Molecular docking protocol

Molecular docking was carried out using Iterated Local Search global optimizer implemented in AutoDock Vina (Trott and Olson 2010) with the help of a graphical user interface program, PyRx (Dallakyan and Olson 2015). Free water molecules were deleted from the crystallographic structures of 3CLpro proteins, while the RdRp model structures of both SARS-CoV and SARS-CoV-2 were used as obtained from SWISS-MODEL webserver. All the protein structures were examined for gabs and hydrogen added before docking simulation. Throughout the docking experiment, the protein structures were kept rigid, while the torsions or degrees of freedom for the ligands were allowed full rotations. Conformational space for docking simulation was sampled following the literature reports of known active sites for 1UJ1 and 6LU7 3CLpro proteins (Jin et al. 2020; Yang et al. 2003). The ligand-binding sites for SARS-CoV and SARS-CoV-2 RdRps are shown in Fig. 3, similar to the reports of (Gao et al. 2020a, b; Kirchdoerfer and Ward 2019). A total of 173 inhibitors are considered in this molecular docking study and their structural representations are given in Figs. ​Figs.11 and ​and2.2. The grid dimensions that were used are contained in Supplementary Information (SI)1. The visualization tools used in this work are UCSF Chimera (Pettersen et al. 2004) and Discovery Studio 2017 R2.

Non FDA approved nucleotide analogues. 1–4. a R₁ = methyl (CH₃), b R₁ = ethyl (CH₂CH₃), c R₁ = allyl (CH₂CH = CH₂), d R₁ = propyl (CH₂CH₂CH₃),), e R₁ = methoxymethyl (CH₂OCH₃), f R₁ = propargy (CH₂CCH), g R₁ = methylthiomethyl (CH₂SCH₃), h R₁ = azidomethyl (CH₂–N₃). 5–8. a1 R₂ = H, R₁ = a; a2 R₂ = OH, R₁ = a; a3 R₂ = F, R₁ = a; a4 R₂ = OCH₃, R₁ = a. b1 R₂ = H, R₁ = b; b2 R₂ = OH, R₁ = b; b3 R₂ = F, R₁ = b; b4 R₂ = OCH₃, R₁ = b. c1 R₂ = H, R₁ = c; c2 R₂ = OH, R₁ = c; c3 R₂ = F, R₁ = c; c4 R₂ = OCH₃, R₁ = c. d1 R₂ = H, R₁ = d; d2 R₂ = OH, R₁ = d; d3 R₂ = F, R₁ = d; d4 R₂ = OCH₃, R₁ = d. e1 R₂ = H, R₁ = e; e2 R₂ = OH, R₁ = e; e3 R₂ = F, R₁ = e; e4 R₂ = OCH₃, R₁ = e. f1 R₂ = H, R₁ = f; f2 R₂ = OH, R₁ = f; f3 R₂ = F, R₁ = f; f4 R₂ = OCH₃, R₁ = f. g1 R₂ = H, R₁ = g; g2 R₂ = OH, R₁ = g; g3 R₂ = F, R₁ = g; g4 R₂ = OCH₃, R₁ = g. h1 R₂ = H, R₁ = h; h2 R₂ = OH, R₁ = h; h3 R₂ = F, R₁ = h; h4 R₂ = OCH₃, R₁ = h (Ju et al. 2020a, b^a)

Structures of approved antiviral drugs that are also used here for molecular docking, with hyroxychloroquine and quinine, antimalarial drugs where their mechanism of action affect viral RNA polymerase (Ben-Zvi et al. 2012; Fox 1996)

Aligned model structures of SARS-CoV-2 (red) with SARS-CoV (blue) RdRp showing the four catalytic domains; palm, thumb, finger and N-terminal (color figure online)