Crowd Sourcing a New Paradigm for Interactome Driven Drug Target Identification in Mycobacterium tuberculosis

A decade since the availability of Mycobacterium tuberculosis (Mtb) genome sequence, no promising drug has seen the light of the day. This not only indicates the challenges in discovering new drugs but also suggests a gap in our current understanding of Mtb biology. We attempt to bridge this gap by carrying out extensive re-annotation and constructing a systems level protein interaction map of Mtb with an objective of finding novel drug target candidates. Towards this, we synergized crowd sourcing and social networking methods through an initiative `Connect to Decode' (C2D) to generate the first and largest manually curated interactome of Mtb termed `3interactome pathway' (IPW), encompassing a total of 1434 proteins connected through 2575 functional relationships. Interactions leading to gene regulation, signal transduction, metabolism, structural complex formation have been catalogued. In the process, we have functionally annotated 87% of the Mtb genome in context of gene products. We further combine IPW with STRING based network to report central proteins, which may be assessed as potential drug targets for development of drugs with least possible side effects. The fact that five of the 17 predicted drug targets are already experimentally validated either genetically or biochemically lends credence to our unique approach.

Designing carboxymethyl cellulose based layer-by-layer capsules as a carrier for protein delivery

Stable hollow microcapsules composed of sodium carboxymethyl cellulose (CMC) and poly (allylamine hydrochloride) (PAH) were produced by layer-by-layer adsorption of polyelectrolytes onto CaCO 3 microparticles. Subsequently the core was removed by addition of chelating agents for calcium ions. Zeta potential studies showed charge reversal with deposition of successive polyelectrolyte layers, indicating that the alternate electrostatic adsorption of polyelectrolytes of opposite charge was successfully achieved. The size and surface morphology of the capsules was characterized by various microscopy techniques. The pH responsive loading behavior was elucidated by confocal laser scanning microscopy (CLSM) studies using fluorescence labeled dextran (FITC-dextran) and labeled BSA (FITC-BSA). CLSM images confirmed the open (pH ≤ 6) and closed state (pH ≥ 7) of the capsules. A model drug bovine serum albumin (BSA) was spontaneously loaded below its isoelectric point into hollow microcapsules, where BSA is positively charged. The loading of the BSA into the microcapsules was found to be dependent on the feeding concentration and pH of the medium. 65 of the loaded BSA was released over 7h of which about 34 was released in the first hour. These findings demonstrate that (CMC/PAH) 2 hollow capsules can be further exploited as a potential drug delivery system.

An Antitubulin Agent BCFMT Inhibits Proliferation of Cancer Cells and Induces Cell Death by Inhibiting Microtubule Dynamics

Using cell based screening assay, we identified a novel anti-tubulin agent (Z)-5-((5-(4-bromo-3-chlorophenyl)furan-2-yl)methylene)-2-thioxothiazoli din-4-one (BCFMT) that inhibited proliferation of human cervical carcinoma (HeLa) (IC50, 7.2 +/- 1.8 mu M), human breast adenocarcinoma (MCF-7) (IC50, 10.0 +/- 0.5 mu M), highly metastatic breast adenocarcinoma (MDA-MB-231) (IC50, 6.0 +/- 1 mu M), cisplatin-resistant human ovarian carcinoma (A2780-cis) (IC50, 5.8 +/- 0.3 mu M) and multi-drug resistant mouse mammary tumor (EMT6/AR1) (IC50, 6.5 +/- 1 mu M) cells. Using several complimentary strategies, BCFMT was found to inhibit cancer cell proliferation at G2/M phase of the cell cycle apparently by targeting microtubules. In addition, BCFMT strongly suppressed the dynamics of individual microtubules in live MCF-7 cells. At its half maximal proliferation inhibitory concentration (10 mu M), BCFMT reduced the rates of growing and shortening phases of microtubules in MCF-7 cells by 37 and 40%, respectively. Further, it increased the time microtubules spent in the pause (neither growing nor shortening detectably) state by 135% and reduced the dynamicity (dimer exchange per unit time) of microtubules by 70%. In vitro, BCFMT bound to tubulin with a dissociation constant of 8.3 +/- 1.8 mu M, inhibited tubulin assembly and suppressed GTPase activity of microtubules. BCFMT competitively inhibited the binding of BODIPY FL-vinblastine to tubulin with an inhibitory concentration (K-i) of 5.2 +/- 1.5 mu M suggesting that it binds to tubulin at the vinblastine site. In cultured cells, BCFMT-treatment depolymerized interphase microtubules, perturbed the spindle organization and accumulated checkpoint proteins (BubR1 and Mad2) at the kinetochores. BCFMT-treated MCF-7 cells showed enhanced nuclear accumulation of p53 and its downstream p21, which consequently activated apoptosis in these cells. The results suggested that BCFMT inhibits proliferation of several types of cancer cells including drug resistance cells by suppressing microtubule dynamics and indicated that the compound may have chemotherapeutic potential.

