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Jiang Y, Liu L, Geng Y, Li Q, Luo D, Liang L, Liu W, Ouyang W, Hu J. Feasibility of the inhibitor development for cancer: A systematic approach for drug design. PLoS One 2024; 19:e0306632. [PMID: 39173044 PMCID: PMC11341021 DOI: 10.1371/journal.pone.0306632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 06/20/2024] [Indexed: 08/24/2024] Open
Abstract
The traditional Chinese medicine (TCM) bupleurum-ginger-licorice formula presents significant anti-cancer effects, but its active ingredients and inhibitory mechanism remain unclear. In this work, the core effective ingredient quercetin and its signal transducer and activator of transcription 3 (Stat3) receptor both were identified by network pharmacology. Quercetin is a low-toxicity, non-carcinogenic flavonoid with antioxidant, anti-inflammatory and anticancer activities, which is widely distributed in edible plants. Stat3 can bind to specific DNA response elements and serves as a transcription factor to promote the translation of some invasion/migration-related target genes, considered as a potential anticancer target. Here, molecular docking and molecular dynamics (MD) simulation both were used to explore molecular recognition of quercetin with Stat3. The results show that quercetin impairs DNA transcription efficiency by hindering Stat3 dimerization, partially destroying DNA conformation. Specifically, when the ligand occupies the SH2 cavity of the enzyme, spatial rejection is not conductive to phosphokinase binding. It indirectly prevents the phosphorylation of Y705 and the formation of Stat3 dimer. When the inhibitor binds to the DT1005 position, it obviously shortens the distance between DNA and DBD, enhances their binding capacity, and thereby reduces the degree of freedom required for transcription. This work not only provides the binding modes between Stat3 and quercetin, but also contributes to the optimization and design of such anti-cancer inhibitors.
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Affiliation(s)
- Yu Jiang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Ling Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China
| | - Yichao Geng
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China
| | - Qingsong Li
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China
| | - Daxian Luo
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Wei Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Weiwei Ouyang
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
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Liu L, Cheng Y, Zhang Z, Li J, Geng Y, Li Q, Luo D, Liang L, Liu W, Hu J, Ouyang W. Study on the allosteric activation mechanism of SHP2 via elastic network models and neural relational inference molecular dynamics simulation. Phys Chem Chem Phys 2023; 25:23588-23601. [PMID: 37621251 DOI: 10.1039/d3cp02795c] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
As a ubiquitous protein tyrosine phosphatase, SHP2 is involved in PD-1/PD-L1 mediated tumor immune escape and undergoes substantial conformational changes. Therefore, it is considered an ideal target for tumor intervention. However, the allosteric mechanisms of SHP2 binding PD-1 intracellular ITIM/ITSM phosphopeptides remain unclear, which greatly hinders the development of novel structure-based anticancer allosteric inhibitors. In this work, the open and closed structural models of SHP2 are first constructed based on this knowledge; next their motion modes are investigated via elastic network models such as the Gaussian network model (GNM), anisotropic network model (ANM) and adaptive anisotropic network model (aANM); and finally, a possible allosteric signaling pathway is proposed using a neural relational inference molecular dynamics (NRI-MD) simulation embedded with an artificial intelligence (AI) strategy. In GNM and ANM, the N-SH2, C-SH2 and PTP domains all exhibit distinct dynamics partitions, and the N-SH2/C-SH2 regions show a rigid rotation relative to PTP. According to a series of intermediate snapshots given by aANM, N-SH2 is first identified with pY223 specifically, inducing a D'E-loop to change from β-sheets to random coils, and then, C-SH2 serves as a fulcrum to drive N-SH2 to rotate 110° completely away from the original active sites of PTP. Finally, a possible allosteric signaling-transfer path for SHP2, namely R220-R138-T108-R32, is proposed based on NRI-MD sampling. This work provides a possible allosteric mechanism of SHP2, which is helpful for the following design of novel allosteric inhibitors and is expected to be used in clinical synergies with PD-1 monoclonal antibody.
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Affiliation(s)
- Ling Liu
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China.
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Yan Cheng
- Breast Disease Center, Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610000, China
| | - Zhigang Zhang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jing Li
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Yichao Geng
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China.
| | - Qingsong Li
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China.
| | - Daxian Luo
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China.
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Wei Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
| | - Weiwei Ouyang
- Department of Thoracic Oncology, Affiliated Cancer Hospital, Guizhou Medical University, Guiyang, China.
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Wu Z, Duan H, Cheng Y, Guo D, Peng L, Hu Y, Hu J, Luo T. A novel ligand swing-mediated active site coordination change of human apurinic/apyrimidinic endonuclease 1: A potential cytotoxic mechanism of nickel ion in the base excision repair. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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4
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Gao J, Shi X, Luo Y, Zhang Z, Wang Y, Liang L, He G, Liu W, Tang D, Hu J. A promising strategy for increasing phosphorescent quantum yield: The ligand 10‐cyclic chelate of the tetradentate Pt(II) complex. Appl Organomet Chem 2021. [DOI: 10.1002/aoc.6539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jiaxing Gao
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department Chengdu University Chengdu China
| | - Xiaodong Shi
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department Chengdu University Chengdu China
| | - Yafei Luo
- Collaborative Innovation Center of Targeted Therapeutics and Innovation, Chongqing Key Laboratory of Kinase Modulators As Innovative Medicine, Chongqing Engineering Laboratory of Targeted and Innovative Therapeutics, International Academy of Targeted Therapeutics and Innovation Chongqing University of Arts and Sciences Chongqing China
| | - Zelan Zhang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department Chengdu University Chengdu China
| | - Yueteng Wang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department Chengdu University Chengdu China
| | - Li Liang
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department Chengdu University Chengdu China
| | - Gang He
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department Chengdu University Chengdu China
| | - Wei Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department Chengdu University Chengdu China
| | - Dianyong Tang
- Collaborative Innovation Center of Targeted Therapeutics and Innovation, Chongqing Key Laboratory of Kinase Modulators As Innovative Medicine, Chongqing Engineering Laboratory of Targeted and Innovative Therapeutics, International Academy of Targeted Therapeutics and Innovation Chongqing University of Arts and Sciences Chongqing China
| | - Jianping Hu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, School of Pharmacy, Sichuan Industrial Institute of Antibiotics, Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department Chengdu University Chengdu China
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Krause M, von der Stück R, Brünink D, Buss S, Doltsinis NL, Strassert CA, Klein A. Platinum and palladium complexes of tridentate −C^N^N (phen-ide)-pyridine-thiazol ligands – A case study involving spectroelectrochemistry, photoluminescence spectroscopy and TD-DFT calculations. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.120093] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Revealing the marked differences of phosphorescence efficiencies on C
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N
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N‐coordinated Pt(II) complexes: A theoretical study. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.6072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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