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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