Thienopyrimidine scaffolds as promising antimicrobial agents: synthesis, biological evaluation, DFT analysis and molecular docking

Abstract

Thienopyrimidines represent an important class of nitrogen- and sulfur-containing heterocycles with broad pharmacological relevance. In this work, a new series of thienopyrimidine derivatives was efficiently synthesized through a multistep route involving cyclization, Mannich annulation, Schiff-base condensation, dipyrimidinone ring formation, and acylation, affording structurally diverse fused frameworks. The synthesized compounds were fully characterized using IR, NMR, and mass spectrometry. Their antimicrobial activity was evaluated against representative Gram-positive, Gram-negative strains and fungal strains revealing clear structure–activity relationships. Notably, the Mannich derivative 11 exhibited the highest potency toward Bacillus subtilis, while the fused dipyrimidinone compound 13 demonstrated broadened activity, including inhibition of Escherichia coli. Density functional theory (DFT) calculations provided insight into the electronic structure, intramolecular interactions, HOMO–LUMO distributions, electrostatic potential surfaces, and noncovalent interaction patterns responsible for the observed reactivity and binding behavior. Molecular docking studies against B. subtilis and E. coli DNA gyrase B revealed strong and diverse protein–ligand interactions, consistent with the biological findings, and highlighted compound 13 as the most promising candidate due to its favorable Vina score and extensive hydrogen-bonding and hydrophobic contacts. Collectively, the combined synthetic, biological, and computational analyses underscore the potential of thienopyrimidine scaffolds as valuable agents for developing new antimicrobial agents.