IP Library › Granted Patent US 12,485,178

Granted Patent B2

US 12,485,178 · App. 17/695,645 · Granted Dec 2, 2025

Bifunctional small molecules to target the selective degradation of circulating proteins

Inventors: David Spiegel (New Haven, CT); David Caianiello (Brooklyn, NY); Mengwen Zhang (New Haven, CT)

Assignee: YALE UNIVERSITY

A61K47/545 A61K47/54 A61K47/549 A61K47/55 A61K47/64 A61P35/00

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Quick Facts

Patent No.: US 12,485,178
App. No.: 17/695,645
Granted: Dec 2, 2025
Kind: B2

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Abstract

The present disclosure is directed to bifunctional small molecules which contain a circulating protein binding moiety (CPBM) linked through a linker group to a cellular receptor binding moiety (CRBM) which is a membrane receptor of degrading cell such as a hepatocyte or other degrading cell. In certain embodiments, the (CRBM) is a moiety which binds to asialoglycoprotein receptor (an asialoglycoprotein receptor binding moiety, or ASGPRBM) of a hepatocyte. In additional embodiments, the (CRBM) is a moiety which binds to a receptor of other cells which can degrade proteins, such as a LRP1, LDLR, FcγRI, FcRN, Transferrin or Macrophage Scavenger receptor.

Claims (164)

1 . A compound according to the structure:

wherein:

[CPBM] is a means for binding to vascular endothelial growth factor (VEGF);

[CRBM] has the structure

wherein:

Z B is absent, —(CH 2 ) IM —, —C(O)—(CH 2 ) IM —, or —C(O)—(CH 2 ) IM —NR M —:

R M is H or C 1 -C 3 alkyl optionally substituted with one or two hydroxyl groups; and

each occurrence of IM is independently 0, 1, 2, 3, 4, or 5;

each [CON] is independently at each occurrence selected from the group consisting of:

a) a group selected from the group consisting of:

wherein:

each occurrence of X 2 is independently —CH 2 —, —O—, —S—, —N(R 4 )—, —C(O)—, —S(O)—, —S(O) 2 —, —S(O) 2 O—, —OS(O) 2 —, or —OS(O) 2 O—;

each occurrence of X 3 is independently —O—, —S—, or —N(R 4 )—;

each occurrence of R 4 is independently H, C 1 -C 3 alkyl, C 1 -C 3 alkanol, or —C(O)(C 1 -C 3 alkyl);

[LINKER] is independently at each occurrence selected from the group consisting of:

i) a polyethyleneglycol linker having from 2 to 12 ethylene glycol residues,

ii) a polypropylene glycol or polypropylene-co-polyethylene glycol linker containing 1 to 100 alkylene glycol units,

iii) a group according to the structure:

—CH 2 CH 2 (OCH 2 CH 2 ) m OCH 2 —, —(CH 2 ) m CH 2 —, or —[N(R a )—CH(R 3 )(C═O)] m —,

wherein:

each occurrence of m is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15;

R a is independently H, C 1 -C 3 alkyl, or C 1 -C 6 alkanol, or

R a , together with nitrogen atom to which it is attached, combines with R 3 to form a pyrrolidine or hydroxypyrroline group; and

R 3 is independently selected from the group consisting of hydrogen, methyl, isopropyl, —CH(CH 3 )CH 2 CH 3 , —CH 2 CH(CH 3 ) 2 , —(CH 2 ) 3 -guanidine, —CH 2 C(═O)NH 2 , —CH 2 C(═O)OH, —CH 2 SH, —(CH 2 ) 2 C(═O)NH 2 , —(CH 2 ) 2 C(═O)OH, —(CH 2 )imidazole, —(CH 2 ) 4 NH 2 , —CH 2 CH 2 SCH 3 , benzyl, —CH 2 OH, —CH(OH)CH 3 , and —(CH 2 )phenol;

iv) a group according to the formula:

wherein:

