Quick spread of Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has struck the world out of the blue. At the beginning of this global pandemic, there was lack of reliable therapeutics and to this day, national authorities still cannot fully agree on the best approach. One of the possible approaches is to inhibit proteins involved in SARS-CoV-2 life cycle, mainly its key enzyme RNA-dependent RNA polymerase (RdRp). Therefore, we decided to develop new inhibitors of SARS-CoV-2 RdRp. Here we present a project, where we docked a large library of small molecules obtained from Maybridge database into several binding pockets of RdRp. Moreover, we managed to optimize method for production, isolation, and purification of recombinant wild-type RdRp, as well as its mutated forms, which were tailored based on docking studies. Furthermore, we plan to (i) evaluate inhibitory activity of candidate inhibitors on RdRp using quantitative polymerase chain reaction-based assay. (ii) Also, we plan to study conformational changes induction in RdRp structure by these inhibitors using hydrogen-deuterium exchange, and (iii) to evaluate their cytotoxicity in various mammalian cells. We believe that this project will give us much needed insight into how binding of small molecules changes the conformation of RdRp and its enzymatic activity and that it will help us to combat this virus.
This work was supported from the OP RDE registration no.: CZ.02.2.69/0.0/0.0/19_073/0016928, funded by the ESF.