Lead selection and characterization of antitubercular compounds using the Nested Chemical Library

Discovering new drugs to treat tuberculosis more efficiently and to overcome multidrug resistance is a world health priority. To find novel antitubercular agents several approaches have been used in various institutions worldwide, including target-based approaches against several validated mycobacterial enzymes and phenotypic screens. We screened more than 17,000 compounds from Vichem's Nested Chemical Library(TM) using an integrated strategy involving whole cell-based assays with Corynebacterium glutamicum and Mycobacterium tuberculosis, and target-based assays with protein kinases PknA, PknB and PknG as well as other targets such as PimA and bacterial topoisomerases simultaneously. With the help of the target-based approach we have found very potent hits inhibiting the selected target enzymes, but good minimal inhibitory concentrations (MIC) against M. tuberculosis were not achieved. Focussing on the whole cell-based approach several potent hits were found which displayed minimal inhibitory concentrations (MIC) against M. tuberculosis below 10 mu M and were non-mutagenic, non-cytotoxic and the targets of some of the hits were also identified. The most active hits represented various scaffolds. Medicinal chemistry-based lead optimization was performed applying various strategies and, as a consequence, a series of novel potent compounds were synthesized. These efforts resulted in some effective potential antitubercular lead compounds which were confirmed in phenotypic assays. (C) 2015 Elsevier Ltd. All rights reserved.

Molecule Modeling of Human Pentameric alpha(7) Neuronal Nicotinic Acetylcholine Receptor and Its Interaction with its Agonist and Competitive Antagonist

The nicotinic Acetylcholine Receptor (nAChR) is the major class of neurotransmitter receptors that is involved in many neurodegenerative conditions such as schizophrenia, Alzheimer's and Parkinson's diseases. The N-terminal region or Ligand Binding Domain (LBD) of nAChR is located at pre- and post-synaptic nervous system, which mediates synaptic transmission. nAChR acts as the drug target for agonist and competitive antagonist molecules that modulate signal transmission at the nerve terminals. Based on Acetylcholine Binding Protein (AChBP) from Lymnea stagnalis as the structural template, the homology modeling approach was carried out to build three dimensional model of the N-terminal region of human alpha(7)nAChR. This theoretical model is an assembly of five alpha(7) subunits with 5 fold axis symmetry, constituting a channel, with the binding picket present at the interface region of the subunits. alpha-netlrotoxin is a potent nAChR competitive antagonist that readily blocks the channel resulting in paralysis. The molecular interaction of alpha-Bungarotoxin, a long chain alpha-neurotoxin from (Bungarus multicinctus) and human alpha(7)nAChR seas studied. Agonists such as acetylcholine, nicotine, which are used in it diverse array of biological activities, such as enhancements of cognitive performances, were also docked with the theoretical model of human alpha(7)nAChR. These docked complexes were analyzed further for identifying the crucial residues involved i interaction. These results provide the details of interaction of agonists and competitive antagonists with three dimensional model of the N-terminal region of human alpha(7)nAChR and thereby point to the design of novel lead compounds.

Toward the Discovery of Vaccine Adjuvants: Coupling In Silico Screening and In Vitro Analysis of Antagonist Binding to Human and Mouse CCR4 Receptors

Background: Adjuvants enhance or modify an immune response that is made to an antigen. An antagonist of the chemokine CCR4 receptor can display adjuvant-like properties by diminishing the ability of CD4+CD25+ regulatory T cells (Tregs) to down-regulate immune responses. Methodology: Here, we have used protein modelling to create a plausible chemokine receptor model with the aim of using virtual screening to identify potential small molecule chemokine antagonists. A combination of homology modelling and molecular docking was used to create a model of the CCR4 receptor in order to investigate potential lead compounds that display antagonistic properties. Three-dimensional structure-based virtual screening of the CCR4 receptor identified 116 small molecules that were calculated to have a high affinity for the receptor; these were tested experimentally for CCR4 antagonism. Fifteen of these small molecules were shown to inhibit specifically CCR4-mediated cellmigration, including that of CCR4(+) Tregs. Significance: Our CCR4 antagonists act as adjuvants augmenting human T cell proliferation in an in vitro immune response model and compound SP50 increases T cell and antibody responses in vivo when combined with vaccine antigens of Mycobacterium tuberculosis and Plasmodium yoelii in mice.

A cyclic peptide mimic of an RNA recognition motif of human La protein is a potent inhibitor of hepatitis C virus

Due to limited available therapeutic options, developing new lead compounds against hepatitis C virus is an urgent need. Human La protein stimulates hepatitis C virus translation through interaction with the hepatitis C viral RNA. A cyclic peptide mimicking the beta-turn of the human La protein that interacts with the viral RNA was synthesized. It inhibits hepatitis C viral RNA translation significantly better than the corresponding linear peptide at longer post-treatment times. The cyclic peptide also inhibited replication as measured by replicon RNA levels using real time RT-PCR. The cyclic peptide emerges as a promising lead compound against hepatitis C.

