1
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Zhang P, Walko M, Wilson A. Maleimide constrained BAD BH3 domain peptides as BCL-xL Inhibitors: A Versatile Approach to Rapidly Identify Sites Compatible with Peptide Constraining. Bioorg Med Chem Lett 2023; 87:129260. [PMID: 36997005 DOI: 10.1016/j.bmcl.2023.129260] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023]
Abstract
Development of protein-protein interaction (PPI) inhibitors remains a major challenge. A significant number of PPIs are mediated by helical recognition epitopes; although peptides derived from such epitopes are attractive templates for inhibitor design, they may not readily adopt a bioactive conformation, are susceptible to proteolysis and rarely elicit optimal cell uptake properties. Constraining peptides has therefore emerged as a useful method to mitigate against these liabilities in the development of PPI inhibitors. Building on our recently reported method for constraining peptides by reaction of dibromomaleimide derivatives with two cysteines positioned in an i and i + 4 relationship, in this study, we showcase the power of the method for rapid identification of ideal constraining positions using a maleimide-staple scan based on a 19-mer sequence derived from the BAD BH3 domain. We found that the maleimide constraint had little or a detrimental impact on helicity and potency in most sequences, but successfully identified i, i + 4 positions where the maleimide constraint was tolerated. Analyses using modelling and molecular dynamics (MD) simulations revealed that the inactive constrained peptides likely lose interactions with the protein as a result of introducing the constraint.
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2
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Bekker GJ, Kamiya N. Advancing the field of computational drug design using multicanonical molecular dynamics-based dynamic docking. Biophys Rev 2022; 14:1349-1358. [PMID: 36659995 PMCID: PMC9842809 DOI: 10.1007/s12551-022-01010-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/14/2022] [Indexed: 11/20/2022] Open
Abstract
Multicanonical molecular dynamics (McMD)-based dynamic docking is a powerful tool to not only predict the native binding configuration between two flexible molecules, but it can also be used to accurately simulate the binding/unbinding pathway. Furthermore, it can also predict alternative binding sites, including allosteric ones, by employing an exhaustive sampling approach. Since McMD-based dynamic docking accurately samples binding/unbinding events, it can thus be used to determine the molecular mechanism of binding between two molecules. We developed the McMD-based dynamic docking methodology based on the powerful, but woefully underutilized McMD algorithm, combined with a toolset to perform the docking and to analyze the results. Here, we showcase three of our recent works, where we have applied McMD-based dynamic docking to advance the field of computational drug design. In the first case, we applied our method to perform an exhaustive search between Hsp90 and one of its inhibitors to successfully predict the native binding configuration in its binding site, as we refined our analysis methods. For our second case, we performed an exhaustive search of two medium-sized ligands and Bcl-xL, which has a cryptic binding site that differs greatly between the apo and holo structures. Finally, we performed a dynamic docking simulation between a membrane-embedded GPCR molecule and a high affinity ligand that binds deep within its receptor's pocket. These advanced simulations showcase the power that the McMD-based dynamic docking method has, and provide a glimpse of the potential our methodology has to unravel and solve the medical and biophysical issues in the modern world. Supplementary Information The online version contains supplementary material available at 10.1007/s12551-022-01010-z.
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Affiliation(s)
- Gert-Jan Bekker
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Narutoshi Kamiya
- Graduate School of Information Science, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo 650-0047 Japan
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3
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Sora V, Papaleo E. Structural Details of BH3 Motifs and BH3-Mediated Interactions: an Updated Perspective. Front Mol Biosci 2022; 9:864874. [PMID: 35685242 PMCID: PMC9171138 DOI: 10.3389/fmolb.2022.864874] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/13/2022] [Indexed: 11/18/2022] Open
Abstract
Apoptosis is a mechanism of programmed cell death crucial in organism development, maintenance of tissue homeostasis, and several pathogenic processes. The B cell lymphoma 2 (BCL2) protein family lies at the core of the apoptotic process, and the delicate balance between its pro- and anti-apoptotic members ultimately decides the cell fate. BCL2 proteins can bind with each other and several other biological partners through the BCL2 homology domain 3 (BH3), which has been also classified as a possible Short Linear Motif and whose distinctive features remain elusive even after decades of studies. Here, we aim to provide an updated overview of the structural features characterizing BH3s and BH3-mediated interactions (with a focus on human proteins), elaborating on the plasticity of BCL2 proteins and the motif properties. We also discussed the implication of these findings for the discovery of interactors of the BH3-binding groove of BCL2 proteins and the design of mimetics for therapeutic purposes.
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Affiliation(s)
- Valentina Sora
- Cancer Structural Biology, Danish Cancer Society Research Center, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Society Research Center, Copenhagen, Denmark
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Elena Papaleo, ,
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4
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Townsend PA, Kozhevnikova MV, Cexus ONF, Zamyatnin AA, Soond SM. BH3-mimetics: recent developments in cancer therapy. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:355. [PMID: 34753495 PMCID: PMC8576916 DOI: 10.1186/s13046-021-02157-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/26/2021] [Indexed: 01/11/2023]
Abstract
The hopeful outcomes from 30 years of research in BH3-mimetics have indeed served a number of solid paradigms for targeting intermediates from the apoptosis pathway in a variety of diseased states. Not only have such rational approaches in drug design yielded several key therapeutics, such outputs have also offered insights into the integrated mechanistic aspects of basic and clinical research at the genetics level for the future. In no other area of medical research have the effects of such work been felt, than in cancer research, through targeting the BAX-Bcl-2 protein-protein interactions. With these promising outputs in mind, several mimetics, and their potential therapeutic applications, have also been developed for several other pathological conditions, such as cardiovascular disease and tissue fibrosis, thus highlighting the universal importance of the intrinsic arm of the apoptosis pathway and its input to general tissue homeostasis. Considering such recent developments, and in a field that has generated so much scientific interest, we take stock of how the broadening area of BH3-mimetics has developed and diversified, with a focus on their uses in single and combined cancer treatment regimens and recently explored therapeutic delivery methods that may aid the development of future therapeutics of this nature.
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Affiliation(s)
- Paul A Townsend
- University of Surrey, Guildford, UK. .,Sechenov First Moscow State Medical University, Moscow, Russian Federation. .,University of Manchester, Manchester, UK.
| | - Maria V Kozhevnikova
- University of Surrey, Guildford, UK.,Sechenov First Moscow State Medical University, Moscow, Russian Federation
| | | | - Andrey A Zamyatnin
- University of Surrey, Guildford, UK.,Sechenov First Moscow State Medical University, Moscow, Russian Federation.,Lomonosov Moscow State University, Moscow, Russian Federation.,Sirius University of Science and Technology, Sochi, Russian Federation
| | - Surinder M Soond
- University of Surrey, Guildford, UK. .,Sechenov First Moscow State Medical University, Moscow, Russian Federation.
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5
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Discovery, development and application of drugs targeting BCL-2 pro-survival proteins in cancer. Biochem Soc Trans 2021; 49:2381-2395. [PMID: 34515749 PMCID: PMC8589430 DOI: 10.1042/bst20210749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/20/2021] [Accepted: 08/24/2021] [Indexed: 12/13/2022]
Abstract
The discovery of a new class of small molecule compounds that target the BCL-2 family of anti-apoptotic proteins is one of the great success stories of basic science leading to translational outcomes in the last 30 years. The eponymous BCL-2 protein was identified over 30 years ago due to its association with cancer. However, it was the unveiling of the biochemistry and structural biology behind it and its close relatives’ mechanism(s)-of-action that provided the inspiration for what are now known as ‘BH3-mimetics’, the first clinically approved drugs designed to specifically inhibit protein–protein interactions. Herein, we chart the history of how these drugs were discovered, their evolution and application in cancer treatment.
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6
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Nguyen W, Lee EF, Evangelista M, Lee M, Harris TJ, Colman PM, Smith NA, Williams LB, Jarman KE, Lowes KN, Haeberli C, Keiser J, Smith BJ, Fairlie WD, Sleebs BE. Optimization of Benzothiazole and Thiazole Hydrazones as Inhibitors of Schistosome BCL-2. ACS Infect Dis 2021; 7:1143-1163. [PMID: 33523649 DOI: 10.1021/acsinfecdis.0c00700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Limited therapeutic options are available for the treatment of human schistosomiasis caused by the parasitic Schistosoma flatworm. The B cell lymphoma-2 (BCL-2)-regulated apoptotic cell death pathway in schistosomes was recently characterized and shown to share similarities with the intrinsic apoptosis pathway in humans. Here, we exploit structural differences in the human and schistosome BCL-2 (sBCL-2) pro-survival proteins toward a novel treatment strategy for schistosomiasis. The benzothiazole hydrazone scaffold previously employed to target human BCL-XL was repurposed as a starting point to target sBCL-2. We utilized X-ray structural data to inform optimization and then applied a scaffold-hop strategy to identify the 5-carboxamide thiazole hydrazone scaffold (43) with potent sBCL-2 activity (IC50 30 nM). Human BCL-XL potency (IC50 13 nM) was inadvertently preserved during the optimization process. The lead analogues from this study exhibit on-target activity in model fibroblast cell lines dependent on either sBCL-2 or human BCL-XL for survival. Further optimization of the thiazole hydrazone class is required to exhibit activity in schistosomes and enhance the potential of this strategy for treating schistosomiasis.
