Insights into the structural/conformational requirements of cytotoxic oxadiazoles as potential chemotherapeutic target binding agents

Repositioning therapeutics for COVID-19: virtual screening of the potent synthetic and natural compounds as SARS-CoV-2 3CLpro inhibitors

The widespread transmission of SARS-CoV-2 has sparked alarm worldwide. Attaining the best drugs to treat COVID-19 at the shortest possible time is one of the most critical issues in this urgent situation. Molecular docking investigation of the therapeutic potential of marketed drugs is a fast and cost-effective approach to provide a solution to this problem. The recent research efforts have led to the resolving of the 3CLpro structure as a key protease in the lifecycle of coronavirus, which could facilitate in silico evaluation of drug candidates. Herein, the similarity between the SARS-CoV-2-3CL main protease and the other SARS-CoV receptors was evaluated via multiple sequence alignment and phylogenetic tree. The reported structure of the 3CLpro was considered as a target to identify potential inhibitors for treating COVID-19 using molecular docking based virtual screening protocol. Accordingly, a database of 50 synthetic compounds with various pharmacological usage such as antiviral, anti-inflammatory, anti-human immunodeficiency viruses, antimalarial, antibacterial, anticancer, and antioxidant including approved drugs and those undergoing clinical trials, and 40 natural compounds particularly those employed in traditional Iranian medicine was constructed. The output of multiple sequence alignment analysis showed that SARS-CoV-2 main protease shares a similarity of 96% with SARS-CoV. Also, the docking results indicated that the licofelone acyl glucuronide as an anti-inflammatory drug and delta-bilirubin as an antioxidant and anti-inflammatory agent as well as kappa-carrageenan conformer, beta-D-galactopyranosyl and calycosin 7-O-glucoside as natural compounds with minimal side-effects, according to in vitro studies, are good candidates to block the enzymatic activity of SARS-CoV-2 3CLpro. Moreover, the compound 1 with the highest negative binding energy is a chemical compound that due to its favorable interactions with the 3CLpro can be identified as a representative potential drug candidate for COVID-19.

Synthesis of α,β-unsaturated benzotriazolyl-1,3,4-oxadiazole derivatives: anticancer activity, cytotoxicity, and cell imaging

A series of ten α,β-unsaturated benzotriazolyl-1,3,4-oxadiazole derivatives was synthesized and all compounds were evaluated in vitro against three breast cancer cell lines (MCF-7, MDA-MB-231 and 4T1) at different concentrations (0.1, 0.5, 1, 2, 3, 4 and 5 mg/mL). The results showed that compounds 6a, 6c, 6d, 6f, 6g, and 6i displayed acceptable anticancer activity, where compound 6f was the most active on the three cell lines (IC50 = 0.80, 0.07, and 0.30 mg/mL, respectively). Regarding the cytotoxicity assay, the compounds exhibited modest toxicity on murine splenocytes and peripheral human blood cells at the highest concentration tested (5 mg/mL). Compound 6f was further evaluated at different concentrations showing moderate cytotoxicity at the 5 mg/mL concentration and negligible cytotoxicity at the minimum concentration evaluated (0.05 mg/mL). Finally, the compounds 6a, 6c, 6d, 6f, 6g, 6i, and 6j were evaluated as fluorescence markers due to their ability to be internalized into MCF-7 cells.

Identification of a potential SARS-CoV2 inhibitor via molecular dynamics simulations and amino acid decomposition analysis

Considering lack of validated therapeutic drugs or vaccines against contagious SARS-CoV2, various efforts have been focused on repurposing of existing drugs or identifying new agents. In an attempt to identify new and potential SARS-CoV2 inhibitors targeting specific enzyme of the pathogen, a few induced fit models of SARS-CoV2 main protease (Mpro) including N-aryl amide and aryl sulfonamide based fragments were subjected to a multi-step in silico strategy. Sub-structure query of co-crystallographic fragments provided numerous ZINC15 driven commercially available compounds that entered molecular docking stage to find binding interactions/modes inside Mpro active site. Docking results were reevaluated through time dependent stability of top-ranked ligand-protease complexes by molecular dynamics (MD) simulations within 50 ns. Relative contribution of interacted residues in binding to the most probable binding pose was estimated through amino acid decomposition analysis in B3LYP level of theory with Def2-TZVPP split basis set. In confirmation of docking results, MD simulations revealed less perceptible torsional distortions (more stable binding mode) in binding of ZINC_252512772 (ΔG_b −9.18 kcal/mol) into Mpro active site. H-bond interactions and hydrophobic contacts were determinant forces in binding interactions of in silico hit. Quantum chemical calculations confirmed MD results and proved the pivotal role of a conserved residue (Glu166) in making permanent hydrogen bond (98% of MD simulations time) with ZINC_252512772. Drug-like physicochemical properties as well as desirable target binding interactions nominated ZINC_252512772 as a desirable in silico hit for further development toward SARS-CoV2 inhibitors.

Highlights

A few N-aryl amide/aryl sulfonamide based fragments were subjected to a multi-step in silico strategy to afford potential SARS-CoV2 Mpro inhibitors.

MD simulations revealed less perceptible torsional distortions (more stable binding mode) in binding of ZINC_252512772 (ΔG_b -9.18 kcal/mol) into Mpro active site.

H-bond interactions and hydrophobic contacts were determinant forces in binding interactions of in silico hit.

Quantum chemical calculations confirmed MD results and proved pivotal role of a conserved residue (Glu166) in making permanent hydrogen bond (98% of MD simulations time) with ZINC_252512772.

Communicated by Ramaswamy H. Sarma