Discovery of N6-phenyl-1H-pyrazolo[3,4-d]pyrimidine-3,6-diamine derivatives as novel CK1 inhibitors using common-feature pharmacophore model based virtual screening and hit-to-lead optimization.

PubMed

Yang, Ling-Ling; Li, Guo-Bo; Yan, Heng-Xiu; Sun, Qi-Zheng; Ma, Shuang; Ji, Pan; Wang, Ze-Rong; Feng, Shan; Zou, Jun; Yang, Sheng-Yong

2012-10-01

Aberrant activation of casein kinase 1 (CK1) has been demonstrated to be implicated in the pathogenesis of cancer and various central nervous system disorders. Discovery of CK1 inhibitors has thus attracted much attention in recent years. In this account, we describe the discovery of N6-phenyl-1H-pyrazolo[3,4-d]pyrimidine-3,6-diamine derivatives as novel CK1 inhibitors. An optimal common-feature pharmacophore hypothesis, termed Hypo2, was firstly generated, followed by virtual screening using Hypo2 against several chemical databases. One of the best hit compounds, N6-(4-chlorophenyl)-1H-pyrazolo[3,4-d]pyrimidine-3,6-diamine, was chosen for the subsequent hit-to-lead optimization under the guide of Hypo2, which led to the discovery of a new lead compound (1-(3-(3-amino-1H-pyrazolo[3,4-d]pyrimidin-6-ylamino)phenyl)-3-(3-chloro-4-fluorophenyl)urea) that potently inhibits CK1 with an IC(50) value of 78 nM. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

A Role for Fragment-Based Drug Design in Developing Novel Lead Compounds for Central Nervous System Targets.

PubMed

Wasko, Michael J; Pellegrene, Kendy A; Madura, Jeffry D; Surratt, Christopher K

2015-01-01

Hundreds of millions of U.S. dollars are invested in the research and development of a single drug. Lead compound development is an area ripe for new design strategies. Therapeutic lead candidates have been traditionally found using high-throughput in vitro pharmacological screening, a costly method for assaying thousands of compounds. This approach has recently been augmented by virtual screening (VS), which employs computer models of the target protein to narrow the search for possible leads. A variant of VS is fragment-based drug design (FBDD), an emerging in silico lead discovery method that introduces low-molecular weight fragments, rather than intact compounds, into the binding pocket of the receptor model. These fragments serve as starting points for "growing" the lead candidate. Current efforts in virtual FBDD within central nervous system (CNS) targets are reviewed, as is a recent rule-based optimization strategy in which new molecules are generated within a 3D receptor-binding pocket using the fragment as a scaffold. This process not only places special emphasis on creating synthesizable molecules but also exposes computational questions worth addressing. Fragment-based methods provide a viable, relatively low-cost alternative for therapeutic lead discovery and optimization that can be applied to CNS targets to augment current design strategies.

A Role for Fragment-Based Drug Design in Developing Novel Lead Compounds for Central Nervous System Targets

PubMed Central

Wasko, Michael J.; Pellegrene, Kendy A.; Madura, Jeffry D.; Surratt, Christopher K.

2015-01-01

Hundreds of millions of U.S. dollars are invested in the research and development of a single drug. Lead compound development is an area ripe for new design strategies. Therapeutic lead candidates have been traditionally found using high-throughput in vitro pharmacological screening, a costly method for assaying thousands of compounds. This approach has recently been augmented by virtual screening (VS), which employs computer models of the target protein to narrow the search for possible leads. A variant of VS is fragment-based drug design (FBDD), an emerging in silico lead discovery method that introduces low-molecular weight fragments, rather than intact compounds, into the binding pocket of the receptor model. These fragments serve as starting points for “growing” the lead candidate. Current efforts in virtual FBDD within central nervous system (CNS) targets are reviewed, as is a recent rule-based optimization strategy in which new molecules are generated within a 3D receptor-binding pocket using the fragment as a scaffold. This process not only places special emphasis on creating synthesizable molecules but also exposes computational questions worth addressing. Fragment-based methods provide a viable, relatively low-cost alternative for therapeutic lead discovery and optimization that can be applied to CNS targets to augment current design strategies. PMID:26441817

Optimization of 2-Anilino 4-Amino Substituted Quinazolines into Potent Antimalarial Agents with Oral in Vivo Activity.

PubMed

Gilson, Paul R; Tan, Cyrus; Jarman, Kate E; Lowes, Kym N; Curtis, Joan M; Nguyen, William; Di Rago, Adrian E; Bullen, Hayley E; Prinz, Boris; Duffy, Sandra; Baell, Jonathan B; Hutton, Craig A; Jousset Subroux, Helene; Crabb, Brendan S; Avery, Vicky M; Cowman, Alan F; Sleebs, Brad E

2017-02-09

Novel antimalarial therapeutics that target multiple stages of the parasite lifecycle are urgently required to tackle the emerging problem of resistance with current drugs. Here, we describe the optimization of the 2-anilino quinazoline class as antimalarial agents. The class, identified from publicly available antimalarial screening data, was optimized to generate lead compounds that possess potent antimalarial activity against P. falciparum parasites comparable to the known antimalarials, chloroquine and mefloquine. During the optimization process, we defined the functionality necessary for activity and improved in vitro metabolism and solubility. The resultant lead compounds possess potent activity against a multidrug resistant strain of P. falciparum and arrest parasites at the ring phase of the asexual stage and also gametocytogensis. Finally, we show that the lead compounds are orally efficacious in a 4 day murine model of malaria disease burden.

Identification and hit-to-lead optimization of a novel class of CB1 antagonists.

PubMed

Letourneau, Jeffrey J; Jokiel, Patrick; Olson, John; Riviello, Christopher M; Ho, Koc-Kan; McAleer, Lihong; Yang, Jingchun; Swanson, Robert N; Baker, James; Cowley, Phillip; Edwards, Darren; Ward, Nick; Ohlmeyer, Michael H J; Webb, Maria L

2010-09-15

The discovery, synthesis and preliminary structure-activity relationships (SARs) of a novel class of CB1 antagonists is described. Initial optimization of benzimidazole-based screening hit 4 led to the identification of 'inverted' indole-based lead compound 18c with improved properties versus compound 4 including reduced AlogP, improved microsomal stability and improved aqueous solubility. Compound 18c demonstrates in vivo CB1 antagonist efficacy (CB1 agonist induced hypothermia model) and is orally bioavailable in rat. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Fragment-based virtual screening approach and molecular dynamics simulation studies for identification of BACE1 inhibitor leads.

PubMed

Manoharan, Prabu; Ghoshal, Nanda

2018-05-01

Traditional structure-based virtual screening method to identify drug-like small molecules for BACE1 is so far unsuccessful. Location of BACE1, poor Blood Brain Barrier permeability and P-glycoprotein (Pgp) susceptibility of the inhibitors make it even more difficult. Fragment-based drug design method is suitable for efficient optimization of initial hit molecules for target like BACE1. We have developed a fragment-based virtual screening approach to identify/optimize the fragment molecules as a starting point. This method combines the shape, electrostatic, and pharmacophoric features of known fragment molecules, bound to protein conjugate crystal structure, and aims to identify both chemically and energetically feasible small fragment ligands that bind to BACE1 active site. The two top-ranked fragment hits were subjected for a 53 ns MD simulation. Principle component analysis and free energy landscape analysis reveal that the new ligands show the characteristic features of established BACE1 inhibitors. The potent method employed in this study may serve for the development of potential lead molecules for BACE1-directed Alzheimer's disease therapeutics.

Fragment-assisted hit investigation involving integrated HTS and fragment screening: Application to the identification of phosphodiesterase 10A (PDE10A) inhibitors.

PubMed

Varnes, Jeffrey G; Geschwindner, Stefan; Holmquist, Christopher R; Forst, Janet; Wang, Xia; Dekker, Niek; Scott, Clay W; Tian, Gaochao; Wood, Michael W; Albert, Jeffrey S

2016-01-01

Fragment-based drug design (FBDD) relies on direct elaboration of fragment hits and typically requires high resolution structural information to guide optimization. In fragment-assisted drug discovery (FADD), fragments provide information to guide selection and design but do not serve as starting points for elaboration. We describe FADD and high-throughput screening (HTS) campaign strategies conducted in parallel against PDE10A where fragment hit co-crystallography was not available. The fragment screen led to prioritized fragment hits (IC50's ∼500μM), which were used to generate a hypothetical core scaffold. Application of this scaffold as a filter to HTS output afforded a 4μM hit, which, after preparation of a small number of analogs, was elaborated into a 16nM lead. This approach highlights the strength of FADD, as fragment methods were applied despite the absence of co-crystallographical information to efficiently identify a lead compound for further optimization. Copyright © 2015 Elsevier Ltd. All rights reserved.

Disease Severity and Exercise Testing Reduce Subcutaneous Implantable Cardioverter-Defibrillator Left Sternal ECG Screening Success in Hypertrophic Cardiomyopathy.

PubMed

Srinivasan, Neil T; Patel, Kiran H; Qamar, Kashif; Taylor, Amy; Bacà, Marco; Providência, Rui; Tome-Esteban, Maria; Elliott, Perry M; Lambiase, Pier D

2017-04-01

The features of the hypertrophic cardiomyopathy (HCM) ECG make it a challenge for subcutaneous implantable cardioverter-defibrillator (S-ICD) screening. We aimed to investigate the causes of screening failure at rest and on exercise to inform optimal S-ICD ECG vector development. One hundred and thirty-one HCM patients (age, 50±16 years; 92 males and 39 females) with ≥1 HCM risk factor for sudden death underwent S-ICD ECG screening at rest and on exercise. Fifty patients (38%) were ineligible for S-ICD because of screening failure in every lead vector: 33 (66%) failed in the supine position, 12 (24%) failed in the standing position, and 5 (10%) failed on exercise. In patients who could exercise and passed screening at rest, 31 (44%) had 1 vector safety, 16 (23%) had 2 vector safety, and 24 (33%) had 3 vector safety. Increased R:T wave ratio in the S-ICD screening ECG (odds ratio, 4.0; confidence interval, 3.0-5.3; P <0.001) was associated with screening failure, while R/T ratio <3 in aVF (odds ratio, 0.3; confidence interval, 0.12-0.69; P =0.006) and increasing age (odds ratio, 0.97; confidence interval, 0.95-0.99; P =0.03) was associated with reduced screening failure. European Society of Cardiology risk score was higher in those failing screening (risk score 5.5% [interquartile range, 3.2-8.7] in failed versus 4.5% [interquartile range, 2.9-7.4] in passed; P =0.04). HCM patients have a significant incidence of screening failure, which is determined primarily by the increased R:T ratio on the screening ECG and lead aVF. High-risk patients have an increased screening failure rate. Optimization of sensing algorithms is required to ensure that the highest risk HCM patients can benefit from S-ICD implantation. © 2017 American Heart Association, Inc.

Docking ligands into flexible and solvated macromolecules. 7. Impact of protein flexibility and water molecules on docking-based virtual screening accuracy.

PubMed

Therrien, Eric; Weill, Nathanael; Tomberg, Anna; Corbeil, Christopher R; Lee, Devin; Moitessier, Nicolas

2014-11-24

The use of predictive computational methods in the drug discovery process is in a state of continual growth. Over the last two decades, an increasingly large number of docking tools have been developed to identify hits or optimize lead molecules through in-silico screening of chemical libraries to proteins. In recent years, the focus has been on implementing protein flexibility and water molecules. Our efforts led to the development of Fitted first reported in 2007 and further developed since then. In this study, we wished to evaluate the impact of protein flexibility and occurrence of water molecules on the accuracy of the Fitted docking program to discriminate active compounds from inactive compounds in virtual screening (VS) campaigns. For this purpose, a total of 171 proteins cocrystallized with small molecules representing 40 unique enzymes and receptors as well as sets of known ligands and decoys were selected from the Protein Data Bank (PDB) and the Directory of Useful Decoys (DUD), respectively. This study revealed that implementing displaceable crystallographic or computationally placed particle water molecules and protein flexibility can improve the enrichment in active compounds. In addition, an informed decision based on library diversity or research objectives (hit discovery vs lead optimization) on which implementation to use may lead to significant improvements.

Choosing the optimal method in programmatic colorectal cancer screening: current evidence and controversies

PubMed Central

2015-01-01

Colorectal cancer (CRC) is an important health problem all over the world, being the third most common cancer and the second leading cause of cancer-related death in Western countries. The most important strategy for CRC prevention is screening (i.e. secondary prevention). Since it is widely accepted that adenomas and serrated polyps are the precursors of the vast majority of CRC, early detection and removal of these lesions is associated with a reduction of CRC incidence and, consequently, mortality. Moreover, cancers detected by screening are usually diagnosed at early stages and, therefore, curable by endoscopic or surgical procedures. This review will be address CRC screening strategies in average-risk population, which is defined by those individuals, men and women, 50 years of age or older, without any additional personal or familial predisposing risk factor. In order to maximize the impact of screening and ensure high coverage and equity of access, only organized screening programs (i.e. programmatic screening) should be implemented, as opposed to case-finding or opportunistic screening. For that reason and considering that the optimal approach for colorectal screening may differ depending on the scenario, this review will be focused on the advantages and limitations of each screening strategy in an organized setting. PMID:26136839

Modern drug discovery technologies: opportunities and challenges in lead discovery.

PubMed

Guido, Rafael V C; Oliva, Glaucius; Andricopulo, Adriano D

2011-12-01

The identification of promising hits and the generation of high quality leads are crucial steps in the early stages of drug discovery projects. The definition and assessment of both chemical and biological space have revitalized the screening process model and emphasized the importance of exploring the intrinsic complementary nature of classical and modern methods in drug research. In this context, the widespread use of combinatorial chemistry and sophisticated screening methods for the discovery of lead compounds has created a large demand for small organic molecules that act on specific drug targets. Modern drug discovery involves the employment of a wide variety of technologies and expertise in multidisciplinary research teams. The synergistic effects between experimental and computational approaches on the selection and optimization of bioactive compounds emphasize the importance of the integration of advanced technologies in drug discovery programs. These technologies (VS, HTS, SBDD, LBDD, QSAR, and so on) are complementary in the sense that they have mutual goals, thereby the combination of both empirical and in silico efforts is feasible at many different levels of lead optimization and new chemical entity (NCE) discovery. This paper provides a brief perspective on the evolution and use of key drug design technologies, highlighting opportunities and challenges.

Three classes of glucocerebrosidase inhibitors identified by quantitative high-throughput screening are chaperone leads for Gaucher disease

PubMed Central

Zheng, Wei; Padia, Janak; Urban, Daniel J.; Jadhav, Ajit; Goker-Alpan, Ozlem; Simeonov, Anton; Goldin, Ehud; Auld, Douglas; LaMarca, Mary E.; Inglese, James; Austin, Christopher P.; Sidransky, Ellen

2007-01-01

Gaucher disease is an autosomal recessive lysosomal storage disorder caused by mutations in the glucocerebrosidase gene. Missense mutations result in reduced enzyme activity that may be due to misfolding, raising the possibility of small-molecule chaperone correction of the defect. Screening large compound libraries by quantitative high-throughput screening (qHTS) provides comprehensive information on the potency, efficacy, and structure–activity relationships (SAR) of active compounds directly from the primary screen, facilitating identification of leads for medicinal chemistry optimization. We used qHTS to rapidly identify three structural series of potent, selective, nonsugar glucocerebrosidase inhibitors. The three structural classes had excellent potencies and efficacies and, importantly, high selectivity against closely related hydrolases. Preliminary SAR data were used to select compounds with high activity in both enzyme and cell-based assays. Compounds from two of these structural series increased N370S mutant glucocerebrosidase activity by 40–90% in patient cell lines and enhanced lysosomal colocalization, indicating chaperone activity. These small molecules have potential as leads for chaperone therapy for Gaucher disease, and this paradigm promises to accelerate the development of leads for other rare genetic disorders. PMID:17670938

Identifying Novel Molecular Structures for Advanced Melanoma by Ligand-Based Virtual Screening

PubMed Central

Wang, Zhao; Lu, Yan; Seibel, William; Miller, Duane D.; Li, Wei

2009-01-01

We recently discovered a new class of thiazole analogs that are highly potent against melanoma cells. To expand the structure-activity relationship study and to explore potential new molecular scaffolds, we performed extensive ligand-based virtual screening against a compound library containing 342,910 small molecules. Two different approaches of virtual screening were carried out using the structure of our lead molecule: 1) connectivity-based search using Scitegic Pipeline Pilot from Accelerys and 2) molecular shape similarity search using Schrodinger software. Using a testing compound library, both approaches can rank similar compounds very high and rank dissimilar compounds very low, thus validating our screening methods. Structures identified from these searches were analyzed, and selected compounds were tested in vitro to assess their activity against melanoma cancer cell lines. Several molecules showed good anticancer activity. While none of the identified compounds showed better activity than our lead compound, they provided important insight into structural modifications for our lead compound and also provided novel platforms on which we can optimize new classes of anticancer compounds. One of the newly synthesized analogs based on this virtual screening has improved potency and selectivity against melanoma. PMID:19445498

Utilization of in vitro Caco-2 permeability and liver microsomal half-life screens in discovering BMS-488043, a novel HIV-1 attachment inhibitor with improved pharmacokinetic properties.

PubMed

Yang, Zheng; Zadjura, Lisa M; Marino, Anthony M; D'Arienzo, Celia J; Malinowski, Jacek; Gesenberg, Christoph; Lin, Pin-Fang; Colonno, Richard J; Wang, Tao; Kadow, John F; Meanwell, Nicholas A; Hansel, Steven B

2010-04-01

Optimizing pharmacokinetic properties to improve oral exposure is a common theme in modern drug discovery. In the present work, in vitro Caco-2 permeability and microsomal half-life screens were utilized in an effort to guide the structure-activity relationship in order to improve the pharmacokinetic properties of novel HIV-1 attachment inhibitors. The relevance of the in vitro screens to in vivo pharmacokinetic properties was first demonstrated with a number of program compounds at the early stage of lead optimization. The Caco-2 permeability, tested at 200 microM, was quantitatively predictive of in vivo oral absorption, with complete absorption occurring at a Caco-2 permeability of 100 nm/s or higher. The liver microsomal half-life screen, conducted at 1 microM substrate concentration, can readily differentiate low-, intermediate-, and high-clearance compounds in rats, with a nearly 1:1 correlation in 12 out of 13 program compounds tested. Among the >100 compounds evaluated, BMS-488043 emerged as a lead, exhibiting a Caco-2 permeability of 178 nm/s and a microsomal half-life predictive of a low clearance (4 mL/min/kg) in humans. These in vitro characteristics translated well to the in vivo setting. The oral bioavailability of BMS-488043 in rats, dogs, and monkeys was 90%, 57%, and 60%, respectively. The clearance was low in all three species tested, with a terminal half-life ranging from 2.4 to 4.7 h. Furthermore, the oral exposure of BMS-488043 was significantly improved (6- to 12-fold in rats and monkeys) compared to the prototype compound BMS-378806 that had a suboptimal Caco-2 permeability (51 nm/s) and microsomal half-life. More importantly, the improvements in preclinical pharmacokinetics translated well to humans, leading to a >15-fold increase in the human oral exposure of BMS-488043 than BMS-378806 and enabling a clinical proof-of-concept for this novel class of anti-HIV agents. The current studies demonstrated the valuable role of in vitro ADME screens in improving oral pharmacokinetics at the lead optimization stage. 2009 Wiley-Liss, Inc. and the American Pharmacists Association

One Question, Multiple Answers: Biochemical and Biophysical Screening Methods Retrieve Deviating Fragment Hit Lists.

PubMed

Schiebel, Johannes; Radeva, Nedyalka; Köster, Helene; Metz, Alexander; Krotzky, Timo; Kuhnert, Maren; Diederich, Wibke E; Heine, Andreas; Neumann, Lars; Atmanene, Cedric; Roecklin, Dominique; Vivat-Hannah, Valérie; Renaud, Jean-Paul; Meinecke, Robert; Schlinck, Nina; Sitte, Astrid; Popp, Franziska; Zeeb, Markus; Klebe, Gerhard

2015-09-01

Fragment-based lead discovery is gaining momentum in drug development. Typically, a hierarchical cascade of several screening techniques is consulted to identify fragment hits which are then analyzed by crystallography. Because crystal structures with bound fragments are essential for the subsequent hit-to-lead-to-drug optimization, the screening process should distinguish reliably between binders and non-binders. We therefore investigated whether different screening methods would reveal similar collections of putative binders. First we used a biochemical assay to identify fragments that bind to endothiapepsin, a surrogate for disease-relevant aspartic proteases. In a comprehensive screening approach, we then evaluated our 361-entry library by using a reporter-displacement assay, saturation-transfer difference NMR, native mass spectrometry, thermophoresis, and a thermal shift assay. While the combined results of these screening methods retrieve 10 of the 11 crystal structures originally predicted by the biochemical assay, the mutual overlap of individual hit lists is surprisingly low, highlighting that each technique operates on different biophysical principles and conditions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Combining Computational Methods for Hit to Lead Optimization in Mycobacterium tuberculosis Drug Discovery

PubMed Central

Ekins, Sean; Freundlich, Joel S.; Hobrath, Judith V.; White, E. Lucile; Reynolds, Robert C

2013-01-01

Purpose Tuberculosis treatments need to be shorter and overcome drug resistance. Our previous large scale phenotypic high-throughput screening against Mycobacterium tuberculosis (Mtb) has identified 737 active compounds and thousands that are inactive. We have used this data for building computational models as an approach to minimize the number of compounds tested. Methods A cheminformatics clustering approach followed by Bayesian machine learning models (based on publicly available Mtb screening data) was used to illustrate that application of these models for screening set selections can enrich the hit rate. Results In order to explore chemical diversity around active cluster scaffolds of the dose-response hits obtained from our previous Mtb screens a set of 1924 commercially available molecules have been selected and evaluated for antitubercular activity and cytotoxicity using Vero, THP-1 and HepG2 cell lines with 4.3%, 4.2% and 2.7% hit rates, respectively. We demonstrate that models incorporating antitubercular and cytotoxicity data in Vero cells can significantly enrich the selection of non-toxic actives compared to random selection. Across all cell lines, the Molecular Libraries Small Molecule Repository (MLSMR) and cytotoxicity model identified ~10% of the hits in the top 1% screened (>10 fold enrichment). We also showed that seven out of nine Mtb active compounds from different academic published studies and eight out of eleven Mtb active compounds from a pharmaceutical screen (GSK) would have been identified by these Bayesian models. Conclusion Combining clustering and Bayesian models represents a useful strategy for compound prioritization and hit-to lead optimization of antitubercular agents. PMID:24132686

Optimal healthcare decision making under multiple mathematical models: application in prostate cancer screening.

PubMed

Bertsimas, Dimitris; Silberholz, John; Trikalinos, Thomas

2018-03-01

Important decisions related to human health, such as screening strategies for cancer, need to be made without a satisfactory understanding of the underlying biological and other processes. Rather, they are often informed by mathematical models that approximate reality. Often multiple models have been made to study the same phenomenon, which may lead to conflicting decisions. It is natural to seek a decision making process that identifies decisions that all models find to be effective, and we propose such a framework in this work. We apply the framework in prostate cancer screening to identify prostate-specific antigen (PSA)-based strategies that perform well under all considered models. We use heuristic search to identify strategies that trade off between optimizing the average across all models' assessments and being "conservative" by optimizing the most pessimistic model assessment. We identified three recently published mathematical models that can estimate quality-adjusted life expectancy (QALE) of PSA-based screening strategies and identified 64 strategies that trade off between maximizing the average and the most pessimistic model assessments. All prescribe PSA thresholds that increase with age, and 57 involve biennial screening. Strategies with higher assessments with the pessimistic model start screening later, stop screening earlier, and use higher PSA thresholds at earlier ages. The 64 strategies outperform 22 previously published expert-generated strategies. The 41 most "conservative" ones remained better than no screening with all models in extensive sensitivity analyses. We augment current comparative modeling approaches by identifying strategies that perform well under all models, for various degrees of decision makers' conservativeness.

Trace fluorescent labeling for protein crystallization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pusey, Marc, E-mail: marc.pusey@ixpressgenes.com; Barcena, Jorge; Morris, Michelle

2015-06-27

The presence of a covalently bound fluorescent probe at a concentration of <0.5% does not affect the outcome of macromolecule crystallization screening experiments. Additionally, the fluorescence can be used to determine new, not immediately apparent, lead crystallization conditions. Fluorescence can be a powerful tool to aid in the crystallization of proteins. In the trace-labeling approach, the protein is covalently derivatized with a high-quantum-yield visible-wavelength fluorescent probe. The final probe concentration typically labels ≤0.20% of the protein molecules, which has been shown to not affect the crystal nucleation or diffraction quality. The labeled protein is then used in a plate-screening experimentmore » in the usual manner. As the most densely packed state of the protein is the crystalline form, then crystals show as the brightest objects in the well under fluorescent illumination. A study has been carried out on the effects of trace fluorescent labeling on the screening results obtained compared with nonlabeled protein, and it was found that considering the stochastic nature of the crystal nucleation process the presence of the probe did not affect the outcomes obtained. Other effects are realised when using fluorescence. Crystals are clearly seen even when buried in precipitate. This approach also finds ‘hidden’ leads, in the form of bright spots, with ∼30% of the leads found being optimized to crystals in a single-pass optimization trial. The use of visible fluorescence also enables the selection of colors that bypass interfering substances, and the screening materials do not have to be UV-transparent.« less

Biophysics: for HTS hit validation, chemical lead optimization, and beyond.

PubMed

Genick, Christine C; Wright, S Kirk

2017-09-01

There are many challenges to the drug discovery process, including the complexity of the target, its interactions, and how these factors play a role in causing the disease. Traditionally, biophysics has been used for hit validation and chemical lead optimization. With its increased throughput and sensitivity, biophysics is now being applied earlier in this process to empower target characterization and hit finding. Areas covered: In this article, the authors provide an overview of how biophysics can be utilized to assess the quality of the reagents used in screening assays, to validate potential tool compounds, to test the integrity of screening assays, and to create follow-up strategies for compound characterization. They also briefly discuss the utilization of different biophysical methods in hit validation to help avoid the resource consuming pitfalls caused by the lack of hit overlap between biophysical methods. Expert opinion: The use of biophysics early on in the drug discovery process has proven crucial to identifying and characterizing targets of complex nature. It also has enabled the identification and classification of small molecules which interact in an allosteric or covalent manner with the target. By applying biophysics in this manner and at the early stages of this process, the chances of finding chemical leads with novel mechanisms of action are increased. In the future, focused screens with biophysics as a primary readout will become increasingly common.

Development of predictive pharmacophore model for in silico screening, and 3D QSAR CoMFA and CoMSIA studies for lead optimization, for designing of potent tumor necrosis factor alpha converting enzyme inhibitors

NASA Astrophysics Data System (ADS)

Murumkar, Prashant Revan; Zambre, Vishal Prakash; Yadav, Mange Ram

2010-02-01

A chemical feature-based pharmacophore model was developed for Tumor Necrosis Factor-α converting enzyme (TACE) inhibitors. A five point pharmacophore model having two hydrogen bond acceptors (A), one hydrogen bond donor (D) and two aromatic rings (R) with discrete geometries as pharmacophoric features was developed. The pharmacophore model so generated was then utilized for in silico screening of a database. The pharmacophore model so developed was validated by using four compounds having proven TACE inhibitory activity which were grafted into the database. These compounds mapped well onto the five listed pharmacophoric features. This validated pharmacophore model was also used for alignment of molecules in CoMFA and CoMSIA analysis. The contour maps of the CoMFA/CoMSIA models were utilized to provide structural insight for activity improvement of potential novel TACE inhibitors. The pharmacophore model so developed could be used for in silico screening of any commercial/in house database for identification of TACE inhibiting lead compounds, and the leads so identified could be optimized using the developed CoMSIA model. The present work highlights the tremendous potential of the two mutually complementary ligand-based drug designing techniques (i.e. pharmacophore mapping and 3D-QSAR analysis) using TACE inhibitors as prototype biologically active molecules.

Discovery of a novel class of triazolones as checkpoint kinase inhibitors--hit to lead exploration.

PubMed

Oza, Vibha; Ashwell, Susan; Brassil, Patrick; Breed, Jason; Deng, Chun; Ezhuthachan, Jay; Haye, Heather; Horn, Candice; Janetka, James; Lyne, Paul; Newcombe, Nicholas; Otterbien, Ludo; Pass, Martin; Read, Jon; Roswell, Sian; Su, Mei; Toader, Dorin; Yu, Dingwei; Yu, Yan; Valentine, Anna; Webborn, Peter; White, Ann; Zabludoff, Sonya; Zheng, Xiaolan

2010-09-01

Checkpoint Kinase-1 (Chk1, CHK1, CHEK1) is a Ser/Thr protein kinase that mediates cellular responses to DNA-damage. A novel class of Chk1 inhibitors, triazoloquinolones/triazolones (TZ's) was identified by high throughput screening. The optimization of these hits to provide a lead series is described. Copyright 2010 Elsevier Ltd. All rights reserved.

Parameter Optimization for Feature and Hit Generation in a General Unknown Screening Method-Proof of Concept Study Using a Design of Experiment Approach for a High Resolution Mass Spectrometry Procedure after Data Independent Acquisition.

PubMed

Elmiger, Marco P; Poetzsch, Michael; Steuer, Andrea E; Kraemer, Thomas

2018-03-06

High resolution mass spectrometry and modern data independent acquisition (DIA) methods enable the creation of general unknown screening (GUS) procedures. However, even when DIA is used, its potential is far from being exploited, because often, the untargeted acquisition is followed by a targeted search. Applying an actual GUS (including untargeted screening) produces an immense amount of data that must be dealt with. An optimization of the parameters regulating the feature detection and hit generation algorithms of the data processing software could significantly reduce the amount of unnecessary data and thereby the workload. Design of experiment (DoE) approaches allow a simultaneous optimization of multiple parameters. In a first step, parameters are evaluated (crucial or noncrucial). Second, crucial parameters are optimized. The aim in this study was to reduce the number of hits, without missing analytes. The obtained parameter settings from the optimization were compared to the standard settings by analyzing a test set of blood samples spiked with 22 relevant analytes as well as 62 authentic forensic cases. The optimization lead to a marked reduction of workload (12.3 to 1.1% and 3.8 to 1.1% hits for the test set and the authentic cases, respectively) while simultaneously increasing the identification rate (68.2 to 86.4% and 68.8 to 88.1%, respectively). This proof of concept study emphasizes the great potential of DoE approaches to master the data overload resulting from modern data independent acquisition methods used for general unknown screening procedures by optimizing software parameters.

Novel inhibitors to Taenia solium Cu/Zn superoxide dismutase identified by virtual screening

NASA Astrophysics Data System (ADS)

García-Gutiérrez, P.; Landa-Piedra, A.; Rodríguez-Romero, A.; Parra-Unda, R.; Rojo-Domínguez, A.

2011-12-01

We describe in this work a successful virtual screening and experimental testing aimed to the identification of novel inhibitors of superoxide dismutase of the worm Taenia solium ( TsCu/Zn-SOD), a human parasite. Conformers from LeadQuest® database of drug-like compounds were selected and then docked on the surface of TsCu/Zn-SOD. Results were screened looking for ligand contacts with receptor side-chains not conserved in the human homologue, with a subsequent development of a score optimization by a set of energy minimization steps, aimed to identify lead compounds for in vitro experiments. Six out of fifty experimentally tested compounds showed μM inhibitory activity toward TsCu/Zn-SOD. Two of them showed species selectivity since did not inhibit the homologous human enzyme when assayed in vitro.

Optimal design of stormwater basins with bio-sorption activated media (BAM) in karst environments - phase I : site screening and selection.

DOT National Transportation Integrated Search

2015-12-01

Anthropogenic activities within the Silver Springs springshed over recent decades may have contributed : to elevated nutrient concentrations in stormwater runoff and groundwater, leading to the eutrophication : of Silver Springs. To remove the nutrie...

A quartz-based micro catalytic methane sensor by high resolution screen printing

NASA Astrophysics Data System (ADS)

Lu, Wenshuai; Jing, Gaoshan; Bian, Xiaomeng; Yu, Hongyan; Cui, Tianhong

2016-02-01

A micro catalytic methane sensor was proposed and fabricated on a bulk fused quartz substrate using a high resolution screen printing technique for the first time, with reduced power consumption and optimized sensitivity. The sensor was designed by the finite element method and quartz was chosen as the substrate material and alumina support with optimized dimensions. Fabrication of the sensor consisted of two MEMS processes, lift-off and high resolution screen printing, with the advantages of high yield and uniformity. When the sensor’s regional working temperature changes from 250 °C to 470 °C, its sensitivity increases, as well as the power consumption. The highest sensitivity can reach 1.52 mV/% CH4. A temperature of 300 °C was chosen as the optimized working temperature, and the sensor’s sensitivity, power consumption, nonlinearity and response time are 0.77 mV/% CH4, 415 mW, 2.6%, and 35 s, respectively. This simple, but highly uniform fabrication process and the reliable performance of this sensor may lead to wide applications for methane detection.

The University of Kansas High-Throughput Screening Laboratory. Part II: enabling collaborative drug-discovery partnerships through cutting-edge screening technology.

PubMed

McDonald, Peter R; Roy, Anuradha; Chaguturu, Rathnam

2011-07-01

The University of Kansas High-Throughput Screening (KU HTS) core is a state-of-the-art drug-discovery facility with an entrepreneurial open-service policy, which provides centralized resources supporting public- and private-sector research initiatives. The KU HTS core was established in 2002 at the University of Kansas with support from an NIH grant and the state of Kansas. It collaborates with investigators from national and international academic, nonprofit and pharmaceutical organizations in executing HTS-ready assay development and screening of chemical libraries for target validation, probe selection, hit identification and lead optimization. This is part two of a contribution from the KU HTS laboratory.

NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds

PubMed Central

Yu, Jun-lan; Chen, Tian-tian; Zhou, Chen; Lian, Fu-lin; Tang, Xu-long; Wen, Yi; Shen, Jing-kang; Xu, Ye-chun; Xiong, Bing; Zhang, Nai-xia

2016-01-01

Aim: Fragment-based lead discovery (FBLD) is a complementary approach in drug research and development. In this study, we established an NMR-based FBLD platform that was used to screen novel scaffolds targeting human bromodomain of BRD4, and investigated the binding interactions between hit compounds and the target protein. Methods: 1D NMR techniques were primarily used to generate the fragment library and to screen compounds. The inhibitory activity of hits on the first bromodomain of BRD4 [BRD4(I)] was examined using fluorescence anisotropy binding assay. 2D NMR and X-ray crystallography were applied to characterize the binding interactions between hit compounds and the target protein. Results: An NMR-based fragment library containing 539 compounds was established, which were clustered into 56 groups (8–10 compounds in each group). Eight hits with new scaffolds were found to inhibit BRD4(I). Four out of the 8 hits (compounds 1, 2, 8 and 9) had IC50 values of 100–260 μmol/L, demonstrating their potential for further BRD4-targeted hit-to-lead optimization. Analysis of the binding interactions revealed that compounds 1 and 2 shared a common quinazolin core structure and bound to BRD4(I) in a non-acetylated lysine mimetic mode. Conclusion: An NMR-based platform for FBLD was established and used in discovery of BRD4-targeted compounds. Four potential hit-to-lead optimization candidates have been found, two of them bound to BRD4(I) in a non-acetylated lysine mimetic mode, being selective BRD4(I) inhibitors. PMID:27238211

Late-stage optimization of a tercyclic class of S1P3-sparing, S1P1 receptor agonists.

PubMed

Horan, Joshua C; Kuzmich, Daniel; Liu, Pingrong; DiSalvo, Darren; Lord, John; Mao, Can; Hopkins, Tamara D; Yu, Hui; Harcken, Christian; Betageri, Raj; Hill-Drzewi, Melissa; Patenaude, Lori; Patel, Monica; Fletcher, Kimberly; Terenzzio, Donna; Linehan, Brian; Xia, Heather; Patel, Mita; Studwell, Debbie; Miller, Craig; Hickey, Eugene; Levin, Jeremy I; Smith, Dustin; Kemper, Raymond A; Modis, Louise K; Bannen, Lynne C; Chan, Diva S; Mac, Morrison B; Ng, Stephanie; Wang, Yong; Xu, Wei; Lemieux, René M

2016-01-15

Poor solubility and cationic amphiphilic drug-likeness were liabilities identified for a lead series of S1P3-sparing, S1P1 agonists originally developed from a high-throughput screening campaign. This work describes the subsequent optimization of these leads by balancing potency, selectivity, solubility and overall molecular charge. Focused SAR studies revealed favorable structural modifications that, when combined, produced compounds with overall balanced profiles. The low brain exposure observed in rat suggests that these compounds would be best suited for the potential treatment of peripheral autoimmune disorders. Copyright © 2015 Elsevier Ltd. All rights reserved.

Optimization and high-throughput screening of antimicrobial peptides.

PubMed

Blondelle, Sylvie E; Lohner, Karl

2010-01-01

While a well-established process for lead compound discovery in for-profit companies, high-throughput screening is becoming more popular in basic and applied research settings in academia. The development of combinatorial libraries combined with easy and less expensive access to new technologies have greatly contributed to the implementation of high-throughput screening in academic laboratories. While such techniques were earlier applied to simple assays involving single targets or based on binding affinity, they have now been extended to more complex systems such as whole cell-based assays. In particular, the urgent need for new antimicrobial compounds that would overcome the rapid rise of drug-resistant microorganisms, where multiple target assays or cell-based assays are often required, has forced scientists to focus onto high-throughput technologies. Based on their existence in natural host defense systems and their different mode of action relative to commercial antibiotics, antimicrobial peptides represent a new hope in discovering novel antibiotics against multi-resistant bacteria. The ease of generating peptide libraries in different formats has allowed a rapid adaptation of high-throughput assays to the search for novel antimicrobial peptides. Similarly, the availability nowadays of high-quantity and high-quality antimicrobial peptide data has permitted the development of predictive algorithms to facilitate the optimization process. This review summarizes the various library formats that lead to de novo antimicrobial peptide sequences as well as the latest structural knowledge and optimization processes aimed at improving the peptides selectivity.

Structure-Based Optimization of Arylamides as Inhibitors of Soluble Epoxide Hydrolase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eldrup, Anne B.; Soleymanzadeh, Fariba; Taylor, Steven J.

2009-11-04

Inhibition of soluble epoxide hydrolase (sEH) is hypothesized to lead to an increase in circulating levels of epoxyeicosatrienoic acids, resulting in the potentiation of their in vivo pharmacological properties. As part of an effort to identify inhibitors of sEH with high and sustained plasma exposure, we recently performed a high throughput screen of our compound collection. The screen identified N-(3,3-diphenyl-propyl)-nicotinamide as a potent inhibitor of sEH. Further profiling of this lead revealed short metabolic half-lives in microsomes and rapid clearance in the rat. Consistent with these observations, the determination of the in vitro metabolic profile of N-(3,3-diphenyl-propyl)-nicotinamide in rat livermore » microsomes revealed extensive oxidative metabolism and a propensity for metabolite switching. Lead optimization, guided by the analysis of the solid-state costructure of N-(3,3-diphenyl-propyl)-nicotinamide bound to human sEH, led to the identification of a class of potent and selective inhibitors. An inhibitor from this class displayed an attractive in vitro metabolic profile and high and sustained plasma exposure in the rat after oral administration.« less

Free Energy-Based Virtual Screening and Optimization of RNase H Inhibitors of HIV-1 Reverse Transcriptase.

PubMed

Zhang, Baofeng; D'Erasmo, Michael P; Murelli, Ryan P; Gallicchio, Emilio

2016-09-30

We report the results of a binding free energy-based virtual screening campaign of a library of 77 α-hydroxytropolone derivatives against the challenging RNase H active site of the reverse transcriptase (RT) enzyme of human immunodeficiency virus-1. Multiple protonation states, rotamer states, and binding modalities of each compound were individually evaluated. The work involved more than 300 individual absolute alchemical binding free energy parallel molecular dynamics calculations and over 1 million CPU hours on national computing clusters and a local campus computational grid. The thermodynamic and structural measures obtained in this work rationalize a series of characteristics of this system useful for guiding future synthetic and biochemical efforts. The free energy model identified key ligand-dependent entropic and conformational reorganization processes difficult to capture using standard docking and scoring approaches. Binding free energy-based optimization of the lead compounds emerging from the virtual screen has yielded four compounds with very favorable binding properties, which will be the subject of further experimental investigations. This work is one of the few reported applications of advanced-binding free energy models to large-scale virtual screening and optimization projects. It further demonstrates that, with suitable algorithms and automation, advanced-binding free energy models can have a useful role in early-stage drug-discovery programs.

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description.

PubMed

Spyrakis, Francesca; Cavasotto, Claudio N

2015-10-01

Structure-based virtual screening is currently an established tool in drug lead discovery projects. Although in the last years the field saw an impressive progress in terms of algorithm development, computational performance, and retrospective and prospective applications in ligand identification, there are still long-standing challenges where further improvement is needed. In this review, we consider the conceptual frame, state-of-the-art and recent developments of three critical "structural" issues in structure-based drug lead discovery: the use of homology modeling to accurately model the binding site when no experimental structures are available, the necessity of accounting for the dynamics of intrinsically flexible systems as proteins, and the importance of considering active site water molecules in lead identification and optimization campaigns. Copyright © 2015 Elsevier Inc. All rights reserved.

[Parameters optimization and cleaning efficiency evaluation of attrition scrubbing remediation of Pb-contaminated soil].

PubMed

Yang, Wen; Huang, Jin-lou; Peng, Hui-qing; Li, Si-tuo

2013-09-01

Attrition scrubbing was used to remediate lead contaminated-site soil, and the main purpose was to remove fine particles and lead contaminants from the surface of sand. The optimal parameters of attrition scrubbing were determined by orthogonal experiment, and three soil samples with different lead concentration were subjected to attrition scrubbing experiments. The results showed that the optimal scrubbing parameters were: a solid ratio of 70% dry matter, a temperature of 25 degrees C, an attrition time of 30 min, and an attrition speed of 1200 r x min(-1). Before attrition scrubbing, the screening and analysis of soil showed that in all three soil samples, lead was mainly enriched on sand and fine particles, and the distribution of lead was highly correlated to the organic matter. After attrition scrubbing, the washing efficiency of the original state lead contaminated sand soil in triplicates was 67.61%, 31.71% and 41.01%, respectively, which indicates that attrition scrubbing can remove part of the fine soil and lead contaminants from the surface of sand, to accomplish the purpose of pollutants enrichment. Scanning electron microscopy (SEM) analysis showed that the sand surface became smooth after attrition scrubbing. The results above show that attrition scrubbing has a good washing effect for the remediation of lead contaminated sand soil.

Fragment Based Optimization of Metabotropic Glutamate Receptor 2 (mGluR2) Positive Allosteric Modulators in the Absence of Structural Information.

PubMed

Szabó, György; Túrós, György I; Kolok, Sándor; Vastag, Mónika; Sánta, Zsuzsanna; Dékány, Miklós; Lévay, György I; Greiner, István; Natsumi, Minami; Tatsuya, Watanabe; Keserű, György M

2018-03-14

Metabotropic glutamate receptor 2 (mGluR2) positive allosteric modulators (PAMs) have been implicated as potential pharmacotherapy for psychiatric conditions. Screening our corporate compound deck, we identified a benzotriazole fragment (4) that was rapidly optimized to a potent and metabolically stable early lead (16). The highly lipophilic character of 16, together with its limited solubility, permeability, and high protein binding, however, did not allow reaching of the proof of concept in vivo. Since further attempts on the optimization of druglike properties were unsuccessful, the original hit 4 has been revisited and was optimized following the principles of fragment based drug discovery (FBDD). Lacking structural information on the receptor-ligand complex, we implemented a group efficiency (GE) based strategy and identified a new fragment like lead (60) with more balanced profile. Significant improvement achieved on the druglike properties nominated the compound for in vivo proof of concept studies that revealed the chemotype being a promising PAM lead targeting mGluR2 receptors.

The University of Kansas High-Throughput Screening Laboratory. Part II: enabling collaborative drug-discovery partnerships through cutting-edge screening technology

PubMed Central

McDonald, Peter R; Roy, Anuradha; Chaguturu, Rathnam

2011-01-01

The University of Kansas High-Throughput Screening (KU HTS) core is a state-of-the-art drug-discovery facility with an entrepreneurial open-service policy, which provides centralized resources supporting public- and private-sector research initiatives. The KU HTS core was established in 2002 at the University of Kansas with support from an NIH grant and the state of Kansas. It collaborates with investigators from national and international academic, nonprofit and pharmaceutical organizations in executing HTS-ready assay development and screening of chemical libraries for target validation, probe selection, hit identification and lead optimization. This is part two of a contribution from the KU HTS laboratory. PMID:21806374

Estimating the relative utility of screening mammography.

