Computational prediction of the effect of amino acid changes on the binding affinity between SARS-CoV-2 spike RBD and human ACE2.

Journal: Proceedings of the National Academy of Sciences of the United States of America
PMID: 34588290

Abstract

The association of the receptor binding domain (RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with human angiotensin-converting enzyme 2 (hACE2) represents the first required step for cellular entry. SARS-CoV-2 has continued to evolve with the emergence of several novel variants, and amino acid changes in the RBD have been implicated with increased fitness and potential for immune evasion. Reliably predicting the effect of amino acid changes on the ability of the RBD to interact more strongly with the hACE2 can help assess the implications for public health and the potential for spillover and adaptation into other animals. Here, we introduce a two-step framework that first relies on 48 independent 4-ns molecular dynamics (MD) trajectories of RBD-hACE2 variants to collect binding energy terms decomposed into Coulombic, covalent, van der Waals, lipophilic, generalized Born solvation, hydrogen bonding, π-π packing, and self-contact correction terms. The second step implements a neural network to classify and quantitatively predict binding affinity changes using the decomposed energy terms as descriptors. The computational base achieves a validation accuracy of 82.8% for classifying single-amino acid substitution variants of the RBD as worsening or improving binding affinity for hACE2 and a correlation coefficient of 0.73 between predicted and experimentally calculated changes in binding affinities. Both metrics are calculated using a fivefold cross-validation test. Our method thus sets up a framework for screening binding affinity changes caused by unknown single- and multiple-amino acid changes offering a valuable tool to predict host adaptation of SARS-CoV-2 variants toward tighter hACE2 binding.

Authors

  • Chen Chen
    The George Institute for Global Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
  • Veda Sheersh Boorla
    Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802.
  • Deepro Banerjee
    The Bioinformatics and Genomics Program, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802.
  • Ratul Chowdhury
    Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802.
  • Victoria S Cavener
    Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802.
  • Ruth H Nissly
    Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802.
  • Abhinay Gontu
    Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802.
  • Nina R Boyle
    Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802.
  • Kurt Vandegrift
    Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802.
  • Meera Surendran Nair
    Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802.
  • Suresh V Kuchipudi
    Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, PA 16802; costas@psu.edu skuchipudi@psu.edu.
  • Costas D Maranas
    Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, USA. Electronic address: costas@psu.edu.

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