Z and Z′ are each independently a bond, —(CH 2 ) i —O—, —(CH 2 ) i —S—, —(CH 2 ) i —N(R)—,

wherein:

the (CH 2 ) i group, if present in Z or Z′, is bonded to [CON], [CPBM], or [CRBM];

each R is independently H, C 1 -C 3 alkyl, or C 1 -C 3 alkanol;

each R 2 is independently H or C 1 -C 3 alkyl;

each Y is independently a bond, —O—, —S—, or —N(R)—;

each i is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

D is a bond, —(CH 2 ) i —Y—C(O)—Y—(CH 2 ) i —, —(CH 2 ) m′ —, or —[(CH 2 ) n —X 1 ] j —,

with the proviso that Z, Z′, and D are not each simultaneously bonds,

wherein:

each i is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

j is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

m′ is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

X 1 is —O—, —S—, or —N(R)—;

R is H, C 1 -C 3 alkyl, or C 1 -C 3 alkanol;

v) a group according to the structure:

—CH 2 —(OCH 2 CH 2 ) n —CH 2 —, —(CH 2 CH 2 O) n′ CH 2 CH 2 —, or —(CH 2 CH 2 CH 2 O) n —,

wherein:

n is an integer from 1 to 25;

n′ is an integer from 1 to 25;

n″ is 0, 1, 2, 3, 4, 5, 6, 7, or 8;

vi) a group of formula: PEG-[CON]-PEG,

wherein each PEG is independently at each occurrence 1 to 12 ethylene glycol residues and [CON] is

and

vii) a group of formula: —Z-D-Z′—[CON]—Z-D-Z′, wherein [CON] is

wherein:

each occurrence of Z and Z′ is independently a bond or —(CH 2 ) i —O;

D is a bond, —(CH 2 ) m′ —, or —[(CH 2 ) n —X 1 ] j —;

X 1 is —O—;

with the proviso that Z, Z′, and D are not each simultaneously bonds;

i is 2;

n is 2;

each occurrence of j is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; and

each occurrence of m′ is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

k′ is 1;

j′ is 1, 2, or 3;

h is 0, 1, 2, 3, 4, 5, or 6;

h′ is 0, 1, 2, 3, 4, 5, or 6;

i L is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; and

provided that h and h′ are not both 0;

or a pharmaceutically acceptable salt, stereoisomer, or solvate thereof.

2 . The compound of claim 1 , wherein k′, j′, h, h′, and i L are each independently 1, 2, or 3.

3 . The compound of claim 1 , wherein [LINKER] is a group according to the structure:

—Z-D-Z′—[CON]—Z-D-Z′—,

wherein [CON] is

wherein:

each occurrence of Z and Z′ is independently a bond or —(CH 2 ) i —O;

D is a bond, —(CH 2 ) m′ —, or —[(CH 2 ) n —X 1 ] j —;

X 1 is —O—;

with the proviso that Z, Z′, and D are not each simultaneously bonds;

i is 2;

n is 2;

each occurrence of j is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; and

each occurrence of m′ is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.

4 . The compound of claim 1 , wherein:

CON is

each occurrence of [LINKER] is independently —Z-D-Z′— or

wherein:

D is a bond or —(CH 2 ) m′ —;

Z and Z′ are each independently a bond or —(CH 2 ) i —O—, with the proviso that Z, Z′, and D are not each simultaneously bonds;

i is 2; and

m′ is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10.

5 . A pharmaceutical composition comprising a therapeutically effective amount of at least one compound of claim 1 and at least one pharmaceutically acceptable carrier, additive, or excipient, optionally further comprising an additional bioactive agent.

