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Thorman AW, Reigle J, Chutipongtanate S, Yang J, Shamsaei B, Pilarczyk M, Fazel-Najafabadi M, Adamczak R, Kouril M, Bhatnagar S, Hummel S, Niu W, Morrow AL, Czyzyk-Krzeska MF, McCullumsmith R, Seibel W, Nassar N, Zheng Y, Hildeman DA, Medvedovic M, Herr AB, Meller J. Accelerating drug discovery and repurposing by combining transcriptional signature connectivity with docking. SCIENCE ADVANCES 2024; 10:eadj3010. [PMID: 39213358 PMCID: PMC11364105 DOI: 10.1126/sciadv.adj3010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 07/26/2024] [Indexed: 09/04/2024]
Abstract
We present an in silico approach for drug discovery, dubbed connectivity enhanced structure activity relationship (ceSAR). Building on the landmark LINCS library of transcriptional signatures of drug-like molecules and gene knockdowns, ceSAR combines cheminformatic techniques with signature concordance analysis to connect small molecules and their targets and further assess their biophysical compatibility using molecular docking. Candidate compounds are first ranked in a target structure-independent manner, using chemical similarity to LINCS analogs that exhibit transcriptomic concordance with a target gene knockdown. Top candidates are subsequently rescored using docking simulations and machine learning-based consensus of the two approaches. Using extensive benchmarking, we show that ceSAR greatly reduces false-positive rates, while cutting run times by multiple orders of magnitude and further democratizing drug discovery pipelines. We further demonstrate the utility of ceSAR by identifying and experimentally validating inhibitors of BCL2A1, an important antiapoptotic target in melanoma and preterm birth-associated inflammation.
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Affiliation(s)
- Alexander W. Thorman
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - James Reigle
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Somchai Chutipongtanate
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Juechen Yang
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Behrouz Shamsaei
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Marcin Pilarczyk
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Mehdi Fazel-Najafabadi
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Rafal Adamczak
- Department of Informatics, Faculty of Physics, Astronomy an Informatics, Nicolaus Copernicus University, Toruń, Poland
| | - Michal Kouril
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Surbhi Bhatnagar
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Computer Science, University of Cincinnati, Cincinnati, OH, USA
| | - Sarah Hummel
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Wen Niu
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Ardythe L. Morrow
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Maria F. Czyzyk-Krzeska
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Veterans Affairs, Cincinnati Veteran Affairs Medical Center, Cincinnati, OH, USA
| | | | - William Seibel
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Nicolas Nassar
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Yi Zheng
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - David A. Hildeman
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Mario Medvedovic
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati, Cincinnati, OH, USA
| | - Andrew B. Herr
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
| | - Jarek Meller
- Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA
- Department of Biostatistics, Health Informatics and Data Sciences, University of Cincinnati, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA
- Department of Informatics, Faculty of Physics, Astronomy an Informatics, Nicolaus Copernicus University, Toruń, Poland
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Department of Computer Science, University of Cincinnati, Cincinnati, OH, USA
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2
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Suraweera CD, Espinoza B, Hinds MG, Kvansakul M. Mastering Death: The Roles of Viral Bcl-2 in dsDNA Viruses. Viruses 2024; 16:879. [PMID: 38932171 PMCID: PMC11209288 DOI: 10.3390/v16060879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 05/25/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Proteins of the Bcl-2 family regulate cellular fate via multiple mechanisms including apoptosis, autophagy, senescence, metabolism, inflammation, redox homeostasis, and calcium flux. There are several regulated cell death (RCD) pathways, including apoptosis and autophagy, that use distinct molecular mechanisms to elicit the death response. However, the same proteins/genes may be deployed in multiple biochemical pathways. In apoptosis, Bcl-2 proteins control the integrity of the mitochondrial outer membrane (MOM) by regulating the formation of pores in the MOM and apoptotic cell death. A number of prosurvival genes populate the genomes of viruses including those of the pro-survival Bcl-2 family. Viral Bcl-2 proteins are sequence and structural homologs of their cellular counterparts and interact with cellular proteins in apoptotic and autophagic pathways, potentially allowing them to modulate these pathways and determine cellular fate.
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Affiliation(s)
- Chathura D. Suraweera
- Genome Sciences and Cancer Division, The John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia;
| | - Benjamin Espinoza
- Department of Biochemistry and Chemistry, La Trobe University, Melbourne, VIC 3086, Australia;
| | - Mark G. Hinds
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Marc Kvansakul
- Genome Sciences and Cancer Division, The John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia;
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3
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Gielecińska A, Kciuk M, Yahya EB, Ainane T, Mujwar S, Kontek R. Apoptosis, necroptosis, and pyroptosis as alternative cell death pathways induced by chemotherapeutic agents? Biochim Biophys Acta Rev Cancer 2023; 1878:189024. [PMID: 37980943 DOI: 10.1016/j.bbcan.2023.189024] [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: 07/26/2023] [Revised: 08/22/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023]
Abstract
For decades, common chemotherapeutic drugs have been established to trigger apoptosis, the preferred immunologically "silent" form of cell death. The primary objective of this review was to show that various FDA-approved chemotherapeutic drugs, including cisplatin, cyclosporine, doxorubicin, etoposide, 5-fluorouracil, gemcitabine, paclitaxel, or vinblastine can trigger necroptosis and pyroptosis. We aimed to provide the advantages and disadvantages of the induction of the given type of cell death by chemotherapeutical agents. Moreover, we give a short overview of the molecular mechanism of each type of cell death and indicate the existing crosstalks between cell death types. Finally, we provide a comparison of cell death types to facilitate the exploration of cell death types induced by other chemotherapeutical agents. Understanding the cell death pathway induced by a drug can lessen side effects and assist the discovery of new combinations with synergistic effects and low systemic toxicity.
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Affiliation(s)
- A Gielecińska
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Molecular Biotechnology and Genetics, Banacha St. 12/16, 90-237 Lodz, Poland; University of Lodz, Doctoral School of Exact and Natural Sciences, Banacha Street 12/16, 90-237 Lodz, Poland.
| | - M Kciuk
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Molecular Biotechnology and Genetics, Banacha St. 12/16, 90-237 Lodz, Poland
| | - E-B Yahya
- Bioprocess Technology Division, School of Industrial Technology, University Sains Malaysia, Penang 11800, Malaysia
| | - T Ainane
- Superior School of Technology of Khenifra, University of Sultan Moulay Slimane, P.O. Box 170, Khenifra 54000, Morocco
| | - S Mujwar
- Chitkara College of Pharmacy, Chitkara University, Rajpura 140401, Punjab, India
| | - R Kontek
- University of Lodz, Faculty of Biology and Environmental Protection, Department of Molecular Biotechnology and Genetics, Banacha St. 12/16, 90-237 Lodz, Poland
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4
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Wyatt S, Glover K, Dasanna S, Lewison M, González-García M, Colbert CL, Sinha SC. Epstein-Barr Virus Encoded BCL2, BHRF1, Downregulates Autophagy by Noncanonical Binding of BECN1. Biochemistry 2023; 62:2934-2951. [PMID: 37776275 PMCID: PMC11166532 DOI: 10.1021/acs.biochem.3c00225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/02/2023]
Abstract
γ-herpesviruses (γHVs) encode BCL2 homologues (vBCL2) that bind the Bcl-2 homology 3 domains (BH3Ds) of diverse proteins, inhibiting apoptosis and promoting host cell and virus survival. vBCLs encoded by Kaposi sarcoma-associated HV (KSHV) and γHV68 downregulate autophagy, a degradative cellular process crucial for homeostasis and innate immune responses to pathogens, by binding to a BH3D in BECN1, a key autophagy protein. Epstein-Barr virus (EBV) encodes a vBCL2 called BHRF1. Here we show that unlike the KSHV and γHV68 vBCL2s, BHRF1 does not bind the isolated BECN1 BH3D. We use yeast two-hybrid assays to identify the minimal region of BECN1 required and sufficient for binding BHRF1. We confirm that this is a direct, albeit weak, interaction via affinity pull-down assays and isothermal titration calorimetry. To understand the structural bases of BHRF1 specificity, we determined the 2.6 Å crystal structure of BHRF1 bound to the BID BH3D, which binds ∼400-times tighter to BHRF1 than does BECN1, and performed a detailed structural comparison with complexes of diverse BH3Ds bound to BHRF1 and to other antiapoptotic BCL2s. Lastly, we used mammalian cell autophagy assays to demonstrate that BHRF1 downregulates autophagy and that a cell-permeable peptide derived from the BID BH3D inhibits BHRF1-mediated downregulation of autophagy. In summary, our results suggest that BHRF1 downregulates autophagy by noncanonical binding of a flexible region of BECN1 that includes but is not limited to the BH3D and that BH3D-derived peptides that bind better to BHRF1 can block downregulation of autophagy by BHRF1.
