IP Library Granted Patent US 12,410,171
Granted Patent B2
US 12,410,171 · App. 17/904,822 · Granted Sep 9, 2025

Tropomyosin receptor kinase (TRK) degradation compounds and methods of use

Inventors: Jing Liu (Oradell, NJ); Jialiang Wang (Nashville, TN); Xiaoran Han (Shanghai, CN); Liqun Chen (Shanghai, CN); Chengwei Zhang (Shanghai, CN)
Assignee: CULLGEN (SHANGHAI), INC.
C07D487/04C07D405/14C07D417/14C07D471/04
View Patent ↗
Loading inventors, assignments & file history…
Monitor This Case
Get email alerts when status or documents change.
Order Certified Copies
Most orders are placed with the USPTO same day — all within 24 business hours.
Order via The Patent Place →
Pre-filled with this patent's details
Quick Facts
Patent No.
US 12,410,171
App. No.
17/904,822
Granted
Sep 9, 2025
Kind
B2
Abstract

This disclosure relates to bivalent compounds (e.g., bi-functional small molecule compounds), compositions comprising one or more of the bivalent compounds, and to methods of use the bivalent compounds for the treatment of certain disease in a subject in need thereof. The disclosure also relates to methods for identifying such bivalent compounds.

Claims (15)

1. A bivalent compound, selected from the group consisting of:

(S)-N-(5-(3,5-Difluorobenzyl)-1H-indazol-3-yl)-4-(4-((1-(2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-5-yl)azetidin-3-yl)methyl)piperazin-1-yl)-2-((tetrahydro-2H-pyran-4-yl)amino)benzamide (TR-341); and

(R)-N-(5-(3,5-Difluorobenzyl)-1H-indazol-3-yl)-4-(4-((1-(2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-5-yl)azetidin-3-yl)methyl)piperazin-1-yl)-2-((tetrahydro-2H-pyran-4-yl)amino)benzamide (TR-342);

or a pharmaceutically acceptable salt thereof.

2. The bivalent compound of claim 1 , which is(S)-N-(5-(3,5-Difluorobenzyl)-1H-indazol-3-yl)-4-(4-((1-(2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-5-yl)azetidin-3-yl)methyl)piperazin-1-yl)-2-((tetrahydro-2H-pyran-4-yl)amino)benzamide (TR-341), or a pharmaceutically acceptable salt thereof.

3. The bivalent compound of claim 1 , which is (R)-N-(5-(3,5-Difluorobenzyl)-1H-indazol-3-yl)-4-(4-((1-(2-(2,6-dioxopiperidin-3-yl)-1,3-dioxoisoindolin-5-yl)azetidin-3-yl)methyl)piperazin-1-yl)-2-((tetrahydro-2H-pyran-4-yl)amino)benzamide (TR-342), or a pharmaceutically acceptable salt thereof.

4. A pharmaceutical composition comprising a bivalent compound of claim 1 , or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier or diluent.

5. A method of treating a tropomyosin receptor kinase (TRK)-mediated disease, comprising administering to a subject with a TRK-mediated disease a bivalent compound of claim 1 , or a pharmaceutically acceptable salt thereof.

6. The method of claim 5 , wherein the TRK-mediated disease results from TRK expression, mutation, splicing, or fusion.

7. The method of claim 5 , wherein the TRK-mediated disease is cancer.

8. The method of claim 7 , wherein the cancer is a relapsed cancer.

9. The method of claim 7 , wherein the cancer is refractory to one or more previous treatments.

10. The method of claim 7 , further comprising administering to the subject an additional therapeutic regimen for treating cancer.

11. The method of claim 10 , wherein the additional therapeutic regimen is selected from the group consisting of surgery, chemotherapy, radiation therapy, hormone therapy, and immunotherapy.

