1
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Gyebi GA, Afolabi SO, Ogunyemi OM, Ibrahim IM, Olorundare OE, Adebayo JO, Koketsu M. Apoptotic Potential of Iloneoside from Gongronema latifolium Benth against Prostate Cancer Cells Using In Vitro and In Silico Approach. Cell Biochem Biophys 2024:10.1007/s12013-024-01507-2. [PMID: 39302620 DOI: 10.1007/s12013-024-01507-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2024] [Indexed: 09/22/2024]
Abstract
Prostate cancer is a major cause of cancer-related mortality in men worldwide. The anti-proliferative activity of Gongronema latifolium leaf extracts on some cancer cells has been reported. Herein, we investigated the growth inhibitory effect of the Gongronema latilolium leaf methanol extract and isolated pregnane (iloneoside) against prostate cancer cell lines using the MTT cell proliferation assay, apoptosis quantification, cell cycle analysis using flow cytometry and computational analysis molecular docking, molecular dynamics simulation (MDs), binding free energy computation and cluster analysis. In addition, UPLC-ESI-TOFMS chemical fingerprinting of previously isolated compounds was performed. The extract inhibited the growth of the cell lines with an IC50 of 49.3 µg/ml and 28.4 µg/ml for 24 h and 48 h, respectively, for PC3; and 43.7 µg/ml and 22.3 µg/ml for 24 h and 48 h, respectively, for DU145. Iloneoside demonstrated low inhibitory activities against PC3 and DU145 (IC50 > 80 μM). Apoptotic quantification and cell cycle analysis further showed that iloneoside induced apoptosis in a few cells at a dose of 200 uM. The ensemble-based molecular docking of the iloneoside to BCL-XL and BCL-2 proteins, and docking to MCL-1, BCL-A1 and BFL-1 proteins, respectively, presented binding energies of -7.22 ± 0.5, -8.12 ± 0.55, -7.1, -7.2 and -6.3 kcal/mol, while the MM/PBSA binding free energy was -25.72 ± 7.22 and -27.76 ± 11.32 kcal/mol for BCL-XL and BCL-2 proteins. Furthermore, iloneoside was stable during the 100 ns MDs analysis, while the clustering of the MDs trajectories showed that the interactions were strongly preserved. Iloneoside, in part, or in synergy with other constituents, may be responsible for the antiproliferative activities of the leaf, subject to further investigation.
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Affiliation(s)
- Gideon A Gyebi
- Department of Biotechnology and Food Science, Faculty of Applied Sciences, Durban University of Technology, Durban, South Africa.
- Natural Products and Structural (Bio-Chem)-informatics Research Laboratory (NpsBC-RL), Department of Biochemistry, Faculty of Science and Technology, Bingham University, Karu, Nigeria.
| | - Saheed O Afolabi
- Biomolecular Modeling and Nutraceuticals Laboratory, Nutritional and Industrial Biochemistry Research Unit, Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oludare M Ogunyemi
- Faculty of Basic Medical Sciences, Department of Pharmacology and Therapeutics, University of Ilorin, Ilorin, Nigeria
| | - Ibrahim M Ibrahim
- Department of Biophysics, Faculty of Sciences, Cairo University, Giza, Egypt
| | - Olufunke E Olorundare
- Faculty of Basic Medical Sciences, Department of Pharmacology and Therapeutics, University of Ilorin, Ilorin, Nigeria
| | - Joseph O Adebayo
- Department of Biochemistry, Faculty of Life Sciences, University of Ilorin, Ilorin, Nigeria
| | - Mamoru Koketsu
- Faculty of Engineering, Department of Chemistry and Biomolecular Science, Gifu University, Gifu, Japan
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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, Milbradt AG, Blackwell JH, Bonomo S, Brierley A, Cassar DJ, Freeman J, Hadfield TE, Morrill LA, Riemens R, Sarda S, Schiesser S, Wiktelius D, Ahmed S, Bostock MJ, Börjesson U, De Fusco C, Guerot C, Hargreaves D, Hewitt S, Lamb ML, Su N, Whatling R, Wheeler M, Kettle JG. Design of a Lead-Like Cysteine-Targeting Covalent Library and the Identification of Hits to Cys55 of Bfl-1. J Med Chem 2024; 67:11209-11225. [PMID: 38916990 DOI: 10.1021/acs.jmedchem.4c00781] [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: 06/27/2024]
Abstract
Covalent hit identification is a viable approach to identify chemical starting points against difficult-to-drug targets. While most researchers screen libraries of <2k electrophilic fragments, focusing on lead-like compounds can be advantageous in terms of finding hits with improved affinity and with a better chance of identifying cryptic pockets. However, due to the increased molecular complexity, larger numbers of compounds (>10k) are desirable to ensure adequate coverage of chemical space. Herein, the approach taken to build a library of 12k covalent lead-like compounds is reported, utilizing legacy compounds, robust library chemistry, and acquisitions. The lead-like covalent library was screened against the antiapoptotic protein Bfl-1, and six promising hits that displaced the BIM peptide from the PPI interface were identified. Intriguingly, X-ray crystallography of lead-like compound 8 showed that it binds to a previously unobserved conformation of the Bfl-1 protein and is an ideal starting point for the optimization of Bfl-1 inhibitors.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, 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
| | - J Henry Blackwell
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Silvia Bonomo
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Andrew Brierley
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Doyle J Cassar
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Jared Freeman
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolic Disorders (CVRM), Biopharmaceuticals R&D, AstraZeneca, Gothenburg, SE-43183, Sweden
| | - Thomas E Hadfield
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Lucas A Morrill
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Rick Riemens
- Medicinal Chemistry, Oncology R&D, Acerta B. V., a Part of the AstraZeneca Group, Oss 5349, The Netherlands
| | - Sunil Sarda
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Stefan Schiesser
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), Biopharmaceuticals R&D, AstraZeneca, Gothenburg, SE-43183, Sweden
| | - Daniel Wiktelius
- Compound Synthesis and Management, Discovery Sciences, R&D, AstraZeneca, Gothenburg, SE-43183, Sweden
| | - Samiyah Ahmed
- Discovery 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
| | - Ulf Börjesson
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Gothenburg, SE-43183, Sweden
| | - Claudia De Fusco
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Carine Guerot
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - David Hargreaves
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Sarah Hewitt
- 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
| | - Nancy Su
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Ryan Whatling
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Matthew Wheeler
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Jason G Kettle
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
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4
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Paquette AR, Boddy CN. Double Stranded DNA Binding Stapled Peptides: An Emerging Tool for Transcriptional Regulation. Chembiochem 2023; 24:e202300594. [PMID: 37750576 DOI: 10.1002/cbic.202300594] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 09/27/2023]
Abstract
Stapled peptides have rapidly established themselves as a powerful technique to mimic α-helical interactions with a short peptide sequence. There are many examples of stapled peptides that successfully disrupt α-helix-mediated protein-protein interactions, with an example currently in clinical trials. DNA-protein interactions are also often mediated by α-helices and are involved in all transcriptional regulation processes. Unlike DNA-binding small molecules, which typically lack DNA sequence selectivity, DNA-binding proteins bind with high affinity and high selectivity. These are ideal candidates for the design DNA-binding stapled peptides. Despite the parallel to protein-protein interaction disrupting stapled peptides and the need for sequence specific DNA binders, there are very few DNA-binding stapled peptides. In this review we examine all the known DNA-binding stapled peptides. Their design concepts are compared to stapled peptides that disrupt protein-protein interactions and based on the few examples in the literature, DNA-binding stapled peptide trends are discussed.