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Affiliation(s)
- Samuel Wyatt
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
| | - Karen Glover
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
| | - Srinivasulu Dasanna
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
| | - Monica Lewison
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
| | | | - Christopher L. Colbert
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
| | - Sangita C. Sinha
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
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5
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Lim D, Choe SH, Jin S, Lee S, Kim Y, Shin HC, Choi JS, Oh DB, Kim SJ, Seo J, Ku B. Structural basis for proapoptotic activation of Bak by the noncanonical BH3-only protein Pxt1. PLoS Biol 2023; 21:e3002156. [PMID: 37315086 DOI: 10.1371/journal.pbio.3002156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 05/10/2023] [Indexed: 06/16/2023] Open
Abstract
Bak is a critical executor of apoptosis belonging to the Bcl-2 protein family. Bak contains a hydrophobic groove where the BH3 domain of proapoptotic Bcl-2 family members can be accommodated, which initiates its activation. Once activated, Bak undergoes a conformational change to oligomerize, which leads to mitochondrial destabilization and the release of cytochrome c into the cytosol and eventual apoptotic cell death. In this study, we investigated the molecular aspects and functional consequences of the interaction between Bak and peroxisomal testis-specific 1 (Pxt1), a noncanonical BH3-only protein exclusively expressed in the testis. Together with various biochemical approaches, this interaction was verified and analyzed at the atomic level by determining the crystal structure of the Bak-Pxt1 BH3 complex. In-depth biochemical and cellular analyses demonstrated that Pxt1 functions as a Bak-activating proapoptotic factor, and its BH3 domain, which mediates direct intermolecular interaction with Bak, plays a critical role in triggering apoptosis. Therefore, this study provides a molecular basis for the Pxt1-mediated novel pathway for the activation of apoptosis and expands our understanding of the cell death signaling coordinated by diverse BH3 domain-containing proteins.
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Affiliation(s)
- Dahwan Lim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Department of Biochemistry, Chungnam National University, Daejeon, Korea
| | - So-Hui Choe
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sein Jin
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Seulgi Lee
- Department of Biochemistry, Chungnam National University, Daejeon, Korea
| | - Younjin Kim
- Department of Biochemistry, Chungnam National University, Daejeon, Korea
| | - Ho-Chul Shin
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Joon Sig Choi
- Department of Biochemistry, Chungnam National University, Daejeon, Korea
| | - Doo-Byoung Oh
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Korea
| | - Seung Jun Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Critical Diseases Diagnostics Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, Korea
| | - Jinho Seo
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, Korea
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, Korea
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6
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Heckmeier PJ, Ruf J, Janković BG, Hamm P. MCL-1 promiscuity and the structural resilience of its binding partners. J Chem Phys 2023; 158:095101. [PMID: 36889945 DOI: 10.1063/5.0137239] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
Abstract
The allosteric protein MCL-1 and its natural inhibitors, the BH3-only proteins PUMA, BIM, and NOXA regulate apoptosis by interacting promiscuously within an entangled binding network. Little is known about the transient processes and dynamic conformational fluctuations that are the basis for the formation and stability of the MCL-1/BH3-only complex. In this study, we designed photoswitchable versions of MCL-1/PUMA and MCL-1/NOXA, and investigated the protein response after an ultrafast photo-perturbation with transient infrared spectroscopy. We observed partial α-helical unfolding in all cases, albeit on strongly varying timescales (1.6 ns for PUMA, 9.7 ns for the previously studied BIM, and 85 ns for NOXA). These differences are interpreted as a BH3-only-specific "structural resilience" to defy the perturbation while remaining in MCL-1's binding pocket. Thus, the presented insights could help to better understand the differences between PUMA, BIM, and NOXA, the promiscuity of MCL-1, in general, and the role of the proteins in the apoptotic network.
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Affiliation(s)
| | - Jeannette Ruf
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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7
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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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8
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Roy MJ, Vom A, Okamoto T, Smith BJ, Birkinshaw RW, Yang H, Abdo H, White CA, Segal D, Huang DCS, Baell JB, Colman PM, Czabotar PE, Lessene G. Structure-Guided Development of Potent Benzoylurea Inhibitors of BCL-X L and BCL-2. J Med Chem 2021; 64:5447-5469. [PMID: 33904752 DOI: 10.1021/acs.jmedchem.0c01771] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The BCL-2 family of proteins (including the prosurvival proteins BCL-2, BCL-XL, and MCL-1) is an important target for the development of novel anticancer therapeutics. Despite the challenges of targeting protein-protein interaction (PPI) interfaces with small molecules, a number of inhibitors (called BH3 mimetics) have entered the clinic and the BCL-2 inhibitor, ABT-199/venetoclax, is already proving transformative. For BCL-XL, new validated chemical series are desirable. Here, we outline the crystallography-guided development of a structurally distinct series of BCL-XL/BCL-2 inhibitors based on a benzoylurea scaffold, originally proposed as α-helix mimetics. We describe structure-guided exploration of a cryptic "p5" pocket identified in BCL-XL. This work yields novel inhibitors with submicromolar binding, with marked selectivity toward BCL-XL. Extension into the hydrophobic p2 pocket yielded the most potent inhibitor in the series, binding strongly to BCL-XL and BCL-2 (nanomolar-range half-maximal inhibitory concentration (IC50)) and displaying mechanism-based killing in cells engineered to depend on BCL-XL for survival.
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Affiliation(s)
- Michael J Roy
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Amelia Vom
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Toru Okamoto
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Brian J Smith
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Richard W Birkinshaw
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Hong Yang
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Houda Abdo
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Christine A White
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - David Segal
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
| | - David C S Huang
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Jonathan B Baell
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Peter M Colman
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
| | - Guillaume Lessene
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3050, Australia
- Department of Pharmacology and Therapeutics, The University of Melbourne, Parkville, VIC 3050, Australia
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9
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Fairlie WD, Lee EF. Co-Operativity between MYC and BCL-2 Pro-Survival Proteins in Cancer. Int J Mol Sci 2021; 22:2841. [PMID: 33799592 PMCID: PMC8000576 DOI: 10.3390/ijms22062841] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/30/2022] Open
Abstract
B-Cell Lymphoma 2 (BCL-2), c-MYC and related proteins are arguably amongst the most widely studied in all of biology. Every year there are thousands of papers reporting on different aspects of their biochemistry, cellular and physiological mechanisms and functions. This plethora of literature can be attributed to both proteins playing essential roles in the normal functioning of a cell, and by extension a whole organism, but also due to their central role in disease, most notably, cancer. Many cancers arise due to genetic lesions resulting in deregulation of both proteins, and indeed the development and survival of tumours is often dependent on co-operativity between these protein families. In this review we will discuss the individual roles of both proteins in cancer, describe cancers where co-operativity between them has been well-characterised and finally, some strategies to target these proteins therapeutically.
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Affiliation(s)
- Walter Douglas Fairlie
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3084, Australia
| | - Erinna F. Lee
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Melbourne, VIC 3084, Australia
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3084, Australia
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10
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Han CW, Lee HN, Jeong MS, Park SY, Jang SB. Structural basis of the p53 DNA binding domain and PUMA complex. Biochem Biophys Res Commun 2021; 548:39-46. [PMID: 33631672 DOI: 10.1016/j.bbrc.2021.02.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 11/18/2022]
Abstract
PUMA (p53-upregulated modulator of apoptosis) is localized in mitochondria and a direct target in p53-mediated apoptosis. p53 elicits mitochondrial apoptosis via transcription-dependent and independent mechanisms. p53 is known to induce apoptosis via the transcriptional induction of PUMA, which encodes proapoptotic BH3-only members of the Bcl-2 protein family. However, the transcription-independent mechanisms of human PUMA remain poorly defined. For example, it is not known whether PUMA interacts directly with the DNA binding domain (DBD: residues 92-293) of p53 in vitro. Here, the structure of the complex between the DBD of p53 and PUMA peptide was elucidated by X-ray crystallography. Isothermal titration calorimetry showed that PUMA peptide binds strongly with p53 DBD, and the crystal structure of p53-PUMA peptide complex revealed it contains four molecules of p53 DBD and one PUMA peptide per asymmetric unit in space group P1. PUMA peptide bound to the N-terminal residues of p53 DBD. A cell proliferation assay demonstrated PUMA peptide inhibited the growth of a lung cancer cell line. These results contribute to understanding of the mechanism responsible for p53-mediated apoptosis.
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Affiliation(s)
- Chang Woo Han
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea
| | - Han Na Lee
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea
| | - Mi Suk Jeong
- Korea Nanobiotechnology Center, Pusan National University, 2,Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea
| | - So Young Park
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea
| | - Se Bok Jang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, 2Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan, 46241, Republic of Korea.
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11
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Predicted Hotspot Residues Involved in Allosteric Signal Transmission in Pro-Apoptotic Peptide-Mcl1 Complexes. Biomolecules 2020; 10:biom10081114. [PMID: 32731448 PMCID: PMC7463671 DOI: 10.3390/biom10081114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/16/2020] [Accepted: 07/24/2020] [Indexed: 11/30/2022] Open
Abstract
Mcl1 is a primary member of the Bcl–2 family—anti–apoptotic proteins (AAP)—that is overexpressed in several cancer pathologies. The apoptotic regulation is mediated through the binding of pro-apoptotic peptides (PAPs) (e.g., Bak and Bid) at the canonical hydrophobic binding groove (CBG) of Mcl1. Although all PAPs form amphipathic α-helices, their amino acid sequences vary to different degree. This sequence variation exhibits a central role in the binding partner selectivity towards different AAPs. Thus, constructing a novel peptide or small organic molecule with the ability to mimic the natural regulatory process of PAP is essential to inhibit various AAPs. Previously reported experimental binding free energies (BFEs) were utilized in the current investigation aimed to understand the mechanistic basis of different PAPs targeted to mMcl1. Molecular dynamics (MD) simulations used to estimate BFEs between mMcl1—PAP complexes using Molecular Mechanics-Generalized Born Solvent Accessible (MMGBSA) approach with multiple parameters. Predicted BFE values showed an excellent agreement with the experiment (R2 = 0.92). The van–der Waals (ΔGvdw) and electrostatic (ΔGele) energy terms found to be the main energy components that drive heterodimerization of mMcl1—PAP complexes. Finally, the dynamic network analysis predicted the allosteric signal transmission pathway involves more favorable energy contributing residues. In total, the results obtained from the current investigation may provide valuable insights for the synthesis of a novel peptide or small organic inhibitor targeting Mcl1.
