Статья

Rapid prediction of possible inhibitors for SARS-CoV-2 main protease using docking and FPL simulations

M. Pham, K. Vu, T. Han Pham, L. Thuy Huong, L. Tran, N. Tung, V. Vu, T. Nguyen, S. Ngo,
2020

A combination of Autodock Vina and FPL calculations suggested that periandrin V , penimocycline , cis-p-Coumaroylcorosolic acid , glycyrrhizin , and uralsaponin B are able to bind well to SARS-CoV-2 Mpro. Originating for the first time in Wuhan, China, the outbreak of SARS-CoV-2 has caused a serious global health issue. An effective treatment for SARS-CoV-2 is still unavailable. Therefore, in this study, we have tried to predict a list of potential inhibitors for SARS-CoV-2 main protease (Mpro) using a combination of molecular docking and fast pulling of ligand (FPL) simulations. The approaches were initially validated over a set of eleven available inhibitors. Both Autodock Vina and FPL calculations produced consistent results with the experiments with correlation coefficients of R Dock = 0.72 ± 0.14 and R W = −0.76 ± 0.10, respectively. The combined approaches were then utilized to predict possible inhibitors that were selected from a ZINC15 sub-database for SARS-CoV-2 Mpro. Twenty compounds were suggested to be able to bind well to SARS-CoV-2 Mpro. Among them, five top-leads are periandrin V , penimocycline , cis-p-Coumaroylcorosolic acid , glycyrrhizin , and uralsaponin B . The obtained results could probably lead to enhance the COVID-19 therapy.

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Версии

  • 1. Version of Record от 2020-08-28

Метаданные

Об авторах
  • M. Pham
    Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam, Institute of Natural Products Chemistry
  • K. Vu
    School of Biotechnology, International University, Ho Chi Minh City, Vietnam, Vietnam National University
  • T. Han Pham
    Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam
  • L. Thuy Huong
    Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam, Institute of Natural Products Chemistry
  • L. Tran
    Vietnam National University, Ho Chi Minh City, Vietnam, Faculty of Civil Energeering, Ho Chi Minh University of Technology (HCMUT)
  • N. Tung
    Graduate University of Science and Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam, Institute of Materials Science
  • V. Vu
    NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
  • T. Nguyen
    Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam, Faculty of Applied Sciences
  • S. Ngo
    Laboratory of Theoretical and Computational Biophysics, Ton Duc Thang University, Ho Chi Minh City, Vietnam, Faculty of Applied Sciences
Название журнала
  • RSC Advances
Том
  • 10
Выпуск
  • 53
Страницы
  • 31991-31996
Издатель
  • Royal Society of Chemistry (RSC)
Тип документа
  • journal article
Тип лицензии Creative Commons
  • CC BY
Правовой статус документа
  • Свободная лицензия
Источник
  • dimensions