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, C 13 H 15 N 2 Cl [6a] and C 21 H 24 N 3 OCl, CH 4 O [7c] were obtained allowing for structural analysis. [C 13 H 15 N 2 Cl] monoclinic, P2 1 /c, a=9.9763(6)Å, b=9.6777(6)Å, c=13.3002(9)Å, β=106.459(7)°, V=1231.47(14)Å 3 , Z=4, T=173(2)K, μ(Cu Kα)=2.522mm −1 , D calc =1.266g/mm 3 , 7124 reflections, 2404 unique (R int =0.0381), R 1 =0.0420 (I>2σ(I)) and wR 2 =0.1254 (all data). [C 21 H 24 N 3 OCl, CH 4 O] 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)Å 3 , Z=4, T=173(2)K, μ(Cu Kα)=1.744mm −1 , D calc =1.243g/mm 3 , 14238 reflections, 8297 unique (R int =0.0330), R 1 =0.0578 (I>2σ(I)) and wR 2 =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 Bacillus flexus compared to antibiotic Amoxicillin.