Chronic inhibition of phosphodiesterase 5 with tadalafil affords cardioprotection in a mouse model of metabolic syndrome: role of nitric oxide

Molecular and Cellular Biochemistry - Patients with metabolic syndrome (MetS) often exhibit generalized endothelial and cardiac dysfunction with decreased nitric oxide (NO) production and/or...     

Molecular mechanism of transdermal co-delivery of interferon-alpha protein with gold nanoparticle – a molecular dynamics study

The transdermal route provides numerous advantages over conventional drug delivery routes. However, passive delivery of large molecules such as proteins through the skin is challenging due to its barrier function. Therefore, to design a successful formulation, molecular interaction of these proteins with constituent molecules present in the skin responsible for its barrier function, is necessary. In this study, we have shown through extensive computer simulations that the therapeutic protein, interferon alpha (INF), can be co-delivered through the skin using the gold nanoparticle. We carried out both steered (umbrella sampling) and unrestrained coarse-grained molecular dynamics simulation to show the molecular mechanism of absorption/permeation of protein on/through skin layer in the absence/presence of gold nanoparticle. According to the steered simulations, when INF was taken alone, the free energy minimum was observed at the head group of the skin layer, whereas, when co-delivered with AuNP, it was observed in the interior of the bilayer. Unrestrained simulations have also shown that INF was adsorbed on the skin lipid bilayer head group, while in presence of AuNP, it first complexed with the AuNP and then breached the barrier. The MD simulations thus established the transdermal delivery as a possible pathway for delivery of INF protein.     

Mechanistic study of HCV polymerase inhibitors at individual steps of the polymerization reaction

Little is known about the mechanism of HCV polymerase-catalyzed nucleotide incorporation and the individual steps employed by this enzyme during a catalytic cycle. In this paper, we applied various biochemical tools and examined the mechanism of polymerase catalysis. We found that formation of a productive RNA-enzyme complex is the slowest step followed by RNA dissociation and initiation of primer strand synthesis. Various groups have reported several classes of small molecule inhibitors of hepatitis C virus NS5B polymerase; however, the mechanism of inhibition for many of these inhibitors is not clear. We undertook a series of detailed mechanistic studies to characterize the mechanisms of inhibition for these HCV polymerase inhibitors. We found that the diketoacid derivatives competitively bind to the elongation NTP pocket in the active site and inhibit both the initiation and elongation steps of polymerization. While both benzimidazoles and benzothiadiazines are noncompetitive with respect to the active site elongation NTP pocket, benzothiadiazine compounds competitively bind to the initiation pocket in the active site and inhibit only the initiation step of de novo RNA polymerization. The benzimidazoles bind to the thumb allosteric pocket and inhibit the conformational changes during RNA synthesis. We also observed a cross interaction between the thumb allosteric pocket and the initiation pocket using inhibitor-inhibitor cross competition studies. This information will be very important in designing combination therapies using two small molecule drugs to treat hepatitis C virus.     

Complex genetic origin of Indian populations and its implications

Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000?years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India.     

Properties of compatible solutes in aqueous solution

We have performed Molecular Dynamics simulations of ectoine, hydroxyectoine and urea in explicit solvent. Special attention has been spent on the local surrounding structure of water molecules. Our results indicate that ectoine and hydroxyectoine are able to accumulate more water molecules than urea by a pronounced ordering due to hydrogen bonds. We have validated that the charging of the molecules is of main importance resulting in a well defined hydration sphere. The influence of a varying salt concentration is also investigated. Finally we present experimental results of a DPPC monolayer phase transition that validate our numerical findings.     

Methane emission potential and increased efficiency of a phytoremediation system bioaugmented with Bacillus firmus XJSL 1-10

Horizontal subsurface flow constructed wetland mesocosms (HSSCW) designed to treat municipal waste water were bioaugmented with Bacillus firmus XJSL 1-10. The efficiencies of the three HSSCW mesocosms (non-vegetated HSSCW, Schoenoplectus validus HSSCW and Bambusa vulgaris HSSCW) were assessed. Bioaugmentation not only enhanced the efficiency of the phytoremediation system but also reduced methane emission from an average of 51.3 mg/m2/d to 21.6 mg/m2/d in Schoenoplectus validus HSSCW and from an average of 1708 mg/m2/d to 1473 mg/m2/d in Bambusa vulgaris HSSCW. Each of the three types of bioaugmented HSSCWs showed higher purification efficiency with respect to the removal of BOD and NH4-N than the non-bioaugmented HSSCWs. The performance enhancement was most significant in bioaugmented Schoenoplectus validus HSSCW mesocosm with 48.8 and 44.8% lower BOD, and NH4-N, respectively than the non-bioaugmented HSSCW.     

