Subtractive sequence analysis aided druggable targets mining in Burkholderia cepacia complex and finding inhibitors through bioinformatics approach

Burkholderia cepacia complex (BCC) is a group of gram-negative bacteria composed of at least 20 different species that cause diseases in plants, animals as well as humans (cystic fibrosis and airway infection). Here, we analyzed the proteomic data of 47 BCC strains by classifying them in three groups. Phylogenetic analyses were performed followed by individual core region identification for each group. Comparative analysis of the three individual core protein fractions resulted in 1766 ortholog/proteins. Non-human homologous proteins from the core region gave 1680 proteins. Essential protein analyses reduced the target list to 37 proteins, which were further compared to a closely related out-group, Burkholderia gladioli ATCC 10,248 strain, resulting in 21 proteins. 3D structure modeling, validation, and druggability step gave six targets that were subjected to further target prioritization parameters which ultimately resulted in two BCC targets. A library of 12,000 ZINC drug-like compounds was screened, where only the top hits were selected for docking orientations. These included ZINC01405842 (against Chorismate synthase aroC) and ZINC06055530 (against Bifunctional N-acetylglucosamine-1-phosphate uridyltransferase/Glucosamine-1-phosphate acetyltransferase glmU). Finally, dynamics simulation (200 ns) was performed for each ligand-receptor complex, followed by ADMET profiling. Of these targets, details of their applicability as drug targets have not yet been elucidated experimentally, hence making our predictions novel and it is suggested that further wet-lab experimentations should be conducted to test the identified BCC targets and ZINC scaffolds to inhibit them.

The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets

Diphtheria is an acute and highly infectious disease, previously regarded as endemic in nature but vaccine-preventable, is caused by Corynebacterium diphtheriae (Cd). In this work, we used an in silico approach along the 13 complete genome sequences of C. diphtheriae followed by a computational assessment of structural information of the binding sites to characterize the “pocketome druggability.” To this end, we first computed the “modelome” (3D structures of a complete genome) of a randomly selected reference strain Cd NCTC13129; that had 13,763 open reading frames (ORFs) and resulted in 1,253 (∼9%) structure models. The amino acid sequences of these modeled structures were compared with the remaining 12 genomes and consequently, 438 conserved protein sequences were obtained. The RCSB-PDB database was consulted to check the template structures for these conserved proteins and as a result, 401 adequate 3D models were obtained. We subsequently predicted the protein pockets for the obtained set of models and kept only the conserved pockets that had highly druggable (HD) values (137 across all strains). Later, an off-target host homology analyses was performed considering the human proteome using NCBI database. Furthermore, the gene essentiality analysis was carried out that gave a final set of 10-conserved targets possessing highly druggable protein pockets. To check the target identification robustness of the pipeline used in this work, we crosschecked the final target list with another in-house target identification approach for C. diphtheriae thereby obtaining three common targets, these were; hisE-phosphoribosyl-ATP pyrophosphatase, glpX-fructose 1,6-bisphosphatase II, and rpsH-30S ribosomal protein S8. Our predicted results suggest that the in silico approach used could potentially aid in experimental polypharmacological target determination in C. diphtheriae and other pathogens, thereby, might complement the existing and new drug-discovery pipelines.

Comparison between topical honey and mafenide acetate in treatment of burn wounds

Histological and clinical studies of wound healing were performed in comparable cases of fresh partial-thickness burns treated with honey dressing or mafenide acetate in two groups of 50 randomly allocated patients. Of the patients with honey-treated wounds, 84% showed satisfactory epithelialization by day 7 and 100% by day 21. In wounds treated with mafenide acetate, epithelialization occurred by day 7 in 72% of cases and in 84% by day 21. Histological evidence of reparative activity was observed in 80% of wounds treated with honey dressing by day 7 with minimal inflammation. Fifty-two per cent of the mafenide acetate treated wounds showed reparative activity with inflammatory changes by day 7. Reparative activity reached 100% by day 21 with the honey dressing and 84% with mafenide acetate. Thus, in honey-dressed wounds, early subsidence of acute inflammatory changes, better control of infection, and quicker wound healing were observed, while in mafenide acetate treated wounds a sustained inflammatory reaction was noted even on epithelialization.

Prevalence of hepatitis E virus (HEV) antibody in pregnant women of Karachi

BACKGROUND

This study was aimed at determining the prevalence of HEV in Karachi.

METHODS

Prevalence of hepatitis E antibody in pregnant women was carried out in 65 pregnant women. They had history of acute viral hepatitis while 15 control pregnant women were included having no history of jaundice.

RESULTS

The statistical outcome of the present study indicates prevalence of HEV as 57% in pregnant women with jaundice. Majority of the patients (85%) were from lower socio-economic strata., with mean age of 25 years. All these patients had hemoglobin less than 10 gm%. The mean ALT level in HEV positive cases was 452 IU/L over a range of 102-5328. It was also observed that HEV affected more women in the last trimester (62%) and in primigravida (67%). It was observed that it was more common in last trimester and in primigravida. Majority of the patients (85%) were from lower socio-economic strata.

CONCLUSIONS

The findings of the present study proved the presence of HEV in pregnant women and confirmed that HEV is endemic in Karachi. The study confirms that it occurs in last trimester and in young adult.

Dynamic measurement of the torque-speed characteristics of dental high speed air turbine handpieces

The first requirement for adequate performance of an air turbine handpiece is sufficient power. Suppliers of such handpieces do not provide data on the power produced by their equipment. A method for determining the torque, speed and hence power during simulated operation is described. Forty-one new and used handpieces were tested. Maximum speeds up to 500,000 rpm, maximum torques up to 2.33 N.mm and maximum power up to 29.6 watt were observed. The maximum power was produced at between 49 and 79 per cent of the free-running speed. A relationship between maximum power and stall torque was noted. The maximum torque is at stall for ball-bearing units. The stall torque can be easily determined by a simple stall torque test which is described. Using this test, the performance of handpieces can be easily checked in the clinic. The one air-bearing handpiece tested performed in a manner similar to the others, except that stall occurred below 60,000 rpm.