6 . A method of removing excess circulating protein in a subject in need thereof, or treating or ameliorating a disease or disorder associated with the upregulation of a circulating protein in the subject, the method comprising:

administering to the subject a therapeutically effective amount of a compound, which is optionally formulated as pharmaceutical composition comprising at least one pharmaceutically acceptable carrier or excipient,

wherein the compound is:

wherein:

[CPBM] is a means for binding to vascular endothelial growth factor (VEGF);

[CRBM] has the structure

wherein:

Z B is absent, —(CH 2 ) IM —, —C(O)—(CH 2 ) IM —, or —C(O)—(CH 2 ) IM —NR M —;

R M is H or C 1 -C 3 alkyl optionally substituted with one or two hydroxyl groups; and

each occurrence of IM is independently 0, 1, 2, 3, 4, or 5;

each [CON] is independently at each occurrence selected from the group consisting of:

wherein:

each occurrence of X 2 is independently —CH 2 —, —O—, —S—, —N(R 4 )—, —C(O)—, —S(O)—, —S(O) 2 —, —S(O) 2 O—, —OS(O) 2 —, or —OS(O) 2 O—;

each occurrence of X 3 is independently —O—, —S—, or —N(R 4 )—;

each occurrence of R 4 is independently H, C 1 -C 3 alkyl, C 1 -C 3 alkanol, or —C(O)(C 1 -C 3 alkyl);

[LINKER] is independently at each occurrence selected from the group consisting of:

i) a polyethyleneglycol linker having from 2 to 12 ethylene glycol residues,

ii) a polypropylene glycol or polypropylene-co-polyethylene glycol linker containing 1 to 100 alkylene glycol units,

iii) a group according to the structure:

—CH 2 CH 2 (OCH 2 CH 2 ) m OCH 2 —, —(CH 2 ) m CH 2 —, or —[N(R a )—CH(R 3 )(C═O) m —,

wherein:

each occurrence of m is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15,

R a is independently H, C 1 -C 3 alkyl, or C 1 -C 6 alkanol, or

R a , together with nitrogen atom to which it is attached, combines with R 3 to form a pyrrolidine or hydroxypyrroline group; and

iv) a group according to the formula:

wherein:

Z and Z′ are each independently a bond, —(CH 2 ) i —O—, —(CH 2 ) i —S—, —(CH 2 ) i —N(R)—,

wherein:

the (CH 2 ) i group, if present in Z or Z′, is bonded to [CON], [CPBM], or [CRBM],

each R is independently H, C 1 -C 3 alkyl, or C 1 -C 3 alkanol;

each R 2 is independently H or C 1 -C 3 alkyl;

each Y is independently a bond, —O—, —S—, or —N(R)—;

each i is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

D is a bond, —(CH 2 ) i —Y—C(O)—Y—(CH 2 ) i —, —(CH 2 ) m′ —, or —[(CH 2 ) n —X 1 ] i —,

with the proviso that Z, Z′, and D are not each simultaneously bonds,

wherein:

each i is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

j is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

m′ is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

X 1 is —O—, —S—, or —N(R)—;

R is H, C 1 -C 3 alkyl, or C 1 -C 3 alkanol;

v) a group according to the structure:

—CH 2 —(OCH 2 CH 2 ) n —CH 2 —, —(CH 2 CH 2 O) n′ CH 2 CH 2 —, or —(CH 2 CH 2 CH 2 O) n —,

wherein:

n is an integer from 1 to 25;

n′ is an integer from 1 to 25;

n″ is 0, 1, 2, 3, 4, 5, 6, 7, or 8;

vi) a group of formula: PEG-[CON]-PEG,

wherein each PEG is independently at each occurrence 1 to 12 ethylene glycol residues and [CON] is

and

vii) a group of formula: —Z-D-Z′—[CON]—Z-D-Z′, wherein [CON] is

wherein:

each occurrence of Z and Z′ is independently a bond or —(CH 2 ) i —O;

D is a bond, —(CH 2 ) m′ —, or —[(CH 2 ) n —X 1 ] i —;