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12
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Marimuthu P, Razzokov J, Eshonqulov G. Disruption of conserved polar interactions causes a sequential release of Bim mutants from the canonical binding groove of Mcl1. Int J Biol Macromol 2020; 158:364-374. [PMID: 32376253 DOI: 10.1016/j.ijbiomac.2020.04.243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 12/15/2022]
Abstract
Mcl1 is an important anti-apoptotic member of the Bcl2 family proteins that are upregulated in several cancer malignancies. The canonical binding groove (CBG) located at the surface of Mcl1 exhibits a critical role in binding partners selectively via the BH3-domain of pro-apoptotic Bcl2 family members that trigger the downregulation of Mcl1 function. There are several crystal structures of point-mutated pro-apoptotic Bim peptides in complex with Mcl1. However, the mechanistic effects of such point-mutations towards peptide binding and complex stability still remain unexplored. Here, the effects of the reported point mutations in Bim peptides and their binding mechanisms to Mcl1 were computationally evaluated using atomistic-level steered molecular dynamics (SMD) simulations. A range of external-forces and constant-velocities were applied to the Bim peptides to uncover the mechanistic basis of peptide dissociation from the CBG of Mcl1. Although the peptides showed similarities in their dissociation pathways, the peak rupture forces varied significantly. According to simulations results, the disruption of the conserved polar contacts at the complex interface causes a sequential release of the peptides from the CBG of Mcl1. Overall, the results obtained from the current study may provide valuable insights for the development of novel anti-cancer peptide-inhibitors that can downregulate Mcl1's function.
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Affiliation(s)
- Parthiban Marimuthu
- Structural Bioinformatics Laboratory (SBL), Biochemistry and Pharmacy, Faculty of Science and Engineering, Åbo Akademi University, FI-20520 Turku, Finland.
| | - Jamoliddin Razzokov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Gofur Eshonqulov
- Department of Physics, National University of Uzbekistan, 100174 Tashkent, Uzbekistan
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13
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The Bcl-2 Family: Ancient Origins, Conserved Structures, and Divergent Mechanisms. Biomolecules 2020; 10:biom10010128. [PMID: 31940915 PMCID: PMC7022251 DOI: 10.3390/biom10010128] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/18/2019] [Accepted: 01/09/2020] [Indexed: 12/13/2022] Open
Abstract
Intrinsic apoptosis, the response to intracellular cell death stimuli, is regulated by the interplay of the B-cell lymphoma 2 (Bcl-2) family and their membrane interactions. Bcl-2 proteins mediate a number of processes including development, homeostasis, autophagy, and innate and adaptive immune responses and their dysregulation underpins a host of diseases including cancer. The Bcl-2 family is characterized by the presence of conserved sequence motifs called Bcl-2 homology motifs, as well as a transmembrane region, which form the interaction sites and intracellular location mechanism, respectively. Bcl-2 proteins have been recognized in the earliest metazoans including Porifera (sponges), Placozoans, and Cnidarians (e.g., Hydra). A number of viruses have gained Bcl-2 homologs and subvert innate immunity and cellular apoptosis for their replication, but they frequently have very different sequences to their host Bcl-2 analogs. Though most mechanisms of apoptosis initiation converge on activation of caspases that destroy the cell from within, the numerous gene insertions, deletions, and duplications during evolution have led to a divergence in mechanisms of intrinsic apoptosis. Currently, the action of the Bcl-2 family is best understood in vertebrates and nematodes but new insights are emerging from evolutionarily earlier organisms. This review focuses on the mechanisms underpinning the activity of Bcl-2 proteins including their structures and interactions, and how they have changed over the course of evolution.
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14
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Ghufran M, Rehman AU, Shah M, Ayaz M, Ng HL, Wadood A. In-silico design of peptide inhibitors of K-Ras target in cancer disease. J Biomol Struct Dyn 2019; 38:5488-5499. [DOI: 10.1080/07391102.2019.1704880] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mehreen Ghufran
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
- State Key Laboratory of Microbial Metabolism, 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, China
| | - Masaud Shah
- Department of Molecular Science and Technology, Ajou University, South Korea
| | - Muhammad Ayaz
- Department of Pharmacy, University of Malakand, Pakistan
| | - Ho Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, USA
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
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15
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Suraweera CD, Caria S, Järvå M, Hinds MG, Kvansakul M. A structural investigation of NRZ mediated apoptosis regulation in zebrafish. Cell Death Dis 2018; 9:967. [PMID: 30237469 PMCID: PMC6148235 DOI: 10.1038/s41419-018-0992-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/12/2018] [Accepted: 07/16/2018] [Indexed: 01/20/2023]
Abstract
Bcl-2 family proteins play a crucial role in regulating apoptosis, a process critical for development, eliminating damaged or infected cells, host-pathogen interactions and in disease. Dysregulation of Bcl-2 proteins elicits an expansive cell survival mechanism promoting cell migration, invasion and metastasis. Through a network of intra-family protein-protein interactions Bcl-2 family members regulate the release of cell death factors from mitochondria. NRZ is a novel zebrafish pro-survival Bcl-2 orthologue resident on mitochondria and the endoplasmic reticulum (ER). However, the mechanism of NRZ apoptosis inhibition has not yet been clarified. Here we examined the interactions of NRZ with pro-apoptotic members of the Bcl-2 family using a combination of isothermal calorimetry and mutational analysis of NRZ. We show that NRZ binds almost all zebrafish pro-apoptotic proteins and displays a broad range of affinities. Furthermore, we define the structural basis for apoptosis inhibition of NRZ by solving the crystal structure of both apo-NRZ and a holo form bound to a peptide spanning the binding motif of the pro-apoptotic zBad, a BH3-only protein orthologous to mammalian Bad. The crystal structure of NRZ revealed that it adopts the conserved Bcl-2 like fold observed for other cellular pro-survival Bcl-2 proteins and employs the canonical ligand binding groove to bind Bad BH3 peptide. NRZ engagement of Bad BH3 involves the canonical ionic interaction between NRZ R86 and Bad D104 and an additional ionic interaction between NRZ D79 and Bad R100, and substitution of either NRZ R86 or D79 to Ala reduces the binding to Bad BH3 tenfold or more. Our findings provide a detailed mechanistic understanding for NRZ mediated anti-apoptotic activity in zebrafish by revealing binding to both Bad and Noxa, suggesting that NRZ is likely to occupy a unique mechanistic role in zebrafish apoptosis regulation by acting as a highly promiscuous pro-apoptotic Bcl-2 binder.
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Affiliation(s)
- Chathura D Suraweera
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Sofia Caria
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Michael Järvå
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Mark G Hinds
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia.
| | - Marc Kvansakul
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia.
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16
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Huang Z, Lu L, Jiang T, Zhang S, Shen Y, Zheng Z, Zhao A, Gao R, Li R, Zhou S, Liu J. miR-29b affects neurocyte apoptosis by targeting MCL-1 during cerebral ischemia/reperfusion injury. Exp Ther Med 2018; 16:3399-3404. [PMID: 30233687 PMCID: PMC6143871 DOI: 10.3892/etm.2018.6622] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/31/2018] [Indexed: 12/21/2022] Open
Abstract
The present study aimed to determine whether an miRNA (miR)-29b inhibitor protected against cerebral ischemia/reperfusion (I/R) injury in vitro and to investigate the underlying mechanisms. As a model for induced cerebral IR injury, N2a cells were exposed to an oxygen-glucose deprivation/reoxygenation (OGD/R) environment. Using this model, it was demonstrated that miR-29b was significantly upregulated compared with cells in a normal environment. The interactions between miR-29b and myeloid cell leukemia sequence (MCL)-1 were then investigated using dual-luciferase assays, revealing a strong regulation of MCL-1 through the 3'untranslated region. Using the OGD/R model, the present study additionally examined the effects of miR-29b and miR-29b inhibitor on cell viability and apoptosis using Cell Counting kit 8 and flow cytometry assays, respectively. miR-29b transfection led to increased N2a cell apoptosis and reduced cell viability under an OGD/R environment. However, this effect was reversed by the miR-29b inhibitor. Finally, the effects of miR-29b on the expression of several Wnt-associating proteins were examined. It was observed that B cell lymphoma-2 was inhibited by miR-29b, as was MCL-1, whereas caspase-3 expression was promoted. The miR-29b inhibitor demonstrated the opposite effect. Overall, miR-29b promoted neurocyte apoptosis by targeting MCL-1 during cerebral I/R injury. The results of the present study suggest a potential novel therapeutic target for the treatment of ischemic stroke.
