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Chemical space: Big data challenge for molecular diversity

Chemical space describes all possible molecules as well as multi-dimensional conceptual spaces representing the structural diversity of these molecules. Part of this chemical space is available in public databases ranging from thousands to billions of compounds. Exploiting these databases for drug discovery represents a typical big data problem limited by computational power, data storage and data access capacity. Here we review recent developments of our laboratory, including progress in the chemical universe databases (GDB) and the fragment subset FDB-17, tools for ligand-based virtual screening by nearest neighbor searches, such as our multi-fingerprint browser for the ZINC database to select purchasable screening compounds, and their application to discover potent and selective inhibitors for calcium channel TRPV6 and Aurora A kinase, the polypharmacology browser (PPB) for predicting off-target effects, and finally interactive 3D-chemical space visualization using our online tools WebDrugCS and WebMolCS. All resources described in this paper are available for public use at www.gdb.unibe.ch.

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Synthesis of some new 1,3,4-oxadiazole derivatives and evaluation of their antibacterial effects

In the present study, some oxadiazole derivatives have been synthesized by incorporating azetidinyl and thiazolidinyl moieties at its 2-position such as 5-(p-methoxyphenyl)-[2-substitutedbenzylidenylimino]1,3,4- oxadiazole 2-6, 5-(p-methoxyphenyl)-[2-(3´-chloro-2´-oxo-4´-substitutedaryl-1-azetidinyl)1,3,4-oxadiazole 7-11 and 5-(p-methoxyphenyl)-[2-(2´-substitutedaryl-4´-oxo-1´,3´-thiazolidin-3´-yl)1,3,4-oxadiazole 12-16. The structure of these compounds have been elucidated by elemental analysis (C, H, N) and IR, 1H-NMR, Mass spectroscopic techniques. Further, these compounds were subjected to screening for antibacterial activities against different bacterial strains.

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Past, present, and future of antifungal drug development

Fungi are eukaryotic, single cell or multicellular organisms which cause a wide range of human diseases ranging from superficial skin to invasive life-threatening infections. Over the last couple of decades the incidence of life-threatening fungal infections has increased seriously as the patients of AIDS, cancer, organ transplant and immune-compromised population have increased. Though a significant progress has been made in the discovery of antifungal agents in the form of polyenes, azoles and allylamines yet the antifungal therapy poses severe challenge because of the side effects, narrow spectrum of activity and recently development resistance among patients against the present antifungals. This chapter deals with the current antifungal agents, their spectrum of activity, mode of action, limitations, current challenges in antifungal therapy, and new avenues for future developments.

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SLC26A3 inhibitor identified in small molecule screen blocks colonic fluid absorption and reduces constipation

SLC26A3 (downregulated in adenoma; DRA) is a Cl-/anion exchanger expressed in the luminal membrane of intestinal epithelial cells, where it facilitates electroneutral NaCl absorption. SLC26A3 loss of function in humans or mice causes chloride-losing diarrhea. Here, we identified slc26a3 inhibitors in a screen of 50,000 synthetic small molecules done in Fischer rat thyroid (FRT) cells coexpressing slc26a3 and a genetically encoded halide sensor. Structure-Activity relationship studies were done on the most potent inhibitor classes identified in the screen: 4,8-dimethylcoumarins and acetamide-Thioimidazoles. The dimethylcoumarin DRAinh-A250 fully and reversibly inhibited slc26a3-mediated Cl- exchange with HCO3 -, I-, and thiocyanate (SCN-), with an IC50 of ?0.2 muM. DRAinh-A250 did not inhibit the homologous anion exchangers slc26a4 (pendrin) or slc26a6 (PAT-1), nor did it alter activity of other related proteins or intestinal ion channels. In mice, intraluminal DRAinh-A250 blocked fluid absorption in closed colonic loops but not in jejunal loops, while the NHE3 (SLC9A3) inhibitor tenapanor blocked absorption only in the jejunum. Oral DRAinh-A250 and tenapanor comparably reduced signs of constipation in loperamide-Treated mice, with additive effects found on coadministration. DRAinh-A250 was also effective in loperamidetreated cystic fibrosis mice. These studies support a major role of slc26a3 in colonic fluid absorption and suggest the therapeutic utility of SLC26A3 inhibition in constipation.