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Affiliation(s)
- André R Paquette
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, The University of Ottawa, Ottawa, ON, K1N 6N5, Canada
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5
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Gupta SRR, Mittal P, Kundu B, Singh A, Singh IK. Silibinin: an inhibitor for a high-expressed BCL-2A1/BFL1 protein, linked with poor prognosis in breast cancer. J Biomol Struct Dyn 2023:1-11. [PMID: 37837418 DOI: 10.1080/07391102.2023.2268176] [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: 03/14/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Breast cancer (BC) accounts for 30% of all diagnosed cases of cancer in women and remains a leading cause of cancer-related deaths among women worldwide. The current study looks for a protein from the anti-apoptotic/pro-survival BCL-2 family whose overexpression reduces survivability in BC patients and a potential inhibitor for the protein. We found BCL-2A1/BFL1 protein with high expression linked to low survivability in BC. The protein shows prognosis in 8 out of 29 categories, whereas no other family member manifests this property. Out of 7379 compounds, three small molecules (CHEMBL9509, CHEMBL2104550 and CHEMBL3545011) form an H-bond with BCL-2A1/BFL1 protein's unique residue Cys55. Of the three small molecules, we found CHEMBL9509 (Silibinin) to be a potent inhibitor. The compound forms a stable H-bond with the residue Cys55 with the lowest binding energy compared to the other two compounds. It remains stable in the BH3 binding region for more than 100 ns, whereas the other two detach from the region. Additionally, the compound is found to be better than Venetoclax and Nematoclax. We firmly believe in the compound CHEMBL9509 potency to halt BC's progression by inhibiting the BCL-2A1/BFL1 protein, increasing patients' survivability.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shradheya R R Gupta
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Pooja Mittal
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
- Norris Comprehensive Cancer Center, Division of Medical Oncology, University of Southern California, Los Angeles, USA
| | - Bishwajit Kundu
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, New Delhi, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi (South Campus), New Delhi, India
| | - Indrakant K Singh
- Molecular Biology Research Laboratory, Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
- Norris Comprehensive Cancer Center, Division of Medical Oncology, University of Southern California, Los Angeles, USA
- Institute of Eminence, Delhi School of Public Health, University of Delhi, Delhi, India
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6
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Tantawy SI, Timofeeva N, Sarkar A, Gandhi V. Targeting MCL-1 protein to treat cancer: opportunities and challenges. Front Oncol 2023; 13:1226289. [PMID: 37601693 PMCID: PMC10436212 DOI: 10.3389/fonc.2023.1226289] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023] Open
Abstract
Evading apoptosis has been linked to tumor development and chemoresistance. One mechanism for this evasion is the overexpression of prosurvival B-cell lymphoma-2 (BCL-2) family proteins, which gives cancer cells a survival advantage. Mcl-1, a member of the BCL-2 family, is among the most frequently amplified genes in cancer. Targeting myeloid cell leukemia-1 (MCL-1) protein is a successful strategy to induce apoptosis and overcome tumor resistance to chemotherapy and targeted therapy. Various strategies to inhibit the antiapoptotic activity of MCL-1 protein, including transcription, translation, and the degradation of MCL-1 protein, have been tested. Neutralizing MCL-1's function by targeting its interactions with other proteins via BCL-2 interacting mediator (BIM)S2A has been shown to be an equally effective approach. Encouraged by the design of venetoclax and its efficacy in chronic lymphocytic leukemia, scientists have developed other BCL-2 homology (BH3) mimetics-particularly MCL-1 inhibitors (MCL-1i)-that are currently in clinical trials for various cancers. While extensive reviews of MCL-1i are available, critical analyses focusing on the challenges of MCL-1i and their optimization are lacking. In this review, we discuss the current knowledge regarding clinically relevant MCL-1i and focus on predictive biomarkers of response, mechanisms of resistance, major issues associated with use of MCL-1i, and the future use of and maximization of the benefits from these agents.
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Affiliation(s)
- Shady I. Tantawy
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Natalia Timofeeva
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Aloke Sarkar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Varsha Gandhi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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7
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Rehman AU, Khurshid B, Ali Y, Rasheed S, Wadood A, Ng HL, Chen HF, Wei Z, Luo R, Zhang J. Computational approaches for the design of modulators targeting protein-protein interactions. Expert Opin Drug Discov 2023; 18:315-333. [PMID: 36715303 PMCID: PMC10149343 DOI: 10.1080/17460441.2023.2171396] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/18/2023] [Indexed: 01/31/2023]
Abstract
BACKGROUND Protein-protein interactions (PPIs) are intriguing targets for designing novel small-molecule inhibitors. The role of PPIs in various infectious and neurodegenerative disorders makes them potential therapeutic targets . Despite being portrayed as undruggable targets, due to their flat surfaces, disorderedness, and lack of grooves. Recent progresses in computational biology have led researchers to reconsider PPIs in drug discovery. AREAS COVERED In this review, we introduce in-silico methods used to identify PPI interfaces and present an in-depth overview of various computational methodologies that are successfully applied to annotate the PPIs. We also discuss several successful case studies that use computational tools to understand PPIs modulation and their key roles in various physiological processes. EXPERT OPINION Computational methods face challenges due to the inherent flexibility of proteins, which makes them expensive, and result in the use of rigid models. This problem becomes more significant in PPIs due to their flexible and flat interfaces. Computational methods like molecular dynamics (MD) simulation and machine learning can integrate the chemical structure data into biochemical and can be used for target identification and modulation. These computational methodologies have been crucial in understanding the structure of PPIs, designing PPI modulators, discovering new drug targets, and predicting treatment outcomes.
