Search for new antibacterial drugs has continued to be an urgent request. One of the approaches is development of covalent inhibitors using biochemoinformatics at initial stages. In this work, structures of few plant-derived substances with electrophilic unsaturated carbonyl & structures of small synthetic compounds suitable for fragment-based drug discovery (FBDD) with -CH2-Br group were selected as ligands for set of >500 PDB structures of bacterial proteins. Theoretical assessment was carried out using the Autodock Vina program for calculation and FYTdock for organization the process and analysis of results. Based on the docking simulations, ixerin D from dandelion has been identified as a potential covalent inhibitor of mycobacterial lipoyl synthase (PDB code: 5EXI), inosine monophosphate dehydrogenase (4ZQR), beta-ketoacyl-acyl-transferring synthase III proteins with localization of its electrophilic fragment within 0.4 nm from the cysteine sulfur atom and binding energies ranging from -9.0 to -10.7 kcal/mol. For the synthetic ligand 4-(4-(2-bromoethyl)piperazin-1-yl)-7-nitrobenzofurazan, affine binding (docking score from -6.5 to -7.3 kcal/mol) with the orientation of the -CH2-Br to the Cys sulfur atom of Sortase B from Staphylococcus aureus, which is important for pathogenesis, E. coli Gsp amidase and β-lactamase S70C BlaC has been shown. Similar binding of 2-bromo-1-(4-(nitrobenzofurazan-4-yl)piperazin-1-yl)ethanone with respect to histidine residues of Microcin-processing metalloprotease from E. coli, CYP134A1 from Bacillus subtilis and 10 other proteins has been observed. 2-bromo-N-(4-bromophenyl)acetamide demonstrated ability to covalent Cys modification for only A264C of P450 BM3 from E. coli. Thus, the compounds may have potential antibacterial properties opening up promising directions for further experimental studies in vitro.