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drug target disease predict

Siyi Zhu, Jiaxin Bing, Xiaoping Min, Chen Lin, Xiangxiang Zeng
Heterogeneous information networks (HINs) currently play an important role in daily life. HINs are applied in many fields, such as science research, e-commerce, recommendation systems, and bioinformatics. Particularly, HINs have been used in biomedical research. Algorithms have been proposed to calculate the correlations between drugs and targets and between diseases and genes. Recently, the interaction between drugs and human genes has become an important subject in the research on drug efficacy and human genomics...
2018: Frontiers in Genetics
Antal Martinecz, Pia Abel Zur Wiesch
Treatment of infectious diseases is often long and requires patients to take drugs even after they have seemingly recovered. This is because of a phenomenon called persistence, which allows small fractions of the bacterial population to survive treatment despite being genetically susceptible. The surviving subpopulation is often below detection limit and therefore is empirically inaccessible but can cause treatment failure when treatment is terminated prematurely. Mathematical models could aid in predicting bacterial survival and thereby determine sufficient treatment length...
August 9, 2018: Pathogens and Disease
Emily Langron, Stella Prins, Paola Vergani
BACKGROUND AND PURPOSE: Cystic fibrosis (CF) is a debilitating hereditary disease caused by mutations in the CFTR gene, which encodes an anion channel. WT-CFTR gating is a non-equilibrium process. After ATP binding, CFTR enters a stable open state (O1 ). ATP hydrolysis leads it to a short-lived post-hydrolytic open state (O2 ), from which channels close. Here we use mutations to probe the mechanism of VX-770, the first compound directly targeting the CFTR protein approved for treatment of CF...
August 14, 2018: British Journal of Pharmacology
Dana E Rathkopf, Howard I Scher
Five new agents have been shown to prolong survival in patients with metastatic castration-resistant prostate cancer, including two targeting androgen receptor signaling (abiraterone acetate plus prednisone; enzalutamide). Recognition that these tumors remain driven by androgen receptor signaling has prompted clinical evaluation of these agents at earlier states in the prostate cancer disease continuum, along with the continued development of new agents targeting this pathway. Areas covered: This article focuses on apalutamide, a next-generation nonsteroidal antiandrogen, with current literature queried in PubMed/Medline...
September 2018: Expert Review of Anticancer Therapy
Anamika Singh Gaur, Selvaraman Nagamani, Karunakar Tanneeru, Dmitry Druzhilovskiy, Anastassia Rudik, Vladimir Poroikov, G Narahari Sastry
Molecular Property Diagnostic Suite - Diabetes Mellitus (MPDSDM ) is a Galaxy-based, open source disease-specific web portal for diabetes. It consists of three modules namely i) data library ii) data processing and iii) data analysis tools. The data library (target library and literature) module provide extensive and curated information about the genes involved in type 1 and type 2 diabetes onset and progression stage (available at The database also contains information on drug targets, biomarkers, therapeutics and associated genes specific to type 1, and type 2 diabetes...
August 6, 2018: Journal of Biomedical Informatics
Ting-Ting Zhang, Rui Xue, Xin Wang, Shi-Wen Zhao, Lei An, Yun-Feng Li, You-Zhi Zhang, Shao Li
Current target-oriented paradigm for novel antidepressant discovery has been difficult to succeed and the failures always bring huge economic losses. Although abundant ledge of disease related genes and drug action targets has been accumulated, the successful application of the knowledge for new drug discovery is limited. Here, we predicted and validated potential antidepressants and molecular targets from DrugBank recorded drugs using a novel network-based drug repositioning approach. This approach predicted relationships between drug and targets through network-based integration of drug chemical similarity, therapeutic similarity and protein-protein interactions...
August 4, 2018: European Neuropsychopharmacology: the Journal of the European College of Neuropsychopharmacology
Isabelle Serr, Carolin Daniel
T follicular helper (TFH) cells are an integral part of humoral immunity by providing help to B cells to produce high-affinity antibodies. The TFH precursor compartment circulates in the blood and TFH cell dysregulation is implied in various autoimmune diseases including type 1 diabetes (T1D). Symptomatic T1D is preceded by a preclinical phase (indicated by the presence of islet autoantibodies) with a highly variable progression time to the symptomatic disease. This heterogeneity points toward differences in immune activation in children with a fast versus slow progressor phenotype...