Effect of carrier concentration of InN on the transport behavior of InN/GaN heterostructure based Schottky junctions

We present the study involving the dependence of carrier concentration of InN films, grown on GaN templates using the plasma assisted molecular beam epitaxy system, on growth temperature. The influence of InN carrier concentration on the electrical transport behavior of InN/GaN heterostructure based Schottky junctions is also discussed. The optical absorption edge of InN film was found to be strongly dependent on carrier concentration, and was described by Kane's k.p model, with non-parabolic dispersion relation for carrier in the conduction band. The position of the Fermi-level in InN films was modulated by the carrier concentration in the InN films. The barrier height of the heterojunctions as estimated from I-V characteristic was also found to be dependent on the carrier concentration of InN. (C) 2012 Elsevier Ltd. All rights reserved.

Effect of doping concentration on the structural and optical properties of pure and tin doped zinc oxide thin films by nebulizer spray pyrolysis (NSP) technique

Pure and tin doped zinc oxide (Sn:ZnO) thin films were prepared for the first time by NSP technique using aqueous solutions of zinc acetate dehydrate, tin (IV) chloride fendahydrate and methanol. X-ray diffraction patterns confirm that the films are polycrystalline in nature exhibiting hexagonal wurtzite type, with (0 0 2) as preferred orientation. The structural parameters such as lattice constant ('a' and `c'), crystallite size, dislocation density, micro strain, stress and texture coefficient were calculated from X-ray diffraction studies. Surface morphology was found to be modified with increasing Sn doping concentration. The ZnO films have high transmittance 85% in the visible region, and the transmittance is found to be decreased with the increase of Sn doping concentration. The corresponding optical band gap decreases from 3.25 to 3.08 eV. Room temperature photoluminescence reveals the sharp emission of strong UV peak at 400 nm (3.10 eV) and a strong sharp green luminescence at 528 nm (2.34 eV) in the Sn doped ZnO films. The electrical resistivity is found to be 10(6) Omega-cm at higher temperature and 10(5) Omega-cm at lower temperature. (C) 2012 Elsevier Ltd. All rights reserved.

Conformational Polymorphism in a Non-steroidal Anti-inflammatory Drug, Mefenamic Acid

For several years, the non-steroidal anti-inflammatory drug mefenamic acid, MA, has been known to exist as dimorphs (I and II). We report a new metastable polymorph (III) of MA obtained during attempted co-crystallization experiments and establish its stability relationship with existing forms. At elevated temperatures I and III convert to II, as evident from DSC experiments. On the basis of the lattice energy calculations in conjunction with thermal analysis, the stability order is proposed to be I > II > III at ambient conditions, whereas at elevated temperature the order is II > I > III. In either condition III is a metastable form and hence transforms to I at ambient conditions and to II at higher temperatures. Also we report the structural studies of a DMF solvate and a cytosine complex.

Silver nanoparticles modified nanocapsules for ultrasonically activated drug delivery

Novel ultrasound-sensitive nanocapsules were designed via layer-by-layer assembly (LbL) of polyelectrolytes for remote activated release of biomolecules/drug. Nanocapsules embedded with silver nanoparticles in the walls were synthesized by alternate assembly of poly(allylamine hydrochloride) (PAH) and dextran sulfate (DS) on silica template followed by nanoparticle synthesis and subsequent template removal thus yielding nanocapsules. The silver NPs were synthesized in situ within the capsule walls under controlled conditions. The nanocapsules were found to be well dispersed and the silver NPs were evenly distributed within the shell. FITC-dextran permeated easily into the capsules containing silver NP's due to the pores generated during the formation of NP's. When the loaded nanocapsules were sonicated, the presence of the silver NPs in the shell structure led to rupturing of the shell into smaller fragments thus releasing the FITC-dextran. Such nanocapsules have the potential to be used as drug delivery vehicles and offer the scope for further development in the areas of modern medicine, material science, and biochemistry. (C) 2012 Elsevier B.V. All rights reserved.