Synthesis, Antimicrobial and Cytotoxic Activities of Sulfonamidomethane Linked Heterocycles

A new class of sulfonamidomethane pyrrolyl-oxadiazoles/thiadiazoles and pyrazolyl-oxadiazoles/thiadiazoles was prepared from arylsulfonylaminoacetic acid hydrazides and E-cinnamic acid. The lead compounds were tested for antimicrobial and cytotoxic activities. The thiadiazole compounds having chloro substituent on the aromatic ring 4c, 8c and 10c exhibited comparable antibacterial activity against Pseudomonas aeruginosa and also antifungal activity against Penieillium ehrysogenunz. The styryl oxadiazole compound 3c showed appreciable cytotoxic activity on A549 lung carcinoma cells which can be used as a lead compound in the future studies.

Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection

Polypharmacology is beginning to emerge as an important concept in the field of drug discovery. However, there are no established approaches to either select appropriate target sets or design polypharmacological drugs. Here, we propose a structural-proteomics approach that utilizes the structural information of the binding sites at a genome-scale obtained through in-house algorithms to characterize the pocketome, yielding a list of ligands that can participate in various biochemical events in the mycobacterial cell. The pocket-type space is seen to be much larger than the sequence or fold-space, suggesting that variations at the site-level contribute significantly to functional repertoire of the organism. All-pair comparisons of binding sites within Mycobacterium tuberculosis (Mtb), pocket-similarity network construction and clustering result in identification of binding-site sets, each containing a group of similar binding sites, theoretically having a potential to interact with a common set of compounds. A polypharmacology index is formulated to rank targets by incorporating a measure of druggability and similarity to other pockets within the proteome. This study presents a rational approach to identify targets with polypharmacological potential along with possible drugs for repurposing, while simultaneously, obtaining clues on lead compounds for use in new drug-discovery pipelines.

Novel M-Superfamily and T-Superfamily conotoxins and contryphans from the vermivorous snail Conus figulinus

The venom of Conus figulinus, a vermivorous cone snail, found in the south east coast of India, has been studied in an effort to identify novel peptide toxins. The amino acid sequences of seven peptides have been established using de novo mass spectrometric based sequencing methods. Among these, three peptides belong to the M-Superfamily conotoxins, namely, Fi3a, Fi3b, and Fi3c, and one that belongs to the T-Superfamily, namely, Fi5a. The other three peptides are contryphans, namely, contryphans fib, fic, and fid. Of these Fi3b, Fi3c, Fi5a, and contryphan fib are novel and are reported for the first time from venom of C.figulinus. The details of the sequencing methods and the relationship of these peptides with other M'-Superfamily conotoxins from the fish hunting and mollusk hunting clades are discussed. These novel peptides could serve as a lead compounds for the development of neuropharmacologically important drugs. Copyright (c) 2014 European Peptide Society and John Wiley & Sons, Ltd.

Two- and three-dimensional lead-1H-imidazole-4,5-dicarboxylates

Reaction of lead nitrate and 1H-imidazole-4,5-dicarboxylic acid under hydrothermal conditions carried out at different temperatures and pH yields a hybrid Compound Pb-2(1H-imidazole-4,5-dicarboxylate)2, 1, and a three-dimensional coordination polymer Pb(1H-imidazole-4,5-dicarboxylate), It. The two-dimensional double-layered compound, 1, with two-dimensional inorganic connectivities and one-dimensional organic connectivity is novel since hybrid compounds formed by 1H-imidazole-4,5-dicarboxylic acid are uncommon. The lead atoms in I have holodirectional geometry, while those in II show hemidirectionality. In both I and II, 1H-imidazole-4,5-dicarboxylic acid acts as a multi-dentate ligand with both the carboxylic groups and the amine group taking part in coordination. (C) 2009 Elsevier B.V. All rights reserved.

