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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
#1
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/27924269/importance-of-consensus-region-of-multiple-ligand-templates-in-a-virtual-screening-method
#2
Tatsuya Okuno, Koya Kato, Shintaro Minami, Tomoki P Terada, Masaki Sasai, George Chikenji
We discuss methods and ideas of virtual screening (VS) for drug discovery by examining the performance of VS-APPLE, a recently developed VS method, which extensively utilizes the tendency of single binding pockets to bind diversely different ligands, i.e. promiscuity of binding pockets. In VS-APPLE, multiple ligands bound to a pocket are spatially arranged by maximizing structural overlap of the protein while keeping their relative position and orientation with respect to the pocket surface, which are then combined into a multiple-ligand template for screening test compounds...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27923949/novel-bumped-kinase-inhibitors-are-safe-and-effective-therapeutics-in-the-calf-clinical-model-for-cryptosporidiosis
#3
Deborah A Schaefer, Dana P Betzer, Kylie D Smith, Zachary G Millman, Hannah C Michalski, Sarah E Menchaca, Jennifer A Zambriski, Kayode K Ojo, Matthew A Hulverson, Samuel L M Arnold, Kasey L Rivas, Rama S R Vidadala, Wenlin Huang, Lynn K Barrett, Dustin J Maly, Erkang Fan, Wesley C Van Voorhis, Michael W Riggs
Cryptosporidiosis, caused by the apicomplexan parasite Cryptosporidium parvum, is a diarrheal disease that has produced a large global burden in mortality and morbidity in humans and livestock. There are currently no consistently effective parasite-specific pharmaceuticals available for this disease. Bumped kinase inhibitors (BKIs) specific for parasite calcium-dependent protein kinases (CDPKs) have been shown to reduce infection in several parasites having medical and veterinary importance, including Toxoplasma gondii, Plasmodium falciparum, and C...
December 15, 2016: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/27923276/association-between-maternal-circulating-25-hydroxyvitamin-d-concentration-and-placental-volume-in-the-first-trimester
#4
Çiğdem Yayla Abide, Meryem Kurek Eken, Işıl Turan, Enis Özkaya, Oya Pekin, Ateş Karateke
OBJECTIVES: We aimed to assess placental volume and placental mean gray value in vitamin D deficiency and healthy placentas in the first trimester of pregnancy using three-dimensional (3D) ultrasonography and Virtual Organ Computer-aided Analysis (VOCAL). METHODS: This prospective cross sectional study comprised 274 patients, divided into two groups according to the presence or absence of vitamin D deficiency (<20ng/ml deficient, n = 153,>20 ng/ml not deficient, n= 121) in the first trimester of pregnancy...
December 6, 2016: Journal of Maternal-fetal & Neonatal Medicine
https://www.readbyqxmd.com/read/27920524/monte-carlo-simulations-guided-by-imaging-to-predict-the-in-vitro-ranking-of-radiosensitizing-nanoparticles
#5
Paul Retif, Aurélie Reinhard, Héna Paquot, Valérie Jouan-Hureaux, Alicia Chateau, Lucie Sancey, Muriel Barberi-Heyob, Sophie Pinel, Thierry Bastogne
This article addresses the in silico-in vitro prediction issue of organometallic nanoparticles (NPs)-based radiosensitization enhancement. The goal was to carry out computational experiments to quickly identify efficient nanostructures and then to preferentially select the most promising ones for the subsequent in vivo studies. To this aim, this interdisciplinary article introduces a new theoretical Monte Carlo computational ranking method and tests it using 3 different organometallic NPs in terms of size and composition...
2016: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/27920426/crystal-structure-based-discovery-of-a-novel-synthesized-parp1-inhibitor-ol-1-with-apoptosis-inducing-mechanisms-in-triple-negative-breast-cancer
#6
Leilei Fu, Shuya Wang, Xuan Wang, Peiqi Wang, Yaxin Zheng, Dahong Yao, Mingrui Guo, Lan Zhang, Liang Ouyang
Poly (ADP-ribose) polymerase-1 (PARP1) is a highly conserved enzyme focused on the self-repair of cellular DNA damage. Until now, numbers of PARP inhibitors have been reported and used for breast cancer therapy in recent years, especially in TNBC. However, developing a new type PARP inhibitor with distinctive skeleton is alternatively promising strategy for TNBC therapy. In this study, based on co-crystallization studies and pharmacophore-docking-based virtual screening, we discovered a series of dihydrodibenzo[b,e]-oxepin compounds as PARP1 inhibitors...