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Affiliation(s)
- William Nguyen
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Erinna F. Lee
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg 3084, Australia
- School of Cancer Medicine, La Trobe University, Melbourne 3086, Australia
| | - Marco Evangelista
- Olivia Newton-John Cancer Research Institute, Heidelberg 3084, Australia
| | - Mihwa Lee
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Tiffany J. Harris
- Olivia Newton-John Cancer Research Institute, Heidelberg 3084, Australia
| | - Peter M. Colman
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Nicholas A. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - Luke B. Williams
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
| | - Kate E. Jarman
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Kym N. Lowes
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
| | - Cécile Haeberli
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4002, Switzerland
- University of Basel, Basel 4001, Switzerland
| | - Jennifer Keiser
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4002, Switzerland
- University of Basel, Basel 4001, Switzerland
| | - Brian J. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
| | - W. Douglas Fairlie
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne 3086, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg 3084, Australia
- School of Cancer Medicine, La Trobe University, Melbourne 3086, Australia
| | - Brad E. Sleebs
- The Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010, Australia
- Department of Veterinary Biosciences, The University of Melbourne, Parkville 3010, Australia
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7
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Intrinsically Connected: Therapeutically Targeting the Cathepsin Proteases and the Bcl-2 Family of Protein Substrates as Co-regulators of Apoptosis. Int J Mol Sci 2021; 22:ijms22094669. [PMID: 33925117 PMCID: PMC8124540 DOI: 10.3390/ijms22094669] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 12/14/2022] Open
Abstract
Taken with the growing importance of cathepsin-mediated substrate proteolysis in tumor biology and progression, the focus and emphasis placed on therapeutic design and development is coming into fruition. Underpinning this approach is the invariable progression from the direction of fully characterizing cathepsin protease members and their substrate targets, towards targeting such an interaction with tangible therapeutics. The two groups of such substrates that have gained much attention over the years are the pro- and anti- apoptotic protein intermediates from the extrinsic and intrinsic signaling arms of the apoptosis pathway. As proteins that are central to determining cellular fate, some of them present themselves as very favorable candidates for therapeutic targeting. However, considering that both anti- and pro- apoptotic signaling intermediates have been reported to be downstream substrates for certain activated cathepsin proteases, therapeutic targeting approaches based on greater selectivity do need to be given greater consideration. Herein, we review the relationships shared by the cathepsin proteases and the Bcl-2 homology domain proteins, in the context of how the topical approach of adopting 'BH3-mimetics' can be explored further in modulating the relationship between the anti- and pro- apoptotic signaling intermediates from the intrinsic apoptosis pathway and their upstream cathepsin protease regulators. Based on this, we highlight important future considerations for improved therapeutic design.
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8
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Bekker GJ, Fukuda I, Higo J, Fukunishi Y, Kamiya N. Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations. Sci Rep 2021; 11:5046. [PMID: 33658550 PMCID: PMC7930018 DOI: 10.1038/s41598-021-84488-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/17/2021] [Indexed: 01/11/2023] Open
Abstract
We have performed multicanonical molecular dynamics (McMD) based dynamic docking simulations to study and compare the binding mechanism between two medium-sized inhibitors (ABT-737 and WEHI-539) that bind to the cryptic site of Bcl-xL, by exhaustively sampling the conformational and configurational space. Cryptic sites are binding pockets that are transiently formed in the apo state or are induced upon ligand binding. Bcl-xL, a pro-survival protein involved in cancer progression, is known to have a cryptic site, whereby the shape of the pocket depends on which ligand is bound to it. Starting from the apo-structure, we have performed two independent McMD-based dynamic docking simulations for each ligand, and were able to obtain near-native complex structures in both cases. In addition, we have also studied their interactions along their respective binding pathways by using path sampling simulations, which showed that the ligands form stable binding configurations via predominantly hydrophobic interactions. Although the protein started from the apo state, both ligands modulated the pocket in different ways, shifting the conformational preference of the sub-pockets of Bcl-xL. We demonstrate that McMD-based dynamic docking is a powerful tool that can be effectively used to study binding mechanisms involving a cryptic site, where ligand binding requires a large conformational change in the protein to occur.
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Affiliation(s)
- Gert-Jan Bekker
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Ikuo Fukuda
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Junichi Higo
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan
| | - Yoshifumi Fukunishi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Narutoshi Kamiya
- Graduate School of Simulation Studies, University of Hyogo, 7-1-28 Minatojima Minami-machi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.
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9
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Pannecoucke E, Van Trimpont M, Desmet J, Pieters T, Reunes L, Demoen L, Vuylsteke M, Loverix S, Vandenbroucke K, Alard P, Henderikx P, Deroo S, Baatz F, Lorent E, Thiolloy S, Somers K, McGrath Y, Van Vlierberghe P, Lasters I, Savvides SN. Cell-penetrating Alphabody protein scaffolds for intracellular drug targeting. SCIENCE ADVANCES 2021; 7:7/13/eabe1682. [PMID: 33771865 PMCID: PMC7997521 DOI: 10.1126/sciadv.abe1682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 02/05/2021] [Indexed: 05/02/2023]
Abstract
The therapeutic scope of antibody and nonantibody protein scaffolds is still prohibitively limited against intracellular drug targets. Here, we demonstrate that the Alphabody scaffold can be engineered into a cell-penetrating protein antagonist against induced myeloid leukemia cell differentiation protein MCL-1, an intracellular target in cancer, by grafting the critical B-cell lymphoma 2 homology 3 helix of MCL-1 onto the Alphabody and tagging the scaffold's termini with designed cell-penetration polypeptides. Introduction of an albumin-binding moiety extended the serum half-life of the engineered Alphabody to therapeutically relevant levels, and administration thereof in mouse tumor xenografts based on myeloma cell lines reduced tumor burden. Crystal structures of such a designed Alphabody in complex with MCL-1 and serum albumin provided the structural blueprint of the applied design principles. Collectively, we provide proof of concept for the use of Alphabodies against intracellular disease mediators, which, to date, have remained in the realm of small-molecule therapeutics.
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Affiliation(s)
- Erwin Pannecoucke
- VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
| | - Maaike Van Trimpont
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Tim Pieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lindy Reunes
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Lisa Demoen
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | | | | | | | | | | | | | | | | | | | | | - Pieter Van Vlierberghe
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | | | - Savvas N Savvides
- VIB Center for Inflammation Research, 9052 Ghent, Belgium.
- Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, 9052 Ghent, Belgium
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10
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Singh N, Chaput L, Villoutreix BO. Fast Rescoring Protocols to Improve the Performance of Structure-Based Virtual Screening Performed on Protein-Protein Interfaces. J Chem Inf Model 2020; 60:3910-3934. [PMID: 32786511 DOI: 10.1021/acs.jcim.0c00545] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein-protein interactions (PPIs) are attractive targets for drug design because of their essential role in numerous cellular processes and disease pathways. However, in general, PPIs display exposed binding pockets at the interface, and as such, have been largely unexploited for therapeutic interventions with low-molecular weight compounds. Here, we used docking and various rescoring strategies in an attempt to recover PPI inhibitors from a set of active and inactive molecules for 11 targets collected in ChEMBL and PubChem. Our focus is on the screening power of the various developed protocols and on using fast approaches so as to be able to apply such a strategy to the screening of ultralarge libraries in the future. First, we docked compounds into each target using the fast "pscreen" mode of the structure-based virtual screening (VS) package Surflex. Subsequently, the docking poses were postprocessed to derive a set of 3D topological descriptors: (i) shape similarity and (ii) interaction fingerprint similarity with a co-crystallized inhibitor, (iii) solvent-accessible surface area, and (iv) extent of deviation from the geometric center of a reference inhibitor. The derivatized descriptors, together with descriptor-scaled scoring functions, were utilized to investigate possible impacts on VS performance metrics. Moreover, four standalone scoring functions, RF-Score-VS (machine-learning), DLIGAND2 (knowledge-based), Vinardo (empirical), and X-SCORE (empirical), were employed to rescore the PPI compounds. Collectively, the results indicate that the topological scoring algorithms could be valuable both at a global level, with up to 79% increase in areas under the receiver operating characteristic curve for some targets, and in early stages, with up to a 4-fold increase in enrichment factors at 1% of the screened collections. Outstandingly, DLIGAND2 emerged as the best scoring function on this data set, outperforming all rescoring techniques in terms of VS metrics. The described methodology could help in the rational design of small-molecule PPI inhibitors and has direct applications in many therapeutic areas, including cancer, CNS, and infectious diseases such as COVID-19.
