1
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Lucas SCC, Blackwell JH, Börjesson U, Hargreaves D, Milbradt AG, Bostock MJ, Ahmed S, Beaumont K, Cheung T, Demanze S, Gohlke A, Guerot C, Haider A, Kantae V, Kauffman GW, Kinzel O, Kupcova L, Lainchbury MD, Lamb ML, Leon L, Palisse A, Sacchetto C, Storer RI, Su N, Thomson C, Vales J, Chen Y, Hu X. Structure-Based Optimization of a Series of Covalent, Cell Active Bfl-1 Inhibitors. J Med Chem 2024. [PMID: 39291659 DOI: 10.1021/acs.jmedchem.4c01288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Bfl-1, a member of the Bcl-2 family of proteins, plays a crucial role in apoptosis regulation and has been implicated in cancer cell survival and resistance to venetoclax therapy. Due to the unique cysteine residue in the BH3 binding site, the development of covalent inhibitors targeting Bfl-1 represents a promising strategy for cancer treatment. Herein, the optimization of a covalent cellular tool from a lead-like hit using structure based design is described. Informed by a reversible X-ray fragment screen, the strategy to establish interactions with a key glutamic acid residue (Glu78) and optimize binding in a cryptic pocket led to a 1000-fold improvement in biochemical potency without increasing reactivity of the warhead. Compound (R,R,S)-26 has a kinact/KI of 4600 M-1 s-1, shows <1 μM caspase activation in a cellular assay and cellular target engagement, and has good physicochemical properties and a promising in vivo profile.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - J Henry Blackwell
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Ulf Börjesson
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - David Hargreaves
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Alexander G Milbradt
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Mark J Bostock
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Samiyah Ahmed
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | | | - Tony Cheung
- Oncology Bioscience, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Sylvain Demanze
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Andrea Gohlke
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Carine Guerot
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Afreen Haider
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Vasudev Kantae
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Gregory W Kauffman
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Olaf Kinzel
- Medicinal Chemistry, Oncology R&D, Acerta B.V., a Member of the AstraZeneca Group, Oss 5349, The Netherlands
| | - Lea Kupcova
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | | | - Michelle L Lamb
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Leonardo Leon
- Oncology Bioscience, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Adeline Palisse
- Medicinal Chemistry, Oncology R&D, Acerta B.V., a Member of the AstraZeneca Group, Oss 5349, The Netherlands
| | - Claudia Sacchetto
- Bioscience, Oncology R&D, Acerta B.V., a Member of the AstraZeneca Group, Oss 5349, The Netherlands
| | - R Ian Storer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Nancy Su
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Clare Thomson
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - John Vales
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Yunhua Chen
- Pharmaron Beijing Co., Ltd., Beijing 100176, P. R. China
| | - Xiaolong Hu
- Pharmaron Beijing Co., Ltd., Beijing 100176, P. R. China
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2
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Lou J, Zhou Q, Lyu X, Cen X, Liu C, Yan Z, Li Y, Tang H, Liu Q, Ding J, Lu Y, Huang H, Xie H, Zhao Y. Discovery of a Covalent Inhibitor That Overcame Resistance to Venetoclax in AML Cells Overexpressing BFL-1. J Med Chem 2024; 67:10795-10830. [PMID: 38913996 DOI: 10.1021/acs.jmedchem.4c00291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Clinical and biological studies have shown that overexpression of BFL-1 is one contributing factor to venetoclax resistance. The resistance might be overcome by a potent BFL-1 inhibitor, but such an inhibitor is rare. In this study, we show that 56, featuring an acrylamide moiety, inhibited the BFL-1/BID interaction with a Ki value of 105 nM. More interestingly, 56 formed an irreversible conjugation adduct at the C55 residue of BFL-1. 56 was a selective BFL-1 inhibitor, and its MCL-1 binding affinity was 10-fold weaker, while it did not bind BCL-2 and BCL-xL. Mechanistic studies showed that 56 overcame venetoclax resistance in isogenic AML cell lines MOLM-13-OE and MV4-11-OE, which both overexpressed BFL-1. More importantly, 56 and venetoclax combination promoted stronger apoptosis induction than either single agent. Collectively, our data show that 56 overcame resistance to venetoclax in AML cells overexpressing BFL-1. These attributes make 56 a promising candidate for future optimization.
