Potential antimicrobial properties of cytosine β-D-riboside derivatives through molecular dynamics and molecular docking exploration with bacterial and fungal proteins

Nucleoside derivatives have contributed to the clinical and pharmaceutical fields as medicinal agents and approved drugs. The reaction of lauroyl chloride with cytosine β-D-riboside, i.e., cytidine ( 1 ) in DMF/Et 3 N, was the initiator step leading to 5′- O -(lauroyl)cytidine ( 2 ). Compound ( 2 ) was reacted with various acylating agents and penetrated to give 2′,3′-di- O -acyl derivatives ( 3 – 6 ). Physicochemical, spectroscopical, and elemental analysis methods were used to confirm the structure of the synthesized derivatives. In vitro antimicrobial tests, coupled with PASS prediction, revealed that these derivatives are highly effective against distinct pathogenic bacteria. Compared with the standard nystatin, compound 5 exhibited excellent antifungal efficacy against Aspergillus flavus and Aspergillus niger . Molecular docking analysis was performed to evaluate the binding interactions with the FimH lectin domain from E. coli K12 and urate oxidase (Uox) from Aspergillus flavus . For the FimH lectin domain, the binding affinities range from −2.35 to −9.32 kcal/mol (PyRx) and from −0.764 to 115.318 kcal/mol (iGEMDOCK), where compound 2 exhibited the highest binding affinity and outperformed the standard azithromycin, forming hydrogen bonds with ASN A:138, GLN A:133, ASP A:54, ASN A:46, PHE A:1, and ASP A:47, along with Pi-alkyl interactions with TYR A:48. Similarly, compound 5 , among the other synthesized compounds, strongly bound to Uox, with docking scores of −8.65 kcal/mol (PyRx) and −119.145 kcal/mol (iGEMDOCK), interacting with key residues such as THR A:173, LEU A:170, PHE A:258, and HIS A:256 through van der Waals forces, Pi‒Pi hydrophobic interactions, and hydrogen bonding. The RMSD, RMSF, and Rg analyses revealed that the docked complexes 4XO8: 2 and 1R4U: 5 exhibited stable protein‒ligand interactions, with no significant structural deviations observed during the 100 ns MD simulations. The hydrogen bonding and SASA results further support the stability of these complexes. According to DFT and FMO studies, compound 5 should exhibit the highest chemical reactivity because it has the smallest Egap (4.84 eV). In silico, ADMET and toxicity studies were used to evaluate the pharmacokinetic characteristics, drug-likeness, and toxicity parameters of the newly synthesized compounds. Finally, SAR study was performed to predict any subsequent changes in the antimicrobial activities of these compounds modified at various positions in their structure, especially those modified with [CH 3 (CH 2 ) 10 CO] and {CH 3 (CH 2 ) 14 CO}] groups. These results suggest that derivatives of lauroyl cytidine have great promise as antimicrobial agents for treating microbial infections. • Novel cytidine derivatives were synthesized via the direct acylation method. • The in vitro antimicrobial activity was evaluated along with PASS prediction. • DFT, FMO and MEP highlighted potential biological interaction sites. • Molecular docking identified as a strong inhibitor of FimH ( E. coli ) and urate oxidase ( A. flavus ). • Molecular dynamics simulations confirmed the stability of the best-docked derivatives.