PubMed

Abbey, Craig K; Eckstein, Miguel P; Boone, John M

2013-05-01

The concept of diagnostic utility is a fundamental component of signal detection theory, going back to some of its earliest works. Attaching utility values to the various possible outcomes of a diagnostic test should, in principle, lead to meaningful approaches to evaluating and comparing such systems. However, in many areas of medical imaging, utility is not used because it is presumed to be unknown. In this work, we estimate relative utility (the utility benefit of a detection relative to that of a correct rejection) for screening mammography using its known relation to the slope of a receiver operating characteristic (ROC) curve at the optimal operating point. The approach assumes that the clinical operating point is optimal for the goal of maximizing expected utility and therefore the slope at this point implies a value of relative utility for the diagnostic task, for known disease prevalence. We examine utility estimation in the context of screening mammography using the Digital Mammographic Imaging Screening Trials (DMIST) data. We show how various conditions can influence the estimated relative utility, including characteristics of the rating scale, verification time, probability model, and scope of the ROC curve fit. Relative utility estimates range from 66 to 227. We argue for one particular set of conditions that results in a relative utility estimate of 162 (±14%). This is broadly consistent with values in screening mammography determined previously by other means. At the disease prevalence found in the DMIST study (0.59% at 365-day verification), optimal ROC slopes are near unity, suggesting that utility-based assessments of screening mammography will be similar to those found using Youden's index.

Prediction of Phase Behavior of Spray-Dried Amorphous Solid Dispersions: Assessment of Thermodynamic Models, Standard Screening Methods and a Novel Atomization Screening Device with Regard to Prediction Accuracy

PubMed Central

Chavez, Pierre-François; Meeus, Joke; Robin, Florent; Schubert, Martin Alexander; Somville, Pascal

2018-01-01

The evaluation of drug–polymer miscibility in the early phase of drug development is essential to ensure successful amorphous solid dispersion (ASD) manufacturing. This work investigates the comparison of thermodynamic models, conventional experimental screening methods (solvent casting, quench cooling), and a novel atomization screening device based on their ability to predict drug–polymer miscibility, solid state properties (Tg value and width), and adequate polymer selection during the development of spray-dried amorphous solid dispersions (SDASDs). Binary ASDs of four drugs and seven polymers were produced at 20:80, 40:60, 60:40, and 80:20 (w/w). Samples were systematically analyzed using modulated differential scanning calorimetry (mDSC) and X-ray powder diffraction (XRPD). Principal component analysis (PCA) was used to qualitatively assess the predictability of screening methods with regards to SDASD development. Poor correlation was found between theoretical models and experimentally-obtained results. Additionally, the limited ability of usual screening methods to predict the miscibility of SDASDs did not guarantee the appropriate selection of lead excipient for the manufacturing of robust SDASDs. Contrary to standard approaches, our novel screening device allowed the selection of optimal polymer and drug loading and established insight into the final properties and performance of SDASDs at an early stage, therefore enabling the optimization of the scaled-up late-stage development. PMID:29518936

Hit-to-lead optimization of phenylsulfonyl hydrazides for a potent suppressor of PGE2 production: Synthesis, biological activity, and molecular docking study.

PubMed

Kim, Minju; Lee, Sunhoe; Park, Eun Beul; Kim, Kwang Jong; Lee, Hwi Ho; Shin, Ji-Sun; Fischer, Katrin; Koeberle, Andreas; Werz, Oliver; Lee, Kyung-Tae; Lee, Jae Yeol

2016-01-01

Preliminary hit-to-lead optimization of a novel series of phenylsulfonyl hydrazide derivatives, which were derived from the high throughput screening hit compound 1 (IC50=5700nM against PGE2 production), for a potent suppressor of PGE2 production is described. Subsequent optimization led to the identification of the potent lead compound 8n with IC50 values of 4.5 and 6.9nM, respectively, against LPS-induced PGE2 production and NO production in RAW 264.7 macrophage cells. In addition, 8n was about 30- and >150-fold more potent against mPGES-1 enzyme in a cell-free assay (IC50=70nM) than MK-886 and hit compound 1, respectively. Molecular docking suggests that compound 8n could inhibit PGE2 production by blocking the PGH2 binding site of human mPGES-1 enzyme. Copyright © 2015 Elsevier Ltd. All rights reserved.

Using the Multi-Display Teaching System to Lower Cognitive Load

ERIC Educational Resources Information Center

Cheng, Tsung-Sheng; Lu, Yu-Chun; Yang, Chu-Sing

2015-01-01

Multimedia plays a vital role in both learning systems and the actual education process. However, currently used presentation software is often not optimized and generates a great deal of clutter on the screen. Furthermore, there is often insufficient space on a single display, leading to the division of content. These limitations generally…

Identification of a novel multiple kinase inhibitor with potent antiviral activity against influenza virus by reducing viral polymerase activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sasaki, Yutaka; Kakisaka, Michinori; Chutiwitoonchai, Nopporn

Highlights: • Screening of 50,000 compounds and subsequent lead optimization identified WV970. • WV970 has antiviral effects against influenza A, B and highly pathogenic viral strains. • WV970 inhibits viral genome replication and transcription. • A target database search suggests that WV970 may bind to a number of kinases. • KINOMEscan screening revealed that WV970 has inhibitory effects on 15 kinases. - Abstract: Neuraminidase inhibitors are the only currently available influenza treatment, although resistant viruses to these drugs have already been reported. Thus, new antiviral drugs with novel mechanisms of action are urgently required. In this study, we identified amore » novel antiviral compound, WV970, through cell-based screening of a 50,000 compound library and subsequent lead optimization. This compound exhibited potent antiviral activity with nanomolar IC{sub 50} values against both influenza A and B viruses but not non-influenza RNA viruses. Time-of-addition and indirect immunofluorescence assays indicated that WV970 acted at an early stage of the influenza life cycle, but likely after nuclear entry of viral ribonucleoprotein (vRNP). Further analyses of viral RNA expression and viral polymerase activity indicated that WV970 inhibited vRNP-mediated viral genome replication and transcription. Finally, structure-based virtual screening and comprehensive human kinome screening were used to demonstrate that WV970 acts as a multiple kinase inhibitor, many of which are associated with influenza virus replication. Collectively, these results strongly suggest that WV970 is a promising anti-influenza drug candidate and that several kinases associated with viral replication are promising drug targets.« less

Advances in fragment-based drug discovery platforms.

PubMed

Orita, Masaya; Warizaya, Masaichi; Amano, Yasushi; Ohno, Kazuki; Niimi, Tatsuya

2009-11-01

Fragment-based drug discovery (FBDD) has been established as a powerful alternative and complement to traditional high-throughput screening techniques for identifying drug leads. At present, this technique is widely used among academic groups as well as small biotech and large pharmaceutical companies. In recent years, > 10 new compounds developed with FBDD have entered clinical development, and more and more attention in the drug discovery field is being focused on this technique. Under the FBDD approach, a fragment library of relatively small compounds (molecular mass = 100 - 300 Da) is screened by various methods and the identified fragment hits which normally weakly bind to the target are used as starting points to generate more potent drug leads. Because FBDD is still a relatively new drug discovery technology, further developments and optimizations in screening platforms and fragment exploitation can be expected. This review summarizes recent advances in FBDD platforms and discusses the factors important for the successful application of this technique. Under the FBDD approach, both identifying the starting fragment hit to be developed and generating the drug lead from that starting fragment hit are important. Integration of various techniques, such as computational technology, X-ray crystallography, NMR, surface plasmon resonance, isothermal titration calorimetry, mass spectrometry and high-concentration screening, must be applied in a situation-appropriate manner.

Determination of Zinc, Cadmium, Lead, Copper and Silver Using a Carbon Paste Electrode and a Screen Printed Electrode Modified with Chromium(III) Oxide

PubMed Central

Koudelkova, Zuzana; Syrovy, Tomas; Ambrozova, Pavlina; Moravec, Zdenek; Kubac, Lubomir; Hynek, David; Adam, Vojtech

2017-01-01

In this study, the preparation and electrochemical application of a chromium(III) oxide modified carbon paste electrode (Cr-CPE) and a screen printed electrode (SPE), made from the same material and optimized for the simple, cheap and sensitive simultaneous determination of zinc, cadmium, lead, copper and the detection of silver ions, is described. The limits of detection and quantification were 25 and 80 µg·L−1 for Zn(II), 3 and 10 µg·L−1 for Cd(II), 3 and 10 µg·L−1 for Pb(II), 3 and 10 µg·L−1 for Cu(II), and 3 and 10 µg·L−1 for Ag(I), respectively. Furthermore, this promising modification was transferred to the screen-printed electrode. The limits of detection for the simultaneous determination of zinc, cadmium, copper and lead on the screen printed electrodes were found to be 350 µg·L−1 for Zn(II), 25 µg·L−1 for Cd(II), 3 µg·L−1 for Pb(II) and 3 µg·L−1 for Cu(II). Practical usability for the simultaneous detection of these heavy metal ions by the Cr-CPE was also demonstrated in the analyses of wastewaters. PMID:28792450

Determination of Zinc, Cadmium, Lead, Copper and Silver Using a Carbon Paste Electrode and a Screen Printed Electrode Modified with Chromium(III) Oxide.

PubMed

Koudelkova, Zuzana; Syrovy, Tomas; Ambrozova, Pavlina; Moravec, Zdenek; Kubac, Lubomir; Hynek, David; Richtera, Lukas; Adam, Vojtech

2017-08-09

In this study, the preparation and electrochemical application of a chromium(III) oxide modified carbon paste electrode (Cr-CPE) and a screen printed electrode (SPE), made from the same material and optimized for the simple, cheap and sensitive simultaneous determination of zinc, cadmium, lead, copper and the detection of silver ions, is described. The limits of detection and quantification were 25 and 80 µg·L -1 for Zn(II), 3 and 10 µg·L -1 for Cd(II), 3 and 10 µg·L -1 for Pb(II), 3 and 10 µg·L -1 for Cu(II), and 3 and 10 µg·L -1 for Ag(I), respectively. Furthermore, this promising modification was transferred to the screen-printed electrode. The limits of detection for the simultaneous determination of zinc, cadmium, copper and lead on the screen printed electrodes were found to be 350 µg·L -1 for Zn(II), 25 µg·L -1 for Cd(II), 3 µg·L -1 for Pb(II) and 3 µg·L -1 for Cu(II). Practical usability for the simultaneous detection of these heavy metal ions by the Cr-CPE was also demonstrated in the analyses of wastewaters.

Monitoring Pb in Aqueous Samples by Using Low Density Solvent on Air-Assisted Dispersive Liquid-Liquid Microextraction Coupled with UV-Vis Spectrophotometry.

PubMed

Nejad, Mina Ghasemi; Faraji, Hakim; Moghimi, Ali

2017-04-01

In this study, AA-DLLME combined with UV-Vis spectrophotometry was developed for pre-concentration, microextraction and determination of lead in aqueous samples. Optimization of the independent variables was carried out according to chemometric methods in three steps. According to the screening and optimization study, 86 μL of 1-undecanol (extracting solvent), 12 times syringe pumps, pH 2.0, 0.00% of salt and 0.1% DDTP (chelating agent) were chosen as the optimum independent variables for microextraction and determination of lead. Under the optimized conditions, R = 0.9994, and linearity range was 0.01-100 µg mL -1 . LOD and LOQ were 3.4 and 11.6 ng mL -1 , respectively. The method was applied for analysis of real water samples, such as tap, mineral, river and waste water.

CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies.

PubMed

Prakash, Meher K; Lang, Brian; Heinrich, Henriette; Valli, Piero V; Bauerfeind, Peter; Sonnenberg, Amnon; Beerenwinkel, Niko; Misselwitz, Benjamin

2017-06-05

Colorectal cancer (CRC) is a leading cause of cancer-related mortality. CRC incidence and mortality can be reduced by several screening strategies, including colonoscopy, but randomized CRC prevention trials face significant obstacles such as the need for large study populations with long follow-up. Therefore, CRC screening strategies will likely be designed and optimized based on computer simulations. Several computational microsimulation tools have been reported for estimating efficiency and cost-effectiveness of CRC prevention. However, none of these tools is publicly available. There is a need for an open source framework to answer practical questions including testing of new screening interventions and adapting findings to local conditions. We developed and implemented a new microsimulation model, Colon Modeling Open Source Tool (CMOST), for modeling the natural history of CRC, simulating the effects of CRC screening interventions, and calculating the resulting costs. CMOST facilitates automated parameter calibration against epidemiological adenoma prevalence and CRC incidence data. Predictions of CMOST were highly similar compared to a large endoscopic CRC prevention study as well as predictions of existing microsimulation models. We applied CMOST to calculate the optimal timing of a screening colonoscopy. CRC incidence and mortality are reduced most efficiently by a colonoscopy between the ages of 56 and 59; while discounted life years gained (LYG) is maximal at 49-50 years. With a dwell time of 13 years, the most cost-effective screening is at 59 years, at $17,211 discounted USD per LYG. While cost-efficiency varied according to dwell time it did not influence the optimal time point of screening interventions within the tested range. Predictions of CMOST are highly similar compared to a randomized CRC prevention trial as well as those of other microsimulation tools. This open source tool will enable health-economics analyses in for various countries, health-care scenarios and CRC prevention strategies. CMOST is freely available under the GNU General Public License at https://gitlab.com/misselwb/CMOST.

The New US Preventive Services Task Force "C" Draft Recommendation for Prostate Cancer Screening.

PubMed

Cooperberg, Matthew R

2017-09-01

The US Preventive Services Task Force has issued a new draft guideline, with a "C" recommendation that men aged 55-69 yr should be informed about the benefits and harms of screening for prostate cancer, and offered prostate-specific antigen testing if they choose it. For men aged ≥70 yr, the recommendation remains "D", or "do not screen." This draft represents substantial progress in the right direction towards offering men a fair opportunity to discuss the risks and benefits of screening with their primary care providers. However, the evidence review underlying the draft remains fundamentally inadequate, leading to biased presentations of both benefits and harms of screening. The final guideline and future revisions should reflect formal engagement with subject matter experts to optimize the advise given to men and their physicians. Copyright © 2017 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Biosorption process for removing heavy metal ions using water milfoil (Myriophyllum Spicatum) in contaminated water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, T.C.; Weissman, J.C.; Varadarajan, R.

1995-12-31

A small scale biomass metal contacting experiment was performed to screen the optimal plant species for biosorption and bioaccumulation of cadmium, zinc, nickel, lead, and copper. Experiments were also conducted to test the ability of the biomass to lower the metal concentrations below the US Environmental Protection Agency surface water discharge criteria. The minimum residual concentration was 0.1 mg/L for zinc, 0.004 mg/L for lead, and about 0.01 mg/L for cadmium, nickel, and lead. Results indicate that water milfoil can be used for bioremoval of metals.

Homogeneous screening assay for human tankyrase.

PubMed

Narwal, Mohit; Fallarero, Adyary; Vuorela, Pia; Lehtiö, Lari

2012-06-01

Tankyrase, a member of human PARP protein superfamily, catalyzes a covalent post-translational modification of substrate proteins. This modification, poly(ADP-ribos)ylation, leads to changes in protein interactions and modifies downstream signaling events. Tankyrase 1 is a potential drug target due to its functions in telomere homeostasis and in Wnt signaling. We describe here optimization and application of an activity-based homogenous assay for tankyrase inhibitors in a high-throughput screening format. The method measures the consumption of substrate by the chemical conversion of the remaining NAD(+) into a stable fluorescent condensation product. Conditions were optimized to measure the enzymatic auto-modification of a recombinant catalytic fragment of tankyrase 1. The fluorescence assay is inexpensive, operationally easy and performs well according to the statistical analysis (Z'= 0.7). A validatory screen with a natural product library confirmed suitability of the assay for finding new tankyrase inhibitors. Flavone was the most potent (IC(50)=325 nM) hit from the natural compounds. A flavone derivative, apigenin, and isopropyl gallate showed potency on the micromolar range, but displayed over 30-fold selectivity for tankyrase over the studied isoenzymes PARP1 and PARP2. The assay is robust and will be useful for screening new tankyrase inhibitors.

Identification and prioritization of novel anti-Wolbachia chemotypes from screening a 10,000-compound diversity library

PubMed Central

Johnston, Kelly L.; Cook, Darren A. N.; Berry, Neil G.; David Hong, W.; Clare, Rachel H.; Goddard, Megan; Ford, Louise; Nixon, Gemma L.; O’Neill, Paul M.; Ward, Stephen A.; Taylor, Mark J.

2017-01-01

Lymphatic filariasis and onchocerciasis are two important neglected tropical diseases (NTDs) that cause severe disability. Control efforts are hindered by the lack of a safe macrofilaricidal drug. Targeting the Wolbachia bacterial endosymbionts in these parasites with doxycycline leads to a macrofilaricidal outcome, but protracted treatment regimens and contraindications restrict its widespread implementation. The Anti-Wolbachia consortium aims to develop improved anti-Wolbachia drugs to overcome these barriers. We describe the first screening of a large, diverse compound library against Wolbachia. This whole-organism screen, streamlined to reduce bottlenecks, produced a hit rate of 0.5%. Chemoinformatic analysis of the top 50 hits led to the identification of six structurally diverse chemotypes, the disclosure of which could offer interesting avenues of investigation to other researchers active in this field. An example of hit-to-lead optimization is described to further demonstrate the potential of developing these high-quality hit series as safe, efficacious, and selective anti-Wolbachia macrofilaricides. PMID:28959730

Automated Lead Optimization of MMP-12 Inhibitors Using a Genetic Algorithm.

PubMed

Pickett, Stephen D; Green, Darren V S; Hunt, David L; Pardoe, David A; Hughes, Ian

2011-01-13

Traditional lead optimization projects involve long synthesis and testing cycles, favoring extensive structure-activity relationship (SAR) analysis and molecular design steps, in an attempt to limit the number of cycles that a project must run to optimize a development candidate. Microfluidic-based chemistry and biology platforms, with cycle times of minutes rather than weeks, lend themselves to unattended autonomous operation. The bottleneck in the lead optimization process is therefore shifted from synthesis or test to SAR analysis and design. As such, the way is open to an algorithm-directed process, without the need for detailed user data analysis. Here, we present results of two synthesis and screening experiments, undertaken using traditional methodology, to validate a genetic algorithm optimization process for future application to a microfluidic system. The algorithm has several novel features that are important for the intended application. For example, it is robust to missing data and can suggest compounds for retest to ensure reliability of optimization. The algorithm is first validated on a retrospective analysis of an in-house library embedded in a larger virtual array of presumed inactive compounds. In a second, prospective experiment with MMP-12 as the target protein, 140 compounds are submitted for synthesis over 10 cycles of optimization. Comparison is made to the results from the full combinatorial library that was synthesized manually and tested independently. The results show that compounds selected by the algorithm are heavily biased toward the more active regions of the library, while the algorithm is robust to both missing data (compounds where synthesis failed) and inactive compounds. This publication places the full combinatorial library and biological data into the public domain with the intention of advancing research into algorithm-directed lead optimization methods.

Automated Lead Optimization of MMP-12 Inhibitors Using a Genetic Algorithm

PubMed Central

2010-01-01

Traditional lead optimization projects involve long synthesis and testing cycles, favoring extensive structure−activity relationship (SAR) analysis and molecular design steps, in an attempt to limit the number of cycles that a project must run to optimize a development candidate. Microfluidic-based chemistry and biology platforms, with cycle times of minutes rather than weeks, lend themselves to unattended autonomous operation. The bottleneck in the lead optimization process is therefore shifted from synthesis or test to SAR analysis and design. As such, the way is open to an algorithm-directed process, without the need for detailed user data analysis. Here, we present results of two synthesis and screening experiments, undertaken using traditional methodology, to validate a genetic algorithm optimization process for future application to a microfluidic system. The algorithm has several novel features that are important for the intended application. For example, it is robust to missing data and can suggest compounds for retest to ensure reliability of optimization. The algorithm is first validated on a retrospective analysis of an in-house library embedded in a larger virtual array of presumed inactive compounds. In a second, prospective experiment with MMP-12 as the target protein, 140 compounds are submitted for synthesis over 10 cycles of optimization. Comparison is made to the results from the full combinatorial library that was synthesized manually and tested independently. The results show that compounds selected by the algorithm are heavily biased toward the more active regions of the library, while the algorithm is robust to both missing data (compounds where synthesis failed) and inactive compounds. This publication places the full combinatorial library and biological data into the public domain with the intention of advancing research into algorithm-directed lead optimization methods. PMID:24900251

Identification of ligand efficient, fragment-like hits from an HTS library: structure-based virtual screening and docking investigations of 2H- and 3H-pyrazolo tautomers for Aurora kinase A selectivity.

PubMed

Sarvagalla, Sailu; Singh, Vivek Kumar; Ke, Yi-Yu; Shiao, Hui-Yi; Lin, Wen-Hsing; Hsieh, Hsing-Pang; Hsu, John T A; Coumar, Mohane Selvaraj

2015-01-01

Furanopyrimidine 1 (IC50 = 273 nM, LE = 0.36, LELP = 10.28) was recently identified by high-throughput screening (HTS) of an in-house library (125,000 compounds) as an Aurora kinase inhibitor. Structure-based hit optimization resulted in lead molecules with in vivo efficacy in a mouse tumour xenograft model, but no oral bioavailability. This is attributed to "molecular obesity", a common problem during hit to lead evolution during which degradation of important molecular properties such as molecular weight (MW) and lipophilicity occurs. This could be effectively tackled by the right choice of hit compounds for optimization. In this regard, ligand efficiency (LE) and ligand efficiency dependent lipophilicity (LELP) indices are more often used to choose fragment-like hits for optimization. To identify hits with appropriate LE, we used a MW cut-off <250, and pyrazole structure to filter HTS library. Next, structure-based virtual screening using software (Libdock and Glide) in the Aurora A crystal structure (PDB ID: 3E5A) was carried out, and the top scoring 18 compounds tested for Aurora A enzyme inhibition. This resulted in the identification of a novel tetrahydro-pyrazolo-isoquinoline hit 7 (IC50 = 852 nM, LE = 0.44, LELP = 8.36) with fragment-like properties suitable for further hit optimization. Moreover, hit 7 was found to be selective for Aurora A (Aurora B IC50 = 35,150 nM) and the possible reasons for selectivity investigated by docking two tautomeric forms (2H- and 3H-pyrazole) of 7 in Auroras A and B (PDB ID: 4AF3) crystal structures. This docking study shows that the major 3H-pyrazole tautomer of 7 binds in Aurora A stronger than in Aurora B.

Identification of ligand efficient, fragment-like hits from an HTS library: structure-based virtual screening and docking investigations of 2 H- and 3 H-pyrazolo tautomers for Aurora kinase A selectivity

NASA Astrophysics Data System (ADS)

Sarvagalla, Sailu; Singh, Vivek Kumar; Ke, Yi-Yu; Shiao, Hui-Yi; Lin, Wen-Hsing; Hsieh, Hsing-Pang; Hsu, John T. A.; Coumar, Mohane Selvaraj

2015-01-01

Furanopyrimidine 1 (IC50 = 273 nM, LE = 0.36, LELP = 10.28) was recently identified by high-throughput screening (HTS) of an in-house library (125,000 compounds) as an Aurora kinase inhibitor. Structure-based hit optimization resulted in lead molecules with in vivo efficacy in a mouse tumour xenograft model, but no oral bioavailability. This is attributed to "molecular obesity", a common problem during hit to lead evolution during which degradation of important molecular properties such as molecular weight (MW) and lipophilicity occurs. This could be effectively tackled by the right choice of hit compounds for optimization. In this regard, ligand efficiency (LE) and ligand efficiency dependent lipophilicity (LELP) indices are more often used to choose fragment-like hits for optimization. To identify hits with appropriate LE, we used a MW cut-off <250, and pyrazole structure to filter HTS library. Next, structure-based virtual screening using software (Libdock and Glide) in the Aurora A crystal structure (PDB ID: 3E5A) was carried out, and the top scoring 18 compounds tested for Aurora A enzyme inhibition. This resulted in the identification of a novel tetrahydro-pyrazolo-isoquinoline hit 7 (IC50 = 852 nM, LE = 0.44, LELP = 8.36) with fragment-like properties suitable for further hit optimization. Moreover, hit 7 was found to be selective for Aurora A (Aurora B IC50 = 35,150 nM) and the possible reasons for selectivity investigated by docking two tautomeric forms (2 H- and 3 H-pyrazole) of 7 in Auroras A and B (PDB ID: 4AF3) crystal structures. This docking study shows that the major 3 H-pyrazole tautomer of 7 binds in Aurora A stronger than in Aurora B.

Discovery of novel inhibitors of Mycobacterium tuberculosis MurG: homology modelling, structure based pharmacophore, molecular docking, and molecular dynamics simulations.

PubMed

Saxena, Shalini; Abdullah, Maaged; Sriram, Dharmarajan; Guruprasad, Lalitha

2017-10-17

MurG (Rv2153c) is a key player in the biosynthesis of the peptidoglycan layer in Mycobacterium tuberculosis (Mtb). This work is an attempt to highlight the structural and functional relationship of Mtb MurG, the three-dimensional (3D) structure of protein was constructed by homology modelling using Discovery Studio 3.5 software. The quality and consistency of generated model was assessed by PROCHECK, ProSA and ERRAT. Later, the model was optimized by molecular dynamics (MD) simulations and the optimized model complex with substrate Uridine-diphosphate-N-acetylglucosamine (UD1) facilitated us to employ structure-based virtual screening approach to obtain new hits from Asinex database using energy-optimized pharmacophore modelling (e-pharmacophore). The pharmacophore model was validated using enrichment calculations, and finally, validated model was employed for high-throughput virtual screening and molecular docking to identify novel Mtb MurG inhibitors. This study led to the identification of 10 potential compounds with good fitness, docking score, which make important interactions with the protein active site. The 25 ns MD simulations of three potential lead compounds with protein confirmed that the structure was stable and make several non-bonding interactions with amino acids, such as Leu290, Met310 and Asn167. Hence, we concluded that the identified compounds may act as new leads for the design of Mtb MurG inhibitors.

Discovery of highly selective inhibitors of p38alpha.

PubMed

Popa-Burke, Ioana; Birkos, Steve; Blackwell, Leonard; Cheatham, Lynn; Clark, Jennifer; Dickson, John K; Galasinski, Scott; Janzen, William P; Mendoza, Jose; Miller, Jennifer L; Mohney, Robert P; Steed, Paul M; Hodge, C Nicholas

2005-01-01

The p38 MAP kinases are a family of serine/threonine protein kinases that play a key role in cellular pathways leading to pro-inflammatory responses. We have developed and implemented a method for rapidly identifying and optimizing potent and selective p38alpha inhibitors, which is amenable to other targets and target classes. A diverse library of druggable, purified and quantitated molecules was assembled and standardized enzymatic assays were performed in a microfluidic format that provided very accurate and precise inhibition data allowing for development of SAR directly from the primary HTS. All compounds were screened against a collection of more than 60 enzymes (kinases, proteases and phosphatases), allowing for removal of promiscuous and non-selective inhibitors very early in the discovery process. Follow-up enzymological studies included measurement of concentration of compound in buffer, yielding accurate determination of K(i) and IC50 values, as well as mechanism of action. In addition, active compounds were screened against less desirable properties such as inhibition of the enzyme activity by aggregation, irreversible binding, and time-dependence. Screening of an 88,634-compound library through the above-described process led to the rapid identification of multiple scaffolds (>5 active compounds per scaffold) of potential drug leads for p38alpha that are highly selective against all other enzymes tested, including the three other p38 isoforms. Potency and selectivity data allowed prioritization of the identified scaffolds for optimization. Herein we present results around our 3-thio-1,2,4-triazole lead series of p38- selective inhibitors, including identification, SAR, synthesis, selectivity profile, enzymatic and cellular data in their progression towards drug candidates.

Fragment-based approaches to the discovery of kinase inhibitors.

PubMed

Mortenson, Paul N; Berdini, Valerio; O'Reilly, Marc

2014-01-01

Protein kinases are one of the most important families of drug targets, and aberrant kinase activity has been linked to a large number of disease areas. Although eminently targetable using small molecules, kinases present a number of challenges as drug targets, not least obtaining selectivity across such a large and relatively closely related target family. Fragment-based drug discovery involves screening simple, low-molecular weight compounds to generate initial hits against a target. These hits are then optimized to more potent compounds via medicinal chemistry, usually facilitated by structural biology. Here, we will present a number of recent examples of fragment-based approaches to the discovery of kinase inhibitors, detailing the construction of fragment-screening libraries, the identification and validation of fragment hits, and their optimization into potent and selective lead compounds. The advantages of fragment-based methodologies will be discussed, along with some of the challenges associated with using this route. Finally, we will present a number of key lessons derived both from our own experience running fragment screens against kinases and from a large number of published studies.

The discovery of tricyclic pyridone JAK2 inhibitors. Part 1: hit to lead.

PubMed

Siu, Tony; Kozina, Ekaterina S; Jung, Joon; Rosenstein, Craig; Mathur, Anjili; Altman, Michael D; Chan, Grace; Xu, Lin; Bachman, Eric; Mo, Jan-Rung; Bouthillette, Melaney; Rush, Thomas; Dinsmore, Christopher J; Marshall, C Gary; Young, Jonathan R

2010-12-15

This paper describes the discovery and design of a novel class of JAK2 inhibitors. Furthermore, we detail the optimization of a screening hit using ligand binding efficiency and log D. These efforts led to the identification of compound 41, which demonstrates in vivo activity in our study. Copyright © 2010 Elsevier Ltd. All rights reserved.

Strategies for the generation, validation and application of in silico ADMET models in lead generation and optimization.

PubMed

Gleeson, Matthew Paul; Montanari, Dino

2012-11-01

The most desirable chemical starting point in drug discovery is a hit or lead with a good overall profile, and where there may be issues; a clear SAR strategy should be identifiable to minimize the issue. Filtering based on drug-likeness concepts are a first step, but more accurate theoretical methods are needed to i) estimate the biological profile of molecule in question and ii) based on the underlying structure-activity relationships used by the model, estimate whether it is likely that the molecule in question can be altered to remove these liabilities. In this paper, the authors discuss the generation of ADMET models and their practical use in decision making. They discuss the issues surrounding data collation, experimental errors, the model assessment and validation steps, as well as the different types of descriptors and statistical models that can be used. This is followed by a discussion on how the model accuracy will dictate when and where it can be used in the drug discovery process. The authors also discuss how models can be developed to more effectively enable multiple parameter optimization. Models can be applied in lead generation and lead optimization steps to i) rank order a collection of hits, ii) prioritize the experimental assays needed for different hit series, iii) assess the likelihood of resolving a problem that might be present in a particular series in lead optimization and iv) screen a virtual library based on a hit or lead series to assess the impact of diverse structural changes on the predicted properties.

Synthesis and structure-activity relationship of piperidine-derived non-urea soluble epoxide hydrolase inhibitors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pecic, Stevan; Pakhomova, Svetlana; Newcomer, Marcia E.

2013-09-27

A series of potent amide non-urea inhibitors of soluble epoxide hydrolase (sEH) is disclosed. The inhibition of soluble epoxide hydrolase leads to elevated levels of epoxyeicosatrienoic acids (EETs), and thus inhibitors of sEH represent one of a novel approach to the development of vasodilatory and anti-inflammatory drugs. Structure–activities studies guided optimization of a lead compound, identified through high-throughput screening, gave rise to sub-nanomolar inhibitors of human sEH with stability in human liver microsomal assay suitable for preclinical development.

Development of a systems-based in situ multiplex biomarker screening approach for the assessment of immunopathology and neural tissue plasticity in male rats after traumatic brain injury.

PubMed

Bogoslovsky, Tanya; Bernstock, Joshua D; Bull, Greg; Gouty, Shawn; Cox, Brian M; Hallenbeck, John M; Maric, Dragan

2018-04-01

Traumatic brain injuries (TBIs) pose a massive burden of disease and continue to be a leading cause of morbidity and mortality throughout the world. A major obstacle in developing effective treatments is the lack of comprehensive understanding of the underlying mechanisms that mediate tissue damage and recovery after TBI. As such, our work aims to highlight the development of a novel experimental platform capable of fully characterizing the underlying pathobiology that unfolds after TBI. This platform encompasses an empirically optimized multiplex immunohistochemistry staining and imaging system customized to screen for a myriad of biomarkers required to comprehensively evaluate the extent of neuroinflammation, neural tissue damage, and repair in response to TBI. Herein, we demonstrate that our multiplex biomarker screening platform is capable of evaluating changes in both the topographical location and functional states of resident and infiltrating cell types that play a role in neuropathology after controlled cortical impact injury to the brain in male Sprague-Dawley rats. Our results demonstrate that our multiplex biomarker screening platform lays the groundwork for the comprehensive characterization of changes that occur within the brain after TBI. Such work may ultimately lead to the understanding of the governing pathobiology of TBI, thereby fostering the development of novel therapeutic interventions tailored to produce optimal tissue protection, repair, and/or regeneration with minimal side effects, and may ultimately find utility in a wide variety of other neurological injuries, diseases, and disorders that share components of TBI pathobiology. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Inhibiting Mycobacterium tuberculosis within and without.

PubMed

Cole, Stewart T

2016-11-05

Tuberculosis remains a scourge of global health with shrinking treatment options due to the spread of drug-resistant strains of Mycobacterium tuberculosis Intensive efforts have been made in the past 15 years to find leads for drug development so that better, more potent drugs inhibiting new targets could be produced and thus shorten treatment duration. Initial attempts focused on repurposing drugs that had been developed for other therapeutic areas but these agents did not meet their goals in clinical trials. Attempts to find new lead compounds employing target-based screens were unsuccessful as the leads were inactive against M. tuberculosis Greater success was achieved using phenotypic screening against live tubercle bacilli and this gave rise to the drugs bedaquiline, pretomanid and delamanid, currently in phase III trials. Subsequent phenotypic screens also uncovered new leads and targets but several of these targets proved to be promiscuous and inhibited by a variety of seemingly unrelated pharmacophores. This setback sparked an interest in alternative screening approaches that mimic the disease state more accurately. Foremost among these were cell-based screens, often involving macrophages, as these should reflect the bacterium's niche in the host more faithfully. A major advantage of this approach is its ability to uncover functions that are central to infection but not necessarily required for growth in vitro For instance, inhibition of virulence functions mediated by the ESX-1 secretion system severely attenuates intracellular M. tuberculosis, preventing intercellular spread and ultimately limiting tissue damage. Cell-based screens have highlighted the druggability of energy production via the electron transport chain and cholesterol metabolism. Here, I review the scientific progress and the pipeline, but warn against over-optimism due to the lack of industrial commitment for tuberculosis drug development and other socio-economic factors.This article is part of the themed issue 'The new bacteriology'. © 2016 The Author(s).

Screening for colorectal cancer in defunctioned colons.

PubMed

Akbar, Fayyaz; Quyn, Aaron; Steele, Robert

2018-01-01

Objectives Population-based colorectal (bowel) cancer screening using faecal occult blood tests leads to a reduction in cause-specific mortality. However, in people where the colon is defunctioned, the use of standard faecal occult blood test is not appropriate. The aim of this study was to examine the current trends of clinical practice for colorectal cancer screening in people with defunctioned colons. Methods An online survey was performed using SurveyMonkey. All members of the Association of Coloproctology of Great Britain and Ireland were invited by email to participate. Reminders were sent to non-responders and partial responders till six weeks. All responses were included in our analysis. Results Of the 206 (34.59%) questionnaires completed, all questions were answered in 110 (55.8%). Among responders, 94 (85.4%) were colorectal consultant surgeons, 72% had worked in their current capacity for more than five years, and 105 (50.9%) had encountered colorectal cancer in defunctioned colons during their career. Some 72.2% of responders stated that a screening test for colorectal cancer in patients with defunctioned colons was currently not offered, or that they did not know whether or not it was offered in their area. Conclusions Bowel screening in the United Kingdom is currently not offered to 72.2% of the age appropriate population with defunctioned colons. Among responding colorectal surgeons, 50% had encountered colorectal cancer in such patients. There is considerable variability in clinical practice regarding the optimal age for onset of screening, time interval, and the optimal modality to offer for screening in such cases.

Lead Quantification in Urine Samples of Athletes by Coupling DLLME with UV-Vis Spectrophotometry.

PubMed

Faraji, Hakim; Helalizadeh, Masoumeh

2017-04-01

Urine lead level is one of the most employed measures of lead exposure and risk. The urine samples used in this study were obtained from ten healthy male cyclists. Dispersive liquid-liquid microextraction combined with ultraviolet and visible spectrophotometry was utilized for preconcentration, extraction, and determination of lead in urine samples. Optimization of the independent variables was carried out based on chemometric methods in three steps. According to the screening and optimization study, 133 μL of CCl 4 (extracting solvent), 1.34 mL ethanol (dispersing solvent), pH 2.0, 0.00 % of salt, and 0.1 % O,O-diethyl dithiophosphoric (chelating agent) were used as the optimum independent variables for microextraction and determination of lead. Under the optimized conditions, R 2 was 0.9991, and linearity range was 0.01-100 μg L -1 . Precision was evaluated in terms of repeatability and intermediate precision, with relative standard deviations being <9.1 and <15.3 %, respectively. The accuracy was estimated using urine samples of cyclists as real samples and it was confirmed. The relative error of ≤5 % was considered significant in the method specificity study. The lead concentration mean for the cyclists was 3.79 μg L -1 in urine samples. As a result, the proposed method is a robust technique to quantify lead concentrations higher than 11.6 ng L -1 in urine samples.

Discovery of novel drugs for promising targets.

PubMed

Martell, Robert E; Brooks, David G; Wang, Yan; Wilcoxen, Keith

2013-09-01

Once a promising drug target is identified, the steps to actually discover and optimize a drug are diverse and challenging. The goal of this study was to provide a road map to navigate drug discovery. Review general steps for drug discovery and provide illustrating references. A number of approaches are available to enhance and accelerate target identification and validation. Consideration of a variety of potential mechanisms of action of potential drugs can guide discovery efforts. The hit to lead stage may involve techniques such as high-throughput screening, fragment-based screening, and structure-based design, with informatics playing an ever-increasing role. Biologically relevant screening models are discussed, including cell lines, 3-dimensional culture, and in vivo screening. The process of enabling human studies for an investigational drug is also discussed. Drug discovery is a complex process that has significantly evolved in recent years. © 2013 Elsevier HS Journals, Inc. All rights reserved.

[Clinical economics: a concept to optimize healthcare services].

PubMed

Porzsolt, F; Bauer, K; Henne-Bruns, D

2012-03-01

Clinical economics strives to support healthcare decisions by economic considerations. Making economic decisions does not mean saving costs but rather comparing the gained added value with the burden which has to be accepted. The necessary rules are offered in various disciplines, such as economy, epidemiology and ethics. Medical doctors have recognized these rules but are not applying them in daily clinical practice. This lacking orientation leads to preventable errors. Examples of these errors are shown for diagnosis, screening, prognosis and therapy. As these errors can be prevented by application of clinical economic principles the possible consequences for optimization of healthcare are discussed.

Genetic screens and functional genomics using CRISPR/Cas9 technology.

PubMed

Hartenian, Ella; Doench, John G

2015-04-01

Functional genomics attempts to understand the genome by perturbing the flow of information from DNA to RNA to protein, in order to learn how gene dysfunction leads to disease. CRISPR/Cas9 technology is the newest tool in the geneticist's toolbox, allowing researchers to edit DNA with unprecedented ease, speed and accuracy, and representing a novel means to perform genome-wide genetic screens to discover gene function. In this review, we first summarize the discovery and characterization of CRISPR/Cas9, and then compare it to other genome engineering technologies. We discuss its initial use in screening applications, with a focus on optimizing on-target activity and minimizing off-target effects. Finally, we comment on future challenges and opportunities afforded by this technology. © 2015 FEBS.

Using Partially Observed Markov Decision Processes (POMDPs) to Implement a Response to Intervention (RTI) Framework for Early Reading

ERIC Educational Resources Information Center

Tokac, Umit

2016-01-01

The dissertation explored the efficacy of using a POMDP to select and apply appropriate instruction. POMDPs are a tool for planning: selecting a sequence of actions that will lead to an optimal outcome. RTI is an approach to instruction, where teachers craft individual plans for students based on the results of screening test. The goal is to…

Pharmacophore Models and Pharmacophore-Based Virtual Screening: Concepts and Applications Exemplified on Hydroxysteroid Dehydrogenases.

PubMed

Kaserer, Teresa; Beck, Katharina R; Akram, Muhammad; Odermatt, Alex; Schuster, Daniela

2015-12-19

Computational methods are well-established tools in the drug discovery process and can be employed for a variety of tasks. Common applications include lead identification and scaffold hopping, as well as lead optimization by structure-activity relationship analysis and selectivity profiling. In addition, compound-target interactions associated with potentially harmful effects can be identified and investigated. This review focuses on pharmacophore-based virtual screening campaigns specifically addressing the target class of hydroxysteroid dehydrogenases. Many members of this enzyme family are associated with specific pathological conditions, and pharmacological modulation of their activity may represent promising therapeutic strategies. On the other hand, unintended interference with their biological functions, e.g., upon inhibition by xenobiotics, can disrupt steroid hormone-mediated effects, thereby contributing to the development and progression of major diseases. Besides a general introduction to pharmacophore modeling and pharmacophore-based virtual screening, exemplary case studies from the field of short-chain dehydrogenase/reductase (SDR) research are presented. These success stories highlight the suitability of pharmacophore modeling for the various application fields and suggest its application also in futures studies.

Discovery of thienoquinolone derivatives as selective and ATP non-competitive CDK5/p25 inhibitors by structure-based virtual screening

PubMed Central

Chatterjee, Arindam; Doerksen, Robert J.; Khan, Ikhlas A.

2014-01-01

Calpain mediated cleavage of CDK5 natural precursor p35 causes a stable complex formation of CDK5/p25, which leads to hyperphosphorylation of tau. Thus inhibition of this complex is a viable target for numerous acute and chronic neurodegenerative diseases involving tau protein, including Alzheimer’s disease. Since CDK5 has the highest sequence homology with its mitotic counterpart CDK2, our primary goal was to design selective CDK5/p25 inhibitors targeting neurodegeneration. A novel structure-based virtual screening protocol comprised of e-pharmacophore models and virtual screening work-flow was used to identify nine compounds from a commercial database containing 2.84 million compounds. An ATP non-competitive and selective thieno[3,2-c]quinolin-4(5H)-one inhibitor (10) with ligand efficiency (LE) of 0.3 was identified as the lead molecule. Further SAR optimization led to the discovery of several low micromolar inhibitors with good selectivity. The research represents a new class of potent ATP non-competitive CDK5/p25 inhibitors with good CDK2/E selectivity. PMID:25438765

Novel Antitubercular 6-Dialkylaminopyrimidine Carboxamides from Phenotypic Whole-Cell High Throughput Screening of a SoftFocus Library: Structure–Activity Relationship and Target Identification Studies

PubMed Central

2017-01-01

A BioFocus DPI SoftFocus library of ∼35 000 compounds was screened against Mycobacterium tuberculosis (Mtb) in order to identify novel hits with antitubercular activity. The hits were evaluated in biology triage assays to exclude compounds suggested to function via frequently encountered promiscuous mechanisms of action including inhibition of the QcrB subunit of the cytochrome bc1 complex, disruption of cell–wall homeostasis, and DNA damage. Among the hits that passed this screening cascade, a 6-dialkylaminopyrimidine carboxamide series was prioritized for hit to lead optimization. Compounds from this series were active against clinical Mtb strains, while no cross-resistance to conventional antituberculosis drugs was observed. This suggested a novel mechanism of action, which was confirmed by chemoproteomic analysis leading to the identification of BCG_3193 and BCG_3827 as putative targets of the series with unknown function. Initial structure–activity relationship studies have resulted in compounds with moderate to potent antitubercular activity and improved physicochemical properties. PMID:29148755

Optimal electrocardiographic limb lead set for rapid emphysema screening

PubMed Central

Bajaj, Rishi; Chhabra, Lovely; Basheer, Zainab; Spodick, David H

2013-01-01

Background Pulmonary emphysema of any etiology has been shown to be strongly and quasidiagnostically associated with a vertical frontal P wave axis. A vertical P wave axis (>60 degrees) during sinus rhythm can be easily determined by a P wave in lead III greater than the P wave in lead I (bipolar lead set) or a dominantly negative P wave in aVL (unipolar lead set). The purpose of this investigation was to determine which set of limb leads may be better for identifying the vertical P vector of emphysema in adults. Methods Unselected consecutive electrocardiograms from 100 patients with a diagnosis of emphysema were analyzed to determine the P wave axis. Patients aged younger than 45 years, those not in sinus rhythm, and those with poor quality tracings were excluded. The electrocardiographic data were divided into three categories depending on the frontal P wave axis, ie, >60 degrees, 60 degrees, or <60 degrees, by each criterion (P amplitude lead III > lead I and a negative P wave in aVL). Results Sixty-six percent of patients had a P wave axis > 60 degrees based on aVL, and 88% of patients had a P wave axis > 60 degrees based on the P wave in lead III being greater than in lead I. Conclusion A P wave in lead III greater than that in lead I is a more sensitive marker than a negative P wave in aVL for diagnosing emphysema and is recommended for rapid routine screening. PMID:23378754

Docking and scoring in virtual screening for drug discovery: methods and applications.