Evidence for double valence fluctuation in metallic oxides of lead

The possible role of double valence fluctuation in both lead and oxide ions with reference to metallization in oxides of lead is examined by x-ray-photoemission spectroscopy, ultraviolet-photoemission spectroscopy (UPS), and 207Pb NMR studies. The double valence fluctuations may be viewed as Pb4++2O2-⇄Pb2+O22-. While the insulating oxides PbO, Pb3O4, and Sr2PbO4 show a single oxide ion, O2- characterized by O(1s) at 529.7 eV, the insulating peroxide BaO2 is characterized by the ion O22- with a single O(1s) at 533 eV. The metallic PbO2, BaPbO3, BaBiPbO3, and SrPbO3 showed the occurrence of both O2- and O22- ions. The valence band in these compounds has also been studied by UPS, and clear evidence for the coexistence of O2- and O22- is seen in PbO2. A simultaneous study of 207Pb NMR suggests that the Pb ion could also exist in mixed-valence states. Qualitative arguments are presented to rationalize the existence of such mixed valences of the anion in metal oxides in general and their role in superconductivity.

Lead Stereochemistry in Incommensurate Ferroelectric Perovskites and in Incommensurate Lead Monoxide

We have performed Rietveld refinements on neutron and synchrotron diffraction patterns and density functional calculations on various ferroelectric lead perovskites and on α lead monoxide (litharge). These structural data have allowed to shed some light on lead stereochemistry in these compounds. In particular, we discuss the changing in the lead behaviour between the paraelectric cubic phases and the low temperature anti or ferroelectric phases in Pb2CoWO6 and Pb2MgTeO6 (both incommensurate), in Pb2MgWO6 (antiferroelectric) and in PbMg1/3Nb2/3O3 (relaxor). The possible phase transition mechanisms are reviewed and the bonds are compared to those in the aperiodic structure of α-lead monoxide.

Gibbs energy formation of lead titanate

The Gibbs energy of formation of titania-saturated lead titanate has been determined by e.m.f. measurements on the solid state cell;Pt,Ir,Pb + Pb1−xTiO3−x + TiO2(rutile)/CaO-ZrO2/Ni + NiO,Pt in the temperature range 1075–1350 K. The results obtained are significantly different from those reported in the literature based upon vapour pressure measurements, employing Knudsen effusion and transportation techniques, and assuming that the vapor phase consisted entirely of monomeric PbO molecules. A reanalysis of the data obtained in the earlier vapor pressure studies using mass spectrometric measurements on polymeric PbO species in the gas phase, gives Gibbs energies of formation of lead titanate which are in better agreement with those obtained in this study. Earlier electrochemical measurements by Mehrotra et al. and more recent electrochemical measurements by Schmahl et al. both employing CaO-ZrO2 solid electrolytes are in good agreement with the present study. The electro-chemical measurements by Schmahl et al. using PbF 2 solid electrolyte give a slightly more positive Gibbs energy of formation. There was no evidence supporting the formation of compounds other than Pb1−xTiO3−x from yellow PbO and rutile form of TiO2 in the temperature range covered in this study.Résumé L'enthalpie libre de formation du titanate de plomb saturé en oxyde de titane a été déterminée par des mesures de FEM de la pile: Pt,Ir,Pb + Pb1−xTiO3−x + TiO2(rutile)/CaO-ZrO2/Ni + NiO,Pt dans le domaine de températures 1075–1350 K. Les résultats obtenus, different appréciablement de ceux publiés, déterminés par mesures de tensions de vapeur (techniques de transport et d'effusion de Knudsen) en supposant que la phase gazeuse etait uniquement constituée de molécules monomériques de PbO. Une réanalyse des résultats de la littérature, à partir de mesures par spectrométrie de masse sur les polymères de PbO gazeux, donne des enthalpies libres de formation du titanate de plomb se rapprochant de celles obtenues dans cette étude. Les mesures de Mehrotra et al. et plus récemment de Schmahl et al. utilisant toutes deux l'électrolyte CaO-ZrO2 concordent bien avec celles de la présente étude. Les mesures de Schmahl et al., à l'aide de l' électrolyte solide PbF2, donnent une enthalpie de formation légèrement plus positive. Pour la gammede températures étudiée, rien ne permet de supposer que des composés autres que Pb1−x TiO3−x puissent se former à partir du PbO Gaune) et du rutile (TiO2).

Potentiometric determination of the Gibbs energies of formation of lead aluminates

The Gibbs energies of formation of three compounds in the PbO-Al2O3 system—2PbO · Al2O3, PbO · Al2O3, andPbO· 6Al2O3—have been determined from potentiometric measurements on reversible solid-state galvanic cells [dformula Pt, Ir | Pb, alpha-Al[sub 2]O[sub 3], PbO [center-dot] 6Al[sub 2]O[sub 3] | ZrO[sub 2]-CaO | NiO, Ni | Pt] [dformula Pt | NiO, Ni | ZrO[sub 2]-CaO | Pb, PbO [center-dot] 6Al[sub 2]O[sub 3], PbO [center-dot] Al[sub 2]O[sub 3] | Ir, Pt] and [dformula Pt | NiO, Ni | ZrO[sub 2]-CaO | Pb, PbO [center-dot] Al[sub 2]O[sub 3], 2PbO [center-dot] Al[sub 2]O[sub 3] | Ir, Pt] in the temperature range 850–1375 K. The results are discussed in the light of reported phase diagrams for the PbO-Al2O3system. The partial pressures of different lead oxide species, PbnOn, n = 1–6, in the gas phase in equilibrium withthe aluminates are calculated by combining the results of this study with the mass-spectrometric data of Drowart et al.(1) for polymerization equilibria in the gas phase. The concentration of oxygen in lead in equilibrium with the aluminatesare also derived from the results and the literature data on the Gibbs energy of solution of oxygen in liquid lead.

