Structural and energetic features of the dimerization of the main proteinase of SARS-CoV-2 using molecular dynamic...

The COVID-19 pandemic caused by SARS-CoV-2 has been declared a global health crisis. The development of anti-SARS-CoV-2 drugs heavily depends on the systematic study of the critical biological processes of key proteins of coronavirus among which the main proteinase (M^pro) dimerization is a key step for virus maturation. Because inhibiting the M^pro dimerization can efficiently suppress virus maturation, the key residues that mediate dimerization can be treated as targets of drug and antibody developments. In this work, the structure and energy features of the M^pro dimer of SARS-CoV-2 and SARS-CoV were studied using molecular dynamics (MD) simulations. The free energy calculations using the Generalized Born (GB) model showed that the dimerization free energy of the SARS-CoV-2 M^pro dimer (-107.5 ± 10.89 kcal mol^-1) is larger than that of the SARS-CoV M^pro dimer (-92.83 ± 9.81 kcal mol^-1), indicating a more stable and possibly a quicker formation of the M^pro dimer of SARS-CoV-2. In addition, the energy decomposition of each residue revealed 11 key attractive residues. Furthermore, Thr285Ala weakens the steric hindrance between the two protomers of SARS-CoV-2 that can form more intimate interactions. It is interesting to find 11 repulsive residues which effectively inhibit the dimerization process. At the interface of the M^pro dimer, we detected three regions that are rich in interfacial water which stabilize the SARS-CoV-2 M^pro dimer by forming hydrogen bonds with two protomers. The key residues and rich water regions provide important targets for the future design of anti-SARS-CoV-2 drugs through inhibiting M^pro dimerization.