PubMed

Kitchen, Douglas B; Decornez, Hélène; Furr, John R; Bajorath, Jürgen

2004-11-01

Computational approaches that 'dock' small molecules into the structures of macromolecular targets and 'score' their potential complementarity to binding sites are widely used in hit identification and lead optimization. Indeed, there are now a number of drugs whose development was heavily influenced by or based on structure-based design and screening strategies, such as HIV protease inhibitors. Nevertheless, there remain significant challenges in the application of these approaches, in particular in relation to current scoring schemes. Here, we review key concepts and specific features of small-molecule-protein docking methods, highlight selected applications and discuss recent advances that aim to address the acknowledged limitations of established approaches.

A Cellular High-Throughput Screening Approach for Therapeutic trans-Cleaving Ribozymes and RNAi against Arbitrary mRNA Disease Targets

PubMed Central

Yau, Edwin H.; Butler, Mark C.; Sullivan, Jack M.

2016-01-01

Major bottlenecks in development of therapeutic post transcriptional gene silencing (PTGS) agents (e.g. ribozymes, RNA interference, antisense) include the challenge of mapping rare accessible regions of the mRNA target that are open for annealing and cleavage, testing and optimization of agents in human cells to identify lead agents, testing for cellular toxicity, and preclinical evaluation in appropriate animal models of disease. Methods for rapid and reliable cellular testing of PTGS agents are needed to identify potent lead candidates for optimization. Our goal was to develop a means of rapid assessment of many RNA agents to identify a lead candidate for a given mRNA associated with a disease state. We developed a rapid human cell-based screening platform to test efficacy of hammerhead ribozyme (hhRz) or RNA interference (RNAi) constructs, using a model retinal degeneration target, human rod opsin (RHO) mRNA. The focus is on RNA Drug Discovery for diverse retinal degeneration targets. To validate the approach, candidate hhRzs were tested against NUH↓ cleavage sites (N=G,C,A,U; H=C,A,U) within the target mRNA of secreted alkaline phosphatase (SEAP), a model gene expression reporter, based upon in silico predictions of mRNA accessibility. HhRzs were embedded in a larger stable adenoviral VAI RNA scaffold for high cellular expression, cytoplasmic trafficking, and stability. Most hhRz expression plasmids exerted statistically significant knockdown of extracellular SEAP enzyme activity when readily assayed by a fluorescence enzyme assay intended for high throughput screening (HTS). Kinetics of PTGS knockdown of cellular targets is measureable in live cells with the SEAP reporter. The validated SEAP HTS platform was transposed to identify lead PTGS agents against a model hereditary retinal degeneration target, RHO mRNA. Two approaches were used to physically fuse the model retinal gene target mRNA to the SEAP reporter mRNA. The most expedient way to evaluate a large set of potential VAI-hhRz expression plasmids against diverse NUH↓ cleavage sites uses cultured human HEK293S cells stably expressing a dicistronic Target-IRES-SEAP target fusion mRNA. Broad utility of this rational RNA drug discovery approach is feasible for any ophthalmological disease-relevant mRNA targets and any disease mRNA targets in general. The approach will permit rank ordering of PTGS agents based on potency to identify a lead therapeutic compound for further optimization. PMID:27233447

In-silico guided discovery of novel CCR9 antagonists

NASA Astrophysics Data System (ADS)

Zhang, Xin; Cross, Jason B.; Romero, Jan; Heifetz, Alexander; Humphries, Eric; Hall, Katie; Wu, Yuchuan; Stucka, Sabrina; Zhang, Jing; Chandonnet, Haoqun; Lippa, Blaise; Ryan, M. Dominic; Baber, J. Christian

2018-03-01

Antagonism of CCR9 is a promising mechanism for treatment of inflammatory bowel disease, including ulcerative colitis and Crohn's disease. There is limited experimental data on CCR9 and its ligands, complicating efforts to identify new small molecule antagonists. We present here results of a successful virtual screening and rational hit-to-lead campaign that led to the discovery and initial optimization of novel CCR9 antagonists. This work uses a novel data fusion strategy to integrate the output of multiple computational tools, such as 2D similarity search, shape similarity, pharmacophore searching, and molecular docking, as well as the identification and incorporation of privileged chemokine fragments. The application of various ranking strategies, which combined consensus and parallel selection methods to achieve a balance of enrichment and novelty, resulted in 198 virtual screening hits in total, with an overall hit rate of 18%. Several hits were developed into early leads through targeted synthesis and purchase of analogs.

Ranking the selectivity of PubChem screening hits by activity-based protein profiling: MMP13 as a case study.

PubMed

Nakai, Ryuichiro; Salisbury, Cleo M; Rosen, Hugh; Cravatt, Benjamin F

2009-02-01

High-throughput screening (HTS) has become an integral part of academic and industrial efforts aimed at developing new chemical probes and drugs. These screens typically generate several 'hits', or lead active compounds, that must be prioritized for follow-up medicinal chemistry studies. Among primary considerations for ranking lead compounds is selectivity for the intended target, especially among mechanistically related proteins. Here, we show how the chemical proteomic technology activity-based protein profiling (ABPP) can serve as a universal assay to rank HTS hits based on their selectivity across many members of an enzyme superfamily. As a case study, four metalloproteinase-13 (MMP13) inhibitors of similar potency originating from a publically supported HTS and reported in PubChem were tested by ABPP for selectivity against a panel of 27 diverse metalloproteases. The inhibitors could be readily separated into two groups: (1) those that were active against several metalloproteases and (2) those that showed high selectivity for MMP13. The latter set of inhibitors was thereby designated as more suitable for future medicinal chemistry optimization. We anticipate that ABPP will find general utility as a platform to rank the selectivity of lead compounds emerging from HTS assays for a wide variety of enzymes.

Trace lead analysis based on carbon-screen-printed-electrodes modified via 4-carboxy-phenyl diazonium salt electroreduction.

PubMed

Bouden, Sarra; Chaussé, Annie; Dorbes, Stephane; El Tall, Omar; Bellakhal, Nizar; Dachraoui, Mohamed; Vautrin-Ul, Christine

2013-03-15

This paper describes the use of 4-carboxyphenyl-grafted screen-printed carbon electrodes (4-CP-SPEs) for trace lead analysis. These novel and simple use of electrodes were easily prepared by the electrochemical reduction of the corresponding diazonium salt. Pb detection was then performed by a three-steps method in order to avoid oxygen interference: (i) immersion of the grafted screen-printed electrode (SPE) in the sample and adsorption of Pb(II), (ii) reduction of adsorbed Pb(II) by chronoamperometry (CA), and (iii) oxidation of Pb by Anodic Square Wave Voltammetry (SWV). The reoxidation response was exploited for lead detection and quantification. In order to optimize the analytical responses, the influence of the adsorption medium pH and the adsorption time were investigated. Moreover, an interference study was carried out with Cu(II), Hg(II), Al(III), Mn(II), Zn(II), Cd(II) and no major interference can be expected to quantify Pb(II). The described method provided a limit of detection and a limit of quantification of 1.2 × 10(-9)M and 4.1 × 10(-9)M, respectively. These performances indicate that the 4-CP-SPE could be considered as an efficient tool for environmental analysis. Copyright © 2013 Elsevier B.V. All rights reserved.

Screening of charged impurities as a possible mechanism for conductance change in graphene gas sensing

NASA Astrophysics Data System (ADS)

Liang, Sang-Zi; Chen, Gugang; Harutyunyan, Avetik R.; Sofo, Jorge O.

2014-09-01

In carbon nanotube and graphene gas sensing, the measured conductance change after the sensor is exposed to target molecules has been traditionally attributed to carrier density change due to charge transfer between the sample and the adsorbed molecule. However, this explanation has many problems when it is applied to graphene: The increased amount of Coulomb impurities should lead to decrease in carrier mobility which was not observed in many experiments, carrier density is controlled by the gate voltage in the experimental setup, and there are inconsistencies in the energetics of the charge transfer. In this paper we explore an alternative mechanism. Charged functional groups and dipolar molecules on the surface of graphene may counteract the effect of charged impurities on the substrate. Because scattering of electrons with these charged impurities has been shown to be the limiting factor in graphene conductivity, this leads to significant changes in the transport behavior. A model for the conductivity is established using the random phase approximation dielectric function of graphene and the first-order Born approximation for scattering. The model predicts optimal magnitudes for the charge and dipole moment which maximally screen a given charged impurity. The dipole screening is shown to be generally weaker than the charge screening although the former becomes more effective with higher gate voltage away from the charge neutrality point. The model also predicts that with increasing amount of adsorbates, the charge impurities eventually become saturated and additional adsorption always lead to decreasing conductivity.

An NMR-Guided Screening Method for Selective Fragment Docking and Synthesis of a Warhead Inhibitor.

PubMed

Khattri, Ram B; Morris, Daniel L; Davis, Caroline M; Bilinovich, Stephanie M; Caras, Andrew J; Panzner, Matthew J; Debord, Michael A; Leeper, Thomas C

2016-07-16

Selective hits for the glutaredoxin ortholog of Brucella melitensis are determined using STD NMR and verified by trNOE and (15)N-HSQC titration. The most promising hit, RK207, was docked into the target molecule using a scoring function to compare simulated poses to experimental data. After elucidating possible poses, the hit was further optimized into the lead compound by extension with an electrophilic acrylamide warhead. We believe that focusing on selectivity in this early stage of drug discovery will limit cross-reactivity that might occur with the human ortholog as the lead compound is optimized. Kinetics studies revealed that lead compound 5 modified with an ester group results in higher reactivity than an acrylamide control; however, after modification this compound shows little selectivity for bacterial protein versus the human ortholog. In contrast, hydrolysis of compound 5 to the acid form results in a decrease in the activity of the compound. Together these results suggest that more optimization is warranted for this simple chemical scaffold, and opens the door for discovery of drugs targeted against glutaredoxin proteins-a heretofore untapped reservoir for antibiotic agents.

Simple many-body based screening mixing ansatz for improvement of G W /Bethe-Salpeter equation excitation energies of molecular systems

NASA Astrophysics Data System (ADS)

Ziaei, Vafa; Bredow, Thomas

2017-11-01

We propose a simple many-body based screening mixing strategy to considerably enhance the performance of the Bethe-Salpeter equation (BSE) approach for prediction of excitation energies of molecular systems. This strategy enables us to closely reproduce results of highly correlated equation of motion coupled cluster singles and doubles (EOM-CCSD) through optimal use of cancellation effects. We start from the Hartree-Fock (HF) reference state and take advantage of local density approximation (LDA) based random phase approximation (RPA) screening, denoted as W0-RPA@LDA with W0 as the dynamically screened interaction built upon LDA wave functions and energies. We further use this W0-RPA@LDA screening as an initial screening guess for calculation of quasiparticle energies in the framework of G0W0 @HF. The W0-RPA@LDA screening is further injected into the BSE. By applying such an approach on a set of 22 molecules for which the traditional G W /BSE approaches fail, we observe good agreement with respect to EOM-CCSD references. The reason for the observed good accuracy of this mixing ansatz (scheme A) lies in an optimal damping of HF exchange effect through the W0-RPA@LDA strong screening, leading to substantial decrease of typically overestimated HF electronic gap, and hence to better excitation energies. Further, we present a second multiscreening ansatz (scheme B), which is similar to scheme A with the exception that now the W0-RPA@HF screening is used in the BSE in order to further improve the overestimated excitation energies of carbonyl sulfide (COS) and disilane (Si2H6 ). The reason for improvement of the excitation energies in scheme B lies in the fact that W0-RPA@HF screening is less effective (and weaker than W0-RPA@LDA), which gives rise to stronger electron-hole effects in the BSE.

Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles

PubMed Central

2016-01-01

Ensemble docking can be a successful virtual screening technique that addresses the innate conformational heterogeneity of macromolecular drug targets. Yet, lacking a method to identify a subset of conformational states that effectively segregates active and inactive small molecules, ensemble docking may result in the recommendation of a large number of false positives. Here, three knowledge-based methods that construct structural ensembles for virtual screening are presented. Each method selects ensembles by optimizing an objective function calculated using the receiver operating characteristic (ROC) curve: either the area under the ROC curve (AUC) or a ROC enrichment factor (EF). As the number of receptor conformations, N, becomes large, the methods differ in their asymptotic scaling. Given a set of small molecules with known activities and a collection of target conformations, the most resource intense method is guaranteed to find the optimal ensemble but scales as O(2N). A recursive approximation to the optimal solution scales as O(N2), and a more severe approximation leads to a faster method that scales linearly, O(N). The techniques are generally applicable to any system, and we demonstrate their effectiveness on the androgen nuclear hormone receptor (AR), cyclin-dependent kinase 2 (CDK2), and the peroxisome proliferator-activated receptor δ (PPAR-δ) drug targets. Conformations that consisted of a crystal structure and molecular dynamics simulation cluster centroids were used to form AR and CDK2 ensembles. Multiple available crystal structures were used to form PPAR-δ ensembles. For each target, we show that the three methods perform similarly to one another on both the training and test sets. PMID:27097522

Opportunistic mammography screening provides effective detection rates in a limited resource healthcare system.

PubMed

Teh, Yew-Ching; Tan, Gie-Hooi; Taib, Nur Aishah; Rahmat, Kartini; Westerhout, Caroline Judy; Fadzli, Farhana; See, Mee-Hoong; Jamaris, Suniza; Yip, Cheng-Har

2015-05-15

Breast cancer is the leading cause of cancer deaths in women world-wide. In low and middle income countries, where there are no population-based mammographic screening programmes, late presentation is common, and because of inadequate access to optimal treatment, survival rates are poor. Mammographic screening is well-studied in high-income countries in western populations, and because it has been shown to reduce breast cancer mortality, it has become part of the healthcare systems in such countries. However the performance of mammographic screening in a developing country is largely unknown. This study aims to evaluate the performance of mammographic screening in Malaysia, a middle income country, and to compare the stage and surgical treatment of screen-detected and symptomatic breast cancer. A retrospective review of 2510 mammograms performed from Jan to Dec 2010 in a tertiary medical centre is carried out. The three groups identified are the routine (opportunistic) screening group, the targeted (high risk) screening group and the diagnostic group. The performance indicators of each group is calculated, and stage at presentation and treatment between the screening and diagnostic group is analyzed. The cancer detection rate in the opportunistic screening group, targeted screening group, and the symptomatic group is 0.5 %, 1.25 % and 26 % respectively. The proportion of ductal carcinoma in situ is 23.1 % in the two screening groups compared to only 2.5 % in the diagnostic group. Among the opportunistic screening group, the cancer detection rate was 0.2 % in women below 50 years old compared to 0.65 % in women 50 years and above. The performance indicators are within international standards. Early-staged breast cancer (Stage 0-2) were 84.6 % in the screening groups compared to 61.1 % in the diagnostic group. From the results, in a setting with resource constraints, targeted screening of high risk individuals will give a higher yield, and if more resources are available, population-based screening of women 50 and above is effective. Opportunistic mammographic screening is feasible and effective in a middle income country with performance indicators within international standards. Waiting until women are symptomatic will lead to more advanced cancers.

Structure-Guided Discovery of Novel, Potent, and Orally Bioavailable Inhibitors of Lipoprotein-Associated Phospholipase A2.

PubMed

Liu, Qiufeng; Huang, Fubao; Yuan, Xiaojing; Wang, Kai; Zou, Yi; Shen, Jianhua; Xu, Yechun

2017-12-28

Lipoprotein-associated phospholipase A2 (Lp-PLA2) is a promising therapeutic target for atherosclerosis, Alzheimer's disease, and diabetic macular edema. Here we report the identification of novel sulfonamide scaffold Lp-PLA2 inhibitors derived from a relatively weak fragment. Similarity searching on this fragment followed by molecular docking leads to the discovery of a micromolar inhibitor with a 300-fold potency improvement. Subsequently, by the application of a structure-guided design strategy, a successful hit-to-lead optimization was achieved and a number of Lp-PLA2 inhibitors with single-digit nanomolar potency were obtained. After preliminary evaluation of the properties of drug-likeness in vitro and in vivo, compound 37 stands out from this congeneric series of inhibitors for good inhibitory activity and favorable oral bioavailability in male Sprague-Dawley rats, providing a quality candidate for further development. The present study thus clearly demonstrates the power and advantage of integrally employing fragment screening, crystal structures determination, virtual screening, and medicinal chemistry in an efficient lead discovery project, providing a good example for structure-based drug design.

Hit to Lead optimization of a novel class of squarate-containing polo-like kinases inhibitors.

PubMed

Zhang, Qingwei; Xia, Zhiren; Mitten, Michael J; Lasko, Loren M; Klinghofer, Vered; Bouska, Jennifer; Johnson, Eric F; Penning, Thomas D; Luo, Yan; Giranda, Vincent L; Shoemaker, Alexander R; Stewart, Kent D; Djuric, Stevan W; Vasudevan, Anil

2012-12-15

A high throughput screening (HTS) hit, 1 (Plk1 K(i)=2.2 μM) was optimized and evaluated for the enzymatic inhibition of Plk-1 kinase. Molecular modeling suggested the importance of adding a hydrophobic aromatic amine side chain in order to improve the potency by a classic kinase H-donor-acceptor binding mode. Extensive SAR studies led to the discovery of 49 (Plk1 K(i)=5 nM; EC(50)=1.05 μM), which demonstrated moderate efficacy at 100 mpk in a MiaPaCa tumor model, with no overt toxicity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Discovery and hit-to-lead optimization of 2,6-diaminopyrimidine inhibitors of interleukin-1 receptor-associated kinase 4

DOE Office of Scientific and Technical Information (OSTI.GOV)

McElroy, William T.; Michael Seganish, W.; Jason Herr, R.

2015-05-01

Interleukin receptor-associated kinase 4 (IRAK4) is a critical element of the Toll-like/interleukin-1 receptor inflammation signaling pathway. A screening campaign identified a novel diaminopyrimidine hit that exhibits weak IRAK4 inhibitory activity and a ligand efficiency of 0.25. Hit-to-lead activities were conducted through independent SAR studies of each of the four pyrimidine substituents. Optimal activity was observed upon removal of the pyrimidine C-4 chloro substituent. The intact C-6 carboribose is required for IRAK4 inhibition. Numerous heteroaryls were tolerated at the C-5 position, with azabenzothiazoles conferring the best activities. Aminoheteroaryls were preferred at the C-2 position. These studies led to the discovery ofmore » inhibitors 35, 36, and 38 that exhibit nanomolar inhibition of IRAK4, improved ligand efficiencies, and modest kinase selectivities.« less

Discovery and hit-to-lead optimization of 2,6-diaminopyrimidine inhibitors of interleukin-1 receptor-associated kinase 4.

PubMed

McElroy, William T; Michael Seganish, W; Jason Herr, R; Harding, James; Yang, Jinhai; Yet, Larry; Komanduri, Venukrishnan; Prakash, Koraboina Chandra; Lavey, Brian; Tulshian, Deen; Greenlee, William J; Sondey, Christopher; Fischmann, Thierry O; Niu, Xiaoda

2015-05-01

Interleukin receptor-associated kinase 4 (IRAK4) is a critical element of the Toll-like/interleukin-1 receptor inflammation signaling pathway. A screening campaign identified a novel diaminopyrimidine hit that exhibits weak IRAK4 inhibitory activity and a ligand efficiency of 0.25. Hit-to-lead activities were conducted through independent SAR studies of each of the four pyrimidine substituents. Optimal activity was observed upon removal of the pyrimidine C-4 chloro substituent. The intact C-6 carboribose is required for IRAK4 inhibition. Numerous heteroaryls were tolerated at the C-5 position, with azabenzothiazoles conferring the best activities. Aminoheteroaryls were preferred at the C-2 position. These studies led to the discovery of inhibitors 35, 36, and 38 that exhibit nanomolar inhibition of IRAK4, improved ligand efficiencies, and modest kinase selectivities. Copyright © 2015 Elsevier Ltd. All rights reserved.

Buccal Epithelium, Cigarette Smoking, and Lung Cancer: Review of the Literature.

PubMed

Saba, Raya; Halytskyy, Oleksandr; Saleem, Nasir; Oliff, Ira A

2017-01-01

Lung cancer is currently the leading cause of cancer-related mortality among men and women in the United States, and optimal screening methods are still lacking. The field effect is a well-supported phenomenon wherein a noxious stimulus triggers genetic, epigenetic and molecular changes that are widespread throughout the entire exposed organ system. The buccal epithelium is an easily accessible part of the respiratory tree that has good potential of yielding a surrogate marker for the field effect in cigarette smokers, and thus, a noninvasive, reliable lung cancer screening method. Herein, we review the literature on the relationship between the buccal epithelium, cigarette smoking, and lung cancer. © 2017 S. Karger AG, Basel.

Large-scale microfluidics providing high-resolution and high-throughput screening of Caenorhabditis elegans poly-glutamine aggregation model

NASA Astrophysics Data System (ADS)

Mondal, Sudip; Hegarty, Evan; Martin, Chris; Gökçe, Sertan Kutal; Ghorashian, Navid; Ben-Yakar, Adela

2016-10-01

Next generation drug screening could benefit greatly from in vivo studies, using small animal models such as Caenorhabditis elegans for hit identification and lead optimization. Current in vivo assays can operate either at low throughput with high resolution or with low resolution at high throughput. To enable both high-throughput and high-resolution imaging of C. elegans, we developed an automated microfluidic platform. This platform can image 15 z-stacks of ~4,000 C. elegans from 96 different populations using a large-scale chip with a micron resolution in 16 min. Using this platform, we screened ~100,000 animals of the poly-glutamine aggregation model on 25 chips. We tested the efficacy of ~1,000 FDA-approved drugs in improving the aggregation phenotype of the model and identified four confirmed hits. This robust platform now enables high-content screening of various C. elegans disease models at the speed and cost of in vitro cell-based assays.

Macrocyclic BACE inhibitors: Optimization of a micromolar hit to nanomolar leads.

PubMed

Huang, Yifang; Strobel, Eric D; Ho, Chih Y; Reynolds, Charles H; Conway, Kelly A; Piesvaux, Jennifer A; Brenneman, Douglas E; Yohrling, George J; Moore Arnold, H; Rosenthal, Daniel; Alexander, Richard S; Tounge, Brett A; Mercken, Marc; Vandermeeren, Marc; Parker, Michael H; Reitz, Allen B; Baxter, Ellen W

2010-05-15

We have identified macrocyclic inhibitors of the aspartic protease BACE, implicated in the etiology of Alzheimer's disease. An X-ray structure of screening hit 1 in the BACE active site revealed a hairpin conformation suggesting that constrained macrocyclic derivatives may also bind there. Several of the analogs we prepared were >100x more potent than 1, such as 7 (5 nM K(i)). Copyright 2010 Elsevier Ltd. All rights reserved.

A logical approach to optimize the nanostructured lipid carrier system of irinotecan: efficient hybrid design methodology

NASA Astrophysics Data System (ADS)

Mohan Negi, Lalit; Jaggi, Manu; Talegaonkar, Sushama

2013-01-01

Development of an effective formulation involves careful optimization of a number of excipient and process variables. Sometimes the number of variables is so large that even the most efficient optimization designs require a very large number of trials which put stress on costs as well as time. A creative combination of a number of design methods leads to a smaller number of trials. This study was aimed at the development of nanostructured lipid carriers (NLCs) by using a combination of different optimization methods. A total of 11 variables were first screened using the Plackett-Burman design for their effects on formulation characteristics like size and entrapment efficiency. Four out of 11 variables were found to have insignificant effects on the formulation parameters and hence were screened out. Out of the remaining seven variables, four (concentration of tween-80, lecithin, sodium taurocholate, and total lipid) were found to have significant effects on the size of the particles while the other three (phase ratio, drug to lipid ratio, and sonication time) had a higher influence on the entrapment efficiency. The first four variables were optimized for their effect on size using the Taguchi L9 orthogonal array. The optimized values of the surfactants and lipids were kept constant for the next stage, where the sonication time, phase ratio, and drug:lipid ratio were varied using the Box-Behnken design response surface method to optimize the entrapment efficiency. Finally, by performing only 38 trials, we have optimized 11 variables for the development of NLCs with a size of 143.52 ± 1.2 nm, zeta potential of -32.6 ± 0.54 mV, and 98.22 ± 2.06% entrapment efficiency.

Fragment virtual screening based on Bayesian categorization for discovering novel VEGFR-2 scaffolds.

PubMed

Zhang, Yanmin; Jiao, Yu; Xiong, Xiao; Liu, Haichun; Ran, Ting; Xu, Jinxing; Lu, Shuai; Xu, Anyang; Pan, Jing; Qiao, Xin; Shi, Zhihao; Lu, Tao; Chen, Yadong

2015-11-01

The discovery of novel scaffolds against a specific target has long been one of the most significant but challengeable goals in discovering lead compounds. A scaffold that binds in important regions of the active pocket is more favorable as a starting point because scaffolds generally possess greater optimization possibilities. However, due to the lack of sufficient chemical space diversity of the databases and the ineffectiveness of the screening methods, it still remains a great challenge to discover novel active scaffolds. Since the strengths and weaknesses of both fragment-based drug design and traditional virtual screening (VS), we proposed a fragment VS concept based on Bayesian categorization for the discovery of novel scaffolds. This work investigated the proposal through an application on VEGFR-2 target. Firstly, scaffold and structural diversity of chemical space for 10 compound databases were explicitly evaluated. Simultaneously, a robust Bayesian classification model was constructed for screening not only compound databases but also their corresponding fragment databases. Although analysis of the scaffold diversity demonstrated a very unevenly distribution of scaffolds over molecules, results showed that our Bayesian model behaved better in screening fragments than molecules. Through a literature retrospective research, several generated fragments with relatively high Bayesian scores indeed exhibit VEGFR-2 biological activity, which strongly proved the effectiveness of fragment VS based on Bayesian categorization models. This investigation of Bayesian-based fragment VS can further emphasize the necessity for enrichment of compound databases employed in lead discovery by amplifying the diversity of databases with novel structures.

Modern approaches to accelerate discovery of new antischistosomal drugs.

PubMed

Neves, Bruno Junior; Muratov, Eugene; Machado, Renato Beilner; Andrade, Carolina Horta; Cravo, Pedro Vitor Lemos

2016-06-01

The almost exclusive use of only praziquantel for the treatment of schistosomiasis has raised concerns about the possible emergence of drug-resistant schistosomes. Consequently, there is an urgent need for new antischistosomal drugs. The identification of leads and the generation of high quality data are crucial steps in the early stages of schistosome drug discovery projects. Herein, the authors focus on the current developments in antischistosomal lead discovery, specifically referring to the use of automated in vitro target-based and whole-organism screens and virtual screening of chemical databases. They highlight the strengths and pitfalls of each of the above-mentioned approaches, and suggest possible roadmaps towards the integration of several strategies, which may contribute for optimizing research outputs and led to more successful and cost-effective drug discovery endeavors. Increasing partnerships and access to funding for drug discovery have strengthened the battle against schistosomiasis in recent years. However, the authors believe this battle also includes innovative strategies to overcome scientific challenges. In this context, significant advances of in vitro screening as well as computer-aided drug discovery have contributed to increase the success rate and reduce the costs of drug discovery campaigns. Although some of these approaches were already used in current antischistosomal lead discovery pipelines, the integration of these strategies in a solid workflow should allow the production of new treatments for schistosomiasis in the near future.

Fragment-based drug discovery using rational design.

PubMed

Jhoti, H

2007-01-01

Fragment-based drug discovery (FBDD) is established as an alternative approach to high-throughput screening for generating novel small molecule drug candidates. In FBDD, relatively small libraries of low molecular weight compounds (or fragments) are screened using sensitive biophysical techniques to detect their binding to the target protein. A lower absolute affinity of binding is expected from fragments, compared to much higher molecular weight hits detected by high-throughput screening, due to their reduced size and complexity. Through the use of iterative cycles of medicinal chemistry, ideally guided by three-dimensional structural data, it is often then relatively straightforward to optimize these weak binding fragment hits into potent and selective lead compounds. As with most other lead discovery methods there are two key components of FBDD; the detection technology and the compound library. In this review I outline the two main approaches used for detecting the binding of low affinity fragments and also some of the key principles that are used to generate a fragment library. In addition, I describe an example of how FBDD has led to the generation of a drug candidate that is now being tested in clinical trials for the treatment of cancer.

Bioactivity-guided mixed synthesis accelerate the serendipity in lead optimization: Discovery of fungicidal homodrimanyl amides.

PubMed

Li, Dangdang; Zhang, Shasha; Song, Zehua; Wang, Guotong; Li, Shengkun

2017-08-18

The bioactivity-guided mixed synthesis was conceived, in which the designed mix-reactions were run in parallel for simultaneous construction of different kinds of analogs. The valuable ones were protruded by biological screening. This tactic will facilitate more rapid incorporation of bioactive candidates into pesticide chemists' repertoire, exemplified by the optimization of less explored homodrimanes as antifungal ingredients. The discovery of D9 as a potent fungicidal agent can be completed in <2 weeks by one student, with EC 50 of 3.33 mg/L and 2.45 mg/L against S. sclerotiorum and B. cinerea, respectively. To confirm the practicability, time-efficiency, and reliability, specific homodrimanes (82 derivatives) were synthesized and elucidated separately and determined for EC 50 values. The SAR correlated well with the intentionally mixed synthesis and the potential was further confirmed by the in vivo bioassay. This methodology will foster more efficient exploration of biologically relevant chemical space of natural products in pesticide discovery, and can also be tailored readily for the lead optimization in medicinal chemistry. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Refined docking as a valuable tool for lead optimization: application to histamine H3 receptor antagonists.

PubMed

Levoin, Nicolas; Calmels, Thierry; Poupardin-Olivier, Olivia; Labeeuw, Olivier; Danvy, Denis; Robert, Philippe; Berrebi-Bertrand, Isabelle; Ganellin, C Robin; Schunack, Walter; Stark, Holger; Capet, Marc

2008-10-01

Drug-discovery projects frequently employ structure-based information through protein modeling and ligand docking, and there is a plethora of reports relating successful use of them in virtual screening. Hit/lead optimization, which represents the next step and the longest for the medicinal chemist, is very rarely considered. This is not surprising because lead optimization is a much more complex task. Here, a homology model of the histamine H(3) receptor was built and tested for its ability to discriminate ligands above a defined threshold of affinity. In addition, drug safety is also evaluated during lead optimization, and "antitargets" are studied. So, we have used the same benchmarking procedure with the HERG channel and CYP2D6 enzyme, for which a minimal affinity is strongly desired. For targets and antitargets, we report here an accuracy as high as at least 70%, for ligands being classified above or below the chosen threshold. Such a good result is beyond what could have been predicted, especially, since our test conditions were particularly stringent. First, we measured the accuracy by means of AUC of ROC plots, i. e. considering both false positive and false negatives. Second, we used as datasets extensive chemical libraries (nearly a thousand ligands for H(3)). All molecules considered were true H(3) receptor ligands with moderate to high affinity (from microM to nM range). Third, the database is issued from concrete SAR (Bioprojet H(3) BF2.649 library) and is not simply constituted by few active ligands buried in a chemical catalogue.

Thin-Film Thermoelectric Module for Power Generator Applications Using a Screen-Printing Method

NASA Astrophysics Data System (ADS)

Lee, Heon-Bok; Yang, Hyun Jeong; We, Ju Hyung; Kim, Kukjoo; Choi, Kyung Cheol; Cho, Byung Jin

2011-05-01

A new process for fabricating a low-cost thermoelectric module using a screen-printing method has been developed. Thermoelectric properties of screen-printed ZnSb films were investigated in an effort to develop a thermoelectric module with low cost per watt. The screen-printed Zn x Sb1- x films showed a low carrier concentration and high Seebeck coefficient when x was in the range of 0.5 to 0.57 and the annealing temperature was kept below 550°C. When the annealing temperature was higher than 550°C, the carrier concentration of the Zn x Sb1- x films reached that of a metal, leading to a decrease of the Seebeck coefficient. In the present experiment, the optimized carrier concentration of screen-printed ZnSb was 7 × 1018/cm3. The output voltage and power density of the ZnSb film were 10 mV and 0.17 mW/cm2, respectively, at Δ T = 50 K. A thermoelectric module was produced using the proposed screen-printing approach with ZnSb and CoSb3 as p-type and n-type thermoelectric materials, respectively, and copper as the pad metal.

Improving the photostability of bright monomeric orange and red fluorescent proteins.

PubMed

Shaner, Nathan C; Lin, Michael Z; McKeown, Michael R; Steinbach, Paul A; Hazelwood, Kristin L; Davidson, Michael W; Tsien, Roger Y

2008-06-01

All organic fluorophores undergo irreversible photobleaching during prolonged illumination. Although fluorescent proteins typically bleach at a substantially slower rate than many small-molecule dyes, in many cases the lack of sufficient photostability remains an important limiting factor for experiments requiring large numbers of images of single cells. Screening methods focusing solely on brightness or wavelength are highly effective in optimizing both properties, but the absence of selective pressure for photostability in such screens leads to unpredictable photobleaching behavior in the resulting fluorescent proteins. Here we describe an assay for screening libraries of fluorescent proteins for enhanced photostability. With this assay, we developed highly photostable variants of mOrange (a wavelength-shifted monomeric derivative of DsRed from Discosoma sp.) and TagRFP (a monomeric derivative of eqFP578 from Entacmaea quadricolor) that maintain most of the beneficial qualities of the original proteins and perform as reliably as Aequorea victoria GFP derivatives in fusion constructs.

Developing a Screening Algorithm for Type II Diabetes Mellitus in the Resource-Limited Setting of Rural Tanzania.

PubMed

West, Caroline; Ploth, David; Fonner, Virginia; Mbwambo, Jessie; Fredrick, Francis; Sweat, Michael

2016-04-01

Noncommunicable diseases are on pace to outnumber infectious disease as the leading cause of death in sub-Saharan Africa, yet many questions remain unanswered with concern toward effective methods of screening for type II diabetes mellitus (DM) in this resource-limited setting. We aim to design a screening algorithm for type II DM that optimizes sensitivity and specificity of identifying individuals with undiagnosed DM, as well as affordability to health systems and individuals. Baseline demographic and clinical data, including hemoglobin A1c (HbA1c), were collected from 713 participants using probability sampling of the general population. We used these data, along with model parameters obtained from the literature, to mathematically model 8 purposed DM screening algorithms, while optimizing the sensitivity and specificity using Monte Carlo and Latin Hypercube simulation. An algorithm that combines risk assessment and measurement of fasting blood glucose was found to be superior for the most resource-limited settings (sensitivity 68%, sensitivity 99% and cost per patient having DM identified as $2.94). Incorporating HbA1c testing improves the sensitivity to 75.62%, but raises the cost per DM case identified to $6.04. The preferred algorithms are heavily biased to diagnose those with more severe cases of DM. Using basic risk assessment tools and fasting blood sugar testing in lieu of HbA1c testing in resource-limited settings could allow for significantly more feasible DM screening programs with reasonable sensitivity and specificity. Copyright © 2016 Southern Society for Clinical Investigation. Published by Elsevier Inc. All rights reserved.

Using a Geographic Information System to Improve Childhood Lead-Screening Efforts

PubMed Central

2013-01-01

The Idaho Division of Public Health conducted a pilot study to produce a lead-exposure–risk map to help local and state agencies better target childhood lead-screening efforts. Priority lead-screening areas, at the block group level, were created by using county tax assessor data and geographic information system software. A series of maps were produced, indicating childhood lead-screening prevalence in areas in which there was high potential for exposure to lead. These maps could enable development of more systematically targeted and cost-effective childhood lead-screening efforts. PMID:23764346

Kinase inhibitor profiling reveals unexpected opportunities to inhibit disease-associated mutant kinases

PubMed Central

Duong-Ly, Krisna C.; Devarajan, Karthik; Liang, Shuguang; Horiuchi, Kurumi Y.; Wang, Yuren; Ma, Haiching; Peterson, Jeffrey R.

2016-01-01

Summary Small-molecule kinase inhibitors have typically been designed to inhibit wild-type kinases rather than the mutant forms that frequently arise in diseases such as cancer. Mutations can have serious clinical implications by increasing kinase catalytic activity or conferring therapeutic resistance. To identify opportunities to repurpose inhibitors against disease-associated mutant kinases, we conducted a large-scale functional screen of 183 known kinase inhibitors against 76 recombinant, mutant kinases. The results revealed lead compounds with activity against clinically important mutant kinases including ALK, LRRK2, RET, and EGFR as well as unexpected opportunities for repurposing FDA-approved kinase inhibitors as leads for additional indications. Furthermore, using T674I PDGFRα as an example, we show how single-dose screening data can provide predictive structure-activity data to guide subsequent inhibitor optimization. This study provides a resource for the development of inhibitors against numerous disease-associated mutant kinases and illustrates the potential of unbiased profiling as an approach to compound-centric inhibitor development. PMID:26776524

Debiasing comparative optimism and increasing worry for health outcomes.

PubMed

Rose, Jason P

2012-11-01

Comparative optimism - feeling at less personal risk for negative outcomes than one's peers - has been linked to reduced prevention efforts. This study examined a novel debiasing technique aimed at simultaneously reducing both indirectly and directly measured comparative optimism. Before providing direct comparative estimates, participants provided absolute self and peer estimates in a joint format (same computer screen) or a separate format (different computer screens). Relative to the separate format condition, participants in the joint format condition showed (1) lower comparative optimism in absolute/indirect measures, (2) lower direct comparative optimism, and (3) heightened worry. Implications for risk perception screening are discussed.

Optimal Methods to Screen Men and Women for Intimate Partner Violence: Results from an Internal Medicine Residency Continuity Clinic

ERIC Educational Resources Information Center

Kapur, Nitin A.; Windish, Donna M.

2011-01-01

Contradictory data exist regarding optimal methods and instruments for intimate partner violence (IPV) screening in primary care settings. The purpose of this study was to determine the optimal method and screening instrument for IPV among men and women in a primary-care resident clinic. We conducted a cross-sectional study at an urban, academic,…

Recommendations From the International Colorectal Cancer Screening Network on the Evaluation of the Cost of Screening Programs.

PubMed

Subramanian, Sujha; Tangka, Florence K L; Hoover, Sonja; Nadel, Marion; Smith, Robert; Atkin, Wendy; Patnick, Julietta

2016-01-01

Worldwide, colorectal cancer is the fourth leading cause of death from cancer and the incidence is projected to increase. Many countries are exploring the introduction of organized screening programs, but there is limited information on the resources required and guidance for cost-effective implementation. To facilitate the generating of the economics evidence base for program implementation, we collected and analyzed detailed program cost data from 5 European members of the International Colorectal Cancer Screening Network. The cost per person screened estimates, often used to compare across programs as an overall measure, varied significantly across the programs. In addition, there were substantial differences in the programmatic and clinical cost incurred, even when the same type of screening test was used. Based on these findings, several recommendations are provided to enhance the underlying methodology and validity of the comparative economic assessments. The recommendations include the need for detailed activity-based cost information, the use of a comprehensive set of effectiveness measures to adequately capture differences between programs, and the incorporation of data from multiple programs in cost-effectiveness models to increase generalizability. Economic evaluation of real-world colorectal cancer-screening programs is essential to derive valuable insights to improve program operations and ensure optimal use of available resources.

Diabetic Retinopathy Screening and Monitoring of Early Stage Disease in Australian General Practice: Tackling Preventable Blindness within a Chronic Care Model.

PubMed

Crossland, Lisa; Askew, Deborah; Ware, Robert; Cranstoun, Peter; Mitchell, Paul; Bryett, Andrew; Jackson, Claire

2016-01-01

Diabetic retinopathy (DR) is the leading cause of preventable blindness in Australia. Up to 50% of people with proliferative DR who do not receive timely treatment will become legally blind within five years. Innovative and accessible screening, involving a variety of primary care providers, will become increasingly important if patients with diabetes are to receive optimal eye care. An open controlled trial design was used. Five intervention practices in urban, regional, and rural Australia partnered with ophthalmologists via telehealth undertook DR screening and monitoring of type 2 diabetes patients and were compared with control practices undertaking usual care 2011-2014. Recorded screening rates were 100% across intervention practices, compared with 22-53% in control practices. 31/577 (5%) of patients in the control practices were diagnosed with mild-moderate DR, of whom 9 (29%) had appropriate follow-up recorded. This was compared with 39/447 (9%) of patients in the intervention group, of whom 37 (95%) had appropriate follow-up recorded. General practice-based DR screening via Annual Cycle of Care arrangements is effective across differing practice locations. It offers improved recording of screening outcomes for Australians with type 2 diabetes and better follow-up of those with screen abnormalities.

Optimizing the Readout of Lanthanide-DOTA Complexes for the Detection of Ligand-Bound Copper(I).

PubMed

Hanna, Jill R; Allan, Christopher; Lawrence, Charlotte; Meyer, Odile; Wilson, Neil D; Hulme, Alison N

2017-05-14

The CuAAC 'click' reaction was used to couple alkyne-functionalized lanthanide-DOTA complexes to a range of fluorescent antennae. Screening of the antenna components was aided by comparison of the luminescent output of the resultant sensors using data normalized to account for reaction conversion as assessed by IR. A maximum 82-fold enhanced signal:background luminescence output was achieved using a Eu(III)-DOTA complex coupled to a coumarin-azide, in a reaction which is specific to the presence of copper(I). This optimized complex provides a new lead design for lanthanide-DOTA complexes which can act as irreversible 'turn-on' catalytic sensors for the detection of ligand-bound copper(I).

Fragment-based hit discovery and structure-based optimization of aminotriazoloquinazolines as novel Hsp90 inhibitors.

PubMed

Casale, Elena; Amboldi, Nadia; Brasca, Maria Gabriella; Caronni, Dannica; Colombo, Nicoletta; Dalvit, Claudio; Felder, Eduard R; Fogliatto, Gianpaolo; Galvani, Arturo; Isacchi, Antonella; Polucci, Paolo; Riceputi, Laura; Sola, Francesco; Visco, Carlo; Zuccotto, Fabio; Casuscelli, Francesco

2014-08-01

In the last decade the heat shock protein 90 (Hsp90) has emerged as a major therapeutic target and many efforts have been dedicated to the discovery of Hsp90 inhibitors as new potent anticancer agents. Here we report the identification of a novel class of Hsp90 inhibitors by means of a biophysical FAXS-NMR based screening of a library of fragments. The use of X-ray structure information combined with modeling studies enabled the fragment evolution of the initial triazoloquinazoline hit to a class of compounds with nanomolar potency and drug-like properties suited for further lead optimization. Copyright © 2014 Elsevier Ltd. All rights reserved.

Automated Protocol for Large-Scale Modeling of Gene Expression Data.

PubMed

Hall, Michelle Lynn; Calkins, David; Sherman, Woody

2016-11-28

With the continued rise of phenotypic- and genotypic-based screening projects, computational methods to analyze, process, and ultimately make predictions in this field take on growing importance. Here we show how automated machine learning workflows can produce models that are predictive of differential gene expression as a function of a compound structure using data from A673 cells as a proof of principle. In particular, we present predictive models with an average accuracy of greater than 70% across a highly diverse ∼1000 gene expression profile. In contrast to the usual in silico design paradigm, where one interrogates a particular target-based response, this work opens the opportunity for virtual screening and lead optimization for desired multitarget gene expression profiles.

Integration of fragment screening and library design.

PubMed

Siegal, Gregg; Ab, Eiso; Schultz, Jan

2007-12-01

With more than 10 years of practical experience and theoretical analysis, fragment-based drug discovery (FBDD) has entered the mainstream of the pharmaceutical and biotech industries. An array of biophysical techniques has been used to detect the weak interaction between a fragment and the target. Each technique presents its own requirements regarding the fragment collection and the target; therefore, in order to optimize the potential of FBDD, the nature of the target should be a driving factor for simultaneous development of both the library and the screening technology. A roadmap is now available to guide fragment-to-lead evolution when structural information is available. The next challenge is to apply FBDD to targets for which high-resolution structural information is not available.

Identification and Optimization of New Leads for Malaria Vector Control.

PubMed

Hueter, Ottmar F; Hoppé, Mark; Wege, Philip; Maienfisch, Peter

2016-10-01

A significant proportion of the world's population remains at risk from malaria, and whilst great progress has been made in reducing the number of malaria cases globally through the use of vector control insecticides, these gains are under threat from the emergence of insecticide resistance. The spread of resistance in the vector populations, principally to pyrethroids, is driving the need for the development of new tools for malaria vector control. In order to identify new leads 30,000 compounds from the Syngenta corporate chemical collection were tested in a newly developed screening platform. More than 3000 compounds (10%) showed activity at ≤200 mg active ingredient (AI) litre -1 against Anopheles stephensi. Further evaluation resulted in the identification of 12 viable leads for the control of adult mosquitoes, most originating from current or former insecticide projects. Surprisingly, one of these leads emerged from a former PPO herbicide project and one from a former complex III fungicide project. This indicates that representatives of certain herbicide and fungicide projects and modes of action can also represent a valuable source of leads for malaria vector control. Optimization of the diphenyl ether lead 1 resulted in the identification of the cyano-pyridyl compound 31. This compound 31 exhibits good activity against mosquito species including rdl resistant Anopheles. It is only slightly weaker than permethrin and does not show relevant levels of cross-resistance to the organochlorine insecticide dieldrin.

Quality assurance manual of endoscopic screening for gastric cancer in Japanese communities.

