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The recent outbreak caused by SARS-CoV-2 continues to threat and take many lives all over the world. The lack of an efficient pharmacological treatments are serious problems to be faced by scientists and medical staffs worldwide. In this work, an  in silico  approach based on the combination of molecular docking, dynamics simulations, and quantum biochemistry revealed that the synthetic peptides  RcAlb -PepI, PepGAT, and PepKAA, strongly interact with the main protease (Mpro) a pivotal protein for SARS-CoV-2 replication. Although not binding to the proteolytic site of SARS-CoV-2 Mpro,  RcAlb -PepI, PepGAT, and PepKAA interact with other protein domain and allosterically altered the protease topology. Indeed, such peptide-SARS-CoV-2 Mpro complexes provoked dramatic alterations in the three-dimensional structure of Mpro leading to area and volume shrinkage of the proteolytic site, which could affect the protease activity and thus the virus replication. Based on these findings, it is suggested that  RcAlb -PepI, PepGAT, and PepKAA could interfere with SARS-CoV-2 Mpro role  in vivo . Also, unlike other antiviral drugs, these peptides have no toxicity to human cells. This pioneering  in  silico investigation opens up opportunity for further  in vivo  research on these peptides, towards discovering new drugs and entirely new perspectives to treat COVID-19. Communicated by Ramaswamy H. Sarma

journal of biomolecular structure and dynamics

Quantum biochemistry, molecular docking, and dynamics simulation revealed synthetic peptides induced conformational changes affecting the topology of the catalytic site of SARS-CoV-2 main protease