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Affiliation(s)
- Natesh Singh
- Université de Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Ludovic Chaput
- Université de Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Bruno O Villoutreix
- Université de Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
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11
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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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12
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Katigbak J, Li H, Rooklin D, Zhang Y. AlphaSpace 2.0: Representing Concave Biomolecular Surfaces Using β-Clusters. J Chem Inf Model 2020; 60:1494-1508. [PMID: 31995373 PMCID: PMC7093224 DOI: 10.1021/acs.jcim.9b00652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Modern rational modulator design and structure-function characterization often concentrate on concave regions of biomolecular surfaces, ranging from well-defined small-molecule binding sites to large protein-protein interaction interfaces. Here, we introduce a β-cluster as a pseudomolecular representation of fragment-centric pockets detected by AlphaSpace [J. Chem. Inf. Model. 2015, 55, 1585], a recently developed computational analysis tool for topographical mapping of biomolecular concavities. By mimicking the shape as well as atomic details of potential molecular binders, this new β-cluster representation allows direct pocket-to-ligand shape comparison and can be used to guide ligand optimization. Furthermore, we defined the β-score, the optimal Vina score of the β-cluster, as an indicator of pocket ligandability and developed an ensemble β-cluster approach, which allows one-to-one pocket mapping and comparison among aligned protein structures. We demonstrated the utility of β-cluster representation by applying the approach to a wide variety of problems including binding site detection and comparison, characterization of protein-protein interactions, and fragment-based ligand optimization. These new β-cluster functionalities have been implemented in AlphaSpace 2.0, which is freely available on the web at http://www.nyu.edu/projects/yzhang/AlphaSpace2.
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Affiliation(s)
- Joseph Katigbak
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Haotian Li
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - David Rooklin
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Yingkai Zhang
- Department of Chemistry, New York University, New York, New York 10003, United States
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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13
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Sale MJ, Minihane E, Monks NR, Gilley R, Richards FM, Schifferli KP, Andersen CL, Davies EJ, Vicente MA, Ozono E, Markovets A, Dry JR, Drew L, Flemington V, Proia T, Jodrell DI, Smith PD, Cook SJ. Targeting melanoma's MCL1 bias unleashes the apoptotic potential of BRAF and ERK1/2 pathway inhibitors. Nat Commun 2019; 10:5167. [PMID: 31727888 PMCID: PMC6856071 DOI: 10.1038/s41467-019-12409-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 09/06/2019] [Indexed: 01/01/2023] Open
Abstract
BRAF and MEK1/2 inhibitors are effective in melanoma but resistance inevitably develops. Despite increasing the abundance of pro-apoptotic BIM and BMF, ERK1/2 pathway inhibition is predominantly cytostatic, reflecting residual pro-survival BCL2 family activity. Here, we show that uniquely low BCL-XL expression in melanoma biases the pro-survival pool towards MCL1. Consequently, BRAF or MEK1/2 inhibitors are synthetic lethal with the MCL1 inhibitor AZD5991, driving profound tumour cell death that requires BAK/BAX, BIM and BMF, and inhibiting tumour growth in vivo. Combination of ERK1/2 pathway inhibitors with BCL2/BCL-w/BCL-XL inhibitors is stronger in CRC, correlating with a low MCL1:BCL-XL ratio; indeed the MCL1:BCL-XL ratio is predictive of ERK1/2 pathway inhibitor synergy with MCL1 or BCL2/BCL-w/BCL-XL inhibitors. Finally, AZD5991 delays acquired BRAFi/MEKi resistance and enhances the efficacy of an ERK1/2 inhibitor in a model of acquired BRAFi + MEKi resistance. Thus combining ERK1/2 pathway inhibitors with MCL1 antagonists in melanoma could improve therapeutic index and patient outcomes.
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Affiliation(s)
- Matthew J Sale
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Emma Minihane
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Noel R Monks
- Oncology R&D, AstraZeneca, One Medimmune Way, Gaithersburg, MD, 20878, USA
| | - Rebecca Gilley
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Frances M Richards
- Pharmacology and Drug Development Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Kevin P Schifferli
- Oncology R&D, AstraZeneca, One Medimmune Way, Gaithersburg, MD, 20878, USA
| | | | - Emma J Davies
- Oncology R&D, AstraZeneca, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Mario Aladren Vicente
- CRUK Therapeutic Discovery Laboratories, Jonas Webb Building, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Eiko Ozono
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | | | - Jonathan R Dry
- Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA
| | - Lisa Drew
- Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA
| | - Vikki Flemington
- Oncology R&D, AstraZeneca, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Theresa Proia
- Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, MA, 02451, USA
| | - Duncan I Jodrell
- Pharmacology and Drug Development Group, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Paul D Smith
- Oncology R&D, AstraZeneca, Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Simon J Cook
- Signalling Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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14
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Luptak J, Bista M, Fisher D, Flavell L, Gao N, Wickson K, Kazmirski SL, Howard T, Rawlins PB, Hargreaves D. Antibody fragments structurally enable a drug-discovery campaign on the cancer target Mcl-1. Acta Crystallogr D Struct Biol 2019; 75:1003-1014. [PMID: 31692474 PMCID: PMC6834078 DOI: 10.1107/s2059798319014116] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 10/16/2019] [Indexed: 11/23/2022] Open
Abstract
Apoptosis is a crucial process by which multicellular organisms control tissue growth, removal and inflammation. Disruption of the normal apoptotic function is often observed in cancer, where cell death is avoided by the overexpression of anti-apoptotic proteins of the Bcl-2 (B-cell lymphoma 2) family, including Mcl-1 (myeloid cell leukaemia 1). This makes Mcl-1 a potential target for drug therapy, through which normal apoptosis may be restored by inhibiting the protective function of Mcl-1. Here, the discovery and biophysical properties of an anti-Mcl-1 antibody fragment are described and the utility of both the scFv and Fab are demonstrated in generating an Mcl-1 crystal system amenable to iterative structure-guided drug design.
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Affiliation(s)
- Jakub Luptak
- Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge CB4 0WG, England
| | - Michal Bista
- Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge CB4 0WG, England
| | - David Fisher
- Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge CB4 0WG, England
| | - Liz Flavell
- Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge CB4 0WG, England
| | - Ning Gao
- Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Waltham, MA 02451, USA
| | - Kate Wickson
- Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge CB4 0WG, England
| | - Steven L. Kazmirski
- Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Waltham, MA 02451, USA
| | - Tina Howard
- Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge CB4 0WG, England
| | - Philip B. Rawlins
- Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge CB4 0WG, England
| | - David Hargreaves
- Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Cambridge CB4 0WG, England
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15
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Denis C, Sopková-de Oliveira Santos J, Bureau R, Voisin-Chiret AS. Hot-Spots of Mcl-1 Protein. J Med Chem 2019; 63:928-943. [DOI: 10.1021/acs.jmedchem.9b00983] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Camille Denis
- Normandie Univiversité, UNICAEN, CERMN, 14000 Caen, France
| | | | - Ronan Bureau
- Normandie Univiversité, UNICAEN, CERMN, 14000 Caen, France
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16
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Discovery of novel biaryl sulfonamide based Mcl-1 inhibitors. Bioorg Med Chem Lett 2019; 29:2375-2382. [DOI: 10.1016/j.bmcl.2019.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/02/2019] [Accepted: 06/05/2019] [Indexed: 01/05/2023]
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17
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Structures of BCL-2 in complex with venetoclax reveal the molecular basis of resistance mutations. Nat Commun 2019; 10:2385. [PMID: 31160589 PMCID: PMC6547681 DOI: 10.1038/s41467-019-10363-1] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 05/08/2019] [Indexed: 12/16/2022] Open
Abstract
Venetoclax is a first-in-class cancer therapy that interacts with the cellular apoptotic machinery promoting apoptosis. Treatment of patients suffering chronic lymphocytic leukaemia with this BCL-2 antagonist has revealed emergence of a drug-selected BCL-2 mutation (G101V) in some patients failing therapy. To understand the molecular basis of this acquired resistance we describe the crystal structures of venetoclax bound to both BCL-2 and the G101V mutant. The pose of venetoclax in its binding site on BCL-2 reveals small but unexpected differences as compared to published structures of complexes with venetoclax analogues. The G101V mutant complex structure and mutant binding assays reveal that resistance is acquired by a knock-on effect of V101 on an adjacent residue, E152, with venetoclax binding restored by a E152A mutation. This provides a framework for considering analogues of venetoclax that might be effective in combating this mutation. The BCL-2 mutation G101V reduces venetoclax affinity and confers drug resistance in patients with chronic lymphocytic leukaemia. Here, the authors present crystal structures and biochemical analyses of venetoclax bound to BCL-2 and the G101V mutant, revealing the structural basis for venetoclax resistance.
