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Gray JL, von Delft F, Brennan PE. Targeting the Small GTPase Superfamily through Their Regulatory Proteins. Angew Chem Int Ed Engl 2020; 59:6342-6366. [PMID: 30869179 PMCID: PMC7204875 DOI: 10.1002/anie.201900585] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/11/2019] [Indexed: 12/11/2022]
Abstract
The Ras superfamily of small GTPases are guanine-nucleotide-dependent switches essential for numerous cellular processes. Mutations or dysregulation of these proteins are associated with many diseases, but unsuccessful attempts to target the small GTPases directly have resulted in them being classed as "undruggable". The GTP-dependent signaling of these proteins is controlled by their regulators; guanine nucleotide exchange factors (GEFs), GTPase activating proteins (GAPs), and in the Rho and Rab subfamilies, guanine nucleotide dissociation inhibitors (GDIs). This review covers the recent small molecule and biologics strategies to target the small GTPases through their regulators. It seeks to critically re-evaluate recent chemical biology practice, such as the presence of PAINs motifs and the cell-based readout using compounds that are weakly potent or of unknown specificity. It highlights the vast scope of potential approaches for targeting the small GTPases in the future through their regulatory proteins.
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Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
| | - Frank von Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Diamond Light SourceHarwell Science and Innovation CampusDidcotOX11 0QXUK
- Department of BiochemistryUniversity of JohannesburgAuckland Park2006South Africa
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRBOld Road CampusOxfordOX3 7DQUK
- Target Discovery InstituteNuffield Department of MedicineUniversity of OxfordOld Road CampusOxfordOX3 7FZUK
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of OxfordOxfordOX3 7FZUK
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2
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Gray JL, Delft F, Brennan PE. Targeting der kleinen GTPasen über ihre regulatorischen Proteine. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201900585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Janine L. Gray
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
| | - Frank Delft
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Diamond Light Source Harwell Science and Innovation Campus Didcot OX11 0QX Großbritannien
- Department of BiochemistryUniversity of Johannesburg Auckland Park 2006 Südafrika
| | - Paul E. Brennan
- Structural Genomics ConsortiumUniversity of Oxford, NDMRB Old Road Campus Oxford OX3 7DQ Großbritannien
- Target Discovery InstituteNuffield Department of MedicineUniversity of Oxford Old Road Campus Oxford OX3 7FZ Großbritannien
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of Oxford Oxford OX3 7FZ Großbritannien
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3
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Martín-Gago P, Fansa EK, Klein CH, Murarka S, Janning P, Schürmann M, Metz M, Ismail S, Schultz-Fademrecht C, Baumann M, Bastiaens PIH, Wittinghofer A, Waldmann H. A PDE6δ-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2. Angew Chem Int Ed Engl 2017; 56:2423-2428. [PMID: 28106325 DOI: 10.1002/anie.201610957] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Indexed: 12/11/2022]
Abstract
Small-molecule inhibition of the interaction between the KRas oncoprotein and the chaperone PDE6δ impairs KRas spatial organization and signaling in cells. However, despite potent binding in vitro (KD <10 nm), interference with Ras signaling and growth inhibition require 5-20 μm compound concentrations. We demonstrate that these findings can be explained by fast release of high-affinity inhibitors from PDE6δ by the release factor Arl2. This limitation is overcome by novel highly selective inhibitors that bind to PDE6δ with up to 7 hydrogen bonds, resulting in picomolar affinity. Their release by Arl2 is greatly decreased, and representative compounds selectively inhibit growth of KRas mutated and -dependent cells with the highest activity recorded yet. Our findings indicate that very potent inhibitors of the KRas-PDE6δ interaction may impair the growth of tumors driven by oncogenic KRas.
