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

TL;DR

This study introduces a new computational method based on MM/PBSA to accurately evaluate the binding free energies of SARS-CoV-2 RBD with ACE2 and antibodies, aiding therapeutic development.

Contribution

The paper presents a novel, efficient computational approach for accurately calculating SARS-CoV-2 RBD binding free energies and identifying key interaction residues.

Findings

Calculated binding free energies agree with experimental data.

Identified key residues and driving forces for RBD-antibody interactions.

Validated the method with multiple SARS-CoV-2 related protein interactions.

Abstract

The spread of the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has become a global health crisis. The binding affinity of SARS-CoV-2 (in particular the receptor binding domain, RBD) to its receptor angiotensin converting enzyme 2 (ACE2) and the antibodies is of great importance in understanding the infectivity of COVID-19 and evaluating the candidate therapeutic for COVID-19. In this work, we propose a new method based on molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) to accurately calculate the free energy of SARS-CoV-2 RBD binding to ACE2 and antibodies. The calculated binding free energy of SARS-CoV-2 RBD to ACE2 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 the example, and calculate the free energy of antibodies binding to SARS-CoV-2 RBD, which is also consistent with the experimental findings. Further, within the framework of the modified MM/PBSA, we determine the key residues and the main driving forces for the SARS-CoV-2 RBD/CB6 interaction by the computational alanine scanning method. The present study offers a computationally efficient and numerically reliable method to evaluate the free energy of SARS-CoV-2 binding to other proteins, which may stimulate the development of the therapeutics against the COVID-19 disease in real applications.