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Affiliation(s)
- Zhi Huang
- Department of Intervention, The Affiliated Baiyun Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China.,Department of Intervention, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China
| | - Lu Lu
- Shenzhen Key Laboratory of Ophthalmoloy, Shenzhen Eye Hospital, Shenzhen, Guangdong 518040, P.R. China
| | - Tianpeng Jiang
- Department of Intervention, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China
| | - Shuai Zhang
- Department of Intervention, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China
| | - Yaping Shen
- Department of Intervention, The Affiliated Baiyun Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China
| | - Zhu Zheng
- School of Biology and Engineering, Guizhou Medical University, Guiyang, Guizhou 550001, P.R. China
| | - Ansu Zhao
- School of Biology and Engineering, Guizhou Medical University, Guiyang, Guizhou 550001, P.R. China
| | - Rui Gao
- Guizhou Entry-Exit Inspection and Quarantine Bureau of The People's Republic of China, Guiyang, Guizhou 550002, P.R. China
| | - Rui Li
- Department of Rehabilitation, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550002, P.R. China
| | - Shi Zhou
- Department of Intervention, The Affiliated Baiyun Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China.,Department of Intervention, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China
| | - Jing Liu
- Department of Intervention, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550002, P.R. China
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17
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Promiscuous and Selective: How Intrinsically Disordered BH3 Proteins Interact with Their Pro-survival Partner MCL-1. J Mol Biol 2018; 430:2468-2477. [DOI: 10.1016/j.jmb.2018.04.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 10/17/2022]
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18
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Crabtree MD, Mendonça CATF, Bubb QR, Clarke J. Folding and binding pathways of BH3-only proteins are encoded within their intrinsically disordered sequence, not templated by partner proteins. J Biol Chem 2018; 293:9718-9723. [PMID: 29716994 PMCID: PMC6016464 DOI: 10.1074/jbc.ra118.002791] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/24/2018] [Indexed: 12/03/2022] Open
Abstract
Intrinsically disordered regions are present in one-third of eukaryotic proteins and are overrepresented in cellular processes such as signaling, suggesting that intrinsically disordered proteins (IDPs) may have a functional advantage over folded proteins. Upon interacting with a partner macromolecule, a subset of IDPs can fold and bind to form a well-defined three-dimensional conformation. For example, disordered BH3-only proteins bind promiscuously to a large number of homologous BCL-2 family proteins, where they fold to a helical structure in a groove on the BCL-2–like protein surface. As two protein chains are involved in the folding reaction, and the structure is only formed in the presence of the partner macromolecule, this raises the question of where the folding information is encoded. Here, we examine these coupled folding and binding reactions to determine which component determines the folding and binding pathway. Using Φ value analysis to compare transition state interactions between the disordered BH3-only proteins PUMA and BID and the folded BCL-2–like proteins A1 and MCL-1, we found that, even though the BH3-only protein is disordered in isolation and requires a stabilizing partner to fold, its folding and binding pathway is encoded in the IDP itself; the reaction is not templated by the folded partner. We suggest that, by encoding both its transition state and level of residual structure, an IDP can evolve a specific kinetic profile, which could be a crucial functional advantage of disorder.
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Affiliation(s)
- Michael D Crabtree
- From the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Carolina A T F Mendonça
- From the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Quenton R Bubb
- From the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jane Clarke
- From the Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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19
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Chen Y, Wang J, Zhang J, Wang W. Binding modes of Bcl-2 homology 3 (BH3) peptides with anti-apoptotic protein A1 and redesign of peptide inhibitors: a computational study. J Biomol Struct Dyn 2017; 36:3967-3977. [DOI: 10.1080/07391102.2017.1404933] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yantao Chen
- Shenzhen Key Laboratory of Environmental Chemistry and Ecological Remediation, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jun Wang
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Jian Zhang
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Wei Wang
- National Laboratory of Solid State Microstructure, Department of Physics, and Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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20
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Fitzsimmons L, Kelly GL. EBV and Apoptosis: The Viral Master Regulator of Cell Fate? Viruses 2017; 9:E339. [PMID: 29137176 PMCID: PMC5707546 DOI: 10.3390/v9110339] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 12/14/2022] Open
Abstract
Epstein-Barr virus (EBV) was first discovered in cells from a patient with Burkitt lymphoma (BL), and is now known to be a contributory factor in 1-2% of all cancers, for which there are as yet, no EBV-targeted therapies available. Like other herpesviruses, EBV adopts a persistent latent infection in vivo and only rarely reactivates into replicative lytic cycle. Although latency is associated with restricted patterns of gene expression, genes are never expressed in isolation; always in groups. Here, we discuss (1) the ways in which the latent genes of EBV are known to modulate cell death, (2) how these mechanisms relate to growth transformation and lymphomagenesis, and (3) how EBV genes cooperate to coordinately regulate key cell death pathways in BL and lymphoblastoid cell lines (LCLs). Since manipulation of the cell death machinery is critical in EBV pathogenesis, understanding the mechanisms that underpin EBV regulation of apoptosis therefore provides opportunities for novel therapeutic interventions.
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Affiliation(s)
- Leah Fitzsimmons
- Institute of Cancer and Genomic Sciences and Centre for Human Virology, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
| | - Gemma L Kelly
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute for Medical Research, Parkville, Melbourne, VIC 3052, Australia.
- Department of Medical Biology, The University of Melbourne, Parkville, Melbourne, VIC 3052, Australia.
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21
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Structural and Functional Insight into Canarypox Virus CNP058 Mediated Regulation of Apoptosis. Viruses 2017; 9:v9100305. [PMID: 29053589 PMCID: PMC5691656 DOI: 10.3390/v9100305] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 10/15/2017] [Accepted: 10/18/2017] [Indexed: 12/21/2022] Open
Abstract
Programmed cell death or apoptosis is an important component of host defense systems against viral infection. The B-cell lymphoma 2 (Bcl-2) proteins family is the main arbiter of mitochondrially mediated apoptosis, and viruses have evolved sequence and structural mimics of Bcl-2 to subvert premature host cell apoptosis in response to viral infection. The sequencing of the canarypox virus genome identified a putative pro-survival Bcl-2 protein, CNP058. However, a role in apoptosis inhibition for CNP058 has not been identified to date. Here, we report that CNP058 is able to bind several host cell pro-death Bcl-2 proteins, including Bak and Bax, as well as several BH3 only-proteins including Bim, Bid, Bmf, Noxa, Puma, and Hrk with high to moderate affinities. We then defined the structural basis for CNP058 binding to pro-death Bcl-2 proteins by determining the crystal structure of CNP058 bound to Bim BH3. CNP058 adopts the conserved Bcl-2 like fold observed in cellular pro-survival Bcl-2 proteins, and utilizes the canonical ligand binding groove to bind Bim BH3. We then demonstrate that CNP058 is a potent inhibitor of ultraviolet (UV) induced apoptosis in a cell culture model. Our findings suggest that CNP058 is a potent inhibitor of apoptosis that is able to bind to BH3 domain peptides from a broad range of pro-death Bcl-2 proteins, and may play a key role in countering premature host apoptosis.
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22
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Ivanov SM, Cawley A, Huber RG, Bond PJ, Warwicker J. Protein-protein interactions in paralogues: Electrostatics modulates specificity on a conserved steric scaffold. PLoS One 2017; 12:e0185928. [PMID: 29016650 PMCID: PMC5634604 DOI: 10.1371/journal.pone.0185928] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/21/2017] [Indexed: 12/05/2022] Open
Abstract
An improved knowledge of protein-protein interactions is essential for better understanding of metabolic and signaling networks, and cellular function. Progress tends to be based on structure determination and predictions using known structures, along with computational methods based on evolutionary information or detailed atomistic descriptions. We hypothesized that for the case of interactions across a common interface, between proteins from a pair of paralogue families or within a family of paralogues, a relatively simple interface description could distinguish between binding and non-binding pairs. Using binding data for several systems, and large-scale comparative modeling based on known template complex structures, it is found that charge-charge interactions (for groups bearing net charge) are generally a better discriminant than buried non-polar surface. This is particularly the case for paralogue families that are less divergent, with more reliable comparative modeling. We suggest that electrostatic interactions are major determinants of specificity in such systems, an observation that could be used to predict binding partners.
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Affiliation(s)
- Stefan M. Ivanov
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Andrew Cawley
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Roland G. Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, Singapore
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Jim Warwicker
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, United Kingdom
- * E-mail:
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23
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The Bcl-2 Family in Host-Virus Interactions. Viruses 2017; 9:v9100290. [PMID: 28984827 PMCID: PMC5691641 DOI: 10.3390/v9100290] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 10/01/2017] [Accepted: 10/03/2017] [Indexed: 12/13/2022] Open
Abstract
Members of the B cell lymphoma-2 (Bcl-2) family are pivotal arbiters of mitochondrially mediated apoptosis, a process of fundamental importance during tissue development, homeostasis, and disease. At the structural and mechanistic level, the mammalian members of the Bcl-2 family are increasingly well understood, with their interplay ultimately deciding the fate of a cell. Dysregulation of Bcl-2-mediated apoptosis underlies a plethora of diseases, and numerous viruses have acquired homologs of Bcl-2 to subvert host cell apoptosis and autophagy to prevent premature death of an infected cell. Here we review the structural biology, interactions, and mechanisms of action of virus-encoded Bcl-2 proteins, and how they impact on host-virus interactions to ultimately enable successful establishment and propagation of viral infections.
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24
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Anasir MI, Caria S, Skinner MA, Kvansakul M. Structural basis of apoptosis inhibition by the fowlpox virus protein FPV039. J Biol Chem 2017; 292:9010-9021. [PMID: 28411240 DOI: 10.1074/jbc.m116.768879] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/13/2017] [Indexed: 11/06/2022] Open
Abstract
Programmed cell death or apoptosis of infected host cells is an important defense mechanism in response to viral infections. This process is regulated by proapoptotic and prosurvival members of the B-cell lymphoma 2 (Bcl-2) protein family. To counter premature death of a virus-infected cell, poxviruses use a range of different molecular strategies including the mimicry of prosurvival Bcl-2 proteins. One such viral prosurvival protein is the fowlpox virus protein FPV039, which is a potent apoptosis inhibitor, but the precise molecular mechanism by which FPV039 inhibits apoptosis is unknown. To understand how fowlpox virus inhibits apoptosis, we examined FPV039 using isothermal titration calorimetry, small-angle X-ray scattering, and X-ray crystallography. Here, we report that the fowlpox virus prosurvival protein FPV039 promiscuously binds to cellular proapoptotic Bcl-2 and engages all major proapoptotic Bcl-2 proteins. Unlike other identified viral Bcl-2 proteins to date, FPV039 engaged with cellular proapoptotic Bcl-2 with affinities comparable with those of Bcl-2's endogenous cellular counterparts. Structural studies revealed that FPV039 adopts the conserved Bcl-2 fold observed in cellular prosurvival Bcl-2 proteins and closely mimics the structure of the prosurvival Bcl-2 family protein Mcl-1. Our findings suggest that FPV039 is a pan-Bcl-2 protein inhibitor that can engage all host BH3-only proteins, as well as Bcl-2-associated X, apoptosis regulator (Bax) and Bcl-2 antagonist/killer (Bak) proteins to inhibit premature apoptosis of an infected host cell. This work therefore provides a mechanistic platform to better understand FPV039-mediated apoptosis inhibition.