PubMed

Hamashima, Chisato; Fukao, Akira

2016-09-02

The Japanese government introduced endoscopic screening for gastric cancer in 2015 as a public policy based on the Japanese guidelines on gastric cancer screening. To provide appropriate endoscopic screening for gastric cancer in Japanese communities, we developed a quality assurance manual of endoscopic screening and recommend 10 strategies with their brief descriptions as follows: (i) Formulation of a committee responsible for implementing and managing endoscopic screening, and for deciding the suitable implementation methods in consideration of the local context; (ii) Development of an interpretation system that leads to a final judgement to standardize endoscopic examination and improve its accuracy; (iii) Preparation of management and reporting systems for adverse effects by the committee for safety management; (iv) Obtaining informed consent before operation following adequate explanations regarding the benefits and harms of endoscopic screening; (v) Avoidance of frequent screenings to reduce false-positive results and overdiagnosis. As a reference, the target age group is ≥50 years, and the screening interval is 2 years; (vi) Keeping the biopsy rate within 10% as post-biopsy bleeding may occur. Before endoscopic screening, any history of antithrombotic drug usage should be checked; (vii) Nonadministration of sedation in endoscopic screening for safety management; (viii) Adherence to proper endoscopic cleaning and disinfection to reduce infection; (ix) Use of a checklist to achieve optimal program preparation when municipal governments introduce endoscopic screening; (x) Identification of the aims and roles by referring to a checklist if primary care physicians decide to participate in endoscopic screening. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Pharmacophore modeling and virtual screening studies to design some potential histone deacetylase inhibitors as new leads.

PubMed

Vadivelan, S; Sinha, B N; Rambabu, G; Boppana, Kiran; Jagarlapudi, Sarma A R P

2008-02-01

Histone deacetylase is one of the important targets in the treatment of solid tumors and hematological cancers. A total of 20 well-defined inhibitors were used to generate Pharmacophore models using and HypoGen module of Catalyst. These 20 molecules broadly represent 3 different chemotypes. The best HypoGen model consists of four-pharmacophore features--one hydrogen bond acceptor, one hydrophobic aliphatic and two ring aromatic centers. This model was validated against 378 known HDAC inhibitors with a correlation of 0.897 as well as enrichment factor of 2.68 against a maximum value of 3. This model was further used to retrieve molecules from NCI database with 238,819 molecules. A total of 4638 molecules from a pool of 238,819 molecules were identified as hits while 297 molecules were indicated as highly active. Also, a Similarity analysis has been carried out for set of 4638 hits with respect to most active molecule of each chemotypes which validated not only the Virtual Screening potential of the model but also identified the possible new Chemotypes. This type of Similarity analysis would prove to be efficient not only for lead generation but also for lead optimization.

Cost-Effectiveness of Screening Individuals With Cystic Fibrosis for Colorectal Cancer.

PubMed

Gini, Andrea; Zauber, Ann G; Cenin, Dayna R; Omidvari, Amir-Houshang; Hempstead, Sarah E; Fink, Aliza K; Lowenfels, Albert B; Lansdorp-Vogelaar, Iris

2017-12-27

Individuals with cystic fibrosis are at increased risk of colorectal cancer (CRC) compared to the general population, and risk is higher among those who received an organ transplant. We performed a cost-effectiveness analysis to determine optimal CRC screening strategies for patients with cystic fibrosis. We adjusted the existing Microsimulation Screening Analysis-Colon microsimulation model to reflect increased CRC risk and lower life expectancy in patients with cystic fibrosis. Modeling was performed separately for individuals who never received an organ transplant and patients who had received an organ transplant. We modeled 76 colonoscopy screening strategies that varied the age range and screening interval. The optimal screening strategy was determined based on a willingness to pay threshold of $100,000 per life-year gained. Sensitivity and supplementary analyses were performed, including fecal immunochemical test (FIT) as an alternative test, earlier ages of transplantation, and increased rates of colonoscopy complications, to assess whether optimal screening strategies would change. Colonoscopy every 5 years, starting at age 40 years, was the optimal colonoscopy strategy for patients with cystic fibrosis who never received an organ transplant; this strategy prevented 79% of deaths from CRC. Among patients with cystic fibrosis who had received an organ transplant, optimal colonoscopy screening should start at an age of 30 or 35 years, depending on the patient's age at time of transplantation. Annual FIT screening was predicted to be cost-effective for patients with cystic fibrosis. However, the level of accuracy of the FIT in population is not clear. Using a Microsimulation Screening Analysis-Colon microsimulation model, we found screening of patients with cystic fibrosis for CRC to be cost-effective. Due to the higher risk in these patients for CRC, screening should start at an earlier age with a shorter screening interval. The findings of this study (especially those on FIT screening) may be limited by restricted evidence available for patients with cystic fibrosis. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

Cost Effectiveness of Screening Individuals With Cystic Fibrosis for Colorectal Cancer.

PubMed

Gini, Andrea; Zauber, Ann G; Cenin, Dayna R; Omidvari, Amir-Houshang; Hempstead, Sarah E; Fink, Aliza K; Lowenfels, Albert B; Lansdorp-Vogelaar, Iris

2018-02-01

Individuals with cystic fibrosis are at increased risk of colorectal cancer (CRC) compared with the general population, and risk is higher among those who received an organ transplant. We performed a cost-effectiveness analysis to determine optimal CRC screening strategies for patients with cystic fibrosis. We adjusted the existing Microsimulation Screening Analysis-Colon model to reflect increased CRC risk and lower life expectancy in patients with cystic fibrosis. Modeling was performed separately for individuals who never received an organ transplant and patients who had received an organ transplant. We modeled 76 colonoscopy screening strategies that varied the age range and screening interval. The optimal screening strategy was determined based on a willingness to pay threshold of $100,000 per life-year gained. Sensitivity and supplementary analyses were performed, including fecal immunochemical test (FIT) as an alternative test, earlier ages of transplantation, and increased rates of colonoscopy complications, to assess if optimal screening strategies would change. Colonoscopy every 5 years, starting at an age of 40 years, was the optimal colonoscopy strategy for patients with cystic fibrosis who never received an organ transplant; this strategy prevented 79% of deaths from CRC. Among patients with cystic fibrosis who had received an organ transplant, optimal colonoscopy screening should start at an age of 30 or 35 years, depending on the patient's age at time of transplantation. Annual FIT screening was predicted to be cost-effective for patients with cystic fibrosis. However, the level of accuracy of the FIT in this population is not clear. Using a Microsimulation Screening Analysis-Colon model, we found screening of patients with cystic fibrosis for CRC to be cost effective. Because of the higher risk of CRC in these patients, screening should start at an earlier age with a shorter screening interval. The findings of this study (especially those on FIT screening) may be limited by restricted evidence available for patients with cystic fibrosis. Copyright © 2018 AGA Institute. Published by Elsevier Inc. All rights reserved.

Fragment informatics and computational fragment-based drug design: an overview and update.

PubMed

Sheng, Chunquan; Zhang, Wannian

2013-05-01

Fragment-based drug design (FBDD) is a promising approach for the discovery and optimization of lead compounds. Despite its successes, FBDD also faces some internal limitations and challenges. FBDD requires a high quality of target protein and good solubility of fragments. Biophysical techniques for fragment screening necessitate expensive detection equipment and the strategies for evolving fragment hits to leads remain to be improved. Regardless, FBDD is necessary for investigating larger chemical space and can be applied to challenging biological targets. In this scenario, cheminformatics and computational chemistry can be used as alternative approaches that can significantly improve the efficiency and success rate of lead discovery and optimization. Cheminformatics and computational tools assist FBDD in a very flexible manner. Computational FBDD can be used independently or in parallel with experimental FBDD for efficiently generating and optimizing leads. Computational FBDD can also be integrated into each step of experimental FBDD and help to play a synergistic role by maximizing its performance. This review will provide critical analysis of the complementarity between computational and experimental FBDD and highlight recent advances in new algorithms and successful examples of their applications. In particular, fragment-based cheminformatics tools, high-throughput fragment docking, and fragment-based de novo drug design will provide the focus of this review. We will also discuss the advantages and limitations of different methods and the trends in new developments that should inspire future research. © 2012 Wiley Periodicals, Inc.

Optimization of PSA screening policies: a comparison of the patient and societal perspectives.

PubMed

Zhang, Jingyu; Denton, Brian T; Balasubramanian, Hari; Shah, Nilay D; Inman, Brant A

2012-01-01

To estimate the benefit of PSA-based screening for prostate cancer from the patient and societal perspectives. A partially observable Markov decision process model was used to optimize PSA screening decisions. Age-specific prostate cancer incidence rates and the mortality rates from prostate cancer and competing causes were considered. The model trades off the potential benefit of early detection with the cost of screening and loss of patient quality of life due to screening and treatment. PSA testing and biopsy decisions are made based on the patient's probability of having prostate cancer. Probabilities are inferred based on the patient's complete PSA history using Bayesian updating. The results of all PSA tests and biopsies done in Olmsted County, Minnesota, from 1993 to 2005 (11,872 men and 50,589 PSA test results). Patients' perspective: to maximize expected quality-adjusted life years (QALYs); societal perspective: to maximize the expected monetary value based on societal willingness to pay for QALYs and the cost of PSA testing, prostate biopsies, and treatment. From the patient perspective, the optimal policy recommends stopping PSA testing and biopsy at age 76. From the societal perspective, the stopping age is 71. The expected incremental benefit of optimal screening over the traditional guideline of annual PSA screening with threshold 4.0 ng/mL for biopsy is estimated to be 0.165 QALYs per person from the patient perspective and 0.161 QALYs per person from the societal perspective. PSA screening based on traditional guidelines is found to be worse than no screening at all. PSA testing done with traditional guidelines underperforms and therefore underestimates the potential benefit of screening. Optimal screening guidelines differ significantly depending on the perspective of the decision maker.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stachel, Shawn J.; Sanders, John M.; Henze, Darrell A.

We have identified several series of small molecule inhibitors of TrkA with unique binding modes. The starting leads were chosen to maximize the structural and binding mode diversity derived from a high throughput screen of our internal compound collection. These leads were optimized for potency and selectivity employing a structure based drug design approach adhering to the principles of ligand efficiency to maximize binding affinity without overly relying on lipophilic interactions. This endeavor resulted in the identification of several small molecule pan-Trk inhibitor series that exhibit high selectivity for TrkA/B/C versus a diverse panel of kinases. We have also demonstratedmore » efficacy in both inflammatory and neuropathic pain models upon oral dosing. Herein we describe the identification process, hit-to-lead progression, and binding profiles of these selective pan-Trk kinase inhibitors.« less

Suicide Risk Screening in Healthcare Settings: Identifying Males and Females at Risk

PubMed Central

King, Cheryl A.; Horwitz, Adam; Czyz, Ewa; Lindsay, Rebecca

2017-01-01

Suicide is the 10th leading cause of death in the United States, accounting for more than 42,000 deaths in 2014. Although this tragedy cuts across groups defined by age, sex, race/ethnicity, and geographic location, it is striking that nearly four times as many males as females die by suicide in the U.S. We describe the current regulations and recommendations for suicide risk screening in healthcare systems and also describe the aspirational goal of “Zero Suicide,” put forth by the National Action Alliance for Suicide Prevention. We then provide information about suicide risk screening tools and steps to take when a patient screens positive for suicide risk. Given the substantially higher suicide rate among males than females, we argue that it is important to consider how we could optimize suicide risk screening strategies to identify males and females at risk. Further research is needed to accomplish this. It is recommended that we consider multi-factorial suicide risk screens that incorporate risk factors known to be particularly important for males as well computerized, adaptive screens that are tailored for the specific risk considerations of the individual patient, male or female. These strategies are not mutually exclusive. Finally, universal suicide risk screening in healthcare settings, especially primary care, specialty medical care, and emergency department settings, is recommended. PMID:28251427

Regenerator Operation at Very High Frequencies for Microcryocoolers

NASA Astrophysics Data System (ADS)

Radebaugh, Ray; O'Gallagher, Agnes

2006-04-01

The size of Stirling and Stirling-type pulse tube cryocoolers is dominated by the size of the pressure oscillator. Such cryocoolers typically operate at frequencies up to about 60 Hz for cold-end temperatures above about 60 K. Higher operating frequencies would allow the size and mass of the pressure oscillator to be reduced for a given power input. However, simply increasing the operating frequency leads to large losses in the regenerator. The simple analytical equations derived here show how the right combination of frequency and pressure, along with optimized regenerator geometry, can lead to successful regenerator operation at frequencies up to 1 kHz. Efficient regenerator operation at such high frequencies is possible only with pressures of about 5 to 8 MPa and with very small hydraulic diameters and lengths. Other geometrical parameters must also be optimized for such conditions. The analytical equations are used to provide guidance to the right combination of parameters. We give example numerical calculations with REGEN3.2 in the paper for 60 Hz, 400 Hz, and 1000 Hz operation of optimized screen regenerators and show that the coefficient of performance at 400 Hz and 1000 Hz is about 78 % and 68 %, respectively, of that for 60 Hz when an average pressure of 7 MPa is used with the higher frequency, compared with 2.5 MPa for 60 Hz operation. The 1000 Hz coefficient of performance for parallel tubes is about the same as that of the screen geometry at 60 Hz. The compressor and cold-end swept volumes are reduced by a factor of 47 at 1000 Hz, compared with the 60 Hz case for the same input acoustic power, which can enable the development of microcryocoolers for MEMS applications.

Discovery of a Small-Molecule Inhibitor of Interleukin 15: Pharmacophore-Based Virtual Screening and Hit Optimization.

PubMed

Quéméner, Agnès; Maillasson, Mike; Arzel, Laurence; Sicard, Benoit; Vomiandry, Romy; Mortier, Erwan; Dubreuil, Didier; Jacques, Yannick; Lebreton, Jacques; Mathé-Allainmat, Monique

2017-07-27

Interleukin (IL)-15 is a pleiotropic cytokine, which is structurally close to IL-2 and shares with it the IL-2 β and γ receptor (R) subunits. By promoting the activation and proliferation of NK, NK-T, and CD8+ T cells, IL-15 plays important roles in innate and adaptative immunity. Moreover, the association of high levels of IL-15 expression with inflammatory and autoimmune diseases has led to the development of various antagonistic approaches targeting IL-15. This study is an original approach aimed at discovering small-molecule inhibitors impeding IL-15/IL-15R interaction. A pharmacophore and docking-based virtual screening of compound libraries led to the selection of 240 high-scoring compounds, 36 of which were found to bind IL-15, to inhibit the binding of IL-15 to the IL-2Rβ chain or the proliferation of IL-15-dependent cells or both. One of them was selected as a hit and optimized by a structure-activity relationship approach, leading to the first small-molecule IL-15 inhibitor with sub-micromolar activity.

A library synthesis of 4-hydroxy-3-methyl-6-phenylbenzofuran-2-carboxylic acid ethyl ester derivatives as anti-tumor agents.

PubMed

Hayakawa, Ichiro; Shioya, Rieko; Agatsuma, Toshinori; Furukawa, Hidehiko; Naruto, Shunji; Sugano, Yuichi

2004-09-06

As a result of a hit-to-lead program using a technique of solution-phase parallel synthesis, a highly potent (2,4-dimethoxyphenyl)-[6-(3-fluorophenyl)-4-hydroxy-3-methylbenzofuran-2-yl]methanone (15b) was synthesized as an optimized derivative of 4-hydroxy-3-methyl-6-phenylbenzofuran-2-carboxylic acid ethyl ester (1), which was discovered as a screening hit from small-molecule libraries and exhibited selective cytotoxicity against a tumorigenic cell line.

Fragment-based lead generation: identification of seed fragments by a highly efficient fragment screening technology

NASA Astrophysics Data System (ADS)

Neumann, Lars; Ritscher, Allegra; Müller, Gerhard; Hafenbradl, Doris

2009-08-01

For the detection of the precise and unambiguous binding of fragments to a specific binding site on the target protein, we have developed a novel reporter displacement binding assay technology. The application of this technology for the fragment screening as well as the fragment evolution process with a specific modelling based design strategy is demonstrated for inhibitors of the protein kinase p38alpha. In a fragment screening approach seed fragments were identified which were then used to build compounds from the deep-pocket towards the hinge binding area of the protein kinase p38alpha based on a modelling approach. BIRB796 was used as a blueprint for the alignment of the fragments. The fragment evolution of these deep-pocket binding fragments towards the fully optimized inhibitor BIRB796 included the modulation of the residence time as well as the affinity. The goal of our study was to evaluate the robustness and efficiency of our novel fragment screening technology at high fragment concentrations, compare the screening data with biochemical activity data and to demonstrate the evolution of the hit fragments with fast kinetics, into slow kinetic inhibitors in an in silico approach.

Population-based V3 genotypic tropism assay: a retrospective analysis using screening samples from the A4001029 and MOTIVATE studies.

PubMed

McGovern, Rachel A; Thielen, Alexander; Mo, Theresa; Dong, Winnie; Woods, Conan K; Chapman, Douglass; Lewis, Marilyn; James, Ian; Heera, Jayvant; Valdez, Hernan; Harrigan, P Richard

2010-10-23

The MOTIVATE-1 and 2 studies compared maraviroc (MVC) along with optimized background therapy (OBT) vs. placebo along with OBT in treatment-experienced patients screened as having R5-HIV (original Monogram Trofile). A subset screened with non-R5 HIV were treated with MVC or placebo along with OBT in a sister safety trial, A4001029. This analysis retrospectively examined the performance of population-based sequence analysis of HIV-1 env V3-loop to predict coreceptor tropism. Triplicate V3-loop sequences were generated using stored screening plasma samples and data was processed using custom software ('ReCall'), blinded to clinical response. Tropism was inferred using geno2pheno ('g2p'; 5% false positive rate). Primary outcomes were viral load changes after starting maraviroc; and concordance with prior screening Trofile results. Genotype and Trofile results were available for 1164 individuals with virological outcome data (N = 169 non-R5 by Trofile). Compared with Trofile, V3 genotyping had a specificity of 92.6% and a sensitivity of 67.4% for detecting non-R5 virus. However, when compared with clinical outcome, virological responses were consistently similar between Trofile and V3 genotype at weeks 8 and 24 following the initiation of therapy for patients categorized as R5. Despite differences in sensitivity for predicting non-R5 HIV, week 8 and 24 week virological responses were similar in this treatment-experienced population. These findings suggest the potential utility of V3 genotyping as an accessible assay to select patients who may benefit from maraviroc treatment. Optimization of the predictive tropism algorithm may lead to further improvement in the clinical utility of HIV genotypic tropism assays.

Virtual gastrointestinal colonoscopy in combination with large bowel endoscopy: Clinical application

PubMed Central

He, Qing; Rao, Ting; Guan, Yong-Song

2014-01-01

Although colorectal cancer (CRC) has no longer been the leading cancer killer worldwide for years with the exponential development in computed tomography (CT) or magnetic resonance imaging, and positron emission tomography/CT as well as virtual colonoscopy for early detection, the CRC related mortality is still high. The objective of CRC screening is to reduce the burden of CRC and thereby the morbidity and mortality rates of the disease. It is believed that this goal can be achieved by regularly screening the average-risk population, enabling the detection of cancer at early, curable stages, and polyps before they become cancerous. Large-scale screening with multimodality imaging approaches plays an important role in reaching that goal to detect polyps, Crohn’s disease, ulcerative colitis and CRC in early stage. This article reviews kinds of presentative imaging procedures for various screening options and updates detecting, staging and re-staging of CRC patients for determining the optimal therapeutic method and forecasting the risk of CRC recurrence and the overall prognosis. The combination use of virtual colonoscopy and conventional endoscopy, advantages and limitations of these modalities are also discussed. PMID:25320519

Structure-Guided Design of EED Binders Allosterically Inhibiting the Epigenetic Polycomb Repressive Complex 2 (PRC2) Methyltransferase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lingel, Andreas; Sendzik, Martin; Huang, Ying

2017-01-12

PRC2 is a multisubunit methyltransferase involved in epigenetic regulation of early embryonic development and cell growth. The catalytic subunit EZH2 methylates primarily lysine 27 of histone H3, leading to chromatin compaction and repression of tumor suppressor genes. Inhibiting this activity by small molecules targeting EZH2 was shown to result in antitumor efficacy. Here, we describe the optimization of a chemical series representing a new class of PRC2 inhibitors which acts allosterically via the trimethyllysine pocket of the noncatalytic EED subunit. Deconstruction of a larger and complex screening hit to a simple fragment-sized molecule followed by structure-guided regrowth and careful propertymore » modulation were employed to yield compounds which achieve submicromolar inhibition in functional assays and cellular activity. The resulting molecules can serve as a simplified entry point for lead optimization and can be utilized to study this new mechanism of PRC2 inhibition and the associated biology in detail.« less

Discovery of ONO-7300243 from a Novel Class of Lysophosphatidic Acid Receptor 1 Antagonists: From Hit to Lead

PubMed Central

2016-01-01

Lysophosphatidic acid (LPA) evokes various physiological responses through a series of G protein-coupled receptors known as LPA1–6. A high throughput screen against LPA1 gave compound 7a as a hit. The subsequent optimization of 7a led to ONO-7300243 (17a) as a novel, potent LPA1 antagonist, which showed good efficacy in vivo. The oral dosing of 17a at 30 mg/kg led to reduced intraurethral pressure in rats. Notably, this compound was equal in potency to the α1 adrenoceptor antagonist tamsulosin, which is used in clinical practice to treat dysuria with benign prostatic hyperplasia (BPH). In contrast to tamsulosin, compound 17a had no impact on the mean blood pressure at this dose. These results suggest that LPA1 antagonists could be used to treat BPH without affecting the blood pressure. Herein, we report the hit-to-lead optimization of a unique series of LPA1 antagonists and their in vivo efficacy. PMID:27774128

Identification of small molecule lead compounds for visceral leishmaniasis using a novel ex vivo splenic explant model system.

PubMed

Osorio, Yaneth; Travi, Bruno L; Renslo, Adam R; Peniche, Alex G; Melby, Peter C

2011-02-15

New drugs are needed to treat visceral leishmaniasis (VL) because the current therapies are toxic, expensive, and parasite resistance may weaken drug efficacy. We established a novel ex vivo splenic explant culture system from hamsters infected with luciferase-transfected Leishmania donovani to screen chemical compounds for anti-leishmanial activity. THIS MODEL HAS ADVANTAGES OVER IN VITRO SYSTEMS IN THAT IT: 1) includes the whole cellular population involved in the host-parasite interaction; 2) is initiated at a stage of infection when the immunosuppressive mechanisms that lead to progressive VL are evident; 3) involves the intracellular form of Leishmania; 4) supports parasite replication that can be easily quantified by detection of parasite-expressed luciferase; 5) is adaptable to a high-throughput screening format; and 6) can be used to identify compounds that have both direct and indirect anti-parasitic activity. The assay showed excellent discrimination between positive (amphotericin B) and negative (vehicle) controls with a Z' Factor >0.8. A duplicate screen of 4 chemical libraries containing 4,035 compounds identified 202 hits (5.0%) with a Z score of <-1.96 (p<0.05). Eighty-four (2.1%) of the hits were classified as lead compounds based on the in vitro therapeutic index (ratio of the compound concentration causing 50% cytotoxicity in the HepG(2) cell line to the concentration that caused 50% reduction in the parasite load). Sixty-nine (82%) of the lead compounds were previously unknown to have anti-leishmanial activity. The most frequently identified lead compounds were classified as quinoline-containing compounds (14%), alkaloids (10%), aromatics (11%), terpenes (8%), phenothiazines (7%) and furans (5%). The ex vivo splenic explant model provides a powerful approach to identify new compounds active against L. donovani within the pathophysiologic environment of the infected spleen. Further in vivo evaluation and chemical optimization of these lead compounds may generate new candidates for preclinical studies of treatment for VL.

Performance of handheld electrocardiogram devices to detect atrial fibrillation in a cardiology and geriatric ward setting.

PubMed

Desteghe, Lien; Raymaekers, Zina; Lutin, Mark; Vijgen, Johan; Dilling-Boer, Dagmara; Koopman, Pieter; Schurmans, Joris; Vanduynhoven, Philippe; Dendale, Paul; Heidbuchel, Hein

2017-01-01

To determine the usability, accuracy, and cost-effectiveness of two handheld single-lead electrocardiogram (ECG) devices for atrial fibrillation (AF) screening in a hospital population with an increased risk for AF. Hospitalized patients (n = 445) at cardiological or geriatric wards were screened for AF by two handheld ECG devices (MyDiagnostick and AliveCor). The performance of the automated algorithm of each device was evaluated against a full 12-lead or 6-lead ECG recording. All ECGs and monitor tracings were also independently reviewed in a blinded fashion by two electrophysiologists. Time investments by nurses and physicians were tracked and used to estimate cost-effectiveness of different screening strategies. Handheld recordings were not possible in 7 and 21.4% of cardiology and geriatric patients, respectively, because they were not able to hold the devices properly. Even after the exclusion of patients with an implanted device, sensitivity and specificity of the automated algorithms were suboptimal (Cardiology: 81.8 and 94.2%, respectively, for MyDiagnostick; 54.5 and 97.5%, respectively, for AliveCor; Geriatrics: 89.5 and 95.7%, respectively, for MyDiagnostick; 78.9 and 97.9%, respectively, for AliveCor). A scenario based on automated AliveCor evaluation in patients without AF history and without an implanted device proved to be the most cost-effective method, with a provider cost to identify one new AF patient of €193 and €82 at cardiology and geriatrics, respectively. The cost to detect one preventable stroke per year would be €7535 and €1916, respectively (based on average CHA 2 DS 2 -VASc of 3.9 ± 2.0 and 5.0 ± 1.5, respectively). Manual interpretation increases sensitivity, but decreases specificity, doubling the cost per detected patient, but remains cheaper than sole 12-lead ECG screening. Using AliveCor or MyDiagnostick handheld recorders requires a structured screening strategy to be effective and cost-effective in a hospital setting. It must exclude patients with implanted devices and known AF, and requires targeted additional 12-lead ECGs to optimize specificity. Under these circumstances, the expenses per diagnosed new AF patient and preventable stroke are reasonable. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2016. For permissions please email: journals.permissions@oup.com.

Thrombophilia testing has limited usefulness in clinical decision-making and should be used selectively.

PubMed

Masuda, Elna M; Lee, Raymond W; Okazaki, Ian J; Benyamini, Pouya; Kistner, Robert L

2015-04-01

Management of venous thromboembolism (VTE) includes evaluation for hypercoagulable state, especially if the VTE occurs in young patients, is recurrent, or is associated with a positive family history. These laboratory tests are costly, and surprisingly, there is little evidence showing that testing leads to improved clinical outcomes. Evidence based on observational prospective studies suggests that optimal duration of anticoagulation should be based on clinical risks resulting in VTE, such as transient, permanent, and idiopathic or unprovoked risks, and less on abnormal thrombophilia values. Thrombophilia screening is important in a subgroup of clinical scenarios, such as when there is clinical suspicion of antiphospholipid antibody syndrome, heparin resistance, or warfarin necrosis; with thrombosis occurring in unusual sites (such as mesenteric or cerebral deep venous thrombosis); and for pregnant women or those seeking pregnancy or considering estrogen-based agents. Thrombophilia screening is not likely to be helpful in most cases of first-time unprovoked VTE in the setting of transient risks, active malignant disease, deep venous thrombosis of upper extremity veins or from central lines, two or more VTEs, or arterial thrombosis with pre-existing atherosclerotic risk factors. The desire by both patient and physician for a scientific explanation of the clotting event may alone lead to testing, and if so, it should be with the understanding that an abnormal test result will likely not change management, and normal results do not accurately exclude a thrombophilic defect because there are likely factors yet to be discovered. Such false assumptions may lead to shorter durations of treatment than are optimal. Copyright © 2015 Society for Vascular Surgery. Published by Elsevier Inc. All rights reserved.

Computational databases, pathway and cheminformatics tools for tuberculosis drug discovery

PubMed Central

Ekins, Sean; Freundlich, Joel S.; Choi, Inhee; Sarker, Malabika; Talcott, Carolyn

2010-01-01

We are witnessing the growing menace of both increasing cases of drug-sensitive and drug-resistant Mycobacterium tuberculosis strains and the challenge to produce the first new tuberculosis (TB) drug in well over 40 years. The TB community, having invested in extensive high-throughput screening efforts, is faced with the question of how to optimally leverage this data in order to move from a hit to a lead to a clinical candidate and potentially a new drug. Complementing this approach, yet conducted on a much smaller scale, cheminformatic techniques have been leveraged and are herein reviewed. We suggest these computational approaches should be more optimally integrated in a workflow with experimental approaches to accelerate TB drug discovery. PMID:21129975

Theory of inhomogeneous quantum systems. III. Variational wave functions for Fermi fluids

NASA Astrophysics Data System (ADS)

Krotscheck, E.

1985-04-01

We develop a general variational theory for inhomogeneous Fermi systems such as the electron gas in a metal surface, the surface of liquid 3He, or simple models of heavy nuclei. The ground-state wave function is expressed in terms of two-body correlations, a one-body attenuation factor, and a model-system Slater determinant. Massive partial summations of cluster expansions are performed by means of Born-Green-Yvon and hypernetted-chain techniques. An optimal single-particle basis is generated by a generalized Hartree-Fock equation in which the two-body correlations screen the bare interparticle interaction. The optimization of the pair correlations leads to a state-averaged random-phase-approximation equation and a strictly microscopic determination of the particle-hole interaction.

Optimization of memory use of fragment extension-based protein-ligand docking with an original fast minimum cost flow algorithm.

PubMed

Yanagisawa, Keisuke; Komine, Shunta; Kubota, Rikuto; Ohue, Masahito; Akiyama, Yutaka

2018-06-01

The need to accelerate large-scale protein-ligand docking in virtual screening against a huge compound database led researchers to propose a strategy that entails memorizing the evaluation result of the partial structure of a compound and reusing it to evaluate other compounds. However, the previous method required frequent disk accesses, resulting in insufficient acceleration. Thus, more efficient memory usage can be expected to lead to further acceleration, and optimal memory usage could be achieved by solving the minimum cost flow problem. In this research, we propose a fast algorithm for the minimum cost flow problem utilizing the characteristics of the graph generated for this problem as constraints. The proposed algorithm, which optimized memory usage, was approximately seven times faster compared to existing minimum cost flow algorithms. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Discovery of novel hedgehog antagonists from cell-based screening: Isosteric modification of p38 bisamides as potent inhibitors of SMO.

PubMed

Yang, Bin; Hird, Alexander W; Russell, Daniel John; Fauber, Benjamin P; Dakin, Les A; Zheng, Xiaolan; Su, Qibin; Godin, Robert; Brassil, Patrick; Devereaux, Erik; Janetka, James W

2012-07-15

Cell-based subset screening of compounds using a Gli transcription factor reporter cell assay and shh stimulated cell differentiation assay identified a series of bisamide compounds as hedgehog pathway inhibitors with good potency. Using a ligand-based optimization strategy, heteroaryl groups were utilized as conformationally restricted amide isosteres replacing one of the amides which significantly increased their potency against SMO and the hedgehog pathway while decreasing activity against p38α kinase. We report herein the identification of advanced lead compounds such as imidazole 11c and 11f encompassing good p38α selectivity, low nanomolar potency in both cell assays, excellent physiochemical properties and in vivo pharmacokinetics. Copyright © 2012 Elsevier Ltd. All rights reserved.

Chemical chronobiology: Toward drugs manipulating time.

PubMed

Wallach, Thomas; Kramer, Achim

2015-06-22

Circadian clocks are endogenous timing systems orchestrating the daily regulation of a huge variety of physiological, metabolic and behavioral processes. These clocks are important for health - in mammals, their disruption leads to a diverse number of pathologies. While genetic and biochemical approaches largely uncovered the molecular bases of circadian rhythm generation, chemical biology strategies targeting the circadian oscillator by small chemical compounds are increasingly developed. Here, we review the recent progress in the identification of small molecules modulating circadian rhythms. We focus on high-throughput screening approaches using circadian bioluminescence reporter cell lines as well as describe alternative mechanistic screens. Furthermore, we discuss the potential for chemical optimization of small molecule ligands with regard to the recent progress in structural chronobiology. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

Bis-Benzimidazole Hits against Naegleria fowleri Discovered with New High-Throughput Screens

PubMed Central

Rice, Christopher A.; Colon, Beatrice L.; Alp, Mehmet; Göker, Hakan; Boykin, David W.

2015-01-01

Naegleria fowleri is a pathogenic free-living amoeba (FLA) that causes an acute fatal disease known as primary amoebic meningoencephalitis (PAM). The major problem for infections with any pathogenic FLA is a lack of effective therapeutics, since PAM has a case mortality rate approaching 99%. Clearly, new drugs that are potent and have rapid onset of action are needed to enhance the treatment regimens for PAM. Diamidines have demonstrated potency against multiple pathogens, including FLA, and are known to cross the blood-brain barrier to cure other protozoan diseases of the central nervous system. Therefore, amidino derivatives serve as an important chemotype for discovery of new drugs. In this study, we validated two new in vitro assays suitable for medium- or high-throughput drug discovery and used these for N. fowleri. We next screened over 150 amidino derivatives of multiple structural classes and identified two hit series with nM potency that are suitable for further lead optimization as new drugs for this neglected disease. These include both mono- and diamidino derivatives, with the most potent compound (DB173) having a 50% inhibitory concentration (IC50) of 177 nM. Similarly, we identified 10 additional analogues with IC50s of <1 μM, with many of these having reasonable selectivity indices. The most potent hits were >500 times more potent than pentamidine. In summary, the mono- and diamidino derivatives offer potential for lead optimization to develop new drugs to treat central nervous system infections with N. fowleri. PMID:25605363

Road screening and distribution route multi-objective robust optimization for hazardous materials based on neural network and genetic algorithm.

PubMed

Ma, Changxi; Hao, Wei; Pan, Fuquan; Xiang, Wang

2018-01-01

Route optimization of hazardous materials transportation is one of the basic steps in ensuring the safety of hazardous materials transportation. The optimization scheme may be a security risk if road screening is not completed before the distribution route is optimized. For road screening issues of hazardous materials transportation, a road screening algorithm of hazardous materials transportation is built based on genetic algorithm and Levenberg-Marquardt neural network (GA-LM-NN) by analyzing 15 attributes data of each road network section. A multi-objective robust optimization model with adjustable robustness is constructed for the hazardous materials transportation problem of single distribution center to minimize transportation risk and time. A multi-objective genetic algorithm is designed to solve the problem according to the characteristics of the model. The algorithm uses an improved strategy to complete the selection operation, applies partial matching cross shift and single ortho swap methods to complete the crossover and mutation operation, and employs an exclusive method to construct Pareto optimal solutions. Studies show that the sets of hazardous materials transportation road can be found quickly through the proposed road screening algorithm based on GA-LM-NN, whereas the distribution route Pareto solutions with different levels of robustness can be found rapidly through the proposed multi-objective robust optimization model and algorithm.

Automated detection of neovascularization for proliferative diabetic retinopathy screening.

PubMed

Roychowdhury, Sohini; Koozekanani, Dara D; Parhi, Keshab K

2016-08-01

Neovascularization is the primary manifestation of proliferative diabetic retinopathy (PDR) that can lead to acquired blindness. This paper presents a novel method that classifies neovascularizations in the 1-optic disc (OD) diameter region (NVD) and elsewhere (NVE) separately to achieve low false positive rates of neovascularization classification. First, the OD region and blood vessels are extracted. Next, the major blood vessel segments in the 1-OD diameter region are classified for NVD, and minor blood vessel segments elsewhere are classified for NVE. For NVD and NVE classifications, optimal region-based feature sets of 10 and 6 features, respectively, are used. The proposed method achieves classification sensitivity, specificity and accuracy for NVD and NVE of 74%, 98.2%, 87.6%, and 61%, 97.5%, 92.1%, respectively. Also, the proposed method achieves 86.4% sensitivity and 76% specificity for screening images with PDR from public and local data sets. Thus, the proposed NVD and NVE detection methods can play a key role in automated screening and prioritization of patients with diabetic retinopathy.

Discovery of Novel HIV-1 Integrase Inhibitors Using QSAR-Based Virtual Screening of the NCI Open Database.

PubMed

Ko, Gene M; Garg, Rajni; Bailey, Barbara A; Kumar, Sunil

2016-01-01

Quantitative structure-activity relationship (QSAR) models can be used as a predictive tool for virtual screening of chemical libraries to identify novel drug candidates. The aims of this paper were to report the results of a study performed for descriptor selection, QSAR model development, and virtual screening for identifying novel HIV-1 integrase inhibitor drug candidates. First, three evolutionary algorithms were compared for descriptor selection: differential evolution-binary particle swarm optimization (DE-BPSO), binary particle swarm optimization, and genetic algorithms. Next, three QSAR models were developed from an ensemble of multiple linear regression, partial least squares, and extremely randomized trees models. A comparison of the performances of three evolutionary algorithms showed that DE-BPSO has a significant improvement over the other two algorithms. QSAR models developed in this study were used in consensus as a predictive tool for virtual screening of the NCI Open Database containing 265,242 compounds to identify potential novel HIV-1 integrase inhibitors. Six compounds were predicted to be highly active (plC50 > 6) by each of the three models. The use of a hybrid evolutionary algorithm (DE-BPSO) for descriptor selection and QSAR model development in drug design is a novel approach. Consensus modeling may provide better predictivity by taking into account a broader range of chemical properties within the data set conducive for inhibition that may be missed by an individual model. The six compounds identified provide novel drug candidate leads in the design of next generation HIV- 1 integrase inhibitors targeting drug resistant mutant viruses.

Pharmacokinetic de-risking tools for selection of monoclonal antibody lead candidates

PubMed Central

Dostalek, Miroslav; Prueksaritanont, Thomayant; Kelley, Robert F.

2017-01-01

ABSTRACT Pharmacokinetic studies play an important role in all stages of drug discovery and development. Recent advancements in the tools for discovery and optimization of therapeutic proteins have created an abundance of candidates that may fulfill target product profile criteria. Implementing a set of in silico, small scale in vitro and in vivo tools can help to identify a clinical lead molecule with promising properties at the early stages of drug discovery, thus reducing the labor and cost in advancing multiple candidates toward clinical development. In this review, we describe tools that should be considered during drug discovery, and discuss approaches that could be included in the pharmacokinetic screening part of the lead candidate generation process to de-risk unexpected pharmacokinetic behaviors of Fc-based therapeutic proteins, with an emphasis on monoclonal antibodies. PMID:28463063

Experimental design methodologies in the optimization of chiral CE or CEC separations: an overview.

PubMed

Dejaegher, Bieke; Mangelings, Debby; Vander Heyden, Yvan

2013-01-01

In this chapter, an overview of experimental designs to develop chiral capillary electrophoresis (CE) and capillary electrochromatographic (CEC) methods is presented. Method development is generally divided into technique selection, method optimization, and method validation. In the method optimization part, often two phases can be distinguished, i.e., a screening and an optimization phase. In method validation, the method is evaluated on its fit for purpose. A validation item, also applying experimental designs, is robustness testing. In the screening phase and in robustness testing, screening designs are applied. During the optimization phase, response surface designs are used. The different design types and their application steps are discussed in this chapter and illustrated by examples of chiral CE and CEC methods.

OPTIMAL WELL LOCATOR (OWL): A SCREENING TOOL FOR EVALUATING LOCATIONS OF MONITORING WELLS

EPA Science Inventory

The Optimal Well Locator ( OWL) program was designed and developed by USEPA to be a screening tool to evaluate and optimize the placement of wells in long term monitoring networks at small sites. The first objective of the OWL program is to allow the user to visualize the change ...

Selecting a mix of prevention strategies against cervical cancer for maximum efficiency with an optimization program.

PubMed

Demarteau, Nadia; Breuer, Thomas; Standaert, Baudouin

2012-04-01

Screening and vaccination against human papillomavirus (HPV) can protect against cervical cancer. Neither alone can provide 100% protection. Consequently it raises the important question about the most efficient combination of screening at specified time intervals and vaccination to prevent cervical cancer. Our objective was to identify the mix of cervical cancer prevention strategies (screening and/or vaccination against HPV) that achieves maximum reduction in cancer cases within a fixed budget. We assessed the optimal mix of strategies for the prevention of cervical cancer using an optimization program. The evaluation used two models. One was a Markov cohort model used as the evaluation model to estimate the costs and outcomes of 52 different prevention strategies. The other was an optimization model in which the results of each prevention strategy of the previous model were entered as input data. The latter model determined the combination of the different prevention options to minimize cervical cancer under budget, screening coverage and vaccination coverage constraints. We applied the model in two countries with different healthcare organizations, epidemiology, screening practices, resource settings and treatment costs: the UK and Brazil. 100,000 women aged 12 years and above across the whole population over a 1-year period at steady state were included. The intervention was papanicolaou (Pap) smear screening programmes and/or vaccination against HPV with the bivalent HPV 16/18 vaccine (Cervarix® [Cervarix is a registered trademark of the GlaxoSmithKline group of companies]). The main outcome measures were optimal distribution of the population between different interventions (screening, vaccination, screening plus vaccination and no screening or vaccination) with the resulting number of cervical cancer and associated costs. In the base-case analysis (= same budget as today), the optimal prevention strategy would be, after introducing vaccination with a coverage rate of 80% in girls aged 12 years and retaining screening coverage at pre-vaccination levels (65% in the UK, 50% in Brazil), to increase the screening interval to 6 years (from 3) in the UK and to 5 years (from 3) in Brazil. This would result in a reduction of cervical cancer by 41% in the UK and by 54% in Brazil from pre-vaccination levels with no budget increase. Sensitivity analysis shows that vaccination alone at 80% coverage with no screening would achieve a cervical cancer reduction rate of 20% in the UK and 43% in Brazil compared with the pre-vaccination situation with a budget reduction of 30% and 14%, respectively. In both countries, the sharp reduction in cervical cancer is seen when the vaccine coverage rate exceeds the maximum screening coverage rate, or when screening coverage rate exceeds the maximum vaccine coverage rate, while maintaining the budget. As with any model, there are limitations to the value of predictions depending upon the assumptions made in each model. Spending the same budget that was used for screening and treatment of cervical cancer in the pre-vaccination era, results of the optimization program show that it would be possible to substantially reduce the number of cases by implementing an optimal combination of HPV vaccination (80% coverage) and screening at pre-vaccination coverage (65% UK, 50% Brazil) while extending the screening interval to every 6 years in the UK and 5 years in Brazil.

Microbial production of next-generation stevia sweeteners.

PubMed

Olsson, Kim; Carlsen, Simon; Semmler, Angelika; Simón, Ernesto; Mikkelsen, Michael Dalgaard; Møller, Birger Lindberg

2016-12-07

The glucosyltransferase UGT76G1 from Stevia rebaudiana is a chameleon enzyme in the targeted biosynthesis of the next-generation premium stevia sweeteners, rebaudioside D (Reb D) and rebaudioside M (Reb M). These steviol glucosides carry five and six glucose units, respectively, and have low sweetness thresholds, high maximum sweet intensities and exhibit a greatly reduced lingering bitter taste compared to stevioside and rebaudioside A, the most abundant steviol glucosides in the leaves of Stevia rebaudiana. In the metabolic glycosylation grid leading to production of Reb D and Reb M, UGT76G1 was found to catalyze eight different reactions all involving 1,3-glucosylation of steviol C 13 - and C 19 -bound glucoses. Four of these reactions lead to Reb D and Reb M while the other four result in formation of side-products unwanted for production. In this work, side-product formation was reduced by targeted optimization of UGT76G1 towards 1,3 glucosylation of steviol glucosides that are already 1,2-diglucosylated. The optimization of UGT76G1 was based on homology modelling, which enabled identification of key target amino acids present in the substrate-binding pocket. These residues were then subjected to site-saturation mutagenesis and a mutant library containing a total of 1748 UGT76G1 variants was screened for increased accumulation of Reb D or M, as well as for decreased accumulation of side-products. This screen was performed in a Saccharomyces cerevisiae strain expressing all enzymes in the rebaudioside biosynthesis pathway except for UGT76G1. Screening of the mutant library identified mutations with positive impact on the accumulation of Reb D and Reb M. The effect of the introduced mutations on other reactions in the metabolic grid was characterized. This screen made it possible to identify variants, such as UGT76G1 Thr146Gly and UGT76G1 His155Leu , which diminished accumulation of unwanted side-products and gave increased specific accumulation of the desired Reb D or Reb M sweeteners. This improvement in a key enzyme of the Stevia sweetener biosynthesis pathway represents a significant step towards the commercial production of next-generation stevia sweeteners.

Test and treat DC: forecasting the impact of a comprehensive HIV strategy in Washington DC.

