Background It is prudent that novel classes of antibiotics be urgently developed to manage the WHO prioritized multi-drug resistant (MDR) pathogens posing an unprecedented medical crisis. Simultaneously, multiple essential proteins have to be targeted to prevent easy resistance development. Methods An integration of structure-based virtual screening and ligand-based virtual screening was employed to explore the antimicrobial properties of indole derivatives from a compound database. Results Whole-genome sequences of the target pathogens were aligned exploiting DNA alignment potential of MAUVE to identify putative common lead target proteins. S-adenosyl methionine (SAM) biosynthesizing MetK was taken as the lead target and various literature searches revealed that SAM is a critical metabolite. Furthermore, SAM utilizing CobA involved in the B12 biosynthesis pathway, Dam in the regulation of replication and protein expression, and TrmD in methylation of tRNA were also taken as drug targets. The ligand library of 715 indole derivatives chosen based on kinase inhibition potential of indoles was created from which 102 were pursued based on ADME/T scores. Among these, 5 potential inhibitors of MetK in N. gonorrhoeae were further expanded to molecular docking studies in MetK proteins of all nine pathogens among which 3 derivatives exhibited inhibition potential. These 3 upon docking in other SAM utilizing enzymes, CobA, Dam, and TrmD gave 2 potential compounds with multiple targets. Further, docking with human MetK homolog also showed probable inhibitory effects however SAM requirements can be replenished from external sources since SAM transporters are present in humans. Conclusions We believe these molecules 3-[(4-hydroxyphenyl)methyl]-6-(1H-indol-3-ylmethyl)piperazine-2,5-dione (ZINC04899565) and 1-[(3S)-3-[5-(1H-indol-3-ylmethyl)-1,3,4-oxadiazol-2-yl]pyrrolidin-1-yl]ethanone (ZINC49171024) could be a starting point to help develop broad-spectrum antibiotics against infections caused by N. gonorrhoeae, A. baumannii, C. coli, K. pneumoniae, E. faecium, H. pylori, P. aeruginosa, S. aureus and S. typhi.

Background The rapid emergence of bacterial resistance and decreased efficacy of most antibiotics is a burning issue in the present medical world demanding swift development of novel classes of potent antibiotics. This study focuses on the robust assay of screening antimicrobials speeding up the antibiotics discovery process. Results Putative Streptomyces designated as LAf4 isolated from a soil sample of Lamjung, mid-hills of Nepal, screened from 141 putative Streptomyces isolates had the highest inhibitory effect among all the strains that showed inhibition potential against two of the ‘critical’ WHO prioritized pathogens including Klebsiella pneumoniae and Pseudomonas aeruginosa,. The results from Resazurin based assays were all verified using broth assays for antimicrobial studies. The proposed method was efficient, easy to observe and gave results a lot faster than the conventional antimicrobial study. Also, a novel spectrophotometric analysis method has been proposed to access the potency of thus screened antimicrobials. GCMS analysis of LAf4 extract indicated the presence of 2,3-butanediol, Naphthalene, and Tributyl phosphate as major constituents exhibiting antimicrobial properties whereas Pyrrolo (1, 2- a) pyrazine -1,4-dione, hexahydro-3-(2-methylpropyl)- which is an antioxidant and an anticancer agent was also recorded.Conclusion The present study validates and exhibits the time and cost effective resazurin based antimicrobial assay as the best one, for preliminary screening of antimicrobial producers compared to conventional disc/well diffusion assays since very small concentration of antimicrobials irrespective of their polarity can be detected unlike the latter methods.