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Affiliation(s)
- Pablo Martín-Gago
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Eyad K Fansa
- Structural Biology Group, Max Planck Institute for Molecular Physiology, 44227, Dortmund, Germany
| | - Christian H Klein
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Sandip Murarka
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Petra Janning
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Marc Schürmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Malte Metz
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Shehab Ismail
- Structural Biology Group, Max Planck Institute for Molecular Physiology, 44227, Dortmund, Germany
| | | | | | - Philippe I H Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- TU Dortmund, Faculty of Chemistry and Chemical Biology, 44227, Dortmund, Germany
| | - Alfred Wittinghofer
- Structural Biology Group, Max Planck Institute for Molecular Physiology, 44227, Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- TU Dortmund, Faculty of Chemistry and Chemical Biology, 44227, Dortmund, Germany
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4
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Martín-Gago P, Fansa EK, Klein CH, Murarka S, Janning P, Schürmann M, Metz M, Ismail S, Schultz-Fademrecht C, Baumann M, Bastiaens PIH, Wittinghofer A, Waldmann H. A PDE6δ-KRas Inhibitor Chemotype with up to Seven H-Bonds and Picomolar Affinity that Prevents Efficient Inhibitor Release by Arl2. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610957] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Pablo Martín-Gago
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
| | - Eyad K. Fansa
- Structural Biology Group; Max Planck Institute for Molecular Physiology; 44227 Dortmund Germany
| | - Christian H. Klein
- Department of Systemic Cell Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
| | - Sandip Murarka
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
| | - Petra Janning
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
| | - Marc Schürmann
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
| | - Malte Metz
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
| | - Shehab Ismail
- Structural Biology Group; Max Planck Institute for Molecular Physiology; 44227 Dortmund Germany
| | | | | | - Philippe I. H. Bastiaens
- Department of Systemic Cell Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
- TU Dortmund; Faculty of Chemistry and Chemical Biology; 44227 Dortmund Germany
| | - Alfred Wittinghofer
- Structural Biology Group; Max Planck Institute for Molecular Physiology; 44227 Dortmund Germany
| | - Herbert Waldmann
- Department of Chemical Biology; Max Planck Institute of Molecular Physiology; 44227 Dortmund Germany
- TU Dortmund; Faculty of Chemistry and Chemical Biology; 44227 Dortmund Germany
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5
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Marín-Ramos NI, Piñar C, Vázquez-Villa H, Martín-Fontecha M, González Á, Canales Á, Algar S, Mayo PP, Jiménez-Barbero J, Gajate C, Mollinedo F, Pardo L, Ortega-Gutiérrez S, Viso A, López-Rodríguez ML. Development of a Nucleotide Exchange Inhibitor That Impairs Ras Oncogenic Signaling. Chemistry 2016; 23:1676-1685. [PMID: 27885731 DOI: 10.1002/chem.201604905] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Indexed: 12/11/2022]
Abstract
Despite more than three decades of intense effort, no anti-Ras therapies have reached clinical application. Contributing to this failure has been an underestimation of Ras complexity and a dearth of structural information. In this regard, recent studies have revealed the highly dynamic character of the Ras surface and the existence of transient pockets suitable for small-molecule binding, opening up new possibilities for the development of Ras modulators. Herein, a novel Ras inhibitor (compound 12) is described that selectively impairs mutated Ras activity in a reversible manner without significantly affecting wild-type Ras, reduces the Ras-guanosine triphosphate (GTP) levels, inhibits the activation of the mitogen-activated protein kinase (MAPK) pathway, and exhibits remarkable cytotoxic activity in Ras-driven cellular models. The use of molecular dynamics simulations and NMR spectroscopy experiments has enabled the molecular bases responsible for the interactions between compound 12 and Ras protein to be explored. The new Ras inhibitor binds partially to the GTP-binding region and extends into the adjacent hydrophobic pocket delimited by switch II. Hence, Ras inhibitor 12 could represent a new compound for the development of more efficacious drugs to target Ras-driven cancers; a currently unmet clinical need.
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Affiliation(s)
- Nagore I Marín-Ramos
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain.,CEI Campus Moncloa, UCM-UPM and CSIC, 28040, Madrid, Spain
| | - Carmen Piñar
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Mar Martín-Fontecha
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Ángel González
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Ángeles Canales
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Sergio Algar
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Paloma P Mayo
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Parque Tecnológico de Bizkaia, Edif. 801A, 48160, Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48103, Bilbao, Spain
| | - Consuelo Gajate
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Faustino Mollinedo
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Leonardo Pardo
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Silvia Ortega-Gutiérrez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Alma Viso
- Instituto de Química Orgánica General, IQOG-CSIC, Juan de la Cierva, 3, 28006, Madrid, Spain
| | - María L López-Rodríguez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
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6
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Sautier B, Nising CF, Wortmann L. Fortschritte bei der Ras-Inhibition aus medizinisch-chemischer Perspektive. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Brice Sautier
- Bayer Pharma AG, Drug Discovery; Medicinal Chemistry Berlin; Muellerstraße 178 13353 Berlin Deutschland
| | - Carl F. Nising
- Bayer Pharma AG, Drug Discovery; Medicinal Chemistry Berlin; Muellerstraße 178 13353 Berlin Deutschland
| | - Lars Wortmann
- Bayer Pharma AG, Drug Discovery; Medicinal Chemistry Berlin; Muellerstraße 178 13353 Berlin Deutschland
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7
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Sautier B, Nising CF, Wortmann L. Latest Advances Towards Ras Inhibition: A Medicinal Chemistry Perspective. Angew Chem Int Ed Engl 2016; 55:15982-15988. [PMID: 27635522 DOI: 10.1002/anie.201608270] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Indexed: 12/17/2022]
Abstract
Owing to their high occurrence rate across many human cancers and their lack of druggability so far, mutant forms of the signaling protein Ras are currently among the most attractive (and elusive) oncology targets. This strong appeal explains the sustained effort in the field, and the ensuing progress has rekindled optimism regarding the discovery of Ras inhibitors. In this Minireview, we discuss the most recent advances towards irreversible inhibitors, and highlight approaches to inhibitors of Ras-effector interactions that have been overshadowed by the current focus on direct Ras inhibition. At the same time, we provide a critical assessment from a medicinal chemistry perspective.
