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Drug prediction

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https://www.readbyqxmd.com/read/27926382/prediction-of-anti-cancer-drug-response-by-kernelized-multi-task-learning
#1
Mehmet Tan
MOTIVATION: Chemotherapy or targeted therapy are two of the main treatment options for many types of cancer. Due to the heterogeneous nature of cancer, the success of the therapeutic agents differs among patients. In this sense, determination of chemotherapeutic response of the malign cells is essential for establishing a personalized treatment protocol and designing new drugs. With the recent technological advances in producing large amounts of pharmacogenomic data, in silico methods have become important tools to achieve this aim...
October 2016: Artificial Intelligence in Medicine
https://www.readbyqxmd.com/read/27925651/model-based-dose-selection-for-intravaginal-ring-formulations-releasing-anastrozole-and-levonorgestrel-intended-for-the-treatment-of-endometriosis-symptoms
#2
Isabel Reinecke, Marcus-Hillert Schultze-Mosgau, Rüdiger Nave, Heinz Schmitz, Bart A Ploeger
Pharmacokinetics (PK) of anastrozole (ATZ) and levonorgestrel (LNG) released from an intravaginal ring (IVR) intended to treat endometriosis symptoms were characterized, and the exposure-response relationship focusing on the development of large ovarian follicle-like structures was investigated by modeling and simulation to support dose selection for further studies. A population PK analysis and simulations were performed for ATZ and LNG based on clinical phase 1 study data from 66 healthy women. A PK/PD model was developed to predict the probability of a maximum follicle size ≥30 mm and the potential contribution of ATZ beside the known LNG effects...
December 7, 2016: Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/27924615/a-model-for-predicting-the-interindividual-variability-of-drug-drug-interactions
#3
M Tod, L Bourguignon, N Bleyzac, S Goutelle
Pharmacokinetic drug-drug interactions are frequently characterized and quantified by an AUC ratio (Rauc). The typical value of the AUC ratio in case of cytochrome-mediated interactions may be predicted by several approaches, based on in vitro or in vivo data. Prediction of the interindividual variability of Rauc would help to anticipate more completely the consequences of a drug-drug interaction. We propose and evaluate a simple approach for predicting the standard deviation (sd) of Ln(Rauc), a metric close to the interindividual coefficient of variation of Rauc...
December 6, 2016: AAPS Journal
https://www.readbyqxmd.com/read/27924481/machine-learning-approaches-toward-building-predictive-models-for-small-molecule-modulators-of-mirna-and-its-utility-in-virtual-screening-of-molecular-databases
#4
Vinita Periwal, Vinod Scaria
The ubiquitous role of microRNAs (miRNAs) in a number of pathological processes has suggested that they could act as potential drug targets. RNA-binding small molecules offer an attractive means for modulating miRNA function. The availability of bioassay data sets for a variety of biological assays and molecules in public domain provides a new opportunity toward utilizing them to create models and further utilize them for in silico virtual screening approaches to prioritize or assign potential functions for small molecules...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924364/metabolic-characterization-of-1-5-fluoropentyl-1h-indol-3-yl-4-methyl-1-naphthalenyl-methanone-mam-2201-using-human-liver-microsomes-and-cdna-overexpressed-cytochrome-p450-enzymes
#5
Tae Yeon Kong, Ju-Hyun Kim, Won Gu Choi, Joo Young Lee, Hee Seung Kim, Jin Young Kim, Moon Kyo In, Hye Suk Lee
MAM-2201 is a synthetic cannabinoid that is increasingly found in recreational drug abusers and cases of severe intoxication. Thus, characterization of the metabolic pathways of MAM-2201 is necessary to predict individual pharmacokinetics and toxicity differences, and to avoid toxic drug-drug interactions. Collectively, 19 phase 1 metabolites of MAM-2201 were identified using liquid chromatography-Orbitrap mass spectrometry following human liver microsomal incubations in the presence of NADPH: 7 hydroxy-MAM-2201 (M1-M7), 4 dihydroxy-MAM-2201 (M8-M11), dihydrodiol-MAM-2201 (M12), N-(5-hydroxypentyl)-MAM-2201 (M13), hydroxy-M13 (M14), N-dealkyl-MAM-2201 (M15), 2 hydroxy-M15 (M16, M17), MAM-2201 N-pentanoic acid (M18), and hydroxy-M18 (M19)...
