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https://www.readbyqxmd.com/read/28923386/structure-based-design-synthesis-and-biological-evaluation-of-withaferin-a-analogues-as-potent-apoptotic-inducers
#1
Gabriel G Llanos, Liliana M Araujo, Ignacio A Jiménez, Laila M Moujir, Jaime Rodríguez, Carlos Jiménez, Isabel L Bazzocchi
Apoptosis inducers represent an attractive approach for the discovery and development of anticancer agents. Herein, we report on the development by molecular fine tuning of a withaferin A-based library of 63 compounds (2-64), 53 of them reported for the first time. Their antiproliferative evaluation on HeLa, A-549 and MCF-7 human tumor cell lines identified fifteen analogues displaying higher activity (IC50 values ranging 0.3-4.8 μM) than the lead (IC50 values ranging 1.3-10.1 μM) either in lag or log growth phases...
September 6, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28922416/multi-level-computational-methods-for-interdisciplinary-research-in-the-hathitrust-digital-library
#2
Jaimie Murdock, Colin Allen, Katy Börner, Robert Light, Simon McAlister, Andrew Ravenscroft, Robert Rose, Doori Rose, Jun Otsuka, David Bourget, John Lawrence, Chris Reed
We show how faceted search using a combination of traditional classification systems and mixed-membership topic models can go beyond keyword search to inform resource discovery, hypothesis formulation, and argument extraction for interdisciplinary research. Our test domain is the history and philosophy of scientific work on animal mind and cognition. The methods can be generalized to other research areas and ultimately support a system for semi-automatic identification of argument structures. We provide a case study for the application of the methods to the problem of identifying and extracting arguments about anthropomorphism during a critical period in the development of comparative psychology...
2017: PloS One
https://www.readbyqxmd.com/read/28921904/developing-a-dna-barcode-library-for-perciform-fishes-in-the-south-china-sea-species-identification-accuracy-and-cryptic-diversity
#3
Gang Hou, Wei-Tao Chen, Huo-Sheng Lu, Fei Cheng, Song-Guang Xie
DNA barcodes were studied for 1,353 specimens representing 272 morphological species belonging to 149 genera and 55 families of Perciformes from the South China Sea (SCS). The average Kimura 2-parameter (K2P) distances within species, genera, and families were 0.31%, 8.71%, and 14.52%, respectively. A Neighbor-joining (NJ) tree, Bayesian inference (BI) and maximum-likelihood (ML) trees and Automatic Barcode Gap Discovery (ABGD) revealed 260, 253 and 259 single-species-representing clusters, respectively. Barcoding Gap Analysis (BGA) demonstrated that barcode gaps were present for 178 of 187 species analysed with multiple specimens (95...
September 15, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28917310/screening-of-a-small-well-curated-natural-product-based-library-identifies-two-rotenoids-with-potent-nematocidal-activity-against-haemonchus-contortus
#4
H M P Dilrukshi Herath, Sarah Preston, Andreas Hofmann, Rohan A Davis, Anson V Koehler, Bill C H Chang, Abdul Jabbar, Robin B Gasser
The control of parasitic roundworms (nematodes) is heavily reliant on the use of a limited number of anthelmintic drugs. However, drug resistance is now very widespread and no vaccines are available, such that the discovery of new chemical entities is crucial. Within this context, we screened a library of pure natural products (n=400) against exsheathed third-stage (xL3) larvae of the parasitic nematode Haemonchus contortus using a whole-organism screening method. We identified two plant-derived rotenoids, deguelin and rotenone, with inhibitory activity on xL3 motility...
September 15, 2017: Veterinary Parasitology
https://www.readbyqxmd.com/read/28916338/structure-activity-relationship-study-of-small-molecule-inhibitors-of-the-deptor-mtor-interaction
#5
Jihye Lee, Yijiang Shi, Mario Vega, Yonghui Yang, Joseph Gera, Michael E Jung, Alan Lichtenstein
DEPTOR is a 48kDa protein that binds to mTOR and inhibits this kinase within mTORC1 and mTORC2 complexes. Over-expression of DEPTOR specifically occurs in the multiple myeloma (MM) tumor model and DEPTOR knockdown is cytotoxic to MM cells, suggesting it is a potential therapeutic target. Since mTORC1 paralysis protects MM cells against DEPTOR knockdown, it indicates that the protein-protein interaction between DEPTOR and mTOR is key to MM viability vs death. In a previous study, we used a yeast two-hybrid screen of a small inhibitor library to identify a compound that inhibited DEPTOR/mTOR binding in yeast...