12. The method of claim 5 , wherein the TRK-mediated disease is acute pain or chronic pain.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Jan 9, 2023
From: LIU, JING; PLEWE, MICHAEL BRUNO; WANG, JIALIANG; HAN, XIAORAN; CHEN, LIQUN; ZHANG, CHENGWEI
To: CULLGEN (SHANGHAI), INC.
Reel/Frame 062314/0507 →
Priority Claims (1)
WO PCT/CN2020/076748 · Feb 26, 2020 · international
Continuity (1)
Related Publication 20230257380A1 · Aug 17, 2023
References Cited (169)
US 6306663B1 · Kenten et al. · 2001 [cited by applicant]
US 6559280B2 · Kenten et al. · 2003 [cited by applicant]
US 7074620B2 · Kenten et al. · 2006 [cited by applicant]
US 7273920B2 · Kenten et al. · 2007 [cited by applicant]
US 8299057B2 · Lombardi Borgia et al. · 2012 [cited by applicant]
US 8507488B2 · Albaugh et al. · 2013 [cited by applicant]
US 8673893B2 · Lombardi Borgia et al. · 2014 [cited by applicant]
US 9029356B2 · Lombardi Borgia et al. · 2015 [cited by applicant]
US 9085558B2 · Lombardi Borgia et al. · 2015 [cited by applicant]
US 9102662B2 · Lombardi Borgia et al. · 2015 [cited by applicant]
US 9255087B2 · Lombardi Borgia et al. · 2016 [cited by applicant]
US 9500653B2 · Crews et al. · 2016 [cited by applicant]
US 9616059B2 · Lombardi Borgia et al. · 2017 [cited by applicant]
US 9632089B2 · Crews et al. · 2017 [cited by applicant]
US 9758522B2 · Gray et al. · 2017 [cited by applicant]
US 9765019B2 · Hedstrom et al. · 2017 [cited by applicant]
US 9821068B2 · Bradner et al. · 2017 [cited by applicant]
US 9938264B2 · Crews et al. · 2018 [cited by applicant]
US 9938302B2 · Chan et al. · 2018 [cited by applicant]
US 10040804B2 · Chan et al. · 2018 [cited by applicant]
US 10081622B2 · Lombardi Borgia et al. · 2018 [cited by applicant]
US 10144745B2 · Chan et al. · 2018 [cited by applicant]
US 10145848B2 · Crews et al. · 2018 [cited by applicant]
US 10730862B2 · Crews et al. · 2020 [cited by applicant]
US 10730870B2 · Crew et al. · 2020 [cited by applicant]
US 10849980B2 · Bradner et al. · 2020 [cited by applicant]
US 12065442B2 · Liu · 2024 [cited by examiner]
US 20110263595A1 · Zhang et al. · 2011 [cited by applicant]
US 20120065233A1 · Gregor et al. · 2012 [cited by applicant]
US 20120108568A1 · Allen et al. · 2012 [cited by applicant]
US 20140356322A1 · Crews et al. · 2014 [cited by applicant]
US 20150119435A1 · Crews et al. · 2015 [cited by applicant]
US 20150291562A1 · Crew et al. · 2015 [cited by applicant]
US 20160058872A1 · Crew et al. · 2016 [cited by applicant]
US 20160272639A1 · Crew et al. · 2016 [cited by applicant]
US 20170037004A1 · Crew et al. · 2017 [cited by applicant]
US 20170065719A1 · Qian et al. · 2017 [cited by applicant]
US 20180050021A1 · Ciulli et al. · 2018 [cited by applicant]
US 20180118733A1 · Harling et al. · 2018 [cited by applicant]
US 20180186785A1 · Crews et al. · 2018 [cited by applicant]
US 20180215731A1 · Crew et al. · 2018 [cited by applicant]
US 20180228907A1 · Crew et al. · 2018 [cited by applicant]
US 20180298027A1 · Chan et al. · 2018 [cited by applicant]
US 20190127359A1 · Crews et al. · 2019 [cited by applicant]
US 20190151457A1 · Bradner et al. · 2019 [cited by applicant]
US 20190241546A1 · Lombardi Borgia et al. · 2019 [cited by applicant]
US 20200155689A1 · Crew et al. · 2020 [cited by applicant]
US 20200155690A1 · Crew et al. · 2020 [cited by applicant]
US 20200306273A1 · Yang et al. · 2020 [cited by applicant]
