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Dang F, Bai L, Dong J, Hu X, Wang J, Paulo JA, Xiong Y, Liang X, Sun Y, Chen Y, Guo M, Wang X, Huang Z, Inuzuka H, Chen L, Chu C, Liu J, Zhang T, Rezaeian AH, Liu J, Kaniskan HÜ, Zhong B, Zhang J, Letko M, Jin J, Lan K, Wei W. USP2 inhibition prevents infection with ACE2-dependent coronaviruses in vitro and is protective against SARS-CoV-2 in mice. Sci Transl Med 2023; 15:eadh7668. [PMID: 38055802 PMCID: PMC10787358 DOI: 10.1126/scitranslmed.adh7668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
Targeting angiotensin-converting enzyme 2 (ACE2) represents a promising and effective approach to combat not only the COVID-19 pandemic but also potential future pandemics arising from coronaviruses that depend on ACE2 for infection. Here, we report ubiquitin specific peptidase 2 (USP2) as a host-directed antiviral target; we further describe the development of MS102, an orally available USP2 inhibitor with viable antiviral activity against ACE2-dependent coronaviruses. Mechanistically, USP2 serves as a physiological deubiquitinase of ACE2, and targeted inhibition with specific small-molecule inhibitor ML364 leads to a marked and reversible reduction in ACE2 protein abundance, thereby blocking various ACE2-dependent coronaviruses tested. Using human ACE2 transgenic mouse models, we further demonstrate that ML364 efficiently controls disease caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), as evidenced by reduced viral loads and ameliorated lung inflammation. Furthermore, we improved the in vivo performance of ML364 in terms of both pharmacokinetics and antiviral activity. The resulting lead compound, MS102, holds promise as an oral therapeutic option for treating infections with coronaviruses that are reliant on ACE2.
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Affiliation(s)
- Fabin Dang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Lei Bai
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Jiazhen Dong
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoping Hu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jingchao Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Joao A. Paulo
- Department of Cell Biology, Blavatnik Institute at Harvard Medical School, Boston, MA 02115, USA
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xiaowei Liang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yishuang Sun
- Medical Research Institute, Wuhan University, Wuhan 430071, China
| | - Yuncai Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Ming Guo
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xin Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Zhixiang Huang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Li Chen
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Chen Chu
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Jianping Liu
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tao Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Abdol-Hossein Rezaeian
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Husnu Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bo Zhong
- Medical Research Institute, Wuhan University, Wuhan 430071, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Jinfang Zhang
- Medical Research Institute, Wuhan University, Wuhan 430071, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Michael Letko
- Paul G. Allen School for Global Health, Washington State University, Pullman, WA 99163 USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ke Lan
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Medical Research Institute, Wuhan University, Wuhan 430071, China
- TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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Salas-Estrada L, Provasi D, Qiu X, Kaniskan HÜ, Huang XP, DiBerto JF, Lamim Ribeiro JM, Jin J, Roth BL, Filizola M. De Novo Design of κ-Opioid Receptor Antagonists Using a Generative Deep-Learning Framework. J Chem Inf Model 2023; 63:5056-5065. [PMID: 37555591 PMCID: PMC10466374 DOI: 10.1021/acs.jcim.3c00651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Indexed: 08/10/2023]
Abstract
Likely effective pharmacological interventions for the treatment of opioid addiction include attempts to attenuate brain reward deficits during periods of abstinence. Pharmacological blockade of the κ-opioid receptor (KOR) has been shown to abolish brain reward deficits in rodents during withdrawal, as well as to reduce the escalation of opioid use in rats with extended access to opioids. Although KOR antagonists represent promising candidates for the treatment of opioid addiction, very few potent selective KOR antagonists are known to date and most of them exhibit significant safety concerns. Here, we used a generative deep-learning framework for the de novo design of chemotypes with putative KOR antagonistic activity. Molecules generated by models trained with this framework were prioritized for chemical synthesis based on their predicted optimal interactions with the receptor. Our models and proposed training protocol were experimentally validated by binding and functional assays.