PubMed

Walensky, Rochelle P; Paltiel, A David; Losina, Elena; Morris, Bethany L; Scott, Callie A; Rhode, Erin R; Seage, George R; Freedberg, Kenneth A

2010-08-15

The United States and international agencies have signaled their commitment to containing the human immunodeficiency virus (HIV) epidemic via early case identification and linkage to antiretroviral therapy (ART) immediately at diagnosis. We forecast outcomes of this approach if implemented in Washington DC. Using a mathematical model of HIV case detection and treatment, we evaluated combinations of HIV screening and ART initiation strategies. We define current practice as no regular screening program and ART at CD4 counts < or = 350 cells/microL, and we define test and treat as annual screening and administration of ART at diagnosis. Outcomes include life expectancy of HIV-infected persons and changes in the population time with transmissible HIV RNA levels. Data, largely from Washington DC, include undiagnosed HIV prevalence of 0.6%, annual incidence of 0.13%, 31% rate of test offer, 60% rate of acceptance, and 50% linkage to care. Input parameters, including optimized ART efficacy, are varied in sensitivity analyses. Projected life expectancies, from an initial mean age of 41 years, are 23.9, 25.0, and 25.6 years for current practice, test and treat, and test and treat with optimized ART, respectively. Compared with current practice, test and treat leads to a 14.7% reduction in time spent with transmissible HIV RNA level in the next 5 years; test and treat with optimized ART results in a 27.3% reduction. An expanded HIV test and treat program in Washington DC will increase life expectancy of HIV-infected patients but will have a modest impact on HIV transmission over the next 5 years and is unlikely to halt the HIV epidemic.

Target discovery focused approaches to overcome bottlenecks in the exploitation of antimycobacterial natural products.

PubMed

Baptista, Rafael; Bhowmick, Sumana; Nash, Robert J; Baillie, Les; Mur, Luis Aj

2018-04-01

Tuberculosis is a major global health hazard. The search for new antimycobacterials has focused on such as screening combinational chemistry libraries or designing chemicals to target predefined pockets of essential bacterial proteins. The relative ineffectiveness of these has led to a reappraisal of natural products for new antimycobacterial drug leads. However, progress has been limited, we suggest through a failure in many cases to define the drug target and optimize the hits using this information. We highlight methods of target discovery needed to develop a drug into a candidate for clinical trials. We incorporate these into suggested analysis pipelines which could inform the research strategies to accelerate the development of new drug leads from natural products.

OPTIMAL WELL LOCATOR (OWL): A SCREENING TOOL FOR EVALUATING LOCATIONS OF MONITORING WELLS: USER'S GUIDE VERSION 1.2

EPA Science Inventory

The Optimal Well Locator ( OWL) program was designed and developed by USEPA to be a screening tool to evaluate and optimize the placement of wells in long term monitoring networks at small sites. The first objective of the OWL program is to allow the user to visualize the change ...

Determining Childhood Blood Lead Level Screening Compliance Among Physicians.

PubMed

Haboush-Deloye, Amanda; Marquez, Erika R; Gerstenberger, Shawn L

2017-08-01

Childhood Lead Poisoning Prevention Programs throughout the U.S. have addressed childhood lead poisoning by implementing primary and secondary prevention efforts. While many programs have helped increase screening rates, in some states children under the age of six still have not been tested for lead. This study aims to identify the barriers to childhood blood lead testing and develop a strategy to increase the number of children tested. Clark County physicians who work with children six and under were surveyed about blood lead level (BLL) testing practices, particularly, adherence to Centers for Disease Control and Prevention (CDC) guidelines, and parental compliance with orders to have their children tested to determine their blood lead levels. In addition, select in-person interviews were conducted with physicians who reported high parental compliance to identify best practices and barriers. Of the 77 physicians that provided data, 48% indicated they did not follow CDC guideline compared to 52% who follow guidelines. 18 of the 30 (or 60%) physicians reported more than 80% of parents complied with doctor recommended BLL testing. Twelve physicians identified cost, lack of insurance, and absence of symptomology as persistent barriers to lead screening. This study identified barriers to childhood lead screening including inadequate parental adherence to physician-ordered screenings and physician non-compliance with screening recommendations are two primary contributors. Addressing these issues could increase screening in children and reduce the risk of lead poisoning.

Optimal Interval for Repeated Gastric Cancer Screening in Normal-Risk Healthy Korean Adults: A Retrospective Cohort Study

PubMed Central

Bae, Jong-Myon; Shin, Sang Yop; Kim, Eun Hee

2015-01-01

Purpose This retrospective cohort study was conducted to estimate the optimal interval for gastric cancer screening in Korean adults with initial negative screening results. Materials and Methods This study consisted of voluntary Korean screenees aged 40 to 69 years who underwent subsequent screening gastroscopies after testing negative in the baseline screening performed between January 2007 and December 2011. A new case was defined as the presence of gastric cancer cells in biopsy specimens obtained upon gastroscopy. The follow-up periods were calculated during the months between the date of baseline screening gastroscopy and positive findings upon subsequent screenings, stratified by sex and age group. The mean sojourn time (MST) for determining the screening interval was estimated using the prevalence/incidence ratio. Results Of the 293,520 voluntary screenees for the gastric cancer screening program, 91,850 (31.29%) underwent subsequent screening gastroscopies between January 2007 and December 2011. The MSTs in men and women were 21.67 months (95% confidence intervals [CI], 17.64 to 26.88 months) and 15.14 months (95% CI, 9.44 to 25.85 months), respectively. Conclusion These findings suggest that the optimal interval for subsequent gastric screening in both men and women is 24 months, supporting the 2-year interval recommended by the nationwide gastric cancer screening program. PMID:25687874

The Role of Conventional and Right-Sided ECG Screening for Subcutaneous ICD in a Tetralogy of Fallot Population.

PubMed

Alonso, Pau; Osca, Joaquín; Cano, Oscar; Pimenta, Pedro; Andrés, Ana; Yagüe, Jaime; Millet, José; Rueda, Joaquín; Sancho-Tello, María José

2017-02-01

Information regarding suitability for subcutaneous implantable cardioverter-defibrillator (S-ICD) implant in tetralogy of Fallot (ToF) population is scarce and needs to be further explored. (1) to determine the proportion of patients with ToF eligible for S-ICD, (2) to identify the optimal sensing vector in ToF patients, (3) to test specifically the eligibility for S-ICD with right-sided screening, and (4) to compare with the proportion of eligible patients in a nonselected ICD population. We recruited 60 consecutive patients with ToF and 40 consecutive nonselected patients. Conventional electrocardiographic screening was performed as usual. Right-sided alternative screening was studied by positioning the left arm and right arm electrodes 1 cm right lateral to the xiphoid midline. The Boston Scientific electrocardiogram (ECG) screening tool was utilized. We found a higher proportion of patients with right-sided positive screening in comparison with standard screening (77 ± 0.4% vs. 67 ± 0.4%; P < 0.0001) and a trend to higher number of appropriate leads in right-sided screening (1.3 ± 1 vs. 1.1 ± 1 ms; P = 0.07). Patients who failed the screening had a longer QRS duration and longer QT interval. Standard and right-sided screening showed a higher percent of positive patients in the control group compared to ToF patients (P < 0.001). Right-sided screening was associated with a significant 10% increase in S-ICD eligibility in ToF patients. When comparing with an acquired cardiomyopathies group, ToF showed a lower eligibility for S-ICD. The most appropriate ECG vector was the alternate vector in contrast to what is observed in the general population. © 2017 Wiley Periodicals, Inc.

Discovery of imidazo[1,2-b]pyridazine derivatives as IKKbeta inhibitors. Part 1: Hit-to-lead study and structure-activity relationship.

PubMed

Shimizu, Hiroki; Tanaka, Shinji; Toki, Tadashi; Yasumatsu, Isao; Akimoto, Toshihiko; Morishita, Kaoru; Yamasaki, Tomonori; Yasukochi, Takanori; Iimura, Shin

2010-09-01

Imidazo[1,2-b]pyridazine derivatives from high-throughput screening were developed as IKKbeta inhibitors. By the optimization of the 3- and 6-position of imidazo[1,2-b]pyridazine scaffold, cell-free IKKbeta inhibitory activity and TNFalpha inhibitory activity in THP-1 cell increased. Also, these compounds showed high kinase selectivity. The structure-activity relationship was revealed and the interaction model of imidazo[1,2-b]pyridazine compounds with IKKbeta was constructed. Copyright 2010. Published by Elsevier Ltd.

Large Scale Bacterial Colony Screening of Diversified FRET Biosensors

PubMed Central

Litzlbauer, Julia; Schifferer, Martina; Ng, David; Fabritius, Arne; Thestrup, Thomas; Griesbeck, Oliver

2015-01-01

Biosensors based on Förster Resonance Energy Transfer (FRET) between fluorescent protein mutants have started to revolutionize physiology and biochemistry. However, many types of FRET biosensors show relatively small FRET changes, making measurements with these probes challenging when used under sub-optimal experimental conditions. Thus, a major effort in the field currently lies in designing new optimization strategies for these types of sensors. Here we describe procedures for optimizing FRET changes by large scale screening of mutant biosensor libraries in bacterial colonies. We describe optimization of biosensor expression, permeabilization of bacteria, software tools for analysis, and screening conditions. The procedures reported here may help in improving FRET changes in multiple suitable classes of biosensors. PMID:26061878

Two High Throughput Screen Assays for Measurement of TNF-α in THP-1 Cells

PubMed Central

Leister, Kristin P; Huang, Ruili; Goodwin, Bonnie L; Chen, Andrew; Austin, Christopher P; Xia, Menghang

2011-01-01

Tumor Necrosis Factor-α (TNF-α), a secreted cytokine, plays an important role in inflammatory diseases and immune disorders, and is a potential target for drug development. The traditional assays for detecting TNF-α, enzyme linked immunosorbent assay (ELISA) and radioimmunoassay, are not suitable for the large size compound screens. Both assays suffer from a complicated protocol, multiple plate wash steps and/or excessive radioactive waste. A simple and quick measurement of TNF-α production in a cell based assay is needed for high throughput screening to identify the lead compounds from the compound library. We have developed and optimized two homogeneous TNF-α assays using the HTRF (homogeneous time resolved fluorescence) and AlphaLISA assay formats. We have validated the HTRF based TNF-α assay in a 1536-well plate format by screening a library of 1280 pharmacologically active compounds. The active compounds identified from the screen were confirmed in the AlphaLISA TNF-α assay using a bead-based technology. These compounds were also confirmed in a traditional ELISA assay. From this study, several beta adrenergic agonists have been identified as TNF-α inhibitors. We also identified several novel inhibitors of TNF-α, such as BTO-1, CCG-2046, ellipticine, and PD 169316. The results demonstrated that both homogeneous TNF-α assays are robust and suitable for high throughput screening. PMID:21643507

Evaluating Oral Fluid as a Screening Tool for Lead Poisoning.

PubMed

Gardner, Sher Lynn; Geller, Robert J; Hannigan, Robyn; Sun, Yu; Mangla, Anil

2016-11-01

Screening for lead poisoning is necessary in young children, but obtaining the needed blood sample is unpleasant and sometimes very difficult. Use of an alternative screening method that is less unpleasant and less difficult would likely help to increase the percent of children receiving screening. To evaluate the correlation of oral fluid and blood lead in a clinical setting, and to ascertain the acceptability and feasibility of obtaining oral fluid from a young child in the clinical setting. Oral fluid samples were collected from a convenience sample of 431 children aged 6 months to 5 years already due to receive a blood lead test in a primary care clinic. Blood lead results obtained at the same time were available for 407 children. The results of the two tests were compared with the blood lead test considered to be the "gold standard". Data analysis used Pearson correlations, scatter plots, linear regression, ANOVA and Bland-Altman analysis. 431 patients had oral fluid samples available for analysis, and 407 patients had blood samples available. Patients who had both blood concentrations <5 µg/dL and oral fluid values below the screening cutoff value were 223, while eight had both blood concentrations ≥ 5 µg/dL and oral fluid values above the screening threshold. Elevated oral fluid but blood lead values less than the value recommended for further intervention occurred in 176; no patients had elevated blood lead values with below-intervention oral fluid values. The negative predictive value of an oral fluid lead below the screening cutoff value was 100%. The use of oral fluid to screen for elevated body burdens of lead instead of the usual blood lead sample is feasible with a negative predictive value of 100%, while eliminating the need for blood for lead screening in more than half of these children. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Novel 1,2-dihydroquinazolin-2-ones: Design, synthesis, and biological evaluation against Trypanosoma brucei.

PubMed

Pham, ThanhTruc; Walden, Madeline; Butler, Christopher; Diaz-Gonzalez, Rosario; Pérez-Moreno, Guiomar; Ceballos-Pérez, Gloria; Gomez-Pérez, Veronica; García-Hernández, Raquel; Zecca, Henry; Krakoff, Emma; Kopec, Brian; Ichire, Ogar; Mackenzie, Caden; Pitot, Marika; Ruiz, Luis Miguel; Gamarro, Francisco; González-Pacanowska, Dolores; Navarro, Miguel; Dounay, Amy B

2017-08-15

In 2014, a published report of the high-throughput screen of>42,000 kinase inhibitors from GlaxoSmithKline against T. brucei identified 797 potent and selective hits. From this rich data set, we selected NEU-0001101 (1) for hit-to-lead optimization. Through our preliminary compound synthesis and SAR studies, we have confirmed the previously reported activity of 1 in a T. brucei cell proliferation assay and have identified alternative groups to replace the pyridyl ring in 1. Pyrazole 24 achieves improvements in both potency and lipophilicity relative to 1, while also showing good in vitro metabolic stability. The SAR developed on 24 provides new directions for further optimization of this novel scaffold for anti-trypanosomal drug discovery. Copyright © 2017 Elsevier Ltd. All rights reserved.

[Maternal phenylketonuria].

PubMed

Bókay, János; Kiss, Erika; Simon, Erika; Szőnyi, László

2013-05-05

Elevated maternal phenylalanine levels during pregnancy are teratogenic, and may result in embryo-foetopathy, which could lead to stillbirth, significant psychomotor handicaps and birth defects. This foetal damage is known as maternal phenylketonuria. Women of childbearing age with all forms of phenylketonuria, including mild variants such as hyperphenylalaninaemia, should receive detailed counselling regarding their risks for adverse foetal effects, optimally before contemplating pregnancy. The most assured way to prevent maternal phenylketonuria is to maintain the maternal phenylalanine levels within the optimal range already before conception and throughout the whole pregnancy. Authors review the comprehensive programme for prevention of maternal phenylketonuria at the Metabolic Center of Budapest, they survey the practical approach of the continuous maternal metabolic control and delineate the outcome of pregnancies of mothers with phenylketonuria from the introduction of newborn screening until most recently.

Discovery of Potent Non-Nucleoside Inhibitors of Dengue Viral RNA-Dependent RNA Polymerase from a Fragment Hit Using Structure-Based Drug Design.

PubMed

Yokokawa, Fumiaki; Nilar, Shahul; Noble, Christian G; Lim, Siew Pheng; Rao, Ranga; Tania, Stefani; Wang, Gang; Lee, Gladys; Hunziker, Jürg; Karuna, Ratna; Manjunatha, Ujjini; Shi, Pei-Yong; Smith, Paul W

2016-04-28

The discovery and optimization of non-nucleoside dengue viral RNA-dependent-RNA polymerase (RdRp) inhibitors are described. An X-ray-based fragment screen of Novartis' fragment collection resulted in the identification of a biphenyl acetic acid fragment 3, which bound in the palm subdomain of RdRp. Subsequent optimization of the fragment hit 3, relying on structure-based design, resulted in a >1000-fold improvement in potency in vitro and acquired antidengue activity against all four serotypes with low micromolar EC50 in cell-based assays. The lead candidate 27 interacts with a novel binding pocket in the palm subdomain of the RdRp and exerts a promising activity against all clinically relevant dengue serotypes.

Design of Potent and Druglike Nonphenolic Inhibitors for Catechol O-Methyltransferase Derived from a Fragment Screening Approach Targeting the S-Adenosyl-l-methionine Pocket.

PubMed

Lerner, Christian; Jakob-Roetne, Roland; Buettelmann, Bernd; Ehler, Andreas; Rudolph, Markus; Rodríguez Sarmiento, Rosa María

2016-11-23

A fragment screening approach designed to target specifically the S-adenosyl-l-methionine pocket of catechol O-methyl transferase allowed the identification of structurally related fragments of high ligand efficiency and with activity on the described orthogonal assays. By use of a reliable enzymatic assay together with X-ray crystallography as guidance, a series of fragment modifications revealed an SAR and, after several expansions, potent lead compounds could be obtained. For the first time nonphenolic and small low nanomolar potent, SAM competitive COMT inhibitors are reported. These compounds represent a novel series of potent COMT inhibitors that might be further optimized to new drugs useful for the treatment of Parkinson's disease, as adjuncts in levodopa based therapy, or for the treatment of schizophrenia.

A new efficient mixture screening design for optimization of media.

PubMed

Rispoli, Fred; Shah, Vishal

2009-01-01

Screening ingredients for the optimization of media is an important first step to reduce the many potential ingredients down to the vital few components. In this study, we propose a new method of screening for mixture experiments called the centroid screening design. Comparison of the proposed design with Plackett-Burman, fractional factorial, simplex lattice design, and modified mixture design shows that the centroid screening design is the most efficient of all the designs in terms of the small number of experimental runs needed and for detecting high-order interaction among ingredients. (c) 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009.

A new insight into mushroom tyrosinase inhibitors: docking, pharmacophore-based virtual screening, and molecular modeling studies.

PubMed

Bagherzadeh, Kowsar; Shirgahi Talari, Faezeh; Sharifi, Amirhossein; Ganjali, Mohammad Reza; Saboury, Ali Akbar; Amanlou, Massoud

2015-01-01

Tyrosinase, a widely spread enzyme in micro-organisms, animals, and plants, participates in two rate-limiting steps in melanin formation pathway which is responsible for skin protection against UV lights' harm whose functional deficiency result in serious dermatological diseases. This enzyme seems to be responsible for neuromelanin formation in human brain as well. In plants, the enzyme leads the browning pathway which is commonly observed in injured tissues that is economically very unfavorable. Among different types of tyrosinase, mushroom tyrosinase has the highest homology with the mammalian tyrosinase and the only commercial tyrosinase available. In this study, ligand-based pharmacophore drug discovery method was applied to rapidly identify mushroom tyrosinase enzyme inhibitors using virtual screening. The model pharmacophore of essential interactions was developed and refined studying already experimentally discovered potent inhibitors employing Docking analysis methodology. After pharmacophore virtual screening and binding modes prediction, 14 compounds from ZINC database were identified as potent inhibitors of mushroom tyrosinase which were classified into five groups according to their chemical structures. The inhibition behavior of the discovered compounds was further studied through Classical Molecular Dynamic Simulations and the conformational changes induced by the presence of the studied ligands were discussed and compared to those of the substrate, tyrosine. According to the obtained results, five novel leads are introduced to be further optimized or directly used as potent inhibitors of mushroom tyrosinase.

The Screening Compound Collection: A Key Asset for Drug Discovery.

PubMed

Boss, Christoph; Hazemann, Julien; Kimmerlin, Thierry; von Korff, Modest; Lüthi, Urs; Peter, Oliver; Sander, Thomas; Siegrist, Romain

2017-10-25

In this case study on an essential instrument of modern drug discovery, we summarize our successful efforts in the last four years toward enhancing the Actelion screening compound collection. A key organizational step was the establishment of the Compound Library Committee (CLC) in September 2013. This cross-functional team consisting of computational scientists, medicinal chemists and a biologist was endowed with a significant annual budget for regular new compound purchases. Based on an initial library analysis performed in 2013, the CLC developed a New Library Strategy. The established continuous library turn-over mode, and the screening library size of 300'000 compounds were maintained, while the structural library quality was increased. This was achieved by shifting the selection criteria from 'druglike' to 'leadlike' structures, enriching for non-flat structures, aiming for compound novelty, and increasing the ratio of higher cost 'Premium Compounds'. Novel chemical space was gained by adding natural compounds, macrocycles, designed and focused libraries to the collection, and through mutual exchanges of proprietary compounds with agrochemical companies. A comparative analysis in 2016 provided evidence for the positive impact of these measures. Screening the improved library has provided several highly promising hits, including a macrocyclic compound, that are currently followed up in different Hit-to-Lead and Lead Optimization programs. It is important to state that the goal of the CLC was not to achieve higher HTS hit rates, but to increase the chances of identified hits to serve as the basis of successful early drug discovery programs. The experience gathered so far legitimates the New Library Strategy.

Towards a Normalised 3D Geovisualisation: The Viewpoint Management

NASA Astrophysics Data System (ADS)

Neuville, R.; Poux, F.; Hallot, P.; Billen, R.

2016-10-01

This paper deals with the viewpoint management in 3D environments considering an allocentric environment. The recent advances in computer sciences and the growing number of affordable remote sensors lead to impressive improvements in the 3D visualisation. Despite some research relating to the analysis of visual variables used in 3D environments, we notice that it lacks a real standardisation of 3D representation rules. In this paper we study the "viewpoint" as being the first considered parameter for a normalised visualisation of 3D data. Unlike in a 2D environment, the viewing direction is not only fixed in a top down direction in 3D. A non-optimal camera location means a poor 3D representation in terms of relayed information. Based on this statement we propose a model based on the analysis of the computational display pixels that determines a viewpoint maximising the relayed information according to one kind of query. We developed an OpenGL prototype working on screen pixels that allows to determine the optimal camera location based on a screen pixels colour algorithm. The viewpoint management constitutes a first step towards a normalised 3D geovisualisation.

Identification of a Novel Class of BRD4 Inhibitors by Computational Screening and Binding Simulations

PubMed Central

2017-01-01

Computational screening is a method to prioritize small-molecule compounds based on the structural and biochemical attributes built from ligand and target information. Previously, we have developed a scalable virtual screening workflow to identify novel multitarget kinase/bromodomain inhibitors. In the current study, we identified several novel N-[3-(2-oxo-pyrrolidinyl)phenyl]-benzenesulfonamide derivatives that scored highly in our ensemble docking protocol. We quantified the binding affinity of these compounds for BRD4(BD1) biochemically and generated cocrystal structures, which were deposited in the Protein Data Bank. As the docking poses obtained in the virtual screening pipeline did not align with the experimental cocrystal structures, we evaluated the predictions of their precise binding modes by performing molecular dynamics (MD) simulations. The MD simulations closely reproduced the experimentally observed protein–ligand cocrystal binding conformations and interactions for all compounds. These results suggest a computational workflow to generate experimental-quality protein–ligand binding models, overcoming limitations of docking results due to receptor flexibility and incomplete sampling, as a useful starting point for the structure-based lead optimization of novel BRD4(BD1) inhibitors. PMID:28884163

Early Probe and Drug Discovery in Academia: A Minireview.

PubMed

Roy, Anuradha

2018-02-09

Drug discovery encompasses processes ranging from target selection and validation to the selection of a development candidate. While comprehensive drug discovery work flows are implemented predominantly in the big pharma domain, early discovery focus in academia serves to identify probe molecules that can serve as tools to study targets or pathways. Despite differences in the ultimate goals of the private and academic sectors, the same basic principles define the best practices in early discovery research. A successful early discovery program is built on strong target definition and validation using a diverse set of biochemical and cell-based assays with functional relevance to the biological system being studied. The chemicals identified as hits undergo extensive scaffold optimization and are characterized for their target specificity and off-target effects in in vitro and in animal models. While the active compounds from screening campaigns pass through highly stringent chemical and Absorption, Distribution, Metabolism, and Excretion (ADME) filters for lead identification, the probe discovery involves limited medicinal chemistry optimization. The goal of probe discovery is identification of a compound with sub-µM activity and reasonable selectivity in the context of the target being studied. The compounds identified from probe discovery can also serve as starting scaffolds for lead optimization studies.

Comparison of DNQ/novolac resists for e-beam exposure

NASA Astrophysics Data System (ADS)

Fedynyshyn, Theodore H.; Doran, Scott P.; Lind, Michele L.; Lyszczarz, Theodore M.; DiNatale, William F.; Lennon, Donna; Sauer, Charles A.; Meute, Jeff

1999-12-01

We have surveyed the commercial resist market with the dual purpose of identifying diazoquinone/novolac based resists that have potential for use as e-beam mask making resists and baselining these resists for comparison against future mask making resist candidates. For completeness, this survey would require that each resist be compared with an optimized developer and development process. To accomplish this task in an acceptable time period, e-beam lithography modeling was employed to quickly identify the resist and developer combinations that lead to superior resist performance. We describe the verification of a method to quickly screen commercial i-line resists with different developers, by determining modeling parameters for i-line resists from e-beam exposures, modeling the resist performance, and comparing predicted performance versus actual performance. We determined the lithographic performance of several DNQ/novolac resists whose modeled performance suggests that sensitivities of less than 40 (mu) C/cm2 coupled with less than 10-nm CD change per percent change in dose are possible for target 600-nm features. This was accomplished by performing a series of statistically designed experiments on the leading resists candidates to optimize processing variables, followed by comparing experimentally determined resist sensitivities, latitudes, and profiles of the DNQ/novolac resists a their optimized process.

Depression screening optimization in an academic rural setting.

PubMed

Aleem, Sohaib; Torrey, William C; Duncan, Mathew S; Hort, Shoshana J; Mecchella, John N

2015-01-01

Primary care plays a critical role in screening and management of depression. The purpose of this paper is to focus on leveraging the electronic health record (EHR) as well as work flow redesign to improve the efficiency and reliability of the process of depression screening in two adult primary care clinics of a rural academic institution in USA. The authors utilized various process improvement tools from lean six sigma methodology including project charter, swim lane process maps, critical to quality tree, process control charts, fishbone diagrams, frequency impact matrix, mistake proofing and monitoring plan in Define-Measure-Analyze-Improve-Control format. Interventions included change in depression screening tool, optimization of data entry in EHR. EHR data entry optimization; follow up of positive screen, staff training and EHR redesign. Depression screening rate for office-based primary care visits improved from 17.0 percent at baseline to 75.9 percent in the post-intervention control phase (p<0.001). Follow up of positive depression screen with Patient History Questionnaire-9 data collection remained above 90 percent. Duplication of depression screening increased from 0.6 percent initially to 11.7 percent and then decreased to 4.7 percent after optimization of data entry by patients and flow staff. Impact of interventions on clinical outcomes could not be evaluated. Successful implementation, sustainability and revision of a process improvement initiative to facilitate screening, follow up and management of depression in primary care requires accounting for voice of the process (performance metrics), system limitations and voice of the customer (staff and patients) to overcome various system, customer and human resource constraints.

[China National Lung Cancer Screening Guideline with Low-dose Computed 
Tomography (2018 version)].

PubMed

Zhou, Qinghua; Fan, Yaguang; Wang, Ying; Qiao, Youlin; Wang, Guiqi; Huang, Yunchao; Wang, Xinyun; Wu, Ning; Zhang, Guozheng; Zheng, Xiangpeng; Bu, Hong; Li, Yin; Wei, Sen; Chen, Liang'an; Hu, Chengping; Shi, Yuankai; Sun, Yan

2018-02-20

Lung cancer is the leading cause of cancer-related death in China. The results from a randomized controlled trial using annual low-dose computed tomography (LDCT) in specific high-risk groups demonstrated a 20% reduction in lung cancer mortality. The aim of tihs study is to establish the China National lung cancer screening guidelines for clinical practice. The China lung cancer early detection and treatment expert group (CLCEDTEG) established the China National Lung Cancer Screening Guideline with multidisciplinary representation including 4 thoracic surgeons, 4 thoracic radiologists, 2 medical oncologists, 2 pulmonologists, 2 pathologist, and 2 epidemiologist. Members have engaged in interdisciplinary collaborations regarding lung cancer screening and clinical care of patients with at risk for lung cancer. The expert group reviewed the literature, including screening trials in the United States and Europe and China, and discussed local best clinical practices in the China. A consensus-based guidelines, China National Lung Cancer Screening Guideline (CNLCSG), was recommended by CLCEDTEG appointed by the National Health and Family Planning Commission, based on results of the National Lung Screening Trial, systematic review of evidence related to LDCT screening, and protocol of lung cancer screening program conducted in rural China. Annual lung cancer screening with LDCT is recommended for high risk individuals aged 50-74 years who have at least a 20 pack-year smoking history and who currently smoke or have quit within the past five years. Individualized decision making should be conducted before LDCT screening. LDCT screening also represents an opportunity to educate patients as to the health risks of smoking; thus, education should be integrated into the screening process in order to assist smoking cessation. A lung cancer screening guideline is recommended for the high-risk population in China. Additional research , including LDCT combined with biomarkers, is needed to optimize the approach to low-dose CT screening in the future.

Structure-based design of Aurora A & B inhibitors

NASA Astrophysics Data System (ADS)

Poulsen, Anders; William, Anthony; Lee, Angeline; Blanchard, Stéphanie; Teo, Eeling; Deng, Weiping; Tu, Noah; Tan, Evelyn; Sun, Eric; Goh, Kay Lin; Ong, Wai Chung; Ng, Chee Pang; Goh, Kee Chuan; Bonday, Zahid

2008-12-01

The Aurora family of serine/threonine kinases are mitotic regulators involved in centrosome duplication, formation of the bipolar mitotic spindle and the alignment of the chromosomes along the spindle. These proteins are frequently overexpressed in tumor cells as compared to normal cells and are therefore potential therapeutic oncology targets. An Aurora A high throughput screen revealed a promising sub-micromolar indazole-benzimidazole lead. Modification of the benzimidazole portion of the lead to a C2 linker with a phenyl ring was proposed to achieve novelty. Docking revealed that a conjugated linker was optimal and the resulting compounds were equipotent with the lead. Further structure-guided optimization of substituents on the 5 & 6 position of the indazole led to single digit nanomolar potency. The homology between the Aurora A & Aurora B kinase domains is 71% but their binding sites only differ at residues 212 & 217 (Aurora A numbering). However interactions with only the latter residue may be used for obtaining selectivity. An analysis of published Aurora A and Aurora B X-ray structures reveals subtle differences in the shape of the binding sites. This was exploited by introduction of appropriately sized substituents in the 4 & 6 position of the indazole leading to Aurora B selective inhibitors. Finally we calculate the conformational energy penalty of the putative bioactive conformation of our inhibitors and show that this property correlates well with the Aurora A binding affinity.

Planning multi-arm screening studies within the context of a drug development program

PubMed Central

Wason, James M S; Jaki, Thomas; Stallard, Nigel

2013-01-01

Screening trials are small trials used to decide whether an intervention is sufficiently promising to warrant a large confirmatory trial. Previous literature examined the situation where treatments are tested sequentially until one is considered sufficiently promising to take forward to a confirmatory trial. An important consideration for sponsors of clinical trials is how screening trials should be planned to maximize the efficiency of the drug development process. It has been found previously that small screening trials are generally the most efficient. In this paper we consider the design of screening trials in which multiple new treatments are tested simultaneously. We derive analytic formulae for the expected number of patients until a successful treatment is found, and propose methodology to search for the optimal number of treatments, and optimal sample size per treatment. We compare designs in which only the best treatment proceeds to a confirmatory trial and designs in which multiple treatments may proceed to a multi-arm confirmatory trial. We find that inclusion of a large number of treatments in the screening trial is optimal when only one treatment can proceed, and a smaller number of treatments is optimal when more than one can proceed. The designs we investigate are compared on a real-life set of screening designs. Copyright © 2013 John Wiley & Sons, Ltd. PMID:23529936

X-ray transparent microfluidic chips for high-throughput screening and optimization of in meso membrane protein crystallization

PubMed Central

Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.; Wan, Frank; Sheraden, Paige N.; Broecker, Jana; Ernst, Oliver P.; Gennis, Robert B.

2017-01-01

Elucidating and clarifying the function of membrane proteins ultimately requires atomic resolution structures as determined most commonly by X-ray crystallography. Many high impact membrane protein structures have resulted from advanced techniques such as in meso crystallization that present technical difficulties for the set-up and scale-out of high-throughput crystallization experiments. In prior work, we designed a novel, low-throughput X-ray transparent microfluidic device that automated the mixing of protein and lipid by diffusion for in meso crystallization trials. Here, we report X-ray transparent microfluidic devices for high-throughput crystallization screening and optimization that overcome the limitations of scale and demonstrate their application to the crystallization of several membrane proteins. Two complementary chips are presented: (1) a high-throughput screening chip to test 192 crystallization conditions in parallel using as little as 8 nl of membrane protein per well and (2) a crystallization optimization chip to rapidly optimize preliminary crystallization hits through fine-gradient re-screening. We screened three membrane proteins for new in meso crystallization conditions, identifying several preliminary hits that we tested for X-ray diffraction quality. Further, we identified and optimized the crystallization condition for a photosynthetic reaction center mutant and solved its structure to a resolution of 3.5 Å. PMID:28469762

Calculating Water Thermodynamics in the Binding Site of Proteins - Applications of WaterMap to Drug Discovery.

PubMed

Cappel, Daniel; Sherman, Woody; Beuming, Thijs

2017-01-01

The ability to accurately characterize the solvation properties (water locations and thermodynamics) of biomolecules is of great importance to drug discovery. While crystallography, NMR, and other experimental techniques can assist in determining the structure of water networks in proteins and protein-ligand complexes, most water molecules are not fully resolved and accurately placed. Furthermore, understanding the energetic effects of solvation and desolvation on binding requires an analysis of the thermodynamic properties of solvent involved in the interaction between ligands and proteins. WaterMap is a molecular dynamics-based computational method that uses statistical mechanics to describe the thermodynamic properties (entropy, enthalpy, and free energy) of water molecules at the surface of proteins. This method can be used to assess the solvent contributions to ligand binding affinity and to guide lead optimization. In this review, we provide a comprehensive summary of published uses of WaterMap, including applications to lead optimization, virtual screening, selectivity analysis, ligand pose prediction, and druggability assessment. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Design, synthesis, in vitro Evaluation and docking studies on dihydropyrimidine-based urease inhibitors.

PubMed

Iftikhar, Fatima; Ali, Yousaf; Ahmad Kiani, Farooq; Fahad Hassan, Syed; Fatima, Tabeer; Khan, Ajmal; Niaz, Basit; Hassan, Abbas; Latif Ansari, Farzana; Rashid, Umer

2017-10-01

In our previous report, we have identified 3,4-dihydropyrimidine scaffold as promising class of urease inhibitor in a structure based virtual screen (SBVS) experiment. In present study, we attempted to optimize the scaffold by varying C-5 substituent. The elongation of the C-5 chain was achieved by the reaction of C-5 ester with hydrazine leading to C-5 carbohydrazides which were further used as building blocks for the synthesis of fifteen new compounds having diverse moieties. A significantly higher in vitro urease inhibitory activity with IC 50 values in submicromolar range was observed for semithiocarbazide derivatives (4a-c, 0.58-0.79µM) and isatin Schiff base derivative 5a (0.23µM). Docking analysis suggests that the synthesized compounds were anchored well in the catalytic site and extending to the entrance of binding pocket and thus restrict the mobility of the flap by interacting with its key amino acid residues. The overall results of urease inhibition have shown that these compounds can be further optimized and developed as lead urease inhibitors. Copyright © 2017 Elsevier Inc. All rights reserved.

Fragment-Based Discovery of a Potent, Orally Bioavailable Inhibitor That Modulates the Phosphorylation and Catalytic Activity of ERK1/2.

PubMed

Heightman, Tom D; Berdini, Valerio; Braithwaite, Hannah; Buck, Ildiko M; Cassidy, Megan; Castro, Juan; Courtin, Aurélie; Day, James E H; East, Charlotte; Fazal, Lynsey; Graham, Brent; Griffiths-Jones, Charlotte M; Lyons, John F; Martins, Vanessa; Muench, Sandra; Munck, Joanne M; Norton, David; O'Reilly, Marc; Palmer, Nick; Pathuri, Puja; Reader, Michael; Rees, David C; Rich, Sharna J; Richardson, Caroline; Saini, Harpreet; Thompson, Neil T; Wallis, Nicola G; Walton, Hugh; Wilsher, Nicola E; Woolford, Alison J-A; Cooke, Michael; Cousin, David; Onions, Stuart; Shannon, Jonathan; Watts, John; Murray, Christopher W

2018-05-31

Aberrant activation of the MAPK pathway drives cell proliferation in multiple cancers. Inhibitors of BRAF and MEK kinases are approved for the treatment of BRAF mutant melanoma, but resistance frequently emerges, often mediated by increased signaling through ERK1/2. Here, we describe the fragment-based generation of ERK1/2 inhibitors that block catalytic phosphorylation of downstream substrates such as RSK but also modulate phosphorylation of ERK1/2 by MEK without directly inhibiting MEK. X-ray crystallographic and biophysical fragment screening followed by structure-guided optimization and growth from the hinge into a pocket proximal to the C-α helix afforded highly potent ERK1/2 inhibitors with excellent kinome selectivity. In BRAF mutant cells, the lead compound suppresses pRSK and pERK levels and inhibits proliferation at low nanomolar concentrations. The lead exhibits tumor regression upon oral dosing in BRAF mutant xenograft models, providing a promising basis for further optimization toward clinical pERK1/2 modulating ERK1/2 inhibitors.

Use of geographic information system technology to aid Health Department decision making about childhood lead poisoning prevention activities.

PubMed Central

Reissman, D B; Staley, F; Curtis, G B; Kaufmann, R B

2001-01-01

The Centers for Disease Control and Prevention recommend that local public health agencies use local data to identify children at risk for lead exposure to ensure that they receive preventive services. The objective of this study was to demonstrate the usefulness of a geographic information system (GIS) in identifying children at risk for lead exposure. We conducted a descriptive study, using GIS technology, of the blood lead (BPb) levels and residential location of at-risk children screened for lead exposure. "At-risk children" were defined as those children living in housing built before 1950 or in an area with a high proportion of older housing. The study was conducted in Jefferson County, Kentucky, USA. Participants were the cohort of children born in 1995 and screened from 1996 through 1997, and children younger than age 7 years who were screened from 1994 through 1998. Outcome measures were the BPb level and residential location (address or target zone) of at-risk children screened from 1996 through 1997, and the number and location of homes where more than one child had been poisoned by lead from 1994 through 1998. The proportion of children screened who live within zones targeted for universal screening varied from 48% to 53%, while only 50% of the at-risk children in the entire county were screened. Between 1994 and 1998, 79 homes housed 35% of the 524 children with lead poisoning. These housing units were prioritized for lead-hazard remediation. Significant numbers of at-risk children throughout the county were not being tested for lead exposure, even in prioritized areas. GIS can be very useful to health departments in planning lead exposure screening strategies and measuring program performance. PMID:11171530

A probabilistic method for the estimation of residual risk in donated blood.

PubMed

Bish, Ebru K; Ragavan, Prasanna K; Bish, Douglas R; Slonim, Anthony D; Stramer, Susan L

2014-10-01

The residual risk (RR) of transfusion-transmitted infections, including the human immunodeficiency virus and hepatitis B and C viruses, is typically estimated by the incidence[Formula: see text]window period model, which relies on the following restrictive assumptions: Each screening test, with probability 1, (1) detects an infected unit outside of the test's window period; (2) fails to detect an infected unit within the window period; and (3) correctly identifies an infection-free unit. These assumptions need not hold in practice due to random or systemic errors and individual variations in the window period. We develop a probability model that accurately estimates the RR by relaxing these assumptions, and quantify their impact using a published cost-effectiveness study and also within an optimization model. These assumptions lead to inaccurate estimates in cost-effectiveness studies and to sub-optimal solutions in the optimization model. The testing solution generated by the optimization model translates into fewer expected infections without an increase in the testing cost. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Newborn screening of glucose-6-phosphate dehydrogenase deficiency in Guangxi, China: determination of optimal cutoff value to identify heterozygous female neonates.

PubMed

Fu, Chunyun; Luo, Shiyu; Li, Qifei; Xie, Bobo; Yang, Qi; Geng, Guoxing; Lin, Caijuan; Su, Jiasun; Zhang, Yue; Wang, Jin; Qin, Zailong; Luo, Jingsi; Chen, Shaoke; Fan, Xin

2018-01-16

The aim of this study is to assess the disease incidence and mutation spectrum of glucose-6-phosphate dehydrogenase (G6PD) deficiency in Guangxi, China, and to determine an optimal cutoff value to identify heterozygous female neonates. A total of 130, 635 neonates were screened from the year of 2013 to 2017. Neonates suspected for G6PD deficiency were further analyzed by quantitatively enzymatic assay and G6PD mutation analysis. The overall incidence of G6PD deficiency was 7.28%. A total of 14 G6PD mutations were identified, and different mutations lead to varying levels of G6PD enzymatic activities. The best cut-off value of G6PD activity in male subjects is 2.2 U/g Hb, same as conventional setting. In female population, however, the cut-off value is found to be 2.8 U/g Hb (sensitivity: 97.5%, specificity: 87.7%, AUC: 0.964) to best discriminate between normal and heterozygotes, and 1.6 U/g Hb (sensitivity: 82.2%, specificity: 85.9%, AUC: 0.871) between heterozygotes and deficient subjects. In conclusion, we have conducted a comprehensive newborn screening of G6PD deficiency in a large cohort of population from Guangxi, China, and first established a reliable cut-off value of G6PD activity to distinguish heterozygous females from either normal or deficient subjects.

Bis-benzimidazole hits against Naegleria fowleri discovered with new high-throughput screens.

PubMed

Rice, Christopher A; Colon, Beatrice L; Alp, Mehmet; Göker, Hakan; Boykin, David W; Kyle, Dennis E

2015-04-01

Naegleria fowleri is a pathogenic free-living amoeba (FLA) that causes an acute fatal disease known as primary amoebic meningoencephalitis (PAM). The major problem for infections with any pathogenic FLA is a lack of effective therapeutics, since PAM has a case mortality rate approaching 99%. Clearly, new drugs that are potent and have rapid onset of action are needed to enhance the treatment regimens for PAM. Diamidines have demonstrated potency against multiple pathogens, including FLA, and are known to cross the blood-brain barrier to cure other protozoan diseases of the central nervous system. Therefore, amidino derivatives serve as an important chemotype for discovery of new drugs. In this study, we validated two new in vitro assays suitable for medium- or high-throughput drug discovery and used these for N. fowleri. We next screened over 150 amidino derivatives of multiple structural classes and identified two hit series with nM potency that are suitable for further lead optimization as new drugs for this neglected disease. These include both mono- and diamidino derivatives, with the most potent compound (DB173) having a 50% inhibitory concentration (IC50) of 177 nM. Similarly, we identified 10 additional analogues with IC50s of <1 μM, with many of these having reasonable selectivity indices. The most potent hits were >500 times more potent than pentamidine. In summary, the mono- and diamidino derivatives offer potential for lead optimization to develop new drugs to treat central nervous system infections with N. fowleri. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Structure based virtual screening of the Ebola virus trimeric glycoprotein using consensus scoring.

PubMed

Onawole, Abdulmujeeb T; Kolapo, Temitope U; Sulaiman, Kazeem O; Adegoke, Rukayat O

2018-02-01

Ebola virus (EBOV) causes zoonotic viral infection with a potential risk of global spread and a highly fatal effect on humans. Till date, no drug has gotten market approval for the treatment of Ebola virus disease (EVD), and this perhaps allows the use of both experimental and computational approaches in the antiviral drug discovery process. The main target of potential vaccines that are recently undergoing clinical trials is trimeric glycoprotein (GP) of the EBOV and its exact crystal structure was used in this structure based virtual screening study, with the aid of consensus scoring to select three possible hit compounds from about 36 million compounds in MCULE's database. Amongst these three compounds, (5R)-5-[[5-(4-chlorophenyl)-1,2,4-oxadiazol-3-yl]methyl]-N-[(4-methoxyphenyl)methyl]-4,5-dihydroisoxazole-3-carboxamide (SC-2, C 21 H 19 ClN 4 O 4 ) showed good features with respect to drug likeness, ligand efficiency metrics, solubility, absorption and distribution properties and non-carcinogenicity to emerge as the most promising compound that can be optimized to lead compound against the GP EBOV. The binding mode showed that SC-2 is well embedded within the trimeric chains of the GP EBOV with molecular interactions with some amino acids. The SC-2 hit compound, upon its optimization to lead, might be a good potential candidate with efficacy against the EBOV pathogen and subsequently receive necessary approval to be used as antiviral drug for the treatment of EVD. Copyright © 2017 Elsevier Ltd. All rights reserved.

Stringent and reproducible tetracycline-regulated transgene expression by site-specific insertion at chromosomal loci with pre-characterised induction characteristics

PubMed Central

Brough, Rachel; Papanastasiou, Antigoni M; Porter, Andrew CG

2007-01-01

Background The ability to regulate transgene expression has many applications, mostly concerning the analysis of gene function. Desirable induction characteristics, such as low un-induced expression, high induced expression and limited cellular heterogeneity, can be seriously impaired by chromosomal position effects at the site of transgene integration. Many clones may therefore need to be screened before one with optimal induction characteristics is identified. Furthermore, such screens must be repeated for each new transgene investigated, and comparisons between clones with different transgenes is complicated by their different integration sites. Results To circumvent these problems we have developed a "screen and insert" strategy in which clones carrying a transgene for a fluorescent reporter are first screened for those with optimal induction characteristics. Site-specific recombination (SSR) is then be used repeatedly to insert any new transgene at the reporter transgene locus of such clones so that optimal induction characteristics are conferred upon it. Here we have tested in a human fibrosarcoma cell line (HT1080) two of many possible implementations of this approach. Clones (e.g. Rht14-10) in which a GFP reporter gene is very stringently regulated by the tetracycline (tet) transactivator (tTA) protein were first identified flow-cytometrically. Transgenes encoding luciferase, I-SceI endonuclease or Rad52 were then inserted by SSR at a LoxP site adjacent to the GFP gene resulting stringent tet-regulated transgene expression. In clone Rht14-10, increases in expression from essentially background levels (+tet) to more than 104-fold above background (-tet) were reproducibly detected after Cre-mediated insertion of either the luciferase or the I-SceI transgenes. Conclusion Although previous methods have made use of SSR to integrate transgenes at defined sites, none has effectively combined this with a pre-selection step to identify integration sites that support optimal regulatory characteristics. Rht14-10 and similar HT1080-derived clones can now be used in conjunction with a convenient delivery vector (pIN2-neoMCS), in a simple 3-step protocol leading to stringent and reproducible transgene regulation. This approach will be particularly useful for transgenes whose products are very active at low concentrations and/or for comparisons of multiple related transgenes. PMID:17493262

Improving participation by Aboriginal children in blood lead screening services in Broken Hill, NSW.