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MESH Headings
- Humans
- Sulfonamides/pharmacology
- Sulfonamides/chemistry
- Sulfonamides/chemical synthesis
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Bridged Bicyclo Compounds, Heterocyclic/chemistry
- Drug Resistance, Neoplasm/drug effects
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Proto-Oncogene Proteins c-bcl-2/antagonists & inhibitors
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/chemical synthesis
- Cell Line, Tumor
- Minor Histocompatibility Antigens/metabolism
- Apoptosis/drug effects
- Drug Discovery
- Structure-Activity Relationship
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Affiliation(s)
- Jianfeng Lou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Qianqian Zhou
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xilin Lyu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
| | - Xinyi Cen
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chen Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Ziqin Yan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
| | - Yan Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
| | - Haotian Tang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Qiupei Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
| | - Jian Ding
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Ye Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - He Huang
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hua Xie
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, PR China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Yujun Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Rd. Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- Shandong Provincial Key Laboratory of Biopharmaceuticals, Shandong Academy of Pharmaceutical Sciences, Jinan 250101, China
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, School of Pharmacy, Ningxia Medical University, Yinchuan 750004, China
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3
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Lucas SCC, Blackwell JH, Börjesson U, Hargreaves D, Milbradt AG, Ahmed S, Bostock MJ, Guerot C, Gohlke A, Kinzel O, Lamb ML, Selmi N, Stubbs CJ, Su N, Su Q, Luo H, Xiong T, Zuo X, Bazzaz S, Bienstock C, Centrella PA, Denton KE, Gikunju D, Guié MA, Guilinger JP, Hupp C, Keefe AD, Satoh T, Zhang Y, Rivers EL. Identification and Evaluation of Reversible Covalent Binders to Cys55 of Bfl-1 from a DNA-Encoded Chemical Library Screen. ACS Med Chem Lett 2024; 15:791-797. [PMID: 38894895 PMCID: PMC11181504 DOI: 10.1021/acsmedchemlett.4c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Bfl-1 is overexpressed in both hematological and solid tumors; therefore, inhibitors of Bfl-1 are highly desirable. A DNA-encoded chemical library (DEL) screen against Bfl-1 identified the first known reversible covalent small-molecule ligand for Bfl-1. The binding was validated through biophysical and biochemical techniques, which confirmed the reversible covalent mechanism of action and pointed to binding through Cys55. This represented the first identification of a cyano-acrylamide reversible covalent compound from a DEL screen and highlights further opportunities for covalent drug discovery through DEL screening. A 10-fold improvement in potency was achieved through a systematic SAR exploration of the hit. The more potent analogue compound 13 was successfully cocrystallized in Bfl-1, revealing the binding mode and providing further evidence of a covalent interaction with Cys55.
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Affiliation(s)
- Simon C. C. Lucas
- Hit
Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
| | - J. Henry Blackwell
- Hit
Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
| | - Ulf Börjesson
- Hit
Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - David Hargreaves
- Mechanistic
and Structural Biology, Discovery Sciences, R&DAstraZeneca, Cambridge CB2 0AA, U.K.
| | - Alexander G. Milbradt
- Mechanistic
and Structural Biology, Discovery Sciences, R&DAstraZeneca, Cambridge CB2 0AA, U.K.
| | - Samiyah Ahmed
- Discovery
Biology, Discovery Sciences, R&DAstraZeneca, Cambridge CB2 0AA, U.K.
| | - Mark J. Bostock
- Mechanistic
and Structural Biology, Discovery Sciences, R&DAstraZeneca, Cambridge CB2 0AA, U.K.
| | - Carine Guerot
- Medicinal
Chemistry, Oncology, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
| | - Andrea Gohlke
- Mechanistic
and Structural Biology, Discovery Sciences, R&DAstraZeneca, Cambridge CB2 0AA, U.K.
