In silico prediction of drug targets in Vibrio cholerae

Repurposing of FDA approved drugs and their validation against potential drug targets for Salmonella enterica through molecular dynamics simulation

Salmonella is a widely distributed pathogen causing infection of intestinal tract, typhoid, and paratyphoid fever. Number of drugs was developed against salmonella, but in the last few decades due to the emergence of drug resistant strains, most of these drugs became dormant. As a result Salmonellosis emerges as a trivial cause of human mortality worldwide; therefore, there is an urgent need for unexploited drug targets and drugs to treat Salmonellosis. As development of new drug molecules is very time consuming and costly, drug repurposing is in consideration as a better alternative. With the aim to identify a new drug molecule against the Salmonella through repurposing approach, we utilized 14 well reported druggable targets known to play a vital role in the life cycle of pathogens. These targets were used to screen DrugBank and got 53 FDA approved drugs against them. To find the interaction between considered target proteins and screened drugs, molecular docking was performed. Fourteen docked drug-target complexes with reasonable binding affinities were subjected to Molecular Dynamics Simulation (MDS) at 150 ns, using Amber18. At the end MMPBSA and MMGBSA calculations were performed for all stable complexes and finally, got 3 precise and favourable complexes, i.e. ArcB-Cefpiramide, MrcB-Cefoperazone, and PhoQ-Carindacillin. Rigorous structural and energetic analysis for these complexes validates the potential of drug molecules to act as therapeutic drugs against Salmonella enterica. With this study we hypothesize that the drugs Cefpiramide (DB00430), Cefoperazone (DB01329) and Carindacillin (DB09319) will be the good repurposed-drugs for the treatment of Salmonellosis.Communicated by Ramaswamy H. Sarma.

Comparative genomic analysis of Rickettsia rickettsii for identification of drug and vaccine targets: tolC as a proposed candidate for case study

BACKGROUND

Antibiotic resistance is increasing rapidly in pathogenic organisms, creating more complications for treatment of diseases. Rocky Mountain spotted fever (RMSF) is a neglected tropical disease in humans caused by Rickettsia rickettsii for which no effective therapeutic is available. Subtractive genomics methods facilitate the characterization of non-homologous essential proteins that could be targeted for the discovery of potential therapeutic compounds against R. rickettsii to combat RMSF. Present study followed an in-silico based methodology, involving scanning and filtering the complete proteome of Rickettsia rickettsii by using several prioritization parameters in the search of potential candidates for drug development. Further the putative targets were subjected to series of molecular dockings with ligands obtained from PDB ligand database to identify suitable potential inhibitors. The comparative genomic analysis revealed 606 non-homologous proteins and 233 essential non-homologous proteins of R. rickettsii. The metabolic pathway analysis predicted 120 proteins as putative drug targets, out of which 56 proteins were found to be associated with metabolic pathways unique to the bacteria and further subcellular localization analysis revealed that 9 proteins as potential drug targets which are secretion proteins, involved in peptidoglycan biosynthesis, folate biosynthesis and bacterial secretion system. As secretion proteins are more feasible as vaccine candidates, we have selected a most potential target i.e. tolC, an outer membrane efflux protein that belongs to type I secretion system and has major role in pathogen survival as well as MDR persistence. So for case study, we have modelled the three dimensional structure of tolC (tunnel protein). The model was further subjected to virtual screening and in-silico docking. The study identified three potential inhibitors having PDB Id 19V, 6Q8 and 39H. Further we have suggested that the above study would be most important while considering the selection of candidate targets and drug or vaccine designing against R. rickettsii.

Analysis of the contribution of bacteriophage ST64B to in vitro virulence traits of Salmonella enterica serovar Typhimurium

Comparison of the publicly available genomes of the virulent Salmonella enterica serovar Typhimurium (S. Typhimurium) strains SL1344, 14028s and D23580 to that of the virulence-attenuated isolate LT2 revealed the absence of a full sequence of bacteriophage ST64B in the latter. Four selected ST64B regions of unknown function (sb7-sb11, sb46, sb49-sb50 and sb54) were mapped by PCR in two strain collections: (i) 310 isolates of S. Typhimurium from human blood or stool samples, and from food, animal and environmental reservoirs; and (ii) 90 isolates belonging to other serovars. The region sb49-sb50 was found to be unique to S. Typhimurium and was strongly associated with strains isolated from blood samples (100  and 28.4 % of the blood and non-blood isolates, respectively). The region was cloned into LT2 and knocked out in SL1344, and these strains were compared to wild-type isogenic strains in in vitro assays used to predict virulence association. No difference in invasion of the Int407 human cell line was observed between the wild-type and mutated strains, but the isolate carrying the whole ST64B prophage was found to have a slightly better survival in blood. The study showed a high prevalence and a strong association between the prophage ST64B and isolates of S. Typhimurium collected from blood, and may indicate that such strains constitute a selected subpopulation within this serovar. Further studies are indicated to determine whether the slight increase in blood survival observed in the strain carrying ST64B genes is of paramount importance for systemic infections.

In silico prediction of drug targets in phytopathogenic Pseudomonas syringae pv. phaseolicola: charting a course for agrigenomics translation research

Pseudomonas syringae pv. phaseolicola is a major plant pathogen causing halo blight disease and has world-wide importance. The emerging post-genomics field of agrigenomics, together with the availability of whole genome sequences of a number of pathogens and host organisms, offer the promise for identification of potential drug targets using sequence comparison approaches. On the other hand, lack of gene expression data for most of the phytopathogenic microbes still remains a formidable barrier. The present study aimed at the prediction of drug targets in Pseudomonas syringae pv. phaseolicola by exploiting the knowledge of Codon Usage bias for gene expression subtractively, supported by gene expression analysis and sequence comparisons. Based on screening of the Database of Essential Genes using blastx, 158 of the total 5172 genes of P. syringae pv. phaseolicola were enlisted as vitally essential genes. Similarity search for these 158 essential genes against available host-plant sequences (Phaseolous vulgaris) led to the identification of homologues of 21 genes in the host genome, thus leaving behind a subset of 137 genes. Expression analysis of these 137 genes using RSCU(gene,) validated by microarray gene expression data suggested 22 genes had higher expression levels in the cell, and therefore their products have been identified as putative drug targets. The gene ontology analysis of these 22 genes revealed their indispensable roles in pivotal metabolic pathways of P. syringae pv. phaseolicola. Upon comparison of the sequences of these genes with other soil bacteria, we identified two genes that were unique to P. syringae pv. phaseolicola. The products of these genes can potentially be utilized for drug development so as to control the halo blight disease and thereby accelerate translation research in the nascent field of agrigenomics.