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Affiliation(s)
- Ashfaq Ur Rehman
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California Irvine, Irvine, California, USA
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, Zhejiang, China
| | - Beenish Khurshid
- Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan
| | - Yasir Ali
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Salman Rasheed
- National Center for Bioinformatics, Quaid-e-Azam University, Islamabad, Pakistan
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Pakistan
| | - Ho-Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, USA
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, Zhejiang, China
| | - Zhiqiang Wei
- Medicinal Chemistry and Bioinformatics Center, Ocean University of China, Qingdao, Shandong, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, Graduate Program in Chemical and Materials Physics, University of California Irvine, Irvine, California, USA
| | - Jian Zhang
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Medicinal Bioinformatics Center, Shanghai Jiao-Tong University School of Medicine, Shanghai, Zhejiang, China
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
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8
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Paulussen FM, Grossmann TN. Peptide-based covalent inhibitors of protein-protein interactions. J Pept Sci 2023; 29:e3457. [PMID: 36239115 PMCID: PMC10077911 DOI: 10.1002/psc.3457] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 12/13/2022]
Abstract
Protein-protein interactions (PPI) are involved in all cellular processes and many represent attractive therapeutic targets. However, the frequently rather flat and large interaction areas render the identification of small molecular PPI inhibitors very challenging. As an alternative, peptide interaction motifs derived from a PPI interface can serve as starting points for the development of inhibitors. However, certain proteins remain challenging targets when applying inhibitors with a competitive mode of action. For that reason, peptide-based ligands with an irreversible binding mode have gained attention in recent years. This review summarizes examples of covalent inhibitors that employ peptidic binders and have been tested in a biological context.
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Affiliation(s)
- Felix M Paulussen
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Molecular Microbiology, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Chemistry and Pharmaceutical Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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9
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Lou J, Lu Y, Cheng J, Zhou F, Yan Z, Zhang D, Meng X, Zhao Y. A chemical perspective on the modulation of TEAD transcriptional activities: Recent progress, challenges, and opportunities. Eur J Med Chem 2022; 243:114684. [DOI: 10.1016/j.ejmech.2022.114684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/02/2022] [Accepted: 08/11/2022] [Indexed: 11/30/2022]
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10
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Wang Y, Zhao R, Wan C, Guo X, Yang F, Hou Z, Wang R, Li S, Feng T, Yin F, Li Z. A Peptide-Based Ligand-Directed Chemistry Enables Protein Functionalization. Org Lett 2022; 24:7205-7209. [PMID: 36169233 DOI: 10.1021/acs.orglett.2c02974] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ligand-directed (LD) chemistry provides powerful tools for site-specific modification of proteins. We utilized a peptide with an appended methionine (Met) as a ligand; then, the Met thioether was modified into sulfonium which enabled a proximity induced group transfer onto protein cysteine in the vicinity upon peptide-target binding. The sulfonium warhead could be easily constructed with unprotected peptides, and the transferable group scope was conducted on model protein PDZ and its ligand peptides. In addition, a living cell labeling was successfully achieved.
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Affiliation(s)
- Yuena Wang
- Center for Disease Control and Prevention, Shenzhen, 518055, China.,State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Rongtong Zhao
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Chuan Wan
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Xiaochun Guo
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Fenfang Yang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Zhanfeng Hou
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China
| | - Shuiming Li
- Shenzhen Key Laboratory of Microbiology and Gene Engineering, Shenzhen University, Shenzhen, 518055, China
| | - Tiejian Feng
- Center for Disease Control and Prevention, Shenzhen, 518055, China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China
| | - Zigang Li
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.,Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China
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11
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Last but not least: BFL-1 as an emerging target for anti-cancer therapies. Biochem Soc Trans 2022; 50:1119-1128. [PMID: 35900226 PMCID: PMC9444066 DOI: 10.1042/bst20220153] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/13/2022] [Accepted: 07/14/2022] [Indexed: 11/17/2022]
Abstract
BFL-1 is an understudied pro-survival BCL-2 protein. The expression of BFL-1 is reported in many cancers, but it is yet to be clarified whether high transcript expression also always correlates with a pro-survival function. However, recent applications of BH3-mimetics for the treatment of blood cancers identified BFL-1 as a potential resistance factor in this type of cancer. Hence, understanding the role of BFL-1 in human cancers and how its up-regulation leads to therapy resistance has become an area of great clinical relevance. In addition, deletion of the murine homologue of BFL-1, called A1, in mice showed only minimal impacts on the well-being of these animals, suggesting drugs targeting BFL-1 would exhibit limited on-target toxicities. BFL-1 therefore represents a good clinical cancer target. Currently, no effective BFL-1 inhibitors exist, which is likely due to the underappreciation of BFL-1 as a potential target in the clinic and lack of understanding of the BFL-1 protein. In this review, the roles of BFL-1 in the development of different types of cancers and drug resistant mechanisms are discussed and some recent advances in the generation of BFL-1 inhibitors highlighted.