| | - Olaf Kinzel
- Medicinal
Chemistry, Oncology, R&D, Acerta B.V.,
a member of the AstraZeneca Group, Oss 5349, The Netherlands
| | - Michelle L. Lamb
- Medicinal
Chemistry, Oncology, R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Nidhal Selmi
- Compound
Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - Christopher J. Stubbs
- Mechanistic
and Structural Biology, Discovery Sciences, R&DAstraZeneca, Cambridge CB2 0AA, U.K.
| | - Nancy Su
- Mechanistic
and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Qibin Su
- Medicinal
Chemistry, Oncology, R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Haiou Luo
- Pharmaron Beijing Co., Ltd., Beijing 100176, P. R. China
| | - Ting Xiong
- Pharmaron Beijing Co., Ltd., Beijing 100176, P. R. China
| | - Xiaoqian Zuo
- Pharmaron Beijing Co., Ltd., Beijing 100176, P. R. China
| | - Sana Bazzaz
- X-Chem Inc., Waltham, Massachusetts 02453, United States
| | | | | | - Kyle E. Denton
- X-Chem Inc., Waltham, Massachusetts 02453, United States
| | - Diana Gikunju
- X-Chem Inc., Waltham, Massachusetts 02453, United States
| | | | | | | | | | - Takashi Satoh
- X-Chem Inc., Waltham, Massachusetts 02453, United States
| | - Ying Zhang
- X-Chem Inc., Waltham, Massachusetts 02453, United States
| | - Emma L. Rivers
- Hit
Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.
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4
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Niu P, Xu H, Fan M. Discovery and optimization of (2-naphthylthio)acetic acid derivative as selective Bfl-1 inhibitor. Bioorg Med Chem Lett 2024; 101:129658. [PMID: 38373466 DOI: 10.1016/j.bmcl.2024.129658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/10/2024] [Accepted: 02/14/2024] [Indexed: 02/21/2024]
Abstract
Bcl-2 anti-apoptotic protein family suppresses cell death by deploying a surface groove to capture the critical BH3 α-helix of pro-apoptotic members. Bfl-1 is a relatively understudied member of this family, though it has been implicated in the pathogenesis and chemoresistance of a variety of human cancers. Reported small molecular Bfl-1 inhibitors encountered the issue of either lack in potency or poor selectivity against its most homologous member Mcl-1. In order to tackle this issue, compound library was screened and a hit compound UMI-77 was identified. We modified its chemical structure to remove the characteristic of PAINS (pan-assay interference compounds), demonstrated the real binding affinity and achieved selectivity against Mcl-1 under the guidance of computational modeling. After optimization 15 was obtained as leading compound to block Bfl-1/BIM interaction in vitro with more than 10-fold selectivity over Mcl-1. We believe 15 is of great value for the exploration of Bfl-1 biological function and its potential as therapeutic target.
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Affiliation(s)
- Pengpeng Niu
- Academy of Medical Engineering and Translational Medicine (AMT), Tianjin University, Tianjin 300072, China; Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China
| | - Huiqi Xu
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Mengyang Fan
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou, Zhejiang 310018, China; Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, China.
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5
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Feng X, Yan Z, Zhou F, Lou J, Lyu X, Ren X, Zeng Z, Liu C, Zhang S, Zhu D, Huang H, Yang J, Zhao Y. Discovery of a selective and covalent small-molecule inhibitor of BFL-1 protein that induces robust apoptosis in cancer cells. Eur J Med Chem 2022; 236:114327. [DOI: 10.1016/j.ejmech.2022.114327] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 11/30/2022]
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6
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Li X, Dou J, You Q, Jiang Z. Inhibitors of BCL2A1/Bfl-1 protein: Potential stock in cancer therapy. Eur J Med Chem 2021; 220:113539. [PMID: 34034128 DOI: 10.1016/j.ejmech.2021.113539] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/23/2021] [Accepted: 05/09/2021] [Indexed: 02/09/2023]
Abstract
The Bcl-2 family members rigorously regulate cell endogenous apoptosis, and targeting anti-apoptotic members is a hot topic in design of anti-cancer drugs. At present, FDA and EMA have approved Bcl-2 inhibitor Venetoclax (ABT-199) for treating chronic lymphocytic leukemia (CLL). However, inhibitors of anti-apoptotic protein BCL2A1/Bfl-1 have not been vigorously developed, and no molecule with ideal activity and selectivity has been found yet. Here we review the biological function and protein structure of Bfl-1, discuss the therapeutic potential and list the currently reported inhibitory peptides and small molecules. This will provide a reference for Bfl-1 targeting drug discovery in the future.
