In 2020, we initiated studies of SARS-CoV-2 RNA-dependent RNAP, RdRp. Like bacterial RNAPs, RdRp is a multi-subunit enzyme. However, the catalytic subunit of RdRp, nsp12, contains two active sites: Active Site 1 mediates RNA synthesis and is homologous to other viral RdRps; Active Site 2 in the NiRAN domain is unique to nidoviruses and mediates protein NMPylation and RNA capping. Both active sites are essential for viral replication, making them promising targets for antivirals.
We aimed to identify new RdRp inhibitors and to correct errors introduced during rapid expansion of this field. We published three papers that uncovered flaws in data interpretation based on hasty structural and computational studies. In the first paper, we showed that RdRp used in a series of high-impact structural studies was largely inactive, making it unsuitable for drug discovery. In the second paper, we showed that the published structure of a “capping intermediate” represents a dead-end complex in which an artificially extended viral protein highjacks the NiRAN active site. In the third paper, we described shortcomings of rigid-body in silico docking for identification of antivirals and demonstrated that two FDA-approved natural products antibiotics inhibit viral RNA synthesis.
We are pursuing fundamental studies of the SARS-CoV-2 RdRp mechanism and, working with an international consortium of medicinal chemists and structural biologists, intend to apply our findings to the design of novel antivirals. We are currently (i) developing rifamycins, the first-line drugs against tuberculosis, into potent RdRp inhibitors; (ii) studying the mechanism of NiRAN catalysis; and (iii) identifying nucleotide analogs selective against NiRAN.