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The spread of the coronavirus disease 2019 (COVID-19) caused by severe acuterespiratory syndrome coronavirus-2 (SARS-CoV-2) has become a global healthcrisis. The binding affinity of SARS-CoV-2 (in particular the receptor bindingdomain, RBD) to its receptor angiotensin converting enzyme 2 (ACE2) and theantibodies is of great importance in understanding the infectivity of COVID-19and evaluating the candidate therapeutic for COVID-19. In this work, we proposea new method based on molecular mechanics/Poisson-Boltzmann surface area(MM/PBSA) to accurately calculate the free energy of SARS-CoV-2 RBD binding toACE2 and antibodies. The calculated binding free energy of SARS-CoV-2 RBD toACE2 is -13.3 kcal/mol, and that of SARS-CoV RBD to ACE2 is -11.4 kcal/mol,which agrees well with experimental result (-11.3 kcal/mol and -10.1 kcal/mol,respectively). Moreover, we take two recently reported antibodies as theexample, and calculate the free energy of antibodies binding to SARS-CoV-2 RBD,which is also consistent with the experimental findings. Further, within theframework of the modified MM/PBSA, we determine the key residues and the maindriving forces for the SARS-CoV-2 RBD/CB6 interaction by the computationalalanine scanning method. The present study offers a computationally efficientand numerically reliable method to evaluate the free energy of SARS-CoV-2binding to other proteins, which may stimulate the development of thetherapeutics against the COVID-19 disease in real applications.

Accurate Evaluation on the Interactions of SARS-CoV-2 with Its Receptor ACE2 and Antibodies CR3022/CB6