US 20200392131A1 · Crew et al. · 2020 [cited by applicant]
US 20210315999A1 · Liu et al. · 2021 [cited by applicant]
US 20210363146A1 · Liu et al. · 2021 [cited by applicant]
US 20240400570A1 · Liu et al. · 2024 [cited by applicant]
CA 3085645A1 · 2019 [cited by examiner]
CN 104736569A · 2015 [cited by applicant]
CN 105085620A · 2015 [cited by applicant]
CN 106456582A · 2017 [cited by applicant]
CN 106458993A · 2017 [cited by applicant]
CN 106543185A · 2017 [cited by applicant]
CN 108366992A · 2018 [cited by applicant]
CN 108601764A · 2018 [cited by applicant]
CN 109912655A · 2019 [cited by applicant]
EP 3131588A4 · 2018 [cited by applicant]
EP 3608317A1 · 2020 [cited by applicant]
WO WO2007027527A2 · 2007 [cited by applicant]
WO WO2009013126A1 · 2009 [cited by applicant]
WO WO2013106643A2 · 2013 [cited by applicant]
WO WO2013170147A1 · 2013 [cited by applicant]
WO WO2015112445A1 · 2015 [cited by applicant]
WO WO2015160845A2 · 2015 [cited by applicant]
WO WO2016096709A1 · 2016 [cited by applicant]
WO WO2016146985A1 · 2016 [cited by applicant]
WO WO2016149668A1 · 2016 [cited by applicant]
WO WO2016169989A1 · 2016 [cited by applicant]
WO WO2016201328A1 · 2016 [cited by applicant]
WO WO2017011371A1 · 2017 [cited by applicant]
WO WO2017176957A1 · 2017 [cited by applicant]
WO WO2017176958A1 · 2017 [cited by applicant]
WO WO2017180417A1 · 2017 [cited by applicant]
WO WO2017197046A1 · 2017 [cited by applicant]
WO WO2017197051A1 · 2017 [cited by applicant]
WO WO2017197055A1 · 2017 [cited by applicant]
WO WO2017204445A2 · 2017 [cited by applicant]
WO WO2017212329A1 · 2017 [cited by applicant]
WO WO2017223452A1 · 2017 [cited by applicant]
WO WO2018052949A1 · 2018 [cited by applicant]
WO WO2018071606A1 · 2018 [cited by applicant]
WO WO2018089736A1 · 2018 [cited by applicant]
WO WO2018102067A2 · 2018 [cited by applicant]
WO WO2018118598A1 · 2018 [cited by applicant]
WO WO2018119357A1 · 2018 [cited by applicant]
WO WO2018119441A1 · 2018 [cited by applicant]
WO WO2018119448A1 · 2018 [cited by applicant]
WO WO2018140809A1 · 2018 [cited by applicant]
WO WO2018144649A1 · 2018 [cited by applicant]
WO WO2018189554A1 · 2018 [cited by applicant]
WO WO2018223909A1 · 2018 [cited by applicant]
WO WO2018226542A1 · 2018 [cited by applicant]
WO WO2019114770A1 · 2019 [cited by applicant]
WO WO2020023549A1 · 2020 [cited by applicant]
WO WO2020038415A1 · 2020 [cited by applicant]
WO WO2021170109A1 · 2021 [cited by applicant]
WO WO2023055952A1 · 2023 [cited by applicant]
Golub et al., Science, vol. 286, Oct. 15, 1999, pp. 531-537 (Year: 1999). [cited by examiner]
Aguilar et al. Discovery of 4-((3′R,4′S,5′R)-6″-Chloro-4′-(3-chloro-2-fluorophenyl)-1′-ethyl-2″-oxodispiro[cyclohexane-1,2′-pyrrolidine-3′,3″-indoline]-5′-carboxamido)bicyclo[2.2.2]octane-1-carboxylic Acid (AA-115/APG-1… [cited by applicant]
Amatu et al. NTRK gene fusions as novel targets of cancer therapy across multiple tumour types. ESMO Open 1(2):e000023 (2016). [cited by applicant]
Bailey et al. Tropomyosin receptor kinase inhibitors: an updated patent review for 2010-2016—Part II. Expert Opinion on Therapeutic Patents 27(7):831-849 (2017). [cited by applicant]
Blake et al. The development of LOXO-195, a second generation TRK kinase inhibitor that overcomes acquired resistance to 1st generation inhibitors observed in patients with TRK-fusion cancers. Eur J Cancer 69:S144-S145 … [cited by applicant]
