The accuracy of protein structure alignment servers

Background: Protein structural alignment is one of the most fundamental and crucial areas of research in the domain of computational structural biology. Comparison of a protein structure with known structures helps to classify it as a new or belonging to a known group of proteins. This, in turn, is useful to determine the function of protein, its evolutionary relationship with other protein molecules and grasping principles underlying protein architecture and folding. Results: A large number of protein structure alignment methods are available. Each protein structure alignment tool has its own strengths andweaknesses that need to be highlighted.We compared and presented results of six most popular and publically available servers for protein structure comparison. These web-based servers were compared with the respect to functionality (features provided by these servers) and accuracy (how well the structural comparison is performed). The CATH was used as a reference. The results showed that overall CE was top performer. DALI and PhyreStorm showed similar results whereas PDBeFold showed the lowest performance. In case of few secondary structural elements, CE, DALI and PhyreStorm gave 100% success rate. Conclusion: Overall none of the structural alignment servers showed 100% success rate. Studies of overall performance, effect of mainly alpha and effect of mainly beta showed consistent performance. CE, DALI, FatCat and PhyreStorm showed more than 90% success rate.

Bioadhesive drug delivery system of diltiazem hydrochloride for improved bioavailability in cardiac therapy

Purpose: To prepare and evaluate bioadhesive buccal films of diltiazem hydrochloride (a L-type calcium channel blocker) for overcoming the limitations of frequent dosing, low bioavailability and gastrointestinal discomfort of oral delivery. Methods: Buccal films were prepared by solvent casting technique using sodium carboxymethylcellulose, polyvinyl pyrrolidone K-30 and polyvinyl alcohol. The films were evaluated for weight, thickness, surface pH, swelling index, in vitro residence time, folding endurance, in vitro release, ex-vivo permeation (across porcine buccal mucosa) and drug content uniformity. Results: The drug content of the formulations was uniform with a range of 18.94 ± 0.066 (F2) to 20.08 ± 0.07 mg per unit film (F1). The films exhibited controlled release ranging from 58.76 ± 1.62 to 91.45 ± 1.02 % over a period > 6 h. The films containing 20 mg diltiazem hydrochloride, polyvinyl alcohol (10 %) and polyvinyl pyrrolidone (1 % w/v) i.e. formulation F5, showed moderate swelling, convenient residence time and promising drug release, and thus can be selected for further development of a buccal film for potential therapeutic uses. Conclusion: The developed formulation is a potential bioadhesive buccal system for delivering diltiazem directly to systemic circulation, circumventing first-pass metabolism, avoiding gastric discomfort and improving bioavailability at a minimal dose.

Mitigating effects of Jambul against lead induced toxicity in epididymis and vas deferens of mice

Background: Precious fruits like jambul are neglected and wasted while environmental pollutants like lead intake remain overlooked. Objective: The aim of this study was to investigate the effects of the Jambul pulp extract on lead detrimental effects in pseudostratified epithelium and the stereocilia of mice epididymis and vas deferens. Materials and Methods: Thirty young males mice (Mus musculus) were distributed randomly in 3 groups (n= 10) called control, Pb (Lead) and Pb-J (Lead-Jambul). The Pb and Pb-J were provided 50ppm Pb in drinking water ad libitum for 15 days and Pb free water for the next 5 days. The Pb-J group received 0.2ml jambul pulp extract on 12 hourly bases. Control group was not given any treatment. Organs (epididymis and vas deference) were recovered on 21st day after euthanasia. The organs were finally processed for histological and micrometric studies. Results: Marked histologic and micrometric changes in both organs were noted in Pb group. These include significant (P ≤ 0.05) decrease in cross sectional area of caput and cauda epididymis folding tubing along with evident alterations of their endothelial thickness. Prominent signs of apoptosis (vacuolations) in the corpus pseudostratified endothelium and the destruction of stereocilia of the epididymis and vas deferens in Pb compared to control group were observed. Evident signs of recovery, in both organs, such as proliferation and rearrangements in pseudostratified endothelium and the stereocilia along with convincing recovery in micrometric parameters were observed in Pb-J group. Conclusion: The results indicate that epididymis and vas deferens are highly sensitive to Pb exposure while Jambul pulp extract has shown rich mitigating potentials against such histopathologies.