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Synthesis and biological evaluation of some new benzofuran derivatives

5-Chloro-3-methyl-2-benzofuran carbohydrazide (4) upon treatment with potassium isothiocynate in presence of hydrochloric acid in water gave 5-chloro-3-methylbenzofuran-2-carbo-N-thiosemicarbazide (5). The cyclisation of 5-chloro-3-methylbenzofuran-2-carbo-N-thiosemicarbazide (5) under different reaction conditions offered 1,3,4-oxadiazole, 1,3,4-thiadiazole, 1,2,4-triazole, thiazolidinone and thiopyrimidinone. The structures of these compounds were established on the basis of spectral data. Some of these compounds exhibited good antimicrobial activity.

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Synthesis of a series of thiazolidinone derivatives and evaluation of their antimicrobial properties

A series of thiazolidinone derivatives with various aromatic aldehyde substitution were synthesized and characterized by physical (TLC and M.P.) and spectral data (IR, NMR and MASS). They were evaluated for antimicrobial potential against Gram positive Staphylococcus aureus, Bacillus subtilis, gram-negative Escherichia coli, Pseudomonas aeuroginosa, Shigella and fungi Candida albicans and Aspergillus niger. The initial screening using zones of inhibition at 50 mul concentration revealed that they are moderately active against the tested strains.

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1, 3-thiazolidin-4-one derivatives bearing pyrimidine moieties: Design, computational studies, synthesis, characterization, antimicrobial, MTT assessment and molecular docking assessment

1, 3-thiazolidin-4-one derivatives bearing 5,6-dihydrothieno[2,3-d]pyrimidine moiety (1-10) were designed and assessed for the level of bioactivity, computationally. Computational findings revealed that compounds 1-8 were exhibiting very good bioactivity score as GPCR ligand, and lying in the zone for active drug molecule, while compounds 9-10, were lying under the zone of moderately active drug molecule. The bioactive compounds (1-10) were then synthesized, characterized and assessed for antimicrobial potential and percent viability of cells. All the compounds (1-10) were found to have very good antimicrobial potential, although some of the members of the series possessed better antimicrobial potential than the reference drug ?Ciprofloxacin?. In Addition, molecular docking assessment was carried out for all the synthesized compounds against the protein GlcN-6-P-synthase to embed both in-silico and in vitro results. The findings revealed that most of the compounds were found to exhibit significant hydrogen bonding to the residues of GlcN-6-P-synthase with a binding affinity -6.9 to -5.3 Kcal/mole. The compounds were also tested for percent viability of cells by MTT assay, and the results revealed that ? 90 % viability of the cells was found @ 3.12 muM and ? 70 @ 100 muM.

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Design, synthesis, anticancer screening, docking studies and in silico ADME prediction of some beta-carboline derivatives

Background: Medicinal interest has focused on beta-carbolines as anticancer agents. Methodology/Results: Several beta-carbolines were designed, synthesized and evaluated for their cytotoxic activity against MCF-7 and A-549 cancer cell lines using MTT assay. Compounds 13a, 13c, 13d and 20a were the most promising showing high selectivity indices. Compounds 13c and 20a showed potent inhibition of topoisomerase (topo-I) and kinesin spindle protein (KSP/Eg5 ATPase) which was confirmed by their docking results into the active site of both enzymes. In silico physicochemical calculations predicted that compounds 13a, 13d and 20a obeyed Lipinski’s rule of five. Conclusion: Compounds 13c and 20a are multitarget anticancer leads that act as potent inhibitors for both topo-I and/or KSP ATPase.

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First catalytic enantioselective synthesis of P-stereogenic phosphoramides via kinetic resolution promoted by a chiral bicyclic imidazole nucleophilic catalyst

A novel method toward the synthesis of P-stereogenic organophosphorus compounds via kinetic resolution by a catalytic asymmetric phosphorylation through P-N bond formation has been developed. Using a chiral bicyclic imidazole nucleophilic catalyst, chiral phosphoramide compounds were prepared in high conversions and with moderate enantioselectivity. This is also the first example of the catalytic asymmetric synthesis of chiral phosphoramide compounds.

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Studies on schiff bases from methyl-1-naphthyl ketone. Part-II: Synthesis and characterization of ketimines from 1-acetylnaphthalene with derivatives of aniline

The Ketimines (Schiff bases) were prepared from Methyl-1-naphthyl-ketone with Aniline, 2-Chloro-aniline, 3- Chloro-aniline, 4-Chloro-aniline and 2-Nitroaniline using toluene as solvent by azeotropic(reflux) method using Dean and Stark. The synthesized ketimines were characterized and confirmed by colour, physical constant, TLC and spectral(UV-Vis and FTIR) information.

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