 25 65 96
11 Br 4.6 .+-. 1.1 12 96 ND: not determined. DC.sub.50:
concentration at which 50% degradation is observed. D.sub.max:
maximal degradation observed. Data represent the mean of .gtoreq.2
determinations.
[0241] Maximal efficacy (>90% degradation) was achieved with
PROTACs that had TBK1 affinities of .ltoreq.245 nM, beyond which
degradation begins to drop off although remain significant (70%)
even in the case of Compound 22 that has a Kd of 1 .mu.M. That
cellular degradation potency shown so high (65 nM) given that the
affinities for the component ligands of PROTAC 28 to its TBK1 and
VHL proteins be so modest (245 and 800 nM, respectively), is likely
due to the ability of the PROTAC to initiate multiple cycles of
degradation and drive a process and not an equilibrium mechanism
such as traditional inhibition.
[0242] Next, the effect of changing the linker and VHL affinity was
evaluated on degradation (Table 3 and Table 4). PROTACs 11 and
29-33 differ in the side chain chemistry of the glycine component
of the VHL ligand which, as for the TBK1 ligand, do not grossly
change the molecular properties of the PROTACs (PSA 219
.ANG..sup.2) yet do alter their VHL affinity. Maximal efficacy was
only seen with the parent PROTAC 11 (R=tBu) although, robust
degradation (>70%) was seen with PROTAC 31 (R=Et).
TABLE-US-00003 TABLE 3 Effect of VHL affinity on degradation
activity ##STR00043## Cmpd R.sub.2 VHL Ligand IC.sub.50 (.mu.M)
DC.sub.50 (nM) D.sub.max (%) 29 H 106 >1000 0 30 Me 23.6
>1000 34 31 Et 70.4 864 71 32 .sup.nPr 6.2 288 75 33 .sup.iPr
1.45 44 88 11 .sup.tBu 0.8 12 96
TABLE-US-00004 TABLE 4 Effect of linker and VHL structure on TBK1
degradation % TBK1 Com- remaining pound at 1 uM # Structure Cmpd**
34 ##STR00044## B 35 ##STR00045## C 36 ##STR00046## C 37
##STR00047## C 38 ##STR00048## C 39 ##STR00049## C 40 ##STR00050##
C 41 ##STR00051## C 42 ##STR00052## B 43 ##STR00053## B 44
##STR00054## B 45 ##STR00055## B 46 ##STR00056## B 47 ##STR00057##
B 48 ##STR00058## A 49 ##STR00059## C 50 ##STR00060## C 51
##STR00061## C 52 ##STR00062## C 53 ##STR00063## C 54 ##STR00064##
B **A: 0-40% B: 41-80% C: .gtoreq.81%
[0243] The effect of potent TBK1 degrader, PROTAC 11 was also
evaluated on cell lines harbouring either wild-type or mutant KRAS.
72 Hour treatment of KRAS mutant cell lines H23, A549 and H1792,
and KRAS wild type cell line H2110 with PROTAC 11, while effecting
near complete degradation of TBK1, caused no differential effect on
the proliferation of these cells, thus supporting the literature
reports that TBK1 was not synthetically lethal in KRAS mutant
versus wild type cells (FIGS. 8A & 8B)..sup.refs
[0244] Assessment of the affinity of PROTAC 11 to the closely
related kinase IKK.epsilon. confirmed robust binding with a K.sub.d
70 nM. In the case of TBK1 this is clearly a sufficient level of
affinity for degradation (Table 2, e.g. Compound 27), however
interestingly was insufficient for IKK.epsilon. as negligible
degradation was observed (FIG. 9).
[0245] It was hypothesized that this introduction of degradation
selectivity into a relatively unselective ligand may result from a
differential presentation of TBK1 and its surface lysines to VHL
and its reactive E2-ubiquitin thioester component, as compared to
IKK.epsilon., and therefore a different efficiency of the transfer
of ubiquitin to TBK1 (FIG. 1). Other potential explanations include
an increased rate of deubiquitinylation in the case of
IKK.epsilon., or that IKK.epsilon. ubiquitinylation leads to
compartmentalization versus degradation in the case of
IKK.epsilon..
[0246] In conclusion, a process for the rapid generation of potent,
VHL and proteasome-dependent PROTAC degraders of TBK1, through a
systematic survey of connector length and ligand affinities has
been described. It has been also demonstrated that PROTACs can
provide greater degradation potency and selectivity than that
anticipated based on the potency and selectivity of the component
ligands. In concert with the prevailing literature opinion, it has
been also demonstrated that deletion of TBK1 via PROTAC-mediated
degradation caused no differential effect on the proliferation
between KRAS mutant and KRAS wild type cells.
Assays, Synthetic and Analytical Methods
[0247] In vitro degradation assay protocol for compounds 3-33:
Panc02.13 cells were purchased from ATCC and cultured in RPMI-1640
(Gibco), supplemented with 15% FBS (ATCC) and 10 Units/mL human
recombinant insulin (Gibco). PROTAC treatments were carried out in
12-well plates for 16 h. TLR3 agonist Poly I:C (Invivogen;
tlrl-pic) was added for the final 3 h. Cells were harvested, and
lysed in RIPA buffer (50 mM Tris pH8, 150 mM NaCl, 1% Tx-100, 0.1%
SDS, 0.5% Sodium Deoxycholate) supplemented with protease and
phosphatase inhibitors. Lysates were clarified at 16,000 g for 10
minutes, and supernatants were separated by SDS-PAGE.
