Potent Dual Polymerase/Exonuclease Inhibitory Activities of Antioxidant Aminothiadiazoles Against the COVID-19 Omicron Virus: A Promising In Silico/In Vitro Repositioning Research Study

Abstract

Recently, natural and synthetic nitrogenous heterocyclic antivirals topped the scene as first choices for the treatment of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their accompanying disease, the coronavirus disease 2019 (COVID-19). Meanwhile, the mysterious evolution of a new strain of SARS-CoV-2, the Omicron variant and its sublineages, caused a new defiance in the continual COVID-19 battle. Hitting the two principal coronaviral-2 multiplication enzymes RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN) synchronously using the same ligand is a highly effective novel dual pathway to hinder SARS-CoV-2 reproduction and stop COVID-19 progression irrespective of the SARS-CoV-2 variant type since RdRps and ExoNs are widely conserved among all SARS-CoV-2 strains. Herein, the present computational/biological study screened our previous small libraries of nitrogenous heterocyclic compounds, searching for the most ideal drug candidates predictably able to efficiently act through this double approach. Theoretical filtration gave rise to three promising antioxidant nitrogenous heterocyclic compounds of the 1,3,4-thiadiazole type, which are CoViTris2022, Taroxaz-26, and ChloViD2022. Further experimental evaluation proved for the first time, utilizing the in vitro anti-RdRp/ExoN and anti-SARS-CoV-2 bioassays, that ChloViD2022, CoViTris2022, and Taroxaz-26 could effectively inhibit the replication of the new virulent strains of SARS-CoV-2 with extremely minute in vitro anti-RdRp and anti-SARS-CoV-2 EC₅₀ values of 0.17 and 0.41 μM for ChloViD2022, 0.21 and 0.69 μM for CoViTris2022, and 0.23 and 0.73 μM for Taroxaz-26, respectively, transcending the anti-COVID-19 drug molnupiravir. The preliminary in silico outcomes greatly supported these biochemical results, proposing that the three molecules potently strike the key catalytic pockets of the SARS-CoV-2 (Omicron variant) RdRp's and ExoN's vital active sites. Moreover, the idealistic pharmacophoric hallmarks of CoViTris2022, Taroxaz-26, and ChloViD2022 molecules relatively make them typical dual-action inhibitors of SARS-CoV-2 replication and proofreading, with their highly flexible structures open for various kinds of chemical derivatization. To cut it short, the present pivotal findings of this comprehensive work disclosed the promising repositioning potentials of the three 2-aminothiadiazoles, CoViTris2022, Taroxaz-26, and ChloViD2022, to successfully interfere with the crucial biological interactions of the coronaviral-2 polymerase/exoribonuclease with the four principal RNA nucleotides, and, as a result, cure COVID-19 infection, encouraging us to rapidly start the three drugs' broad preclinical/clinical anti-COVID-19 evaluations.

Keywords: 2-Amino-1,3,4-thiadiazole Derivative; Anti-COVID-19 Drug; Anti-Omicron Agent; ChloViD2022; Coronaviral-2 RNA-dependent RNA Polymerase (RdRp); SARS-CoV-2 Proofreading 3′-to-5′ Exoribonuclease (ExoN).

Fig. 1

A Chemical structures of the reference anti-SARS-CoV-2 drug molnupiravir and the investigated three aminothiadiazoles, CoViTris2022, Taroxaz-26, and ChloViD2022. B Rational design of 5-substituted-2-amino-1,3,4-thiadiazoles, e.g., ChloViD2022 molecule as a displayed ideal example, as potential dual-action inhibitors of SARS-CoV-2 RdRp/ExoN acting through nucleoside mimicry strategy

Fig. 2

RMSD trajectories (during a simulation period of 100 ns) of the α-carbon of amino acid residues of the protein (blue color) and the ligand (maroon color) in the protein–ligand complexes of the three aminothiadiazoles, CoViTris2022, Taroxaz-26, and ChloViD2022, and the reference drug, molnupiravir, respectively, with: A SARS-CoV-2 RdRp “nsp12” enzyme cocrystallized with its protein cofactors nsp7 and nsp8 (PDB ID: 7BV2). B SARS-CoV-2 ExoN “nsp14” enzyme cocrystallized with its protein cofactor nsp10 (PDB ID: 7MC6). The apoprotein RMSD trajectories of the 7BV2 and 7MC6 were, respectively, displayed for comparison purposes