PubMed

Thomas, Susan L; Boreland, Frances; Lyle, David M

2013-03-01

Lead poses a health risk to young children with detrimental effects on their intellectual development. Attendance rates for Aboriginal children at routine blood lead screening and at follow-up appointments in Broken Hill, NSW, have declined in recent years. This study sought to identify strategies to improve the participation of Aboriginal children aged 1-4 years in blood lead screening services in Broken Hill. Attendance rates during the period 2000-2010 were determined using the Broken Hill Lead Management database. From June to August 2011, Aboriginal community members, service providers and public health staff were invited to interviews and focus groups to explore barriers, enablers and suggestions for improving participation. In 2009, 27% of Aboriginal children aged 1-4 years attended blood lead screening and 29% of these children with blood lead levels over 15 µg/dL attended follow-up appointments. Barriers to participation in lead screening services included community perceptions, reduced service capacity, socio-economic and interorganisational factors. Enablers included using a culturally acceptable model, linking lead screening with routine health checks and using the finger-prick method of testing. The final report for the study included recommendations to improve participation rates of Aboriginal children including using social marketing, formalising collaboration between health services, supporting disadvantaged families and employing an Aboriginal Health Worker.

Cost of a recall of a single-center experience managing the Riata defibrillator lead.

PubMed

Hussain, Sarah; Moorman, Liza; Moorman, J Randall; DiMarco, John P; Malhotra, Rohit; Darby, Andrew; Bilchick, Kenneth; Mangrum, J Michael; Ferguson, John D; Mason, Pamela K

2015-01-15

Riata and Riata ST defibrillator leads (St. Jude Medical, Sylmar, California) were recalled in 2011 due to increased risk of insulation failure leading to externalized cables. Fluoroscopic screening can identify insulation failure, although the relation between mechanical failure and electrical failure is unclear. At the time of the recall, the University of Virginia developed a screening program, including fluoroscopic evaluation, education sessions, device interrogation, and remote monitoring for patients with this defibrillator lead. The aim of this study was to review the outcomes of the screening program, including costs, which were absorbed by our institution. Costs were calculated using Medicare reimbursement estimates. Forty-eight patients participated in the screening program. At initial screening, 31% were found to have evidence of insulation failure but electrical function was normal in all leads. The cost of this program was $35,358.72. The cost per diagnosis of mechanical lead failure was $2,357.25. During 2 years of follow-up, 1 patient experienced Riata lead electrical failure without fluoroscopic evidence of insulation failure. Patients were more likely to have a lead revision if there was evidence of insulation failure. Lead revisions occurred at the time of generator change in 88% of patients with insulation failure but in only 14% of patients with a fluoroscopically normal lead (p = 0.04). The cost of recall-related defibrillator lead revisions was $81,704.55. In conclusion, our Riata screening program added expense without clear benefit to patients. In fact, patients may have been put at more risk by undergoing defibrillator lead revisions based solely on the results of the fluoroscopic screening. Copyright © 2015 Elsevier Inc. All rights reserved.

Community- and family-level factors influence care-giver choice to screen blood lead levels of children in a mining community.

PubMed

Moodie, S M; Tsui, E K; Silbergeld, E K

2010-07-01

Bunker Hill, in Kellogg, Idaho, formerly a lead mine (1884-1981) and smelter (1917-1981), is now a Superfund site listed on the Environmental Protection Agency's (EPA) National Priorities List. Lead contamination from the site is widespread due to past smelter discharges to land, water, and air, placing children at risk for both exposure to lead and resultant health effects of lead. Since 1983, the EPA has used child blood lead levels to inform the clean-up standards for the Bunker Hill Superfund site. This study was undertaken to examine factors that have contributed to the significant fall-off in the rates and numbers of children being screened for blood lead in Kellogg (number screened decreased from 195 to 8 from 2002 to 2007). The goal of this research project was to define community- and family-level factors which influence care-giver choice to screen blood lead levels of their children in this environment. This formative research study used mixed methods and was comprised of three research components: (1) preliminary interviews using community-based participatory research methods to define key research questions of relevance to community members, government and NGOs working in relation to the Bunker Hill clean-up; (2) a quantitative analysis of a cross-sectional household survey conducted with adult care-givers about child blood lead screening in Kellogg; and (3) ethnographic community rapid assessment methods formed the in-depth interview process and qualitative analysis. The survey showed the likelihood of blood lead screening that for children under the age of 18 years increases 34% with each one-year increase in current age of the child (95% CI, 1.08-1.67, p-value=0.009), and decreases 45% with annual household income greater than $10,000 (95% CI, 0.35-0.88, p-value=0.013). Sibling birth order increased the likelihood of blood lead screening by 61% (95% CI, 1.04-2.48, p-value=0.032) for each successive child. Female children were rated by their care-givers as 3.7 times less agitated or easily angered than male children (95% CI, 1.5-8.8, p-value=0.005). Across all levels of interviews, regulators, residents, and non-governmental organization representatives reported that Kellogg's long history as a mining town has continued to influence attitudes and actions of care-givers to access blood lead screening for their children. The mining context has been described as instilling stigmas, parental blame and a sense of shame about lead exposure and resultant health effects. Children under 6 years of age are currently the least likely to have been screened for lead in Kellogg and screening rates decreased in the 2000s. According to most indicators, socio-economic status did not influence the likelihood of a care-giver to screen children's blood lead levels. However, children in homes with an annual income below $10,000 were more likely to have been screened than the rest of the population. Former concerted screening efforts, including outreach, support, follow-up, and financial incentives in the 1980s-1990s to screen children, may have influenced low-income residents. Programmatic outreach for children under 6 years of age in Kellogg should focus on increasing female child and first child blood lead screening, rather than targeting only low-income families, by improving approaches to promotion, implementation and environmental follow-up for child lead screening. Some families have resided in Kellogg for five to six generations, and the long-term mining context influences community values and perceptions of lead exposure and screening for children through a conflicted combination of pride in the mining history, attachment to the past economy that supported the community in juxtaposition to the personalized blame, shame, guilt, and stigma associated with children having high blood lead levels. Health communication and other programs should prioritize methods of reducing parental feelings of blame, shame and guilt, and stigmas associated with the health effects of lead in a way that respects the pride of former mine workers, their families, and the history of the town. 2010 Elsevier Inc. All rights reserved.

Transungual Gel of Terbinafine Hydrochloride for the Management of Onychomycosis: Formulation, Optimization, and Evaluation.

PubMed

Thatai, Purva; Sapra, Bharti

2017-08-01

The present study was aimed to optimize, develop, and evaluate microemulsion and microemulsion-based gel as a vehicle for transungual drug delivery of terbinafine hydrochloride for the treatment of onychomycosis. D-optimal mixture experimental design was adopted to optimize the composition of microemulsion having amount of oil (X 1 ), Smix (mixture of surfactant and cosurfactant; X 2 ), and water (X 3 ) as the independent variables. The formulations were assessed for permeation (micrograms per square centimeter per hour; Y 1 ), particle size (nanometer; Y 2 ), and solubility of the drug in the formulation (milligrams per milliliter; Y 3 ). The microemulsion containing 3.05% oil, 24.98% Smix, and 71.96% water was selected as the optimized formulation. The microemulsion-based gel showed better penetration (∼5 folds) as well as more retention (∼9 fold) in the animal hoof as compared to the commercial cream. The techniques used to screen penetration enhancers (hydration enhancement factor, ATR-FTIR, SEM, and DSC) revealed the synergistic effect of combination of urea and n-acetyl cysteine in disruption of the structure of hoof and hence, leading to enhanced penetration of drug.

Quality of life, optimism/pessimism, and knowledge and attitudes toward HIV Screening among pregnant women in Ghana.

PubMed

Moyer, Cheryl A; Ekpo, Geraldine; Calhoun, Cecilia L; Greene, Jonathan; Naik, Sujata; Sippola, Emily; Stern, David T; Adanu, Richard M; Koranteng, Isaac O; Kwawukume, Enyonam Yao; Anderson, Frank J

2008-01-01

We sought to explore optimism/pessimism, knowledge of HIV, and attitudes toward HIV screening and treatment among Ghanaian pregnant women. Pregnant women in Accra, Ghana, completed a self-administered questionnaire including the Life Orientation Test-Revised (LOT-R, an optimism/pessimism measure), an HIV knowledge and screening attitudes questionnaire, the Short Form 12 (SF-12, a measure of health-related quality of life [HRQOL]), and a demographic questionnaire. Data were analyzed using t-tests, ANOVA, correlations, and the chi2 test. There were 101 participants; 28% were nulliparous. Mean age was 29.7 years, and mean week of gestation was 31.8. All women had heard of AIDS, 27.7% had been tested for HIV before this pregnancy, 46.5% had been tested during this pregnancy, and 59.4% of the sample had ever been tested for HIV. Of those not tested during this pregnancy, 64.2% were willing to be tested. Of all respondents, 89% said they would get tested if antiretroviral drugs (ARVs) were readily available and might prevent maternal-to-child transmission. Neither optimism/pessimism nor HRQOL was associated with attitudes toward HIV screening. Optimism was negatively correlated with HIV knowledge (p = .001) and was positively correlated with having never been tested before this pregnancy (p = .007). The relationship between optimism/pessimism and HIV knowledge and screening behavior is worthy of further study using larger samples and objective measures of testing beyond self-report.

Clinical outcomes and a high prevalence of abnormalities on comprehensive arterial and venous thrombophilia screening in TIA or ischaemic stroke patients with a patent foramen ovale, an inter-atrial septal aneurysm or both.

PubMed

Lim, Soon Tjin; Murphy, Stephen J X; Smith, Deirdre R; Williams, Jennifer; Navarro, Silvia Gil; McCabe, John; Moore, David P; McHugh, Johnny; McCabe, Dominick J H

2017-06-15

Data are limited on the optimal management of cryptogenic TIA/stroke patients with a patent foramen ovale (PFO)±inter-atrial septal aneurysm (IASA), especially with an inherited thrombophilia. Prospectively-collected data on TIA/ischaemic stroke patients with PFO, IASA or both who received 'goal-directed secondary-prevention medical treatment' were analysed. All patients had trans-oesophageal echocardiography, anti-nuclear, anti-cardiolipin, anti-beta 2 glycoprotein I antibodies, rheumatoid factor, lupus anticoagulant, protein C&S, anti-thrombin, factor VIII activity, activated protein C resistance, Factor V Leiden, prothrombin gene and MTHFR-c.677C>T mutation screening. ENA and homocysteine were assessed in the latter study period. Eighty-three patients were recruited. Mean follow-up: 48.1months. Forty-seven patients (56.6%) had an isolated PFO, 32 (38.6%) a PFO and an IASA, and 4 (4.8%) an IASA alone. Eighteen (21.7%) had ≥1 abnormality on thrombophilia screening. The most important abnormalities which lead to treatment changes in 11 patients (13.3%) were primary anti-phospholipid syndrome (N=3; 3.6%), protein S deficiency (N=2; 2.4%) hyper-homocysteinaemia (N=6/72 screened, 8.3%). Four patients (4.8%) opted for PFO closure: two with protein S deficiency, and two with no identified thrombophilia. Seven (8.4%) had recurrent TIA/ischaemic stroke during follow-up (overall annualised incidence: 2.1%), of whom five had a PFO alone and two a PFO and IASA. Comprehensive arterial and venous thrombophilia screening is warranted in TIA/ischaemic stroke patients with a PFO±IASA, is conclusively abnormal in over a fifth, and informed important decision-making regarding individualised therapy in 13.3% of patients. The incidence of recurrent vascular events in this population is low on optimal, personalised secondary-prevention treatment, even with an underlying thrombophilia. Copyright © 2017 Elsevier B.V. All rights reserved.

Biomaterial based cardiac tissue engineering and its applications

PubMed Central

Huyer, Locke Davenport; Montgomery, Miles; Zhao, Yimu; Xiao, Yun; Conant, Genevieve; Korolj, Anastasia; Radisic, Milica

2015-01-01

Cardiovascular disease is a leading cause of death worldwide, necessitating the development of effective treatment strategies. A myocardial infarction involves the blockage of a coronary artery leading to depletion of nutrient and oxygen supply to cardiomyocytes and massive cell death in a region of the myocardium. Cardiac tissue engineering is the growth of functional cardiac tissue in vitro on biomaterial scaffolds for regenerative medicine application. This strategy relies on the optimization of the complex relationship between cell networks and biomaterial properties. In this review, we discuss important biomaterial properties for cardiac tissue engineering applications, such as elasticity, degradation, and induced host response, and their relationship to engineered cardiac cell environments. With these properties in mind, we also emphasize in vitro use of cardiac tissues for high-throughput drug screening and disease modelling. PMID:25989939

Optimization on Fc for Improvement of Stability and Aggregation Resistance.

PubMed

Chen, Xiaobo; Zeng, Fang; Huang, Tao; Cheng, Liang; Liu, Huan; Gong, Rui

2016-01-01

Fc-based therapeutics including therapeutic full-size monoclonal antibodies (mAbs) and Fcfusion proteins represent fastest-growing market in biopharmaceutical industrial. However, one major challenge during development of Fc-based therapeutics is how to maintain their efficacy in clinic use. Many factors may lead to failure in final marketing. For example, the stability and aggregation resistance might not be high enough for bearing the disadvantages during fermentation, purification, formulation, storage, shipment and other steps in manufacture and sale. Low stability and high aggregation tendency lead to decreased bioactivity and increased risk of immunogenicity resulting in serious side effect. Because Fc is one of the major parts in monoclonal antibodies and Fc-fusion proteins, engineering of Fc to increase its stability and reduce or eliminate aggregation due to incorrect association are of great importance and could further extend the potential of Fc-based therapeutics. Lots of studies focus on Fc optimization for better physical and chemical characteristics and function by structured-based computer-aid rational design, high-throughput screening expression system selection and other methods. The identification of optimized Fc mutants increases the clinic potential of currently existed therapeutics mAbs and Fc-fusion proteins, and accelerates the development of new Fc-based therapeutics. Here we provide an overview of the related field, and discuss recent advances and future directions in optimization of Fc-based therapeutics with modified stability and aggregation resistance. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The demographic, system, and psychosocial origins of mammographic screening disparities: prediction of initiation versus maintenance screening among immigrant and non-immigrant women.

PubMed

Consedine, Nathan S

2012-08-01

Disparities in breast screening are well documented. Less clear are differences within groups of immigrant and non-immigrant minority women or differences in adherence to mammography guidelines over time. A sample of 1,364 immigrant and non-immigrant women (African American, English Caribbean, Haitian, Dominican, Eastern European, and European American) were recruited using a stratified cluster-sampling plan. In addition to measuring established predictors of screening, women reported mammography frequency in the last 10 years and were (per ACS guidelines at the time) categorized as never, sub-optimal (<1 screen/year), or adherent (1+ screens/year) screeners. Multinomial logistic regression showed that while ethnicity infrequently predicted the never versus sub-optimal comparison, English Caribbean, Haitian, and Eastern European women were less likely to screen systematically over time. Demographics did not predict the never versus sub-optimal distinction; only regular physician, annual exam, physician recommendation, and cancer worry showed effects. However, the adherent categorization was predicted by demographics, was less likely among women without insurance, a regular physician, or an annual exam, and more likely among women reporting certain patterns of emotion (low embarrassment and greater worry). Because regular screening is crucial to breast health, there is a clear need to consider patterns of screening among immigrant and non-immigrant women as well as whether the variables predicting the initiation of screening are distinct from those predicting systematic screening over time.

[Maternal and neonatal vitamin B12 deficiency detected by expanded newborn screening].

PubMed

Papp, Ferenc; Rácz, Gábor; Lénárt, István; Kóbor, Jenő; Bereczki, Csaba; Karg, Eszter; Baráth, Ákos

2017-12-01

Infant vitamin B 12 deficiency can manifest as a severe neurodegenerative disorder and is usually caused by maternal deficiency due to vegetarian diet or pernicious anaemia. Its early recognition and treatment can prevent potentially serious and irreversible neurologic damage. Biochemically, vitamin B 12 deficiency leads to an accumulation of methylmalonic acid, homocysteine, and propionylcarnitine. Expanded newborn screening using tandem mass spectrometry may identify neonatal and maternal vitamin B 12 deficiency by measurement of propionylcarnitine and other metabolites in the dried blood spot sample of newborns. To summarize our experiences gained by screening for vitamin B 12 deficiency. Clinical and laboratory data of vitamin B 12 -deficient infants diagnosed in Szeged Screening Centre were retrospectively analysed. In Hungary, expanded newborn screening was introduced in 2007. Since then approximately 395 000 newborns were screened in our centre and among them, we identified four newborns with vitamin B 12 deficiency based on their screening results. In three cases an elevated propionylcarnitine level and in the fourth one a low methionine level were indicative of vitamin B 12 deficiency. We also detected an additional vitamin B 12 -deficient infant with neurological symptoms at 4 months of age, after a normal newborn screening, because of elevated urinary methylmalonic acid concentration. Vitamin B 12 deficiency was secondary to maternal autoimmune pernicious anaemia in all the five infants. As a result of the recognized cases the incidence of infant vitamin B 12 deficiency in the East-Hungarian region was 1.26/100 000 births, but the real frequency may be higher. Conslusions: Optimizing the cut off values of current screening parameters and measuring of methylmalonic acid and/or homocysteine in the dried blood spot, as a second tier test, can improve recognition rate of vitamin B 12 deficiency. Orv Hetil. 2017; 158(48): 1909-1918.

Development and Implementation of a High Throughput Screen for the Human Sperm-Specific Isoform of Glyceraldehyde 3-Phosphate Dehydrogenase (GAPDHS)

PubMed Central

Sexton, Jonathan Z; Danshina, Polina V; Lamson, David R; Hughes, Mark; House, Alan J; Yeh, Li-An; O’Brien, Deborah A; Williams, Kevin P

2011-01-01

Glycolytic isozymes that are restricted to the male germline are potential targets for the development of reversible, non-hormonal male contraceptives. GAPDHS, the sperm-specific isoform of glyceraldehyde-3-phosphate dehydrogenase, is an essential enzyme for glycolysis making it an attractive target for rational drug design. Toward this goal, we have optimized and validated a high-throughput spectrophotometric assay for GAPDHS in 384-well format. The assay was stable over time and tolerant to DMSO. Whole plate validation experiments yielded Z’ values >0.8 indicating a robust assay for HTS. Two compounds were identified and confirmed from a test screen of the Prestwick collection. This assay was used to screen a diverse chemical library and identified fourteen small molecules that modulated the activity of recombinant purified GAPDHS with confirmed IC50 values ranging from 1.8 to 42 µM. These compounds may provide useful scaffolds as molecular tools to probe the role of GAPDHS in sperm motility and long term to develop potent and selective GAPDHS inhibitors leading to novel contraceptive agents. PMID:21760877

Recent Advances in Screening of Anti-Campylobacter Activity in Probiotics for Use in Poultry

PubMed Central

Saint-Cyr, Manuel J.; Guyard-Nicodème, Muriel; Messaoudi, Soumaya; Chemaly, Marianne; Cappelier, Jean-Michel; Dousset, Xavier; Haddad, Nabila

2016-01-01

Campylobacteriosis is the most common cause of bacterial gastroenteritis worldwide. Campylobacter species involved in this infection usually include the thermotolerant species Campylobacter jejuni. The major reservoir for C. jejuni leading to human infections is commercial broiler chickens. Poultry flocks are frequently colonized by C. jejuni without any apparent symptoms. Risk assessment analyses have identified the handling and consumption of poultry meat as one of the most important sources of human campylobacteriosis, so elimination of Campylobacter in the poultry reservoir is a crucial step in the control of this foodborne infection. To date, the use of probiotics has demonstrated promising results to reduce Campylobacter colonization. This review provides recent insights into methods used for probiotic screening to reduce the prevalence and colonization of Campylobacter at the farm level. Different eukaryotic epithelial cell lines are employed to screen probiotics with an anti-Campylobacter activity and yield useful information about the inhibition mechanism involved. These in vitro virulence models involve only human intestinal or cervical cell lines whereas the use of avian cell lines could be a preliminary step to investigate mechanisms of C. jejuni colonization in poultry in the presence of probiotics. In addition, in vivo trials to evaluate the effect of probiotics on Campylobacter colonization are conducted, taking into account the complexity introduced by the host, the feed, and the microbiota. However, the heterogeneity of the protocols used and the short time duration of the experiments lead to results that are difficult to compare and draw conclusions at the slaughter-age of broilers. Nevertheless, the combined approach using complementary in vitro and in vivo tools (cell cultures and animal experiments) leads to a better characterization of probiotic strains and could be employed to assess reduced Campylobacter spp. colonization in chickens if some parameters are optimized. PMID:27303366

Virtual High-Throughput Screening To Identify Novel Activin Antagonists

PubMed Central

Zhu, Jie; Mishra, Rama K.; Schiltz, Gary E.; Makanji, Yogeshwar; Scheidt, Karl A.; Mazar, Andrew P.; Woodruff, Teresa K.

2015-01-01

Activin belongs to the TGFβ superfamily, which is associated with several disease conditions, including cancer-related cachexia, preterm labor with delivery, and osteoporosis. Targeting activin and its related signaling pathways holds promise as a therapeutic approach to these diseases. A small-molecule ligand-binding groove was identified in the interface between the two activin βA subunits and was used for a virtual high-throughput in silico screening of the ZINC database to identify hits. Thirty-nine compounds without significant toxicity were tested in two well-established activin assays: FSHβ transcription and HepG2 cell apoptosis. This screening workflow resulted in two lead compounds: NUCC-474 and NUCC-555. These potential activin antagonists were then shown to inhibit activin A-mediated cell proliferation in ex vivo ovary cultures. In vivo testing showed that our most potent compound (NUCC-555) caused a dose-dependent decrease in FSH levels in ovariectomized mice. The Blitz competition binding assay confirmed target binding of NUCC-555 to the activin A:ActRII that disrupts the activin A:ActRII complex’s binding with ALK4-ECD-Fc in a dose-dependent manner. The NUCC-555 also specifically binds to activin A compared with other TGFβ superfamily member myostatin (GDF8). These data demonstrate a new in silico-based strategy for identifying small-molecule activin antagonists. Our approach is the first to identify a first-in-class small-molecule antagonist of activin binding to ALK4, which opens a completely new approach to inhibiting the activity of TGFβ receptor superfamily members. in addition, the lead compound can serve as a starting point for lead optimization toward the goal of a compound that may be effective in activin-mediated diseases. PMID:26098096

[Thoughts on optimizing the breast cancer screening strategies and implementation effects].

PubMed

Wu, K J

2018-02-01

Reasonable and effective breast cancer screening can make early diagnosis of breast cancer, improve the cure rate, prolong survival and improve the patients' quality of life. China has made preliminary exploration and attempt in breast cancer screening, however, there are still some problems that have not been solved in terms of the proportion of opportunistic screening, the selection of screening targets, methods and frequency, and the judgment of screening results. Therefore, this article analyzes the above problems in details, and presents some thoughts and recommendations on how to optimize the breast cancer screening strategies and implementation effects in China, from the experience of clinical practice, under the background of constantly emerging new research results and techniques and the rapid development of artificial intelligence, that is, to adjust measures to local conditions, provide personalized strategies, achieve precise screening, preach and educate, ensure health insurance coverage, improve quality control, offer technical support and employ artificial intelligence.

[Evaluating the effectiveness of child lead poisoning prevention programs].

PubMed

Ginot, L; Fontaine, A; Cheymol, J; Peyr, C

2003-09-01

A multi annual screening and prevention program against lead poisoning was implemented in a suburb of the Paris area. We attempted to assess the effectiveness of this program based on data available from children screening and follow-up. Indicators of effectiveness included the evolution of blood lead levels at screening and the frequency of secondary increases in blood lead levels. Buildings inclusion dates were used to control for the increasing selection of less exposed children. A total of 3,660 children were screened between 1992 and 2000. We observed a regular decrease in blood lead levels at screening, in the highest blood lead levels obtained for each child and in the proportion of children whose blood lead levels increased after screening: the proportion of children with initial blood lead levels >=15 micro g/dl fell from 17.4% in the 1992-1996 period to 4.1% in the 1997-2000 period. A multivariate analysis taking into account the first year that children were screened in a given building showed that less exposed children were included over time, but found also an additional independent decrease in blood lead levels that can be related to the effectiveness of prevention efforts. A "building by building" analysis of 30 buildings where more than 20 children were located over the whole study period confirmed that the incidence of lead poisoning decreased within most of these buildings. Taking into account buildings'inclusion dates makes it possible to distinguish program effectiveness from the consequences of including less exposed children The effectiveness of preventive actions is associated with several interacting factors, including the participation of families and the active involvement of local technical staff and policy makers. The finding that the decrease in blood lead levels leveled off after 1997 calls for further actions.

A biosensor generated via high throughput screening quantifies cell edge Src dynamics

PubMed Central

Gulyani, Akash; Vitriol, Eric; Allen, Richard; Wu, Jianrong; Gremyachinskiy, Dmitriy; Lewis, Steven; Dewar, Brian; Graves, Lee M.; Kay, Brian K.; Kuhlman, Brian; Elston, Tim; Hahn, Klaus M.

2011-01-01

Fluorescent biosensors for living cells currently require laborious optimization and a unique design for each target. They are limited by the availability of naturally occurring ligands with appropriate target specificity. Here we describe a biosensor based on an engineered fibronectin monobody scaffold that can be tailored to bind different targets via high throughput screening. This Src family kinase (SFK) biosensor was made by derivatizing a monobody specific for activated SFK with a bright dye whose fluorescence increases upon target binding. We identified sites for dye attachment and alterations to eliminate vesiculation in living cells, providing a generalizable scaffold for biosensor production. This approach minimizes cell perturbation because it senses endogenous, unmodified target, and because sensitivity is enhanced by direct dye excitation. Automated correlation of cell velocities and SFK activity revealed that SFK are activated specifically during protrusion. Activity correlates with velocity, and peaks 1–2 microns from the leading edge. PMID:21666688

Quantification of a bacterial secondary metabolite by SERS combined with SLM extraction for bioprocess monitoring.

PubMed

Morelli, Lidia; Andreasen, Sune Zoëga; Jendresen, Christian Bille; Nielsen, Alex Toftgaard; Emnéus, Jenny; Zór, Kinga; Boisen, Anja

2017-11-20

During the last few decades, great advances have been reached in high-throughput design and building of genetically engineered microbial strains, leading to a need for fast and reliable screening methods. We developed and optimized a microfluidic supported liquid membrane (SLM) extraction device and combined it with surface enhanced Raman scattering (SERS) sensing for the screening of a biological process, namely for the quantification of a bacterial secondary metabolite, p-coumaric acid (pHCA), produced by Escherichia coli. The microfluidic device proved to be robust and reusable, enabling efficient removal of interfering compounds from the real samples, reaching more than 13-fold up-concentration of the donor at 10 μL min -1 flow rate. With this method, we quantified pHCA directly from the bacterial supernatant, distinguishing between various culture conditions based on the pHCA production yield. The obtained data showed good correlation with HPLC analysis.

Research on atmospheric transmission distortion of Gauss laser using multiple phase screen method

NASA Astrophysics Data System (ADS)

Zhang, Yizhuo; Wang, Qiushi; Gu, Haidong

2018-02-01

The laser beam is attenuated, broadened, defocused and may even be deflected from its initial propagation direction as it propagates through the atmosphere. It leads to the decrease of the laser intensity of the receiving surface. Gauss beam is the fundamental components of all possible laser waveforms. Therefore, research on the transmission of the Gauss laser has far-reaching consequences in optical communication, weaponry, target designation, ranging, remote sensing and other applications that require transmission of laser beams through the atmosphere. In this paper, we propose a laboratory simulation method using multi-phase screen to calculate the effects of atmospheric turbulence. Theoretical analysis of Gauss laser transmission in the atmosphere is given. By calculating the propagation of the Gauss beam TEM00, the far field intensity and phase distribution is shown. By the given method, the optical setup is presented and used for optimizing the adaptive optics algorithm.

Optimum concentration gradient of the electrocatalyst, Nafion® and poly(tetrafluoroethylene) in a membrane-electrode-assembly for enhanced performance of direct methanol fuel cells.

PubMed

Liu, Jing Hua; Jeon, Min Ku; Lee, Ki Rak; Woo, Seong Ihl

2010-12-14

A combinatorial library of membrane-electrode-assemblies (MEAs) which consisted of 27 different compositions was fabricated to optimize the multilayer structure of direct methanol fuel cells. Each spot consisted of three layers of ink and a gradient was generated by employing different concentrations of the three components (Pt catalyst, Nafion® and polytetrafluoroethylene (PTFE)) of each layer. For quick evaluation of the library, a high-throughput optical screening technique was employed for methanol electro-oxidation reaction (MOR) activity. The screening results revealed that gradient layers could lead to higher MOR activity than uniform layers. It was found that the MOR activity was higher when the concentrations of Pt catalyst and Nafion ionomer decreased downward from the top layer to the bottom layer. On the other hand, higher MOR activity was observed when PTFE concentration increased downward from the top to the bottom layer.

A method for direct assessment of tissue-nonspecific alkaline phosphatase (TNAP) inhibitors in blood samples.

PubMed

Sergienko, Eduard A; Sun, Qing; Ma, Chen-Ting

2013-01-01

Tissue nonspecific alkaline phosphatase (TNAP) is one of four human alkaline phosphatases (AP), a family of exocytic enzymes that catalyze hydrolysis of phospho-monoesters in bone, liver, kidney, and various other tissues. Overexpression of TNAP gives rise to excessive bone and soft tissue mineralization, including blood vessel calcification. Our prior screening campaigns have found several leads against this attractive therapeutic target using in vitro assay with a recombinant enzyme; these compounds were further optimized using medicinal chemistry approaches. To prioritize compounds for their use in animal models, we have designed and developed a biomarker assay for in situ detection of TNAP activity within human and mouse blood samples at physiological pH. This assay is suitable for screening compounds in 1,536-well plates using blood plasma from different mammalian species. The user may choose from two different substrates based on the need for greater assay simplicity or sensitivity.

A kinase-focused compound collection: compilation and screening strategy.

PubMed

Sun, Dongyu; Chuaqui, Claudio; Deng, Zhan; Bowes, Scott; Chin, Donovan; Singh, Juswinder; Cullen, Patrick; Hankins, Gretchen; Lee, Wen-Cherng; Donnelly, Jason; Friedman, Jessica; Josiah, Serene

2006-06-01

Lead identification by high-throughput screening of large compound libraries has been supplemented with virtual screening and focused compound libraries. To complement existing approaches for lead identification at Biogen Idec, a kinase-focused compound collection was designed, developed and validated. Two strategies were adopted to populate the compound collection: a ligand shape-based virtual screening and a receptor-based approach (structural interaction fingerprint). Compounds selected with the two approaches were cherry-picked from an existing high-throughput screening compound library, ordered from suppliers and supplemented with specific medicinal compounds from internal programs. Promising hits and leads have been generated from the kinase-focused compound collection against multiple kinase targets. The principle of the collection design and screening strategy was validated and the use of the kinase-focused compound collection for lead identification has been added to existing strategies.

Lead selection and characterization of antitubercular compounds using the Nested Chemical Library.

PubMed

Sipos, Anna; Pató, János; Székely, Rita; Hartkoorn, Ruben C; Kékesi, László; Őrfi, László; Szántai-Kis, Csaba; Mikušová, Katarína; Svetlíková, Zuzana; Korduláková, Jana; Nagaraja, Valakunja; Godbole, Adwait Anand; Bush, Natassja; Collin, Frédéric; Maxwell, Anthony; Cole, Stewart T; Kéri, György

2015-06-01

Discovering new drugs to treat tuberculosis more efficiently and to overcome multidrug resistance is a world health priority. To find novel antitubercular agents several approaches have been used in various institutions worldwide, including target-based approaches against several validated mycobacterial enzymes and phenotypic screens. We screened more than 17,000 compounds from Vichem's Nested Chemical Library™ using an integrated strategy involving whole cell-based assays with Corynebacterium glutamicum and Mycobacterium tuberculosis, and target-based assays with protein kinases PknA, PknB and PknG as well as other targets such as PimA and bacterial topoisomerases simultaneously. With the help of the target-based approach we have found very potent hits inhibiting the selected target enzymes, but good minimal inhibitory concentrations (MIC) against M. tuberculosis were not achieved. Focussing on the whole cell-based approach several potent hits were found which displayed minimal inhibitory concentrations (MIC) against M. tuberculosis below 10 μM and were non-mutagenic, non-cytotoxic and the targets of some of the hits were also identified. The most active hits represented various scaffolds. Medicinal chemistry-based lead optimization was performed applying various strategies and, as a consequence, a series of novel potent compounds were synthesized. These efforts resulted in some effective potential antitubercular lead compounds which were confirmed in phenotypic assays. Copyright © 2015 Elsevier Ltd. All rights reserved.

Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets.

PubMed

Feinstein, Wei P; Brylinski, Michal

2015-01-01

Computational approaches have emerged as an instrumental methodology in modern research. For example, virtual screening by molecular docking is routinely used in computer-aided drug discovery. One of the critical parameters for ligand docking is the size of a search space used to identify low-energy binding poses of drug candidates. Currently available docking packages often come with a default protocol for calculating the box size, however, many of these procedures have not been systematically evaluated. In this study, we investigate how the docking accuracy of AutoDock Vina is affected by the selection of a search space. We propose a new procedure for calculating the optimal docking box size that maximizes the accuracy of binding pose prediction against a non-redundant and representative dataset of 3,659 protein-ligand complexes selected from the Protein Data Bank. Subsequently, we use the Directory of Useful Decoys, Enhanced to demonstrate that the optimized docking box size also yields an improved ranking in virtual screening. Binding pockets in both datasets are derived from the experimental complex structures and, additionally, predicted by eFindSite. A systematic analysis of ligand binding poses generated by AutoDock Vina shows that the highest accuracy is achieved when the dimensions of the search space are 2.9 times larger than the radius of gyration of a docking compound. Subsequent virtual screening benchmarks demonstrate that this optimized docking box size also improves compound ranking. For instance, using predicted ligand binding sites, the average enrichment factor calculated for the top 1 % (10 %) of the screening library is 8.20 (3.28) for the optimized protocol, compared to 7.67 (3.19) for the default procedure. Depending on the evaluation metric, the optimal docking box size gives better ranking in virtual screening for about two-thirds of target proteins. This fully automated procedure can be used to optimize docking protocols in order to improve the ranking accuracy in production virtual screening simulations. Importantly, the optimized search space systematically yields better results than the default method not only for experimental pockets, but also for those predicted from protein structures. A script for calculating the optimal docking box size is freely available at www.brylinski.org/content/docking-box-size. Graphical AbstractWe developed a procedure to optimize the box size in molecular docking calculations. Left panel shows the predicted binding pose of NADP (green sticks) compared to the experimental complex structure of human aldose reductase (blue sticks) using a default protocol. Right panel shows the docking accuracy using an optimized box size.

Community-based prevention of hepatitis-B-related liver cancer: Australian insights

PubMed Central

Kansil, Melanie Q; Porwal, Mamta; Penman, Andrew G; George, Jacob

2014-01-01

Abstract Problem Although most primary hepatocellular cancers (HCCs) are attributable to chronic viral hepatitis and largely preventable, such cancers remain a leading cause of cancer-related mortality wherever chronic hepatitis B is endemic. Approach Many HCCs could be prevented by increasing awareness and knowledge of hepatitis B, optimizing the monitoring of chronic hepatitis B and using antiviral treatments – but there are gaps in the implementation of such strategies. Local setting The “B Positive” programme, based in Sydney, Australia, is designed to improve hepatitis-B-related health outcomes among immigrants from countries with endemic hepatitis B. The programme offers information about disease screening, vaccination and treatment options, as well as optimized access to care. Relevant changes The B Positive programme has been informed by economic modelling. The programme offers culturally tailored education on chronic hepatitis B to target communities and their health practitioners and regular follow-up through a population-based registry of cases. Lessons learnt As the costs of screening for chronic hepatitis B and follow-up are relatively low and less than one in every four cases may require antiviral drugs, optimizing access to treatment seems an appropriate and cost-effective management option. The identification and accurate staging of cases and the judicious use of antiviral medications are predicated upon an informed and educated health workforce. As establishing community trust is a lengthy process, delaying the implementation of programmes against chronic hepatitis B until antiviral drugs become cheaper is unwarranted. PMID:24839327

Identification of two integration sites in favor of transgene expression in Trichoderma reesei.

PubMed

Qin, Lina; Jiang, Xianzhang; Dong, Zhiyang; Huang, Jianzhong; Chen, Xiuzhen

2018-01-01

The ascomycete fungus Trichoderma reesei was widely used as a biotechnological workhorse for production of cellulases and recombinant proteins due to its large capacity of protein secretion. Transgenesis by random integration of a gene of interest (GOI) into the genome of T. reesei can generate series of strains that express different levels of the indicated transgene. The insertion site of the GOI plays an important role in the ultimate production of the targeted proteins. However, so far no systematic studies have been made to identify transgene integration loci for optimal expression of the GOI in T. reesei . Currently, only the locus of exocellobiohydrolases I encoding gene ( cbh1) is widely used as a promising integration site to lead to high expression level of the GOI. No additional sites associated with efficient gene expression have been characterized. To search for gene integration sites that benefit for the secreted expression of GOI, the food-and-mouth disease virus 2A protein was applied for co-expression of an Aspergillus niger lipA gene and Discosoma sp. DsRed1 gene in T. reesei, by random integration of the expression cassette into the genome. We demonstrated that the fluorescent intensity of RFP (red fluorescent protein) inside of the cell was well correlated with the secreted lipase yields, based on which, we successfully developed a high-throughput screening method to screen strains with relatively higher secreted expression of the GOI (in this study, lipase). The copy number and the insertion sites of the transgene were investigated among the selected highly expressed strains. Eventually, in addition to cbh1 gene locus, two other genome insertion loci that efficiently facilitate gene expression in T. reesei were identified. We have successfully developed a high-throughput screening method to screen strains with optimal expression of the indicated secreted proteins in T. reesei . Moreover, we identified two optimal genome loci for transgene expression, which could provide new approach to modulate gene expression levels while retaining the indicated promoter and culture conditions.

Bayesian lead time estimation for the Johns Hopkins Lung Project data.

PubMed

Jang, Hyejeong; Kim, Seongho; Wu, Dongfeng

2013-09-01

Lung cancer screening using X-rays has been controversial for many years. A major concern is whether lung cancer screening really brings any survival benefits, which depends on effective treatment after early detection. The problem was analyzed from a different point of view and estimates were presented of the projected lead time for participants in a lung cancer screening program using the Johns Hopkins Lung Project (JHLP) data. The newly developed method of lead time estimation was applied where the lifetime T was treated as a random variable rather than a fixed value, resulting in the number of future screenings for a given individual is a random variable. Using the actuarial life table available from the United States Social Security Administration, the lifetime distribution was first obtained, then the lead time distribution was projected using the JHLP data. The data analysis with the JHLP data shows that, for a male heavy smoker with initial screening ages at 50, 60, and 70, the probability of no-early-detection with semiannual screens will be 32.16%, 32.45%, and 33.17%, respectively; while the mean lead time is 1.36, 1.33 and 1.23 years. The probability of no-early-detection increases monotonically when the screening interval increases, and it increases slightly as the initial age increases for the same screening interval. The mean lead time and its standard error decrease when the screening interval increases for all age groups, and both decrease when initial age increases with the same screening interval. The overall mean lead time estimated with a random lifetime T is slightly less than that with a fixed value of T. This result is hoped to be of benefit to improve current screening programs. Copyright © 2013 Ministry of Health, Saudi Arabia. Published by Elsevier Ltd. All rights reserved.

Comparison of Adsorbed Mercury Screening Method With Cold-Vapor Atomic Absorption Spectrophotometry for Determination of Mercury in Soil

NASA Technical Reports Server (NTRS)

Easterling, Donald F.; Hovanitz, Edward S.; Street, Kenneth W.

2000-01-01

A field screening method for the determination of elemental mercury in environmental soil samples involves the thermal desorption of the mercury from the sample onto gold and then the thermal desorption from the gold to a gold-film mercury vapor analyzer. This field screening method contains a large number of conditions that could be optimized for the various types of soils encountered. In this study, the conditions were optimized for the determination of mercury in silty clay materials, and the results were comparable to the cold-vapor atomic absorption spectrophotometric method of determination. This paper discusses the benefits and disadvantages of employing the field screening method and provides the sequence of conditions that must be optimized to employ this method of determination on other soil types.

Simulation optimization of PSA-threshold based prostate cancer screening policies

PubMed Central

Zhang, Jingyu; Denton, Brian T.; Shah, Nilay D.; Inman, Brant A.

2013-01-01

We describe a simulation optimization method to design PSA screening policies based on expected quality adjusted life years (QALYs). Our method integrates a simulation model in a genetic algorithm which uses a probabilistic method for selection of the best policy. We present computational results about the efficiency of our algorithm. The best policy generated by our algorithm is compared to previously recommended screening policies. Using the policies determined by our model, we present evidence that patients should be screened more aggressively but for a shorter length of time than previously published guidelines recommend. PMID:22302420

Screening for Colorectal Cancer: US Preventive Services Task Force Recommendation Statement.

PubMed

Bibbins-Domingo, Kirsten; Grossman, David C; Curry, Susan J; Davidson, Karina W; Epling, John W; García, Francisco A R; Gillman, Matthew W; Harper, Diane M; Kemper, Alex R; Krist, Alex H; Kurth, Ann E; Landefeld, C Seth; Mangione, Carol M; Owens, Douglas K; Phillips, William R; Phipps, Maureen G; Pignone, Michael P; Siu, Albert L

2016-06-21

Colorectal cancer is the second leading cause of cancer death in the United States. In 2016, an estimated 134,000 persons will be diagnosed with the disease, and about 49,000 will die from it. Colorectal cancer is most frequently diagnosed among adults aged 65 to 74 years; the median age at death from colorectal cancer is 68 years. To update the 2008 US Preventive Services Task Force (USPSTF) recommendation on screening for colorectal cancer. The USPSTF reviewed the evidence on the effectiveness of screening with colonoscopy, flexible sigmoidoscopy, computed tomography colonography, the guaiac-based fecal occult blood test, the fecal immunochemical test, the multitargeted stool DNA test, and the methylated SEPT9 DNA test in reducing the incidence of and mortality from colorectal cancer or all-cause mortality; the harms of these screening tests; and the test performance characteristics of these tests for detecting adenomatous polyps, advanced adenomas based on size, or both, as well as colorectal cancer. The USPSTF also commissioned a comparative modeling study to provide information on optimal starting and stopping ages and screening intervals across the different available screening methods. The USPSTF concludes with high certainty that screening for colorectal cancer in average-risk, asymptomatic adults aged 50 to 75 years is of substantial net benefit. Multiple screening strategies are available to choose from, with different levels of evidence to support their effectiveness, as well as unique advantages and limitations, although there are no empirical data to demonstrate that any of the reviewed strategies provide a greater net benefit. Screening for colorectal cancer is a substantially underused preventive health strategy in the United States. The USPSTF recommends screening for colorectal cancer starting at age 50 years and continuing until age 75 years (A recommendation). The decision to screen for colorectal cancer in adults aged 76 to 85 years should be an individual one, taking into account the patient's overall health and prior screening history (C recommendation).

Systematic review of colorectal cancer screening guidelines for average-risk adults: Summarizing the current global recommendations.

PubMed

Bénard, Florence; Barkun, Alan N; Martel, Myriam; von Renteln, Daniel

2018-01-07

To summarize and compare worldwide colorectal cancer (CRC) screening recommendations in order to identify similarities and disparities. A systematic literature search was performed using MEDLINE, EMBASE, Scopus, CENTRAL and ISI Web of knowledge identifying all average-risk CRC screening guideline publications within the last ten years and/or position statements published in the last 2 years. In addition, a hand-search of the webpages of National Gastroenterology Society websites, the National Guideline Clearinghouse, the BMJ Clinical Evidence website, Google and Google Scholar was performed. Fifteen guidelines were identified. Six guidelines were published in North America, four in Europe, four in Asia and one from the World Gastroenterology Organization. The majority of guidelines recommend screening average-risk individuals between ages 50 and 75 using colonoscopy (every 10 years), or flexible sigmoidoscopy (FS, every 5 years) or fecal occult blood test (FOBT, mainly the Fecal Immunochemical Test, annually or biennially). Disparities throughout the different guidelines are found relating to the use of colonoscopy, rank order between test, screening intervals and optimal age ranges for screening. Average risk individuals between 50 and 75 years should undergo CRC screening. Recommendations for optimal surveillance intervals, preferred tests/test cascade as well as the optimal timing when to start and stop screening differ regionally and should be considered for clinical decision making. Furthermore, local resource availability and patient preferences are important to increase CRC screening uptake, as any screening is better than none.