December 6, 2016: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/27924273/molecular-dynamics-analysis-to-evaluate-docking-pose-prediction
#6
Takako Sakano, Md Iqbal Mahamood, Takefumi Yamashita, Hideaki Fujitani
The accurate prediction of a ligand-protein complex structure is important for computer-assisted drug development. Although many docking methods have been developed over the last three decades, the success of binding structure prediction remains greatly limited. The purpose of this study was to demonstrate the usefulness of molecular dynamics (MD) simulation in assessing a docking pose predicted using a docking program. If the predicted pose is not unstable in an aqueous environment, MD simulation equilibrates the system and removes the ligand from the predicted position...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27924018/disgenet-a-comprehensive-platform-integrating-information-on-human-disease-associated-genes-and-variants
#7
Janet Piñero, Àlex Bravo, Núria Queralt-Rosinach, Alba Gutiérrez-Sacristán, Jordi Deu-Pons, Emilio Centeno, Javier García-García, Ferran Sanz, Laura I Furlong
The information about the genetic basis of human diseases lies at the heart of precision medicine and drug discovery. However, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, availability and different conceptualization of the data must be overcome. To provide the community with a resource free of these hurdles, we have developed DisGeNET (http://www.disgenet.org), one of the largest available collections of genes and variants involved in human diseases...
October 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923859/non-growing-follicle-density-is-increased-following-adriamycin-bleomycin-vinblastine-and-dacarbazine-abvd-chemotherapy-in-the-adult-human-ovary
#8
M McLaughlin, T W Kelsey, W H B Wallace, R A Anderson, E E Telfer
STUDY QUESTION: Do the chemotherapeutic regimens of ABVD (adriamycin, bleomycin, vinblastine and dacarbazine) or OEPA-COPDAC (combined vincristine, etoposide, prednisone, doxorubicin (OEPA) and cyclophosphamide, vincristine, prednisone, dacarbazine (COPDAC)) used to treat Hodgkin lymphoma (HL), affect the density, morphology and in vitro developmental potential of human ovarian follicles? SUMMARY ANSWER: Ovarian tissue from women treated with ABVD contained a higher density of non-growing follicles (NGFs) per cubic millimetre and increased numbers of multiovular follicles but showed reduced in vitro growth compared with patients with lymphoma who had not received chemotherapy, patients treated with OEPA-COPDAC, age-matched healthy women and age-related model-predicted values...
December 5, 2016: Human Reproduction
https://www.readbyqxmd.com/read/27923842/predicting-mek-inhibitor-response-in-lung-cancer-a-proper-signature-is-required
#9
Yaohua Xue, Piro Lito
The ERK signaling pathway is one of the most commonly deregulated pathways in cancer. Assays that accurately measure ERK signaling output in clinical specimens would be extremely helpful not only in determining the parmacodynamic effects of drug treatment but also in selecting those patients most likely to respond to therapy.
December 6, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/27923476/establishment-of-quantitative-retention-activity-model-by-optimized-microemulsion-liquid-chromatography
#10
Liyuan Xu, Haoshi Gao, Liangxing Li, Yinnong Li, Liuyun Wang, Chongkai Gao, Ning Li
The effective permeability coefficient is of theoretical and practical importance in evaluation of the bioavailability of drug candidates. However, most methods currently used to measure this coefficient are expensive and time-consuming. In this paper, we addressed these problems by proposing a new measurement method which is based on the microemulsion liquid chromatography. First, the parallel artificial membrane permeability assays model was used to determine the effective permeability of drug so that quantitative retention-activity relationships could be established, which were used to optimize the microemulsion liquid chromatography...
November 4, 2016: Journal of Chromatography. A
https://www.readbyqxmd.com/read/27923250/clinical-evaluation-of-the-first-automated-assay-for-the-detection-of-stimulating-tsh-receptor-autoantibodies
#11
S Allelein, M Ehlers, S Goretzki, D Hermsen, J Feldkamp, M Haase, T Dringenberg, C Schmid, H Hautzel, M Schott
Until recently, stimulating TSH receptor autoantibodies (sTRAbs) could only be measured by bioassays. A new assay system, which directly detects sTRAb in sera by applying bridge technology, has been established and is now available as automated chemiluminescence (bridge) immunoassay. We evaluated the automated bridge assay in clinical routine and compared it with a conventional automated TRAb assay (competition assay). Altogether, 226 Graves' disease (GD), 57 autoimmune thyroiditis, 74 non-autoimmune nodular goiter and 49 thyroid cancer patients, as well as 41 healthy controls were retrospectively evaluated...