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Affiliation(s)
- Mohd Ishtiaq Anasir
- From the Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia and
| | - Sofia Caria
- From the Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia and
| | - Michael A Skinner
- Section of Virology, Faculty of Medicine, Imperial College London, London W2 1PZ, United Kingdom
| | - Marc Kvansakul
- From the Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia and
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25
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Banjara S, Caria S, Dixon LK, Hinds MG, Kvansakul M. Structural Insight into African Swine Fever Virus A179L-Mediated Inhibition of Apoptosis. J Virol 2017; 91:e02228-16. [PMID: 28053104 PMCID: PMC5331815 DOI: 10.1128/jvi.02228-16] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 12/21/2016] [Indexed: 11/20/2022] Open
Abstract
Programmed cell death is a tightly controlled process critical for the removal of damaged or infected cells. Pro- and antiapoptotic proteins of the Bcl-2 family are pivotal mediators of this process. African swine fever virus (ASFV) is a large DNA virus, the only member of the Asfarviridae family, and harbors A179L, a putative Bcl-2 like protein. A179L has been shown to bind to several proapoptotic Bcl-2 proteins; however, the hierarchy of binding and the structural basis for apoptosis inhibition are currently not understood. We systematically evaluated the ability of A179L to bind proapoptotic Bcl-2 family members and show that A179L is the first antiapoptotic Bcl-2 protein to bind to all major death-inducing mammalian Bcl-2 proteins. We then defined the structural basis for apoptosis inhibition of A179L by determining the crystal structures of A179L bound to both Bid and Bax BH3 motifs. Our findings provide a mechanistic understanding for the potent antiapoptotic activity of A179L by identifying it as the first panprodeath Bcl-2 binder and serve as a platform for more-detailed investigations into the role of A179L during ASFV infection.IMPORTANCE Numerous viruses have acquired strategies to subvert apoptosis by encoding proteins capable of sequestering proapoptotic host proteins. African swine fever virus (ASFV), a large DNA virus and the only member of the Asfarviridae family, encodes the protein A179L, which functions to prevent apoptosis. We show that A179L is unusual among antiapoptotic Bcl-2 proteins in being able to physically bind to all core death-inducing mammalian Bcl-2 proteins. Currently, little is known regarding the molecular interactions between A179L and the proapoptotic Bcl-2 members. Using the crystal structures of A179L bound to two of the identified proapoptotic Bcl-2 proteins, Bid and Bax, we now provide a three-dimensional (3D) view of how A179L sequesters host proapoptotic proteins, which is crucial for subverting premature host cell apoptosis.
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Affiliation(s)
- Suresh Banjara
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Sofia Caria
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | | | - Mark G Hinds
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Marc Kvansakul
- Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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26
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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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27
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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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28
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Ivanov S, Huber R, Warwicker J, Bond P. Energetics and Dynamics Across the Bcl-2-Regulated Apoptotic Pathway Reveal Distinct Evolutionary Determinants of Specificity and Affinity. Structure 2016; 24:2024-2033. [DOI: 10.1016/j.str.2016.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 09/05/2016] [Accepted: 09/28/2016] [Indexed: 12/21/2022]
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29
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Luna-Vargas MP, Chipuk JE. The deadly landscape of pro-apoptotic BCL-2 proteins in the outer mitochondrial membrane. FEBS J 2016; 283:2676-89. [PMID: 26662859 PMCID: PMC4907887 DOI: 10.1111/febs.13624] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/11/2015] [Accepted: 12/08/2015] [Indexed: 01/06/2023]
Abstract
Apoptosis is a biological process that removes damaged, excess or infected cells through a genetically controlled mechanism. This process plays a crucial role in organismal development, immunity and tissue homeostasis, and alterations in apoptosis contribute to human diseases including cancer and auto-immunity. In the past two decades, significant efforts have focused on understanding the function of the BCL-2 proteins, a complex family of pro-survival and pro-apoptotic α-helical proteins that directly control the mitochondrial pathway of apoptosis. Diverse structural investigations of the BCL-2 family members have broadened our mechanistic understanding of their individual functions. However, an often over-looked aspect of the mitochondrial pathway of apoptosis is how the BCL-2 family specifically interacts with and targets the outer mitochondrial membrane to initiate apoptosis. Structural information on the relationship between the BCL-2 family and the outer mitochondrial membrane is missing; likewise, knowledge of the biophysical mechanisms by which the outer mitochondrial membrane affects and effects apoptosis is lacking. In this mini-review, we provide a current overview of the BCL-2 family members and discuss the latest structural insights into BAK/BAX activation and oligomerization in the context of the outer mitochondrial membrane and mitochondrial biology.
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Affiliation(s)
- Mark P.A. Luna-Vargas
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
| | - Jerry E. Chipuk
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- The Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
- The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY, 10029, USA
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30
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Abstract
High-resolution protein structures determined by X-ray crystallography or NMR have proven invaluable for deciphering the molecular mechanisms underlying the function of a vast range of proteins. Here, we describe methods to generate complexes of proteins belonging to the Bcl-2 family of proteins with either biological ligands or small molecule antagonists.
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Affiliation(s)
- Marc Kvansakul
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Physical Sciences 4, Room 205, Kingsbury Drive, Bundoora, Melbourne, VIC, 3086, Australia.,La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Peter E Czabotar
- The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3052, Australia.
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31
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Hoggard LR, Zhang Y, Zhang M, Panic V, Wisniewski JA, Ji H. Rational design of selective small-molecule inhibitors for β-catenin/B-cell lymphoma 9 protein-protein interactions. J Am Chem Soc 2015; 137:12249-60. [PMID: 26352795 DOI: 10.1021/jacs.5b04988] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Selective inhibition of α-helix-mediated protein-protein interactions (PPIs) with small organic molecules provides great potential for the discovery of chemical probes and therapeutic agents. Protein Data Bank data mining using the HippDB database indicated that (1) the side chains of hydrophobic projecting hot spots at positions i, i + 3, and i + 7 of an α-helix had few orientations when interacting with the second protein and (2) the hot spot pockets of PPI complexes had different sizes, shapes, and chemical groups when interacting with the same hydrophobic projecting hot spots of α-helix. On the basis of these observations, a small organic molecule, 4'-fluoro-N-phenyl-[1,1'-biphenyl]-3-carboxamide, was designed as a generic scaffold that itself directly mimics the binding mode of the side chains of hydrophobic projecting hot spots at positions i, i + 3, and i + 7 of an α-helix. Convenient decoration of this generic scaffold led to the selective disruption of α-helix-mediated PPIs. A series of small-molecule inhibitors selective for β-catenin/B-cell lymphoma 9 (BCL9) over β-catenin/cadherin PPIs was designed and synthesized. The binding mode of new inhibitors was characterized by site-directed mutagenesis and structure-activity relationship studies. This new class of inhibitors can selectively disrupt β-catenin/BCL9 over β-catenin/cadherin PPIs, suppress the transactivation of canonical Wnt signaling, downregulate the expression of Wnt target genes, and inhibit the growth of Wnt/β-catenin-dependent cancer cells.
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Affiliation(s)
- Logan R Hoggard
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Yongqiang Zhang
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Min Zhang
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Vanja Panic
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - John A Wisniewski
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Haitao Ji
- Department of Chemistry, Center for Cell and Genome Science, University of Utah , Salt Lake City, Utah 84112-0850, United States
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32
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Checco JW, Lee EF, Evangelista M, Sleebs NJ, Rogers K, Pettikiriarachchi A, Kershaw NJ, Eddinger GA, Belair DG, Wilson JL, Eller CH, Raines RT, Murphy WL, Smith BJ, Gellman SH, Fairlie WD. α/β-Peptide Foldamers Targeting Intracellular Protein-Protein Interactions with Activity in Living Cells. J Am Chem Soc 2015; 137:11365-75. [PMID: 26317395 DOI: 10.1021/jacs.5b05896] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptides can be developed as effective antagonists of protein-protein interactions, but conventional peptides (i.e., oligomers of l-α-amino acids) suffer from significant limitations in vivo. Short half-lives due to rapid proteolytic degradation and an inability to cross cell membranes often preclude biological applications of peptides. Oligomers that contain both α- and β-amino acid residues ("α/β-peptides") manifest decreased susceptibility to proteolytic degradation, and when properly designed these unnatural oligomers can mimic the protein-recognition properties of analogous "α-peptides". This report documents an extension of the α/β-peptide approach to target intracellular protein-protein interactions. Specifically, we have generated α/β-peptides based on a "stapled" Bim BH3 α-peptide, which contains a hydrocarbon cross-link to enhance α-helix stability. We show that a stapled α/β-peptide can structurally and functionally mimic the parent stapled α-peptide in its ability to enter certain types of cells and block protein-protein interactions associated with apoptotic signaling. However, the α/β-peptide is nearly 100-fold more resistant to proteolysis than is the parent stapled α-peptide. These results show that backbone modification, a strategy that has received relatively little attention in terms of peptide engineering for biomedical applications, can be combined with more commonly deployed peripheral modifications such as side chain cross-linking to produce synergistic benefits.
