Investigation of Some Nanobodies against SARS-C۰V-۲ Spike protein by immune-bioinformatics tools

Antibody-antigen interactions and understanding binding a nity for predictive computational Modeling is a main part of the drug discovery process, ensuring that therapeutic antibodies that bind their targets selectively and specifically. Following the SARS-CoV-۲ pandemic, Nanobodies were selected as an e↵ective particle in the treatment of COVID-۱۹. Small size, simple structure, ease to use and relatively low cost, low immunogenicity, and high a nity, make them special in research fields such as treatment and diagnosis. We selected ۱۷ nanobodies from PDB and investigated their structure and function in relationship to spike glycoprotein, among them, some are synthetic antibody (sybody) and we focused on their IC۵۰ and KD. IC۵۰ is the concentration of neutralizing antibody that displaces ۵۰% of the specifically bound labeled antigen and KD is the equilibrium dissociation constant, a calculated ratio of Ko↵ / Kon, between the antibody and its antigen. KD is inversely proportional to a nity, so the lower the KD value (the lower the concentration), the higher the a nity of the antibody. Among ۱۷ nanobodies, only ۲ nanobodies pose either low IC۵۰ or low Kd in the amount of pico mol. According to structural studies the conformational flexibility of the SARS-CoV-۲ trimer S protein allows each of its RBD to exist in two main conformations: up and down. the “up” conformation is easily bound by ACE۲ and most neutralizing antibodies, so these antibodies compete with ACE۲ to bind to the S protein of RBD in an upward conformation thereby preventing viral infection. The “down” conformation is not easy to be accessed by ACE۲ or most neutralizing antibodies. Nanobodies as a small particle with high a nity can bind to and stabilize the “down” conformation of the S protein, thereby preventing the conformational changes required for the virus to enter the host.

کلیدواژه ها:

nanobody ، a nity ، SARS-CoV-۲