Comparative molecular dynamics study of receptor-binding domains in wild type and Omicron (B.۱.۱.۵۲۹) variant of SARS-CoV-۲

The new variant of SARS-CoV-۲, Omicron (B.۱.۱.۵۲۹), first reported in November ۲۰۲۱ is currentlyinfecting people around the world. Since the spike glycoprotein plays a key role in the early events in viralreplication through a receptor binding domain (RBD) which bindes to angiotensin-converting enzyme ۲(ACE۲), it is important to study the effects of mutations on the structure of receptor binding domain (RBD).Based on Structural analysis, ۱۵ substitution mutations were identified in RBD of this new variant. In thispaper, we used computational comparison of receptor-binding domain (RBD) in wild-type (WT) SARSCoV-۲ and Omicron variant of concern (VOC) in free forms and structural models were built using the ITASSERserver. Based on our molecular dynamics simulation results, mutations can affect the RBD structureand in this new variant of concern, RBD structure is more open than the wild-type (WT) RBD. The resultsof this study could help to achieve a better understanding for researchers, and be effective in the developmentof novel therapies.

Keywords:

Receptor-binding domain (RBD) , SARS-CoV-۲ , Omicron (B.۱.۱.۵۲۹) , Molecular dynamics simulations