YspC: A Unique Translocator Exhibits Structural Alteration in the Complex form with Chaperone SycB

YspC is an annotated translocator of Yersinia secretion apparatus-Yersinia secretion protein type three secretion system of Yersinia enterocolitica, it forms an 1:1 complex with its cognate chaperone SycB. Unlike other translocators, YspC is highly soluble inspite of having a transmembrane region. Size exclusion chromatography shows that YspC exists predominantly in a monomeric form. Multiple sequence alignment and ConSurf (a web based bioinformatic tool) analysis confirm its significant deviation from the closest class of minor translocators. YspC also possesses a tertiary structure signal seen from near UV CD, further confirming its unique nature amongst the groups of translocators. Far UV CD depicts that YspC is predominantly an ??-helical protein; however, its secondary structure alters in the YspC-SycB complex. Thermal denaturation curve predicts a cooperative melting behaviour for YspC which is altered in the YspC-SycB complex. Furthermore, trypsinolysis data confirms a different digestion pattern for YspC in isolation, when compared to the complex form with SycB. From the Forsters resonance energy transfer analysis, it can be predicted that the two tetratricopeptide repeat regions of SycB are masked while it forms a complex with YspC and this is further confirmed by the interaction studies of YspC with two truncated forms of SycB. YspC interacted with ?SycB_(1?C114) and ?SycB_(36?C114) (possessing only the two TPR regions). However, the complexes formed between YspC and truncated forms of SycB have altered physiological states.     

Taxonomic studies on genus Tetramorium Mayr (Hymenoptera, Formicidae) with report of two new species and three new records including a tramp species from India with a revised key

Two new species of Tetramorium Mayr, namely Tetramorium shivalikensesp. n. and Tetramorium triangulatumsp. n. are described. Tetramorium triangulatumsp. n. belongs to the inglebyi-species group and is described based on worker, queen and male caste, while Tetramorium shivalikensesp. n. belongs to the ciliatum-species group and is described based on worker caste only. Three species viz., Tetramorium caldarium (Roger), Tetramorium tonganum Mayr and Tetramorium urbanii Bolton represent first records from India. The male caste is described for the first time in the case of Tetramorium tonganum. Among these, Tetramorium caldarium is a tramp species which extends its limit to India as well. A revised key to the Indian ants of this genus is also provided herewith.     

Efficacy of a non-hypercalcemic vitamin-D2 derived anti-cancer agent (MT19c) and inhibition of fatty acid synthesis in an ovarian cancer xenograft model

Background

Numerous vitamin-D analogs exhibited poor response rates, high systemic toxicities and hypercalcemia in human trials to treat cancer. We identified the first non-hypercalcemic anti-cancer vitamin D analog MT19c by altering the A-ring of ergocalciferol. This study describes the therapeutic efficacy and mechanism of action of MT19c in both in vitro and in vivo models.

Methodology/Principal Finding

Antitumor efficacy of MT19c was evaluated in ovarian cancer cell (SKOV-3) xenografts in nude mice and a syngenic rat ovarian cancer model. Serum calcium levels of MT19c or calcitriol treated animals were measured. In-silico molecular docking simulation and a cell based VDR reporter assay revealed MT19c–VDR interaction. Genomewide mRNA analysis of MT19c treated tumors identified drug targets which were verified by immunoblotting and microscopy. Quantification of cellular malonyl CoA was carried out by HPLC-MS. A binding study with PPAR-Y receptor was performed. MT19c reduced ovarian cancer growth in xenograft and syngeneic animal models without causing hypercalcemia or acute toxicity. MT19c is a weak vitamin-D receptor (VDR) antagonist that disrupted the interaction between VDR and coactivator SRC2-3. Genome-wide mRNA analysis and western blot and microscopy of MT19c treated xenograft tumors showed inhibition of fatty acid synthase (FASN) activity. MT19c reduced cellular levels of malonyl CoA in SKOV-3 cells and inhibited EGFR/phosphoinositol-3kinase (PI-3K) activity independently of PPAR-gamma protein.

Significance

Antitumor effects of non-hypercalcemic agent MT19c provide a new approach to the design of vitamin-D based anticancer molecules and a rationale for developing MT19c as a therapeutic agent for malignant ovarian tumors by targeting oncogenic de novo lipogenesis.