In silico design of miniprotein to inhibit SARS-CoV-2 variant Omicron spike protein

Abstract

Omicron is a novel variant of SARS-CoV-2 that is currently spreading globally as the dominant strain. The virus first enters the host cell through the receptor binding domain (RBD) of the spike protein by interacting with the angiotensin-converting enzyme 2 (ACE2). Thus, the RBD protein is an ideal target for the design of drugs against the Omicron variant. Here, we designed several miniprotein inhibitors in silico to combat the SARS-CoV-2 Omicron variant using single- and double-point mutation approaches, based on the structure of the initial inhibitor AHB2. Also, two parallel molecular dynamics (MD) simulations were performed for each system to reproduce the calculated results, and the binding free energy was evaluated with the MM/PBSA method. The evaluated values showed that all inhibitors, including AHB2, M7E, M7E + M43W, and M7E + M43Y, were energetically more beneficial to the binding with the RBD than ACE2. In particular, the mutant inhibitor M7E + M43Y possessed the highest binding affinity to RBD and was selected as the most promising “best” inhibitor among all inhibitors. In addition, the combination of multiple analysis methods, such as free energy landscape analysis (FEL), principal component analysis (PCA), dynamic cross-correlation matrix analysis (DCCM), and hydrogen bond, salt bridge, and hydrophobic interaction analysis, also demonstrated that the mutations significantly affect the dynamical behavior and binding pattern of the inhibitor binding to the RBD protein. The current work suggested that miniprotein inhibitors can form stable complex structures with the RBD protein and exert a blocking or inhibitory effect on the SARS-CoV-2 variant Omicron. In conclusion, this study has identified several novel mutant inhibitors with enhanced affinity to the RBD protein, and provided potential guidance and insights for the rational design of therapeutic approaches for the new SARS-CoV-2 variant Omicron.