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Selected lipopeptides of Bacillus as plausible inhibitors of SARS-COV-2 chymotrypsin-like protease 3CLPro: an in-silico analysis
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  • Samya Sen,
  • Saikat Banerjee,
  • Atreyee Ghosh,
  • Keka Sarkar
Samya Sen
Indian Institute of Technology Jodhpur
Author Profile
Saikat Banerjee
University of Kalyani
Atreyee Ghosh
The Medical Academy named after S. I. Georgievsky of Vernadsky
Keka Sarkar
University of Kalyani

Abstract

A coronavirus disease pandemic caused by the novel severe acute respiratory syndrome virus-2 or nCoV-2 has escalated to a global health emergency. In search of prospective therapeutics against the virus from the microbial treasure trove, three classes of cyclic lipopeptides produced by the bacterial genus Bacillus, namely Surfactins, Fengycins, and Iturins, were chosen as exploitative targets against the main viral protease, 3CLPro, in turn, responsible for the ordered transcription and replication of the virus. On performing molecular docking analysis using AutoDock Vina, all the annotated lipopeptides showed promising binding stability, ranging from -6.1 to -7.4 kcal/mol, compared with the control inhibitor Darunavir (-7.2 kcal/mol). The lowest binding energy was observed for Fengycin 35518574 whereas the highest was for Surfactin B, but due to the richness in forming effective interactions with the target, Surfactin C was adjudged the most potent among all others. Molecular dynamics simulation analysis using iMODs server strengthened our claim that the 3CLPro-Surfactin C complex was stable, based on Deformability, Bfactor, Eigenvalue, Covariance, and Elastic network modeling. All the lipopeptides were found to form multiple hydrogen-bonded and hydrophobic interactions with the enzyme, in-silico, due to the exposed polyhydroxyl moieties and prenyl groups in their peptide structures. As most of these lipopeptides are non-toxic to human cells, the results of this study emphasize the need for research using these wonder molecules and their derivatives as pharmaceuticals in combating notorious viruses like nCoV-2.