September 6, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28916042/urinary-intermediates-of-tryptophan-as-indicators-of-the-gut-microbial-metabolism
#6
Tereza Pavlova, Veronika Vidova, Julie Bienertova-Vasku, Petr Janku, Martina Almasi, Jana Klanova, Zdenek Spacil
While over 10% of the human metabolome is directly associated with the gut microbial metabolism, specific metabolites are largely uncharacterized. Therefore, methods for the identification and quantification of microbiota-associated metabolites in biological fluids such as urine or plasma are necessary in order to elucidate the molecular basis of host-microbiota interaction. In this study, we focused on the tryptophan metabolism, employing quantitative assays by ultra-high performance liquid chromatography (UHPLC) and tandem mass spectrometry, specifically selected reaction monitoring (SRM)...
September 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28915268/large-scale-cross-species-chemogenomic-platform-proposes-a-new-drug-discovery-strategy-of-veterinary-drug-from-herbal-medicines
#7
Chao Huang, Yang Yang, Xuetong Chen, Chao Wang, Yan Li, Chunli Zheng, Yonghua Wang
Veterinary Herbal Medicine (VHM) is a comprehensive, current, and informative discipline on the utilization of herbs in veterinary practice. Driven by chemistry but progressively directed by pharmacology and the clinical sciences, drug research has contributed more to address the needs for innovative veterinary medicine for curing animal diseases. However, research into veterinary medicine of vegetal origin in the pharmaceutical industry has reduced, owing to questions such as the short of compatibility of traditional natural-product extract libraries with high-throughput screening...
2017: PloS One
https://www.readbyqxmd.com/read/28915003/the-evolution-of-dna-templated-synthesis-as-a-tool-for-materials-discovery
#8
Rachel K O'Reilly, Andrew J Turberfield, Thomas R Wilks
Precise control over reactivity and molecular structure is a fundamental goal of the chemical sciences. Billions of years of evolution by natural selection have resulted in chemical systems capable of information storage, self-replication, catalysis, capture and production of light, and even cognition. In all these cases, control over molecular structure is required to achieve a particular function: without structural control, function may be impaired, unpredictable, or impossible. The search for molecules with a desired function is often achieved by synthesizing a combinatorial library, which contains many or all possible combinations of a set of chemical building blocks (BBs), and then screening this library to identify "successful" structures...
September 15, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28912539/diphenyleneiodonium-chloride-dpic-displays-broad-spectrum-bactericidal-activity
#9
Manitosh Pandey, Alok Kumar Singh, Ritesh Thakare, Sakshi Talwar, Pratiksha Karaulia, Arunava Dasgupta, Sidharth Chopra, Amit Kumar Pandey
Indiscriminate use of antibiotics globally has lead to an increase in emergence of drug-resistant pathogens under both nosocomial, as well as more worryingly, in community setting as well. Further, a decrease in the corporate interest and financial commitment has exerted increasing pressure on a rapidly dwindling antimicrobial drug discovery and developmental program. In this context, we have screened the Library of Pharmacologically Active Compounds (LOPAC, Sigma) against Staphylococcus aureus and Mycobacterium tuberculosis to identify potent novel antimicrobial molecules amongst non-antibiotic molecules...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28894419/molecular-connectivity-predefines-polypharmacology-aliphatic-rings-chirality-and-sp-3-centers-enhance-target-selectivity
#10
Stefania Monteleone, Julian E Fuchs, Klaus R Liedl
Dark chemical matter compounds are small molecules that have been recently identified as highly potent and selective hits. For this reason, they constitute a promising class of possible candidates in the process of drug discovery and raise the interest of the scientific community. To this purpose, Wassermann et al. (2015) have described the application of 2D descriptors to characterize dark chemical matter. However, their definition was based on the number of reported positive assays rather than the number of known targets...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28894353/optimized-next-generation-sequencing-genotype-haplotype-calling-for-genome-variability-analysis
#11
Javier Navarro, Bruno Nevado, Porfidio Hernández, Gonzalo Vera, Sebastián E Ramos-Onsins
The accurate estimation of nucleotide variability using next-generation sequencing data is challenged by the high number of sequencing errors produced by new sequencing technologies, especially for nonmodel species, where reference sequences may not be available and the read depth may be low due to limited budgets. The most popular single-nucleotide polymorphism (SNP) callers are designed to obtain a high SNP recovery and low false discovery rate but are not designed to account appropriately the frequency of the variants...