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18
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The Structural Biology of Bcl-x L. Int J Mol Sci 2019; 20:ijms20092234. [PMID: 31067648 PMCID: PMC6540150 DOI: 10.3390/ijms20092234] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 01/12/2023] Open
Abstract
Interactions between the pro-survival and pro-apoptotic members of the Bcl-2 family of proteins dictate whether a cell lives or dies. Much of our knowledge of the molecular details of these interactions has come from biochemical and structural studies on the pro-survival protein Bcl-xL. The first high-resolution structure of any Bcl-2 family member was of Bcl-xL, which revealed the conserved topology amongst all family members. Subsequent structures of Bcl-xL complexes with pro-apoptotic ligands demonstrated the general features of all pro-survival:pro-apoptotic complexes. Structural studies involving Bcl-xL were also the basis for the discovery of the first small-molecule pro-survival protein inhibitors, leading ultimately to the development of a new class of drugs now successfully used for cancer treatment in the clinic. This article will review our current knowledge of the structural biology of Bcl-xL and how this has impacted our understanding of the molecular details of the intrinsic apoptotic pathway.
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19
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Knight T, Luedtke D, Edwards H, Taub JW, Ge Y. A delicate balance - The BCL-2 family and its role in apoptosis, oncogenesis, and cancer therapeutics. Biochem Pharmacol 2019; 162:250-261. [PMID: 30668936 DOI: 10.1016/j.bcp.2019.01.015] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 01/18/2019] [Indexed: 01/06/2023]
Abstract
Evasion of apoptosis is fundamental to the pathogenesis of cancer. Members of the B-cell Lymphoma 2 (BCL-2) protein family are key pro- and anti-apoptotic regulators, and in healthy cells are held in a fine, delicate balance - perturbations of which may tip a cell irreversibly towards cellular death or, conversely, allow a cell to permanently escape apoptosis and immortalize itself as a malignant clone. The restoration of this balance or, indeed, adjustment in favor of apoptosis via manipulation of the BCL-2 family, is a promising area in the realm of molecular therapeutics, and one in which breathtaking advances are currently being made. The purpose of this review is to outline the role of the BCL-2 family in apoptosis, to contrast its optimal functioning with those disruptions seen in malignancy, and to provide an overview of the medications both presently available and currently under development which selectively target members of this family.
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Affiliation(s)
- Tristan Knight
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Children's Hospital of Michigan, Detroit, MI, USA; Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Daniel Luedtke
- Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI, USA
| | - Holly Edwards
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Jeffrey W Taub
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Children's Hospital of Michigan, Detroit, MI, USA; Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yubin Ge
- Department of Pediatrics, Wayne State University School of Medicine, Detroit, MI, USA; Cancer Biology Graduate Program, Wayne State University School of Medicine, Detroit, MI, USA; Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Molecular Therapeutics Program, Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA.
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20
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Lee EF, Smith NA, Soares da Costa TP, Meftahi N, Yao S, Harris TJ, Tran S, Pettikiriarachchi A, Perugini MA, Keizer DW, Evangelista M, Smith BJ, Fairlie WD. Structural insights into BCL2 pro-survival protein interactions with the key autophagy regulator BECN1 following phosphorylation by STK4/MST1. Autophagy 2019; 15:785-795. [PMID: 30626284 DOI: 10.1080/15548627.2018.1564557] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
BECN1/Beclin 1 is a critical protein in the initiation of autophagosome formation. Recent studies have shown that phosphorylation of BECN1 by STK4/MST1 at threonine 108 (T108) within its BH3 domain blocks macroautophagy/autophagy by increasing BECN1 affinity for its negative regulators, the anti-apoptotic proteins BCL2/Bcl-2 and BCL2L1/Bcl-xL. It was proposed that this increased binding is due to formation of an electrostatic interaction with a conserved histidine residue on the anti-apoptotic molecules. Here, we performed biophysical studies which demonstrated that a peptide corresponding to the BECN1 BH3 domain in which T108 is phosphorylated (p-T108) does show increased affinity for anti-apoptotic proteins that is significant, though only minor (<2-fold). We also determined X-ray crystal structures of BCL2 and BCL2L1 with T108-modified BECN1 BH3 peptides, but only showed evidence of an interaction between the BH3 peptide and the conserved histidine residue when the histidine flexibility was restrained due to crystal contacts. These data, together with molecular dynamics studies, indicate that the histidine is highly flexible, even when complexed with BECN1 BH3. Binding studies also showed that detergent can increase the affinity of the interaction. Although this increase was similar for both the phosphorylated and non-phosphorylated peptides, it suggests factors such as membranes could impact on the interaction between BECN1 and BCL2 proteins, and therefore, on the regulation of autophagy. Hence, we propose that phosphorylation of BECN1 by STK4/MST1 can increase the affinity of the interaction between BECN1 and anti-apoptotic proteins and this interaction can be stabilized by local environmental factors. Abbreviations: asu: asymmetric unit; BH3: BCL2/Bcl-2 homology 3; DAPK: death associated protein kinase; MD: molecular dynamics; MST: microscale thermophoresis; NMR: nuclear magnetic resonance; PDB: protein data bank; p-T: phosphothreonine; SPR: surface plasmon resonance; STK4/MST1: serine/threonine kinase 4.
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Affiliation(s)
- Erinna F Lee
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia.,b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia.,c School of Cancer Medicine , La Trobe University , Melbourne , Australia
| | - Nicholas A Smith
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
| | | | - Nastaran Meftahi
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
| | - Shenggen Yao
- d Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , Australia
| | - Tiffany J Harris
- b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia
| | - Sharon Tran
- b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia.,c School of Cancer Medicine , La Trobe University , Melbourne , Australia
| | - Anne Pettikiriarachchi
- e Structural Biology Division , The Walter and Eliza Hall Institute of Medical Research , Parkville , Australia
| | - Matthew A Perugini
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
| | - David W Keizer
- d Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , Australia
| | - Marco Evangelista
- b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia
| | - Brian J Smith
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
| | - W Douglas Fairlie
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia.,b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia.,c School of Cancer Medicine , La Trobe University , Melbourne , Australia
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21
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Abstract
BCL-2 family proteins interact in a network that regulates apoptosis. The BH3 amino acid sequence motif serves to bind together this conglomerate protein family, both literally and figuratively. BH3 motifs are present in antiapoptotic and proapoptotic BCL-2 homologs, and in a separate group of unrelated BH3-only proteins often appended to the BCL-2 family. BH3-containing helices mediate many of their physical interactions to determine cell death versus survival, leading to the development of BH3 mimetics as therapeutics. Here we provide an overview of BCL-2 family interactions, their relevance in health and disease, and the progress toward regulating their interactions therapeutically.
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Affiliation(s)
- Jason D Huska
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Heather M Lamb
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - J Marie Hardwick
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA.