December 2016: Scientific Reports
https://www.readbyqxmd.com/read/27918689/vertical-jump-biomechanics-altered-with-virtual-overhead-goal
#7
Kevin R Ford, Anh-Dung Nguyen, Eric J Hegedus, Jeffrey B Taylor
Virtual environments with real-time feedback can simulate extrinsic goals that mimic real life conditions. The purpose was to compare jump performance and biomechanics with a physical overhead goal (POG) and with a virtual overhead goal (VOG). Fourteen female subjects participated (age: 18.8±1.1 years, height: 163.2±8.1 cm, weight 63.0±7.9 kg). Sagittal plane trunk, hip, and knee biomechanics were calculated during the landing and take-off phases of DVJ with different goal conditions. Repeated measures ANOVAs determined differences between goal conditions...
December 5, 2016: Journal of Applied Biomechanics
https://www.readbyqxmd.com/read/27916800/lead-discovery-strategies-for-identification-of-chlamydia-pneumoniae-inhibitors
#8
REVIEW
Leena Hanski, Pia Vuorela
Throughout its known history, the gram-negative bacterium Chlamydia pneumoniae has remained a challenging target for antibacterial chemotherapy and drug discovery. Owing to its well-known propensity for persistence and recent reports on antimicrobial resistence within closely related species, new approaches for targeting this ubiquitous human pathogen are urgently needed. In this review, we describe the strategies that have been successfully applied for the identification of nonconventional antichlamydial agents, including target-based and ligand-based virtual screening, ethnopharmacological approach and pharmacophore-based design of antimicrobial peptide-mimicking compounds...
November 28, 2016: Microorganisms
https://www.readbyqxmd.com/read/27914361/development-of-cxcr4-modulators-by-virtual-hts-of-a-novel-amide-sulfamide-compound-library
#9
Renren Bai, Qi Shi, Zhongxing Liang, Younghyoun Yoon, Yiran Han, Amber Feng, Shuangping Liu, Yoonhyeun Oum, C Chris Yun, Hyunsuk Shim
CXCR4 plays a crucial role in recruitment of inflammatory cells to inflammation sites at the beginning of the disease process. Modulating CXCR4 functions presents a new avenue for anti-inflammatory strategies. However, using CXCR4 antagonists for a long term usage presents potential serious side effect due to their stem cell mobilizing property. We have been developing partial CXCR4 antagonists without such property. A new computer-aided drug design program, the FRESH workflow, was used for anti-CXCR4 lead compound discovery and optimization, which coupled both compound library building and CXCR4 docking screens in one campaign...
November 24, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27913182/virtual-screening-and-biophysical-studies-lead-to-hsp90-inhibitors
#10
Renjie Huang, Daniel M Ayine-Tora, M Nasri Muhammad Rosdi, Yu Li, Jóhannes Reynisson, Ivanhoe K H Leung
Heat shock protein 90 (HSP90) is a molecular chaperone that plays important functional roles in cells. The chaperone activity of HSP90 is regulated by the hydrolysis of ATP at the protein's N-terminal domain. HSP90, in particular the N-terminal domain, is a current inhibition target for therapeutic treatments of cancers. This paper describes an application of virtual screening, thermal shift assaying and protein NMR spectroscopy leading to the discovery of HSP90 inhibitors that contain the resorcinol structure...