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Affiliation(s)
- Xue Li
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Junwei Dou
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Zhengyu Jiang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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7
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Kump KJ, Miao L, Mady ASA, Ansari NH, Shrestha UK, Yang Y, Pal M, Liao C, Perdih A, Abulwerdi FA, Chinnaswamy K, Meagher JL, Carlson JM, Khanna M, Stuckey JA, Nikolovska-Coleska Z. Discovery and Characterization of 2,5-Substituted Benzoic Acid Dual Inhibitors of the Anti-apoptotic Mcl-1 and Bfl-1 Proteins. J Med Chem 2020; 63:2489-2510. [PMID: 31971799 DOI: 10.1021/acs.jmedchem.9b01442] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Anti-apoptotic Bcl-2 family proteins are overexpressed in a wide spectrum of cancers and have become well validated therapeutic targets. Cancer cells display survival dependence on individual or subsets of anti-apoptotic proteins that could be effectively targeted by multimodal inhibitors. We designed a 2,5-substituted benzoic acid scaffold that displayed equipotent binding to Mcl-1 and Bfl-1. Structure-based design was guided by several solved cocrystal structures with Mcl-1, leading to the development of compound 24, which binds both Mcl-1 and Bfl-1 with Ki values of 100 nM and shows appreciable selectivity over Bcl-2/Bcl-xL. The selective binding profile of 24 was translated to on-target cellular activity in model lymphoma cell lines. These studies lay a foundation for developing more advanced dual Mcl-1/Bfl-1 inhibitors that have potential to provide greater single agent efficacy and broader coverage to combat resistance in several types of cancer than selective Mcl-1 inhibitors alone.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Andrej Perdih
- National Institute of Chemistry, Ljubljana 1000, Slovenia
| | | | | | | | - Jacob M Carlson
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States.,Center for Innovation in Brain Science, Tucson, Arizona 85721, United States
| | - May Khanna
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, Arizona 85724, United States.,Center for Innovation in Brain Science, Tucson, Arizona 85721, United States
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8
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Modi V, Sankararamakrishnan R. Binding affinity of pro-apoptotic BH3 peptides for the anti-apoptotic Mcl-1 and A1 proteins: Molecular dynamics simulations of Mcl-1 and A1 in complex with six different BH3 peptides. J Mol Graph Model 2017; 73:115-128. [PMID: 28279820 DOI: 10.1016/j.jmgm.2016.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/29/2016] [Accepted: 12/08/2016] [Indexed: 02/07/2023]
Abstract
The anti-apoptotic members of Bcl-2 family of proteins bind to their pro-apoptotic counterparts to induce or prevent cell death.Based on the distinct binding profiles for specific pro-apoptotic BH3 peptides, the anti-apoptotic Bcl-2 proteins can be divided into at least two subclasses. The subclass that includes Bcl-XL binds strongly to Bad BH3 peptide while it has weak binding affinity for the second subclass of Bcl-2 proteins such as Mcl-1 and A1. Anti-apoptotic Bcl-2 proteins are considered to be attractive drug targets for anti-cancer drugs. BH3-mimetic inhibitors such as ABT-737 have been shown to be specific to Bcl-XL subclass while Mcl-1 and A1 show resistance to the same drug. An efficacious inhibitor should target all the anti-apoptotic Bcl-2 proteins. Hence, development of inhibitors selective to Mcl-1 and A1 is of prime importance for targeted cancer therapeutics. The first step to achieve this goal is to understand the molecular basis of high binding affinities of specific pro-apoptotic BH3 peptides for Mcl-1 and A1. To understand the interactions between the BH3 peptides and Mcl-1/A1, we performed multi-nanosecond molecular dynamics (MD) simulations of six complex structures of Mcl-1 and A1. With the exception of Bad, all complex structures were experimentally determined. Bad complex structures were modeled. Our simulation studies identified specific pattern of polar interactions between Mcl-1/A1 and high-affinity binding BH3 peptides. The lack of such polar interactions in Bad peptide complex is attributed to specific basic residues present before and after the highly conserved Leu residue. The close approach of basic residues in Bad and Mcl-1/A1 is hypothesized to be the cause of weak binding affinity. To test this hypothesis, we generated in silico mutants of these basic residues in Bad peptide and Mcl-1/A1 proteins. MD simulations of the mutant systems established the pattern of stable polar interactions observed in high-affinity binding BH3 peptides. We have thus identified specific residue positions in Bad and Mcl-1/A1 responsible for the weak binding affinity. Results from these simulation studies will aid in the development of inhibitors specific to Mcl-1 and A1 proteins.