Immunoblotting was performed using standard protocols. The
antibodies used were TBK1 (Cell Signaling#3504), pIRF3
(abcam#ab76493), and GAPDH (Cell Signaling#5174).
[0248] In Vitro Degradation Assay Protocol for Compounds 34-57
[0249] MDA MB 231 cells were purchased from ATCC and cultured in
RPMI-1640 (Gibco), supplemented with 10% FBS (Gibco). PROTAC
treatments were carried out in 24-well plates for 16 h. Cells were
harvested, and lysed in RIPA buffer (50 mM Tris pH8, 150 mM NaCl,
1% Tx-100, 0.1% SDS, 0.5% Sodium Deoxycholate) supplemented with
protease and phosphatase inhibitors. Lysates were clarified at
16,000 g for 10 minutes, and supernatants were separated by
SDS-PAGE. Immunoblotting was performed using standard protocols.
The antibodies used were TBK1 (Cell Signaling#3504) and GAPDH (Cell
Signaling#5174).
[0250] Representative Experimental Procedure (Compound 11)
##STR00065##
1,2-Di(1,3-dioxan-2-yl)ethane
[0251] A mixture of 2,5-dimethoxytetrahydrofuran (20 g, 132 mmol),
1,3-propanediol (120 g, 1.5 mol) and p-TsOH.H.sub.2O (2.5 g, 15.1
mmol) in DCM (500 mL) was stirred at 40.degree. C. for 16 h. The
reaction was quenched with 1N NaHCO.sub.3. The organic phase was
washed with water, brine, dried over Na.sub.2SO.sub.4, filtered and
concentrated. The residue was purified by silica gel chromatography
eluting with 10-30% EtOAc in hexane to afford
1,2-di(1,3-dioxan-2-yl)ethane (22.5 g, 74%) as white solid. .sup.1
HNMR (400 MHz, CDCl.sub.3): .delta. 1.30-1.34 (m, 2H), 1.69-1.70
(m, 4H), 2.01-2.11 (m, 2H), 3.71-3.78 (m, 4H), 4.07-4.11 (m, 4H),
4.51-4.55 (m, 2H).
3,3'-(Butane-1,4-diylbis(oxy))bis(propan-1-ol)
[0252] To a solution of 1,2-di(1,3-dioxan-2-yl)ethane (22.5 g, 113
mmol) in THF (400 mL) was added BH.sub.3 THF complex (1M, 282 mmol,
282 mL) slowly at 0.degree. C. After the addition, the reaction was
stirred at reflux for 48 h. TLC showed the reaction was complete.
MeOH (40 mL) was carefully added into the reaction mixture at
0.degree. C. and the resulting solution was stirred at room
temperature for additional 2 h. The volatiles were evaporated and
the residue was purified by silica gel chromatography eluting with
6-8% MeOH in DCM to afford
3,3'-(butane-1,4-diylbis(oxy))bis(propan-1-ol) (7.5 g, 32%) as
colorless oil. .sup.1HNMR (400 MHz, CDCl.sub.3): .delta. 1.62-1.65
(m, 4H), 1.79-1.85 (m, 4H), 2.79 (br, 2H), 3.45-3.47 (m, 4H), 3.60
(t, J=6.0 Hz, 4H), 3.75 (t, J=5.6 Hz, 4H).
3-(4-(3-(Benzyloxy)propoxy)butoxy)propan-1-ol
[0253] To a mixture of
3,3'-(butane-1,4-diylbis(oxy))bis(propan-1-ol) (14 g, 68 mmol),
Ag.sub.2O (23.6 g, 102 mmol) and KI (4.5 g, 27 mmol) in DCM (120
mL) was added benzyl bromide (12.8 g, 74.7 mmol) dropwise at room
temperature. The resulting mixture was stirred at room temperature
for 12 h. The solid was removed by filtration and washed with DCM.
The combined organic solution was concentrated and the residue was
purified by silica gel chromatography eluting with 20% EtOAc in
hexane to afford 3-(4-(3-(benzyloxy)propoxy)butoxy)propan-1-ol (7.8
g, 39%) as colorless oil. LCMS: 297.3 [M+1].sup.+. .sup.1HNMR (400
MHz, CDCl.sub.3): .delta. 1.60-1.63 (m, 4H), 1.80-1.89 (m, 4H),
2.52 (t, J=5.6 Hz, 1H), 3.40-3.46 (m, 4H), 3.49-3.62 (m, 6H),
3.74-3.78 (m, 2H), 4.50 (s, 2H), 7.27-7.34 (m, 5H).
.sup.tButyl 1-phenyl-2,6,11,15-tetraoxaheptadecan-17-oate
[0254] To a mixture of
3-(4-(3-(benzyloxy)propoxy)butoxy)propan-1-ol (7.8 g, 26.3 mmol) in
dry DMF (75 mL) was added NaH (60%, 1.9 g, 47.3 mmol) at 0.degree.
C. slowly, and the resulting mixture was stirred at room
temperature for 1.5 h. t-Butyl bromoacetate (12.7 g, 65.8 mmol) was
added into the reaction mixture at 0.degree. C. dropwise and the
resulting mixture was allowed to stir at room temperature for 15 h.