Bondeson, et al., Catalytic in vivo protein knockdown by small-molecule PROTACs. Nat Chem Biol 11(8):611-617 (Aug. 2015). [cited by applicant]
Brasca et al. Identification of N, 1,4,4-tetramethyl-8-{[4-(4-methylpiperazin-1-yl)phenyl]amino}-4,5-dihydro-1H-py razolo[4,3-h]quinazoline-3-carboxamide (PHA-848125), a potent, orally available cyclin dependent kinase … [cited by applicant]
Buckley et al. HaloPROTACS: Use of Small Molecule PROTACs to Induce Degradation of HaloTag Fusion Proteins. ACS Chem Biol 10:1831-1837 (2015). [cited by applicant]
Buckley et al. Small-molecule control of intracellular protein levels through modulation of the ubiquitin proteasome system. Angew Chem Int Ed Engl 53:2312-2330 (2014). [cited by applicant]
Buckley et al. Small-molecule inhibitors of the interaction between the E3 ligase VHL and HIF1α. Angew Chem Int Ed Engl 51:11463-11467 (2012). [cited by applicant]
Buckley et al. Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1alpha interaction. J Am Chem Soc 134:4465-4468 (2012). [cited by applicant]
Chamberlain et al. Structure of the human Cereblon-DDB1-lenalidomide complex reveals basis for responsiveness to thalidomide analogs. Nat Struct Mol Biol 21:803-809 (2014). [cited by applicant]
Chen et al., Discovery of first-in-class potent and selective tropomyosin receptor kinase degraders. J. Med. Chem. 63(23):14562-14575 (2020). [cited by applicant]
Choi et al. (R)-2-Phenylpyrrolidine Substituted Imidazopyridazines: A New Class of Potent and Selective Pan-TRK Inhibitors. ACS Med Chem Lett 6:562-567 (2015). [cited by applicant]
Chong et al. Identification of Existing Drugs That Effectively Target NTRK1 and ROS1 Rearrangements in Lung Cancer. Clin Cancer Res 23:204-213 (2017). [cited by applicant]
Cranston et al. Tropomyosin Receptor Antagonism in Cylindromatosis (TRAC), an early phase trial of a topical tropomyosin kinase inhibitor as a treatment for inherited CYLD defective skin tumours: study protocol for a ra… [cited by applicant]
Cui et al. TPX-0005, a novel ALK/ROS1/TRK inhibitor, effectively inhibited a broad spectrum of mutations including solvent front ALK G1202R, ROS1 G2032R and TRKA G595R mutants. Eur J Cancer 69:S32 (2016). [cited by applicant]
Davies et al. Monoacidic Inhibitors of the Kelch-like ECH-Associated Protein 1: Nuclear Factor Erythroid 2-Related Factor 2 (KEAP1:NRF2) Protein-Protein Interaction with High Cell Potency Identified by Fragment-Based Di… [cited by applicant]
Denk et al. Nerve Growth Factor and Pain Mechanisms. Annual review of neuroscience 40:307-325 (2017). [cited by applicant]
Drilon et al. Efficacy of Larotrectinib in TRK Fusion-Positive Cancers in Adults and Children. N Engl J Med 378:731-739 (2018). [cited by applicant]
Drilon et al. Safety and Antitumor Activity of the Multitargeted Pan-TRK, ROS1, and ALK Inhibitor Entrectinib: Combined Results from Two Phase I Trials (ALKA-372-001 and STARTRK-1). Cancer discovery 7:400-409 (2017). [cited by applicant]
Fischer et al. Structure of the DDB1-CRBN E3 ubiquitin ligase in complex with thalidomide. Nature 512:49-53 (2014). [cited by applicant]
Fujiwara et al. Safety and pharmacokinetics of DS-6051b in Japanese patients with non-small cell lung cancer harboring ROS1 fusions: a phase I study. Oncotarget 9:23729-23737 (2018). [cited by applicant]
Fuse et al. Mechanisms of Resistance to NTRK Inhibitors and Therapeutic Strategies in NTRK1-Rearranged Cancers. Mol Cancer Ther 16, 2130-2143 (2017). [cited by applicant]
