Synthesis, crystal structure, molecular docking and antimicrobial evaluation of new pyrrolo[3,2-c]pyridine derivatives

•A new series of pyrrolo[3,2-c]pyridine derivatives were designed and synthesized.•The molecular docking of the GlcN-6-P synthase with target compounds was carried out.•X-ray crystal structure determination and analysis of 6a and 7c were carried out.•In vitro antibacterial and antifungal screening was carried out.•Compound 7e showed substantial antibacterial activity against B. flexus.

New antibacterial agents, pyrrolo[3,2-c]pyridine derivatives have been designed and synthesized. The structural considerations of the designed molecules were further supported by the docking study with GlcN-6-P synthase. The chemical structures of the new compounds were characterized by NMR, mass spectral analysis and elemental analysis. Single crystals of two compounds, C13H15N2Cl [6a] and C21H24N3OCl, CH4O [7c] were obtained allowing for structural analysis. [C13H15N2Cl] monoclinic, P21/c, a = 9.9763(6) Å, b = 9.6777(6) Å, c = 13.3002(9) Å, β = 106.459(7)°, V = 1231.47(14) Å3, Z = 4, T = 173(2) K, μ(Cu Kα) = 2.522 mm−1, Dcalc = 1.266 g/mm3, 7124 reflections, 2404 unique (Rint = 0.0381), R1 = 0.0420 (I > 2σ(I)) and wR2 = 0.1254 (all data). [C21H24N3OCl, CH4O] triclinic, P−1, a = 10.1478(7) Å, b = 12.0945(8) Å, c = 18.3244(10) Å, α = 104.369(5)°, β = 90.766(5)°, γ = 99.235(6)°, V = 2147.1(2) Å3, Z = 4, T = 173(2) K, μ(Cu Kα) = 1.744 mm−1, Dcalc = 1.243 g/mm3, 14238 reflections, 8297 unique (Rint = 0.0330), R1 = 0.0578 (I > 2σ(I)) and wR2 = 0.1773 (all data). The in vitro antimicrobial activities of the compounds were conducted against various Gram-negative, Gram-positive bacteria and fungi. Amongst the tested compounds 7e displayed promising antibacterial activity against Gram-positive bacteria Bacillusflexus compared to antibiotic Amoxicillin.

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