The Unusual Architecture of RNA-Dependent RNA Polymerase (RdRp)'s Catalytic Chamber Provides a Potential Strategy for Combination Therapy against COVID-19

Abstract

The unusual and interesting architecture of the catalytic chamber of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) was recently explored using Cryogenic Electron Microscopy (Cryo-EM), which revealed the presence of two distinctive binding cavities within the catalytic chamber. In this report, first, we mapped out and fully characterized the variations between the two binding sites, BS1 and BS2, for significant differences in their amino acid architecture, size, volume, and hydrophobicity. This was followed by investigating the preferential binding of eight antiviral agents to each of the two binding sites, BS1 and BS2, to understand the fundamental factors that govern the preferential binding of each drug to each binding site. Results showed that, in general, hydrophobic drugs, such as remdesivir and sofosbuvir, bind better to both binding sites than relatively less hydrophobic drugs, such as alovudine, molnupiravir, zidovudine, favilavir, and ribavirin. However, suramin, which is a highly hydrophobic drug, unexpectedly showed overall weaker binding affinities in both binding sites when compared to other drugs. This unexpected observation may be attributed to its high binding solvation energy, which disfavors overall binding of suramin in both binding sites. On the other hand, hydrophobic drugs displayed higher binding affinities towards BS1 due to its higher hydrophobic architecture when compared to BS2, while less hydrophobic drugs did not show a significant difference in binding affinities in both binding sites. Analysis of binding energy contributions revealed that the most favorable components are the ΔE_ele, ΔE_vdw, and ΔG_gas, whereas ΔG_sol was unfavorable. The ΔE_ele and ΔG_gas for hydrophobic drugs were enough to balance the unfavorable ΔG_sol, leaving the ΔE_vdw to be the most determining factor of the total binding energy. The information presented in this report will provide guidelines for tailoring SARS-CoV-2 inhibitors with enhanced binding profiles.

Keywords: COVID-19; RNA-dependent RNA polymerase; catalytic chamber; combination therapy.

Figure 1

Surface view of RNA-dependent RNA Polymerase (RdRp) (PDB ID: 7D4F) [11], (shows the “catalytic chamber” housing two distinct binding sites/cavities, estimated with the Maestro Schrödinger [13]. The amino acid residues of binding site1 (BS1) and binding site2 (BS2) are also shown.

Figure 2

List of the two-dimensional structure of the eight antiviral drugs used for this study.

Figure 3

Binding site size and volume analysis. (A) BS1 and BS2 of the catalytic chamber amino acid molecular number surface view. (B) Binding pockets size comparison of BS1 and BS2. Difference of red and blue motion of both pocket sites. (C) The volume of the specificity conferring moiety of the pocket sites, estimated [13], differs significantly between BS1 and BS2.

Figure 4

Analyzing the hydrophobic (red) and hydrophilic (blue) regions of (A), (a) BS1 and (B), (b) BS2. Both binding pockets have large regions that are hydrophilic, although there are a few hydrophobic regions.