Role of ATP in the RNA Translocation Mechanism of SARS-CoV-2 NSP13 Helicase

The COVID-19 pandemic has demonstrated the need to develop potent and transferable therapeutics treat coronavirus infections. Numerous antiviral targets are being investigated, but nonstructural protein 13 (nsp13) stands out as a highly conserved yet understudied target. Nsp13 is superfamily 1 (SF1) helicase that translocates along unwinds viral RNA in an ATP-dependent manner. Currently, there no available structures of nsp13 from SARS-CoV-1 or SARS-CoV-2 with either ATP bound, which presents significant hurdle rational design therapeutics. To address this knowledge gap, we have built models Apo, ATP, ssRNA ssRNA+ATP substrate states. Using 30 μs Gaussian-accelerated molecular dynamics simulation (at least 6 per state), these were confirmed maintain binding poses similar other SF1 helicases. A Gaussian mixture model linear discriminant analysis structural clustering protocol was used identify key states translocation mechanism. Namely, four RNA-nsp13 identified exhibit populations support inchworm mechanism for translocation. These characterized by different RNA-binding motifs Ia, IV, V suggest power stroke-like motion domain 2A relative 1A. This mechanistic insight novel further development antivirals.