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22
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Ivanov SM, Huber RG, Alibay I, Warwicker J, Bond PJ. Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway. J Chem Inf Model 2018; 59:245-261. [DOI: 10.1021/acs.jcim.8b00765] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefan M. Ivanov
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix 07-01, 30 Biopolis Street, Singapore 138671, Singapore
| | - Roland G. Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix 07-01, 30 Biopolis Street, Singapore 138671, Singapore
| | - Irfan Alibay
- Division of Pharmacy and Optometry, School of Health Sciences, The University of Manchester, Oxford Road, Manchester M13 9PT, U.K
| | - Jim Warwicker
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Peter J. Bond
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix 07-01, 30 Biopolis Street, Singapore 138671, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
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23
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Hedir S, De Giorgi M, Fogha J, De Pascale M, Weiswald LB, Brotin E, Marekha B, Denoyelle C, Denis C, Suzanne P, Gautier F, Juin P, Ligat L, Lopez F, Carlier L, Legay R, Bureau R, Rault S, Poulain L, Oliveira Santos JSD, Voisin-Chiret AS. Structure-guided design of pyridoclax derivatives based on Noxa / Mcl-1 interaction mode. Eur J Med Chem 2018; 159:357-380. [PMID: 30308410 DOI: 10.1016/j.ejmech.2018.10.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/28/2018] [Accepted: 10/01/2018] [Indexed: 11/18/2022]
Abstract
Protein-protein interactions are attractive targets because they control numerous cellular processes. In oncology, apoptosis regulating Bcl-2 family proteins are of particular interest. Apoptotic cell death is controlled via PPIs between the anti-apoptotic proteins hydrophobic groove and the pro-apoptotic proteins BH3 domain. In ovarian carcinoma, it has been previously demonstrated that Bcl-xL and Mcl-1 cooperate to protect tumor cells against apoptosis. Moreover, Mcl-1 is a key regulator of cancer cell survival and is a known resistance factor to Bcl-2/Bcl-xL pharmacological inhibitors making it an attractive therapeutic target. Here, using a structure-guided design from the oligopyridine lead Pyridoclax based on Noxa/Mcl-1 interaction we identified a new derivative, active at lower concentration as compared to Pyridoclax. This new derivative selectively binds to the Mcl-1 hydrophobic groove and releases Bak and Bim from Mcl-1 to induce cell death and sensitize cancer cells to Bcl-2/Bcl-xL targeting strategies.
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Affiliation(s)
- Siham Hedir
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France; UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France
| | - Marcella De Giorgi
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Jade Fogha
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Martina De Pascale
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Louis-Bastien Weiswald
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France; UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France
| | - Emilie Brotin
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France; UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France
| | - Bogdan Marekha
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Christophe Denoyelle
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France; UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France
| | - Camille Denis
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Peggy Suzanne
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Fabien Gautier
- Team 8 "Stress adaptation and tumor escape", CRCINA, UMR 1232 INSERM, Université de Nantes, Université d'Angers, Institut de Recherche en Santé-Université de Nantes, Nantes, France; ICO site René Gauducheau, Boulevard Jacques Monod, Saint Herblain, 44805, France
| | - Philippe Juin
- Team 8 "Stress adaptation and tumor escape", CRCINA, UMR 1232 INSERM, Université de Nantes, Université d'Angers, Institut de Recherche en Santé-Université de Nantes, Nantes, France; ICO site René Gauducheau, Boulevard Jacques Monod, Saint Herblain, 44805, France
| | - Laetitia Ligat
- INSERM UMR1037-Plateforme Protéomique-Pôle Technologique du Centre de Recherches en Cancérologie de Toulouse, 2 avenue Hubert Curien, 31100 Toulouse, France; Université Toulouse III-Paul Sabatier, UMR1037 CRCT, 31000 Toulouse, France
| | - Frédéric Lopez
- INSERM UMR1037-Plateforme Protéomique-Pôle Technologique du Centre de Recherches en Cancérologie de Toulouse, 2 avenue Hubert Curien, 31100 Toulouse, France; Université Toulouse III-Paul Sabatier, UMR1037 CRCT, 31000 Toulouse, France
| | - Ludovic Carlier
- Sorbonne Université, Ecole normale supérieure, PSL University, CNRS, Laboratoire des Biomolécules (LBM), 75005 Paris, France
| | - Rémi Legay
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Ronan Bureau
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Sylvain Rault
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France
| | - Laurent Poulain
- Normandie Univ, UNICAEN, Inserm U1086 ANTICIPE «Interdisciplinary Research Unit for Cancer Prevention and Treatment», Biology and Innovative Therapeutics for Ovarian Cancers Group (BioTICLA), Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France; UNICANCER, Centre de Lutte Contre le Cancer F. Baclesse, 3 avenue du Général Harris, 14076, Caen, France.
| | - Jana Sopková-de Oliveira Santos
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France.
| | - Anne Sophie Voisin-Chiret
- Normandie Univ, UNICAEN, EA 4258 CERMN (Centre d'Etudes et de Recherche sur le Médicament de Normandie) - FR CNRS INC3M, Caen, France.
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24
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Maity A, Majumdar S, Ghosh Dastidar S. Flexibility enables to discriminate between ligands: Lessons from structural ensembles of Bcl-xl and Mcl-1. Comput Biol Chem 2018; 77:17-27. [PMID: 30195235 DOI: 10.1016/j.compbiolchem.2018.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/24/2018] [Accepted: 08/17/2018] [Indexed: 12/19/2022]
Abstract
The proteins of Bcl-2 family, which are promising anti-cancer-drug targets, have substantial similarity in primary sequence and share homologous domains as well as similar structural folds. In spite of similarities in sequence and structures, the members of its pro- and anti- apoptotic subgroups form complexes with different type of partners with discriminating binding affinities. Understanding the origin of this discrimination is very important for designing ligands that can either selectively target a protein or could be made broad ranged as necessary. Using principal component analysis (PCA) of the available structures and from the analysis of the evolution of the binding pocket residues, the correlation has been investigated considering two important anti-apoptotic protein Bcl-xl and Mcl-1, which serve as two ideal representatives of this family. The flexibility of the receptor enables them to discriminate between the ligands or the binding partners. It has been observed that although Bcl-xl and Mcl-1 are classified as homologous proteins, through the course of evolution the binding pocket residues are highly conserved for Bcl-xl; whereas they have been substituted frequently in Mcl-1. The investigation has revealed that the Bcl-xl can adjust the backbone conformation of the binding pocket residues to a larger extent to complement with the shape of different binding partners whereas the Mcl-1 shows more variation in the side chain conformation of binding pocket residues for the same purpose.
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Affiliation(s)
- Atanu Maity
- Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700054, India
| | - Sarmistha Majumdar
- Bioinformatics Centre, Bose Institute, P-1/12 CIT Scheme VII M, Kolkata 700054, India
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25
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Oudenaarden CRL, van de Ven RAH, Derksen PWB. Re-inforcing the cell death army in the fight against breast cancer. J Cell Sci 2018; 131:131/16/jcs212563. [DOI: 10.1242/jcs.212563] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
ABSTRACT
Metastatic breast cancer is responsible for most breast cancer-related deaths. Disseminated cancer cells have developed an intrinsic ability to resist anchorage-dependent apoptosis (anoikis). Anoikis is caused by the absence of cellular adhesion, a process that underpins lumen formation and maintenance during mammary gland development and homeostasis. In healthy cells, anoikis is mostly governed by B-cell lymphoma-2 (BCL2) protein family members. Metastatic cancer cells, however, have often developed autocrine BCL2-dependent resistance mechanisms to counteract anoikis. In this Review, we discuss how a pro-apoptotic subgroup of the BCL2 protein family, known as the BH3-only proteins, controls apoptosis and anoikis during mammary gland homeostasis and to what extent their inhibition confers tumor suppressive functions in metastatic breast cancer. Specifically, the role of the two pro-apoptotic BH3-only proteins BCL2-modifying factor (BMF) and BCL2-interacting mediator of cell death (BIM) will be discussed here. We assess current developments in treatment that focus on mimicking the function of the BH3-only proteins to induce apoptosis, and consider their applicability to restore normal apoptotic responses in anchorage-independent disseminating tumor cells.
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Affiliation(s)
- Clara R. L. Oudenaarden
- UMC Utrecht, Department of Pathology, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Lund University, Department of Experimental Oncology, Scheelevägen 2, 22363 Lund, Sweden
| | - Robert A. H. van de Ven
- UMC Utrecht, Department of Pathology, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
- Harvard Medical School, Department of Cell Biology, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Patrick W. B. Derksen
- UMC Utrecht, Department of Pathology, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
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26
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Cook SJ, Stuart K, Gilley R, Sale MJ. Control of cell death and mitochondrial fission by ERK1/2 MAP kinase signalling. FEBS J 2017; 284:4177-4195. [PMID: 28548464 PMCID: PMC6193418 DOI: 10.1111/febs.14122] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 05/08/2017] [Accepted: 05/24/2017] [Indexed: 12/14/2022]
Abstract
The ERK1/2 signalling pathway is best known for its role in connecting activated growth factor receptors to changes in gene expression due to activated ERK1/2 entering the nucleus and phosphorylating transcription factors. However, active ERK1/2 also translocate to a variety of other organelles including the endoplasmic reticulum, endosomes, golgi and mitochondria to access specific substrates and influence cell physiology. In this article, we review two aspects of ERK1/2 signalling at the mitochondria that are involved in regulating cell fate decisions. First, we describe the prominent role of ERK1/2 in controlling the BCL2-regulated, cell-intrinsic apoptotic pathway. In most cases ERK1/2 signalling promotes cell survival by activating prosurvival BCL2 proteins (BCL2, BCL-xL and MCL1) and repressing prodeath proteins (BAD, BIM, BMF and PUMA). This prosurvival signalling is co-opted by oncogenes to confer cancer cell-specific survival advantages and we describe how this information has been used to develop new drug combinations. However, ERK1/2 can also drive the expression of the prodeath protein NOXA to control 'autophagy or apoptosis' decisions during nutrient starvation. We also describe recent studies demonstrating a link between ERK1/2 signalling, DRP1 and the mitochondrial fission machinery and how this may influence metabolic reprogramming during tumorigenesis and stem cell reprogramming. With advances in subcellular proteomics it is likely that new roles for ERK1/2, and new substrates, remain to be discovered at the mitochondria and other organelles.
