Affinity maturation of cross-reactive CR3022 antibody against the receptor binding domain of SARS-CoV-2 via in silico site-directed mutagenesis

Abstract

Background: The coronavirus disease 2019 (COVID-19) has unequivocally affected the lives of people across the planet and has imposed an unprecedented burden on our healthcare systems. With no potent regimen for treatment, there is a dire need for finding promising candidates. Receptor binding domain (RBD) of the spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has proven to be a promising target owing to its role in viral invasion. Methods: Our study aimed at generating antibody candidates from the human antibody CR3022 (derived from convalescent SARS patient) against the RBD of SARS-CoV-2 via in silico affinity maturation. We optimized the paratope of the CR3022 antibody towards the RBD of SARS-CoV-2 for better binding affinity and stability, employing molecular modeling, docking, and dynamics simulations. Results: Out of seven antibody leads generated post in silico site-directed mutagenesis followed by preliminary screening, antibody named SAM3 was predicted to have the highest binding affinity towards RBD. However, molecular dynamics simulation of fifty nanoseconds set the seal on SAM1 and SAM2. Both demonstrated a higher binding affinity and stability compared to other counterparts and CR3022. Conclusion: We hypothesize that SAM1, SAM2, and SAM3 antibody candidates can bind to the RBD and potentially disrupt the viral invasion. All three antibody candidates to bind residues on the human ACE-2 binding site of SARS-CoV-2 which were not conserved from SARS-CoV. Our study calls for further in vitro and in vivo testing of SAM1, SAM2, and SAM3 candidates for COVID-19 treatment.

Affinity maturation of cross-reactive CR3022 antibody against the receptor binding domain of SARS-CoV-2 via in silico site-directed mutagenesis

“…The trends of binding a nities computed are in agreement with previously reported studies on the interaction between SARS-CoV-2 RBD and CR3022 [23,24]. The computed binding a nity between SARS-CoV RBD and CR3022 (PDB ID: 7JN5) is higher than that found between SARS-CoV-2 RBD and CR3022.…”