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12
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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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13
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Zhang Z, Bai L, Hou L, Deng H, Luan S, Liu D, Huang M, Zhao L. Trends in targeting Bcl-2 anti-apoptotic proteins for cancer treatment. Eur J Med Chem 2022; 232:114184. [DOI: 10.1016/j.ejmech.2022.114184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/24/2022] [Accepted: 02/03/2022] [Indexed: 12/12/2022]
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14
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Lee EF, Fairlie WD. Discovery, development and application of drugs targeting BCL-2 pro-survival proteins in cancer. Biochem Soc Trans 2021; 49:2381-2395. [PMID: 34515749 PMCID: PMC8589430 DOI: 10.1042/bst20210749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022]
Abstract
The discovery of a new class of small molecule compounds that target the BCL-2 family of anti-apoptotic proteins is one of the great success stories of basic science leading to translational outcomes in the last 30 years. The eponymous BCL-2 protein was identified over 30 years ago due to its association with cancer. However, it was the unveiling of the biochemistry and structural biology behind it and its close relatives' mechanism(s)-of-action that provided the inspiration for what are now known as 'BH3-mimetics', the first clinically approved drugs designed to specifically inhibit protein-protein interactions. Herein, we chart the history of how these drugs were discovered, their evolution and application in cancer treatment.
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Affiliation(s)
- Erinna F. Lee
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
- Cell Death and Survival Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia
| | - W. Douglas Fairlie
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
- Cell Death and Survival Laboratory, Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, Victoria 3086, Australia
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15
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Perez JJ, Perez RA, Perez A. Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering. Front Mol Biosci 2021; 8:681617. [PMID: 34095231 PMCID: PMC8173110 DOI: 10.3389/fmolb.2021.681617] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/05/2021] [Indexed: 12/13/2022] Open
Abstract
Protein-protein interactions (PPIs) mediate a large number of important regulatory pathways. Their modulation represents an important strategy for discovering novel therapeutic agents. However, the features of PPI binding surfaces make the use of structure-based drug discovery methods very challenging. Among the diverse approaches used in the literature to tackle the problem, linear peptides have demonstrated to be a suitable methodology to discover PPI disruptors. Unfortunately, the poor pharmacokinetic properties of linear peptides prevent their direct use as drugs. However, they can be used as models to design enzyme resistant analogs including, cyclic peptides, peptide surrogates or peptidomimetics. Small molecules have a narrower set of targets they can bind to, but the screening technology based on virtual docking is robust and well tested, adding to the computational tools used to disrupt PPI. We review computational approaches used to understand and modulate PPI and highlight applications in a few case studies involved in physiological processes such as cell growth, apoptosis and intercellular communication.
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Affiliation(s)
- Juan J Perez
- Department of Chemical Engineering, Universitat Politecnica de Catalunya, Barcelona, Spain
| | - Roman A Perez
- Bioengineering Institute of Technology, Universitat Internacional de Catalunya, Sant Cugat, Spain
| | - Alberto Perez
- The Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, FL, United States
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16
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Design, Synthesis, and Anticancer Screening for Repurposed Pyrazolo[3,4-d]pyrimidine Derivatives on Four Mammalian Cancer Cell Lines. Molecules 2021; 26:molecules26102961. [PMID: 34065773 PMCID: PMC8156061 DOI: 10.3390/molecules26102961] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 12/24/2022] Open
Abstract
The present study reports the synthesis of new purine bioisosteres comprising a pyrazolo[3,4-d]pyrimidine scaffold linked to mono-, di-, and trimethoxy benzylidene moieties through hydrazine linkages. First, in silico docking experiments of the synthesized compounds against Bax, Bcl-2, Caspase-3, Ki67, p21, and p53 were performed in a trial to rationalize the observed cytotoxic activity for the tested compounds. The anticancer activity of these compounds was evaluated in vitro against Caco-2, A549, HT1080, and Hela cell lines. Results revealed that two (5 and 7) of the three synthesized compounds (5, 6, and 7) showed high cytotoxic activity against all tested cell lines with IC50 values in the micro molar concentration. Our in vitro results show that there is no significant apoptotic effect for the treatment with the experimental compounds on the viability of cells against A549 cells. Ki67 expression was found to decrease significantly following the treatment of cells with the most promising candidate: drug 7. The overall results indicate that these pyrazolopyrimidine derivatives possess anticancer activity at varying doses. The suggested mechanism of action involves the inhibition of the proliferation of cancer cells.
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17
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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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18
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Cohen DT, Wales TE, McHenry MW, Engen JR, Walensky LD. Site-Dependent Cysteine Lipidation Potentiates the Activation of Proapoptotic BAX. Cell Rep 2021; 30:3229-3239.e6. [PMID: 32160532 PMCID: PMC7343539 DOI: 10.1016/j.celrep.2020.02.057] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 12/23/2019] [Accepted: 02/11/2020] [Indexed: 11/19/2022] Open
Abstract
BCL-2 family proteins converge at the mitochondrial outer membrane to regulate apoptosis and maintain the critical balance between cellular life and death. This physiologic process is essential to organism homeostasis and relies on protein-protein and protein-lipid interactions among BCL-2 family proteins in the mitochondrial lipid environment. Here, we find that trans-2-hexadecenal (t-2-hex), previously implicated in regulating BAX-mediated apoptosis, does so by direct covalent reaction with C126, which is located on the surface of BAX at the junction of its α5/α6 core hydrophobic hairpin. The application of nuclear magnetic resonance spectroscopy, hydrogen-deuterium exchange mass spectrometry, specialized t-2-hex-containing liposomes, and BAX mutational studies in mitochondria and cells reveals structure-function insights into the mechanism by which covalent lipidation at the mitochondria sensitizes direct BAX activation. The functional role of BAX lipidation as a control point of mitochondrial apoptosis could provide a therapeutic strategy for BAX modulation by chemical modification of C126. Cohen et al. show that trans-2-hexadecenal (t-2-hex) potentiates BAX-mediated apoptosis by non-enzymatic covalent lipidation of BAX C126. t-2-hex derivatization induces BAX-activating conformational changes and enhances BH3-triggered BAX poration of liposomal and mitochondrial membranes in a C126-dependent manner. This mechanism informs a therapeutic strategy for modulating BAX-mediated apoptosis by targeting C126.