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Affiliation(s)
| | - Erinna F Lee
- The Walter and Eliza Hall Institute of Medical Research , Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne , Parkville, Victoria 3010, Australia
| | - Marco Evangelista
- The Walter and Eliza Hall Institute of Medical Research , Parkville, Victoria 3052, Australia
| | - Nerida J Sleebs
- The Walter and Eliza Hall Institute of Medical Research , Parkville, Victoria 3052, Australia
| | - Kelly Rogers
- The Walter and Eliza Hall Institute of Medical Research , Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne , Parkville, Victoria 3010, Australia
| | - Anne Pettikiriarachchi
- The Walter and Eliza Hall Institute of Medical Research , Parkville, Victoria 3052, Australia
| | - Nadia J Kershaw
- The Walter and Eliza Hall Institute of Medical Research , Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne , Parkville, Victoria 3010, Australia
| | | | | | | | | | | | | | - Brian J Smith
- Department of Chemistry and Physics, La Trobe Institute of Molecular Science , Melbourne, Victoria 3086, Australia
| | | | - W Douglas Fairlie
- The Walter and Eliza Hall Institute of Medical Research , Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne , Parkville, Victoria 3010, Australia
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33
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Foight GW, Keating AE. Locating Herpesvirus Bcl-2 Homologs in the Specificity Landscape of Anti-Apoptotic Bcl-2 Proteins. J Mol Biol 2015; 427:2468-2490. [PMID: 26009469 DOI: 10.1016/j.jmb.2015.05.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/13/2015] [Accepted: 05/17/2015] [Indexed: 12/31/2022]
Abstract
Viral homologs of the anti-apoptotic Bcl-2 proteins are highly diverged from their mammalian counterparts, yet they perform overlapping functions by binding and inhibiting BH3 (Bcl-2 homology 3)-motif-containing proteins. We investigated the BH3 binding properties of the herpesvirus Bcl-2 homologs KSBcl-2, BHRF1, and M11, as they relate to those of the human Bcl-2 homologs Mcl-1, Bfl-1, Bcl-w, Bcl-xL, and Bcl-2. Analysis of the sequence and structure of the BH3 binding grooves showed that, despite low sequence identity, M11 has structural similarities to Bcl-xL, Bcl-2, and Bcl-w. BHRF1 and KSBcl-2 are more structurally similar to Mcl-1 than to the other human proteins. Binding to human BH3-like peptides showed that KSBcl-2 has similar specificity to Mcl-1, and BHRF1 has a restricted binding profile; M11 binding preferences are distinct from those of Bcl-xL, Bcl-2, and Bcl-w. Because KSBcl-2 and BHRF1 are from human herpesviruses associated with malignancies, we screened computationally designed BH3 peptide libraries using bacterial surface display to identify selective binders of KSBcl-2 or BHRF1. The resulting peptides bound to KSBcl-2 and BHRF1 in preference to Bfl-1, Bcl-w, Bcl-xL, and Bcl-2 but showed only modest specificity over Mcl-1. Rational mutagenesis increased specificity against Mcl-1, resulting in a peptide with a dissociation constant of 2.9nM for binding to KSBcl-2 and >1000-fold specificity over other Bcl-2 proteins, as well as a peptide with >70-fold specificity for BHRF1. In addition to providing new insights into viral Bcl-2 binding specificity, this study will inform future work analyzing the interaction properties of homologous binding domains and designing specific protein interaction partners.
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Affiliation(s)
- Glenna Wink Foight
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Amy E Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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34
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Rajan S, Choi M, Baek K, Yoon HS. Bh3 induced conformational changes in Bcl-Xl revealed by crystal structure and comparative analysis. Proteins 2015; 83:1262-72. [PMID: 25907960 DOI: 10.1002/prot.24816] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 04/09/2015] [Accepted: 04/17/2015] [Indexed: 01/08/2023]
Abstract
Apoptosis or programmed cell death is a regulatory process in cells in response to stimuli perturbing physiological conditions. The Bcl-2 family of proteins plays an important role in regulating homeostasis during apoptosis. In the process, the molecular interactions among the three members of this family, the pro-apoptotic, anti-apoptotic and BH3-only proteins at the mitochondrial outer membrane define the fate of a cell. Here, we report the crystal structures of the human anti-apoptotic protein Bcl-XL in complex with BH3-only BID(BH3) and BIM(BH3) peptides determined at 2.0 Å and 1.5 Å resolution, respectively. The BH3 peptides bind to the canonical hydrophobic pocket in Bcl-XL and adopt an alpha helical conformation in the bound form. Despite a similar structural fold, a comparison with other BH3 complexes revealed structural differences due to their sequence variations. In the Bcl-XL-BID(BH3) complex we observed a large pocket, in comparison with other BH3 complexes, lined by residues from helices α1, α2, α3, and α5 located adjacent to the canonical hydrophobic pocket. These results suggest that there are differences in the mode of interactions by the BH3 peptides that may translate into functional differences in apoptotic regulation.
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Affiliation(s)
- Sreekanth Rajan
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Minjoo Choi
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Kwanghee Baek
- Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-Si, Gyeonggi-Do, 446-701, Republic of Korea
| | - Ho Sup Yoon
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.,Department of Genetic Engineering, College of Life Sciences, Kyung Hee University, Yongin-Si, Gyeonggi-Do, 446-701, Republic of Korea
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35
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Lang MJ, Brennan MS, O'Reilly LA, Ottina E, Czabotar PE, Whitlock E, Fairlie WD, Tai L, Strasser A, Herold MJ. Characterisation of a novel A1-specific monoclonal antibody. Cell Death Dis 2014; 5:e1553. [PMID: 25476901 PMCID: PMC4649835 DOI: 10.1038/cddis.2014.519] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- M J Lang
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - M S Brennan
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - L A O'Reilly
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - E Ottina
- Division of Developmental Immunology, Biocenter, Innsbruck Medical University, Innsbruck, Austria
| | - P E Czabotar
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - E Whitlock
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - W D Fairlie
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - L Tai
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - A Strasser
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - M J Herold
- Molecular Genetics of Cancer Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
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36
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Lee EF, Dewson G, Evangelista M, Pettikiriarachchi A, Gold GJ, Zhu H, Colman PM, Fairlie WD. The functional differences between pro-survival and pro-apoptotic B cell lymphoma 2 (Bcl-2) proteins depend on structural differences in their Bcl-2 homology 3 (BH3) domains. J Biol Chem 2014; 289:36001-17. [PMID: 25371206 DOI: 10.1074/jbc.m114.610758] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Bcl-2 homology 3 (BH3) domains are short sequence motifs that mediate nearly all protein-protein interactions between B cell lymphoma 2 (Bcl-2) family proteins in the intrinsic apoptotic cell death pathway. These sequences are found on both pro-survival and pro-apoptotic members, although their primary function is believed to be associated with induction of cell death. Here, we identify critical features of the BH3 domains of pro-survival proteins that distinguish them functionally from their pro-apoptotic counterparts. Biochemical and x-ray crystallographic studies demonstrate that these differences reduce the capacity of most pro-survival proteins to form high affinity "BH3-in-groove" complexes that are critical for cell death induction. Switching these residues for the corresponding residues in Bcl-2 homologous antagonist/killer (Bak) increases the binding affinity of isolated BH3 domains for pro-survival proteins; however, their exchange in the context of the parental protein causes rapid proteasomal degradation due to protein destabilization. This is supported by further x-ray crystallographic studies that capture elements of this destabilization in one pro-survival protein, Bcl-w. In pro-apoptotic Bak, we demonstrate that the corresponding distinguishing residues are important for its cell-killing capacity and antagonism by pro-survival proteins.
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Affiliation(s)
- Erinna F Lee
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville, Victoria 3052, Australia and the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Grant Dewson
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville, Victoria 3052, Australia and the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marco Evangelista
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville, Victoria 3052, Australia and
| | - Anne Pettikiriarachchi
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville, Victoria 3052, Australia and
| | - Grace J Gold
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville, Victoria 3052, Australia and the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Haoran Zhu
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville, Victoria 3052, Australia and the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peter M Colman
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville, Victoria 3052, Australia and the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - W Douglas Fairlie
- From the Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde, Parkville, Victoria 3052, Australia and the Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
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37
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Edwards AL, Gavathiotis E, LaBelle JL, Braun CR, Opoku-Nsiah KA, Bird GH, Walensky LD. Multimodal interaction with BCL-2 family proteins underlies the proapoptotic activity of PUMA BH3. ACTA ACUST UNITED AC 2014; 20:888-902. [PMID: 23890007 DOI: 10.1016/j.chembiol.2013.06.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/21/2013] [Accepted: 06/09/2013] [Indexed: 12/15/2022]
Abstract
PUMA is a proapoptotic BCL-2 family member that drives the apoptotic response to a diversity of cellular insults. Deciphering the spectrum of PUMA interactions that confer its context-dependent proapoptotic properties remains a high priority goal. Here, we report the synthesis of PUMA SAHBs, structurally stabilized PUMA BH3 helices that, in addition to broadly targeting antiapoptotic proteins, directly bind to proapoptotic BAX. NMR, photocrosslinking, and biochemical analyses revealed that PUMA SAHBs engage an α1/α6 trigger site on BAX to initiate its functional activation. We further demonstrated that a cell-permeable PUMA SAHB analog induces apoptosis in neuroblastoma cells and, like expressed PUMA protein, engages BCL-2, MCL-1, and BAX. Thus, we find that PUMA BH3 is a dual antiapoptotic inhibitor and proapoptotic direct activator, and its mimetics may serve as effective pharmacologic triggers of apoptosis in resistant human cancers.