Conducting polymer-carbon black nanocomposite sensor for volatile organic compounds and correlating sensor response by molecular dynamics

Volatile organic compounds (VOCs) are present in our every day used products such as plastics, cosmetics, air fresheners, paint, etc. The determination of amount of VOC present in atmosphere can be carried out via various sensors. In this work a nanocomposite of a novel thiophene based conducting polymer and carbon black is used as a volatile organic compound sensor. The fabricated 2 lead chemiresistor sensor was tested for vapours of toluene, acetone, cylcohexane, and carbon tetrachloride. The sensor responds to all the vapours, however, exhibit maximum response to toluene vapours. The sensor was evaluated for various concentrations of toluene. The lower limit of detection of the sensor is 15 +/- 10 ppm. The study of the effect of humidity on senor response to toluene showed that the response decreases at higher humidity conditions. The surface morphology of the nanocomposite was characterized by scanning electron microscopy. Diffuse reflectance spectroscopy was used to investigate the absorption of vapours by the nanocomposite film. Contact angle measurements were used to present the effect of water vapour on the toluene response of nanocomposite film. Solubility parameter of the conducting polymer is predicted by molecular dynamics. The sensing behaviour of the conducting polymer is correlated with solubility parameter of the polymer. Dispersion interaction of conducting polymer with toluene is believed to be the reason for the selective response towards toluene. (C) 2014 Elsevier B.V. All rights reserved.

Metastable monoclinic and orthorhombic phases and electric field induced irreversible phase transformation at room temperature in the lead-free classical ferroelectric BaTiO3

For decades it has been a well-known fact that among the few ferroelectric compounds in the perovskite family, namely, BaTiO3, KNbO3, PbTiO3, and Na1/2Bi1/2TiO3, the dielectric and piezoelectric properties of BaTiO3 are considerably higher than the others in polycrystalline form at room temperature. Further, similar to ferroelectric alloys exhibiting morphotropic phase boundary, single crystals of BaTiO3 exhibit anomalously large piezoelectric response when poled away from the direction of spontaneous polarization at room temperature. These anomalous features in BaTiO3 remained unexplained so far from the structural standpoint. In this work, we have used high-resolution synchrotron x-ray powder diffraction, atomic resolution aberration-corrected transmission electron microscopy, in conjunction with a powder poling technique, to reveal that at 300 K (i) the equilibrium state of BaTiO3 is characterized by coexistence of metastable monoclinic Pm and orthorhombic (Amm2) phases along with the tetragonal phase, and (ii) strong electric field switches the polarization direction from the 001] direction towards the 101] direction. These results suggest that BaTiO3 at room temperature is within an instability regime, and that this instability is the fundamental factor responsible for the anomalous dielectric and piezoelectric properties of BaTiO3 as compared to the other homologous ferroelectric perovskite compounds at room temperature. Pure BaTiO3 at room temperature is therefore more akin to lead-based ferroelectric alloys close to the morphotropic phase boundary where polarization rotation and field induced ferroelectric-ferroelectric phase transformations play a fundamental role in influencing the dielectric and piezoelectric behavior.

High thermopower and ultra low thermal conductivity in Cd-based Zintl phase compounds

By combining first principles density functional theory and electronic as well as lattice Boltzmann transport calculations, we unravel the excellent thermoelectric properties of Zintl phase compounds ACd(2)Sb(2) (where, A = Ca, Ba, Sr). The calculated electronic structures of these compounds show charge carrier pockets and heavy light bands near the band edge, which lead to a large power factor. Furthermore, we report large Gruneisen parameters and low phonon group velocity indicating essential strong anharmonicity in these compounds, which resulted in low lattice thermal conductivity. The combination of low thermal conductivity and the excellent transport properties give a high ZT value of similar to 1.4-1.9 in CaCd2Sb2 and BaCd2Sb2 at moderate p and n-type doping. Our results indicate that well optimized Cd-based Zintl phase compounds have the potential to match the performance of conventional thermoelectric materials.