2018: Frontiers in Immunology
Haroon Khan, Dima A Sabbah, Muhammad Zafar, Mohammad S Mubarak
Fungal diseases could be serious and, in some cases, life-threatening. Considering the limited availability of antifungal agents in use, and the emergence of multi drug resistance (MDR) in fungal infections, there is a pressing need for the development of novel broad spectrum antifungal drugs with better efficacy. Coruscanone A analogues, natural derivatives which target the fungal lanosterol enzyme, were docked against lanosterol 14 α-demethylase (CYP51A1) that converts lanosterol to 4,4-dimethylcholesta-8,14,24-trien-3β-ol in the ergosterol biosynthesis pathway in order to stabilize the plasma membrane of the fungal species, and hence can be targeted for an effective antifungal therapy...
August 1, 2018: Life Sciences
Cyrille Touzeau, Paulo Maciag, Martine Amiot, Philippe Moreau
Despite advances in the treatment of multiple myeloma, the disease still remains incurable for the majority of patients. The overexpression of anti-apoptotic proteins (i.e., Bcl-2, Bcl-XL or Mcl-1) is a hallmark of cancer and favors tumor cell survival and resistance to therapy. The oral drug venetoclax is the first-in-class Bcl-2-specific BH3 mimetic. In myeloma, in vitro sensitivity to venetoclax is mainly observed in plasma cells harboring the t(11;14) translocation, a molecular subgroup associated with high Bcl-2 and low Mcl-1/Bcl-XL expression...
August 3, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Sunyong Yoo, Hojung Nam, Doheon Lee
Although natural compounds have provided a wealth of leads and clues in drug development, the process of identifying their pharmacological effects is still a challenging task. Over the last decade, many in vitro screening methods have been developed to identify the pharmacological effects of natural compounds, but they are still costly processes with low productivity. Therefore, in silico methods, primarily based on molecular information, have been proposed. However, large-scale analysis is rarely considered, since many natural compounds do not have molecular structure and target protein information...
August 3, 2018: Scientific Reports
Erika Cecchin, Elena De Mattia, Fabrizio Ecca, Giuseppe Toffoli
Adverse events affect the pharmacological treatment of approximately 90% of colorectal cancer (CRC) patients at any stage of the disease. Chemotherapy including fluoropyrimidines, irinotecan, and oxaliplatin is the cornerstone of the pharmacological treatment of CRC. The introduction of novel targeted agents, as anti-EGFR (i.e. cetuximab, panitumumab) and antiangiogenic (i.e. bevacizumab, ziv-aflibercept, regorafenib, and ramucirumab) molecules, into the oncologist's toolbox has led to significant improvements in the life expectancy of advanced CRC patients, but with a substantial increase in toxicity burden...
July 2018: Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy
Eva-Maria Didden, Yann Ruffieux, Noemi Hummel, Orestis Efthimiou, Stephan Reichenbach, Sandro Gsteiger, Axel Finckh, Christine Fletcher, Georgia Salanti, Matthias Egger
BACKGROUND: Decision makers often need to assess the real-world effectiveness of new drugs prelaunch, when phase II/III randomized controlled trials (RCTs) but no other data are available. OBJECTIVE: To develop a method to predict drug effectiveness prelaunch and to apply it in a case study in rheumatoid arthritis (RA). METHODS: The approach 1) identifies a market-approved treatment ( S) currently used in a target population similar to that of the new drug ( N); 2) quantifies the impact of treatment, prognostic factors, and effect modifiers on clinical outcome; 3) determines the characteristics of patients likely to receive N in routine care; and 4) predicts treatment outcome in simulated patients with these characteristics...
August 2018: Medical Decision Making: An International Journal of the Society for Medical Decision Making
Marc Sala, Manu Jain
Cystic fibrosis (CF) is the most common, life-limiting autosomal recessive disease in Caucasians, and is caused by defects in production of the CFTR ion channel. Until recently, there were no available treatments targeting the disease-causing defects in CFTR but newly developed CFTR modulators are changing the course of disease in CF. The newest modulator, tezacaftor, is a CFTR corrector that was recently approved by the FDA to be used in combination with the first approved CFTR potentiator, ivacaftor. Areas Covered: A detailed review of the clinical trials and published literature, focusing on safety and efficacy, leading to the approval of tezacaftor in cystic fibrosis...
August 3, 2018: Expert Review of Respiratory Medicine
Yan Li, Fiona Clow, John D Fraser, Feng Lin
Previous studies have demonstrated that staphylococcal superantigen-like protein 7 (SSL7), a protein produced by Staphylococcus aureus, potently inhibits the formation of the complement membrane attack complex by binding to complement component 5 (C5). However, because of the predicted immunogenicity of SSL7 as a foreign protein in humans, its potential as a new complement inhibitor for treating complement-mediated diseases is uncertain. In this study, we found that administration of SSL7 significantly prevented complement-mediated hemolysis and reduced hemoglobinuria in a mouse model of complement-mediated intravascular hemolysis...
