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Yang W, Wang S, Zhang X, Sun H, Zhang M, Chen H, Cui J, Li J, Peng F, Zhu M, Yu B, Li Y, Yang L, Min W, Xue M, Pan L, Zhu H, Wu B, Gu Y. New natural compound inhibitors of PDGFRA (platelet-derived growth factor receptor α) based on computational study for high-grade glioma therapy. Front Neurosci 2023; 16:1060012. [PMID: 36685223 PMCID: PMC9845622 DOI: 10.3389/fnins.2022.1060012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 12/01/2022] [Indexed: 01/06/2023] Open
Abstract
Background High-grade glioma (HGG) is a malignant brain tumor that is common and aggressive in children and adults. In the current medical paradigm, surgery and radiotherapy are the standard treatments for HGG patients. Despite this, the overall prognosis is still very bleak. Studies have shown that platelet-derived growth factor receptor α (PDGFRA) is an essential target to treat tumors and inhibiting the activity of PDGFRA can improve the prognosis of HGG. Thus, PDGFRA inhibitors are critical to developing drugs and cancer treatment. Objective The purpose of this study was to screen lead compounds and candidate drugs with potential inhibitors against platelet-derived growth factor receptor α (PDGFRA) from the drug library (ZINC database) in order to improve the prognosis of patients with high-grade glioma (HGG). Materials and methods In our study, we selected Imatinib as the reference drug. A series of computer-aided technologies, such as Discovery Studio 2019 and Schrodinger, were used to screen and assess potential inhibitors of PDGFRA. The first step was to calculate the LibDock scores and then analyze the pharmacological and toxicological properties. Following this, we docked the small molecules selected in the previous steps with PDGFRA to study their docking mechanism and affinity. In addition, molecular dynamics simulation was used to determine whether the ligand-PDGFRA complex was stable in nature. Results Two novel natural compounds 1 and 2 (ZINC000008829785 and ZINC000013377891) from the ZINC database were found binding to PDGFRA with more favorable interaction energy. Also, they were predicted with less Ames mutagenicity, rodent carcinogenicity, non-developmental toxic potential, and tolerant with cytochrome P450 2D6 (CYP2D6). The dynamic simulation analysis demonstrated that ZINC000008829785-PDGFRA and ZINC000013377891-PDGFRA dimer complex had more favorable potential energy compared with Imatinib, and they can exist in natural environments stably. Conclusion ZINC000008829785 and ZINC000013377891 might provide a solid foundation for drugs that inhibit PDGFRA in HGG. In addition to being safe drug candidates, these compounds had important implications for improving drugs targeting PDGFRA.
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Affiliation(s)
- Wenzhuo Yang
- Department of Neurosurgery, Zibo Central Hospital, Zibo, China,Department of Neurosurgery, Cancer Hospital of Sun Yat-sen University, Guangzhou, China
| | - Shengnan Wang
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Xiangmao Zhang
- Department of Neurosurgery, Zibo Central Hospital, Zibo, China
| | - Hu Sun
- Department of Neurosurgery, Zibo Central Hospital, Zibo, China
| | - Menghan Zhang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Xinxiang Medical College, Xinxiang, China
| | - Hongyu Chen
- Department of Neurosurgery, Cancer Hospital of Sun Yat-sen University, Guangzhou, China
| | - Junxiang Cui
- School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Jinyang Li
- School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Fei Peng
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Mingqin Zhu
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Bingcheng Yu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yifan Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Liu Yang
- Department of Neurosurgical Oncology, The First Hospital of Jilin University, Changchun, China
| | - Wanwan Min
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Mengru Xue
- Department of Neurology, The First Hospital of Jilin University, Changchun, China
| | - Lin Pan
- School of Clinical Medicine, Jilin University, Changchun, China
| | - Hao Zhu
- Department of Hepatology, The First Hospital of Jilin University, Changchun, China
| | - Bo Wu
- Department of Orthopaedics, The First Hospital of Jilin University, Changchun, China
| | - Yinghao Gu
- Department of Neurosurgery, Zibo Central Hospital, Zibo, China,*Correspondence: Yinghao Gu,
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Ma L, Li R, Yao Z, Wang B, Liu Y, Liu C, Wang H, Chen S, Sun D. Computational study on new natural compound inhibitors of Traf2 and Nck-interacting kinase (TNIK). Aging (Albany NY) 2022; 14:8394-8410. [DOI: 10.18632/aging.204349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/05/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Lushun Ma
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Rui Li
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhiwei Yao
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Bo Wang
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Yong Liu
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Chunxiang Liu
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Heng Wang
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
- Department of Gastrointestinal Surgery/Pediatric Surgery, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Shuxian Chen
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Daqing Sun
- Department of Paediatric Surgery, Tianjin Medical University General Hospital, Tianjin, China
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