The mixture was carefully quenched with water with ice-water
cooling and extracted with EtOAc. The organic phase was washed with
brine, dried over anhydrous Na.sub.2SO.sub.4, filtered and
concentrated. The residue was purified by silica gel chromatography
eluting with 20-50% EtOAc in hexane to afford the title compound
(2.4 g, 22%). LCMS: 469.4 [M+1].sup.+. .sup.1HNMR (400 MHz,
CDCl.sub.3): .delta. 1.47 (s, 9H), 1.59-1.62 (m, 4H), 1.86-1.91 (m,
4H), 3.40-3.43 (m, 4H), 3.49-3.57 (m, 6H), 3.64 (t, J=6.4 Hz, 2H),
4.18 (s, 2H), 4.50 (s, 2H), 4.56 (s, 2H), 7.27-7.36 (m, 5H).
.sup.tButyl 2-(3-(4-(3-hydroxypropoxy)butoxy)propoxy)acetate
[0255] A solution of tert-butyl
1-phenyl-2,6,11,15-tetraoxaheptadecan-17-oate (2.4 g, 5.1 mmol),
Pd/C (10%, 100 mg) in EtOH (50 mL) was stirred at room temperature
16 h under H.sub.2 atmosphere. Pd/C was removed by filtration and
washed with EtOH. The combined organic phase was concentrated to
afford the title compound (1.8 g, 93%) as brown oil. It was used in
next step without further purification.
[0256] .sup.1HNMR (400 MHz, CDCl.sub.3): .delta. 1.48 (s, 9H),
1.62-1.63 (m, 4H), 1.81-1.91 (m, 4H), 2.55 (br, 1H), 1.86-1.91 (m,
4H), 3.41-3.47 (m, 4H), 3.51 (t, J=6.4 Hz, 2H), 3.60-3.66 (m, 4H),
3.77 (t, J=5.4 Hz, 2H), 4.19 (s, 2H), 4.57 (s, 2H).
.sup.tButyl 2-(3-(4-(3-(tosyloxy)propoxy)butoxy)propoxy)acetate
[0257] A mixture of tert-butyl
2-(3-(4-(3-hydroxypropoxy)butoxy)propoxy)acetate (800 mg, 2.11
mmol), TsCl (420 mg, 2.54 mmol), TEA (260 mmol, 2.54 mmol) and DMAP
(10 mg) in DCM (15 mL) was stirred at room temperature for 8 h. The
reaction mixture was diluted with DCM and washed with water and
brine. The organic layer was dried over Na.sub.2SO.sub.4, filtered
and concentrated. The residue was purified by silica gel
chromatography eluting with 10-15% EtOAc in hexane to afford the
title compound (850 mg, 73%) as colorless oil. LCMS:
533.3[M+1].sup.+. .sup.1HNMR (400 MHz, CDCl.sub.3): .delta. 1.48
(s, 9H), 1.53-1.55 (m, 4H), 1.86-1.92 (m, 4H), 2.45 (s, 3H),
3.31-3.34 (m, 2H), 3.39-3.43 (m, 4H), 3.50 (t, J=6.2 Hz, 2H), 3.64
(t, J=6.4 Hz, 2H), 4.13 (t, J=6.2 Hz, 2H), 4.18 (s, 2H), 4.57 (s,
2H), 7.34 (d, J=8.0 Hz, 2H), 7.80 (d, J=8.4 Hz, 2H).
.sup.tButyl
2-(3-(4-(3-(4-nitrophenoxy)propoxy)butoxy)propoxy)acetate
[0258] A mixture of tert-butyl
2-(3-(4-(3-(tosyloxy)propoxy)butoxy)propoxy)acetate (850 mg, 1.6
mmol), K.sub.2CO3 (552 mg, 4 mmol) and 4-nitrophenol (244 mg, 1.76
mmol) in DMF (5 mL) was stirred at 70.degree. C. for 16 h. The
mixture was partitioned between EtOAc and water. The organic phase
was washed with brine, dried over anhydrous Na.sub.2SO.sub.4,
filtered and concentrated. The residue was purified by silica gel
chromatography eluting with 20-50% EtOAc in hexane to afford the
title compound (650 mg, 81%) as light yellow solid. .sup.1H NMR
(400 MHz, CDCl.sub.3): .delta. 1.47 (s, 9H), 1.61-1.63 (m, 4H),
1.85-1.91 (m, 2H), 2.06-2.09 (m, 2H), 3.41-3.52 (m, 6H), 3.57-3.65
(m, 4H), 4.18 (s, 2H), 4.57 (s, 2H), 6.96 (d, J=9.2 Hz, 2H), 8.20
(d, J=9.2 Hz, 2H).
.sup.tButyl
2-(3-(4-(3-(4-aminophenoxy)propoxy)butoxy)propoxy)acetate
[0259] A solution of tert-butyl
2-(3-(4-(3-(4-nitrophenoxy)propoxy)butoxy)propoxy)acetate (200 mg,
0.4 mmol), Pd/C (10%, 20 mg) in EtOH (20 mL) was stirred at room
temperature under H.sub.2 atmosphere. Pd/C was removed by
filtration and washed with EtOH. The combined organic phase was
concentrated to afford the title compound (120 mg, 64%) as brown
oil. The crude product was used directly without purification.