2017: Evolutionary Bioinformatics Online
https://www.readbyqxmd.com/read/28892616/chemoproteomics-enabled-covalent-ligand-screening-reveals-a-thioredoxin-caspase-3-interaction-disruptor-that-impairs-breast-cancer-pathogenicity
#12
Kimberly E Anderson, Milton To, James A Olzmann, Daniel K Nomura
Covalent ligand discovery is a promising strategy to develop small-molecule effectors against therapeutic targets. Recent studies have shown that dichlorotriazines are promising reactive scaffolds that preferentially react with lysines. Here, we have synthesized a series of dichlorotriazine-based covalent ligands and have screened this library to reveal small molecules that impair triple-negative breast cancer cell survival. Upon identifying a lead hit from this screen KEA1-97, we used activity-based protein profiling (ABPP)-based chemoproteomic platforms to identify that this compound targets lysine 72 of thioredoxin-a site previously shown to be important in protein interactions with caspase 3 to inhibit caspase 3 activity and suppress apoptosis...
September 13, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28888997/discovery-of-peptide-drug-carrier-candidates-for-targeted-multi-drug-delivery-into-prostate-cancer-cells
#13
O Bashari, B Redko, A Cohen, G Luboshits, G Gellerman, M A Firer
Metastatic castration-resistant prostate cancer (mCRPC) remains essentially incurable. Targeted Drug Delivery (TDD) systems may overcome the limitations of current mCRPC therapies. We describe the use of strict criteria to isolate novel prostate cancer cell targeting peptides that specifically deliver drugs into target cells. Phage from a libraries displaying 7mer peptides were exposed to PC-3 cells and only internalized phage were recovered. The ability of these phage to internalize into other prostate cancer cells (LNCaP, DU-145) was validated...
September 6, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28885764/porphyrin-derivatives-inhibit-the-interaction-between-receptor-activator-of-nf-%C3%AE%C2%BAb-and-its-ligand
#14
Melanie Chypre, Maria-Bernadette Madel, Olivier Chaloin, Chlaudine Blin-Wakkach, Christophe Morice, Christopher G Mueller
Receptor Activator of NF-κB (RANK), a member of the TNF-receptor superfamily, plays an important role in bone resorption and stimulates immune and epithelial cell activation. Denosumab, a human monoclonal antibody blocking RANK ligand (RANKL), is approved for the treatment of osteoporosis and bone metastasis. However, a small molecule inhibiting RANK-RANKL interaction would be beneficial to reduce costs and to facilitate treatments with orally available therapeutic agents. Here, we report the discovery of the first non-peptidic inhibitors of RANK-RANKL interactions...
September 8, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28882677/protein-biomarkers-for-early-detection-of-diseases-the-decisive-contribution-of-combinatorial-peptide-ligand-libraries
#15
Egisto Boschetti, Alfonsina D'Amato, Giovanni Candiano, Pier Giorgio Righetti
The present review deals with biomarker discovery, especially in regard to sample treatment via combinatorial peptide ligand libraries, perhaps the only technique at present allowing deep exploration of biological fluids and tissue extracts in search for low- to very-low-abundance proteins, which could possibly mark the onset of most pathologies. Early-stage biomarkers, in fact, might be the only way to detect the beginning of most diseases thus permitting proper intervention and care. The following cancers are reviewed, with lists of potential biomarkers suggested in various reports: hepatocellular carcinoma, ovarian cancer, breast cancer and pancreatic cancer, together with some other interesting applications...
