Identification and evaluation of antiviral activity of novel compounds targeting SARS-CoV-2 virus by enzymatic and antiviral assays, and computational analysis

Figures

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  Figure 1.. Left. Reaction of the 1,5-diaryl-3-oxo-1,4-pentadienyl pharmacophore with thiol group at the catalytic site (showing Cys111 and His272) of SARS-CoV-2 PLpro. Initially, a non-covalent enzyme-inhibitor association is formed (E:I, 1) leading to a covalent adduct. Right. Structure of BBC DU-UC15 (2c) with the 1,5-diaryl-3-oxo-1,4-pentadienyl pharmacophore in red.

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  Scheme 1.. Synthesis of bis(benzylidene)cyclohexanone inhibitors.

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  Figure 2.. Left: 3D structure of the SARS-CoV-2 PLpro-GRL0617 complex (PDB entry 7CMD62). The inhibitor GRL0617 that occupies the S4 - S3 pockets of the substrate binding cleft is shown in the CPK representation. Catalytic triad of PLpro: Cys111 - His272 - Asp286 coloured purple shows the location of the catalytic site. Right: 2D scheme of inhibitor - residue interactions. Binding of GRL0617 induces closure of the flexible blocking loop BL2 (Gly266 - Gly271) and narrows the substrate binding cleft. The residues Tyr268 and Gln269 in the BL2 loop shift towards the bound GRL0617.

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  Figure 3.. Evaluation of antiviral efficacy with calculation of the effective inhibitory concentration EC50 for compounds: T98 (A1, B1), T120 (A2, B2), T121 (A3, B3), T122 (A4, B4) and T124 (A5, B5). Monitoring the trend of decreasing the SARS-CoV-2 virus titre (normalised to untreated control, presented as mean with SEM) with increasing compound concentration (A1-A5). Determination of half-maximal effective concentrations EC50 [M] (B1-B5) from the sigmoidal model with the corresponding regression coefficient R2 (the goodness of fit). Data (B1-B5) are presented as mean and error with SEM.

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  Figure 4.. Left: Molecular surface of the binding site of GRL0617 that occupies the S4 - S3 pockets of the substrate binding cleft S4 - S3 - S2 - S1 of PLpro of SARS-CoV-2. The flexible BL2 loop G266-NYQC-G271 stabilises the bound ligand in its position by closing on the inhibitor (PDB entry 7CMD) 62. Right: Binding site of the model of noncovalent complex PLpro - T98. The partially transparent molecular surface of the enzyme illustrates the shape of the pockets of the substrate binding cleft. The amine tail is oriented downward and is not fully visible. Atom colouring scheme: H, white; C, yellow; N, blue; O, red. Only polar hydrogens are shown.