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Qi X, Li G, Liu J, Mou L, Zhang Y, Guo S, Chen X, Li W. Structural and energetic insights into the selective inhibition of PKMYT1 against WEE1. J Biomol Struct Dyn 2024; 42:3010-3018. [PMID: 37345529 DOI: 10.1080/07391102.2023.2225106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/30/2023] [Indexed: 06/23/2023]
Abstract
Protein kinase, membrane-associated tyrosine/threonine 1 (PKMYT1), a member of the WEE family and responsible for the regulation of CDK1 phosphorylation, has been considered a promising therapeutic target for cancer therapy. However, the highly structural conservation of the ATP-binding sites of the WEE family poses a challenge to the design of selective inhibitors for PKMYT1. Here, molecular docking, multiple microsecond-length molecular dynamics (MD) simulations and end-point free energy calculations were performed to uncover the molecular mechanism of the binding selectivity of RP-6306 toward PKMYT1 over its highly homologous kinase WEE1. The binding specificity of RP-6306 reported in previous experimental bioassays was clarified by MD simulations and binding free energy calculations. Further, the binding free energy prediction indicated that the binding selectivity of RP-6306 largely derived from the difference in the protein-ligand electrostatic interactions. The per-residue free energy decomposition suggested that the non-conserved gatekeeper residue in the hinge domain of PKMYT1/WEE1, Thr187/Asn376, is the critical factor responsible for the binding selectivity of RP-6306 toward PKMYT1. In addition, a water-mediated hydrogen bond was formed between RP-6306 and Gly191 at the hinge domain in the PKMYT1/RP-6306 complex, which was absent in the WEE1/RP-6306 complex. This study is expected to offer useful information for the design of more potent and selective PKMYT1 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xuesen Qi
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Guozhen Li
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Jiahai Liu
- Department of Gastrointestinal and Anal Diseases Surgery, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Linkai Mou
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Yusheng Zhang
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Shilin Guo
- Department of Urology, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
| | - Xiangyu Chen
- School of Medical Laboratory, Weifang Medical University, Weifang, Shandong, China
| | - Wenxing Li
- Pathology Department, The Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong, China
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Olawale F, Ogunyemi O, Folorunso IM. Repurposing clinically approved drugs as Wee1 checkpoint kinase inhibitors: an in silico investigation integrating molecular docking, ensemble QSAR modelling and molecular dynamics simulation. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2101673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Femi Olawale
- Nano-Gene and Drug Delivery Group, Department of Biochemistry, School of life science, University of KwaZulu Natal, Durban, South Africa
| | - Oludare Ogunyemi
- Human Nutraceuticals and Bioinformatics Research Unit, Department of Biochemistry, Salem University, Lokoja, Nigeria
| | - Ibukun Mary Folorunso
- Bioinformatics and Molecular Biology Unit, Department of Biochemistry, Federal University of Technology Akure, Akure, Nigeria
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Comparing the interaction of four structurally similar coumarins from Fraxinus Chinensis Roxb. with HSA through multi-spectroscopic and docking studies. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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