.sup.1H NMR (400 MHz, CDCl.sub.3): .delta. 1.47 (s, 9H), 1.56-1.63
(m, 4H), 1.87-1.90 (m, 2H), 1.97-2.03 (m, 2H), 3.40-3.45 (m, 4H),
3.50 (t, J=6.4 Hz, 2H), 3.57 (t, J=6.2 Hz, 2H), 3.64 (t, J=6.4 Hz,
2H), 3.98 (t, J=6.4 Hz, 2H), 4.18 (s, 2H), 4.57 (s, 2H), 6.64 (d,
J=8.8 Hz, 2H), 6.74 (d, J=8.8 Hz, 2H).
.sup.tButyl
2-(3-(4-(3-(4-((5-bromo-4-((3-(N-methylcyclobutanecarboxamido)-propyl)-am-
ino)pyrimidin-2-yl)amino)phenoxy)propoxy)butoxy)propoxy)acetate
[0260] A mixture of tert-butyl
2-(3-(4-(3-(4-aminophenoxy)propoxy)butoxy)propoxy)acetate (120 mg,
0.26 mmol),
N-[3-[(5-bromo-2-chloropyrimidin-4-yl)amino]propyl]-N-methylcyclob-
utanecarboxamide (96 mg. 0.26 mmol) and TsOH H.sub.2O (23 mg, 0.12
mmol) in dioxane (3 mL) was stirred at 100.degree. C. for 16 h. The
reaction mixture was cooled to room temperature, and partitioned
between EtOAc and 1N NaHCO.sub.3. The organic phase was washed with
water, brine, dried over anhydrous Na.sub.2SO.sub.4, concentrated.
The residue was purified by silica gel chromatography eluting with
2%-5% MeOH in DCM to afford the title compound (120 mg, 58%) as
yellow oil. LCMS: 796.3 [M+1].sup.+.
2-(3-(4-(3-(4-((5-Bromo-4-((3-(N-methylcyclobutanecarboxamido)-propyl)amin-
o)pyrimidin-2-yl)amino)phenoxy)propoxy)butoxy)propoxy)acetic
Acid
[0261] A mixture of tert-butyl
2-(3-(4-(3-(4-((5-bromo-4-((3-(N-methylcyclobutanecarboxamido)-propyl)ami-
no)pyrimidin-2-yl)amino)phenoxy)propoxy)butoxy)propoxy)acetate (120
mg, 0.15 mmol) and LiOH H.sub.2O (17 mg, 0.4 mmol) in THF (2 mL)
and water (0.5 mL) was stirred at room temperature for 2 h. TLC
showed the reaction was complete. The reaction mixture was
acidified to pH 3-4 with 1M HCl, and the mixture was extracted with
DCM, dried over anhydrous Na.sub.2SO.sub.4, filtered and
concentrated to afford the title compound (100 mg, 98%) as yellow
oil which was used in the next step without further purification.
LCMS: 682.3 [M+1].sup.+.
(2S,4R)-1-((S)-18-(4-((5-Bromo-4-((3-(N-methylcyclobutanecarboxamido)-prop-
yl)
amino)pyrimidin-2-yl)amino)phenoxy)-2-(tert-butyl)-4-oxo-6,10,15-triox-
a-3-azaoctadecan-1-oyl)-4-hydroxy-N-(4-(4-methylthiazol-5-yl)benzyl)pyrrol-
idine-2-carboxamide
[0262] To a mixture of
2-(3-(4-(3-(4-((5-bromo-4-((3-(N-methylcyclobutanecarboxamido)-propyl)ami-
no)pyrimidin-2-yl)amino)phenoxy)propoxy)butoxy)propoxy)acetic acid
(100 mg, 0.147 mmol),
(2S,4R)-1-((S)-2-amino-3,3-dimethylbutanoyl)-4-hydroxy-N-((S)-1-(4-(4-met-
hylthiazol-5-yl)phenyl)ethyl)pyrrolidine-2-carboxamide
hydrochloride (68 mg, 0.147 mmol), and DIPEA (77 mg, 0.6 mmol) in
dry DMF (3 mL) was added HATU (114 mg, 0.3 mmol) at 0.degree. C.
The resulting mixture was allowed to stir at room temperature for
0.5 h. TLC showed the reaction was complete. The mixture was
partitioned between EtOAc and water. The organic phase was washed
with water, brine and dried over anhydrous Na.sub.2SO.sub.4,
filtered and concentrated. The residue was purified by preparative
TLC to afford the title compound as white solid (22.5 mg, 15%).
LCMS: 1094.4 [M+1].sup.+. .sup.1H NMR (400 MHz, CD.sub.3OD):
.delta. 1.05 (s, 9H), 1.60-1.64 (m, 4H), 1.80-2.26 (m, 15H), 2.48
(s, 3H), 2.86-2.91 (m, 3H), 3.26-3.28 (m, 1H), 3.40-3.54 (m, 9H),
3.59-3.64 (m, 4H), 3.83-3.88 (m, 2H), 3.97-4.06 (m, 4H), 4.34-4.38
(m, 1H), 4.52-4.61 (m, 3H), 4.71-4.72 (m, 1H), 6.87-6.90 (m, 2H),
7.41-7.49 (m, 6H), 7.87-7.90 (m, 1H), 8.88 (s, 1H).
