Integrated CDFT, Biological Evaluation, Molecular Docking Simulation, Molecular Motion Dynamics, and Pharmacokinetic Properties of Pyrimidine Nucleoside Derivatives as Potential Antimicrobial Agents

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Abstract
Pyrimidine nucleoside derivatives have attracted considerable attention because of their broad therapeutic potential. In this study, a novel and efficient synthetic route was developed for accessing thymidine‐based nucleoside derivatives, affording high yields and confirming their structures through physicochemical, elemental, and spectroscopic analyses. The antimicrobial and antibiofilm activities of the synthesized compounds were evaluated against four bacterial strains and two fungal strains. Both the experimental and PASS‐predicted results revealed stronger antifungal activity than antibacterial activity, with remarkable potency against Aspergillus niger and Candida albicans . Notably, Compound 6 presented the lowest MIC value (e.g., 8 μg/mL) against C. albicans , which was comparable to or better than that of the standard antifungal drug fluconazole (MIC = 16 μg/mL). In addition, Compound 6 demonstrated strong antibiofilm inhibition, indicating its potential as an alternative biofilm‐targeting agent. Structure–activity relationship analysis suggested that derivatives containing long acyl chains [CH 3 (CH 2 ) 7 CO–], [CH 3 (CH 2 ) 8 CO–], and [CH 3 (CH 2 ) 14 CO–] enhanced antimicrobial efficacy. Computational studies (MEP, CDFT, and molecular docking) revealed that Compound 1 was the most stable and that Compound 7 was the most chemically reactive, while docking of the R‐7 isomer with human serum albumin and DNA suggested potential anticancer effects. The dynamic stability of the docked complexes was confirmed through MM‐PBSA and molecular dynamics analyses. ADMET profiling indicated favorable pharmacokinetic properties. Overall, these thymidine derivatives display potent antimicrobial, antifungal, and antibiofilm activities, as supported by strong in silico validation, and hold promise as next‐generation antimicrobial agents.
Funding Information
  • Ministry of Science and Technology, Government of the People’s Republic of Bangladesh (SRG-246485)

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