Synthesis of new pyrido[2,3-b]pyrazine derivatives: Crystal structures, spectroscopic characterizations, molecular docking studies, DFT calculations, and antibacterial activity

Pyrido[2,3-b]pyrazine derivatives have attracted considerable attention in medicinal chemistry due to their multifaceted biological properties. In this work, a novel and efficient synthetic strategy was developed for the preparation of 7-bromo-1,4-dihydropyrido[2,3-b]pyrazine-2,3-dione and its N1,N4-dialkylated derivatives (2a–2f) using phase-transfer catalysis under mild conditions. The synthesized compounds were characterized by NMR spectroscopy, mass spectrometry, and melting point analysis. To evaluate their antibacterial potential, minimum inhibitory concentrations (MICs) were determined against clinically relevant bacterial strains, including Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Salmonella spp. Compounds 2a and 2c exhibited the most significant activity, with compound 2d also showing noteworthy inhibition against Escherichia coli.

Complementary computational studies were undertaken to rationalize the observed biological activities. Density Functional Theory (DFT) was used to calculate electronic parameters such as HOMO-LUMO energy gaps, chemical hardness, electrophilicity, dipole moment, and molecular electrostatic potential (MEP) surfaces. These calculations revealed that compound 2a had the highest reactivity, while 2c exhibited the strongest electrophilic character and polarizability. Molecular docking simulations further demonstrated strong interactions of these compounds—especially 2c—with DNA gyrase from various bacterial pathogens. Compound 2c showed superior binding affinities and multiple hydrogen bonding interactions across bacterial targets, aligning with experimental MIC results. These findings confirm the potential of alkylated pyridopyrazines as a scaffold for developing new antibacterial agents, supported by both in vitro and in silico analyses.