December 2016: Hormone and Metabolic Research, Hormon- und Stoffwechselforschung, Hormones et Métabolisme
https://www.readbyqxmd.com/read/27922627/blood-based-and-urinary-prostate-cancer-biomarkers-a-review-and-comparison-of-novel-biomarkers-for-detection-and-treatment-decisions
#12
REVIEW
R J Hendriks, I M van Oort, J A Schalken
BACKGROUND: The diagnosis of prostate cancer (PCa) is currently based on serum PSA testing and/or abnormal digital rectal examination and histopathologic evaluation of prostate biopsies. The main drawback of PSA testing is the lack of specificity for PCa. To improve early detection of PCa more specific biomarkers are needed. In the past few years, many new promising biomarkers have been identified; however, to date, only a few have reached clinical practice. METHODS: In this review, we discuss new blood-based and urinary biomarker models that are promising for usage in PCa detection, follow-up and treatment decision-making...
December 6, 2016: Prostate Cancer and Prostatic Diseases
https://www.readbyqxmd.com/read/27922541/effects-of-the-5-ht1a-receptor-agonists-buspirone-and-8-oh-dpat-on-pupil-size-in-common-marmosets
#13
Manato Kotani, Naoko Urushino, Itaru Natsutani, Yuji Ogi, Kazuhito Ikeda
As pupil size is affected by psychotropic drugs in all mammals, it has been used as a well-established clinical indicator for the preclinical and clinical development of novel drugs. It has been reported that activation of the serotonin (5-HT)1A receptor differently affects pupil response in rodents (mydriasis) and humans (miosis). Thus, it is important to establish a quantitative system for measuring pupil size using other species, such as nonhuman primates. Common marmosets have recently attracted a great deal of attention as suitable experimental animals in the psychoneurological field because of handling ease compared with other nonhuman primates and the requirement for small amounts of test drugs...
December 2, 2016: Behavioural Pharmacology
https://www.readbyqxmd.com/read/27922344/predictors-of-mortality-in-a-paediatric-intensive-care-unit-in-kigali-rwanda
#14
Rosine Nyirasafari, Mark H Corden, Angélique Charlie Karambizi, Jean Claude Kabayiza, Jean Damascene Makuza, Rex Wong, Michael F Canarie
BACKGROUND: The enormous burden of critical illness in resource-limited settings has led to a growing interest in paediatric critical care in these regions. However, published data on the practice of critical care and patient outcomes in these settings are scant. OBJECTIVE: This study sought to identify risk factors associated with mortality in the newly established Paediatric Intensive Care Unit (PICU) at Kigali University Teaching Hospital (KUTH) in Rwanda and test the predictive ability of a newly devised mortality risk score, the modified PRISM (MP) score...
December 6, 2016: Paediatrics and International Child Health
https://www.readbyqxmd.com/read/27922047/new-arylated-benzo-h-quinolines-induce-anti-cancer-activity-by-oxidative-stress-mediated-dna-damage
#15
Dharmendra K Yadav, Reeta Rai, Naresh Kumar, Surjeet Singh, Sanjeev Misra, Praveen Sharma, Priyanka Shaw, Horacio Pérez-Sánchez, Ricardo L Mancera, Eun Ha Choi, Mi-Hyun Kim, Ramendra Pratap
The anti-cancer activity of the benzo[h]quinolines was evaluated on cultured human skin cancer (G361), lung cancer (H460), breast cancer (MCF7) and colon cancer (HCT116) cell lines. The inhibitory effect of these compounds on the cell growth was determined by the MTT assay. The compounds 3e, 3f, 3h and 3j showed potential cytotoxicity against these human cancer cell lines. Effect of active compounds on DNA oxidation and expression of apoptosis related gene was studied. We also developed a quantitative method to measure the activity of cyclin-dependent kinases-2 (CDK2) by western blotting in the presence of active compound...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27921285/spatiotemporal-distribution-modeling-of-pet-tracer-uptake-in-solid-tumors
#16
Madjid Soltani, Mostafa Sefidgar, Hossein Bazmara, Michael E Casey, Rathan M Subramaniam, Richard L Wahl, Arman Rahmim
OBJECTIVE: Distribution of PET tracer uptake is elaborately modeled via a general equation used for solute transport modeling. This model can be used to incorporate various transport parameters of a solid tumor such as hydraulic conductivity of the microvessel wall, transvascular permeability as well as interstitial space parameters. This is especially significant because tracer delivery and drug delivery to solid tumors are determined by similar underlying tumor transport phenomena, and quantifying the former can enable enhanced prediction of the latter...