X 1 is —O—;

with the proviso that Z, Z′, and D are not each simultaneously bonds;

i is 2;

n is 2;

each occurrence of j is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; and

each occurrence of m′ is independently 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;

k′ is 1;

j′ is 1, 2, or 3;

h is 0, 1, 2, 3, 4, 5, or 6;

h′ is 0, 1, 2, 3, 4, 5, or 6;

i L is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10; and

provided that h and h′ are not both 0;

or a pharmaceutically acceptable salt, stereoisomer, or solvate thereof,

wherein the circulating protein is VEGF; and

wherein the disease or disorder is selected from the group consisting of prostate cancer, metastatic prostate cancer, stomach cancer, colon cancer, rectal cancer, liver cancer, pancreatic cancer, lung cancer, breast cancer, cervical cancer, ovarian cancer, testicular cancer, bladder cancer, renal cancer, brain/CNS cancer, head and neck cancer, throat cancer, Hodgkin's disease, non-Hodgkin's lymphoma, multiple myeloma, leukemia, melanoma, non-melanoma skin cancer, acute lymphocytic leukemia, acute myelogenous leukemia, Ewing's sarcoma, small cell lung cancer, choriocarcinoma, rhabdomyosarcoma, Wilms' tumor, neuroblastoma, hairy cell leukemia, mouth/pharynx cancer, esophageal cancer, kidney cancer, and lymphoma.

7 . The method of claim 6 , wherein the pharmaceutical composition further comprises at least one agent 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, a VEGFR inhibitor, an EGFR TK inhibitor, an aurora kinase inhibitor, a PIK-1 modulator, a Bcl-2 inhibitor, an HDAC inhibitor, 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 inhibitor, 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 1 KRX-0402, lucanthone, LY 317615, neuradiab, vitespan, RTA 744, SDX 102, talampanel, atrasentan, XR 311, romidepsin, ADS-100380, sunitinib, 5-fluorouracil, vorinostat, etoposide, gemcitabine, doxorubicin, irinotecan, liposomal doxorubicin, 5′-deoxy-5-fluorouridine, vincristine, temozolomide, ZK-304709, seliciclib, PD0325901, AZD-6244, capecitabine, camptothecin, PEG-labeled irinotecan, tamoxifen, toremifene citrate, anastrozole, exemestane, letrozole, diethylstilbestrol, estradiol, estrogen, conjugated estrogen, bevacizumab, IMC-1C11, CHIR-258, 3-[5-(methylsulfonylpiperadinemethyl)-indolyl-quinolone, vatalanib, AG-013736, AVE-0005, pyro-Glu-His-Trp-Ser-Tyr-D-Ser(But)-Leu-Arg-Pro-Azgly-NH 2 acetate [C 59 H 84 N 18 O 14 ·(C 2 H 4 O 2 ) x , where x is 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, lonafarnib, BMS-214662, tipifarnib, amifostine, NVP-L AQ824, suberoyl analide hydroxamic acid, valproic acid, trichostatin A, FK-228, SU11248, sorafenib, KRN951, aminoglutethimide, arnsacrine, anagrelide, L-asparaginase, Bacillus Calmette-Guerin (BCG) vaccine, bleomycin, buserelin, busulfan, carboplatin, carmustine, chlorambucil, cisplatin, cladribine, clodronate, cyproterone, cytarabine, dacarbazine, dactinomycin, daunorubicin, diethylstilbestrol, epirubicin, fludarabine, fludrocortisone, fluoxymesterone, flutamide, 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, irinotecan, topotecan, doxorubicin, docetaxel, vinorelbine, bevacizumab, erbitux, cremophor-free paclitaxel, epithilone B, BMS-247550, BMS-310705, droloxifene, 4-hydroxytamoxifen, pipendoxifene, ERA-923, arzoxifene, fulvestrant, acolbifene, lasofoxifene, idoxifene, TSE-424, HMR-3339, ZK186619, 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-trans retinoic 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 and darbepoetin alfa, vemurafenib, a PD-L1 inhibitor, a PD-1 inhibitor, and a CTLA-4 inhibitor.

8 . The method of claim 6 , wherein the administration is by a route selected from the group consisting of subcutaneous, intravenous, intramuscular, intraperitoneal, transdermal, oral, buccal, sublingual, and ocular.

9 . The method of claim 6 , wherein the compound is administered in a dose of about 1 mg/kg to about 50 mg/kg.

Continuity (4)

Continuation In Part 17046221

Provisional Application 62788040 · Jan 3, 2019

Provisional Application 62655055 · Apr 9, 2018

Related Publication 20230083388A1 · Mar 16, 2023

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