On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2

Carolina Corrêa Giron; Aatto Laaksonen; Fernando L. Barroso da Silva

Computational virology is an emergent research field that takes advantage of the progress from molecular and structural biology, immunology, bioinformatics and related areas to foster the understanding of virus, their evolutionary dynamics in nature, infectivity, pathogenesis, cell/hosttropism, viral assembly and their molecular interactions in general (including how to predict epitopes, how to design specific neutralizing antibodies and basically any drug design & discovery related to viral infections). [27] [28] [29] [30] [31] [32] [33] [34] In particular, structural and interactive aspects can benefit from the solid foundations that computational molecular simulation methods such as Molecular Dynamics (MD) 35, 36 and Monte Carlo (MC) 35, 37 have achieved to probe the thermodynamic, dynamics and interactive properties of biomolecules in material science, food and pharma (see refs. 38, 39 for reviews). Here, we applied a fast constant-pH MC scheme 40, 41 for protein-protein studies 42, 43 to improve our understanding of the molecular interactions involving SARS-CoV-1 and 2 S RBD proteins and to identify key amino acids for the host-pathogen interactions.