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Affiliation(s)
- Vivek Modi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, 208016, India
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9
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Schenk RL, Strasser A, Dewson G. BCL-2: Long and winding path from discovery to therapeutic target. Biochem Biophys Res Commun 2017; 482:459-469. [PMID: 28212732 DOI: 10.1016/j.bbrc.2016.10.100] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 02/09/2023]
Abstract
In 1988, the BCL-2 protein was found to promote cancer by limiting cell death rather than enhancing proliferation. This discovery set the wheels in motion for an almost 30 year journey involving many international research teams that has recently culminated in the approval for a drug, ABT-199/venetoclax/Venclexta that targets this protein in the treatment of cancer. This review will describe the long and winding path from the discovery of this protein and understanding the fundamental process of apoptosis that BCL-2 and its numerous homologues control, through to its exploitation as a drug target that is set to have significant benefit for cancer patients.
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Affiliation(s)
- Robyn L Schenk
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
| | - Andreas Strasser
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia
| | - Grant Dewson
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Melbourne, Victoria 3010, Australia.
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10
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Jenson JM, Ryan JA, Grant RA, Letai A, Keating AE. Epistatic mutations in PUMA BH3 drive an alternate binding mode to potently and selectively inhibit anti-apoptotic Bfl-1. eLife 2017; 6:e25541. [PMID: 28594323 PMCID: PMC5464773 DOI: 10.7554/elife.25541] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 05/16/2017] [Indexed: 01/07/2023] Open
Abstract
Overexpression of anti-apoptotic Bcl-2 family proteins contributes to cancer progression and confers resistance to chemotherapy. Small molecules that target Bcl-2 are used in the clinic to treat leukemia, but tight and selective inhibitors are not available for Bcl-2 paralog Bfl-1. Guided by computational analysis, we designed variants of the native BH3 motif PUMA that are > 150-fold selective for Bfl-1 binding. The designed peptides potently trigger disruption of the mitochondrial outer membrane in cells dependent on Bfl-1, but not in cells dependent on other anti-apoptotic homologs. High-resolution crystal structures show that designed peptide FS2 binds Bfl-1 in a shifted geometry, relative to PUMA and other binding partners, due to a set of epistatic mutations. FS2 modified with an electrophile reacts with a cysteine near the peptide-binding groove to augment specificity. Designed Bfl-1 binders provide reagents for cellular profiling and leads for developing enhanced and cell-permeable peptide or small-molecule inhibitors.
