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Xiaoli A, Yuzhen N, Qiong Y, Yang L, Yao X, Bing Z. Investigating the Dynamic Binding Behavior of PMX53 Cooperating with Allosteric Antagonist NDT9513727 to C5a Anaphylatoxin Chemotactic Receptor 1 through Gaussian Accelerated Molecular Dynamics and Free-Energy Perturbation Simulations. ACS Chem Neurosci 2022; 13:3502-3511. [PMID: 36428153 DOI: 10.1021/acschemneuro.2c00556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
C5a anaphylatoxin chemotactic receptor 1 (C5aR1) is an important target in anti-inflammatory therapeutics. The cyclic peptide antagonist PMX53 binds to the orthosteric site located in the extracellular vestibule of C5aR1, and the non-peptide antagonist NDT9513727 binds to the allosteric site formed by the middle region of TM3 (trans-membrane helix), TM4, and TM5. We catch a sight of the variational binding mode of PMX53 during the Gaussian accelerated molecular dynamic (GaMD) simulations. In the binary complex of C5aR1 and PMX53, the PMX53 takes a dynamic binding mechanism during the simulation. Namely, the side chain of Arg6 of PMX53 extends to TM6-TM7 (pose 1) or swings to TM5 (pose 2), forming a salt bridge with Glu199. Meanwhile, in the ternary complex of C5aR1 with PMX53 and NDT9513727, the side chain of Arg6 of PMX53 swings to TM5 (pose 2) from extending to TM6-TM7 (pose 1) at the beginning of the GaMD simulation. In subsequent simulation, PMX53 stabilizes in the pose 2 binding mode by forming a stable salt bridge with Glu199. The free-energy perturbation (FEP) calculations demonstrate that pose 1 (ΔGbinding = -10.94 kcal/mol) is more stable in the binary complex and pose 2 (ΔGbinding = -7.91 kcal/mol) is unstable because of highly dynamic TM5. NDT9513727 interacts directly with TM4 and TM5 and stabilizes the hydrophobic stack between the extracellular sides of the two helices. Therefore, pose 2 (ΔGbinding = -16.27 kcal/mol) is notably stable than pose 1 (ΔGbinding = -9.78 kcal/mol) in the ternary complex. The identification of a novel binding mode of PMX53 and the detailed structural information of PMX53 interacting with a receptor obtained by GaMD simulations will be helpful in designing potent antagonists of C5aR1.
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Affiliation(s)
- An Xiaoli
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou 730000, China
| | - Niu Yuzhen
- Shandong Laboratory of Yantai Advanced Materials and Green Manufacturing, Yantai 264006, China.,Yantai Zhongke Research Institute of Advanced Materials and Green Chemical Engineering, Yantai 264006, China
| | - Yang Qiong
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou 730000, China
| | - Lei Yang
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou 730000, China
| | - Xiaojun Yao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China
| | - Zhitong Bing
- Institute of Modern Physics, Chinese Academy of Science, Lanzhou 730000, China.,Advanced Energy Science and Technology Guangdong Laboratory, Huizhou 516000, China
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Mortier J, Friberg A, Badock V, Moosmayer D, Schroeder J, Steigemann P, Siegel F, Gradl S, Bauser M, Hillig RC, Briem H, Eis K, Bader B, Nguyen D, Christ CD. Computationally Empowered Workflow Identifies Novel Covalent Allosteric Binders for KRAS G12C. ChemMedChem 2020; 15:827-832. [PMID: 32237114 PMCID: PMC7318243 DOI: 10.1002/cmdc.201900727] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 01/25/2023]
Abstract
Due to its frequent mutations in multiple lethal cancers, KRAS is one of the most-studied anticancer targets nowadays. Since the discovery of the druggable allosteric binding site containing a G12C mutation, KRASG12C has been the focus of attention in oncology research. We report here a computationally driven approach aimed at identifying novel and selective KRASG12C covalent inhibitors. The workflow involved initial enumeration of virtual molecules tailored for the KRAS allosteric binding site. Tools such as pharmacophore modeling, docking, and free-energy perturbations were deployed to prioritize the compounds with the best profiles. The synthesized naphthyridinone scaffold showed the ability to react with G12C and inhibit KRASG12C . Analogues were prepared to establish structure-activity relationships, while molecular dynamics simulations and crystallization of the inhibitor-KRASG12C complex highlighted an unprecedented binding mode.
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Affiliation(s)
- Jérémie Mortier
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Anders Friberg
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Volker Badock
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Dieter Moosmayer
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Jens Schroeder
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Patrick Steigemann
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Franziska Siegel
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Stefan Gradl
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Marcus Bauser
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Roman C Hillig
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Hans Briem
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Knut Eis
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Benjamin Bader
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Duy Nguyen
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
| | - Clara D Christ
- Bayer AG, Research & Development, Pharmaceuticals, Müllerstrasse 178, 13342, Berlin, Germany
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