Multi-model climate change projections for India under representative concentration pathways

Climate projections for the Fifth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC) are made using the newly developed representative concentration pathways (RCPs) under the Coupled Model Inter-comparison Project 5 (CMIP5). This article provides multi-model and multi-scenario temperature and precipitation projections for India for the period 1860-2099 based on the new climate data. We find that CMIP5 ensemble mean climate is closer to observed climate than any individual model. The key findings of this study are: (i) under the business-as-usual (between RCP6.0 and RCP8.5) scenario, mean warming in India is likely to be in the range 1.7-2 degrees C by 2030s and 3.3-4.8 degrees C by 2080s relative to pre-industrial times; (ii) all-India precipitation under the business-as-usual scenario is projected to increase from 4% to 5% by 2030s and from 6% to 14% towards the end of the century (2080s) compared to the 1961-1990 baseline; (iii) while precipitation projections are generally less reliable than temperature projections, model agreement in precipitation projections increases from RCP2.6 to RCP8.5, and from short-to long-term projections, indicating that long-term precipitation projections are generally more robust than their short-term counterparts and (iv) there is a consistent positive trend in frequency of extreme precipitation days (e.g. > 40 mm/day) for decades 2060s and beyond. These new climate projections should be used in future assessment of impact of climate change and adaptation planning. There is need to consider not just the mean climate projections, but also the more important extreme projections in impact studies and as well in adaptation planning.

Rationalization and prediction of drug resistant mutations in targets for clinical anti-tubercular drugs

Resistance to therapy limits the effectiveness of drug treatment in many diseases. Drug resistance can be considered as a successful outcome of the bacterial struggle to survive in the hostile environment of a drug-exposed cell. An important mechanism by which bacteria acquire drug resistance is through mutations in the drug target. Drug resistant strains (multi-drug resistant and extensively drug resistant) of Mycobacterium tuberculosis are being identified at alarming rates, increasing the global burden of tuberculosis. An understanding of the nature of mutations in different drug targets and how they achieve resistance is therefore important. An objective of this study is to first decipher sequence as well as structural bases for the observed resistance in known drug resistant mutants and then to predict positions in each target that are more prone to acquiring drug resistant mutations. A curated database containing hundreds of mutations in the 38 drug targets of nine major clinical drugs, associated with resistance is studied here. Mutations have been classified into those that occur in the binding site itself, those that occur in residues interacting with the binding site and those that occur in outer zones. Structural models of the wild type and mutant forms of the target proteins have been analysed to seek explanations for reduction in drug binding. Stability analysis of an entire array of 19 mutations at each of the residues for each target has been computed using structural models. Conservation indices of individual residues, binding sites and whole proteins are computed based on sequence conservation analysis of the target proteins. The analyses lead to insights about which positions in the polypeptide chain have a higher propensity to acquire drug resistant mutations. Thus critical insights can be obtained about the effect of mutations on drug binding, in terms of which amino acid positions and therefore which interactions should not be heavily relied upon, which in turn can be translated into guidelines for modifying the existing drugs as well as for designing new drugs. The methodology can serve as a general framework to study drug resistant mutants in other micro-organisms as well.

Near-infrared light-responsive graphene oxide composite multilayer capsules: a novel route for remote controlled drug delivery

A novel and simple route for near-infrared (NIR)-light controlled release of drugs has been demonstrated using graphene oxide (GO) composite microcapsules based on the unique optical properties of GO. Upon NIR-laser irradiation, the microcapsules were ruptured in a point-wise fashion due to local heating which in turn triggers the light-controlled release of the encapsulated anticancer drug doxorubicin (Dox) from these capsules.