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Affiliation(s)
- Amanda L Edwards
- Department of Pediatric Oncology, Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
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38
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Abulwerdi FA, Liao C, Mady AS, Gavin J, Shen C, Cierpicki T, Stuckey JA, Showalter HDH, Nikolovska-Coleska Z. 3-Substituted-N-(4-hydroxynaphthalen-1-yl)arylsulfonamides as a novel class of selective Mcl-1 inhibitors: structure-based design, synthesis, SAR, and biological evaluation. J Med Chem 2014; 57:4111-33. [PMID: 24749893 PMCID: PMC4033665 DOI: 10.1021/jm500010b] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Mcl-1, an antiapoptotic member of the Bcl-2 family of proteins, is a validated and attractive target for cancer therapy. Overexpression of Mcl-1 in many cancers results in disease progression and resistance to current chemotherapeutics. Utilizing high-throughput screening, compound 1 was identified as a selective Mcl-1 inhibitor and its binding to the BH3 binding groove of Mcl-1 was confirmed by several different, but complementary, biochemical and biophysical assays. Guided by structure-based drug design and supported by NMR experiments, comprehensive SAR studies were undertaken and a potent and selective inhibitor, compound 21, was designed which binds to Mcl-1 with a Ki of 180 nM. Biological characterization of 21 showed that it disrupts the interaction of endogenous Mcl-1 and biotinylated Noxa-BH3 peptide, causes cell death through a Bak/Bax-dependent mechanism, and selectively sensitizes Eμ-myc lymphomas overexpressing Mcl-1, but not Eμ-myc lymphoma cells overexpressing Bcl-2. Treatment of human leukemic cell lines with compound 21 resulted in cell death through activation of caspase-3 and induction of apoptosis.
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Affiliation(s)
- Fardokht A Abulwerdi
- Department of Pathology, University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
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39
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Control of apoptosis by the BCL-2 protein family: implications for physiology and therapy. Nat Rev Mol Cell Biol 2014; 15:49-63. [PMID: 24355989 DOI: 10.1038/nrm3722] [Citation(s) in RCA: 2182] [Impact Index Per Article: 218.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The BCL-2 protein family determines the commitment of cells to apoptosis, an ancient cell suicide programme that is essential for development, tissue homeostasis and immunity. Too little apoptosis can promote cancer and autoimmune diseases; too much apoptosis can augment ischaemic conditions and drive neurodegeneration. We discuss the biochemical, structural and genetic studies that have clarified how the interplay between members of the BCL-2 family on mitochondria sets the apoptotic threshold. These mechanistic insights into the functions of the BCL-2 family are illuminating the physiological control of apoptosis, the pathological consequences of its dysregulation and the promising search for novel cancer therapies that target the BCL-2 family.
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40
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α-Helix mimetics: outwards and upwards. Bioorg Med Chem Lett 2013; 24:717-24. [PMID: 24433858 DOI: 10.1016/j.bmcl.2013.12.003] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 11/23/2013] [Accepted: 12/01/2013] [Indexed: 01/28/2023]
Abstract
α-Helices are common secondary structural elements forming key parts of the large, generally featureless interfacial regions of many therapeutically-relevant protein-protein interactions (PPIs). The rational design of helix mimetics is an appealing small-molecule strategy for the mediation of aberrant PPIs, however the first generation of scaffolds presented a relatively small number of residues on a single recognition surface. Increasingly, helices involved in PPIs are found to have more complex binding modes, utilizing two or three recognition surfaces, or binding with extended points of contact. To address these unmet needs the design and synthesis of new generations of multi-sided, extended, and supersecondary structures are underway.
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41
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Modi V, Sankararamakrishnan R. Antiapoptotic Bcl-2 homolog CED-9 in Caenorhabditis elegans
: Dynamics of BH3 and CED-4 binding regions and comparison with mammalian antiapoptotic Bcl-2 proteins. Proteins 2013; 82:1035-47. [DOI: 10.1002/prot.24476] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Revised: 10/16/2013] [Accepted: 11/04/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Vivek Modi
- Department of Biological Sciences & Bioengineering; Indian Institute of Technology Kanpur; Kanpur 208016 India
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42
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Structural biology of the Bcl-2 family and its mimicry by viral proteins. Cell Death Dis 2013; 4:e909. [PMID: 24201808 PMCID: PMC3847314 DOI: 10.1038/cddis.2013.436] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/09/2013] [Accepted: 10/02/2013] [Indexed: 12/16/2022]
Abstract
Intrinsic apoptosis in mammals is regulated by protein–protein interactions among the B-cell lymphoma-2 (Bcl-2) family. The sequences, structures and binding specificity between pro-survival Bcl-2 proteins and their pro-apoptotic Bcl-2 homology 3 motif only (BH3-only) protein antagonists are now well understood. In contrast, our understanding of the mode of action of Bax and Bak, the two necessary proteins for apoptosis is incomplete. Bax and Bak are isostructural with pro-survival Bcl-2 proteins and also interact with BH3-only proteins, albeit weakly. Two sites have been identified; the in-groove interaction analogous to the pro-survival BH3-only interaction and a site on the opposite molecular face. Interaction of Bax or Bak with activator BH3-only proteins and mitochondrial membranes triggers a series of ill-defined conformational changes initiating their oligomerization and mitochondrial outer membrane permeabilization. Many actions of the mammalian pro-survival Bcl-2 family are mimicked by viruses. By expressing proteins mimicking mammalian pro-survival Bcl-2 family proteins, viruses neutralize death-inducing members of the Bcl-2 family and evade host cell apoptosis during replication. Remarkably, structural elements are preserved in viral Bcl-2 proteins even though there is in many cases little discernible sequence conservation with their mammalian counterparts. Some viral Bcl-2 proteins are dimeric, but they have distinct structures to those observed for mammalian Bcl-2 proteins. Furthermore, viral Bcl-2 proteins modulate innate immune responses regulated by NF-κB through an interface separate from the canonical BH3-binding groove. Our increasing structural understanding of the viral Bcl-2 proteins is leading to new insights in the cellular Bcl-2 network by exploring potential alternate functional modes in the cellular context. We compare the cellular and viral Bcl-2 proteins and discuss how alterations in their structure, sequence and binding specificity lead to differences in behavior, and together with the intrinsic structural plasticity in the Bcl-2 fold enable exquisite control over critical cellular signaling pathways.
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43
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Building blocks of the apoptotic pore: how Bax and Bak are activated and oligomerize during apoptosis. Cell Death Differ 2013; 21:196-205. [PMID: 24162660 DOI: 10.1038/cdd.2013.139] [Citation(s) in RCA: 292] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2013] [Revised: 09/03/2013] [Accepted: 09/03/2013] [Indexed: 12/18/2022] Open
Abstract
The central role of the Bcl-2 family in regulating apoptotic cell death was first identified in the 1980s. Since then, significant in-roads have been made in identifying the multiple members of this family, characterizing their form and function and understanding how their interactions determine whether a cell lives or dies. In this review we focus on the recent progress made in characterizing the proapoptotic Bcl-2 family members, Bax and Bak. This progress has resolved longstanding controversies, but has also challenged established theories in the apoptosis field. We will discuss different models of how these two proteins become activated and different 'modes' by which they are inhibited by other Bcl-2 family members. We will also discuss novel conformation changes leading to Bak and Bax oligomerization and speculate how these oligomers might permeabilize the mitochondrial outer membrane.
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44
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Fais F, Tenca C, Ghiotto F, Bruno S. Targeting the Bcl-2 family in B-cell chronic lymphocytic leukemia. Int J Hematol Oncol 2013. [DOI: 10.2217/ijh.13.43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
SUMMARY B-cell chronic lymphocytic leukemia (CLL) is the most common leukemia in human adults of the western world and no definitive cure is yet available. One key factor in CLL pathogenesis and disease progression is misbalanced Bcl-2 cell death machinery that is shifted towards protection from apoptosis. Thus, strategies to counteract the antiapoptotic action of the Bcl-2 family in CLL cells are being explored. The Bcl-2 family is composed of a growing number of proteins related to Bcl-2 by sequence homology and their interactions regulate the cell’s decision to die. The features of one particular subclass, the BH3-only proteins, are being studied and exploited for the development of therapeutic anticancer approaches that specifically target antiapoptotic Bcl-2 proteins overexpressed in tumors, including CLL. Preclinical and clinical efficacy and toxicity of the most effective among these ‘BH3 mimetics’ are presented, together with a model that accounts for the differential sensitivity of CLL and normal cells to Bcl-2 neutralization.
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Affiliation(s)
- Franco Fais
- Department of Experimental Medicine (DIMES), University of Genoa, Human Anatomy Section, Via De Toni 14, Genoa 16132, Italy
| | - Claudya Tenca
- Department of Experimental Medicine (DIMES), University of Genoa, Human Anatomy Section, Via De Toni 14, Genoa 16132, Italy
| | - Fabio Ghiotto
- Department of Experimental Medicine (DIMES), University of Genoa, Human Anatomy Section, Via De Toni 14, Genoa 16132, Italy
| | - Silvia Bruno
- Department of Experimental Medicine (DIMES), University of Genoa, Human Anatomy Section, Via De Toni 14, Genoa 16132, Italy
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Ilizaliturri-Flores I, Correa-Basurto J, Benítez-Cardoza CG, Zamorano-Carrillo A. A study of the structural properties and thermal stability of human Bcl-2 by molecular dynamics simulations. J Biomol Struct Dyn 2013; 32:1707-19. [PMID: 24028527 DOI: 10.1080/07391102.2013.833858] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The anti-apoptotic B-cell lymphoma 2 (Bcl-2) protein interacts with several proteins that regulate the apoptotic properties of cells. In this research, we conduct several all-atom molecular dynamics (MD) simulations under high-temperature unfolding conditions, from 400 to 800 K, for 25 ns. These simulations were performed using a model of an engineered Bcl-2 human protein (Bcl-2-Δ22Σ3), which lacks 22 C-terminal residues of the transmembrane domain. The aim of this study is to gain insight into the structural behavior of Bcl-2-Δ22Σ3 by mapping the conformational movements involved in Bcl-2 stability and its biological function. To build a Bcl-2-Δ22Σ3 three-dimensional model, the protein core was built by homology modeling and the flexible loop domain (FLD, residues 33-91) by ab initio methods. Further, the entire protein model was refined by MD simulations. Afterwards, the production MD simulations showed that the FLD at 400 and 500 K has several conformations reaching into the protein core, whereas at 600 K some of the alpha-helices were lost. At 800 K, the Bcl-2 core is destabilized suggesting a possible mechanism for protein unfolding, where the alpha helices 1 and 6 were the most stable, and a reduction in the number of hydrogen bonds initially occurs. In conclusion, the structural changes and the internal protein interactions suggest that the core and the FLD are crucial components of Bcl-2 in its function of regulate ng access to the recognition sites of kinases and caspases.
