Novel Investigational Anti-SARS-CoV-2 Agent Ensitrelvir "S-217622": A Very Promising Potential Universal Broad-Spectrum Antiviral at the Therapeutic Frontline of Coronavirus Species

Abstract

Lately, nitrogenous heterocyclic antivirals, such as nucleoside-like compounds, oxadiazoles, thiadiazoles, triazoles, quinolines, and isoquinolines, topped the therapeutic scene as promising agents of choice for the treatment of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and their accompanying ailment, the coronavirus disease 2019 (COVID-19). At the same time, the continuous emergence of new strains of SARS-CoV-2, like the Omicron variant and its multiple sublineages, resulted in a new defiance in the enduring COVID-19 battle. Ensitrelvir (S-217622) is a newly discovered orally active noncovalent nonpeptidic agent with potential strong broad-spectrum anticoronaviral activities, exhibiting promising nanomolar potencies against the different SARS-CoV-2 variants. S-217622 effectively and nonspecifically hits the main protease (M^pro) enzyme of a broad scope of coronaviruses. Herein, in the present computational/biological study, we tried to extend these previous findings to prove the universal activities of this investigational agent against any coronavirus, irrespective of its type, through synchronously acting on most of its main unchanged replication enzymes/proteins, including (in addition to the M^pro), e.g., the highly conserved RNA-dependent RNA polymerase (RdRp) and 3'-to-5' exoribonuclease (ExoN). Biochemical evaluation proved, using the in vitro anti-RdRp/ExoN bioassay, that S-217622 can potently inhibit the replication of coronaviruses, including the new virulent strains of SARS-CoV-2, with extremely minute in vitro anti-RdRp and anti-RdRp/ExoN half-maximal effective concentration (EC₅₀) values of 0.17 and 0.27 μM, respectively, transcending the anti-COVID-19 drug molnupiravir. The preliminary in silico results greatly supported these biochemical results, proposing that the S-217622 molecule strongly and stabilizingly strikes the key catalytic pockets of the SARS-CoV-2 RdRp's and ExoN's principal active sites predictably via the nucleoside analogism mode of anti-RNA action (since the S-217622 molecule can be considered as a uridine analog). Moreover, the idealistic druglikeness and pharmacokinetic characteristics of S-217622 make it ready for pharmaceutical formulation with the expected very good clinical behavior as a drug for the infections caused by coronaviruses, e.g., COVID-19. To cut it short, the current critical findings of this extension work significantly potentiate and extend the S-217622's previous in vitro/in vivo (preclinical) results since they showed that the striking inhibitory activities of this novel anti-SARS-CoV-2 agent on the M^pro could be extended to other replication enzymes like RdRp and ExoN, unveiling the possible universal use of the compound against the next versions of the virus (i.e., disclosing the nonspecific anticoronaviral properties of this compound against almost any coronavirus strain), e.g., SARS-CoV-3, and encouraging us to rapidly start the compound's vast clinical anti-COVID-19 evaluations.

Figure 1

(A) Chemical structures of the investigational anticoronaviral agent S-217622 (along with its expected comprehensive extended and broad-spectrum anticoronaviral activities against the diverse nonspecific proteins of coronaviruses) and the reference anti-SARS-CoV-2 drug molnupiravir, respectively. (B) Comparative physicochemical radar (preliminary in silico pharmacokinetics/druglikeness assessment; LIPO: Lipophilicity, INSOLU: Insolubility, INSATU: Insaturation, and FLEX: Flexibility) of S-217622 versus molnupiravir, generated using the SwissADME webserver.

Figure 2

2D images of the postdocking interactions of S-217622 and 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).

Figure 3

3D images of the postdocking interactions of S-217622 and 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).

Figure 4

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 S-217622 and 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).

Figure 5

RMSF trajectories (along the different residue regions) of the α-carbon of amino acid residues of the protein in the protein–ligand complexes of S-217622 and 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).

Figure 6

Collective post-MD simulation analysis of the protein–ligand complexes properties (RMSD, rGyr, MolSA, SASA, and PSA) of S-217622 and 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).

Figure 7

Histograms of the protein–ligand interactions fractions throughout the simulative interaction trajectories of S-217622 and 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).

Figure 8

Plots of the distribution of the total number of interactions (contacts) in each trajectory framework of the protein–ligand complexes of S-217622 and 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).