Fig. 2

RMSD trajectories (during a simulation period of 100 ns) of the α-carbon of amino acid residues of the protein (blue color) and the ligand (maroon color) in the protein–ligand complexes of the three aminothiadiazoles, CoViTris2022, Taroxaz-26, and ChloViD2022, and the reference drug, molnupiravir, respectively, with: A SARS-CoV-2 RdRp “nsp12” enzyme cocrystallized with its protein cofactors nsp7 and nsp8 (PDB ID: 7BV2). B SARS-CoV-2 ExoN “nsp14” enzyme cocrystallized with its protein cofactor nsp10 (PDB ID: 7MC6). The apoprotein RMSD trajectories of the 7BV2 and 7MC6 were, respectively, displayed for comparison purposes

Fig. 3

RMSF trajectories (along the different residue regions) of the α-carbon of amino acid residues of the protein in the protein–ligand complexes of the three aminothiadiazoles, CoViTris2022, Taroxaz-26, and ChloViD2022, and the reference drug, molnupiravir, respectively, with: A SARS-CoV-2 RdRp “nsp12” enzyme cocrystallized with its protein cofactors nsp7 and nsp8 (PDB ID: 7BV2). B SARS-CoV-2 ExoN “nsp14” enzyme cocrystallized with its protein cofactor nsp10 (PDB ID: 7MC6). The apoprotein RMSF trajectories of the 7BV2 and 7MC6 were, respectively, displayed for comparison purposes

Fig. 3

RMSF trajectories (along the different residue regions) of the α-carbon of amino acid residues of the protein in the protein–ligand complexes of the three aminothiadiazoles, CoViTris2022, Taroxaz-26, and ChloViD2022, and the reference drug, molnupiravir, respectively, with: A SARS-CoV-2 RdRp “nsp12” enzyme cocrystallized with its protein cofactors nsp7 and nsp8 (PDB ID: 7BV2). B SARS-CoV-2 ExoN “nsp14” enzyme cocrystallized with its protein cofactor nsp10 (PDB ID: 7MC6). The apoprotein RMSF trajectories of the 7BV2 and 7MC6 were, respectively, displayed for comparison purposes

Fig. 4

Collective post-MD simulation analysis of the protein–ligand complexes properties (RMSD, rGyr, MolSA, SASA, and PSA) of the three aminothiadiazoles, CoViTris2022, Taroxaz-26, and ChloViD2022, and the reference drug, molnupiravir, respectively, with: A SARS-CoV-2 RdRp “nsp12” enzyme cocrystallized with its protein cofactors nsp7 and nsp8 (PDB ID: 7BV2). B SARS-CoV-2 ExoN “nsp14” enzyme cocrystallized with its protein cofactor nsp10 (PDB ID: 7MC6)

Fig. 5

Histograms of fractions of the most predominant and stable protein–ligand interactions throughout the 100-ns simulative interaction trajectories of the three aminothiadiazoles, CoViTris2022, Taroxaz-26, and ChloViD2022, and the reference drug, molnupiravir, respectively, with: A SARS-CoV-2 RdRp “nsp12” enzyme cocrystallized with its protein cofactors nsp7 and nsp8 (PDB ID: 7BV2). B SARS-CoV-2 ExoN “nsp14” enzyme cocrystallized with its protein cofactor nsp10 (PDB ID: 7MC6)

Fig. 6

Plots of distribution of the total number of the most predominant and stable interactions (contacts) in each trajectory framework of the protein–ligand complexes of the three aminothiadiazoles, CoViTris2022, Taroxaz-26, and ChloViD2022, and the reference drug, molnupiravir, respectively, with: A SARS-CoV-2 RdRp “nsp12” enzyme cocrystallized with its protein cofactors nsp7 and nsp8 (PDB ID: 7BV2). B SARS-CoV-2 ExoN “nsp14” enzyme cocrystallized with its protein cofactor nsp10 (PDB ID: 7MC6)