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 angiotensin-converting enzyme 2 (ACE2) and other
viral RBDs or hemagglutinins (HAs). The successful development of these Nbs
demonstrates the potential of molecular modeling as a low-cost 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.