November 23, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27911347/smartphone-applications-for-immersive-virtual-reality-therapy-for-internet-addiction-and-internet-gaming-disorder
#11
Melvyn W B Zhang, Roger C M Ho
There have been rapid advances in technologies over the past decade and virtual reality technology is an area which is increasingly utilized as a healthcare intervention in many disciplines including that of Medicine, Surgery and Psychiatry. In Psychiatry, most of the current interventions involving the usage of virtual reality technology is limited to its application for anxiety disorders. With the advances in technology, Internet addiction and Internet gaming disorders are increasingly prevalent. To date, these disorders are still being treated using conventional psychotherapy methods such as cognitive behavioural therapy...
November 25, 2016: Technology and Health Care: Official Journal of the European Society for Engineering and Medicine
https://www.readbyqxmd.com/read/27905473/carcinogenic-human-papillomavirus-infection
#12
Mark Schiffman, John Doorbar, Nicolas Wentzensen, Silvia de Sanjosé, Carole Fakhry, Bradley J Monk, Margaret A Stanley, Silvia Franceschi
Infections with human papillomavirus (HPV) are common and transmitted by direct contact. Although the great majority of infections resolve within 2 years, 13 phylogenetically related, sexually transmitted HPV genotypes, notably HPV16, cause - if not controlled immunologically or by screening - virtually all cervical cancers worldwide, a large fraction of other anogenital cancers and an increasing proportion of oropharyngeal cancers. The carcinogenicity of these HPV types results primarily from the activity of the oncoproteins E6 and E7, which impair growth regulatory pathways...
December 1, 2016: Nature Reviews. Disease Primers
https://www.readbyqxmd.com/read/27903422/novel-butyrylcholinesterase-inhibitors-through-pharmacophore-modeling-virtual-screening-and-dft-based-approaches-along-with-design-of-bioisosterism-based-analogues
#13
Dhrubajyoti Gogoi, Amrita Kashyap Chaliha, Diganta Sarma, Bibhuti Bhusan Kakoti, Alak Kumar Buragohain
Ligand and structure-based pharmacophore models were used to identify the important chemical features of butyrylcholinesterase (BChE) inhibitors. A training set of 16 known structurally diverse compounds with a wide range of inhibitory activity against BChE was used to develop a quantitative ligand-based pharmacophore (Hypo1) model to identify novel BChE inhibitors in virtual screening databases. A structure-based pharmacophore hypothesis (Phar1) was also developed with the ligand-binding site of BChE in consideration...
November 27, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/27903217/rational-drug-discovery-of-hcv-helicase-inhibitor-improved-docking-accuracy-with-multiple-seedings-of-autodock-vina-and-in-situ-minimization
#14
SeeKhai Lim, Rozana Othman, Rohana Yusof, ChoonHan Heh
BACKGROUND: Hepatitis C is a significant cause for end-stage liver diseases and liver transplantation which affects approximate 3% of the global populations. Despite the present of several direct antiviral agents in the treatment of hepatitis C, the standard treatment for HCV is accompanied by several drawbacks such as adverse side effects, high pricing of medications and the rapid emerging rate of resistant HCV variants. OBJECTIVES: To discover potential inhibitors for HCV helicase through an optimized in silico approach...
November 30, 2016: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/27903215/identification-of-novel-agents-for-the-treatment-of-brain-metastases-of-breast-cancer
#15
Vinay Kumar Venishetty, Werner J Geldenhuys, Tori B Terell-Hall, Jessica I G Griffith, Gregory R Sondag, Fayez F Safadi, Paul R Lockman
BACKGROUND: Brain cancer from metastasized breast cancer has a high mortality rate in women. The treatment of lesions is hampered in large part by the blood-brain barrier (BBB), which prevents adequate distribution of anti-cancer compounds to brain metastases. METHOD: In this study we used a novel screening method to identify candidate molecules that are well-suited to utilizing the BBB choline transporter for distribution into the brain parenchyma. RESULTS: From our screen we identified two compounds, Ch-1 and Ch-2 that were able to reduce the brain tumor burden in a murine mouse model of brain metastasis of breast cancer...
