Favipiravir Analogues as Inhibitors of SARS-CoV-2 RNA-Dependent RNA Polymerase, Combined Quantum Chemical Modeling, Quantitative Structure-Property Relationship, and Molecular Docking Study

Abstract

Our study was motivated by the urgent need to develop or improve antivirals for effective therapy targeting RNA viruses. We hypothesized that analogues of favipiravir (FVP), an inhibitor of RNA-dependent RNA polymerase (RdRp), could provide more effective nucleic acid recognition and binding processes while reducing side effects such as cardiotoxicity, hepatotoxicity, teratogenicity, and embryotoxicity. We proposed a set of FVP analogues together with their forms of triphosphate as new SARS-CoV-2 RdRp inhibitors. The main aim of our study was to investigate changes in the mechanism and binding capacity resulting from these modifications. Using three different approaches, QTAIM, QSPR, and MD, the differences in the reactivity, toxicity, binding efficiency, and ability to be incorporated by RdRp were assessed. Two new quantum chemical reactivity descriptors, the relative electro-donating and electro-accepting power, were defined and successfully applied. Moreover, a new quantitative method for comparing binding modes was developed based on mathematical metrics and an atypical radar plot. These methods provide deep insight into the set of desirable properties responsible for inhibiting RdRp, allowing ligands to be conveniently screened. The proposed modification of the FVP structure seems to improve its binding ability and enhance the productive mode of binding. In particular, two of the FVP analogues (the trifluoro- and cyano-) bind very strongly to the RNA template, RNA primer, cofactors, and RdRp, and thus may constitute a very good alternative to FVP.

Keywords: COVID-2019; RNA viruses; SARS-CoV-2; binding modes; favipiravir analogues; hydrogen bonds; interaction patterns.

Figure 1

Structural formula of Favipiravir (6-fluoro-3-hydroxypyrazine-2-carboxamide, FVP, R = F) and its analogues R = H, Cl, Br, I, CH₃, CF₃ and CN (pro-drug (left), ribofuranosyl-5′-triphosphate active forms (right)) and the Tanimoto coefficient (molecular similarity distance).

Figure 2

Conversion of favipiravir and its analogues to its various metabolites (a series of ribosylation and phosphorylation steps to form the active triphosphate FVP-RTP).

Figure 3

The ligand’s ability to accept (R⁺) and donate (R⁻) charge in relation to FVP: (a) MP2/6-311G(d,p) and (b) M062X/6-311G(d,p) (the ordering of the substituents according to group electronegativity).

Figure 4

The binding mode of FVP-RTP to RdRp in the 7CTT [81] complex.

Figure 5

The docked poses of the ligands in the RdRp binding site. The protein backbone is represented as a cartoon, the binding cavity residues are shown as thin sticks, and the docked ligands are shown as color sticks (FVP in cyan, CN in yellow, and CF₃ in red).

Figure 6

The binding affinity versus ligand’s ability to accept (R⁺) and donate (R⁻) charge.

Figure 7

The comparison of the binding energies of FVR-RTP analogues with the RdRp split to active site residues, RNA primer, RNA template, and cofactor. (FVP*—native ligand).

Figure 8

The overlap of the isosurfaces of RDG (isovalue 0.5a.u.) with sign(λ₂)ρ_BCP mapped over the surface for (a) FVP (red) and the CF₃ derivative (green) and (b) FVP (red) and the CN derivative (green). (Pre-Catalytic State—Productive Mode I).

Figure 9

The binding mode of RDV (7UO4 [80]).

Figure 10

The docked poses of the ligands in the binding site of RdRp (target from 7UO4 [80]). The protein backbone is represented as a cartoon, the binding cavity residues are shown as thin sticks, and the docked ligands are shown as sticks.

Figure 11

The comparison of the binding energies of FVR-RTP analogues with RdRp (selected residues), RNA primer, RNA template, and cofactor (target from 7UO4 [80]). (RDV*—native ligand).

Figure 12

The isosurfaces of RDG (isovalue 0.5a.u.) with sign(λ₂)ρ_BCP mapped over the surface for (a) the CF₃ analogue and (b) the CN analogue.(Pre-Catalytic State—Productive Mode II).

Figure 13

The binding mode of FVP-RTP in 7AAP [84].

Figure 14

The docked poses of the ligands in the binding site of RdRp (target from 7AAP [84]). The protein backbone is represented as a cartoon; the binding cavity residues are shown as thin sticks, and the docked ligands are shown as sticks (FVP-RTP in cyan, the CF3 analogue in pink, and the CN analogue in white).

Figure 15

The comparison of the binding energies of FVR-RTP analogues to RdRp (selected residues), RNA primer, RNA template, and cofactor (target from 7AAP [84]) (FVP-RTP*—native ligand).

Figure 16

The isosurfaces of RDG (isovalue 0.5a.u.) with sign(λ₂)ρ_BCP mapped over the surface for (a) the CF₃ derivative and (b) the CN derivative (Pre-Catalytic State—Non-Productive Mode).

Figure 17

The comparison of the binding energies of the FVR-RMP analogues to RdRp (selected residues) and cofactor (target from 7DFG [85]). (FVP-RMP*—native ligand).

Figure 18

The docked poses of the ligands in the binding site of RdRp (Active state). The protein backbone is represented as a cartoon; the binding cavity residues are shown as thin sticks and docked ligands are shown as sticks (FVP in pink, the CF₃ analogue in yellow, and the CN analogue in green).

Figure 19

The isosurfaces of RDG (isovalue 0.5a.u.) with sign(λ₂)ρ_BCP mapped over the surface for (a) the CF₃ derivative and (b) the CN derivative. (Active state).

Figure 20

The docked poses of the ligands in the binding site of RdRp (the RdRp target from 6M71 [74]). The protein backbone is represented as a cartoon; the binding cavity residues are shown as thin sticks and docked ligands are shown as sticks (FVP in pink, the CF₃ analogue in yellow, and the CN analogue in green).

Figure 21

The comparison of the binding energies of the FVR-RTP analogues to RdRp (the RdRp target from 6M71 [74]).

Figure 22

The isosurfaces of RDG (isovalue 0.5a.u.) with sign(λ₂)ρ_BCP mapped over the surface for (a) the CF₃ derivative and (b) the CN derivative. (Allosteric effect).

Figure 23

The comparison of the binding energies of the FVR-RTP analogues to RdRp of all residues, cofactors Mg²⁺ and Zn²⁺, RNA Template, and RNA Primer; (a) pre-catalytic productive mode I; (b) pre-catalytic productive mode II; (c) non-productive mode. Pop-up peaks represent components with high binding energy.