Development of CXCR4 modulators by virtual HTS of a novel amide-sulfamide compound library.

PubMed

Bai, Renren; Shi, Qi; Liang, Zhongxing; Yoon, Younghyoun; Han, Yiran; Feng, Amber; Liu, Shuangping; Oum, Yoonhyeun; Yun, C Chris; Shim, Hyunsuk

2017-01-27

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. Based on the designed parent framework, 30 prioritized amide-sulfamide structures were obtained after systemic filtering and docking screening. Twelve compounds were prepared from the top-30 list. Most synthesized compounds exhibited good to excellent binding affinity to CXCR4. Compounds Ig and Im demonstrated notable in vivo suppressive activity against xylene-induced mouse ear inflammation (with 56% and 54% inhibition). Western blot analyses revealed that Ig significantly blocked CXCR4/CXCL12-mediated phosphorylation of Akt. Moreover, Ig attenuated the amount of TNF-α secreted by pathogenic E. coli-infected macrophages. More importantly, Ig had no observable cytotoxicity. Our results demonstrated that FRESH virtual high throughput screening program of targeted chemical class could successfully find potent lead compounds, and the amide-sulfamide pharmacophore was a novel and effective framework blocking CXCR4 function. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

A high throughput screen identifies benzoquinoline compounds as inhibitors of Ebola virus replication.

PubMed

Luthra, Priya; Liang, Jue; Pietzsch, Colette A; Khadka, Sudip; Edwards, Megan R; Wei, Shuguang; De, Sampriti; Posner, Bruce; Bukreyev, Alexander; Ready, Joseph M; Basler, Christopher F

2018-02-01

Ebola virus (EBOV) is an enveloped negative-sense, single-stranded RNA virus of the filovirus family that causes severe disease in humans. Approved therapies for EBOV disease are lacking. EBOV RNA synthesis is carried out by a virus-encoded complex with RNA-dependent RNA polymerase activity that is required for viral propagation. This complex and its activities are therefore potential antiviral targets. To identify potential lead inhibitors of EBOV RNA synthesis, a library of small molecule compounds was screened against a previously established assay of EBOV RNA synthesis, the EBOV minigenome assay (MGA), in 384 well microplate format. The screen identified 56 hits that inhibited EBOV MGA activity by more than 70% while exhibiting less than 20% cell cytotoxicity. Inhibitory chemical scaffolds included angelicin derivatives, derivatives of the antiviral compound GSK983 and benzoquinolines. Structure-activity relationship (SAR) studies of the benzoquinoline scaffold produced ∼50 analogs and led to identification of an optimized compound, SW456, with a submicromolar IC 50 in the EBOV MGA and antiviral activity against infectious EBOV in cell culture. The compound was also active against a MGA for another deadly filovirus, Marburg virus. It also exhibited antiviral activity towards a negative-sense RNA virus from the rhabdovirus family, vesicular stomatitis virus, and a positive-sense RNA virus, Zika virus. Overall, these data demonstrate the potential of the EBOV MGA to identify anti-EBOV compounds and identifies the benzoquinoline series as a broad-spectrum antiviral lead. Copyright © 2017. Published by Elsevier B.V.

High-throughput density functional calculations to optimize properties and interfacial chemistry of piezoelectric materials

NASA Astrophysics Data System (ADS)

Barr, Jordan A.; Lin, Fang-Yin; Ashton, Michael; Hennig, Richard G.; Sinnott, Susan B.

2018-02-01

High-throughput density functional theory calculations are conducted to search through 1572 A B O3 compounds to find a potential replacement material for lead zirconate titanate (PZT) that exhibits the same excellent piezoelectric properties as PZT and lacks both its use of the toxic element lead (Pb) and the formation of secondary alloy phases with platinum (Pt) electrodes. The first screening criterion employed a search through the Materials Project database to find A -B combinations that do not form ternary compounds with Pt. The second screening criterion aimed to eliminate potential candidates through first-principles calculations of their electronic structure, in which compounds with a band gap of 0.25 eV or higher were retained. Third, thermodynamic stability calculations were used to compare the candidates in a Pt environment to compounds already calculated to be stable within the Materials Project. Formation energies below or equal to 100 meV/atom were considered to be thermodynamically stable. The fourth screening criterion employed lattice misfit to identify those candidate perovskites that have low misfit with the Pt electrode and high misfit of potential secondary phases that can be formed when Pt alloys with the different A and B components. To aid in the final analysis, dynamic stability calculations were used to determine those perovskites that have dynamic instabilities that favor the ferroelectric distortion. Analysis of the data finds three perovskites warranting further investigation: CsNb O3 , RbNb O3 , and CsTa O3 .

Microseed matrix screening for optimization in protein crystallization: what have we learned?

PubMed

D'Arcy, Allan; Bergfors, Terese; Cowan-Jacob, Sandra W; Marsh, May

2014-09-01

Protein crystals obtained in initial screens typically require optimization before they are of X-ray diffraction quality. Seeding is one such optimization method. In classical seeding experiments, the seed crystals are put into new, albeit similar, conditions. The past decade has seen the emergence of an alternative seeding strategy: microseed matrix screening (MMS). In this strategy, the seed crystals are transferred into conditions unrelated to the seed source. Examples of MMS applications from in-house projects and the literature include the generation of multiple crystal forms and different space groups, better diffracting crystals and crystallization of previously uncrystallizable targets. MMS can be implemented robotically, making it a viable option for drug-discovery programs. In conclusion, MMS is a simple, time- and cost-efficient optimization method that is applicable to many recalcitrant crystallization problems.

Microseed matrix screening for optimization in protein crystallization: what have we learned?

PubMed Central

D’Arcy, Allan; Bergfors, Terese; Cowan-Jacob, Sandra W.; Marsh, May

2014-01-01

Protein crystals obtained in initial screens typically require optimization before they are of X-ray diffraction quality. Seeding is one such optimization method. In classical seeding experiments, the seed crystals are put into new, albeit similar, conditions. The past decade has seen the emergence of an alternative seeding strategy: microseed matrix screening (MMS). In this strategy, the seed crystals are transferred into conditions unrelated to the seed source. Examples of MMS applications from in-house projects and the literature include the generation of multiple crystal forms and different space groups, better diffracting crystals and crystallization of previously uncrystallizable targets. MMS can be implemented robotically, making it a viable option for drug-discovery programs. In conclusion, MMS is a simple, time- and cost-efficient optimization method that is applicable to many recalcitrant crystallization problems. PMID:25195878

Subcutaneous ICD screening with the Boston Scientific ZOOM programmer versus a 12-lead ECG machine.

PubMed

Chang, Shu C; Patton, Kristen K; Robinson, Melissa R; Poole, Jeanne E; Prutkin, Jordan M

2018-02-24

The subcutaneous implantable cardioverter-defibrillator (S-ICD) requires preimplant screening to ensure appropriate sensing and reduce risk of inappropriate shocks. Screening can be performed using either an ICD programmer or a 12-lead electrocardiogram (ECG) machine. It is unclear whether differences in signal filtering and digital sampling change the screening success rate. Subjects were recruited if they had a transvenous single-lead ICD without pacing requirements or were candidates for a new ICD. Screening was performed using both a Boston Scientific ZOOM programmer (Marlborough, MA, USA) and General Electric MAC 5000 ECG machine (Fairfield, CT, USA). A pass was defined as having at least one lead that fit within the screening template in both supine and sitting positions. A total of 69 subjects were included and 27 sets of ECG leads had differing screening results between the two machines (7%). Of these sets, 22 (81%) passed using the ECG machine but failed using the programmer and five (19%) passed using the ECG machine but failed using the programmer (P < 0.001). Four subjects (6%) passed screening using the ECG machine but failed using the programmer. No subject passed screening with the programmer but failed with the ECG machine. There can be occasional disagreement in S-ICD patient screening between an ICD programmer and ECG machine, all of whom passed with the ECG machine but failed using the programmer. On a per lead basis, the ECG machine passes more subjects. It is unknown what the inappropriate shock rate would be if an S-ICD was implanted. Clinical judgment should be used in borderline cases. © 2018 Wiley Periodicals, Inc.

Applications of Biophysics in High-Throughput Screening Hit Validation.

PubMed

Genick, Christine Clougherty; Barlier, Danielle; Monna, Dominique; Brunner, Reto; Bé, Céline; Scheufler, Clemens; Ottl, Johannes

2014-06-01

For approximately a decade, biophysical methods have been used to validate positive hits selected from high-throughput screening (HTS) campaigns with the goal to verify binding interactions using label-free assays. By applying label-free readouts, screen artifacts created by compound interference and fluorescence are discovered, enabling further characterization of the hits for their target specificity and selectivity. The use of several biophysical methods to extract this type of high-content information is required to prevent the promotion of false positives to the next level of hit validation and to select the best candidates for further chemical optimization. The typical technologies applied in this arena include dynamic light scattering, turbidometry, resonance waveguide, surface plasmon resonance, differential scanning fluorimetry, mass spectrometry, and others. Each technology can provide different types of information to enable the characterization of the binding interaction. Thus, these technologies can be incorporated in a hit-validation strategy not only according to the profile of chemical matter that is desired by the medicinal chemists, but also in a manner that is in agreement with the target protein's amenability to the screening format. Here, we present the results of screening strategies using biophysics with the objective to evaluate the approaches, discuss the advantages and challenges, and summarize the benefits in reference to lead discovery. In summary, the biophysics screens presented here demonstrated various hit rates from a list of ~2000 preselected, IC50-validated hits from HTS (an IC50 is the inhibitor concentration at which 50% inhibition of activity is observed). There are several lessons learned from these biophysical screens, which will be discussed in this article. © 2014 Society for Laboratory Automation and Screening.

Application of a High Throughput Method of Biomarker Discovery to Improvement of the EarlyCDT®-Lung Test

PubMed Central

Macdonald, Isabel K.; Murray, Andrea; Healey, Graham F.; Parsy-Kowalska, Celine B.; Allen, Jared; McElveen, Jane; Robertson, Chris; Sewell, Herbert F.; Chapman, Caroline J.; Robertson, John F. R.

2012-01-01

Background The National Lung Screening Trial showed that CT screening for lung cancer led to a 20% reduction in mortality. However, CT screening has a number of disadvantages including low specificity. A validated autoantibody assay is available commercially (EarlyCDT®-Lung) to aid in the early detection of lung cancer and risk stratification in patients with pulmonary nodules detected by CT. Recent advances in high throughput (HTP) cloning and expression methods have been developed into a discovery pipeline to identify biomarkers that detect autoantibodies. The aim of this study was to demonstrate the successful clinical application of this strategy to add to the EarlyCDT-Lung panel in order to improve its sensitivity and specificity (and hence positive predictive value, (PPV)). Methods and Findings Serum from two matched independent cohorts of lung cancer patients were used (n = 100 and n = 165). Sixty nine proteins were initially screened on an abridged HTP version of the autoantibody ELISA using protein prepared on small scale by a HTP expression and purification screen. Promising leads were produced in shake flask culture and tested on the full assay. These results were analyzed in combination with those from the EarlyCDT-Lung panel in order to provide a set of re-optimized cut-offs. Five proteins that still displayed cancer/normal differentiation were tested for reproducibility and validation on a second batch of protein and a separate patient cohort. Addition of these proteins resulted in an improvement in the sensitivity and specificity of the test from 38% and 86% to 49% and 93% respectively (PPV improvement from 1 in 16 to 1 in 7). Conclusion This is a practical example of the value of investing resources to develop a HTP technology. Such technology may lead to improvement in the clinical utility of the EarlyCDT­-Lung test, and so further aid the early detection of lung cancer. PMID:23272083

Knowledge-driven lead discovery.

PubMed

Pirard, Bernard

2005-11-01

Virtual screening encompasses several computational approaches which have proven valuable for identifying novel leads. These approaches rely on available information. Herein, we review recent successful applications of virtual screening. The extension of virtual screening methodologies to target families is also briefly discussed.

A novel microseeding method for the crystallization of membrane proteins in lipidic cubic phase.

PubMed

Kolek, Stefan Andrew; Bräuning, Bastian; Stewart, Patrick Douglas Shaw

2016-04-01

Random microseed matrix screening (rMMS), in which seed crystals are added to random crystallization screens, is an important breakthrough in soluble protein crystallization that increases the number of crystallization hits that are available for optimization. This greatly increases the number of soluble protein structures generated every year by typical structural biology laboratories. Inspired by this success, rMMS has been adapted to the crystallization of membrane proteins, making LCP seed stock by scaling up LCP crystallization conditions without changing the physical and chemical parameters that are critical for crystallization. Seed crystals are grown directly in LCP and, as with conventional rMMS, a seeding experiment is combined with an additive experiment. The new method was used with the bacterial integral membrane protein OmpF, and it was found that it increased the number of crystallization hits by almost an order of magnitude: without microseeding one new hit was found, whereas with LCP-rMMS eight new hits were found. It is anticipated that this new method will lead to better diffracting crystals of membrane proteins. A method of generating seed gradients, which allows the LCP seed stock to be diluted and the number of crystals in each LCP bolus to be reduced, if required for optimization, is also demonstrated.

Accurate Binding Free Energy Predictions in Fragment Optimization.

PubMed

Steinbrecher, Thomas B; Dahlgren, Markus; Cappel, Daniel; Lin, Teng; Wang, Lingle; Krilov, Goran; Abel, Robert; Friesner, Richard; Sherman, Woody

2015-11-23

Predicting protein-ligand binding free energies is a central aim of computational structure-based drug design (SBDD)--improved accuracy in binding free energy predictions could significantly reduce costs and accelerate project timelines in lead discovery and optimization. The recent development and validation of advanced free energy calculation methods represents a major step toward this goal. Accurately predicting the relative binding free energy changes of modifications to ligands is especially valuable in the field of fragment-based drug design, since fragment screens tend to deliver initial hits of low binding affinity that require multiple rounds of synthesis to gain the requisite potency for a project. In this study, we show that a free energy perturbation protocol, FEP+, which was previously validated on drug-like lead compounds, is suitable for the calculation of relative binding strengths of fragment-sized compounds as well. We study several pharmaceutically relevant targets with a total of more than 90 fragments and find that the FEP+ methodology, which uses explicit solvent molecular dynamics and physics-based scoring with no parameters adjusted, can accurately predict relative fragment binding affinities. The calculations afford R(2)-values on average greater than 0.5 compared to experimental data and RMS errors of ca. 1.1 kcal/mol overall, demonstrating significant improvements over the docking and MM-GBSA methods tested in this work and indicating that FEP+ has the requisite predictive power to impact fragment-based affinity optimization projects.

Optimizing Cognitive Load for Learning from Computer-Based Science Simulations

ERIC Educational Resources Information Center

Lee, Hyunjeong; Plass, Jan L.; Homer, Bruce D.

2006-01-01

How can cognitive load in visual displays of computer simulations be optimized? Middle-school chemistry students (N = 257) learned with a simulation of the ideal gas law. Visual complexity was manipulated by separating the display of the simulations in two screens (low complexity) or presenting all information on one screen (high complexity). The…

QSAR-Driven Design and Discovery of Novel Compounds With Antiplasmodial and Transmission Blocking Activities.

PubMed

Lima, Marilia N N; Melo-Filho, Cleber C; Cassiano, Gustavo C; Neves, Bruno J; Alves, Vinicius M; Braga, Rodolpho C; Cravo, Pedro V L; Muratov, Eugene N; Calit, Juliana; Bargieri, Daniel Y; Costa, Fabio T M; Andrade, Carolina H

2018-01-01

Malaria is a life-threatening infectious disease caused by parasites of the genus Plasmodium , affecting more than 200 million people worldwide every year and leading to about a half million deaths. Malaria parasites of humans have evolved resistance to all current antimalarial drugs, urging for the discovery of new effective compounds. Given that the inhibition of deoxyuridine triphosphatase of Plasmodium falciparum ( Pf dUTPase) induces wrong insertions in plasmodial DNA and consequently leading the parasite to death, this enzyme is considered an attractive antimalarial drug target. Using a combi-QSAR (quantitative structure-activity relationship) approach followed by virtual screening and in vitro experimental evaluation, we report herein the discovery of novel chemical scaffolds with in vitro potency against asexual blood stages of both P. falciparum multidrug-resistant and sensitive strains and against sporogonic development of P. berghei . We developed 2D- and 3D-QSAR models using a series of nucleosides reported in the literature as Pf dUTPase inhibitors. The best models were combined in a consensus approach and used for virtual screening of the ChemBridge database, leading to the identification of five new virtual Pf dUTPase inhibitors. Further in vitro testing on P. falciparum multidrug-resistant (W2) and sensitive (3D7) parasites showed that compounds LabMol-144 and LabMol-146 demonstrated fair activity against both strains and presented good selectivity versus mammalian cells. In addition, LabMol-144 showed good in vitro inhibition of P. berghei ookinete formation, demonstrating that hit-to-lead optimization based on this compound may also lead to new antimalarials with transmission blocking activity.

Estimates of over-diagnosis of breast cancer due to population-based mammography screening in South Australia after adjustment for lead time effects.

PubMed

Beckmann, Kerri; Duffy, Stephen W; Lynch, John; Hiller, Janet; Farshid, Gelareh; Roder, David

2015-09-01

To estimate over-diagnosis due to population-based mammography screening using a lead time adjustment approach, with lead time measures based on symptomatic cancers only. Women aged 40-84 in 1989-2009 in South Australia eligible for mammography screening. Numbers of observed and expected breast cancer cases were compared, after adjustment for lead time. Lead time effects were modelled using age-specific estimates of lead time (derived from interval cancer rates and predicted background incidence, using maximum likelihood methods) and screening sensitivity, projected background breast cancer incidence rates (in the absence of screening), and proportions screened, by age and calendar year. Lead time estimates were 12, 26, 43 and 53 months, for women aged 40-49, 50-59, 60-69 and 70-79 respectively. Background incidence rates were estimated to have increased by 0.9% and 1.2% per year for invasive and all breast cancer. Over-diagnosis among women aged 40-84 was estimated at 7.9% (0.1-12.0%) for invasive cases and 12.0% (5.7-15.4%) when including ductal carcinoma in-situ (DCIS). We estimated 8% over-diagnosis for invasive breast cancer and 12% inclusive of DCIS cancers due to mammography screening among women aged 40-84. These estimates may overstate the extent of over-diagnosis if the increasing prevalence of breast cancer risk factors has led to higher background incidence than projected. © The Author(s) 2015.

Screening for major and minor depression in a multiethnic sample of Asian primary care patients: a comparison of the nine-item Patient Health Questionnaire (PHQ-9) and the 16-item Quick Inventory of Depressive Symptomatology - Self-Report (QIDS-SR16 ).

PubMed

Sung, Sharon Cohan; Low, Charity Cheng Hong; Fung, Daniel Shuen Sheng; Chan, Yiong Huak

2013-12-01

Depression is common, disabling, and the single most important factor leading to suicide, yet it is underdiagnosed in busy primary care settings. A key challenge facing primary care clinicians in Asia is the selection of instruments to facilitate depression screening. Although the nine-item Patient Health Questionnaire (PHQ-9) and 16-item Quick Inventory of Depressive Symptomatology - Self-Report (QIDS-SR16 ) are used internationally, they have not been directly compared or widely validated in Asian primary care populations. This study aimed to validate the PHQ-9 and QIDS-SR16 against a structured interview diagnosis of Diagnostic and Statistical Manual, 4th Edition, depression based on the Mini-International Neuropsychiatric Interview in a multiethnic Asian sample. From April through August 2011, we enrolled 400 English-speaking Singaporean primary care patients. Participants completed a demographic data form, the PHQ-9, and the QIDS-SR16 . They were assessed independently for major and minor depression using the Mini-International Neuropsychiatric Interview. Sensitivity and specificity for diagnosing major depression were 91.7% and 72.2%, respectively, for the PHQ-9 (optimal cutoff score of 6), and 83.3% and 84.7%, respectively, for the QIDS-SR16 (optimal cutoff score of 9). The QIDS-SR16 also detected minor depression at an optimal cutoff score of 7, with a sensitivity of 94.4% and specificity of 77.9%. The PHQ-9 and QIDS-SR16 showed good internal consistency (Cronbach's α: 0.87 and 0.79, respectively) and good convergent validity (correlation coefficient: r = 0.73, P < 0.001). The overall prevalence of major and minor depressive disorders was 9%. The PHQ-9 and QIDS-SR16 appear to be valid and reliable for depression screening in Asian primary care settings. Copyright © 2013 Wiley Publishing Asia Pty Ltd.

24 CFR 35.1320 - Lead-based paint inspections, paint testing, risk assessments, lead-hazard screens, and...

Code of Federal Regulations, 2010 CFR

2010-04-01

... POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES Methods and Standards for Lead-Paint Hazard... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false Lead-based paint inspections, paint testing, risk assessments, lead-hazard screens, and reevaluations. 35.1320 Section 35.1320 Housing and...

24 CFR 35.1320 - Lead-based paint inspections, paint testing, risk assessments, lead-hazard screens, and...

Code of Federal Regulations, 2014 CFR

2014-04-01

... POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES Methods and Standards for Lead-Paint Hazard... 24 Housing and Urban Development 1 2014-04-01 2014-04-01 false Lead-based paint inspections, paint testing, risk assessments, lead-hazard screens, and reevaluations. 35.1320 Section 35.1320 Housing and...

24 CFR 35.1320 - Lead-based paint inspections, paint testing, risk assessments, lead-hazard screens, and...

Code of Federal Regulations, 2013 CFR

2013-04-01

... POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES Methods and Standards for Lead-Paint Hazard... 24 Housing and Urban Development 1 2013-04-01 2013-04-01 false Lead-based paint inspections, paint testing, risk assessments, lead-hazard screens, and reevaluations. 35.1320 Section 35.1320 Housing and...

24 CFR 35.1320 - Lead-based paint inspections, paint testing, risk assessments, lead-hazard screens, and...

Code of Federal Regulations, 2012 CFR

2012-04-01

... POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES Methods and Standards for Lead-Paint Hazard... 24 Housing and Urban Development 1 2012-04-01 2012-04-01 false Lead-based paint inspections, paint testing, risk assessments, lead-hazard screens, and reevaluations. 35.1320 Section 35.1320 Housing and...

24 CFR 35.1320 - Lead-based paint inspections, paint testing, risk assessments, lead-hazard screens, and...

Code of Federal Regulations, 2011 CFR

2011-04-01

... POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES Methods and Standards for Lead-Paint Hazard... 24 Housing and Urban Development 1 2011-04-01 2011-04-01 false Lead-based paint inspections, paint testing, risk assessments, lead-hazard screens, and reevaluations. 35.1320 Section 35.1320 Housing and...

Optimization of media components for laccase production by litter dwelling fungal isolate Fusarium incarnatum LD-3.

PubMed

Chhaya, Urvish; Gupte, Akshaya

2010-02-01

Laccase production by solid state fermentation (SSF) using an indigenously isolated litter dwelling fungus Fusarium incarnatum LD-3 was optimized. Fourteen medium components were screened by the initial screening method of Plackett-Burman. Each of the components was screened on the basis of 'p' (probability value) which was above 95% confidence level. Ortho-dianisidine, thiamine HCl and CuSO(4) . 5 H(2)O were identified as significant components for laccase production. The Central Composite Design response surface methodology was then applied to further optimize the laccase production. The optimal concentration of these three medium components for higher laccase production were (g/l): CuSO(4) . 5 H(2)O, 0.01; thiamine HCl, 0.0136 and ortho-dianisidine, 0.388 mM served as an inducer. Wheat straw, 5.0 g was used as a solid substrate. Using this statistical optimization method the laccase production was found to increase from 40 U/g to 650 U/g of wheat straw, which was sixteen times higher than non optimized medium. This is the first report on statistical optimization of laccase production from Fusarium incarnatum LD-3.

[Study on baking processing technology of hui medicine Aconitum flavum].

PubMed

Fu, Xue-yan; Zhang, Bai-tong; Li, Ting-ting; Dong, Lin; Hao, Wen-jing; Yu, Liang

2013-12-01

To screen and optimize the processing technology of Aconitum flavum. The acute-toxicity, anti-inflammatory and analgesic experiments were used as indexes. Four processing methods, including decoction, streaming, baking and processing with Chebulae Fructus decoction, were compared to screen the optimum processing method for Aconitum flavum. The baking time was also optimized. The optimal baked technology was that 1-2 mm decoction pieces was baked at 105 degrees C for 3 hours. The baking method is proved to be the optimal processing method of Aconitum flavum. It is shown that this method is simple and stable.

[Analysis of washing efficiency and change in lead speciation in lead-contaminated soil of a battery factory].

PubMed

Ren, Bei; Huang, Jin-lou; Miao, Ming-sheng

2013-09-01

Lead-contaminated soil with different pollution load in a lead battery factory in the southwest of China was chosen as the research object, the lead content and speciation were analyzed, and different washing agents were screened. The lead washing efficiency and lead speciation were analyzed under different pH conditions, and the soil of different particle size was washed using different duration to determine the best washing time. The results showed that the soil of sites A and B in the factory was severely contaminated, the lead concentration reaching 15,703.22 mg x kg(-1) and 1747.78 mg x kg(-1), respectively, and the proportion of the active-state lead was relatively high, while the residue state accounted for only 17.32%, 11.64%, 14.6% and 10.2%. EDTA and hydrochloric acid showed the best extraction effect in the 5 washing agents tested, which included EDTA, hydrochloric acid, citric acid, rhamnolipid and SDS. Cleaning under acidic conditions could not only effectively extract the total amount of lead but also effectively reduce the environmental risk of active-state lead. pH 4-7 was suggested as the most appropriate condition. The cleaning effect of coarse sand and fine sand was good, while for washing powder clay, it is better to improve the process, with the optimal washing time determined as 240 min.

Engineering of the function of diamond-like carbon binding peptides through structural design.

PubMed

Gabryelczyk, Bartosz; Szilvay, Géza R; Singh, Vivek K; Mikkilä, Joona; Kostiainen, Mauri A; Koskinen, Jari; Linder, Markus B

2015-02-09

The use of phage display to select material-specific peptides provides a general route towards modification and functionalization of surfaces and interfaces. However, a rational structural engineering of the peptides for optimal affinity is typically not feasible because of insufficient structure-function understanding. Here, we investigate the influence of multivalency of diamond-like carbon (DLC) binding peptides on binding characteristics. We show that facile linking of peptides together using different lengths of spacers and multivalency leads to a tuning of affinity and kinetics. Notably, increased length of spacers in divalent systems led to significantly increased affinities. Making multimers influenced also kinetic aspects of surface competition. Additionally, the multivalent peptides were applied as surface functionalization components for a colloidal form of DLC. The work suggests the use of a set of linking systems to screen parameters for functional optimization of selected material-specific peptides.

Deterring Online Advertising Fraud through Optimal Payment in Arrears

NASA Astrophysics Data System (ADS)

Edelman, Benjamin

Online advertisers face substantial difficulty in selecting and supervising small advertising partners: Fraud can be well-hidden, and limited reputation systems reduce accountability. But partners are not paid until after their work is complete, and advertisers can extend this delay both to improve detection of improper partner practices and to punish partners who turn out to be rule-breakers. I capture these relationships in a screening model with delayed payments and probabilistic delayed observation of agents’ types. I derive conditions in which an advertising principal can set its payment delay to deter rogue agents and to attract solely or primarily good-type agents. Through the savings from excluding rogue agents, the principal can increase its profits while offering increased payments to good-type agents. I estimate that a leading affiliate network could have invoked an optimal payment delay to eliminate 71% of fraud without decreasing profit.

Structure-guided design of novel Trypanosoma brucei Methionyl-tRNA synthetase inhibitors.

PubMed

Huang, Wenlin; Zhang, Zhongsheng; Barros-Álvarez, Ximena; Koh, Cho Yeow; Ranade, Ranae M; Gillespie, J Robert; Creason, Sharon A; Shibata, Sayaka; Verlinde, Christophe L M J; Hol, Wim G J; Buckner, Frederick S; Fan, Erkang

2016-11-29

A screening hit 1 against Trypanosoma brucei methionyl-tRNA synthetase was optimized using a structure-guided approach. The optimization led to the identification of two novel series of potent inhibitors, the cyclic linker and linear linker series. Compounds of both series were potent in a T. brucei growth inhibition assay while showing low toxicity to mammalian cells. The best compound of each series, 16 and 31, exhibited EC 50 s of 39 and 22 nM, respectively. Compounds 16 and 31 also exhibited promising PK properties after oral dosing in mice. Moreover, compound 31 had moderately good brain permeability, with a brain/plasma ratio of 0.27 at 60 min after IP injection. This study provides new lead compounds for arriving at new treatments of human African trypanosomiasis (HAT). Copyright © 2016 Elsevier Masson SAS. All rights reserved.

Fragment growing and linking lead to novel nanomolar lactate dehydrogenase inhibitors.

PubMed

Kohlmann, Anna; Zech, Stephan G; Li, Feng; Zhou, Tianjun; Squillace, Rachel M; Commodore, Lois; Greenfield, Matthew T; Lu, Xiaohui; Miller, David P; Huang, Wei-Sheng; Qi, Jiwei; Thomas, R Mathew; Wang, Yihan; Zhang, Sen; Dodd, Rory; Liu, Shuangying; Xu, Rongsong; Xu, Yongjin; Miret, Juan J; Rivera, Victor; Clackson, Tim; Shakespeare, William C; Zhu, Xiaotian; Dalgarno, David C

2013-02-14

Lactate dehydrogenase A (LDH-A) catalyzes the interconversion of lactate and pyruvate in the glycolysis pathway. Cancer cells rely heavily on glycolysis instead of oxidative phosphorylation to generate ATP, a phenomenon known as the Warburg effect. The inhibition of LDH-A by small molecules is therefore of interest for potential cancer treatments. We describe the identification and optimization of LDH-A inhibitors by fragment-based drug discovery. We applied ligand based NMR screening to identify low affinity fragments binding to LDH-A. The dissociation constants (K(d)) and enzyme inhibition (IC(50)) of fragment hits were measured by surface plasmon resonance (SPR) and enzyme assays, respectively. The binding modes of selected fragments were investigated by X-ray crystallography. Fragment growing and linking, followed by chemical optimization, resulted in nanomolar LDH-A inhibitors that demonstrated stoichiometric binding to LDH-A. Selected molecules inhibited lactate production in cells, suggesting target-specific inhibition in cancer cell lines.

Evolution of a designed retro-aldolase leads to complete active site remodeling

PubMed Central

Giger, Lars; Caner, Sami; Obexer, Richard; Kast, Peter; Baker, David; Ban, Nenad; Hilvert, Donald

2013-01-01

Evolutionary advances are often fueled by unanticipated innovation. Directed evolution of a computationally designed enzyme suggests that dramatic molecular changes can also drive the optimization of primitive protein active sites. The specific activity of an artificial retro-aldolase was boosted >4,400 fold by random mutagenesis and screening, affording catalytic efficiencies approaching those of natural enzymes. However, structural and mechanistic studies reveal that the engineered catalytic apparatus, consisting of a reactive lysine and an ordered water molecule, was unexpectedly abandoned in favor of a new lysine residue in a substrate binding pocket created during the optimization process. Structures of the initial in silico design, a mechanistically promiscuous intermediate, and one of the most evolved variants highlight the importance of loop mobility and supporting functional groups in the emergence of the new catalytic center. Such internal competition between alternative reactive sites may have characterized the early evolution of many natural enzymes. PMID:23748672

Optimization of PCR Condition: The First Study of High Resolution Melting Technique for Screening of APOA1 Variance.

PubMed

Wahyuningsih, Hesty; K Cayami, Ferdy; Bahrudin, Udin; A Sobirin, Mochamad; Ep Mundhofir, Farmaditya; Mh Faradz, Sultana; Hisatome, Ichiro

2017-03-01

High resolution melting (HRM) is a post-PCR technique for variant screening and genotyping based on the different melting points of DNA fragments. The advantages of this technique are that it is fast, simple, and efficient and has a high output, particularly for screening of a large number of samples. APOA1 encodes apolipoprotein A1 (apoA1) which is a major component of high density lipoprotein cholesterol (HDL-C). This study aimed to obtain an optimal quantitative polymerase chain reaction (qPCR)-HRM condition for screening of APOA1 variance. Genomic DNA was isolated from a peripheral blood sample using the salting out method. APOA1 was amplified using the RotorGeneQ 5Plex HRM. The PCR product was visualized with the HRM amplification curve and confirmed using gel electrophoresis. The melting profile was confirmed by looking at the melting curve. Five sets of primers covering the translated region of APOA1 exons were designed with expected PCR product size of 100-400 bps. The amplified segments of DNA were amplicons 2, 3, 4A, 4B, and 4C. Amplicons 2, 3 and 4B were optimized at an annealing temperature of 60 °C at 40 PCR cycles. Amplicon 4A was optimized at an annealing temperature of 62 °C at 45 PCR cycles. Amplicon 4C was optimized at an annealing temperature of 63 °C at 50 PCR cycles. In addition to the suitable procedures of DNA isolation and quantification, primer design and an estimated PCR product size, the data of this study showed that appropriate annealing temperature and PCR cycles were important factors in optimization of HRM technique for variant screening in APOA1 .

Optimization of PCR Condition: The First Study of High Resolution Melting Technique for Screening of APOA1 Variance

PubMed Central

Wahyuningsih, Hesty; K Cayami, Ferdy; Bahrudin, Udin; A Sobirin, Mochamad; EP Mundhofir, Farmaditya; MH Faradz, Sultana; Hisatome, Ichiro

2017-01-01

Background High resolution melting (HRM) is a post-PCR technique for variant screening and genotyping based on the different melting points of DNA fragments. The advantages of this technique are that it is fast, simple, and efficient and has a high output, particularly for screening of a large number of samples. APOA1 encodes apolipoprotein A1 (apoA1) which is a major component of high density lipoprotein cholesterol (HDL-C). This study aimed to obtain an optimal quantitative polymerase chain reaction (qPCR)-HRM condition for screening of APOA1 variance. Methods Genomic DNA was isolated from a peripheral blood sample using the salting out method. APOA1 was amplified using the RotorGeneQ 5Plex HRM. The PCR product was visualized with the HRM amplification curve and confirmed using gel electrophoresis. The melting profile was confirmed by looking at the melting curve. Results Five sets of primers covering the translated region of APOA1 exons were designed with expected PCR product size of 100–400 bps. The amplified segments of DNA were amplicons 2, 3, 4A, 4B, and 4C. Amplicons 2, 3 and 4B were optimized at an annealing temperature of 60 °C at 40 PCR cycles. Amplicon 4A was optimized at an annealing temperature of 62 °C at 45 PCR cycles. Amplicon 4C was optimized at an annealing temperature of 63 °C at 50 PCR cycles. Conclusion In addition to the suitable procedures of DNA isolation and quantification, primer design and an estimated PCR product size, the data of this study showed that appropriate annealing temperature and PCR cycles were important factors in optimization of HRM technique for variant screening in APOA1. PMID:28331418

Discovery and SAR of Novel 2,3‐Dihydroimidazo[1,2‐c]quinazoline PI3K Inhibitors: Identification of Copanlisib (BAY 80‐6946)

PubMed Central

Hentemann, Martin F.; Rowley, R. Bruce; Bull, Cathy O.; Jenkins, Susan; Bullion, Ann M.; Johnson, Jeffrey; Redman, Anikó; Robbins, Arthur H.; Esler, William; Fracasso, R. Paul; Garrison, Timothy; Hamilton, Mark; Michels, Martin; Wood, Jill E.; Wilkie, Dean P.; Xiao, Hong; Levy, Joan; Stasik, Enrico; Liu, Ningshu; Schaefer, Martina; Brands, Michael

2016-01-01

Abstract The phosphoinositide 3‐kinase (PI3K) pathway is aberrantly activated in many disease states, including tumor cells, either by growth factor receptor tyrosine kinases or by the genetic mutation and amplification of key pathway components. A variety of PI3K isoforms play differential roles in cancers. As such, the development of PI3K inhibitors from novel compound classes should lead to differential pharmacological and pharmacokinetic profiles and allow exploration in various indications, combinations, and dosing regimens. A screening effort aimed at the identification of PI3Kγ inhibitors for the treatment of inflammatory diseases led to the discovery of the novel 2,3‐dihydroimidazo[1,2‐c]quinazoline class of PI3K inhibitors. A subsequent lead optimization program targeting cancer therapy focused on inhibition of PI3Kα and PI3Kβ. Herein, initial structure–activity relationship findings for this class and the optimization that led to the identification of copanlisib (BAY 80‐6946) as a clinical candidate for the treatment of solid and hematological tumors are described. PMID:27310202

Identification, characterization and initial hit-to-lead optimization of a series of 4-arylamino-3-pyridinecarbonitrile as protein kinase C theta (PKCtheta) inhibitors.

PubMed

Cole, Derek C; Asselin, Magda; Brennan, Agnes; Czerwinski, Robert; Ellingboe, John W; Fitz, Lori; Greco, Rita; Huang, Xinyi; Joseph-McCarthy, Diane; Kelly, Michael F; Kirisits, Matthew; Lee, Julie; Li, Yuanhong; Morgan, Paul; Stock, Joseph R; Tsao, Désirée H H; Wissner, Allan; Yang, Xiaoke; Chaudhary, Divya

2008-10-09

The protein kinase C (PKC) family of serine/threonine kinases is implicated in a wide variety of cellular processes. The PKC theta (PKCtheta) isoform is involved in TCR signal transduction and T cell activation and regulates T cell mediated diseases, including lung inflammation and airway hyperresponsiveness. Thus inhibition of PKCtheta enzyme activity by a small molecule represents an attractive strategy for the treatment of asthma. A PKCtheta high-throughput screening (HTS) campaign led to the identification of 4-(3-bromophenylamino)-5-(3,4-dimethoxyphenyl)-3-pyridinecarbonitrile 4a, a low microM ATP competitive PKCtheta inhibitor. Structure based hit-to-lead optimization led to the identification of 5-(3,4-dimethoxyphenyl)-4-(1H-indol-5-ylamino)-3-pyridinecarbonitrile 4p, a 70 nM PKCtheta inhibitor. Compound 4p was selective for inhibition of novel PKC isoforms over a panel of 21 serine/threonine, tyrosine, and phosphoinositol kinases, in addition to the conventional and atypical PKCs, PKCbeta, and PKCzeta, respectively. Compound 4p also inhibited IL-2 production in antiCD3/anti-CD28 activated T cells enriched from splenocytes.

Optimal use of colonoscopy and fecal immunochemical test for population-based colorectal cancer screening: a cost-effectiveness analysis using Japanese data.

PubMed

Sekiguchi, Masau; Igarashi, Ataru; Matsuda, Takahisa; Matsumoto, Minori; Sakamoto, Taku; Nakajima, Takeshi; Kakugawa, Yasuo; Yamamoto, Seiichiro; Saito, Hiroshi; Saito, Yutaka

2016-02-01

There have been few cost-effectiveness analyses of population-based colorectal cancer screening in Japan, and there is no consensus on the optimal use of total colonoscopy and the fecal immunochemical test for colorectal cancer screening with regard to cost-effectiveness and total colonoscopy workload. The present study aimed to examine the cost-effectiveness of colorectal cancer screening using Japanese data to identify the optimal use of total colonoscopy and fecal immunochemical test. We developed a Markov model to assess the cost-effectiveness of colorectal cancer screening offered to an average-risk population aged 40 years or over. The cost, quality-adjusted life-years and number of total colonoscopy procedures required were evaluated for three screening strategies: (i) a fecal immunochemical test-based strategy; (ii) a total colonoscopy-based strategy; (iii) a strategy of adding population-wide total colonoscopy at 50 years to a fecal immunochemical test-based strategy. All three strategies dominated no screening. Among the three, Strategy 1 was dominated by Strategy 3, and the incremental cost per quality-adjusted life-years gained for Strategy 2 against Strategies 1 and 3 were JPY 293 616 and JPY 781 342, respectively. Within the Japanese threshold (JPY 5-6 million per QALY gained), Strategy 2 was the most cost-effective, followed by Strategy 3; however, Strategy 2 required more than double the number of total colonoscopy procedures than the other strategies. The total colonoscopy-based strategy could be the most cost-effective for population-based colorectal cancer screening in Japan. However, it requires more total colonoscopy procedures than the other strategies. Depending on total colonoscopy capacity, the strategy of adding total colonoscopy for individuals at a specified age to a fecal immunochemical test-based screening may be an optimal solution. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Stability and Change of Behavioral and Emotional Screening Scores

ERIC Educational Resources Information Center

Dever, Bridget V.; Dowdy, Erin; Raines, Tara C.; Carnazzo, Katherine

2015-01-01

Universal screening for behavioral and emotional difficulties is integral to the identification of students needing early intervention and prevention efforts. However, unanswered questions regarding the stability of screening scores impede the ability to determine optimal strategies for subsequent screening. This study examined the 2-year…

Using an Ocean of Data, Researchers Model Real-Life Benefits of Cancer Screening

Cancer.gov

Using the results of screening trials, the NCI Cancer Intervention and Surveillance Modeling Network is trying to estimate the true benefit of cancer screening in the general population and identify the optimal way to implement screening within the health care system.

Optimized Hypernetted-Chain Solutions for Helium -4 Surfaces and Metal Surfaces

NASA Astrophysics Data System (ADS)

Qian, Guo-Xin

This thesis is a study of inhomogeneous Bose systems such as liquid ('4)He slabs and inhomogeneous Fermi systems such as the electron gas in metal films, at zero temperature. Using a Jastrow-type many-body wavefunction, the ground state energy is expressed by means of Bogoliubov-Born-Green-Kirkwood -Yvon and Hypernetted-Chain techniques. For Bose systems, Euler-Lagrange equations are derived for the one- and two -body functions and systematic approximation methods are physically motivated. It is shown that the optimized variational method includes a self-consistent summation of ladder- and ring-diagrams of conventional many-body theory. For Fermi systems, a linear potential model is adopted to generate the optimized Hartree-Fock basis. Euler-Lagrange equations are derived for the two-body correlations which serve to screen the strong bare Coulomb interaction. The optimization of the pair correlation leads to an expression of correlation energy in which the state averaged RPA part is separated. Numerical applications are presented for the density profile and pair distribution function for both ('4)He surfaces and metal surfaces. Both the bulk and surface energies are calculated in good agreement with experiments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Longenecker, Kenton L.; Stamper, Geoffrey F.; Hajduk, Philip J.

In a broad genomics analysis to find novel protein targets for antibiotic discovery, MurF was identified as an essential gene product for Streptococcus pneumonia that catalyzes a critical reaction in the biosynthesis of the peptidoglycan in the formation of the cell wall. Lacking close relatives in mammalian biology, MurF presents attractive characteristics as a potential drug target. Initial screening of the Abbott small-molecule compound collection identified several compounds for further validation as pharmaceutical leads. Here we report the integrated efforts of NMR and X-ray crystallography, which reveal the multidomain structure of a MurF-inhibitor complex in a compact conformation that differsmore » dramatically from related structures. The lead molecule is bound in the substrate-binding region and induces domain closure, suggestive of the domain arrangement for the as yet unobserved transition state conformation for MurF enzymes. The results form a basis for directed optimization of the compound lead by structure-based design to explore the suitability of MurF as a pharmaceutical target.« less

Hit-to-lead evaluation of a novel class of sphingosine 1-phosphate lyase inhibitors.

PubMed

Dinges, Jurgen; Harris, Christopher M; Wallace, Grier A; Argiriadi, Maria A; Queeney, Kara L; Perron, Denise C; Dominguez, Eric; Kebede, Tegest; Desino, Kelly E; Patel, Hetal; Vasudevan, Anil

2016-05-01

Inhibition of sphingosine-1-phosphate lyase has recently been proposed as a potential treatment option for inflammatory disorders such as multiple sclerosis, rheumatoid arthritis, and inflammatory bowel disease. In this report we describe our hit-to-lead evaluation of the isoxazolecarboxamide 6, a high-throughput screening hit (in vitro IC50=1.0 μM, cell IC50=1.8 μM), as a novel S1P lyase inhibitor. We were able to establish basic structure-activity relationships around 6 and succeeded in obtaining X-ray structural information which enabled structure-based design. With the discovery of 28, enzyme activity was quickly improved to IC50=120 nM and cell potency to IC50=230 nM. The main liability in the established isoxazolecarboxamide hit series was determined to be metabolic stability. In particular we identified that future lead-optimization efforts to overcome this problem should focus on blocking the N-dealkylation on the secondary amine. Copyright © 2016 Elsevier Ltd. All rights reserved.

Concept of combinatorial de novo design of drug-like molecules by particle swarm optimization.