Network approaches to drug discovery

Introduction: Advances in genomics technologies are providing a very large amount of data on genome-wide gene expression profiles, protein molecules and their interactions with other macromolecules and metabolites. Molecular interaction networks provide a useful way to capture this complex data and comprehend it. Networks are beginning to be used in drug discovery, in many steps of the modern discovery pipeline, with large-scale molecular networks being particularly useful for the understanding of the molecular basis of the disease. Areas covered: The authors discuss network approaches used for drug target discovery and lead identification in the drug discovery pipeline. By reconstructing networks of targets, drugs and drug candidates as well as gene expression profiles under normal and disease conditions, the paper illustrates how it is possible to find relationships between different diseases, find biomarkers, explore drug repurposing and study emergence of drug resistance. Furthermore, the authors also look at networks which address particular important aspects such as off-target effects, combination-targets, mechanism of drug action and drug safety. Expert opinion: The network approach represents another paradigm shift in drug discovery science. A network approach provides a fresh perspective of understanding important proteins in the context of their cellular environments, providing a rational basis for deriving useful strategies in drug design. Besides drug target identification and inferring mechanism of action, networks enable us to address new ideas that could prove to be extremely useful for new drug discovery, such as drug repositioning, drug synergy, polypharmacology and personalized medicine.

Effect of iodine concentration on the photovoltaic properties of dye sensitized solar cells for various I-2/LiI ratios

In the present study, the effect of iodine concentration on the photovoltaic properties of dye sensitized solar cells (DSSC) based on TiO2 nanoparticles for three different ratios of lithium iodide (LiI) and iodine (I-2) has been investigated. The electron transport properties and interfacial recombination kinetics have been evaluated by electrochemical impedance spectroscopy (EIS). It is found that increasing the concentration of lithium iodide for all ratios of iodine and lithium iodide decreases the open-circuit voltage (V-oc) whereas short circuit current density (J(sc)) and fill factor (FF) shows improvement. The reduction in V-oc and increment in J(sc) is ascribed to the higher concentration of absorptive Li+ cations which shifts the conduction band edge of TiO2 positively. The increase in FF is due to the reduction in electron transport resistance (R-omega) of the cell. In addition for all the ratios of LiI/I-2 increasing the concentration of I-2 decreases the V-oc which is attributed to the increased recombination with tri-iodide ions (I-3(-)) as verified from the low recombination resistance (R-k) and electron lifetime (tau) values obtained by EIS analysis. (C) 2012 Elsevier Ltd. All rights reserved.

Room temperature synthesis of Mn2+ doped ZnS d-dots and observation of tunable dual emission: Effects of doping concentration, temperature, and ultraviolet light illumination

Mn2+ doped (0-50.0 molar %) ZnS d-dots have been synthesized in water medium by using an environment friendly low cost chemical technique. Tunable dual emission in UV and yellow-orange regions is achieved by tailoring the Mn2+ doping concentration in the host ZnS nanocrystal. The optimum doping concentration for achieving efficient photoluminescence (PL) emission is determined to be similar to 1.10 (at. %) corresponding to 40.0 (molar %) of Mn2+ doping concentration used during synthesis. The mechanism of charge transfer from the host to the dopant leading to the intensity modulated tunable (594-610 nm) yellow-orange PL emission is straightforwardly understood as no capping agent is used. The temperature dependent PL emission measurements are carried out, viz., in 1.10 at. % Mn2+ doped sample and the experimental results are explained by using a theoretical PL emission model. It is found that the ratio of non-radiative to radiative recombination rates is temperature dependent and this phenomenon has not been reported, so far, in Mn2+ doped ZnS system. The colour tuning of the emitted light from the samples are evident from the calculated chromaticity coordinates. UV light irradiation for 150 min in 40.0 (molar %) Mn2+ doped sample shows an enhancement of 33% in PL emission intensity. (C) 2013 American Institute of Physics. http://dx.doi.org/10.1063/1.4795779]

Surface modification and paclitaxel drug delivery of folic acid modified polyethylene glycol functionalized hydroxyapatite nanoparticles

Nanoparticles are used for a number of biomedical applications. In this work we report the synthesis of folic acid (FA) modified polyethylene glycol (PEG) functionalized hydroxyapatite (HAp) nanoparticles. The anticancer drug, paclitaxel, is attached to the folic acid modified polyethylene glycol functionalized hydroxyapatite nanoparticles and the in vitro drug release is analyzed. The surface modification and functionalization is confirmed by Fourier transform infrared spectroscopy (FTIR), thermo gravimetric analysis (TGA) and UV spectroscopy. The importance of the paper is the investigation of the release behavior of paclitaxel conjugated folic acid modified polyethylene glycol functionalized hydroxyapatite nanoparticles. The results show an initial rapid release and then a sustained release. (C) 2012 Elsevier B.V. All rights reserved.