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Affiliation(s)
- Daniel T Cohen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Matthew W McHenry
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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19
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Bcl-xL: A Focus on Melanoma Pathobiology. Int J Mol Sci 2021; 22:ijms22052777. [PMID: 33803452 PMCID: PMC7967179 DOI: 10.3390/ijms22052777] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/26/2021] [Accepted: 03/04/2021] [Indexed: 11/17/2022] Open
Abstract
Apoptosis is the main mechanism by which multicellular organisms eliminate damaged or unwanted cells. To regulate this process, a balance between pro-survival and pro-apoptotic proteins is necessary in order to avoid impaired apoptosis, which is the cause of several pathologies, including cancer. Among the anti-apoptotic proteins, Bcl-xL exhibits a high conformational flexibility, whose regulation is strictly controlled by alternative splicing and post-transcriptional regulation mediated by transcription factors or microRNAs. It shows relevant functions in different forms of cancer, including melanoma. In melanoma, Bcl-xL contributes to both canonical roles, such as pro-survival, protection from apoptosis and induction of drug resistance, and non-canonical functions, including promotion of cell migration and invasion, and angiogenesis. Growing evidence indicates that Bcl-xL inhibition can be helpful for cancer patients, but at present, effective and safe therapies targeting Bcl-xL are lacking due to toxicity to platelets. In this review, we summarized findings describing the mechanisms of Bcl-xL regulation, and the role that Bcl-xL plays in melanoma pathobiology and response to therapy. From these findings, it emerged that even if Bcl-xL plays a crucial role in melanoma pathobiology, we need further studies aimed at evaluating the involvement of Bcl-xL and other members of the Bcl-2 family in the progression of melanoma and at identifying new non-toxic Bcl-xL inhibitors.
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20
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Targeting Bfl-1 via acute CDK9 inhibition overcomes intrinsic BH3-mimetic resistance in lymphomas. Blood 2020; 137:2947-2957. [PMID: 33259592 DOI: 10.1182/blood.2020008528] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/21/2020] [Indexed: 12/30/2022] Open
Abstract
BH3 mimetics like venetoclax target prosurvival Bcl-2 family proteins and are important therapeutics in the treatment of hematological malignancies. We demonstrate that endogenous Bfl-1 expression can render preclinical lymphoma tumor models insensitive to Mcl-1 and Bcl-2 inhibitors. However, suppression of Bfl-1 alone was insufficient to fully induce apoptosis in Bfl-1-expressing lymphomas, highlighting the need for targeting additional prosurvival proteins in this context. Importantly, we demonstrated that cyclin-dependent kinase 9 (CDK9) inhibitors rapidly downregulate both Bfl-1 and Mcl-1, inducing apoptosis in BH3-mimetic-resistant lymphoma cell lines in vitro and driving in vivo tumor regressions in diffuse large B-cell lymphoma patient-derived xenograft models expressing Bfl-1. These data underscore the need to clinically develop CDK9 inhibitors, like AZD4573, for the treatment of lymphomas using Bfl-1 as a selection biomarker.
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21
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Reddy CN, Manzar N, Ateeq B, Sankararamakrishnan R. Computational Design of BH3-Mimetic Peptide Inhibitors That Can Bind Specifically to Mcl-1 or Bcl-X L: Role of Non-Hot Spot Residues. Biochemistry 2020; 59:4379-4394. [PMID: 33146015 DOI: 10.1021/acs.biochem.0c00661] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Interactions between pro- and anti-apoptotic Bcl-2 proteins decide the fate of the cell. The BH3 domain of pro-apoptotic Bcl-2 proteins interacts with the exposed hydrophobic groove of their anti-apoptotic counterparts. Through their design and development, BH3 mimetics that target the hydrophobic groove of specific anti-apoptotic Bcl-2 proteins have the potential to become anticancer drugs. We have developed a novel computational method for designing sequences with BH3 domain features that can bind specifically to anti-apoptotic Mcl-1 or Bcl-XL. In this method, we retained the four highly conserved hydrophobic and aspartic residues of wild-type BH3 sequences and randomly substituted all other positions to generate a large number of BH3-like sequences. We modeled 20000 complex structures with Mcl-1 or Bcl-XL using the BH3-like sequences derived from five wild-type pro-apoptotic BH3 peptides. Peptide-protein interaction energies calculated from these models for each set of BH3-like sequences resulted in negatively skewed extreme value distributions. The selected BH3-like sequences from the extreme negative tail regions have highly favorable interaction energies with Mcl-1 or Bcl-XL. They are enriched in acidic and basic residues when they bind to Mcl-1 and Bcl-XL, respectively. With the charged residues often away from the binding interface, the overall electric field generated by the charged residues results in strong long-range electrostatic interaction energies between the peptide and the protein giving rise to high specificity. Cell viability studies of representative BH3-like peptides further validated the predicted specificity. This study has revealed the importance of non-hot spot residues in BH3-mimetic peptides in providing specificity to a particular anti-apoptotic protein.
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22
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Selective Covalent Targeting of Anti-apoptotic BFL-1 by a Sulfonium-Tethered Peptide. Chembiochem 2020; 22:340-344. [PMID: 32790056 DOI: 10.1002/cbic.202000473] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/10/2020] [Indexed: 12/21/2022]
Abstract
Anti-apoptotic B cell lymphoma 2 (BCL-2) family proteins are proven targets for human cancers. Targeting the BH3-binding pockets of these anti-apoptotic proteins could reactivate apoptosis in BCL-2-depedent cancers. BFL-1 is a BCL-2 family protein overexpressed in various chemoresistant cancers. A unique cysteine at the binding interface of the BH3 and BFL-1 was previously proven to be an intriguing targeting site to irreversibly inhibit BFL-1 functions with stabilized cyclic peptide bearing a covalent warhead. Recently, we developed a sulfonium-tethered peptide cyclization strategy to construct peptide ligands that could selectively and efficiently react with the cysteine(s) of target proteins near the interacting interface. Using this method, we constructed a BFL-1 peptide inhibitor, B4-MC, that could selectively conjugate with BFL-1 both in vitro and in cell. B4-MC showed good cellular uptake, colocalized with BFL-1 on mitochondria, and showed obvious growth inhibition of BFL-1 over-expressed cancer cell lines.
