scholarly journals Prediction and Analysis of the Protein Interactome in Pseudomonas aeruginosa to Enable Network-Based Drug Target Selection

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e41202 ◽  
Author(s):  
Minlu Zhang ◽  
Shengchang Su ◽  
Raj K. Bhatnagar ◽  
Daniel J. Hassett ◽  
Long J. Lu
2018 ◽  
Author(s):  
Kalyani B. Karunakaran ◽  
Srilakshmi Chaparala ◽  
Madhavi K. Ganapathiraju

AbstractFrom the schizophrenia drug-target interactome,1we studied the drugs that targeted multiple proteins in the interactome, or those that target proteins with many targets, or those that target novel (computationally predicted) interactors of schizophrenia associated proteins. In schizophrenia, gene expression has been described as a measurable aspect of the disease reflecting the action of risk genes. We studied each of the selected drugs using the NextBio software suite, and shortlisted those that had a negative correlation with gene expression of schizophrenia. This analysis resulted in 12 drugs whose differential gene expression (drug versus normal) had an anti-correlation with differential expression for schizophrenia (disorder versus normal). Some of these drugs were already being tested for their clinical activity in schizophrenia and other neuropsychiatric disorders. Several proteins in the protein interactome of the targets of several of these drugs were associated with various neuropsychiatric disorders. The network of genes which were differentially expressed on drug treatment, and had an anti-correlation with gene expression in schizophrenia, were significantly enriched in pathways relevant to schizophrenia etiology and GWAS genes associated with traits or diseases that had pathophysiological overlap with schizophrenia. Drugs that are structurally similar to the shortlisted drugs, or targeted the same genes as these drugs, have also demonstrated clinical activity in schizophrenia and other related disorders. This integrated computational analysis may help translate insights from the schizophrenia drug-protein interactome to clinical research - an important step, especially in the field of psychiatric drug development, facing a high failure rate.


Author(s):  
Paul McVeigh ◽  
Louise Atkinson ◽  
Nikki J. Marks ◽  
Angela Mousley ◽  
Johnathan J. Dalzell ◽  
...  

PLoS ONE ◽  
2012 ◽  
Vol 7 (4) ◽  
pp. e35973 ◽  
Author(s):  
Thomas C. Eadsforth ◽  
Mary Gardiner ◽  
Fernando V. Maluf ◽  
Stuart McElroy ◽  
Daniel James ◽  
...  

2020 ◽  
Vol 295 (29) ◽  
pp. 10081-10091
Author(s):  
Hyung Jun Kim ◽  
Hyunjung Lee ◽  
Yunmi Lee ◽  
Inhee Choi ◽  
Yoonae Ko ◽  
...  

Thiamine pyrophosphate (TPP) is an essential cofactor for various pivotal cellular processes in all living organisms, including bacteria. Thiamine biosynthesis occurs in bacteria but not in humans; therefore, the enzymes in this pathway are attractive targets for antibiotic development. Among these enzymes, thiamine monophosphate kinase (ThiL) catalyzes the final step of this pathway, phosphorylating thiamine monophosphate to produce TPP. Here, we extensively investigated ThiL in Pseudomonas aeruginosa, a major pathogen responsible for hospital-acquired infections. We demonstrate that thiL deletion abolishes not only thiamine biosynthesis but also thiamine salvage capability and results in growth defects of the ΔthiL strain even in the presence of thiamine derivatives, except for TPP. Most importantly, the pathogenesis of the ΔthiL strain was markedly attenuated, compared with that of WT cells, with lower inflammatory cytokine induction and 103–104-fold decreased bacterial loads in an in vivo infection model in which the intracellular TPP level was in the submicromolar range. To validate P. aeruginosa ThiL (PaThiL) as a drug target, we further characterized its biochemical properties, determining a Vmax of 4.0 ± 0.2 nmol·min−1 and Km values of 111 ± 8 and 8.0 ± 3.5 μm for ATP and thiamine monophosphate, respectively. An in vitro small-molecule screening assay identified PaThiL inhibitors including WAY213613, a noncompetitive inhibitor with a Ki value of 13.4 ± 2.3 μm and potential antibacterial activity against P. aeruginosa. These comprehensive biological and biochemical results indicate that PaThiL represents a potential drug target for the development of an augmented repertoire of antibiotics against P. aeruginosa.


2016 ◽  
Author(s):  
Chris Finan ◽  
Anna Gaulton ◽  
Felix Kruger ◽  
Tom Lumbers ◽  
Tina Shah ◽  
...  

Target identification (identifying the correct drug targets for each disease) and target validation (demonstrating the effect of target perturbation on disease biomarkers and disease end-points) are essential steps in drug development. We showed previously that biomarker and disease endpoint associations of single nucleotide polymorphisms (SNPs) in a gene encoding a drug target accurately depict the effect of modifying the same target with a pharmacological agent; others have shown that genomic support for a target is associated with a higher rate of drug development success. To delineate drug development (including repurposing) opportunities arising from this paradigm, we connected complex disease- and biomarker-associated loci from genome wide association studies (GWAS) to an updated set of genes encoding druggable human proteins, to compounds with bioactivity against these targets and, where these were licensed drugs, to clinical indications. We used this set of genes to inform the design of a new genotyping array, to enable druggable genome-wide association studies for drug target selection and validation in human disease.


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