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Affiliation(s)
- Simon J. Cook
- Signalling ProgrammeThe Babraham InstituteCambridgeUK
| | - Kate Stuart
- Signalling ProgrammeThe Babraham InstituteCambridgeUK
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27
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Fogha J, Marekha B, De Giorgi M, Voisin-Chiret AS, Rault S, Bureau R, Sopkova-de Oliveira Santos J. Toward Understanding Mcl-1 Promiscuous and Specific Binding Mode. J Chem Inf Model 2017; 57:2885-2895. [DOI: 10.1021/acs.jcim.7b00396] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jade Fogha
- Normandie Univ, UNICAEN, CERMN, FR CNRS 3038 INC3M, SF 4206 ICORE bd Becquerel, F-14000 Caen, France
| | - Bogdan Marekha
- Normandie Univ, UNICAEN, CERMN, FR CNRS 3038 INC3M, SF 4206 ICORE bd Becquerel, F-14000 Caen, France
| | - Marcella De Giorgi
- Normandie Univ, UNICAEN, CERMN, FR CNRS 3038 INC3M, SF 4206 ICORE bd Becquerel, F-14000 Caen, France
| | - Anne Sophie Voisin-Chiret
- Normandie Univ, UNICAEN, CERMN, FR CNRS 3038 INC3M, SF 4206 ICORE bd Becquerel, F-14000 Caen, France
| | - Sylvain Rault
- Normandie Univ, UNICAEN, CERMN, FR CNRS 3038 INC3M, SF 4206 ICORE bd Becquerel, F-14000 Caen, France
| | - Ronan Bureau
- Normandie Univ, UNICAEN, CERMN, FR CNRS 3038 INC3M, SF 4206 ICORE bd Becquerel, F-14000 Caen, France
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28
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Progress in targeting the BCL-2 family of proteins. Curr Opin Chem Biol 2017; 39:133-142. [PMID: 28735187 DOI: 10.1016/j.cbpa.2017.06.014] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/14/2017] [Accepted: 06/14/2017] [Indexed: 01/31/2023]
Abstract
The network of protein-protein interactions among the BCL-2 protein family plays a critical role in regulating cellular commitment to mitochondrial apoptosis. Anti-apoptotic BCL-2 proteins are considered promising targets for drug discovery and exciting clinical progress has stimulated intense investigations in the broader family. Here, we discuss recent developments in small molecules targeting anti-apoptotic proteins and alternative approaches to targeting BCL-2 family interactions. These studies advance our understanding of the role of BCL-2 family proteins in physiology and disease, providing unique tools for dissecting these functions. The BCL-2 family of proteins is a prime example of targeting protein-protein interactions and further chemical biology approaches will increase opportunities for novel targeted therapies in cancer, autoimmune and aging-associated diseases.
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29
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Ashkenazi A, Fairbrother WJ, Leverson JD, Souers AJ. From basic apoptosis discoveries to advanced selective BCL-2 family inhibitors. Nat Rev Drug Discov 2017; 16:273-284. [DOI: 10.1038/nrd.2016.253] [Citation(s) in RCA: 508] [Impact Index Per Article: 72.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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30
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Kellici TF, Chatziathanasiadou MV, Lee MS, Sayyad N, Geromichalou EG, Vrettos EI, Tsiailanis AD, Chi SW, Geromichalos GD, Mavromoustakos T, Tzakos AG. Rational design and structure–activity relationship studies of quercetin–amino acid hybrids targeting the anti-apoptotic protein Bcl-xL. Org Biomol Chem 2017; 15:7956-7976. [DOI: 10.1039/c7ob02045g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Anti-apoptotic proteins, like the Bcl-2 family proteins, present an important therapeutic cancer drug target.
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Affiliation(s)
- Tahsin F. Kellici
- Department of Chemistry
- University of Ioannina
- Ioannina 45110
- Greece
- Department of Chemistry
| | | | - Min-Sung Lee
- Disease Target Structure Research Center
- KRIBB
- Daejeon 34141
- Republic of Korea
| | - Nisar Sayyad
- Department of Chemistry
- University of Ioannina
- Ioannina 45110
- Greece
| | - Elena G. Geromichalou
- Laboratory of Pharmacology
- Medical School National and Kapodistrian University of Athens
- Athens 11527
- Greece
| | | | | | - Seung-Wook Chi
- Disease Target Structure Research Center
- KRIBB
- Daejeon 34141
- Republic of Korea
| | - George D. Geromichalos
- Laboratory of Inorganic Chemistry
- Faculty of Chemistry
- Aristotle University of Thessaloniki
- GR-54124 Thessaloniki
- Greece
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31
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Modeling Peptide-Protein Structure and Binding Using Monte Carlo Sampling Approaches: Rosetta FlexPepDock and FlexPepBind. Methods Mol Biol 2017; 1561:139-169. [PMID: 28236237 DOI: 10.1007/978-1-4939-6798-8_9] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Many signaling and regulatory processes involve peptide-mediated protein interactions, i.e., the binding of a short stretch in one protein to a domain in its partner. Computational tools that generate accurate models of peptide-receptor structures and binding improve characterization and manipulation of known interactions, help to discover yet unknown peptide-protein interactions and networks, and bring into reach the design of peptide-based drugs for targeting specific systems of medical interest.Here, we present a concise overview of the Rosetta FlexPepDock protocol and its derivatives that we have developed for the structure-based characterization of peptide-protein binding. Rosetta FlexPepDock was built to generate precise models of protein-peptide complex structures, by effectively addressing the challenge of the considerable conformational flexibility of the peptide. Rosetta FlexPepBind is an extension of this protocol that allows characterizing peptide-binding affinities and specificities of various biological systems, based on the structural models generated by Rosetta FlexPepDock. We provide detailed descriptions and guidelines for the usage of these protocols, and on a specific example, we highlight the variety of different challenges that can be met and the questions that can be answered with Rosetta FlexPepDock.
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32
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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: 26] [Impact Index Per Article: 3.7] [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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33
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Purushotham PM, Kim JM, Jo EK, Senthil K. Withanolides against TLR4-Activated Innate Inflammatory Signalling Pathways: A Comparative Computational and Experimental Study. Phytother Res 2016; 31:152-163. [PMID: 27859734 DOI: 10.1002/ptr.5746] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/23/2016] [Accepted: 10/22/2016] [Indexed: 11/12/2022]
Abstract
Innate inflammations are dominant causes of poor health and high mortality. The pathogen-associated molecular pattern and lipopolysaccharide (LPS) are sensed by immune cells through activation of toll-like receptor 4 leading to mitogen-activated protein kinases (MAPKs) and NF-κB activations. Controlled MAPK and Nf-κB inhibitors have been proposed as potential antiinflammatory drugs. Withania somnifera is an important medicinal herb with known antiinflammatory activity. In this study, the selected Withania somnifera extracts and withanolides were analysed on LPS-induced macrophages comparatively. Molecular docking analysis revealed withaferin A, withanone and withanolide A as effective withanolides against inflammatory target molecules. In experiments, withaferin A and withanone treatment had prominent suppressions on LPS-induced expression of pro-inflammatory cytokines in bone marrow-derived macrophages. Withaferin A regulated all the major four pathways (MAPKs and NF-κB) involved in innate inflammations. Similarly among the Withania extracts analysed, the in vitro propagated leaf and field grown root extracts containing high withaferin A content suppressed the inflammatory molecules through NF-κB and MAPK pathways. Withaferin A was found to be best in suppressing the activated inflammatory pathways among all the analysed withanolides. Therefore, withaferin A and extracts with high withaferin A content can be used as promising drug candidates against innate inflammations. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Preethi M Purushotham
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women University, Coimbatore, 641043, Tamil Nadu, India
| | - Jin-Man Kim
- Department of Pathology, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Eun-Kyeong Jo
- Infection Signaling Network Research Center, College of Medicine, Chungnam National University, Daejeon, Korea
| | - Kalaiselvi Senthil
- Department of Biochemistry, Biotechnology and Bioinformatics, Avinashilingam Institute for Home Science and Higher Education for Women University, Coimbatore, 641043, Tamil Nadu, India
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34
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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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35
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Lee S, Wales TE, Escudero S, Cohen DT, Luccarelli J, Gallagher CG, Cohen NA, Huhn AJ, Bird GH, Engen JR, Walensky LD. Allosteric inhibition of antiapoptotic MCL-1. Nat Struct Mol Biol 2016; 23:600-7. [PMID: 27159560 PMCID: PMC4900187 DOI: 10.1038/nsmb.3223] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 04/06/2016] [Indexed: 11/09/2022]
Abstract
MCL-1 is an antiapoptotic BCL-2 family protein that has emerged as a major pathogenic factor in human cancer. Like BCL-2, MCL-1 bears a surface groove whose function is to sequester the BH3 killer domains of proapoptotic BCL-2 family members, a mechanism harnessed by cancer cells to establish formidable apoptotic blockades. Although drugging the BH3-binding groove has been achieved for BCL-2, translating this approach to MCL-1 has been challenging. Here, we report an alternative mechanism for MCL-1 inhibition by small-molecule covalent modification of C286 at a new interaction site distant from the BH3-binding groove. Our structure-function analyses revealed that the BH3 binding capacity of MCL-1 and its suppression of BAX are impaired by molecular engagement, a phenomenon recapitulated by C286W mutagenic mimicry in vitro and in mouse cells. Thus, we characterize an allosteric mechanism for disrupting the antiapoptotic BH3 binding activity of MCL-1, informing a new strategy for disarming MCL-1 in cancer.
