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Hosen M.J.,Ghent University | Hosen M.J.,Shahjalal University of Science and Technology | Zubaer A.,Swapnojaatra Bioresearch Laboratory | Thapa S.,Swapnojaatra Bioresearch Laboratory | And 3 more authors.
PLoS ONE | Year: 2014

The human ATP-binding cassette family C member 6 (ABCC6) gene encodes an ABC transporter protein (ABCC6), primarily expressed in liver and kidney. Mutations in the ABCC6 gene cause pseudoxanthoma elasticum (PXE), an autosomal recessive connective tissue disease characterized by ectopic mineralization of the elastic fibers. The pathophysiology underlying PXE is incompletely understood, which can at least partly be explained by the undetermined nature of the ABCC6 substrates as well as the unknown substrate recognition and binding sites. Several compounds, including anionic glutathione conjugates (N-ethylmaleimide; NEM-GS) and leukotriene C4 (LTC4) were shown to be modestly transported in vitro; conversely, vitamin K3 (VK3) was demonstrated not to be transported by ABCC6. To predict the possible substrate binding pockets of the ABCC6 transporter, we generated a 3D homology model of ABCC6 in both open and closed conformation, qualified for molecular docking and virtual screening approaches. By docking 10 reported in vitro substrates in our ABCC6 3D homology models, we were able to predict the substrate binding residues of ABCC6. Further, virtual screening of 4651 metabolites from the Human Serum Metabolome Database against our open conformation model disclosed possible substrates for ABCC6, which are mostly lipid and biliary secretion compounds, some of which are found to be involved in mineralization. Docking of these possible substrates in the closed conformation model also showed high affinity. Virtual screening expands this possibility to explore more compounds that can interact with ABCC6, and may aid in understanding the mechanisms leading to PXE. © 2014 Hosen et al.

Mondal S.I.,Shahjalal University of Science and Technology | Mondal S.I.,University of Miyazaki | Khadka B.,Shahjalal University of Science and Technology | Khadka B.,Swapnojaatra Bioresearch Laboratory | And 3 more authors.
Interdisciplinary Sciences: Computational Life Sciences | Year: 2014

Cholera is a severe diarrheal disease caused by Vibrio cholerae and remains as a major health risk in developing countries. The emergence and spread of multi-drug resistant V. cholerae strains during the past two decades is now a major problem in the treatment of cholera and have created the urgent need for the development of novel therapeutic agents. Targeting transcriptional factor is now a novel approach to tackle the development of multi-drug resistant strain. In the recent year virtual high throughput screening has emerged as a widely accepted powerful technology in the identification of novel and diverse lead. This study provides new insight to the search for new potent and selective inhibitors that still remains necessary to avoid the risk of possible resistance and reduce toxicity and side effects of currently available cholera drugs. The publications of high resolution X-ray structure of V. cholerae ToxT has open the way to the structure based virtual screening to identify new small molecular inhibitors which still remain necessary to avoid the risk of possible resistance and reduce toxicity and side effects of currently available cholera drugs. In this study we have performed structure based virtual screening approach using NCI diversity set-II to look for novel inhibitor of ToxT and proposed eight candidate compounds with high scoring function. Thus from complex scoring and binding ability it is elucidated that these compounds could be the promising inhibitors or could be developed as novel lead compounds for drug design against cholera. © 2014 International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg.

Thapa S.,Shahjalal University of Science and Technology | Thapa S.,Swapnojaatra Bioresearch Laboratory | Alum M.A.,Shahjalal University of Science and Technology | Saha C.,Shahjalal University of Science and Technology | And 4 more authors.
Indian Journal of Biotechnology | Year: 2013

Streptococcus pneumoniae is the causative agent of Pneumonia resulting in a substantial portion of childhood deaths in Bangladesh. Though drugs are in sufficient availability but the emergence of multi-drug resistant varieties of S. pneumoniae has led to the search for novel drug targets. The metabolic pathways of host (Homo sapiens) and pathogen (S. pneumoniae serotype-2) were compared where six biochemical pathways of S. pneumonia, distinct from human pathways, were identified. These comprised of 20 unique enzymes, which being non-homologous proteins in contrast to human host proteins, can be considered as probable drug targets. Among them, the 3D structure of an uncharacterized protein molecule was built in by homology modeling and the binding pockets of protein molecule responsible for specific functions were identified. These structural and functional characterizations of the protein, unique in S. pneumoniae in host condition, made the possibility for the sophisticated rational drug design.

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