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Zhao TT, Hu HJ, Gao LX, Zhou YB, Zhu YL, Zhang C, Li J, Wang WL. Exploring the mechanism of the PTP1B inhibitors by molecular dynamics and experimental study. J Mol Graph Model 2023; 125:108585. [PMID: 37544021 DOI: 10.1016/j.jmgm.2023.108585] [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: 06/14/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/08/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) has proven to be an attractive target for the treatment of cancer, diabetes and other diseases. Although many PTP1B inhibitors with various scaffolds have been developed, there is still a lack of PTP1B inhibitor with high specificity and acceptable pharmacological properties. Therefore, it is urgent to develop more methods to explore complex action mode of PTP1B and ligands for designing ideal PTP1B modulators. In this work, we developed a potential molecular dynamics (MD) analytic mode to analyze the mechanism of active compounds 6a and 6e against PTP1B from different perspectives, including the stable ability, interactions and binding site of ligand and protein, the binding energy, relative movement between residues and changes in protein internal interactions. The simulated results demonstrated that compound 6a bound more stably to the active pocket of PTP1B than 6e due to its smaller molecular volume (326 Å3), matched electronegativity, and enhanced the positive correlation motion of residues, especially for WPD loop and P loop. Lastly, compound 6a as a competitive inhibitor for PTP1B was verified by enzyme kinetic assay. This work successfully studied the mechanism of compound 6a against PTP1B from various aspects, enriched the analysis of interaction mode between PTP1B and inhibitors. In summary, we hope that this work could provide more theoretical information for designing and developing more novel and ideal PTP1B inhibitors in the future.
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Affiliation(s)
- Tian-Tian Zhao
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China
| | - Hao-Jie Hu
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China
| | - Li-Xin Gao
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China; State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yu-Bo Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yun-Long Zhu
- Wuxi Maternal and Child Health Hospital, Wuxi School of Medicine, Jiangnan University, Jiangsu, 214002, China.
| | - Chun Zhang
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China.
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Wen-Long Wang
- School of Life Sciences and Health Engineering, Jiangnan University, Jiangsu, 214122, China.
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Isolation and identification of novel angiotensin I-converting enzyme (ACE) inhibitory peptides from Pony Seed and evaluation of the inhibitory mechanisms. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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