N-[3-[(5-Bromo-2-chloropyrimidin-4-yl)amino]propyl]-N-methylcyclobutanecar-
boxamide
##STR00066##
[0263].sup.tButyl
N-[3-(1-cyclobutyl-N-methylformamido)propyl]carbamate
[0264] Into a 250-mL round-bottom flask purged and maintained with
an inert atmosphere of nitrogen, was placed a solution of
cyclobutanecarboxylic acid (2.66 g, 26.6 mmol, 1.00 equiv) in
N,N-dimethylformamide (100 mL), and DIEA (6.86 g, 53.1 mmol, 2.00
equiv). This was followed by the addition of HATU (12.13 g, 31.9
mmol, 1.20 equiv). The mixture was stirred for 30 min at
0-10.degree. C. To this was added tert-butyl
N-[3-(methylamino)propyl]carbamate (5 g, 26.6 mmol, 1.00 equiv).
The resulting solution was stirred for 12 h at room temperature.
The reaction was then quenched by the addition of 500 mL of water.
The resulting solution was extracted with 3.times.100 mL of ethyl
acetate and the organic layers combined. The extracts were washed
with 1.times.100 mL of water and 1.times.100 mL of brine. The
mixture was dried over anhydrous sodium sulfate and concentrated in
vacuo. The residue was purified by silica gel chromatography
eluting with ethyl acetate/petroleum ether (1:1). This resulted in
5.9 g (82%) of tert-butyl
N-[3-(1-cyclobutyl-N-methylformamido)propyl]carbamate as colorless
oil. LC-MS (ES.sup.+): m/z 271.05[MH.sup.+], t.sub.R=0.98 min.
N-(3-Aminopropyl)-N-methylcyclobutanecarboxamide Hydrochloride
[0265] Into a 250-mL round-bottom flask, was placed a solution of
tert-butyl N-[3-(1-cyclobutyl-N-methylformamido)propyl]carbamate
(13 g, 48.1 mmol, 1.00 equiv) in methanol/HCl (g) (200 mL). The
resulting solution was stirred for 1 h at room temperature. The
resulting mixture was concentrated under vacuum. This resulted in
9.6 g (97%) of N-(3-aminopropyl)-N-methylcyclobutanecarboxamide
hydrochloride as a white solid. LC-MS (ES.sup.+): m/z 171.00
[MH.sup.+], t.sub.R=0.34 min.
N-[3-[(5-Bromo-2-chloropyrimidin-4-yl)amino]propyl]-N-methylcyclobutanecar-
boxamide
[0266] Into a 500-mL 3-necked round-bottom flask purged and
maintained with an inert atmosphere of nitrogen, was placed a
solution of 5-bromo-2,4-dichloropyrimidine (10.55 g, 46.3 mmol,
1.00 equiv) in CH.sub.3CN (250 mL). This solution was cooled to
0.degree. C. and treated with dropwise DIEA (18 g, 139.3 mmol, 3.00
equiv) and then N-(3-aminopropyl)-N-methylcyclobutanecarboxamide
hydrochloride (9.6 g, 46.4 mmol, 1.00 equiv) batchwise. The
resulting solution was stirred for 3 h at room temperature then
quenched by the addition of 50 mL of water. The CH.sub.3CN was
removed in vacuo and the resulting solution further diluted with
100 mL of water. This mixture was extracted with 3.times.100 mL of
ethyl acetate and the organic layers combined, washed with
1.times.100 mL of brine and dried over anhydrous sodium sulfate,
and concentrated in vacuo. The resulting residue was washed with
2.times.100 mL of ethyl acetate/petroleum ether (1/5) and the
solids collected by filtration. This resulted in 11.3 g (67%) of
N-[3-[(5-bromo-2-chloropyrimidin-4-yl)amino]propyl]-N-methylcyclobutaneca-
rboxamide as a white solid. .sup.1H NMR (400 MHz, CDCl.sub.3)
.delta. 8.09 (s, 1H), 7.20 (b, 1H), 3.49-3.47 (m, 4H), 3.46-3.28
(m, 2H), 2.41-2.31 (m, 2H), 2.24-2.16 (m, 2H), 2.05-1.80 (m, 2H),
1.80-1.70 (m, 2H); LC-MS (ES.sup.+): m/z 362.90, 364.90 [MH.sup.+],
t.sub.R=2.85 min.
Analytical Characterization of TBK1 Compounds:
TABLE-US-00005 [0267] Compound # MH+ (1) MH+ (2) 7 1038.37 1040.37
34 1054.35 1056.35 16 1170.46 1172.46 3 978.37 980.37 35 1098.39
1100.39 36 1142.41 1144.42 37 1230.47 1232.47 4 994.36 996.36 13
1126.44 1128.44 38 1186.44 1188.44 39 1038.36 1040.37 40 1110.51
1112.51 6 1022.47 1024.47 11 1094.53 1096.54 5 1006.46 1008.46 8
1050.49 1052.49 41 1082.46 1084.46 42 1200.52 1202.53 10 1082.48
1084.48 43 1068.45 1070.45 44 1154.53 1156.53 45 1214.55 1216.55 9
1066.50 1068.50 12 1106.57 1108.57 14 1138.56 1140.56 17 1182.59
1184.59 46 1126.50 1128.51 15 1152.57 1154.58 47 1168.57 1170.57 48
1242.61 1244.61 49 1094.45 1096.46 50 1028.57 -- 51 1054.58 -- 28
1054.58 -- 25 1028.56 -- 26 1042.58 -- 52 1042.58 -- 27 1040.56 --
53 1041.06 -- 54 1040.56 -- 18 1094.43 1096.44 19 1014.52 -- 20
1048.42 1050.42 21 1082.42 -- 24 1032.43 -- 23 1140.33 -- 22
1068.47 -- 29 1038.27 1040.28 30 1052.29 1054.29 31 1066.30 1068.30
32 1080.32 1082.32 33 1080.32 1082.32 55 1210.41 1212.41 56 1238.44
1240.44 57 1294.50 1296.50
[0268] Method to synthesize novel bifunctional molecules, which
contains a TBK1 recruiting moiety and an E3 Ligase recruiting
moiety, through PROTAC technology is described. PROTAC mediated
protein degradation provides a promising strategy in targeting the
"undruggable" pathological proteins by traditional approaches.
