An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review

Madhur Babu Singh, Ritika Sharma, Durgesh Kumar, Pankaj Khanna, Mansi, Leena Khanna, Vinod Kumar, Kamlesh Kumari, Akanksha Gupta, Preeti Chaudhary, Neha Kaushik, Eun Ha Choi, Nagendra Kumar Kaushik, Prashant Singh

Research output: Contribution to journalReview articlepeer-review

10 Scopus citations

Abstract

The first infection case of new coronavirus was reported at the end of 2019 and after then, the cases are reported in all nations across the world in a very short period. Further, the regular news of mutations in the virus has made life restricted with appropriate behavior. To date, a new strain (Omicron and its new subvariant Omicron XE) has brought fear amongst us due to a higher trajectory of increase in the number of cases. The researchers thus started giving attention to this viral infection and discovering drug-like candidates to cure the infections. Finding a drug for any viral infection is not an easy task and takes plenty of time. Therefore, computational chemistry/bioinformatics is followed to get promising molecules against viral infection. Molecular dynamics (MD) simulations are being explored to get drug candidates in a short period. The molecules are screened via molecular docking, which provides preliminary information which can be further verified by molecular dynamics (MD) simulations. To understand the change in structure, MD simulations generated several trajectories such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), hydrogen bonding, and radius of gyration for the main protease (Mpro) of the new coronavirus (nCoV) in the presence of small molecules. Additionally, change in free energy for the formation of complex of Mpro of nCoV with the small molecule can be determined by applying molecular mechanics with generalized born and surface area solvation (MM-GBSA). Thus, the promising molecules can be further explored for clinical trials to combat coronavirus disease-19 (COVID-19).

Original languageEnglish
Pages (from-to)1326-1349
Number of pages24
JournalJournal of Infection and Public Health
Volume15
Issue number11
DOIs
StatePublished - Nov 2022
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2022 The Author(s)

Keywords

  • Molecular dynamics simulations
  • Mpro of nCoV
  • Promising drug like candidate
  • SARS-CoV-2

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