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Insights on 3D Structures of Potential Drug‐targeting Proteins of SARS‐CoV‐2: Application of Cavity Search and Molecular Docking
Author(s) -
Fernandes Mariana S.,
Silva Francielly S.,
Freitas Ana Carolina S. G.,
Melo Eduardo B.,
Trossini Gustavo H. G.,
Paula Fávero R.
Publication year - 2021
Publication title -
molecular informatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.481
H-Index - 68
eISSN - 1868-1751
pISSN - 1868-1743
DOI - 10.1002/minf.202000096
Subject(s) - druggability , docking (animal) , lopinavir , computational biology , drug discovery , protein data bank (rcsb pdb) , covid-19 , ritonavir , structural bioinformatics , drug , chemistry , biology , bioinformatics , virology , protein structure , infectious disease (medical specialty) , medicine , pharmacology , disease , biochemistry , virus , gene , nursing , pathology , antiretroviral therapy , viral load
The emergence of the COVID‐19 has caused public health problems worldwide and there is no effective pharmacological treatment for this disease. Research on 3D models of proteins and the search for active molecular sites are important tools to assist in the discovery of effective antiviral drugs to combat COVID‐19. To address this problem, the 3D protein structures of SARS‐CoV 2 were analyzed and submitted to cavities research, evaluation of their druggabillity and liganbility, and applied to molecular docking studies with potential ligand candidates actually assayed against COVID‐19. Eight druggable potential cavity sites were determined in model structures’ PDB code, 6W4B, 6VWW, 6W01, 6M3M, and 6VYO, and these are the good alternatives to be characterized as targets for antiviral compounds. The good cavity model of the protease 3D structure was used in molecular docking, and this allowed verifying the theoric interactions of this protein and lopinavir and ritonavir antiviral drugs. These results may assist in the use of 3D protein models in drug design studies aiming to develop drugs against the COVID‐19 pandemic.