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Affiliation(s)
- Leslie Salas-Estrada
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Davide Provasi
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xing Qiu
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Husnu Ümit Kaniskan
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xi-Ping Huang
- National
Institute of Mental Health, Psychoactive Drug Screening Program, Department
of Pharmacology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Jeffrey F. DiBerto
- National
Institute of Mental Health, Psychoactive Drug Screening Program, Department
of Pharmacology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - João Marcelo Lamim Ribeiro
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Jian Jin
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
- Mount
Sinai Center for Therapeutics Discovery, Departments of Oncological
Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Bryan L. Roth
- National
Institute of Mental Health, Psychoactive Drug Screening Program, Department
of Pharmacology, University of North Carolina
School of Medicine, Chapel Hill, North Carolina 27599, United States
- Division
of Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill Eshelman School of Pharmacy, Chapel Hill, North Carolina 27599, United States
| | - Marta Filizola
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, New York, New York 10029, United States
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Park K, Qin L, Kabir M, Luo K, Dale B, Zhong Y, Kim A, Wang GG, Kaniskan HÜ, Jin J. Targeted Degradation of PRC1 Components, BMI1 and RING1B, via a Novel Protein Complex Degrader Strategy. Adv Sci (Weinh) 2023; 10:e2205573. [PMID: 36737841 PMCID: PMC10074066 DOI: 10.1002/advs.202205573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Polycomb repressive complex 1 (PRC1) is an essential epigenetic regulator that mainly controls histone H2A Lys119 mono-ubiquitination (H2AK119ub). B cell-specific Moloney murine leukemia virus Integration site 1 (BMI1) and really interesting new gene 1B (RING1B) are PRC1 core components and play critical roles in the development of various cancers. However, therapeutic agents targeting PRC1 are very limited. In this study, MS147, the first degrader of PRC1 core components, BMI1 and RING1B, is discovered via a novel protein complex degradation strategy that utilizes the target protein's interacting partner protein (embryonic ectoderm development (EED)). MS147, which comprises an EED small-molecule binder linked to a ligand of the E3 ligase von Hippel-Lindau (VHL), degrades BMI1/RING1B in an EED-, VHL-, ubiquitination-, and time-dependent manner. MS147 preferentially degrades BMI1/RING1B over polycomb repressive complex 2 (PRC2) core components. Consequently, MS147 effectively reduces H2AK119ub, but not histone H3 Lys27 tri-methylation (H3K27me3), which is catalyzed by PRC2. Furthermore, MS147 effectively inhibits the proliferation of cancer cell lines that are insensitive to PRC2 inhibitors/degraders. Overall, this study provides a novel BMI1/RING1B degrader, which is a useful chemical tool to further investigate the roles of PRC1 in cancer, and a novel protein complex degradation strategy, which can potentially expand the degradable human proteome.
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Affiliation(s)
- Kwang‐Su Park
- Mount Sinai Center for Therapeutics DiscoveryDepartments of Pharmacological SciencesOncological Sciences and NeuroscienceTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNY10029USA
| | - Lihuai Qin
- Mount Sinai Center for Therapeutics DiscoveryDepartments of Pharmacological SciencesOncological Sciences and NeuroscienceTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNY10029USA
| | - Md Kabir
- Mount Sinai Center for Therapeutics DiscoveryDepartments of Pharmacological SciencesOncological Sciences and NeuroscienceTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNY10029USA
| | - Kaixiu Luo
- Mount Sinai Center for Therapeutics DiscoveryDepartments of Pharmacological SciencesOncological Sciences and NeuroscienceTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNY10029USA
| | - Brandon Dale
- Mount Sinai Center for Therapeutics DiscoveryDepartments of Pharmacological SciencesOncological Sciences and NeuroscienceTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNY10029USA
| | - Yue Zhong
- Mount Sinai Center for Therapeutics DiscoveryDepartments of Pharmacological SciencesOncological Sciences and NeuroscienceTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNY10029USA
| | - Arum Kim
- Lineberger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNC27514USA
- Department of Biochemistry and BiophysicsUniversity of North Carolina at Chapel HillChapel HillNC27514USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer CenterUniversity of North Carolina at Chapel HillChapel HillNC27514USA
- Department of Biochemistry and BiophysicsUniversity of North Carolina at Chapel HillChapel HillNC27514USA
- Department of PharmacologyUniversity of North Carolina at Chapel HillChapel HillNC27514USA
| | - Husnu Ümit Kaniskan
- Mount Sinai Center for Therapeutics DiscoveryDepartments of Pharmacological SciencesOncological Sciences and NeuroscienceTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNY10029USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics DiscoveryDepartments of Pharmacological SciencesOncological Sciences and NeuroscienceTisch Cancer InstituteIcahn School of Medicine at Mount SinaiNew YorkNY10029USA
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4
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Kaniskan HÜ, Eram MS, Liu J, Smil D, Martini ML, Shen Y, Santhakumar V, Brown PJ, Arrowsmith C, Vedadi M, Jin J. Design and synthesis of selective, small molecule inhibitors of coactivator-associated arginine methyltransferase 1 (CARM1). Medchemcomm 2016; 7:1793-1796. [PMID: 28042453 DOI: 10.1039/c6md00342g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1) is a type I protein arginine methyltransferase (PRMT) that catalyzes the conversion of arginine into monomethylarginine (MMA) and further into asymmetric dimethylarginine (ADMA). CARM1 methylates histone 3 arginines 17 and 26, as well as numerous non-histone proteins including CBP/p300, SRC-3, NCOA2, PABP1, and SAP49, while also functioning as a coactivator for various proteins that have been linked to cancer such as p53, NF-κβ, β-catenin, E2F1 and steroid hormone receptor ERα. As a result, CARM1 is involved in transcriptional activation, cellular differentiation, cell cycle progression, RNA splicing and DNA damage response. It has been associated with several human cancers including breast, colon, prostate and lung cancers and thus, is a potential oncological target. Herein, we present the design and synthesis of a series of CARM1 inhibitors. Based on a fragment hit, we discovered compound 9 as a potent inhibitor that displayed selectivity for CARM1 over other PRMTs.
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Affiliation(s)
- H Ü Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - M S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - J Liu
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - D Smil
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - M L Martini
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Y Shen
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - V Santhakumar
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - P J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - C Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, Canada
| | - M Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - J Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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