[0269] As described herein, in one aspect the disclosure provides
bifunctional compounds comprising the chemical structure:
TBM-L-ULM, wherein TBM is a TBK1 binding moiety; L is absent (a
bond) or a chemical linker; and ULM is an E3 ubiquitin ligase
binding moiety.
[0270] In any of the aspects or embodiments described herein, the
TBM has the structure:
##STR00067##
Wherein the TBM is covalently coupled to an ULM via an L group.
[0271] In any of the aspects or embodiments described herein, the
ULM is a moiety that binds an E3 ubiquitin ligase selected from the
group consisting of Von Hippel-Lindau (VHL) E3 ubiquitin ligase,
IAP, cereblon, and MDM2 as described herein.
[0272] In any of the aspects or embodiments described herein, the
bifunctional compound comprise a linker (L) group having the
structure: -A.sub.1 . . . A.sub.q-, wherein A.sub.1 is coupled to
the ULM and TBM moiety; and q is an integer greater than or equal
to 0.
[0273] In any of the aspects or embodiments described herein, each
A unit (i.e., A.sub.1 to A.sub.q) is each independently, a bond,
CR.sup.L1R.sup.L2, O, S, SO, SO.sub.2, NR.sup.L3,
SO.sub.2NR.sup.L3, SONR.sup.L3, CONR.sup.L3, NR.sup.L3CONR.sup.L4,
NR.sup.L3SO.sub.2NR.sup.L4, CO, CR.sup.L1.dbd.CR.sup.L2, C.ident.C,
SiR.sup.L1R.sup.L2, P(O)R.sup.L3, P(O)OR.sup.L3,
NR.sup.L3C(.dbd.NCN)NR.sup.L4, NR.sup.L3C(.dbd.NCN),
NR.sup.L3C(.dbd.CNO.sub.2)NR.sup.L4, C.sub.3-11cycloalkyl
optionally substituted with 0-6 R.sup.L1 and/or R.sup.L2 groups,
C.sub.3-11heteocyclyl optionally substituted with 0-6 R.sup.L1
and/or R.sup.L2 groups, aryl optionally substituted with 0-6
R.sup.L1 and/or R.sup.L2 groups, heteroaryl optionally substituted
with 0-6 R.sup.L1 and/or R.sup.L2 groups, wherein R.sup.L1 or
R.sup.L2, each independently, can be linked to other A groups to
form cycloalkyl and/or heterocyclyl moeity which can be further
substituted with 0-4 R.sup.L5 groups; and wherein R.sup.L1,
R.sup.L2, R.sup.L3, R.sup.L4 and R.sup.L5 are, each independently,
H, halo, C.sub.1-8alkyl, OC.sub.1-8alkyl, SC.sub.1-8alkyl,
NHC.sub.1-8alkyl, N(C.sub.1-8alkyl).sub.2, C.sub.3-11cycloalkyl,
aryl, heteroaryl, C.sub.3-11heterocyclyl, OC.sub.1-8cycloalkyl,
SC.sub.1-8cycloalkyl, NHC.sub.1-8cycloalkyl,
N(C.sub.1-8cycloalkyl).sub.2,
N(C.sub.1-8cycloalkyl)(C.sub.1-8alkyl), OH, NH.sub.2, SH,
SO.sub.2C.sub.1-8alkyl, P(O)(OC.sub.1-8alkyl)(C.sub.1-8alkyl),
P(O)(OC.sub.1-8alkyl).sub.2, CC--C.sub.1-8alkyl, CCH,
CH.dbd.CH(C.sub.1-8alkyl),
C(C.sub.1-8alkyl).dbd.CH(C.sub.1-8alkyl),
C(C.sub.1-8alkyl).dbd.C(C.sub.1-8alkyl).sub.2, Si(OH).sub.3,
Si(C.sub.1-8alkyl).sub.3, Si(OH)(C.sub.1-8alkyl).sub.2,
COC.sub.1-8alkyl, CO.sub.2H, halogen, CN, CF.sub.3, CHF.sub.2,
CH.sub.2F, NO.sub.2, SF.sub.5, SO.sub.2NHC.sub.1-8alkyl,
SO.sub.2N(C.sub.1-8alkyl).sub.2, SONHC.sub.1-8alkyl,
SON(C.sub.1-8alkyl).sub.2, CONHC.sub.1-8alkyl,
CON(C.sub.1-8alkyl).sub.2, N(C.sub.1-8alkyl)CONH(C.sub.1-8alkyl),
N(C.sub.1-8alkyl)CON(C.sub.1-8alkyl).sub.2, NHCONH(C.sub.1-8alkyl),
NHCON(C.sub.1-8alkyl).sub.2, NHCONH.sub.2,
N(C.sub.1-8alkyl)SO.sub.2NH(C.sub.1-8alkyl), N(C.sub.1-8alkyl)
SO.sub.2N(C.sub.1-8alkyl).sub.2, NH SO.sub.2NH(C.sub.1-8alkyl), NH
SO.sub.2N(C.sub.1-8alkyl).sub.2, or NH SO.sub.2NH.sub.2.
