Bioisosteric replacement in the search for antimicrobial agents: design, synthesis and activity of novel 6-(1h-Benzimidazol-2-yl)-1-alkyl-3,5-dimethylthieno[2,3-d]pyrimidine-2,4(1h,3h)-dione derivatives

Abstract

The aim. To apply the concept of bioisosterism for the structural optimization of benzimidazole–thieno[2,3-d]pyrimidine hybrids aimed at developing effective antibacterial agents as potential inhibitors of the bacterial enzyme TrmD. Materials and Methods. Organic synthesis methods; structure confirmation by ¹H, ¹³C, and HMBC NMR spectroscopy, LC-MS, and elemental analysis. Molecular docking was performed using AutoDock Vina, AutoDockTools 1.5.6, and Discovery Studio Client. Antimicrobial activity was evaluated using the agar diffusion method, and the impact on biofilm formation/disruption was assessed using the crystal violet assay. Results and Discussion. The bioisosteric modification involved oxidation of the thione group in 3,5-dimethyl-4-oxo-2-thioxothieno[2,3-d]pyrimidine-6-carboxylate. The resulting 2,4-dioxothieno[2,3-d]pyrimidine-6-carboxylic acid was activated with 1,1′-carbonyldiimidazole to form a benzimidazole fragment in a one-pot procedure. Alkylation of the obtained hybrid with chloroacetamides led to regioselective products confirmed by HMBC. All synthesized compounds demonstrated significant antimicrobial activity against both Gram-positive and Gram-negative test strains. Compound 5c with a 4-ethoxyphenyl substituent processed the highest activity, including effectiveness against clinical strains of S. aureus and P. aeruginosa. Compound 5c also demonstrated notable biofilm disruption capacity against S. aureus, E. coli, P. aeruginosa, and C. albicans. Molecular docking to the TrmD bacterial enzyme confirmed the formation of a hydrogen bond between the 2-oxo group and Glu121.

Conclusions. An efficient method was developed for the synthesis of a novel series of 2-[6-(1H-benzimidazol-2-yl)-3,5-dimethyl-2,4-dioxo-3,4-dihydrothieno[2,3-d]pyrimidin-1(2H)-yl]-N-arylacetamides. Bioisosteric hybrids showed enhanced antimicrobial properties and improved binding affinity to bacterial TrmD. Compound 5c demonstrated high activity against both Gram-positive and Gram-negative strains, including clinical isolates, as well as the ability to disrupt biofilms, highlighting its potential as a promising lead for further development