Fig 1.
Interactions (A) and binding pattern (B) of cytochalasin Z8 (11518356) with RdRp of SARS-CoV-2 (7B3B) as a receptor.
Fig 2.
Interactions (A) and binding pattern (B) of aspulvinone D (54678424) with RdRp of HIV-1 (6UK0) as a receptor.
Table 1.
Computation binding energy profiling of secondary metabolites as potential drug candidates against RdRp of five different viruses.
Fig 3.
Interactions (A) and binding pattern (B) of talaromyolide D (146683236) with RdRp of hepatitis C (4OOW) as a receptor.
Fig 4.
Interactions (A) and binding pattern (B) of aspulvinone D (54678424) with RdRp of Ebola (7YER) as a receptor.
Fig 5.
Interactions (A) and binding pattern (B) of talaromyolide D (146683236) with RdRp of dengue (5K5M) as a receptor.
Fig 6.
Chemical structures of the best active antiviral compounds found via molecular docking study.
Table 2.
Evaluation of drug-like properties by rule of five of selected secondary metabolites against viral RdRp enzyme.
Table 3.
ADMET related drug-like parameters of the best selected secondary metabolites against viral RdRp enzyme.
Fig 7.
Root-mean-square deviation (RMSD) values of selected receptor proteins with their best ligands.
(a) RMSD of the C-alpha atoms of RdRp of SARS-CoV-2 and cytochalasin Z8; (b) RMSD of the C-alpha atoms of RdRp of HIV-1 and aspulvinone D with time; (c) RMSD of the C-alpha atoms of RdRp of hepatitis C with talaromyolide D; (d) RMSD of the C-alpha atoms of RdRp of Ebola with aspulvinone D; (e) RMSD of the C-alpha atoms of RdRp of dengue with talaromyolide D; (f) RMSD of C-alpha atoms of RdRp of SARS-CoV2 and remdesivir as a control. The variation of protein RMSD is shown on the left Y-axis through time. The variation of ligand RMSD is shown on the right Y-axis through time.
Fig 8.
Residue wise root mean square fluctuation (RMSF) of RdRp of selected receptor proteins.
(a) SARS-CoV-2 and cytochalasin Z8 complex, (b) HIV-1 and aspulvinone D complex, (c) hepatitis C and talaromyolide D complex, (d) Ebola and aspulvinone D complex, (e) dengue and talaromyolide D complex, (f) SARS-CoV2 and remdesivir (control) complex.
Fig 9.
Protein-ligand contact histograms (H-bond, hydrophobic, ionic, and water bridges) of; (a) RdRp of SARS-CoV-2 and cytochalasin Z8 complex, (b) RdRp of HIV-1 and aspulvinone D complex, (c) RdRp of hepatitis C and talaromyolide D complex, (d) RdRp of Ebola and aspulvinone D complex, (e) RdRp of dengue and talaromyolide D complex, (f) RdRp of SARS-CoV2 and remdesivir (control) complex.
Fig 10.
A timeline representation of the interactions and contacts (H-bonds, hydrophobic, ionic, and water bridges) between; (a) RdRp of SARS-CoV-2 and cytochalasin Z8 complex, (b) RdRp of HIV-1 and aspulvinone D complex, (c) RdRp of hepatitis C and talaromyolide D complex, (d) RdRp of Ebola and aspulvinone D complex, (e) RdRp of dengue and talaromyolide D complex, (f) RdRp of SARS-CoV-2 and remdesivir complex as a control.
Fig 11.
Ligand atom interactions with protein residues.
(a) interaction of cytochalasin Z8 atoms with RdRp of SARS-CoV-2 protein residues; (b) interaction of aspulvinone D atoms with RdRp of HIV-1 protein residues; (c) interaction of talaromyolide D atoms with RdRp of hepatitis C protein residues; (d) interaction of aspulvinone D atoms with RdRp of Ebola protein residues; (e) interaction of talaromyolide D atoms with RdRp of dengue protein residues; (f) interaction of remdesivir atoms with RdRp of SARS-CoV-2 protein residues.
Fig 12.
MM-GBSA method was employed for the prediction of binding energy between five receptor proteins and their respective best ligands.
SAR: SARS-CoV-2, Cyt: Cytochalasin Z8, HIV: HIV-1, Asp: Aspulvinone D, HCV: Hepatitis C, Tal: Talaromyolide D, Ebo: Ebola, Den: Dengue, Rem: Remdesivir.