November 21, 2016: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/27899825/the-role-of-pharmacists-and-pharmacy-education-in-point-of-care-testing
#16
James P Kehrer, Deborah E James
Point-of-care testing (POCT) is defined as laboratory testing conducted close to the site of patient care. Although performed originally primarily by clinical staff for acute conditions, recent advances in technology have made such testing possible for disease screening and prevention across a wide range of conditions in virtually any setting, and often by individuals with little or no training. With the ongoing evolution in POCT, numerous concerns have arisen about the quality and accuracy of the tests, comparability between multiple tests for the same endpoint, interpretation of test results, and whether and how results should be used for therapeutic decisions and included in a patient's medical record...
October 25, 2016: American Journal of Pharmaceutical Education
https://www.readbyqxmd.com/read/27899820/inhibition-of-hedgehog-dependent-tumors-and-cancer-stem-cells-by-a-newly-identified-naturally-occurring-chemotype
#17
Paola Infante, Romina Alfonsi, Cinzia Ingallina, Deborah Quaglio, Francesca Ghirga, Ilaria D'Acquarica, Flavia Bernardi, Laura Di Magno, Gianluca Canettieri, Isabella Screpanti, Alberto Gulino, Bruno Botta, Mattia Mori, Lucia Di Marcotullio
Hedgehog (Hh) inhibitors have emerged as valid tools in the treatment of a wide range of cancers. Indeed, aberrant activation of the Hh pathway occurring either by ligand-dependent or -independent mechanisms is a key driver in tumorigenesis. The smoothened (Smo) receptor is one of the main upstream transducers of the Hh signaling and is a validated target for the development of anticancer compounds, as underlined by the FDA-approved Smo antagonist Vismodegib (GDC-0449/Erivedge) for the treatment of basal cell carcinoma...
September 22, 2016: Cell Death & Disease
https://www.readbyqxmd.com/read/27899265/discovery-of-novel-dna-methyltransferase-3a-inhibitors-via-structure-based-virtual-screening-and-biological-assays
#18
Zhiyuan Shao, Pan Xu, Wen Xu, Linjuan Li, Shien Liu, Rukang Zhang, Yu-Chih Liu, Chenhua Zhang, Shijie Chen, Cheng Luo
DNA methyltransferases are involved in diverse biological processes and abnormal methylation patterns play essential roles in cancer initiation and progression. DNA methyltransferase 3A (DNMT3A) acting as a de novo DNA methyltransferase, has gained widespread attention especially in haematological diseases. To date, large numbers of DNMTs inhibitors have been discovered, however, the small molecular inhibitors targeting DNMT3A are still in its infancy. In this study, structure-based virtual screening in combination with biological assays was performed to discovery potent novel DNMT3A inhibitors...
November 11, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27898018/combating-ebola-with-repurposed-therapeutics-using-the-cando-platform
#19
Gaurav Chopra, Sashank Kaushik, Peter L Elkin, Ram Samudrala
Ebola virus disease (EVD) is extremely virulent with an estimated mortality rate of up to 90%. However, the state-of-the-art treatment for EVD is limited to quarantine and supportive care. The 2014 Ebola epidemic in West Africa, the largest in history, is believed to have caused more than 11,000 fatalities. The countries worst affected are also among the poorest in the world. Given the complexities, time, and resources required for a novel drug development, finding efficient drug discovery pathways is going to be crucial in the fight against future outbreaks...
November 25, 2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/27897029/a-method-for-evaluating-the-performance-of-computer-aided-detection-of-pulmonary-nodules-in-lung-cancer-ct-screening-detection-limit-for-nodule-size-and-density
#20
Hajime Kobayashi, Masaki Ohkubo, Akihiro Narita, Janaka C Marasinghe, Kohei Murao, Toru Matsumoto, Shusuke Sone, Shinichi Wada
OBJECTIVES: We propose the application of virtual nodules to evaluate the performance of computer-aided detection (CAD) of lung nodules in cancer screening using low-dose computed tomography (CT). METHODS: The virtual nodules were generated based on the spatial resolution measured for a CT system used in an institution providing cancer screening and were fused into clinical lung images obtained at that institution, allowing site-specificity. First, we validated the virtual nodules as an alternative to artificial nodules inserted into a phantom...
November 29, 2016: British Journal of Radiology
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