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23
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Diversity in the intrinsic apoptosis pathway of nematodes. Commun Biol 2020; 3:478. [PMID: 32859965 PMCID: PMC7456325 DOI: 10.1038/s42003-020-01208-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/03/2020] [Indexed: 11/08/2022] Open
Abstract
Early studies of the free-living nematode C. elegans informed us how BCL-2-regulated apoptosis in humans is regulated. However, subsequent studies showed C. elegans apoptosis has several unique features compared with human apoptosis. To date, there has been no detailed analysis of apoptosis regulators in nematodes other than C. elegans. Here, we discovered BCL-2 orthologues in 89 free-living and parasitic nematode taxa representing four evolutionary clades (I, III, IV and V). Unlike in C. elegans, 15 species possess multiple (two to five) BCL-2-like proteins, and some do not have any recognisable BCL-2 sequences. Functional studies provided no evidence that BAX/BAK proteins have evolved in nematodes, and structural studies of a BCL-2 protein from the basal clade I revealed it lacks a functionally important feature of the C. elegans orthologue. Clade I CED-4/APAF-1 proteins also possess WD40-repeat sequences associated with apoptosome assembly, not present in C. elegans, or other nematode taxa studied.
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24
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A redox switch regulates the structure and function of anti-apoptotic BFL-1. Nat Struct Mol Biol 2020; 27:781-789. [PMID: 32661419 PMCID: PMC7544158 DOI: 10.1038/s41594-020-0458-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 06/03/2020] [Indexed: 01/27/2023]
Abstract
Apoptosis is regulated by BCL-2 family proteins. Anti-apoptotic members suppress cell death by deploying a surface groove to capture the critical BH3 α-helix of pro-apoptotic members. Cancer cells hijack this mechanism by overexpressing anti-apoptotic BCL-2 family proteins to enforce cellular immortality. We previously identified and harnessed a unique cysteine (C55) in the groove of anti-apoptotic BFL-1 to selectively neutralize its oncogenic activity using a covalent stapled-peptide inhibitor. Here, we find that disulfide bonding between a native cysteine pair at the groove (C55) and C-terminal α9 helix (C175) of BFL-1 operates as a redox switch to control the accessibility of the anti-apoptotic pocket. Reducing the C55-C175 disulfide triggers α9 release, which promotes mitochondrial translocation, groove exposure for BH3 interaction and inhibition of mitochondrial permeabilization by pro-apoptotic BAX. C55-C175 disulfide formation in an oxidative cellular environment abrogates the ability of BFL-1 to bind BH3 domains. Thus, we identify a mechanism of conformational control of BFL-1 by an intramolecular redox switch.
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25
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Hauseman ZJ, Harvey EP, Newman CE, Wales TE, Bucci JC, Mintseris J, Schweppe DK, David L, Fan L, Cohen DT, Herce HD, Mourtada R, Ben-Nun Y, Bloch NB, Hansen SB, Wu H, Gygi SP, Engen JR, Walensky LD. Homogeneous Oligomers of Pro-apoptotic BAX Reveal Structural Determinants of Mitochondrial Membrane Permeabilization. Mol Cell 2020; 79:68-83.e7. [PMID: 32533918 PMCID: PMC7472837 DOI: 10.1016/j.molcel.2020.05.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/13/2020] [Accepted: 05/20/2020] [Indexed: 10/24/2022]
Abstract
BAX is a pro-apoptotic protein that transforms from a cytosolic monomer into a toxic oligomer that permeabilizes the mitochondrial outer membrane. How BAX monomers assemble into a higher-order conformation, and the structural determinants essential to membrane permeabilization, remain a mechanistic mystery. A key hurdle has been the inability to generate a homogeneous BAX oligomer (BAXO) for analysis. Here, we report the production and characterization of a full-length BAXO that recapitulates physiologic BAX activation. Multidisciplinary studies revealed striking conformational consequences of oligomerization and insight into the macromolecular structure of oligomeric BAX. Importantly, BAXO enabled the assignment of specific roles to particular residues and α helices that mediate individual steps of the BAX activation pathway, including unexpected functionalities of BAX α6 and α9 in driving membrane disruption. Our results provide the first glimpse of a full-length and functional BAXO, revealing structural requirements for the elusive execution phase of mitochondrial apoptosis.
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Affiliation(s)
- Zachary J Hauseman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Edward P Harvey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Catherine E Newman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Joel C Bucci
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Devin K Schweppe
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Liron David
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lixin Fan
- Small Angle X-ray Scattering Core, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Daniel T Cohen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Henry D Herce
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Rida Mourtada
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Yael Ben-Nun
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Noah B Bloch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Scott B Hansen
- The Scripps Research Institute-Florida, Jupiter, FL 33458, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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Abstract
For over three decades, a mainstay and goal of clinical oncology has been the development of therapies promoting the effective elimination of cancer cells by apoptosis. This programmed cell death process is mediated by several signalling pathways (referred to as intrinsic and extrinsic) triggered by multiple factors, including cellular stress, DNA damage and immune surveillance. The interaction of apoptosis pathways with other signalling mechanisms can also affect cell death. The clinical translation of effective pro-apoptotic agents involves drug discovery studies (addressing the bioavailability, stability, tumour penetration, toxicity profile in non-malignant tissues, drug interactions and off-target effects) as well as an understanding of tumour biology (including heterogeneity and evolution of resistant clones). While tumour cell death can result in response to therapy, the selection, growth and dissemination of resistant cells can ultimately be fatal. In this Review, we present the main apoptosis pathways and other signalling pathways that interact with them, and discuss actionable molecular targets, therapeutic agents in clinical translation and known mechanisms of resistance to these agents.
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Affiliation(s)
| | - Wafik S El-Deiry
- The Warren Alpert Medical School, Brown University, Providence, RI, USA.
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27
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Harvey EP, Hauseman ZJ, Cohen DT, Rettenmaier TJ, Lee S, Huhn AJ, Wales TE, Seo HS, Luccarelli J, Newman CE, Guerra RM, Bird GH, Dhe-Paganon S, Engen JR, Wells JA, Walensky LD. Identification of a Covalent Molecular Inhibitor of Anti-apoptotic BFL-1 by Disulfide Tethering. Cell Chem Biol 2020; 27:647-656.e6. [PMID: 32413285 DOI: 10.1016/j.chembiol.2020.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/13/2020] [Accepted: 04/03/2020] [Indexed: 02/06/2023]
Abstract
The BCL-2 family is composed of anti- and pro-apoptotic members that respectively protect or disrupt mitochondrial integrity. Anti-apoptotic overexpression can promote oncogenesis by trapping the BCL-2 homology 3 (BH3) "killer domains" of pro-apoptotic proteins in a surface groove, blocking apoptosis. Groove inhibitors, such as the relatively large BCL-2 drug venetoclax (868 Da), have emerged as cancer therapies. BFL-1 remains an undrugged oncogenic protein and can cause venetoclax resistance. Having identified a unique C55 residue in the BFL-1 groove, we performed a disulfide tethering screen to determine if C55 reactivity could enable smaller molecules to block BFL-1's BH3-binding functionality. We found that a disulfide-bearing N-acetyltryptophan analog (304 Da adduct) effectively targeted BFL-1 C55 and reversed BFL-1-mediated suppression of mitochondrial apoptosis. Structural analyses implicated the conserved leucine-binding pocket of BFL-1 as the interaction site, resulting in conformational remodeling. Thus, therapeutic targeting of BFL-1 may be achievable through the design of small, cysteine-reactive drugs.
