Inhibition mechanism and hot-spot prediction of nine potential drugs for SARS-CoV-2 Mproby large-scale molecular dynamic simulations combined with accurate binding free energy calculations

被引:0
|
作者
School of Physics and Electronics, Shandong Normal University, Jinan [1 ]
250014, China
不详 [2 ]
200062, China
不详 [3 ]
200062, China
不详 [4 ]
NY
10003, United States
不详 [5 ]
030006, China
机构
来源
Nanoscale | 2040年 / 17卷 / 8313-8332期
关键词
461.6 Medicine and Pharmacology - 461.7 Health Care - 641.1 Thermodynamics - 801.4 Physical Chemistry - 802.2 Chemical Reactions - 815.1.1 Organic Polymers - 931.3 Atomic and Molecular Physics;
D O I
暂无
中图分类号
学科分类号
摘要
Coronavirus
引用
收藏
相关论文
共 15 条
  • [1] Inhibition mechanism and hot-spot prediction of nine potential drugs for SARS-CoV-2 Mpro by large-scale molecular dynamic simulations combined with accurate binding free energy calculations
    Luo, Song
    Huang, Kaifang
    Zhao, Xiaoyu
    Cong, Yalong
    Zhang, John Z. H.
    Duan, Lili
    NANOSCALE, 2021, 13 (17) : 8313 - 8332
  • [2] Candidate Binding Sites for Allosteric Inhibition of the SARS-CoV-2 Main Protease from the Analysis of Large-Scale Molecular Dynamics Simulations
    Carli, Matteo
    Sormani, Giulia
    Rodriguez, Alex
    Laio, Alessandro
    JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 2021, 12 (01): : 65 - 72
  • [3] Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations
    Sk, Md Fulbabu
    Roy, Rajarshi
    Jonniya, Nisha Amarnath
    Poddar, Sayan
    Kar, Parimal
    JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2021, 39 (10): : 3649 - 3661
  • [4] Exploring the Binding Mechanism of PF-07321332 SARS-CoV-2 Protease Inhibitor through Molecular Dynamics and Binding Free Energy Simulations
    Ahmad, Bilal
    Batool, Maria
    ul Ain, Qurat
    Kim, Moon Suk
    Choi, Sangdun
    INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 2021, 22 (17)
  • [5] Computational Prediction of the Potential Target of SARS-CoV-2 Inhibitor Plitidepsin via Molecular Docking, Dynamic Simulations and MM-PBSA Calculations
    El Hassab, Mahmoud A.
    Hemeda, Loah R.
    Elsayed, Zainab M.
    Al-Rashood, Sara T.
    Amin, Mohammed K. Abdel-Hamid
    Abdel-Aziz, Hatem A.
    Eldehna, Wagdy M.
    CHEMISTRY & BIODIVERSITY, 2022, 19 (02)
  • [6] Ultra-Large-Scale Screening of Natural Compounds and Free Energy Calculations Revealed Potential Inhibitors for the Receptor-Binding Domain (RBD) of SARS-CoV-2
    Guo, Lisha
    Zafar, Faryar
    Moeen, Nawal
    Alshabrmi, Fahad M.
    Lin, Junqi
    Ali, Syed Shujait
    Munir, Muhammad
    Khan, Abbas
    Wei, Dongqing
    MOLECULES, 2022, 27 (21):
  • [7] Multiple protonation states in ligand-free SARS-CoV-2 main protease revealed by large-scale quantum molecular dynamics simulations
    Ono, Junichi
    Koshimizu, Uika
    Fukunishi, Yoshifumi
    Nakai, Hiromi
    CHEMICAL PHYSICS LETTERS, 2022, 794
  • [8] Deciphering the binding mechanism of inhibitors of the SARS-CoV-2 main protease through multiple replica accelerated molecular dynamics simulations and free energy landscapes
    Li, Meng
    Liu, Xinguo
    Zhang, Shaolong
    Liang, Shanshan
    Zhang, Qinggang
    Chen, Jianzhong
    PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2022, 24 (36) : 22129 - 22143
  • [9] Prediction of deleterious non-synonymous SNPs of TMPRSS2 protein combined with Molecular Dynamics Simulations and free energy analysis to identify the potential peptide substrates against SARS-CoV-2
    Ramachandran, Balajee
    Nadeem, Ahmed
    Mohanprasanth, Aruchamy
    Saravanan, Muthupandian
    JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2024,
  • [10] Identification of 1H-purine-2,6-dione derivative as a potential SARS-CoV-2 main protease inhibitor: molecular docking, dynamic simulations, and energy calculations
    Nada, Hossam
    Elkamhawy, Ahmed
    Lee, Kyeong
    PEERJ, 2022, 10