Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV-2), a novel coronavirus, has brought an unprecedented pandemic to the world and affected over 64 million people. The virus infects human using its spike glycoprotein mediated by a crucial area, receptor-binding domain (RBD), to bind to the human ACE2 (hACE2) receptor. Mutations on RBD have been observed in different countries and classified into nine types: A435S, D364Y, G476S, N354D/D364Y, R408I, V341I, V367F, V483A and W436R. Employing molecular dynamics (MD) simulation, we investigated dynamics and structures of the complexes of the prototype and mutant types of SARS-CoV-2 spike RBDs and hACE2. We then probed binding free energies of the prototype and mutant types of RBD with hACE2 protein by using an end-point molecular mechanics Poisson Boltzmann surface area (MM-PBSA) method. According to the result of MM-PBSA binding free energy calculations, we found that V367F and N354D/D364Y mutant types showed enhanced binding affinities with hACE2 compared to the prototype. Our computational protocols were validated by the successful prediction of relative binding free energies between prototype and three mutants: N354D/D364Y, V367F and W436R. Thus, this study provides a reliable computational protocol to fast assess the existing and emerging RBD mutations. More importantly, the binding hotspots identified by using the molecular mechanics generalized Born surface area (MM-GBSA) free energy decomposition approach can guide the rational design of small molecule drugs or vaccines free of drug resistance, to interfere with or eradicate spike-hACE2 binding.
Keywords: COVID-19; Free energy calculation and decomposition; Hotspot residues; MD simulation; Protein–protein interaction; SARS-CoV-2; Spike RBD/hACE2.
【저자키워드】 COVID-19, SARS-CoV-2, MD simulation, Free energy calculation and decomposition, Hotspot residues, Protein–protein interaction, Spike RBD/hACE2., 【초록키워드】 Structure, Vaccine, coronavirus, pandemic, protocol, spike, spike glycoprotein, molecular dynamics, severe acute respiratory syndrome Coronavirus, virus, binding free energy, binding affinity, MD simulation, SARS-CoV-2 Spike RBD, hACE2, free energy, Novel coronavirus, Free energy calculations, human ACE2, Receptor-binding domain, RBD, small molecule, drug resistance, mutant, receptor, molecular, respiratory, binding, RBD mutations, Protein–protein interaction, Molecular mechanics, structures, RBDs, binding affinities, surface area, free energies, acute respiratory syndrome, acute respiratory syndrome coronavirus, domain, prototype, binding free energies, Poisson, V483A, hotspot, decomposition, hACE2 protein, infect, approach, country, V367F, small molecule drugs, G476S, affected, investigated, nine, provide, interfere, complexes, small molecule drug, 【제목키워드】 SARS-CoV-2 spike protein, mutant, binding, human ACE2 receptor,