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Affiliation(s)
- Ian Ilizaliturri-Flores
- a Laboratorio de Investigación Bioquímica, Doctorado en Ciencias en Biotecnología , ENMH, Instituto Politécnico Nacional , Guillermo Massieu Helguera #239 Fracc. "La Escalera" Ticoman, C.P. 07320, D.F. México , Mexico
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46
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Juin P, Geneste O, Gautier F, Depil S, Campone M. Decoding and unlocking the BCL-2 dependency of cancer cells. Nat Rev Cancer 2013; 13:455-65. [PMID: 23783119 DOI: 10.1038/nrc3538] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cancer cells are subject to many apoptotic stimuli that would kill them were it not for compensatory prosurvival alterations. BCL-2-like (BCL-2L) proteins contribute to such aberrant behaviour by engaging a network of interactions that is potent at promoting survival but that is also fragile: inhibition of a restricted number of interactions may suffice to trigger cancer cell death. Currently available and novel compounds that inhibit these interactions could be efficient therapeutic agents if this phenotype of BCL-2L dependence was better understood at a molecular, cellular and systems level and if it could be diagnosed by relevant biomarkers.
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Affiliation(s)
- Philippe Juin
- Team 8 Cell survival and tumor escape in breast cancer, UMR 892 INSERM / 6299 CNRS / Université de Nantes, Institut de Recherche Thérapeutique de l'Université de Nantes, 8 quai Moncousu, BP 70721, 44007 Nantes Cedex, 1 France.
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47
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Santiveri CM, Sborgi L, de Alba E. Nuclear magnetic resonance study of protein-protein interactions involving apoptosis regulator Diva (Boo) and the BH3 domain of proapoptotic Bcl-2 members. J Mol Recognit 2013. [PMID: 23192964 DOI: 10.1002/jmr.2240] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
According to biochemical assays, the Bcl-2 protein Diva from mouse regulates programmed cell death by heterodimerizing with other members of the family and by interacting with the apoptotic protease-activating factor Apaf-1. In typical Bcl-2 heterodimers, peptide fragments comprising the Bcl-2 homology domain 3 (BH3 domain) of proapoptotic members are capable of forming functional complexes with prosurvival proteins. High-resolution structural studies have revealed that the BH3 peptide forms an α-helix positioned in a canonical hydrophobic cleft of the antiapoptotic protein. Because Diva shows mutations in conserved residues within this area, it has been proposed to have a different interacting surface. However, we showed previously that Diva binds through the canonical groove the BH3 peptide of the human Bcl-2 killing member Harakiri. To further test Diva's binding capabilities, here we show Nuclear Magnetic Resonance (NMR) data, indicating that Diva binds peptides derived from the BH3 domain of several other proapoptotic Bcl-2 proteins, including mouse Harakiri, Bid, Bak and Bmf. We have measured the binding affinities of the heterodimers, which show significant variability. Structural models of the protein-peptide complexes based on NMR chemical shift perturbation data indicate that the binding surface is analogous. These models do not rely on NMR NOE (Nuclear Overhauser Effect) data, and thus our results can only suggest that the complexes share similar intermolecular interactions. However, the observed affinity differences correlate with the α-helical population of the BH3-peptides obtained from circular dichroism experiments, which highlights a role of conformational selection in the binding mechanism. Altogether, our results shed light on important factors governing Diva-BH3 peptide molecular recognition mode.
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Affiliation(s)
- Clara M Santiveri
- Chemical and Physical Biology Department, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, 9, Madrid, 28040, Spain
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48
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Structure-guided design of a selective BCL-X(L) inhibitor. Nat Chem Biol 2013; 9:390-7. [PMID: 23603658 DOI: 10.1038/nchembio.1246] [Citation(s) in RCA: 299] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 03/26/2013] [Indexed: 12/14/2022]
Abstract
The prosurvival BCL-2 family protein BCL-X(L) is often overexpressed in solid tumors and renders malignant tumor cells resistant to anticancer therapeutics. Enhancing apoptotic responses by inhibiting BCL-X(L) will most likely have widespread utility in cancer treatment and, instead of inhibiting multiple prosurvival BCL-2 family members, a BCL-X(L)-selective inhibitor would be expected to minimize the toxicity to normal tissues. We describe the use of a high-throughput screen to discover a new series of small molecules targeting BCL-X(L) and their structure-guided development by medicinal chemistry. The optimized compound, WEHI-539 (7), has high affinity (subnanomolar) and selectivity for BCL-X(L) and potently kills cells by selectively antagonizing its prosurvival activity. WEHI-539 will be an invaluable tool for distinguishing the roles of BCL-X(L) from those of its prosurvival relatives, both in normal cells and notably in malignant tumor cells, many of which may prove to rely upon BCL-X(L) for their sustained growth.
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49
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Dutta S, Chen TS, Keating AE. Peptide ligands for pro-survival protein Bfl-1 from computationally guided library screening. ACS Chem Biol 2013; 8:778-88. [PMID: 23363053 DOI: 10.1021/cb300679a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Pro-survival members of the Bcl-2 protein family inhibit cell death by binding short helical BH3 motifs in pro-apoptotic proteins. Mammalian pro-survival proteins Bcl-x(L), Bcl-2, Bcl-w, Mcl-1, and Bfl-1 bind with varying affinities and specificities to native BH3 motifs, engineered peptides, and small molecules. Biophysical studies have determined interaction patterns for these proteins, particularly for the most-studied family members Bcl-x(L) and Mcl-1. Bfl-1 is a pro-survival protein implicated in preventing apoptosis in leukemia, lymphoma, and melanoma. Although Bfl-1 is a promising therapeutic target, relatively little is known about its binding preferences. We explored the binding of Bfl-1 to BH3-like peptides by screening a peptide library that was designed to sample a high degree of relevant sequence diversity. Screening using yeast-surface display led to several novel high-affinity Bfl-1 binders and to thousands of putative binders identified through deep sequencing. Further screening for specificity led to identification of a peptide that bound to Bfl-1 with K(d) < 1 nM and very slow dissociation from Bfl-1 compared to other pro-survival Bcl-2 family members. A point mutation in this sequence gave a peptide with ~50 nM affinity for Bfl-1 that was selective for Bfl-1 in equilibrium binding assays. Analysis of engineered Bfl-1 binders deepens our understanding of how the binding profiles of pro-survival proteins differ and may guide the development of targeted Bfl-1 inhibitors.
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Affiliation(s)
- Sanjib Dutta
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United
States
| | - T. Scott Chen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United
States
| | - Amy E. Keating
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United
States
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50
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Lama D, Modi V, Sankararamakrishnan R. Behavior of solvent-exposed hydrophobic groove in the anti-apoptotic Bcl-XL protein: clues for its ability to bind diverse BH3 ligands from MD simulations. PLoS One 2013; 8:e54397. [PMID: 23468841 PMCID: PMC3585337 DOI: 10.1371/journal.pone.0054397] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 12/13/2012] [Indexed: 11/19/2022] Open
Abstract
Bcl-XL is a member of Bcl-2 family of proteins involved in the regulation of intrinsic pathway of apoptosis. Its overexpression in many human cancers makes it an important target for anti-cancer drugs. Bcl-XL interacts with the BH3 domain of several pro-apoptotic Bcl-2 partners. This helical bundle protein has a pronounced hydrophobic groove which acts as a binding region for the BH3 domains. Eight independent molecular dynamics simulations of the apo/holo forms of Bcl-XL were carried out to investigate the behavior of solvent-exposed hydrophobic groove. The simulations used either a twin-range cut-off or particle mesh Ewald (PME) scheme to treat long-range interactions. Destabilization of the BH3 domain-containing helix H2 was observed in all four twin-range cut-off simulations. Most of the other major helices remained stable. The unwinding of H2 can be related to the ability of Bcl-XL to bind diverse BH3 ligands. The loss of helical character can also be linked to the formation of homo- or hetero-dimers in Bcl-2 proteins. Several experimental studies have suggested that exposure of BH3 domain is a crucial event before they form dimers. Thus unwinding of H2 seems to be functionally very important. The four PME simulations, however, revealed a stable helix H2. It is possible that the H2 unfolding might occur in PME simulations at longer time scales. Hydrophobic residues in the hydrophobic groove are involved in stable interactions among themselves. The solvent accessible surface areas of bulky hydrophobic residues in the groove are significantly buried by the loop LB connecting the helix H2 and subsequent helix. These observations help to understand how the hydrophobic patch in Bcl-XL remains stable in the solvent-exposed state. We suggest that both the destabilization of helix H2 and the conformational heterogeneity of loop LB are important factors for binding of diverse ligands in the hydrophobic groove of Bcl-XL.
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Affiliation(s)
- Dilraj Lama
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Vivek Modi
- Department of Biological Sciences & Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
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