Design, Synthesis, and Antimicrobial Evaluation of Novel 5-Chloropyridine Oxalamide Conjugates as In Vitro and In Silico Inhibitors of E. coli DNA Gyrase and C. albicans Sterol 14α-Demethylase (CYP51)

Objective: A series of novel 5-chloropyridine oxalamide conjugates (IVa–IVl) were designed, synthesized, and evaluated for their in vitro and in silico antimicrobial activity, compared with standard drugs. Methods: The coupling of 2-((5-chloropyridin-2-yl)amino)-2-oxoacetic acid (II) with various ethyl and methyl esters of amino acids (IIIa–IIIi), including glycine, L-histidine, L-alanine, L-phenylalanine, L-valine, and L-tryptophan, was carried out using DIPEA as a base and HATU as a coupling agent to obtain the final targeted 5-chloropyridine oxalamide conjugates (IVa–IVl). Antimicrobial screening was performed using the MTT assay. Further, all hybrids (IVa–IVl) were geometry-optimized using Gaussian09, molecular docking was performed using AutoDock Tool 1.5.7, and in silico ADME analysis was conducted via the online SwissADME server. Results and Discussion: The novel 5-chloropyridine oxalamide conjugates (IVa–IVl) were characterized by IR, ¹H, ¹³C NMR spectroscopy, and mass spectrometry, and screened against two Gram-negative and two Gram-positive bacterial strains, as well as three fungal strains. Compounds methyl (2-((5-chloropyridin-2-yl)amino)-2-oxoacetyl)glycinate (IVb), methyl (2-((5-chloropyridin-2-yl)amino)-2-oxoacetyl)tryptophanate (IVe), and methyl (2-((5-chloropyridin-2-yl)amino)-2-oxoacetyl)phenylalaninate (IVl) exhibited the most potent antibacterial activity against E. coli, with MIC values of 25 μg/mL. Compounds ethyl (2-((5-chloropyridin-2-yl)amino)-2-oxoacetyl)glycinate (IVa), methyl (2-((5-chloropyridin-2-yl)amino)-2-oxoacetyl)histidinate (IVc), and ethyl (2-((5-chloropyridin-2-yl)amino)-2-oxoacetyl)tryptophanate (IVd) exhibited the most potent antifungal activity against C. albicans with MIC values of 250 μg/mL. DFT analysis was performed using the B3LYP/6-311G(d,p) basis set to determine quantum chemical parameters, frontier molecular orbitals (FMO), and molecular electrostatic potential (MEP) of all synthesized compounds (IVa–IVl). Moreover, molecular docking studies revealed that compounds (IVa–IVl) could bind to the active sites of E. coli DNA gyrase (1KZN) and C. albicans sterol 14α-demethylase (CYP51) (5TZ1), forming hydrogen bonds with key active-site amino acid residues. Conclusions: The synthesized hybrids exhibited potent to moderate activity against Gram-positive and Gram-negative bacterial strains, as well as fungal pathogens. This was further supported by molecular docking and ADME analysis, suggesting their potential as promising lead compounds for the development of future antimicrobial drugs.