Abstract
Recent studies have pointed the role of angiotensin-converting enzyme-II (ACE2) in mediating the entry of SARS-CoV-2 to the host cell by binding to the receptor-binding domain (RBD) of viral spike protein, and successive priming by cellular proteases initiates the infection. SARS-CoV replication rate and disease severity is controlled by the binding affinity of RBD with ACE2. To understand, how mutations in the conserved residues of RBD affect the molecular interaction with ACE2, we generated five alanine mutants i.e. Y449A, N487A, Y489A, N501A and Y505A in the receptor binding motif (RBM) of the ACE2-RBD SARS-CoV-2 complex (PDB: 6M0J). Computational site directed mutagenesis induced dynamics in wild-type and mutant complexes were extensively studied through all-atoms molecular dynamics (MD) simulations of 150 ns. In silico mutational analysis revealed loss of important intermolecular hydrogen bonds and other non-bonded contacts, critical for molecular recognition of SARS-CoV-2 RBD to ACE2, which is well supported by saturation mutagenesis study of binding interface residues. MD simulations results showed that RBM motif is flexible, where mutant residues are relatively more mobile than corresponding wild-type residues. Global motion analysis through principal component studies revealed that RBD exhibits protuberant in-ward motion towards the human ACE2 binding interface which may be crucial for molecular interaction. Conclusively, the present finding are in congruence with previous experimental reports and provides detailed information on the structural basis of receptor binding by human SARS-CoV-2, which will crucial for the development of novel inhibitors or drugs to combat against SARS-CoV-2.Communicated by Ramaswamy H. Sarma.
Keywords: MD simulation; SARS-CoV-2; angiotensin-converting enzyme-II; coronavirus; receptor binding motif.
【저자키워드】 SARS-CoV-2, coronavirus, MD simulation, angiotensin-converting enzyme-II, receptor binding motif., 【초록키워드】 ACE2, Mutation, SARS-CoV, disease severity, Infection, drug, molecular dynamics, MD simulations, binding affinity, MD simulation, Spike protein, human ACE2, Receptor-binding domain, RBD, mutant, molecular, inhibitor, information, Critical, receptor binding motif, binding, Replication rate, Mutagenesis, Analysis, angiotensin, Receptor binding, Interface residues, SARS-CoV-2 RBD, host cell, Principal component, hydrogen, viral spike protein, enzyme, complex, residue, ward, Alanine, priming, wild-type, residues, cellular proteases, molecular interaction, human SARS-CoV-2, ACE2-RBD, motif, cellular protease, Affect, recent, FIVE, 6M0J, alanine mutants, Directed mutagenesis, flexible, conserved, supported, provide, the receptor-binding domain, complexes, exhibit, initiate, the binding affinity, alanine mutant, entry of SARS-CoV-2, intermolecular hydrogen bond, RBM, 【제목키워드】 Mutation, Molecular dynamics simulation, Receptor binding domain, host cell receptor, Effect,