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Affiliation(s)
- Justin M Jenson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Jeremy A Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Robert A Grant
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Anthony Letai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States,Department of Biology, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States,
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Villoutreix B. Combining bioinformatics, chemoinformatics and experimental approaches to design chemical probes: Applications in the field of blood coagulation. ANNALES PHARMACEUTIQUES FRANÇAISES 2016; 74:253-66. [DOI: 10.1016/j.pharma.2016.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/21/2016] [Accepted: 03/21/2016] [Indexed: 11/08/2022]
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12
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Besbes S, Mirshahi M, Pocard M, Billard C. New dimension in therapeutic targeting of BCL-2 family proteins. Oncotarget 2016; 6:12862-71. [PMID: 25970783 PMCID: PMC4536985 DOI: 10.18632/oncotarget.3868] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 04/01/2015] [Indexed: 01/22/2023] Open
Abstract
Proteins of the BCL-2 family control the mitochondrial pathway of apoptosis. Targeting these proteins proves to be an attractive strategy for anticancer therapy. The biological context is based on the fact that BH3-only members of the family are specific antagonists of prosurvival members. This prompted the identification of “BH3 mimetic” compounds. These small peptides or organic molecules indeed mimic the BH3 domain of BH3-only proteins: by selectively binding and antagonizing prosurvival proteins, they can induce apoptosis in malignant cells. Some small-molecule inhibitors of prosurvival proteins have already entered clinical trials in cancer patients and two of them have shown significant therapeutic effects. The latest developments in the field of targeting BCL-2 family proteins highlight several new antagonists of prosurvival proteins as well as direct activators of proapoptotic proteins. These compounds open up novel prospects for the development of BH3 mimetic anticancer drugs.
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Affiliation(s)
- Samaher Besbes
- INSERM U 965, Hôpital Lariboisière, Paris, France.,Université Paris Diderot, UMR S965, Paris, France
| | - Massoud Mirshahi
- INSERM U 965, Hôpital Lariboisière, Paris, France.,Université Paris Diderot, UMR S965, Paris, France
| | - Marc Pocard
- INSERM U 965, Hôpital Lariboisière, Paris, France.,Université Paris Diderot, UMR S965, Paris, France
| | - Christian Billard
- INSERM U 965, Hôpital Lariboisière, Paris, France.,Université Paris Diderot, UMR S965, Paris, France
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13
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Besbes S, Mirshahi M, Pocard M, Billard C. Strategies targeting apoptosis proteins to improve therapy of chronic lymphocytic leukemia. Blood Rev 2015; 29:345-50. [DOI: 10.1016/j.blre.2015.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 03/02/2015] [Accepted: 03/26/2015] [Indexed: 12/21/2022]
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14
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Kuenemann MA, Sperandio O, Labbé CM, Lagorce D, Miteva MA, Villoutreix BO. In silico design of low molecular weight protein-protein interaction inhibitors: Overall concept and recent advances. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:20-32. [PMID: 25748546 DOI: 10.1016/j.pbiomolbio.2015.02.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 02/18/2015] [Accepted: 02/24/2015] [Indexed: 12/22/2022]
Abstract
Protein-protein interactions (PPIs) are carrying out diverse functions in living systems and are playing a major role in the health and disease states. Low molecular weight (LMW) "drug-like" inhibitors of PPIs would be very valuable not only to enhance our understanding over physiological processes but also for drug discovery endeavors. However, PPIs were deemed intractable by LMW chemicals during many years. But today, with the new experimental and in silico technologies that have been developed, about 50 PPIs have already been inhibited by LMW molecules. Here, we first focus on general concepts about protein-protein interactions, present a consensual view about ligandable pockets at the protein interfaces and the possibilities of using fast and cost effective structure-based virtual screening methods to identify PPI hits. We then discuss the design of compound collections dedicated to PPIs. Recent financial analyses of the field suggest that LMW PPI modulators could be gaining momentum over biologics in the coming years supporting further research in this area.
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Affiliation(s)
- Mélaine A Kuenemann
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France
| | - Olivier Sperandio
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France; CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse, 59000 Lille, France
| | - Céline M Labbé
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France; CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse, 59000 Lille, France
| | - David Lagorce
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France
| | - Maria A Miteva
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France
| | - Bruno O Villoutreix
- Université Paris Diderot, Sorbonne Paris Cité, UMRS 973 Inserm, Paris 75013, France; Inserm, U973, Paris 75013, France; CDithem, Faculté de Pharmacie, 1 rue du Prof Laguesse, 59000 Lille, France.
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