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Affiliation(s)
- Brice Sautier
- Bayer Pharma AG, Drug Discovery, Medicinal Chemistry Berlin, Muellerstrasse 178, 13353, Berlin, Germany
| | - Carl F Nising
- Bayer Pharma AG, Drug Discovery, Medicinal Chemistry Berlin, Muellerstrasse 178, 13353, Berlin, Germany
| | - Lars Wortmann
- Bayer Pharma AG, Drug Discovery, Medicinal Chemistry Berlin, Muellerstrasse 178, 13353, Berlin, Germany
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8
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Cromm PM, Wallraven K, Glas A, Bier D, Fürstner A, Ottmann C, Grossmann TN. Constraining an Irregular Peptide Secondary Structure through Ring-Closing Alkyne Metathesis. Chembiochem 2016; 17:1915-1919. [PMID: 27596722 PMCID: PMC5096054 DOI: 10.1002/cbic.201600362] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Indexed: 01/04/2023]
Abstract
Macrocyclization can be used to constrain peptides in their bioactive conformations, thereby supporting target affinity and bioactivity. In particular, for the targeting of challenging protein-protein interactions, macrocyclic peptides have proven to be very useful. Available approaches focus on the stabilization of α-helices, which limits their general applicability. Here we report for the first time on the use of ring-closing alkyne metathesis for the stabilization of an irregular peptide secondary structure. A small library of alkyne-crosslinked peptides provided a number of derivatives with improved target affinity relative to the linear parent peptide. In addition, we report the crystal structure of the highest-affinity derivative in a complex with its protein target 14-3-3ζ. It can be expected that the alkyne-based macrocyclization of irregular binding epitopes should give rise to new scaffolds suitable for targeting of currently intractable proteins.
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Affiliation(s)
- Philipp M Cromm
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
| | - Kerstin Wallraven
- VU University Amsterdam, Department of Chemistry and Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Adrian Glas
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany
| | - David Bier
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany
- University of Eindhoven, Department of Biomedical Engineering, Institute of Complex Molecular Systems, Den Dolech 2, 5612 AZ, Eindhoven, The Netherlands
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Alois Fürstner
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim/Ruhr, Germany
| | - Christian Ottmann
- University of Eindhoven, Department of Biomedical Engineering, Institute of Complex Molecular Systems, Den Dolech 2, 5612 AZ, Eindhoven, The Netherlands
- Department of Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141, Essen, Germany
| | - Tom N Grossmann
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, 44227, Dortmund, Germany.
- VU University Amsterdam, Department of Chemistry and Pharmaceutical Sciences, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, 44227, Dortmund, Germany.
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9
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Lu S, Jang H, Zhang J, Nussinov R. Inhibitors of Ras-SOS Interactions. ChemMedChem 2015; 11:814-21. [PMID: 26630662 DOI: 10.1002/cmdc.201500481] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Indexed: 12/18/2022]
Abstract
Activating Ras mutations are found in about 30 % of human cancers. Ras activation is regulated by guanine nucleotide exchange factors, such as the son of sevenless (SOS), which form protein-protein interactions (PPIs) with Ras and catalyze the exchange of GDP by GTP. This is the rate-limiting step in Ras activation. However, Ras surfaces lack any evident suitable pockets where a molecule might bind tightly, rendering Ras proteins still 'undruggable' for over 30 years. Among the alternative approaches is the design of inhibitors that target the Ras-SOS PPI interface, a strategy that is gaining increasing recognition for treating Ras mutant cancers. Herein we focus on data that has accumulated over the past few years pertaining to the design of small-molecule modulators or peptide mimetics aimed at the interface of the Ras-SOS PPI. We emphasize, however, that even if such Ras-SOS therapeutics are potent, drug resistance may emerge. To counteract this development, we propose "pathway drug cocktails", that is, drug combinations aimed at parallel (or compensatory) pathways. A repertoire of classified cancer, cell/tissue, and pathway/protein combinations would be beneficial toward this goal.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China.
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD, 21702, USA. .,Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
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