September 4, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28876963/candidiasis-and-the-impact-of-flow-cytometry-on-antifungal-drug-discovery
#16
Tsun Sheng N Ku, Stella Bernardo, Carla J Walraven, Samuel A Lee
Invasive candidiasis continues to be associated with significant morbidity and mortality as well as substantial health care costs nationally and globally. One of the contributing factors is the development of resistance to antifungal agents that are already in clinical use. Moreover, there are known treatment limitations with all of the available antifungal agents. Since traditional techniques in novel drug discovery are time consuming, high-throughput screening using flow cytometry presents as a potential tool to identify new antifungal agents that would be useful in the management of these patients...
September 6, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28876025/progress-towards-the-broad-use-of-non-peptide-synthetic-macrocycles-in-drug-discovery
#17
Adrian Whitty, Lauren A Viarengo, Mengqi Zhong
We discuss progress towards addressing three key questions pertaining to the design of screening libraries of synthetic non-peptidic macrocycles (MCs) for drug discovery: What structural and physicochemical properties of MCs maximize the likelihood of achieving strong and specific binding to protein targets? What features render a protein target suitable for binding MCs, and can this information be used to identify suitable targets for inhibition by MCs? What properties of synthetic MCs confer good pharmaceutical properties, and particularly good aqueous solubility coupled with passive membrane permeability? We additionally discuss how the criteria that define a meaningful MC screening hit are linked to the size of the screening library and the synthetic methodology employed in its preparation...
September 6, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28873423/an-immunosignature-test-distinguishes-trypanosoma-cruzi-hepatitis-b-hepatitis-c-and-west-nile-virus-seropositivity-among-asymptomatic-blood-donors
#18
Michael Rowe, Jonathan Melnick, Robert Gerwien, Joseph B Legutki, Jessica Pfeilsticker, Theodore M Tarasow, Kathryn F Sykes
BACKGROUND: The complexity of the eukaryotic parasite Trypanosoma (T.) cruzi manifests in its highly dynamic genome, multi-host life cycle, progressive morphologies and immune-evasion mechanisms. Accurate determination of infection or Chagas' disease activity and prognosis continues to challenge researchers. We hypothesized that a diagnostic platform with higher ligand complexity than previously employed may hold value. METHODOLOGY: We applied the ImmunoSignature Technology (IST) for the detection of T...
September 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28870156/generation-of-expressed-sequence-tags-for-discovery-of-genes-responsible-for-floral-traits-of-chrysanthemum-morifolium-by-next-generation-sequencing-technology
#19
Katsutomo Sasaki, Nobutaka Mitsuda, Kenji Nashima, Kyutaro Kishimoto, Yuichi Katayose, Hiroyuki Kanamori, Akemi Ohmiya
BACKGROUND: Chrysanthemum morifolium is one of the most economically valuable ornamental plants worldwide. Chrysanthemum is an allohexaploid plant with a large genome that is commercially propagated by vegetative reproduction. New cultivars with different floral traits, such as color, morphology, and scent, have been generated mainly by classical cross-breeding and mutation breeding. However, only limited genetic resources and their genome information are available for the generation of new floral traits...
September 4, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28866080/the-tartary-buckwheat-genome-provides-insights%C3%A2-into-rutin-biosynthesis-and-abiotic-stress%C3%A2-tolerance
#20
Lijun Zhang, Xiuxiu Li, Bin Ma, Qiang Gao, Huilong Du, Yuanhuai Han, Yan Li, Yinghao Cao, Ming Qi, Yaxin Zhu, Hongwei Lu, Mingchuan Ma, Longlong Liu, Jianping Zhou, Chenghu Nan, Yongjun Qin, Jun Wang, Lin Cui, Huimin Liu, Chengzhi Liang, Zhijun Qiao
Tartary buckwheat (Fagopyrum tataricum) is an important pseudocereal crop that is strongly adapted to growth in adverse environments. Its gluten-free grain contains complete proteins with a well-balanced composition of essential amino acids and is a rich source of beneficial phytochemicals that provide significant health benefits. Here, we report a high-quality, chromosome-scale Tartary buckwheat genome sequence of 489.3 Mb that is assembled by combining whole-genome shotgun sequencing of both Illumina short reads and single-molecule real-time long reads, sequence tags of a large DNA insert fosmid library, Hi-C sequencing data, and BioNano genome maps...
September 12, 2017: Molecular Plant
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