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Affiliation(s)
- Edward P Harvey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Zachary J Hauseman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Daniel T Cohen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - T Justin Rettenmaier
- Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California, 1700 Fourth Street, San Francisco, CA 94143, USA
| | - Susan Lee
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Annissa J Huhn
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, 412 The Fenway, Boston, MA 02115, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - James Luccarelli
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Catherine E Newman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Rachel M Guerra
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Gregory H Bird
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, 412 The Fenway, Boston, MA 02115, USA
| | - James A Wells
- Departments of Pharmaceutical Chemistry and Cellular and Molecular Pharmacology, University of California, 1700 Fourth Street, San Francisco, CA 94143, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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28
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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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29
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Baggio C, Udompholkul P, Gambini L, Jossart J, Salem AF, Håkansson M, Perry JJP, Pellecchia M. N-locking stabilization of covalent helical peptides: Application to Bfl-1 antagonists. Chem Biol Drug Des 2020; 95:412-426. [PMID: 31898401 DOI: 10.1111/cbdd.13661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/16/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022]
Abstract
Recently, it was reported that tetrapeptides cyclized via lactam bond between the amino terminus and a glutamic residue in position 4 (termed here N-lock) can nucleate helix formation in longer peptides. We applied such strategy to derive N-locked covalent BH3 peptides that were designed to selectively target the anti-apoptotic protein Bfl-1. The resulting agents were soluble in aqueous buffer and displayed a remarkable (low nanomolar) affinity for Bfl-1 and cellular activity. The crystal structure of the complex between such N-locked covalent peptide and Bfl-1 provided insights on the geometry of the N-locking strategy and of the covalent bond between the agent and Bfl-1.
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Affiliation(s)
- Carlo Baggio
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Parima Udompholkul
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Luca Gambini
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Jennifer Jossart
- Department of Biochemistry, College of Natural and Agricultural Sciences, University of California Riverside, Riverside, CA, USA
| | - Ahmed F Salem
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
| | | | - J Jefferson P Perry
- Department of Biochemistry, College of Natural and Agricultural Sciences, University of California Riverside, Riverside, CA, USA
| | - Maurizio Pellecchia
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
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30
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Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2. Sci Rep 2019; 9:20219. [PMID: 31882608 PMCID: PMC6934455 DOI: 10.1038/s41598-019-56078-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 12/04/2019] [Indexed: 12/31/2022] Open
Abstract
We have investigated covalent conjugation of VPPPVPPRRRX′ peptide (where X′ denotes Nε-chloroacetyl lysine) to N-terminal SH3 domain from adapter protein Grb2. Our experimental results confirmed that the peptide first binds to the SH3 domain noncovalently before establishing a covalent linkage through reaction of X′ with the target cysteine residue C32. We have also confirmed that this reaction involves a thiolate-anion form of C32 and follows the SN2 mechanism. For this system, we have developed a new MD-based protocol to model the formation of covalent conjugate. The simulation starts with the known coordinates of the noncovalent complex. When two reactive groups come into contact during the course of the simulation, the reaction is initiated. The reaction is modeled via gradual interpolation between the two sets of force field parameters that are representative of the noncovalent and covalent complexes. The simulation proceeds smoothly, with no appreciable perturbations to temperature, pressure or volume, and results in a high-quality MD model of the covalent complex. The validity of this model is confirmed using the experimental chemical shift data. The new MD-based approach offers a valuable tool to explore the mechanics of protein-peptide conjugation and build accurate models of covalent complexes.
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31
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Guerra RM, Bird GH, Harvey EP, Dharia NV, Korshavn KJ, Prew MS, Stegmaier K, Walensky LD. Precision Targeting of BFL-1/A1 and an ATM Co-dependency in Human Cancer. Cell Rep 2019; 24:3393-3403.e5. [PMID: 30257201 DOI: 10.1016/j.celrep.2018.08.089] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 07/24/2018] [Accepted: 08/29/2018] [Indexed: 11/16/2022] Open
Abstract
Cancer cells overexpress a diversity of anti-apoptotic BCL-2 family proteins, such as BCL-2, MCL-1, and BFL-1/A1, to enforce cellular immortality. Thus, intensive drug development efforts have focused on targeting this class of oncogenic proteins to overcome treatment resistance. Whereas a selective BCL-2 inhibitor has been FDA approved and several small molecule inhibitors of MCL-1 have recently entered phase I clinical testing, BFL-1/A1 remains undrugged. Here, we developed a series of stapled peptide design principles to engineer a functionally selective and cell-permeable BFL-1/A1 inhibitor that is specifically cytotoxic to BFL-1/A1-dependent human cancer cells. Because cancers harbor a diversity of resistance mechanisms and typically require multi-agent treatment, we further investigated BFL-1/A1 co-dependencies by mining a genome-scale CRISPR-Cas9 screen. We identified ataxia-telangiectasia-mutated (ATM) kinase as a BFL-1/A1 co-dependency in acute myeloid leukemia (AML), which informed the validation of BFL-1/A1 and ATM inhibitor co-treatment as a synergistic approach to subverting apoptotic resistance in cancer.
