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Structural insights into Nirmatrelvir (PF-07321332)-3C-like SARS-CoV-2 protease complexation: a ligand Gaussian accelerated molecular dynamics study.
Wang, Yeng-Tseng; Liao, Jun-Min; Lin, Wen-Wei; Li, Chia-Ching; Huang, Bo-Cheng; Cheng, Tian-Lu; Chen, Tun-Chieh.
  • Wang YT; School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Taiwan. c00jsw00@kmu.edu.tw.
  • Liao JM; Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
  • Lin WW; Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
  • Li CC; Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
  • Huang BC; Graduate Institute of Medicine, Kaohsiung Medical University, Kaohsiung, 80708, Taiwan.
  • Cheng TL; Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan.
  • Chen TC; School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Taiwan. c00jsw00@kmu.edu.tw.
Phys Chem Chem Phys ; 24(37): 22898-22904, 2022 Sep 28.
Статья в английский | MEDLINE | ID: covidwho-2036937
ABSTRACT
Coronavirus 3C-like protease (3CLpro) is found in SARS-CoV-2 virus, which causes COVID-19. 3CLpro controls virus replication and is a major target for target-based antiviral discovery. As reported by Pfizer, Nirmatrelvir (PF-07321332) is a competitive protein inhibitor and a clinical candidate for orally delivered medication. However, the binding mechanisms between Nirmatrelvir and 3CLpro complex structures remain unknown. This study incorporated ligand Gaussian accelerated molecular dynamics, the one-dimensional and two-dimensional potential of mean force, normal molecular dynamics, and Kramers' rate theory to determine the binding and dissociation rate constants (koff and kon) associated with the binding of the 3CLpro protein to the Nirmatrelvir inhibitor. The proposed approach addresses the challenges in designing small-molecule antiviral drugs.
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Полный текст: Имеется в наличии Коллекция: Международные базы данных база данных: MEDLINE Основная тема: Antiviral Agents / Coronavirus 3C Proteases / SARS-CoV-2 Тип исследования: Прогностическое исследование Язык: английский Журнал: Phys Chem Chem Phys Тематика журнала: Биофизика / Химия Год: 2022 Тип: Статья Аффилированная страна: D2cp02882d

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Полный текст: Имеется в наличии Коллекция: Международные базы данных база данных: MEDLINE Основная тема: Antiviral Agents / Coronavirus 3C Proteases / SARS-CoV-2 Тип исследования: Прогностическое исследование Язык: английский Журнал: Phys Chem Chem Phys Тематика журнала: Биофизика / Химия Год: 2022 Тип: Статья Аффилированная страна: D2cp02882d