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Affiliation(s)
- Susan Lee
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Silvia Escudero
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Daniel T Cohen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - James Luccarelli
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Catherine G Gallagher
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Nicole A Cohen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Annissa J Huhn
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Gregory H Bird
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Division of Hematology/Oncology, Boston Children's Hospital, Boston, Massachusetts, USA
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36
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Hennessy EJ. Selective inhibitors of Bcl-2 and Bcl-xL: Balancing antitumor activity with on-target toxicity. Bioorg Med Chem Lett 2016; 26:2105-14. [DOI: 10.1016/j.bmcl.2016.03.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 03/08/2016] [Accepted: 03/09/2016] [Indexed: 10/22/2022]
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37
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Scott DE, Bayly AR, Abell C, Skidmore J. Small molecules, big targets: drug discovery faces the protein–protein interaction challenge. Nat Rev Drug Discov 2016; 15:533-50. [DOI: 10.1038/nrd.2016.29] [Citation(s) in RCA: 625] [Impact Index Per Article: 78.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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38
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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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Cierpicki T, Grembecka J. Targeting protein-protein interactions in hematologic malignancies: still a challenge or a great opportunity for future therapies? Immunol Rev 2015; 263:279-301. [PMID: 25510283 DOI: 10.1111/imr.12244] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Over the past several years, there has been an increasing research effort focused on inhibition of protein-protein interactions (PPIs) to develop novel therapeutic approaches for cancer, including hematologic malignancies. These efforts have led to development of small molecule inhibitors of PPIs, some of which already advanced to the stage of clinical trials while others are at different stages of preclinical optimization, emphasizing PPIs as an emerging and attractive class of drug targets. Here, we review several examples of recently developed inhibitors of PPIs highly relevant to hematologic cancers. We address the existing skepticism about feasibility of targeting PPIs and emphasize potential therapeutic benefit from blocking PPIs in hematologic malignancies. We then use these examples to discuss the approaches for successful identification of PPI inhibitors and provide analysis of the protein-protein interfaces, with the goal to address 'druggability' of new PPIs relevant to hematology. We discuss lessons learned to improve the success of targeting new PPIs and evaluate prospects and limits of the research in this field. We conclude that not all PPIs are equally tractable for blocking by small molecules, and detailed analysis of PPI interfaces is critical for selection of those with the highest chance of success. Together, our analysis uncovers patterns that should help to advance drug discovery in hematologic malignancies by successful targeting of new PPIs.
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Affiliation(s)
- Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
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40
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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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41
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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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42
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Enrichment of druggable conformations from apo protein structures using cosolvent-accelerated molecular dynamics. BIOLOGY 2015; 4:344-66. [PMID: 25906084 PMCID: PMC4498304 DOI: 10.3390/biology4020344] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 03/27/2015] [Accepted: 04/11/2015] [Indexed: 11/16/2022]
Abstract
Here we describe the development of an improved workflow for utilizing experimental and simulated protein conformations in the structure-based design of inhibitors for anti-apoptotic Bcl-2 family proteins. Traditional structure-based approaches on similar targets are often constrained by the sparsity of available structures and difficulties in finding lead compounds that dock against flat, flexible protein-protein interaction surfaces. By employing computational docking of known small molecule inhibitors, we have demonstrated that structural ensembles derived from either accelerated MD (aMD) or MD in the presence of an organic cosolvent generally give better scores than those assessed from analogous conventional MD. Furthermore, conformations obtained from combined cosolvent aMD simulations started with the apo-Bcl-xL structure yielded better average and minimum docking scores for known binders than an ensemble of 72 experimental apo- and ligand-bound Bcl-xL structures. A detailed analysis of the simulated conformations indicates that the aMD effectively enhanced conformational sampling of the flexible helices flanking the main Bcl-xL binding groove, permitting the cosolvent acting as small ligands to penetrate more deeply into the binding pocket and shape ligand-bound conformations not evident in conventional simulations. We believe this approach could be useful for identifying inhibitors against other protein-protein interaction systems involving highly flexible binding sites, particularly for targets with less accumulated structural data.
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43
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Campbell ST, Carlson KJ, Buchholz CJ, Helmers MR, Ghosh I. Mapping the BH3 Binding Interface of Bcl-xL, Bcl-2, and Mcl-1 Using Split-Luciferase Reassembly. Biochemistry 2015; 54:2632-43. [PMID: 25844633 DOI: 10.1021/bi501505y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The recognition of helical BH3 domains by Bcl-2 homology (BH) receptors plays a central role in apoptosis. The residues that determine specificity or promiscuity in this interactome are difficult to predict from structural and computational data. Using a cell free split-luciferase system, we have generated a 276 pairwise interaction map for 12 alanine mutations at the binding interface for three receptors, Bcl-xL, Bcl-2, and Mcl-1, and interrogated them against BH3 helices derived from Bad, Bak, Bid, Bik, Bim, Bmf, Hrk, and Puma. This panel, in conjunction with previous structural and functional studies, starts to provide a more comprehensive portrait of this interactome, explains promiscuity, and uncovers surprising details; for example, the Bcl-xL R139A mutation disrupts binding to all helices but the Bad-BH3 peptide, and Mcl-1 binding is particularly perturbed by only four mutations of the 12 tested (V220A, N260A, R263A, and F319A), while Bcl-xL and Bcl-2 have a more diverse set of important residues depending on the bound helix.
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Affiliation(s)
- Sean T Campbell
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Kevin J Carlson
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Carl J Buchholz
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Mark R Helmers
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
| | - Indraneel Ghosh
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, Arizona 85721, United States
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44
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Levoin N, Vo DD, Gautier F, Barillé-Nion S, Juin P, Tasseau O, Grée R. A combination of in silico and SAR studies to identify binding hot spots of Bcl-xL inhibitors. Bioorg Med Chem 2015; 23:1747-57. [DOI: 10.1016/j.bmc.2015.02.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/18/2015] [Indexed: 01/01/2023]
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45
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Johnson DK, Karanicolas J. Selectivity by small-molecule inhibitors of protein interactions can be driven by protein surface fluctuations. PLoS Comput Biol 2015; 11:e1004081. [PMID: 25706586 PMCID: PMC4338137 DOI: 10.1371/journal.pcbi.1004081] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 12/10/2014] [Indexed: 12/13/2022] Open
Abstract
Small-molecules that inhibit interactions between specific pairs of proteins have long represented a promising avenue for therapeutic intervention in a variety of settings. Structural studies have shown that in many cases, the inhibitor-bound protein adopts a conformation that is distinct from its unbound and its protein-bound conformations. This plasticity of the protein surface presents a major challenge in predicting which members of a protein family will be inhibited by a given ligand. Here, we use biased simulations of Bcl-2-family proteins to generate ensembles of low-energy conformations that contain surface pockets suitable for small molecule binding. We find that the resulting conformational ensembles include surface pockets that mimic those observed in inhibitor-bound crystal structures. Next, we find that the ensembles generated using different members of this protein family are overlapping but distinct, and that the activity of a given compound against a particular family member (ligand selectivity) can be predicted from whether the corresponding ensemble samples a complementary surface pocket. Finally, we find that each ensemble includes certain surface pockets that are not shared by any other family member: while no inhibitors have yet been identified to take advantage of these pockets, we expect that chemical scaffolds complementing these “distinct” pockets will prove highly selective for their targets. The opportunity to achieve target selectivity within a protein family by exploiting differences in surface fluctuations represents a new paradigm that may facilitate design of family-selective small-molecule inhibitors of protein-protein interactions. Despite intense interest and considerable effort, there are few examples of small molecules that directly inhibit protein-protein interactions. Crystal structures of early successes have highlighted the plasticity of the protein surface, as some inhibitor-bound proteins are captured in conformations that are distinct from both their unbound and their protein-bound conformations. The lack of a single well-defined structure presents a challenge for predicting the members of a protein family to which a given compound will show activity (ligand selectivity). Here we generate ensembles of conformations from simulation, and show that we can predict ligand selectivity based on which family members sample conformations complementary to the ligand. This approach may present a new avenue for designing highly-selective inhibitors of protein-protein interactions.