July 31, 2018: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
Gholamreza Bidkhori, Rui Benfeitas, Ezgi Elmas, Meisam Naeimi Kararoudi, Muhammad Arif, Mathias Uhlen, Jens Nielsen, Adil Mardinoglu
Hepatocellular carcinoma (HCC) is a deadly form of liver cancer with high mortality worldwide. Unfortunately, the large heterogeneity of this disease makes it difficult to develop effective treatment strategies. Cellular network analyses have been employed to study heterogeneity in cancer, and to identify potential therapeutic targets. However, the existing approaches do not consider metabolic growth requirements, i.e., biological network functionality, to rank candidate targets while preventing toxicity to non-cancerous tissues...
2018: Frontiers in Physiology
Claudia Matteucci, Ayele Argaw-Denboba, Emanuela Balestrieri, Alessandro Giovinazzo, Martino Miele, Cartesio D'Agostini, Francesca Pica, Sandro Grelli, Maurizio Paci, Antonio Mastino, Paola Sinibaldi Vallebona, Enrico Garaci, Carlo Tomino
BACKGROUND: Thymosin alpha 1 (Tα1) is a well-recognized immune response modulator in a wide range of disorders, particularly infections and cancer. The bioinformatic analysis of public databases allows drug repositioning, predicting a new potential area of clinical intervention. We aimed to decipher the cellular network induced by Tα1 treatment to confirm present use and identify new potential clinical applications. RESEARCH DESIGN AND METHODS: We used the transcriptional profile of human peripheral blood mononuclear cells treated in vitro with Tα1 to perform the enrichment network analysis by the Metascape online tools and the disease enrichment analysis by the DAVID online tool...
July 2018: Expert Opinion on Biological Therapy
Lucas G Viviani, Erika Piccirillo, Arquimedes Cheffer, Leandro de Rezende, Henning Ulrich, Ana Maria Carmona-Ribeiro, Antonia T-do Amaral
Promiscuous inhibition due to aggregate formation has been recognized as a major concern in drug discovery campaigns. Here, we report some aggregators identified in a virtual screening (VS) protocol to search for inhibitors of human ecto -5'-nucleotidase ( ecto -5'-NT/CD73), a promising target for several diseases and pathophysiological events, including cancer, inflammation and autoimmune diseases. Four compounds ( A , B , C and D ), selected from the ZINC-11 database, showed IC50 values in the micromolar range, being at the same time computationally predicted as potential aggregators...
July 27, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Soumita Ghosh, Sulabha Pathak, Haripalsingh M Sonawat, Shobhona Sharma, Arjun Sengupta
Metabolomics refers to top-down systems biological analysis of metabolites in biological specimens. Phenotypic proximity of metabolites makes them interesting candidates for studying biomarkers of environmental stressors such as parasitic infections. Moreover, the host-parasite interaction directly impinges upon metabolic pathways since the parasite uses the host metabolite pool as a biosynthetic resource. Malarial infection, although not recognized as a classic metabolic disorder, often leads to severe metabolic changes such as hypoglycemia and lactic acidosis...
July 26, 2018: Cytokine
E Siva Sankari, Dr D Manimegalai
Membrane proteins are vital type of proteins that serve as channels, receptors and energy transducers in a cell. They perform various important functions, which are mainly associated with their types. They are also attractive targets of drug discovery for various diseases. So predicting membrane protein types is a crucial and challenging research area in bioinformatics and proteomics. Because of vast investigation of uncharacterized protein sequences in databases, customary biophysical techniques are extremely tedious, costly and vulnerable to mistakes...
July 26, 2018: Journal of Theoretical Biology
Chuanbo Huang, Weili Yang, Junpei Wang, Yuan Zhou, Bin Geng, Georgios Kararigas, Jichun Yang, Qinghua Cui
Enrichment analysis methods, e.g., gene set enrichment analysis, represent one class of important bioinformatical resources for mining patterns in biomedical datasets. However, tools for inferring patterns and rules of a list of drugs are limited. In this study, we developed a web-based tool, DrugPattern, for drug set enrichment analysis. We first collected and curated 7019 drug sets, including indications, adverse reactions, targets, pathways, etc. from public databases. For a list of interested drugs, DrugPattern then evaluates the significance of the enrichment of these drugs in each of the 7019 drug sets...
July 24, 2018: Journal of Genetics and Genomics, Yi Chuan Xue Bao
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