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Affiliation(s)
- Rachel M Guerra
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Gregory H Bird
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Edward P Harvey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Neekesh V Dharia
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Kyle J Korshavn
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Michelle S Prew
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Broad Institute, 415 Main Street, Cambridge, MA 02142, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
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32
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The Structural Biology of Bcl-x L. Int J Mol Sci 2019; 20:ijms20092234. [PMID: 31067648 PMCID: PMC6540150 DOI: 10.3390/ijms20092234] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 01/12/2023] Open
Abstract
Interactions between the pro-survival and pro-apoptotic members of the Bcl-2 family of proteins dictate whether a cell lives or dies. Much of our knowledge of the molecular details of these interactions has come from biochemical and structural studies on the pro-survival protein Bcl-xL. The first high-resolution structure of any Bcl-2 family member was of Bcl-xL, which revealed the conserved topology amongst all family members. Subsequent structures of Bcl-xL complexes with pro-apoptotic ligands demonstrated the general features of all pro-survival:pro-apoptotic complexes. Structural studies involving Bcl-xL were also the basis for the discovery of the first small-molecule pro-survival protein inhibitors, leading ultimately to the development of a new class of drugs now successfully used for cancer treatment in the clinic. This article will review our current knowledge of the structural biology of Bcl-xL and how this has impacted our understanding of the molecular details of the intrinsic apoptotic pathway.
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33
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Ali AM, Atmaj J, Van Oosterwijk N, Groves MR, Dömling A. Stapled Peptides Inhibitors: A New Window for Target Drug Discovery. Comput Struct Biotechnol J 2019; 17:263-281. [PMID: 30867891 PMCID: PMC6396041 DOI: 10.1016/j.csbj.2019.01.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 12/11/2022] Open
Abstract
Protein-protein interaction (PPI) is a hot topic in clinical research as protein networking has a major impact in human disease. Such PPIs are potential drugs targets, leading to the need to inhibit/block specific PPIs. While small molecule inhibitors have had some success and reached clinical trials, they have generally failed to address the flat and large nature of PPI surfaces. As a result, larger biologics were developed for PPI surfaces and they have successfully targeted PPIs located outside the cell. However, biologics have low bioavailability and cannot reach intracellular targets. A novel class -hydrocarbon-stapled α-helical peptides that are synthetic mini-proteins locked into their bioactive structure through site-specific introduction of a chemical linker- has shown promise. Stapled peptides show an ability to inhibit intracellular PPIs that previously have been intractable with traditional small molecule or biologics, suggesting that they offer a novel therapeutic modality. In this review, we highlight what stapling adds to natural-mimicking peptides, describe the revolution of synthetic chemistry techniques and how current drug discovery approaches have been adapted to stabilize active peptide conformations, including ring-closing metathesis (RCM), lactamisation, cycloadditions and reversible reactions. We provide an overview on the available stapled peptide high-resolution structures in the protein data bank, with four selected structures discussed in details due to remarkable interactions of their staple with the target surface. We believe that stapled peptides are promising drug candidates and open the doors for peptide therapeutics to reach currently "undruggable" space.
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Affiliation(s)
| | | | | | | | - Alexander Dömling
- Department of Drug Design, University of Groningen, Antonius Deusinglaan1, 9700AD Groningen, the Netherlands
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34
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Abe H, Sato C, Ohishi Y, Inouye M. Metathesis‐Based Stapling of a Pyridine–Acetylene–Phenol Oligomer Having Alkenyl Side Chains after Intermolecular Templation by Native Saccharides. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800531] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Hajime Abe
- Graduate School of Pharmaceutical Sciences University of Toyama Sugitani 2630 930‐0194 Toyama Japan
- Faculty of Pharmaceutical Sciences Himeji Dokkyo University Kami‐ono 7‐2‐1 670‐8524 Himeji Hyogo Japan
| | - Chihiro Sato
- Graduate School of Pharmaceutical Sciences University of Toyama Sugitani 2630 930‐0194 Toyama Japan
| | - Yuki Ohishi
- Graduate School of Pharmaceutical Sciences University of Toyama Sugitani 2630 930‐0194 Toyama Japan
| | - Masahiko Inouye
- Graduate School of Pharmaceutical Sciences University of Toyama Sugitani 2630 930‐0194 Toyama Japan
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35
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D de Araujo A, Lim J, Wu KC, Xiang Y, Good AC, Skerlj R, Fairlie DP. Bicyclic Helical Peptides as Dual Inhibitors Selective for Bcl2A1 and Mcl-1 Proteins. J Med Chem 2018; 61:2962-2972. [PMID: 29584430 DOI: 10.1021/acs.jmedchem.8b00010] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A 26-residue peptide BimBH3 binds indiscriminately to multiple oncogenic Bcl2 proteins that regulate apoptosis of cancer cells. Specific inhibition of the BimBH3-Bcl2A1 protein-protein interaction was obtained in vitro and in cancer cells by shortening the peptide to 14 residues, inserting two cyclization constraints to stabilize a water-stable α-helix, and incorporating an N-terminal acrylamide electrophile for selective covalent bonding to Bcl2A1. Mass spectrometry of trypsin-digested bands on electrophoresis gels established covalent bonding of an electrophilic helix to just one of the three cysteines in Bcl2A1, the one (Cys55) at the BimBH3-Bcl2A1 protein-protein interaction interface. Optimizing the helix-inducing constraints and the sequence subsequently enabled electrophile removal without loss of inhibitor potency. The bicyclic helical peptides were potent, cell permeable, plasma-stable, dual inhibitors of Bcl2A1 and Mcl-1 with high selectivity over other Bcl2 proteins. One bicyclic peptide was shown to inhibit the interaction between a pro-apoptotic protein (Bim) and either endogenous Bcl2A1 or Mcl-1, to induce apoptosis of SKMel28 human melanoma cells, and to sensitize them for enhanced cell death by the anticancer drug etoposide. These approaches look promising for chemically silencing intracellular proteins.
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Affiliation(s)
- Aline D de Araujo
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience, The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Junxian Lim
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience, The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Kai-Chen Wu
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience, The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Yibin Xiang
- Noliva Therapeutics LLC , Newton , Massachusetts 02465 , United States
| | - Andrew C Good
- Noliva Therapeutics LLC , Newton , Massachusetts 02465 , United States
| | - Renato Skerlj
- Noliva Therapeutics LLC , Newton , Massachusetts 02465 , United States
| | - David P Fairlie
- Division of Chemistry and Structural Biology, ARC Centre of Excellence in Advanced Molecular Imaging , Institute for Molecular Bioscience, The University of Queensland , Brisbane , Queensland 4072 , Australia
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