Iterated Virtual Screening-Assisted Antiviral and Enzyme Inhibition Assays Reveal the Discovery of Novel Promising Anti-SARS-CoV-2 with Dual Activity

Abstract

Unfortunately, COVID-19 is still a threat to humankind and has a dramatic impact on human health, social life, the world economy, and food security. With the limited number of suggested therapies under clinical trials, the discovery of novel therapeutic agents is essential. Here, a previously identified anti-SARS-CoV-2 compound named Compound 13 (1,2,5-Oxadiazole-3-carboximidic acid, 4,4’-(methylenediimino) bis,bis[[(2-hydroxyphenyl)methylene]hydrazide) was subjected to an iterated virtual screening against SARS-CoV-2 Mpro using a combination of Ligand Designer and PathFinder. PathFinder, a computational reaction enumeration tool, was used for the rapid generation of enumerated structures via default reaction library. Ligand designer was employed for the computerized lead optimization and selection of the best structural modification that resulted in a favorable ligand–protein complex. The obtained compounds that showed the best binding to Mpro were re-screened against TMPRSS2, leading to the identification of 20 shared compounds. The compounds were further visually inspected, which resulted in the identification of five shared compounds M1–5 with dual binding affinity. In vitro evaluation and enzyme inhibition assay indicated that M3, an analogue of Compound 13 afforded by replacing the phenolic moiety with pyridinyl, possesses an improved antiviral activity and safety. M3 displayed in vitro antiviral activity with IC50 0.016 µM and Mpro inhibition activity with IC50 0.013 µM, 7-fold more potent than the parent Compound 13 and potent than the antivirals drugs that are currently under clinical trials. Moreover, M3 showed potent activity against human TMPRSS2 and furin enzymes with IC50 0.05, and 0.08 µM, respectively. Molecular docking, WaterMap analysis, molecular dynamics simulation, and R-group analysis confirmed the superiority of the binding fit to M3 with the target enzymes. WaterMap analysis calculated the thermodynamic properties of the hydration site in the binding pocket that significantly affects the biological activity. Loading M3 on zinc oxide nanoparticles (ZnO NPs) increased the antiviral activity of the compound 1.5-fold, while maintaining a higher safety profile. In conclusion, lead optimized discovery following an iterated virtual screening in association with molecular docking and biological evaluation revealed a novel compound named M3 with promising dual activity against SARS-CoV-2. The compound deserves further investigation for potential clinical-based studies.

A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet?

“…Only M-pro inhibitors that have pIC 50 values and can inhibit SARS-CoV-2 replication in a cellular antiviral assay were included. The compound with the CAS number 339096-59-2, also named compound M3 [ 101 ], was obtained from the optimization of a previous SARS-CoV-2 M-pro inhibitor, named compound 13 [ 102 ]. Compound 339096-59-2 inhibited the SARS-CoV-2 M-pro in vitro with an IC 50 of 13 nM and displayed anti-SARS-CoV-2 activity in Vero-E6 cells infected with SARS-CoV-2 [ 101 ].…”

“…Compound 339096-59-2 inhibited the SARS-CoV-2 M-pro in vitro with an IC 50 of 13 nM and displayed anti-SARS-CoV-2 activity in Vero-E6 cells infected with SARS-CoV-2 [ 101 ]. The EC 50 value was 16 nM [ 101 ]. This compound also inhibited in vitro human TMPRSS2 and furin enzymes, which are required for viral entry [ 101 ].…”

“…The EC 50 value was 16 nM [ 101 ]. This compound also inhibited in vitro human TMPRSS2 and furin enzymes, which are required for viral entry [ 101 ]. Compounds with the CAS number 2603242-35-7, 2603242-41-5, 2679814-93-6, 2679814-92-5, 2679814-91-4, 2679814-96-9, 2603242-04-0 are perampanel derivatives that can inhibit the SARS-CoV-2 M-pro in vitro, with IC 50 values between 0.128 and 0.018 μM [ 44 , 46 ].…”

New Bioactive Fused Triazolothiadiazoles as Bcl-2-Targeted Anticancer Agents

“…Structure-activity relationships (SAR) of the most potent and selective compounds (5b, 5e, 5i, 5k and 5l) were studied using the R-group analysis tool [13]. This analysis showed that the different structural substitution resulted in a variance in the biological activity and binding affinity.…”

A Computer-Aided Approach for the Discovery of D-Peptides as Inhibitors of SARS-CoV-2 Main Protease

“…Structure-based virtual screening (SBVS) of diverse ligand databases, many of them containing drug repurposing candidates and natural products, has been extensively applied to identify potential 3CL pro inhibitors (Wu C. et al, 2020;Chowdhury et al, 2020;Jukic et al, 2020;Meyer-Almes, 2020;Olubiyi et al, 2020;Selvaraj et al, 2020;Federico et al, 2021;Gogoi et al, 2021;Guedes et al, 2021;Kumar et al, 2021;Lokhande et al, 2021;Naik et al, 2021;Rajpoot et al, 2021;Rehman et al, 2021;Sisakht et al, 2021). In several cases, this approach has led to the successful identification of compounds displaying in vitro inhibitory activity against 3CL pro (Ghahremanpour et al, 2020;Gupta et al, 2020;Jin et al, 2020;Li et al, 2020;Alves et al, 2021;Banerjee et al, 2021;Gunther et al, 2021;Guo et al, 2021;Gupta et al, 2021;Hamdy et al, 2021;Pathak et al, 2021;Yang et al, 2021). On the other hand, protein-peptide docking remains far more challenging compared to other small molecules due to the higher flexibility of peptides (Rentzsch and Renard, 2015;Ciemny et al, 2018;Hashemi et al, 2021).…”