Fig 1.
(A): Ramachandran plot. SARS-CoV-2 RdRp (pdb: 6M71) protein and (B): Interfaces summary of SARS-CoV-2 RdRp (pdb: 6M71).
Table 1.
Predicted antiviral activities (% inhibition) of cytidine derivatives 2–15, remdesivir, and AZT.
Fig 2.
The designed cytidine (1) and its derivatives (2–15).
Fig 3.
Cytidine (1) and its derivatives (2–15).
Fig 4.
Interactions of control molecule with the enzyme.
Fig 5.
Derivatives (13) with the active site of SARS-CoV-2 (PDB: 6M71) were performed by Discovery Studio.
Fig 6.
(A) Docked 3D pose. Derivative 13 with RdRp (PDB: 6M71). (B) The close viewer of key active site residues involved in interactions with derivative 13.
Table 2.
The binding energy of the cytidine derivatives against RdRp.
Fig 7.
Backbone structural deviations.
Analysis based on molecular dynamics simulations. A. RMSD, B. RMSF and C. RoG.
Fig 8.
Snapshots of compound 13 with the enzyme at different nanoseconds.
Table 3.
Prediction in silico of absorption of cytidine derivatives.
Fig 9.
Charts of the cytidine derivatives where FLEX: Flexibility, LIPO: Lipophilicity, INSATU: Unsaturation. and INSOLU: Insolubility.
Table 4.
Determination of drug-likeness score of cytidine derivatives through Molinspiration cheminformatics online server.
Table 5.
Data of QSAR.
Fig 10.
Determination of drug-likeness.
Score of cytidine derivatives (1–15) through Osiris cheminformatics online server.
Fig 11.
Toxicity risks and drug score calculations of compounds 1–15.
Fig 12.
Calculations of compounds 1–15.
Fig 13.
Antifungal/antiviral pharmacophore site of compound 4 [69–75].