Computational design of novel nanobodies targeting the receptor binding domain of variants of concern of SARS-CoV-2.

The COVID-19 pandemic has created an urgent need for effective therapeutic and diagnostic
strategies to manage the disease caused by the severe acute respiratory syndrome coronavirus
2 (SARS-CoV-2). However, the emergence of numerous variants of concern
(VOCs) has made it challenging to develop targeted therapies that are broadly specific in
neutralizing the virus. In this study, we aimed to develop neutralizing nanobodies (Nbs)
using computational techniques that can effectively neutralize the receptor-binding domain
(RBD) of SARS-CoV-2 VOCs. We evaluated the performance of different protein-protein
docking programs and identified HDOCK as the most suitable program for Nb/RBD docking
with high accuracy. Using this approach, we designed 14 novel Nbs with high binding affinity
to the VOC RBDs. The Nbs were engineered with mutated amino acids that interacted with
key amino acids of the RBDs, resulting in higher binding affinity than human angiotensinconverting
enzyme 2 (ACE2) and other viral RBDs or haemagglutinins (HAs). The successful
development of these Nbs demonstrates the potential of molecular modeling as a lowcost
and time-efficient method for engineering effective Nbs against SARS-CoV-2. The engineered
Nbs have the potential to be employed in RBD-neutralizing assays, facilitating the
identification of novel treatment, prevention, and diagnostic strategies against SARS-CoV-2.