December 5, 2016: Annals of Nuclear Medicine
https://www.readbyqxmd.com/read/27921038/the-clinical-manifestation-and-management-of-autosomal-dominant-polycystic-kidney-disease-in-china
#17
REVIEW
Cheng Xue, Chen-Chen Zhou, Ming Wu, Chang-Lin Mei
BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is the most common monogenic hereditary kidney disease characterized by progressive enlargement of renal cysts. The incidence is 1-2‰ worldwide. Mutations in two genes (PKD1 and PKD2) cause ADPKD. Currently, there is no pharmaceutical treatment available for ADPKD patients in China. Summary: This review focused on advances in clinical manifestation, gene diagnosis, risk factors, and management of ADPKD in China. There is an age-dependent increase in total kidney volume (TKV) and decrease in renal function in Chinese ADPKD patients...
October 2016: Kidney Diseases
https://www.readbyqxmd.com/read/27920722/a-new-structure-activity-relationship-sar-model-for-predicting-drug-induced-liver-injury-based-on-statistical-and-expert-based-structural-alerts
#18
Fabiola Pizzo, Anna Lombardo, Alberto Manganaro, Emilio Benfenati
The prompt identification of chemical molecules with potential effects on liver may help in drug discovery and in raising the levels of protection for human health. Besides in vitro approaches, computational methods in toxicology are drawing attention. We built a structure-activity relationship (SAR) model for evaluating hepatotoxicity. After compiling a data set of 950 compounds using data from the literature, we randomly split it into training (80%) and test sets (20%). We also compiled an external validation set (101 compounds) for evaluating the performance of the model...
2016: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/27919952/molecular-factors-associated-with-pemetrexed-sensitivity-according-to-histological-type-in-non-small-cell-lung-cancer
#19
Tsukihisa Yoshida, Tatsuro Okamoto, Tokujiro Yano, Kazuki Takada, Mikihiro Kohno, Kenichi Suda, Mitsuhiro Takenoyama, Yoshinao Oda, Yoshihiko Maehara
BACKGROUND: This study was designed to investigate potential molecules that predict chemosensitivity to pemetrexed (Alimta®) in surgically resected non-small cell lung cancer (NSCLC). MATERIALS AND METHODS: Chemosensitivity to ALM and other drugs was assessed by succinate dehydrogenase inhibition (SDI) test in 69 NSCLC samples (55 adenocarcinomas, and 14 squamous cell carcinomas). The mRNA expression levels of Alimta®-target enzymes [thymidylate synthase (TYMS); dihydrofolate reductase (DHFR) and glycinamide ribonucleotide formyltransferase (GARFT)], Alimta®-metabolizing enzymes [γ-glutamyl hydrase (GGH) and folylpolyglutamate synthase] and an Alimta® transporter [reduce folate carrier (RFC)] were measured and examined for potential correlations to chemosensitivity...
December 2016: Anticancer Research
https://www.readbyqxmd.com/read/27919903/high-throughput-screening-and-prediction-models-building-for-novel-hemozoin-inhibitors-using-physicochemical-properties
#20
Nguyen Tien Huy, Pham Lan Chi, Jun Nagai, Tran Ngoc Dang, Evaristus Chibunna Mbanefo, Ali Mahmoud Ahmed, Nguyen Phuoc Long, Le Thi Bich Thoa, Le Phi Hung, Titouna Afaf, Kaeko Kamei, Hiroshi Ueda, Kenji Hirayama
It is essential to continue the search for novel antimalarial drugs due to current spread of resistance against artemisinin by Plasmodium falciparum parasites. In this study, we developed in silico models to predict hemozoin inhibitors as a potential first-step screening for novel antimalarials. The in vitro colorimetric high throughput screening assay of hemozoin formation was used to identify hemozoin inhibitors from 9600 structurally diverse compounds. Physicochemical properties of positive hits and randomly selected compounds were extracted from ChemSpider database; they were used for developing prediction models to predict hemozoin inhibitors using two different approaches, i...
December 5, 2016: Antimicrobial Agents and Chemotherapy
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