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Affiliation(s)
- David K. Johnson
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - John Karanicolas
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- * E-mail:
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46
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DeBartolo J, Taipale M, Keating AE. Genome-wide prediction and validation of peptides that bind human prosurvival Bcl-2 proteins. PLoS Comput Biol 2014; 10:e1003693. [PMID: 24967846 PMCID: PMC4072508 DOI: 10.1371/journal.pcbi.1003693] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/13/2014] [Indexed: 01/27/2023] Open
Abstract
Programmed cell death is regulated by interactions between pro-apoptotic and prosurvival members of the Bcl-2 family. Pro-apoptotic family members contain a weakly conserved BH3 motif that can adopt an alpha-helical structure and bind to a groove on prosurvival partners Bcl-xL, Bcl-w, Bcl-2, Mcl-1 and Bfl-1. Peptides corresponding to roughly 13 reported BH3 motifs have been verified to bind in this manner. Due to their short lengths and low sequence conservation, BH3 motifs are not detected using standard sequence-based bioinformatics approaches. Thus, it is possible that many additional proteins harbor BH3-like sequences that can mediate interactions with the Bcl-2 family. In this work, we used structure-based and data-based Bcl-2 interaction models to find new BH3-like peptides in the human proteome. We used peptide SPOT arrays to test candidate peptides for interaction with one or more of the prosurvival proteins Bcl-xL, Bcl-w, Bcl-2, Mcl-1 and Bfl-1. For the 36 most promising array candidates, we quantified binding to all five human receptors using direct and competition binding assays in solution. All 36 peptides showed evidence of interaction with at least one prosurvival protein, and 22 peptides bound at least one prosurvival protein with a dissociation constant between 1 and 500 nM; many peptides had specificity profiles not previously observed. We also screened the full-length parent proteins of a subset of array-tested peptides for binding to Bcl-xL and Mcl-1. Finally, we used the peptide binding data, in conjunction with previously reported interactions, to assess the affinity and specificity prediction performance of different models. Bcl-2 family proteins regulate key cell death vs. survival decisions and are implicated in the development of many cancers. To understand the roles of Bcl-2 family proteins in both normal and diseased cells, it is important to map the interaction network of the family. Low sequence conservation in known Bcl-2 interaction motifs precludes easy identification of possible binding partners, but we developed computational models based on structure and experimental mutation data that show good predictive performance. We used our models to search the human proteome for new Bcl-2 interaction partners. We predicted and experimentally validated more than twice as many tight-binding peptides as were previously known.
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Affiliation(s)
- Joe DeBartolo
- MIT Department of Biology, Cambridge, Massachusetts, United States of America
| | - Mikko Taipale
- MIT Department of Biology, Cambridge, Massachusetts, United States of America
| | - Amy E. Keating
- MIT Department of Biology, Cambridge, Massachusetts, United States of America
- * E-mail:
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47
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Procko E, Berguig GY, Shen BW, Song Y, Frayo S, Convertine AJ, Margineantu D, Booth G, Correia BE, Cheng Y, Schief WR, Hockenbery DM, Press OW, Stoddard BL, Stayton PS, Baker D. A computationally designed inhibitor of an Epstein-Barr viral Bcl-2 protein induces apoptosis in infected cells. Cell 2014; 157:1644-1656. [PMID: 24949974 PMCID: PMC4079535 DOI: 10.1016/j.cell.2014.04.034] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 03/13/2014] [Accepted: 04/15/2014] [Indexed: 11/25/2022]
Abstract
Because apoptosis of infected cells can limit virus production and spread, some viruses have co-opted prosurvival genes from the host. This includes the Epstein-Barr virus (EBV) gene BHRF1, a homolog of human Bcl-2 proteins that block apoptosis and are associated with cancer. Computational design and experimental optimization were used to generate a novel protein called BINDI that binds BHRF1 with picomolar affinity. BINDI recognizes the hydrophobic cleft of BHRF1 in a manner similar to other Bcl-2 protein interactions but makes many additional contacts to achieve exceptional affinity and specificity. BINDI induces apoptosis in EBV-infected cancer lines, and when delivered with an antibody-targeted intracellular delivery carrier, BINDI suppressed tumor growth and extended survival in a xenograft disease model of EBV-positive human lymphoma. High-specificity-designed proteins that selectively kill target cells may provide an advantage over the toxic compounds used in current generation antibody-drug conjugates.
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Affiliation(s)
- Erik Procko
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Geoffrey Y. Berguig
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Betty W. Shen
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Yifan Song
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Shani Frayo
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | | | - Garrett Booth
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Yuanhua Cheng
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | | | | | - Oliver W. Press
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Patrick S. Stayton
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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48
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Liu G, Poppe L, Aoki K, Yamane H, Lewis J, Szyperski T. High-quality NMR structure of human anti-apoptotic protein domain Mcl-1(171-327) for cancer drug design. PLoS One 2014; 9:e96521. [PMID: 24789074 PMCID: PMC4008586 DOI: 10.1371/journal.pone.0096521] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/08/2014] [Indexed: 12/18/2022] Open
Abstract
A high-quality NMR solution structure is presented for protein hMcl-1(171–327) which comprises residues 171–327 of the human anti-apoptotic protein Mcl-1 (hMcl-1). Since this construct contains the three Bcl-2 homology (BH) sequence motifs which participate in forming a binding site for inhibitors of hMcl-1, it is deemed to be crucial for structure-based design of novel anti-cancer drugs blocking the Mcl1 related anti-apoptotic pathway. While the coordinates of an NMR solution structure for a corresponding construct of the mouse homologue (mMcl-1) are publicly available, our structure is the first atomic resolution structure reported for the ‘apo form’ of the human protein. Comparison of the two structures reveals that hMcl-1(171–327) exhibits a somewhat wider ligand/inhibitor binding groove as well as a different charge distribution within the BH3 binding groove. These findings strongly suggest that the availability of the human structure is of critical importance to support future design of cancer drugs.
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Affiliation(s)
- Gaohua Liu
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Leszek Poppe
- Molecular Structure, Amgen, Thousand Oaks, California, United States of America
| | - Ken Aoki
- Protein Science, Amgen, Thousand Oaks, California, United States of America
| | - Harvey Yamane
- Protein Science, Amgen, Thousand Oaks, California, United States of America
| | - Jeffrey Lewis
- Protein Science, Amgen, Thousand Oaks, California, United States of America
| | - Thomas Szyperski
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York, United States of America
- * E-mail:
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49
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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: 2160] [Impact Index Per Article: 216.0] [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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50
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Wysoczanski P, Mart RJ, Loveridge EJ, Williams C, Whittaker SBM, Crump MP, Allemann RK. ¹H, ¹³C and ¹⁵N chemical shift assignments of unliganded Bcl-xL and its complex with a photoresponsive Bak-derived peptide. BIOMOLECULAR NMR ASSIGNMENTS 2013; 7:187-191. [PMID: 22744789 DOI: 10.1007/s12104-012-9407-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 06/21/2012] [Indexed: 06/01/2023]
Abstract
Here we report the (1)H, (13)C and (15)N resonance assignments of free Bcl-x(L) and of Bcl-x(L) in complex with an azobenzene-modified peptide derived from the BH3 domain of the pro-apoptotic Bak. The spectra suggest predominantly folded proteins; chemical shift difference analysis provides a detailed view of the reorganization occurring on peptide binding.
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Affiliation(s)
- Piotr Wysoczanski
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, UK
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