[0274] In any of the aspects or embodiments described herein, the
linker (L) is selected from the group consisting of:
##STR00068## ##STR00069## ##STR00070##
[0275] In an additional aspect, the disclosure provides
compositions comprising an effective amount of the bifunctional
compound as described herein, and a pharmaceutically acceptable
carrier.
[0276] In any of the aspects or embodiments described herein, the
composition can further comprise at least one additional bioactive
agent. In any of the aspects or embodiments described herein, the
bioactive agent is an anti-cancer agent. In any of the aspects or
embodiments described herein, the additional anti-cancer agent is
selected from the group consisting of: everolimus, trabectedin,
abraxane, TLK 286, AV-299, DN-101, pazopanib, GSK690693, RTA 744,
ON 0910.Na, AZD 6244 (ARRY-142886), AMN-107, TKI-258, GSK461364,
AZD 1152, enzastaurin, vandetanib, ARQ-197, MK-0457, MLN8054,
PHA-739358, R-763, AT-9263, a FLT-3 inhibitor, an androgen receptor
inhibitor, a VEGFR inhibitor, an EGFR TK inhibitor, an aurora
kinase inhibitor, a PIK-1 modulator, a Bcl-2 inhibitor, an HDAC
inhbitor, a c-MET inhibitor, a PARP inhibitor, a Cdk inhibitor, an
EGFR TK inhibitor, an IGFR-TK inhibitor, an anti-HGF antibody, a
PI3 kinase inhibitors, an AKT inhibitor, a JAK/STAT inhibitor, a
checkpoint-1 or 2 inhibitor, a focal adhesion kinase inhibitor, a
Map kinase kinase (mek) inhibitor, a VEGF trap antibody,
pemetrexed, erlotinib, dasatanib, nilotinib, decatanib,
panitumumab, amrubicin, oregovomab, Lep-etu, nolatrexed, azd2171,
batabulin, ofatumumab, zanolimumab, edotecarin, tetrandrine,
rubitecan, tesmilifene, oblimersen, ticilimumab, ipilimumab,
gossypol, Bio 111, 131-I-TM-601, ALT-110, BIO 140, CC 8490,
cilengitide, gimatecan, IL13-PE38QQR, INO 1001, IPdR.sub.1
KRX-0402, lucanthone, LY317615, neuradiab, vitespan, Rta 744, Sdx
102, talampanel, atrasentan, Xr 311, romidepsin, ADS-100380,
sunitinib, 5-fluorouracil, vorinostat, etoposide, gemcitabine,
doxorubicin, liposomal doxorubicin, 5'-deoxy-5-fluorouridine,
vincristine, temozolomide, ZK-304709, seliciclib; PD0325901,
AZD-6244, capecitabine, L-Glutamic acid,
N-[4-[2-(2-amino-4,7-dihydro-4-oxo-1
H--pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoyl]-, disodium salt,
heptahydrate, camptothecin, PEG-labeled irinotecan, tamoxifen,
toremifene citrate, anastrazole, exemestane, letrozole,
DES(diethylstilbestrol), estradiol, estrogen, conjugated estrogen,
bevacizumab, IMC-1C11, CHIR-258);
3-[5-(methylsulfonylpiperadinemethyl)-indolylj-quinolone,
vatalanib, AG-013736, AVE-0005, the acetate salt of [D-Ser(But)
6,Azgly 10]
(pyro-Glu-His-Trp-Ser-Tyr-D-Ser(But)-Leu-Arg-Pro-Azgly-NH 2 acetate
[C.sub.59H.sub.84N.sub.18Oi.sub.4-(C.sub.2H.sub.4O.sub.2).sub.x
where x=1 to 2.4], goserelin acetate, leuprolide acetate,
triptorelin pamoate, medroxyprogesterone acetate,
hydroxyprogesterone caproate, megestrol acetate, raloxifene,
bicalutamide, flutamide, nilutamide, megestrol acetate, CP-724714;
TAK-165, HKI-272, erlotinib, lapatanib, canertinib, ABX-EGF
antibody, erbitux, EKB-569, PKI-166, GW-572016, Ionafarnib,
BMS-214662, tipifarnib; amifostine, NVP-LAQ824, suberoyl analide
hydroxamic acid, valproic acid, trichostatin A, FK-228, SU11248,
sorafenib, KRN951, aminoglutethimide, arnsacrine, anagrelide,
L-asparaginase, Bacillus Calmette-Guerin (BCG) vaccine, adriamycin,
bleomycin, buserelin, busulfan, carboplatin, carmustine,
chlorambucil, cisplatin, cladribine, clodronate, cyproterone,
cytarabine, dacarbazine, dactinomycin, daunorubicin,
diethylstilbestrol, epirubicin, fludarabine, fludrocortisone,
fluoxymesterone, flutamide, gleevec, gemcitabine, hydroxyurea,
idarubicin, ifosfamide, imatinib, leuprolide, levamisole,
lomustine, mechlorethamine, melphalan, 6-mercaptopurine, mesna,
methotrexate, mitomycin, mitotane, mitoxantrone, nilutamide,
octreotide, oxaliplatin, pamidronate, pentostatin, plicamycin,
porfimer, procarbazine, raltitrexed, rituximab, streptozocin,
teniposide, testosterone, thalidomide, thioguanine, thiotepa,
tretinoin, vindesine, 13-cis-retinoic acid, phenylalanine mustard,
uracil mustard, estramustine, altretamine, floxuridine,
5-deooxyuridine, cytosine arabinoside, 6-mecaptopurine,
deoxycoformycin, calcitriol, valrubicin, mithramycin, vinblastine,
vinorelbine, topotecan, razoxin, marimastat, COL-3, neovastat,
BMS-275291, squalamine, endostatin, SU5416, SU6668, EMD121974,
interleukin-12, IM862, angiostatin, vitaxin, droloxifene,
idoxyfene, spironolactone, finasteride, cimitidine, trastuzumab,