Galdeano et al. Structure-guided design and optimization of small molecules targeting the protein-protein interaction between the von Hippel-Lindau (VHL) E3 ubiquitin ligase and the hypoxia inducible factor (HIF) alpha … [cited by applicant]
Hiroyuki et al. The structure of bestatin. The Journal of Antibiotic 20:100-101 (1976). [cited by applicant]
Ito et al. Identification of a primary target of thalidomide teratogenicity. Science 327:1345-1350 (2010). [cited by applicant]
Khotskaya et al. Targeting TRK family proteins in cancer. Pharmacol Ther 173:58-66 (2017). [cited by applicant]
Lai et al. Modular PROTAC Design for the Degradation of Oncogenic BCR-ABL. Angew chem Int Ed Engl. 55:807-810 (2016). [cited by applicant]
Li et al. Trk inhibitor attenuates the BDNF/TrkB-induced protection of neuroblastoma cells from etoposide in vitro and in vivo. Cancer Biol Ther 16:477-483 (2015). [cited by applicant]
Lu et al., Hijacking the E3 ubiquitin ligase cereblon to efficiently target BRD4. Chem Biol. 22(6):755-763 (2015). [cited by applicant]
Maniaci et al. Homo-PROTACs: bivalent small-molecule dimerizers of the VHL E3 ubiquitin ligase to induce self-degradation. Nat Commun 8:830 (2017). [cited by applicant]
Menichincheri et al. Discovery of Entrectinib: A New 3-Aminoindazole As a Potent Anaplastic Lymphoma Kinase (ALK), c-ros Oncogene 1 Kinase (ROS1), and Pan-Tropomyosin Receptor Kinases (Pan-TRKs) inhibitor. J Med Chem 59… [cited by applicant]
Miller et al. Nerve growth factor blockade for the management of osteoarthritis pain: what can we learn from clinical trials and preclinical models? Current opinion in rheumatology 29:110-118 (2017). [cited by applicant]
Ohoka et al. In Vivo Knockdown of Pathogenic Proteins via Specific and Nongenetic Inhibitor of Apoptosis Protein (IAP)-dependent Protein Erasers (SNIPERs). J Biol Chem 292:4556-4570 (2017). [cited by applicant]
Okuhira et al. Specific degradation of CRABP-II via cIAP1-mediated ubiquitylation induced by hybrid molecules that crosslink cIAP1 and the target protein. FEBS Lett 585:1147-1152 (2011). [cited by applicant]
Patwardhan et al. Significant blockade of multiple receptor tyrosine kinases by MGCD516 (Sitravatinib), a novel small molecule inhibitor, shows potent anti-tumor activity in preclinical models of sarcoma. Oncotarget 7:4… [cited by applicant]
PCT/CN2019/101850 International Search Report and Written Opinion dated Nov. 20, 2019. [cited by applicant]
PCT/CN2021/078240 International Search Report dated Jul. 7, 2021. [cited by applicant]
Raina and Crews et al., Targeted protein knockdown using small molecule degraders. Curr Opin Chem Biol. 39:46-53 (2017). [cited by applicant]
Ricciuti et al. Targeting NTRK fusion in non-small cell lung cancer: rationale and clinical evidence. Med Oncol 34:105 (2017). [cited by applicant]
Robinson et al. The protein tyrosine kinase family of the human genome. Oncogene 19(49):5548-57 (2000). [cited by applicant]
Sakamoto et al., Protacs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation. PNAS USA 98(15):8554-8559 (2001). [cited by applicant]
Schnitzer et al. A systematic review of the efficacy and general safety of antibodies to NGF in the treatment of OA of the hip or knee. Osteoarthritis and cartilage 23(Suppl 1):S8-17 (2015). [cited by applicant]