denileukin diftitox,gefitinib, bortezimib, paclitaxel,
cremophor-free paclitaxel, docetaxel, epithilone B, BMS-247550,
BMS-310705, droloxifene, 4-hydroxytamoxifen, pipendoxifene,
ERA-923, arzoxifene, fulvestrant, acolbifene, lasofoxifene,
idoxifene, TSE-424, HMR-3339, ZK186619, topotecan, PTK787/ZK
222584, VX-745, PD 184352, rapamycin,
40-O-(2-hydroxyethyl)-rapamycin, temsirolimus, AP-23573, RAD001,
ABT-578, BC-210, LY294002, LY292223, LY292696, LY293684, LY293646,
wortmannin, ZM336372, L-779,450, PEG-filgrastim, darbepoetin,
erythropoietin, granulocyte colony-stimulating factor,
zolendronate, prednisone, cetuximab, granulocyte macrophage
colony-stimulating factor, histrelin, pegylated interferon alfa-2a,
interferon alfa-2a, pegylated interferon alfa-2b, interferon
alfa-2b, azacitidine, PEG-L-asparaginase, lenalidomide, gemtuzumab,
hydrocortisone, interleukin-11, dexrazoxane, alemtuzumab,
all-transretinoic acid, ketoconazole, interleukin-2, megestrol,
immune globulin, nitrogen mustard, methylprednisolone, ibritgumomab
tiuxetan, androgens, decitabine, hexamethylmelamine, bexarotene,
tositumomab, arsenic trioxide, cortisone, editronate, mitotane,
cyclosporine, liposomal daunorubicin, Edwina-asparaginase,
strontium 89, casopitant, netupitant, an NK-1 receptor antagonist,
palonosetron, aprepitant, diphenhydramine, hydroxyzine,
metoclopramide, lorazepam, alprazolam, haloperidol, droperidol,
dronabinol, dexamethasone, methylprednisolone, prochlorperazine,
granisetron, ondansetron, dolasetron, tropisetron, pegfilgrastim,
erythropoietin, epoetin alfa, darbepoetin alfa and mixtures
thereof.
[0277] In any of the aspects or embodiments described herein, the
composition can comprise an effective amount of at least two
different bifunctional compounds as described herein.
[0278] In any of the aspects or embodiments described herein, the
compound as described herein can be selected from the group
consisting of:
##STR00071## ##STR00072## ##STR00073## ##STR00074##
##STR00075##
combinations thereof.
[0279] In any of the aspects or embodiments described herein, the
disclosure includes compositions comprising one or more of the
above-referenced compounds, including effective amounts of the
same. In any of the aspects or embodiments, the compositions can
further include a pharmaceutically acceptable carrier.
[0280] In an additional aspect, the description provides
compositions for use in methods of treating a disease or disorder
in a subject comprising the steps of administering a composition
comprising a pharmaceutically acceptable carrier and an effective
amount of a compound as described herein to a subject in need
thereof, wherein the compound is effective in treating or
ameliorating at least one symptom of the disease or disorder. In
any of the aspects or embodiments, the disease or disorder is at
least one of cancer, an inflammatory disease, an autoimmune
disease, septic shock, or viral infection.
[0281] The contents of all references, patents, pending patent
applications and published patents, cited throughout this
application are hereby expressly incorporated by reference.
[0282] Those skilled in the art will recognize, or be able to
ascertain using no more than routine experimentation, many
equivalents to the specific embodiments of the invention described
herein. Such equivalents are intended to be encompassed by the
following claims. It is understood that the detailed examples and
embodiments described herein are given by way of example for
illustrative purposes only, and are in no way considered to be
limiting to the invention. Various modifications or changes in
light thereof will be suggested to persons skilled in the art and
are included within the spirit and purview of this application and
are considered within the scope of the appended claims. For
example, the relative quantities of the ingredients may be varied
to optimize the desired effects, additional ingredients may be
added, and/or similar ingredients may be substituted for one or
more of the ingredients described. Additional advantageous features
and functionalities associated with the systems, methods, and
processes of the present invention will be apparent from the
appended claims. Moreover, those skilled in the art will recognize,
or be able to ascertain using no more than routine experimentation,
many equivalents to the specific embodiments of the invention
described herein. Such equivalents are intended to be encompassed
by the following claims.
* * * * *