Shibata et al. Development of protein degradation inducers of oncogenic BCR-ABL protein by conjugation of ABL kinase inhibitors and IAP ligands. Cancer Sci 108:1657-1666 (2017). [cited by applicant]
Skerratt et al. The Discovery of a Potent, Selective, and Peripherally Restricted Pan-Trk Inhibitor (PF-06273340) for the Treatment of Pain. J Med Chem 59:10084-10099 (2016). [cited by applicant]
Smith et al. Altiratinib Inhibits Tumor Growth, Invasion, Angiogenesis, and Microenvironment-Mediated Drug Resistance via Balanced Inhibition of MET, TIE2, and VEGFR2. Mol Cancer Ther 14:2023-2034 (2015). [cited by applicant]
Subbiah et al. First-in-human trial of multikinase VEGF inhibitor regorafenib and anti-EGFR antibody cetuximab in advanced cancer patients. JCI Insight 2(8): e90380 (2017). [cited by applicant]
Sun et al. Discovery of AMG 232, a potent, selective, and orally bioavailable MDM2-p53 inhibitor in clinical development. J Med Chem 57:1454-1472 (2014). [cited by applicant]
Tatematsu et al. Investigation of neurotrophic tyrosine kinase receptor 1 fusions and neurotrophic tyrosine kinase receptor family expression in non-small-cell lung cancer and sensitivity to AZD7451 in vitro. Mol Clin O… [cited by applicant]
Varfolomeev et al. IAP antagonists induce autoubiquitination of c-IAPs, NF-kappaB activation, and TNFalpha-dependent apoptosis. Cell 131:669-681 (2007). [cited by applicant]
Vassilev et al. In vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Science 303:844-848 (2004). [cited by applicant]
Vu et al. Discovery of RG7112: A Small-Molecule MDM2 Inhibitor in Clinical Development. ACS Med Chem Lett 4:466-469 (2013). [cited by applicant]
Wakeling. Use of pure antioestrogens to elucidate the mode of action of oestrogens. Biochem Pharmacol 49:1545-1549 (1995). [cited by applicant]
Weisberg et al. Smac mimetics: implications for enhancement of targeted therapies in leukemia. Leukemia 24:2100-2109 (2010). [cited by applicant]
Winter et al. Phthalimide conjugation as a strategy for in vivo target protein degradation. Science 348:1376-1381 (2015). [cited by applicant]
Xie et al. Pharmacological targeting of the pseudokinase Her3. Nat Chem Biol 10, 1006-1012 (2014). [cited by applicant]
Zengerle et al. Selective Small Molecule Induced Degradation of the BET Bromodomain Protein BRD4. ACS Chem Biol 10:1770-1777 (2015). [cited by applicant]
Rolfo, Christian et al. Entrectinib: a potent new Trk, ROS1, and ALK inhibitor. Expert Opin Investig Drugs 24(11):1493-1500 (2015). [cited by applicant]
U.S. Appl. No. 17/239,356 Office Action dated May 31, 2023. [cited by applicant]
U.S. Appl. No. 17/269,670 Office Action dated Sep. 26, 2023. [cited by applicant]
Bailey et al. Tropomyosin receptor kinase inhibitors: an updated patent review for 2010-2016—Part I. Expert Opin Ther Pat 27:733-751 (2017). [cited by applicant]
Dean, Dennis C. Recent Advances in the Synthesis and Applications of Radiolabeled Compounds for Drug Discovery and Development. Current Pharmaceutical Design 6:1-2 (2000). [cited by applicant]
Evans, Anthony E. Synthesis of Radiolabeled Compounds. Journal of Radioanalytical and Nuclear Chemistry 64(1-2):9-32 (1981). [cited by applicant]
Kabalka, George W. et al. The Synthesis of Radiolabeled Compounds via Organometallic Intermediates. Tetrahedron 45(21):6601-6621 (1989). [cited by applicant]
Zhao, Bosheng et al. TrkC-Targeted Kinase Inhibitors And PROTACs. Mol PHarm 16(10):4313-4318 (2019). [cited by applicant]