PubMed

Hartenfeller, Markus; Proschak, Ewgenij; Schüller, Andreas; Schneider, Gisbert

2008-07-01

We present a fast stochastic optimization algorithm for fragment-based molecular de novo design (COLIBREE, Combinatorial Library Breeding). The search strategy is based on a discrete version of particle swarm optimization. Molecules are represented by a scaffold, which remains constant during optimization, and variable linkers and side chains. Different linkers represent virtual chemical reactions. Side-chain building blocks were obtained from pseudo-retrosynthetic dissection of large compound databases. Here, ligand-based design was performed using chemically advanced template search (CATS) topological pharmacophore similarity to reference ligands as fitness function. A weighting scheme was included for particle swarm optimization-based molecular design, which permits the use of many reference ligands and allows for positive and negative design to be performed simultaneously. In a case study, the approach was applied to the de novo design of potential peroxisome proliferator-activated receptor subtype-selective agonists. The results demonstrate the ability of the technique to cope with large combinatorial chemistry spaces and its applicability to focused library design. The technique was able to perform exploitation of a known scheme and at the same time explorative search for novel ligands within the framework of a given molecular core structure. It thereby represents a practical solution for compound screening in the early hit and lead finding phase of a drug discovery project.

Method optimization for drug impurity profiling in supercritical fluid chromatography: Application to a pharmaceutical mixture.

PubMed

Muscat Galea, Charlene; Didion, David; Clicq, David; Mangelings, Debby; Vander Heyden, Yvan

2017-12-01

A supercritical chromatographic method for the separation of a drug and its impurities has been developed and optimized applying an experimental design approach and chromatogram simulations. Stationary phase screening was followed by optimization of the modifier and injection solvent composition. A design-of-experiment (DoE) approach was then used to optimize column temperature, back-pressure and the gradient slope simultaneously. Regression models for the retention times and peak widths of all mixture components were built. The factor levels for different grid points were then used to predict the retention times and peak widths of the mixture components using the regression models and the best separation for the worst separated peak pair in the experimental domain was identified. A plot of the minimal resolutions was used to help identifying the factor levels leading to the highest resolution between consecutive peaks. The effects of the DoE factors were visualized in a way that is familiar to the analytical chemist, i.e. by simulating the resulting chromatogram. The mixture of an active ingredient and seven impurities was separated in less than eight minutes. The approach discussed in this paper demonstrates how SFC methods can be developed and optimized efficiently using simple concepts and tools. Copyright © 2017 Elsevier B.V. All rights reserved.

[Fragment-based drug discovery: concept and aim].

PubMed

Tanaka, Daisuke

2010-03-01

Fragment-Based Drug Discovery (FBDD) has been recognized as a newly emerging lead discovery methodology that involves biophysical fragment screening and chemistry-driven fragment-to-lead stages. Although fragments, defined as structurally simple and small compounds (typically <300 Da), have not been employed in conventional high-throughput screening (HTS), the recent significant progress in the biophysical screening methods enables fragment screening at a practical level. The intention of FBDD primarily turns our attention to weakly but specifically binding fragments (hit fragments) as the starting point of medicinal chemistry. Hit fragments are then promoted to more potent lead compounds through linking or merging with another hit fragment and/or attaching functional groups. Another positive aspect of FBDD is ligand efficiency. Ligand efficiency is a useful guide in screening hit selection and hit-to-lead phases to achieve lead-likeness. Owing to these features, a number of successful applications of FBDD to "undruggable targets" (where HTS and other lead identification methods failed to identify useful lead compounds) have been reported. As a result, FBDD is now expected to complement more conventional methodologies. This review, as an introduction of the following articles, will summarize the fundamental concepts of FBDD and will discuss its advantages over other conventional drug discovery approaches.

Estimate of overdiagnosis of breast cancer due to mammography after adjustment for lead time. A service screening study in Italy

PubMed Central

Paci, Eugenio; Miccinesi, Guido; Puliti, Donella; Baldazzi, Paola; De Lisi, Vincenzo; Falcini, Fabio; Cirilli, Claudia; Ferretti, Stefano; Mangone, Lucia; Finarelli, Alba Carola; Rosso, Stefano; Segnan, Nereo; Stracci, Fabrizio; Traina, Adele; Tumino, Rosario; Zorzi, Manuel

2006-01-01

Introduction Excess of incidence rates is the expected consequence of service screening. The aim of this paper is to estimate the quota attributable to overdiagnosis in the breast cancer screening programmes in Northern and Central Italy. Methods All patients with breast cancer diagnosed between 50 and 74 years who were resident in screening areas in the six years before and five years after the start of the screening programme were included. We calculated a corrected-for-lead-time number of observed cases for each calendar year. The number of observed incident cases was reduced by the number of screen-detected cases in that year and incremented by the estimated number of screen-detected cases that would have arisen clinically in that year. Results In total we included 13,519 and 13,999 breast cancer cases diagnosed in the pre-screening and screening years, respectively. In total, the excess ratio of observed to predicted in situ and invasive cases was 36.2%. After correction for lead time the excess ratio was 4.6% (95% confidence interval 2 to 7%) and for invasive cases only it was 3.2% (95% confidence interval 1 to 6%). Conclusion The remaining excess of cancers after individual correction for lead time was lower than 5%. PMID:17147789

Resource Effective Strategies to Prevent and Treat Cardiovascular Disease

PubMed Central

Schwalm, Jon-David; McKee, Martin; Huffman, Mark D.; Yusuf, Salim

2016-01-01

Cardiovascular disease (CVD) is the leading cause of global deaths, with the majority occurring in low- and middle-income countries (LMIC). The primary and secondary prevention of CVD is suboptimal throughout the world, but the evidence-practice gaps are much more pronounced in LMIC. Barriers at the patient, health-care provider, and health system level prevent the implementation of optimal primary and secondary prevention. Identification of the particular barriers that exist in resource-constrained settings is necessary to inform effective strategies to reduce the identified evidence-practice gaps. Furthermore, targeting modifiable factors that contribute most significantly to the global burden of CVD, including tobacco use, hypertension, and secondary prevention for CVD will lead to the biggest gains in mortality reduction. We review a select number of novel, resource-efficient strategies to reduce premature mortality from CVD, including: (1) effective measures for tobacco control; (2) implementation of simplified screening and management algorithms for those with or at risk of CVD, (3) increasing the availability and affordability of simplified and cost-effective treatment regimens including combination CVD preventive drug therapy, and (4) simplified delivery of health care through task-sharing (non-physician health workers) and optimizing self-management (treatment supporters). Developing and deploying systems of care that address barriers related to the above, will lead to substantial reductions in CVD and related mortality. PMID:26903017

Optimization of a hydrodynamic separator using a multiscale computational fluid dynamics approach.

PubMed

Schmitt, Vivien; Dufresne, Matthieu; Vazquez, Jose; Fischer, Martin; Morin, Antoine

2013-01-01

This article deals with the optimization of a hydrodynamic separator working on the tangential separation mechanism along a screen. The aim of this study is to optimize the shape of the device to avoid clogging. A multiscale approach is used. This methodology combines measurements and computational fluid dynamics (CFD). A local model enables us to observe the different phenomena occurring at the orifice scale, which shows the potential of expanded metal screens. A global model is used to simulate the flow within the device using a conceptual model of the screen (porous wall). After validation against the experimental measurements, the global model was used to investigate the influence of deflectors and disk plates in the structure.

Addressing Unmet Basic Resource Needs as Part of Chronic Cardiometabolic Disease Management.

PubMed

Berkowitz, Seth A; Hulberg, Amy Catherine; Standish, Sara; Reznor, Gally; Atlas, Steven J

2017-02-01

It is unclear if helping patients meet resource needs, such as difficulty affording food, housing, or medications, improves clinical outcomes. To determine the effectiveness of the Health Leads program on improvement in systolic and diastolic blood pressure (SBP and DBP, respectively), low-density lipoprotein cholesterol (LDL-C) level, and hemoglobin A1c (HbA1c) level. A difference-in-difference evaluation of the Health Leads program was conducted from October 1, 2012, through September 30, 2015, at 3 academic primary care practices. Health Leads consists of screening for unmet needs at clinic visits, and offering those who screen positive to meet with an advocate to help obtain resources, or receive brief information provision. Changes in SBP, DBP, LDL-C level, and HbA1c level. We compared those who screened positive for unmet basic needs (Health Leads group) with those who screened negative, using intention-to-treat, and, secondarily, between those who did and did not enroll in Health Leads, using linear mixed modeling, examining the period before and after screening. A total of 5125 people were screened, using a standardized form, for unmet basic resource needs; 3351 screened negative and 1774 screened positive. For those who screened positive, the mean age was 57.6 years and 1811 (56%) were women. For those who screened negative, the mean age was 56.7 years and 909 (57%) were women. Of 5125 people screened, 1774 (35%) reported at least 1 unmet need, and 1021 (58%) of those enrolled in Health Leads. Median follow-up for those who screened positive and negative was 34 and 32 months, respectively. In unadjusted intention-to-treat analyses of 1998 participants with hypertension, the Health Leads group experienced greater reduction in SBP (differential change, -1.2; 95% CI, -2.1 to -0.4) and DBP (differential change, -1.0; 95% CI, -1.5 to -0.5). For 2281 individuals with an indication for LDL-C level lowering, results also favored the Health Leads group (differential change, -3.7; 95% CI -6.7 to -0.6). For 774 individuals with diabetes, the Health Leads group did not show HbA1c level improvement (differential change, -0.04%; 95% CI, -0.17% to 0.10%). Results adjusted for baseline demographic and clinical differences were not qualitatively different. Among those who enrolled in Health Leads program, there were greater BP and LDL-C level improvements than for those who declined (SBP differential change -2.6; 95% CI,-3.5 to -1.7; SBP differential change, -1.4; 95% CI, -1.9 to -0.9; LDL-C level differential change, -6.3; 95% CI, -9.7 to -2.8). Screening for and attempting to address unmet basic resource needs in primary care was associated with modest improvements in blood pressure and lipid, but not blood glucose, levels.

Benefits and harms of CT lung cancer screening strategies. A comparative modeling study for the U.S. Preventive Services Task Force

PubMed Central

de Koning, Harry J.; Meza, Rafael; Plevritis, Sylvia K.; Haaf, Kevin ten; Munshi, Vidit N.; Jeon, Jihyoun; Erdogan, Saadet Ayca; Kong, Chung Yin; Han, Summer S.; van Rosmalen, Joost; Choi, Sung Eun; Pinsky, Paul F.; Berrington de Gonzalez, Amy; Berg, Christine D.; Black, William C.; Tammemägi, Martin C.; Hazelton, William D.; Feuer, Eric J.; McMahon, Pamela M.

2014-01-01

Background The optimal screening policy for lung cancer is unknown. Objective To identify efficient CT-screening scenarios where relatively more lung cancer deaths are averted for fewer CT screens. Design Comparative modeling study using 5 independent models. Data Sources The National Lung Screening Trial, the Prostate, Lung, Colorectal and Ovarian trial, the Surveillance, Epidemiology, and End Results program, and U.S. Smoking History Generator. Target Population U.S. cohort born in 1950. Time Horizon Cohort followed from ages 45 to 90. Perspective Societal. Intervention 576 scenarios with varying eligibility criteria (age, smoking pack-years, years quit) and screening intervals. Outcome Measures Benefits: lung cancer deaths averted or life-years gained; harms: CT-exams, false positives (including biopsy/surgery), overdiagnosed cases, radiation-related deaths. Results of Best-Case Annual screening from age 55 through 80 for ever-smokers with at least 30 pack-years and ex-smokers with less than 15 years since quitting was the most advantageous strategy. It would lead to 50% (45 to 54%) of cancers being detected at an early stage (I/II); 575 screens per lung cancer death averted; a 14% (8.2 to 23.5%) lung cancer mortality reduction; 497 lung cancer deaths averted; and 5,250 life-years gained per the 100,000-member cohort. Harms would include 67,550 false-positive tests, 910 biopsies or surgeries for benign lesions and 190 overdiagnosed cancers (3.7%; 1.4 to 8.3%). Results of Sensitivity Analysis The number of cancer deaths averted for the scenario varied across models between 177 and 862, and for overdiagnosed cancers between 72 and 426. Limitations Scenarios assumed 100% screening adherence. Data derived from trials with short duration were extrapolated to life-time follow-up. Conclusion Annual CT screening for lung cancer has a favorable benefit-harm ratio for individuals aged 55 through 80 years with 30 or more pack-year exposure to smoking. PMID:24379002

Optimization of LC-Orbitrap-HRMS acquisition and MZmine 2 data processing for nontarget screening of environmental samples using design of experiments.

PubMed

Hu, Meng; Krauss, Martin; Brack, Werner; Schulze, Tobias

2016-11-01

Liquid chromatography-high resolution mass spectrometry (LC-HRMS) is a well-established technique for nontarget screening of contaminants in complex environmental samples. Automatic peak detection is essential, but its performance has only rarely been assessed and optimized so far. With the aim to fill this gap, we used pristine water extracts spiked with 78 contaminants as a test case to evaluate and optimize chromatogram and spectral data processing. To assess whether data acquisition strategies have a significant impact on peak detection, three values of MS cycle time (CT) of an LTQ Orbitrap instrument were tested. Furthermore, the key parameter settings of the data processing software MZmine 2 were optimized to detect the maximum number of target peaks from the samples by the design of experiments (DoE) approach and compared to a manual evaluation. The results indicate that short CT significantly improves the quality of automatic peak detection, which means that full scan acquisition without additional MS 2 experiments is suggested for nontarget screening. MZmine 2 detected 75-100 % of the peaks compared to manual peak detection at an intensity level of 10 5 in a validation dataset on both spiked and real water samples under optimal parameter settings. Finally, we provide an optimization workflow of MZmine 2 for LC-HRMS data processing that is applicable for environmental samples for nontarget screening. The results also show that the DoE approach is useful and effort-saving for optimizing data processing parameters. Graphical Abstract ᅟ.

Prenatal screening: current practice, new developments, ethical challenges.

PubMed

de Jong, Antina; Maya, Idit; van Lith, Jan M M

2015-01-01

Prenatal screening pathways, as nowadays offered in most Western countries consist of similar tests. First, a risk-assessment test for major aneuploides is offered to pregnant women. In case of an increased risk, invasive diagnostic tests, entailing a miscarriage risk, are offered. For decades, only conventional karyotyping was used for final diagnosis. Moreover, several foetal ultrasound scans are offered to detect major congenital anomalies, but the same scans also provide relevant information for optimal support of the pregnancy and the delivery. Recent developments in prenatal screening include the application of microarrays that allow for identifying a much broader range of abnomalities than karyotyping, and non-invasive prenatal testing (NIPT) that enables reducing the number of invasive tests for aneuploidies considerably. In the future, broad NIPT may become possible and affordable. This article will briefly address the ethical issues raised by these technological developments. First, a safe NIPT may lead to routinisation and as such challenge the central issue of informed consent and the aim of prenatal screening: to offer opportunity for autonomous reproductive choice. Widening the scope of prenatal screening also raises the question to what extent 'reproductive autonomy' is meant to expand. Finally, if the same test is used for two different aims, namely detection of foetal anomalies and pregnancy-related problems, non-directive counselling can no longer be taken as a standard. Our broad outline of the ethical issues is meant as an introduction into the more detailed ethical discussions about prenatal screening in the other articles of this special issue. © 2014 John Wiley & Sons Ltd.

Patient Navigation for Colonoscopy Completion: Results of an RCT.

PubMed

DeGroff, Amy; Schroy, Paul C; Morrissey, Kerry Grace; Slotman, Beth; Rohan, Elizabeth A; Bethel, James; Murillo, Jennifer; Ren, Weijia; Niwa, Shelley; Leadbetter, Steven; Joseph, Djenaba

2017-09-01

Colorectal cancer is a leading cause of cancer-related death in the U.S. Although screening reduces colorectal cancer incidence and mortality, screening rates among U.S. adults remain less than optimal, especially among disadvantaged populations. This study examined the efficacy of patient navigation to increase colonoscopy screening. RCT. A total of 843 low-income adults, primarily Hispanic and non-Hispanic blacks, aged 50-75 years referred for colonoscopy at Boston Medical Center were randomized into the intervention (n=429) or control (n=427) groups. Participants were enrolled between September 2012 and December 2014, with analysis following through 2015. Two bilingual lay navigators provided individualized education and support to reduce patient barriers and facilitate colonoscopy completion. The intervention was delivered largely by telephone. Colonoscopy completion within 6 months of study enrollment. Colonoscopy completion was significantly higher for navigated patients (61.1%) than control group patients receiving usual care (53.2%, p=0.021). Based on regression analysis, the odds of completing a colonoscopy for navigated patients was one and a half times greater than for controls (95% CI=1.12, 2.03, p=0.007). There were no differences between navigated and control groups in regard to adequacy of bowel preparation (95.3% vs 97.3%, respectively). Navigation significantly improved colonoscopy screening completion among a racially diverse, low-income population. Results contribute to mounting evidence demonstrating the efficacy of patient navigation in increasing colorectal cancer screening. Screening can be further enhanced when navigation is combined with other evidence-based practices implemented in healthcare systems and the community. Copyright © 2017. Published by Elsevier Inc.

Phoenito experiments: combining the strengths of commercial crystallization automation.

PubMed

Newman, Janet; Pham, Tam M; Peat, Thomas S

2008-11-01

The use of crystallization robots for initial screening in macromolecular crystallization is well established. This paper describes how four general optimization techniques, growth-rate modulation, fine screening, seeding and additive screening, have been adapted for automation in a medium-throughput crystallization service facility. The use of automation for more challenging optimization experiments is discussed, as is a novel way of using both the Mosquito and the Phoenix nano-dispensing robots during the setup of a single crystallization plate. This dual-dispenser technique plays to the strengths of both machines.

Phoenito experiments: combining the strengths of commercial crystallization automation

PubMed Central

Newman, Janet; Pham, Tam M.; Peat, Thomas S.

2008-01-01

The use of crystallization robots for initial screening in macromolecular crystallization is well established. This paper describes how four general optimization techniques, growth-rate modulation, fine screening, seeding and additive screening, have been adapted for automation in a medium-throughput crystallization service facility. The use of automation for more challenging optimization experiments is discussed, as is a novel way of using both the Mosquito and the Phoenix nano-dispensing robots during the setup of a single crystallization plate. This dual-dispenser technique plays to the strengths of both machines. PMID:18997323

High-Throughput Screening of Na(V)1.7 Modulators Using a Giga-Seal Automated Patch Clamp Instrument.

PubMed

Chambers, Chris; Witton, Ian; Adams, Cathryn; Marrington, Luke; Kammonen, Juha

2016-03-01

Voltage-gated sodium (Na(V)) channels have an essential role in the initiation and propagation of action potentials in excitable cells, such as neurons. Of these channels, Na(V)1.7 has been indicated as a key channel for pain sensation. While extensive efforts have gone into discovering novel Na(V)1.7 modulating compounds for the treatment of pain, none has reached the market yet. In the last two years, new compound screening technologies have been introduced, which may speed up the discovery of such compounds. The Sophion Qube(®) is a next-generation 384-well giga-seal automated patch clamp (APC) screening instrument, capable of testing thousands of compounds per day. By combining high-throughput screening and follow-up compound testing on the same APC platform, it should be possible to accelerate the hit-to-lead stage of ion channel drug discovery and help identify the most interesting compounds faster. Following a period of instrument beta-testing, a Na(V)1.7 high-throughput screen was run with two Pfizer plate-based compound subsets. In total, data were generated for 158,000 compounds at a median success rate of 83%, which can be considered high in APC screening. In parallel, IC50 assay validation and protocol optimization was completed with a set of reference compounds to understand how the IC50 potencies generated on the Qube correlate with data generated on the more established Sophion QPatch(®) APC platform. In summary, the results presented here demonstrate that the Qube provides a comparable but much faster approach to study Na(V)1.7 in a robust and reliable APC assay for compound screening.

Discovery of orally efficacious RORγt inverse agonists, part 1: Identification of novel phenylglycinamides as lead scaffolds.

PubMed

Shirai, Junya; Tomata, Yoshihide; Kono, Mitsunori; Ochida, Atsuko; Fukase, Yoshiyuki; Sato, Ayumu; Masada, Shinichi; Kawamoto, Tetsuji; Yonemori, Kazuko; Koyama, Ryoukichi; Nakagawa, Hideyuki; Nakayama, Masaharu; Uga, Keiko; Shibata, Akira; Koga, Keiko; Okui, Toshitake; Shirasaki, Mikio; Skene, Robert; Sang, BiChing; Hoffman, Isaac; Lane, Wes; Fujitani, Yasushi; Yamasaki, Masashi; Yamamoto, Satoshi

2018-01-15

A series of novel phenylglycinamides as retinoic acid receptor-related orphan receptor-gamma t (RORγt) inverse agonists were discovered through optimization of a high-throughput screen hit 1. (R)-N-(2-((3,5-Difluoro-4-(trimethylsilyl)phenyl) amino)-1-(4-methoxyphenyl)-2-oxoethyl)-3-hydroxy-N-methylisoxazole-5-carboxamide (22) was identified as one of the best of these compounds. It displayed higher subtype selectivity and specificity over other nuclear receptors and demonstrated in vivo potency to suppress the transcriptional activity of RORγt in a mouse PD (pharmacodynamic) model upon oral administration. Copyright © 2017 Elsevier Ltd. All rights reserved.

Economic Analysis of Screening Strategies for Rupture of Silicone Gel Breast Implants

PubMed Central

Chung, Kevin C.; Malay, Sunitha; Shauver, Melissa J.; Kim, H. Myra

2012-01-01

Background In 2006, the U.S. Food and Drug Administration (FDA) recommended screening of all women with silicone gel breast implants with magnetic resonance imaging (MRI) three years after implantation and every two years thereafter to assess their integrity. The cost for these serial examinations over the lifetime of the breast implants is an added burden to insurance payers and to women. We perform an economic analysis to determine the most optimal screening strategies by considering the diagnostic accuracy of the screening tests, the costs of the tests and subsequent implant removal. Methods We determined aggregate/pooled values for sensitivity and specificity of the screening tests ultrasound (US) and MRI in detecting silicone breast implant ruptures from the data obtained from published literature. We compiled costs, based on Medicare reimbursements for 2011, for the following elements: imaging modalities, anesthesia and 3 surgical treatment options for detected ruptures. We used decision tree to compare three alternate screening strategies of US only, MRI only and US followed by MRI in asymptomatic and symptomatic women. Results The cost per rupture of screening and management of rupture with US in asymptomatic women was $1,090, whereas in symptomatic women it was $1,622. Similar cost for MRI in asymptomatic women was $2,067, whereas in symptomatic women it was $2,143. Similar cost for US followed by MRI in asymptomatic women was $637, whereas in symptomatic women it was $2,908. Conclusion Screening with US followed by MRI was optimal for asymptomatic women and screening with US was optimal for symptomatic women. PMID:22743887

Neighborhood Screening in Communities Throughout the Nation for Children with Elevated Blood Lead Levels

PubMed Central

Anderson, Dudley G.; Clark, John L.

1974-01-01

From the spring of 1971 to September 1973, neighborhood surveys were conducted in 58 communities throughout the nation to determine whether children with confirmed elevated blood lead levels could be identified. Another purpose of these screenings was to assist communities in identifying children with elevated blood lead levels and thereby demonstrate to community officials that such children do exist in communities screened. The children screened were not a random sample. In those communities where the initial elevated blood levels were confirmed all but seven had one or more children requiring followup and/or treatment. Of those children screened, black children had an elevated rate about three times as great as nonblack children. With few exceptions, the homes in the neighborhoods had at least one interior surface with sufficient quantities of lead paint to be dangerous if the paint were ingested. PMID:4831146

Discovery and safety profiling of a potent preclinical candidate, (4-[4-[[(3R)-3-(hydroxycarbamoyl)-8-azaspiro[4.5]decan-3-yl]sulfonyl]phenoxy]-N-methylbenzamide) (CM-352), for the prevention and treatment of hemorrhage.

PubMed

Orbe, Josune; Rodríguez, José A; Sánchez-Arias, Juan A; Salicio, Agustina; Belzunce, Miriam; Ugarte, Ana; Chang, Haisul C Y; Rabal, Obdulia; Oyarzabal, Julen; Páramo, José A

2015-04-09

Discovery of potent and safe therapeutics that improve upon currently available antifibrinolytics, e.g., tranexamic acid (TXA, 1) and aprotinin, has been challenging. Matrix metalloproteinases (MMPs) participate in thrombus dissolution. Then we designed a novel series of optimized MMP inhibitors that went through phenotypic screening consisting of thromboelastometry and mouse tail bleeding. Our optimized lead compound, CM-352 (2), inhibited fibrinolysis in human whole blood functional assays and was more effective than the current standard of care, 1, in the tail-bleeding model using a 30 000 times lower dose. Moreover, 2 reduced blood loss during liver hepatectomy, while 1 and aprotinin had no effect. Molecule 2 displayed optimal pharmacokinetic and safety profiles with no evidence of thrombosis or coagulation impairment. This novel mechanism of action, targeting MMP, defines a new class of antihemorrhagic agents without interfering with normal hemostatic function. Furthermore, 2 represents a preclinical candidate for the acute treatment of bleeding.

Disease modeling and drug screening for neurological diseases using human induced pluripotent stem cells.

PubMed

Xu, Xiao-hong; Zhong, Zhong

2013-06-01

With the general decline of pharmaceutical research productivity, there are concerns that many components of the drug discovery process need to be redesigned and optimized. For example, the human immortalized cell lines or animal primary cells commonly used in traditional drug screening may not faithfully recapitulate the pathological mechanisms of human diseases, leading to biases in assays, targets, or compounds that do not effectively address disease mechanisms. Recent advances in stem cell research, especially in the development of induced pluripotent stem cell (iPSC) technology, provide a new paradigm for drug screening by permitting the use of human cells with the same genetic makeup as the patients without the typical quantity constraints associated with patient primary cells. In this article, we will review the progress made to date on cellular disease models using human stem cells, with a focus on patient-specific iPSCs for neurological diseases. We will discuss the key challenges and the factors that associated with the success of using stem cell models for drug discovery through examples from monogenic diseases, diseases with various known genetic components, and complex diseases caused by a combination of genetic, environmental and other factors.

The development of an inherent safety approach to the prevention of domino accidents.

PubMed

Cozzani, Valerio; Tugnoli, Alessandro; Salzano, Ernesto

2009-11-01

The severity of industrial accidents in which a domino effect takes place is well known in the chemical and process industry. The application of an inherent safety approach for the prevention of escalation events leading to domino accidents was explored in the present study. Reference primary scenarios were analyzed and escalation vectors were defined. Inherent safety distances were defined and proposed as a metric to express the intensity of the escalation vectors. Simple rules of thumb were presented for a preliminary screening of these distances. Swift reference indices for layout screening with respect to escalation hazard were also defined. Two case studies derived from existing layouts of oil refineries were selected to understand the potentialities coming from the application in the methodology. The results evidenced that the approach allows a first comparative assessment of the actual domino hazard in a layout, and the identification of critical primary units with respect to escalation events. The methodology developed also represents a useful screening tool to identify were to dedicate major efforts in the design of add-on measures, optimizing conventional passive and active measures for the prevention of severe domino accidents.

CamMedNP: building the Cameroonian 3D structural natural products database for virtual screening.

PubMed

Ntie-Kang, Fidele; Mbah, James A; Mbaze, Luc Meva'a; Lifongo, Lydia L; Scharfe, Michael; Hanna, Joelle Ngo; Cho-Ngwa, Fidelis; Onguéné, Pascal Amoa; Owono Owono, Luc C; Megnassan, Eugene; Sippl, Wolfgang; Efange, Simon M N

2013-04-16

Computer-aided drug design (CADD) often involves virtual screening (VS) of large compound datasets and the availability of such is vital for drug discovery protocols. We present CamMedNP - a new database beginning with more than 2,500 compounds of natural origin, along with some of their derivatives which were obtained through hemisynthesis. These are pure compounds which have been previously isolated and characterized using modern spectroscopic methods and published by several research teams spread across Cameroon. In the present study, 224 distinct medicinal plant species belonging to 55 plant families from the Cameroonian flora have been considered. About 80 % of these have been previously published and/or referenced in internationally recognized journals. For each compound, the optimized 3D structure, drug-like properties, plant source, collection site and currently known biological activities are given, as well as literature references. We have evaluated the "drug-likeness" of this database using Lipinski's "Rule of Five". A diversity analysis has been carried out in comparison with the ChemBridge diverse database. CamMedNP could be highly useful for database screening and natural product lead generation programs.

Cultural, economic, and psychological predictors of colonoscopy in a national sample.

PubMed

Halbert, Chanita Hughes; Barg, Frances K; Guerra, Carmen E; Shea, Judy A; Armstrong, Katrina; Ferguson, Monica; Weathers, Benita; Coyne, James; Troxel, Andrea B

2011-11-01

Although colorectal cancer (CRC) is the second leading cause of cancer death among adults in the US and colonoscopy is efficacious in reducing morbidity and mortality from CRC, screening rates are sub-optimal. Understanding the socioeconomic, cultural, and health care context within which decisions about colonoscopy are made allows physicians to address patients' most salient beliefs and values and other constraints when making screening recommendations. To evaluate the direct and interactive effects of socioeconomics, health care variables, psychological characteristics, and cultural values on colonoscopy use. National survey completed between January-August 2009 in a random sample of African American, white, and Hispanic adults ages 50-75 without cancer (n = 582). Self-reported colonoscopy use. Only 59% of respondents reported having a colonoscopy. The likelihood of colonoscopy increased with having health insurance (OR = 2.82, 95% CI = 1.24, 6.43, p = 0.004), and increasing age (OR = 1.40, 95% CI = 1.11, 1.77, p = 0.001). In addition, respondents with greater self-efficacy were more likely to have a colonoscopy (OR = 2.41, 95% CI = 1.35, 4.29, p = 0.003). Programs that help patients to overcome access and psychological barriers to screening are needed.

West Nile Virus Drug Discovery

PubMed Central

Lim, Siew Pheng; Shi, Pei-Yong

2013-01-01

The outbreak of West Nile virus (WNV) in 1999 in the USA, and its continued spread throughout the Americas, parts of Europe, the Middle East and Africa, underscored the need for WNV antiviral development. Here, we review the current status of WNV drug discovery. A number of approaches have been used to search for inhibitors of WNV, including viral infection-based screening, enzyme-based screening, structure-based virtual screening, structure-based rationale design, and antibody-based therapy. These efforts have yielded inhibitors of viral or cellular factors that are critical for viral replication. For small molecule inhibitors, no promising preclinical candidate has been developed; most of the inhibitors could not even be advanced to the stage of hit-to-lead optimization due to their poor drug-like properties. However, several inhibitors developed for related members of the family Flaviviridae, such as dengue virus and hepatitis C virus, exhibited cross-inhibition of WNV, suggesting the possibility to re-purpose these antivirals for WNV treatment. Most promisingly, therapeutic antibodies have shown excellent efficacy in mouse model; one of such antibodies has been advanced into clinical trial. The knowledge accumulated during the past fifteen years has provided better rationale for the ongoing WNV and other flavivirus antiviral development. PMID:24300672

West Nile virus drug discovery.

PubMed

Lim, Siew Pheng; Shi, Pei-Yong

2013-12-03

The outbreak of West Nile virus (WNV) in 1999 in the USA, and its continued spread throughout the Americas, parts of Europe, the Middle East and Africa, underscored the need for WNV antiviral development. Here, we review the current status of WNV drug discovery. A number of approaches have been used to search for inhibitors of WNV, including viral infection-based screening, enzyme-based screening, structure-based virtual screening, structure-based rationale design, and antibody-based therapy. These efforts have yielded inhibitors of viral or cellular factors that are critical for viral replication. For small molecule inhibitors, no promising preclinical candidate has been developed; most of the inhibitors could not even be advanced to the stage of hit-to-lead optimization due to their poor drug-like properties. However, several inhibitors developed for related members of the family Flaviviridae, such as dengue virus and hepatitis C virus, exhibited cross-inhibition of WNV, suggesting the possibility to re-purpose these antivirals for WNV treatment. Most promisingly, therapeutic antibodies have shown excellent efficacy in mouse model; one of such antibodies has been advanced into clinical trial. The knowledge accumulated during the past fifteen years has provided better rationale for the ongoing WNV and other flavivirus antiviral development.

Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins

PubMed Central

Li, Liang; Mustafi, Debarshi; Fu, Qiang; Tereshko, Valentina; Chen, Delai L.; Tice, Joshua D.; Ismagilov, Rustem F.

2006-01-01

High-throughput screening and optimization experiments are critical to a number of fields, including chemistry and structural and molecular biology. The separation of these two steps may introduce false negatives and a time delay between initial screening and subsequent optimization. Although a hybrid method combining both steps may address these problems, miniaturization is required to minimize sample consumption. This article reports a “hybrid” droplet-based microfluidic approach that combines the steps of screening and optimization into one simple experiment and uses nanoliter-sized plugs to minimize sample consumption. Many distinct reagents were sequentially introduced as ≈140-nl plugs into a microfluidic device and combined with a substrate and a diluting buffer. Tests were conducted in ≈10-nl plugs containing different concentrations of a reagent. Methods were developed to form plugs of controlled concentrations, index concentrations, and incubate thousands of plugs inexpensively and without evaporation. To validate the hybrid method and demonstrate its applicability to challenging problems, crystallization of model membrane proteins and handling of solutions of detergents and viscous precipitants were demonstrated. By using 10 μl of protein solution, ≈1,300 crystallization trials were set up within 20 min by one researcher. This method was compatible with growth, manipulation, and extraction of high-quality crystals of membrane proteins, demonstrated by obtaining high-resolution diffraction images and solving a crystal structure. This robust method requires inexpensive equipment and supplies, should be especially suitable for use in individual laboratories, and could find applications in a number of areas that require chemical, biochemical, and biological screening and optimization. PMID:17159147

Improved Participation for Blood Lead Screening with In-Home Phlebotomy

ERIC Educational Resources Information Center

Dowling, Kathryn C.; Miranda, Veronica; Galaviz, Vanessa E.

2008-01-01

Both nationally and within the State of California, it is unlikely that those children most susceptible to lead exposure are adequately screened for blood lead levels. New and creative approaches are necessary to reach these individuals. In-home phlebotomy was employed to test blood lead levels of 128 San Diego households containing Latino…

In silico-designed novel non-peptidic ABAD LD hot spot mimetics reverse Aβ-induced mitochondrial impairments in vitro.

PubMed

Viswanath, Ambily Nath Indu; Kim, TaeHun; Jung, Seo Yun; Lim, Sang Min; Pae, Ae Nim

2017-12-01

Present work aimed to introduce non-peptidic ABAD loop D (L D ) hot spot mimetics as ABAD-Aβ inhibitors. A full-length atomistic model of ABAD-Aβ complex was built as a scaffold to launch the lead design and its topology later verified by cross-checking the computational mutagenesis results with that of in vitro data. Thereafter, the interactions of prime Aβ-binding L D residues-Tyr101, Thr108, and Thr110-were translated into specific pharmacophore features and this hypothesis subsequently used as a virtual screen query. ELISA-based screening of 20 hits identified two promising lead candidates, VC15 and VC19 with an IC 50 of 4.4 ± 0.3 and 9.6 ± 0.1 μm, respectively. They productively reversed Aβ-induced mitochondrial dysfunctions such as mitochondrial membrane potential loss (JC-1 assay), toxicity (MTT assay), and ATP reduction (ATP assay) in addition to increased cell viabilities. This is the first reporting of L D hot spot-centric in silico scheme to discover novel compounds with promising ABAD-Aβ inhibitory potential. These chemotypes are proposed for further structural optimization to derive novel Alzheimer's disease (AD) therapeutics. © 2017 John Wiley & Sons A/S.

Changes in Blood Lead Levels Associated with Use of Chloramines in Water Treatment Systems

PubMed Central

Miranda, Marie Lynn; Kim, Dohyeong; Hull, Andrew P.; Paul, Christopher J.; Galeano, M. Alicia Overstreet

2007-01-01

Background More municipal water treatment plants are using chloramines as a disinfectant in order to reduce carcinogenic by-products. In some instances, this has coincided with an increase in lead levels in drinking water in those systems. Lead in drinking water can be a significant health risk. Objectives We sought to test the potential effect of switching to chloramines for disinfection in water treatment systems on childhood blood lead levels using data from Wayne County, located in the central Coastal Plain of North Carolina. Methods We constructed a unified geographic information system (GIS) that links blood lead screening data with age of housing, drinking water source, and census data for 7,270 records. The data were analyzed using both exploratory methods and more formal multivariate techniques. Results The analysis indicates that the change to chloramine disinfection may lead to an increase in blood lead levels, the impact of which is progressively mitigated in newer housing. Conclusions Introducing chloramines to reduce carcinogenic by-products may increase exposure to lead in drinking water. Our research provides guidance on adjustments in the local childhood lead poisoning prevention program that should accompany changes in water treatment. As similar research is conducted in other areas, and the underlying environmental chemistry is clarified, water treatment strategies can be optimized across the multiple objectives that municipalities face in providing high quality drinking water to local residents. PMID:17384768

A systematic review of screening questionnaires for childhood lead poisoning.

PubMed

Ossiander, Eric M

2013-01-01

The Centers for Disease Control and Prevention encourages the use of risk factor questionnaires to screen children for lead poisoning. A majority of state health departments have formal lead screening guidelines that recommend health care providers use questionnaires. We conducted a systematic review to evaluate the ability of lead screening questionnaires to predict lead poisoning risk among children. Articles that reported the evaluation of a predesigned lead screening questionnaire were obtained by searching Medline/PubMed and by examining references of articles obtained through the online search. From each evaluation, we abstracted the number of children that were true positive, false positive, true negative, and false negative, according to the results of the screening questionnaire and the follow-up blood lead test. From these data, we calculated specificity and sensitivity of the questionnaire for each evaluation. Twenty articles met the inclusion criteria: these included 28 separate questionnaire evaluations. Among 17 evaluations of the 1991 Centers for Disease Control and Prevention questionnaire, sensitivity ranged from 0.25 to 0.87, specificity from 0.31 to 0.80, and accuracy (sum of sensitivity and specificity) from 0.74 to 1.39. The pooled mean estimates for this questionnaire were sensitivity 0.61 (95% confidence interval: 0.53-0.68); specificity 0.52 (0.45-0.60); accuracy 1.12 (1.06-1.18). Among 11 evaluations of all other questionnaires, sensitivity ranged from 0.43 to 0.90, specificity from 0.17 to 0.66, and accuracy from 0.94 to 1.27. For these questionnaires, the pooled mean estimates were sensitivity 0.76 (0.68-0.85), specificity 0.41 (0.33-0.49), and accuracy 1.12 (1.06-1.18). Lead screening questionnaires showed a wide range of sensitivity and specificity and performed little better than chance at predicting lead poisoning risk among children.

Optimal screening and donor management in a public stool bank.

PubMed

Kazerouni, Abbas; Burgess, James; Burns, Laura J; Wein, Lawrence M

2015-12-17

Fecal microbiota transplantation is an effective treatment for recurrent Clostridium difficile infection and is being investigated as a treatment for other microbiota-associated diseases. To facilitate these activities, an international public stool bank has been created, which screens donors and processes stools in a standardized manner. The goal of this research is to use mathematical modeling and analysis to optimize screening and donor management at the stool bank. Compared to the current policy of screening active donors every 60 days before releasing their quarantined stools for sale, costs can be reduced by 10.3 % by increasing the screening frequency to every 36 days. In addition, the stool production rate varies widely across donors, and using donor-specific screening, where higher producers are screened more frequently, also reduces costs, as does introducing an interim (i.e., between consecutive regular tests) stool test for just rotavirus and C. difficile. We also derive a donor release (i.e., into the system) policy that allows the supply to approximately match an exponentially increasing deterministic demand. More frequent screening, interim screening for rotavirus and C. difficile, and donor-specific screening, where higher stool producers are screened more frequently, are all cost-reducing measures. If screening costs decrease in the future (e.g., as a result of bringing screening in house), a bottleneck for implementing some of these recommendations may be the reluctance of donors to undergo serum screening more frequently than monthly.

Optimal control problems of epidemic systems with parameter uncertainties: application to a malaria two-age-classes transmission model with asymptomatic carriers.

PubMed

Mwanga, Gasper G; Haario, Heikki; Capasso, Vicenzo

2015-03-01

The main scope of this paper is to study the optimal control practices of malaria, by discussing the implementation of a catalog of optimal control strategies in presence of parameter uncertainties, which is typical of infectious diseases data. In this study we focus on a deterministic mathematical model for the transmission of malaria, including in particular asymptomatic carriers and two age classes in the human population. A partial qualitative analysis of the relevant ODE system has been carried out, leading to a realistic threshold parameter. For the deterministic model under consideration, four possible control strategies have been analyzed: the use of Long-lasting treated mosquito nets, indoor residual spraying, screening and treatment of symptomatic and asymptomatic individuals. The numerical results show that using optimal control the disease can be brought to a stable disease free equilibrium when all four controls are used. The Incremental Cost-Effectiveness Ratio (ICER) for all possible combinations of the disease-control measures is determined. The numerical simulations of the optimal control in the presence of parameter uncertainty demonstrate the robustness of the optimal control: the main conclusions of the optimal control remain unchanged, even if inevitable variability remains in the control profiles. The results provide a promising framework for the designing of cost-effective strategies for disease controls with multiple interventions, even under considerable uncertainty of model parameters. Copyright © 2014 Elsevier Inc. All rights reserved.

Biomarker evidence of tobacco smoke exposure in children participating in lead screening.

PubMed

Joseph, Anne; Spector, Logan; Wickham, Katherine; Janis, Gregory; Winickoff, Jonathan; Lindgren, Bruce; Murphy, Sharon

2013-12-01

We assessed tobacco smoke exposure (TSE), defined according to detection of cotinine, in dried blood spots collected from children for lead screening. Dried blood spots collected from a national sample of 1541 Black and White children and submitted to a commercial laboratory for lead analysis were analyzed for cotinine. We used an anonymous administrative data set including information on children's characteristics to conduct univariate and multivariate analyses. Cotinine was detected in 61% of dried blood spots; 17% of samples had cotinine levels above 3 nanograms per gram. Median cotinine levels were significantly higher among Black than White children (0.66 ng/g vs 0.30 ng/g) and among Medicaid recipients (0.94 ng/g vs < 0.3 ng/g). In multivariate analyses, significant increases in cotinine levels were associated with Black (vs White) race, older age, Medicaid coverage, higher state smoking rate, and higher average winter temperature. Detectable cotinine levels were significantly associated with higher lead levels. TSE is highly prevalent among children undergoing lead screening, and exposure levels are greater among Black children and children on Medicaid. TSE may contribute to lead exposure. Concurrent lead screening and biological screening for TSE may be a feasible approach to increasing childhood TSE detection.

Web-based newborn screening system for metabolic diseases: machine learning versus clinicians.

PubMed

Chen, Wei-Hsin; Hsieh, Sheau-Ling; Hsu, Kai-Ping; Chen, Han-Ping; Su, Xing-Yu; Tseng, Yi-Ju; Chien, Yin-Hsiu; Hwu, Wuh-Liang; Lai, Feipei

2013-05-23

A hospital information system (HIS) that integrates screening data and interpretation of the data is routinely requested by hospitals and parents. However, the accuracy of disease classification may be low because of the disease characteristics and the analytes used for classification. The objective of this study is to describe a system that enhanced the neonatal screening system of the Newborn Screening Center at the National Taiwan University Hospital. The system was designed and deployed according to a service-oriented architecture (SOA) framework under the Web services .NET environment. The system consists of sample collection, testing, diagnosis, evaluation, treatment, and follow-up services among collaborating hospitals. To improve the accuracy of newborn screening, machine learning and optimal feature selection mechanisms were investigated for screening newborns for inborn errors of metabolism. The framework of the Newborn Screening Hospital Information System (NSHIS) used the embedded Health Level Seven (HL7) standards for data exchanges among heterogeneous platforms integrated by Web services in the C# language. In this study, machine learning classification was used to predict phenylketonuria (PKU), hypermethioninemia, and 3-methylcrotonyl-CoA-carboxylase (3-MCC) deficiency. The classification methods used 347,312 newborn dried blood samples collected at the Center between 2006 and 2011. Of these, 220 newborns had values over the diagnostic cutoffs (positive cases) and 1557 had values that were over the screening cutoffs but did not meet the diagnostic cutoffs (suspected cases). The original 35 analytes and the manifested features were ranked based on F score, then combinations of the top 20 ranked features were selected as input features to support vector machine (SVM) classifiers to obtain optimal feature sets. These feature sets were tested using 5-fold cross-validation and optimal models were generated. The datasets collected in year 2011 were used as predicting cases. The feature selection strategies were implemented and the optimal markers for PKU, hypermethioninemia, and 3-MCC deficiency were obtained. The results of the machine learning approach were compared with the cutoff scheme. The number of the false positive cases were reduced from 21 to 2 for PKU, from 30 to 10 for hypermethioninemia, and 209 to 46 for 3-MCC deficiency. This SOA Web service-based newborn screening system can accelerate screening procedures effectively and efficiently. An SVM learning methodology for PKU, hypermethioninemia, and 3-MCC deficiency metabolic diseases classification, including optimal feature selection strategies, is presented. By adopting the results of this study, the number of suspected cases could be reduced dramatically.

Web-Based Newborn Screening System for Metabolic Diseases: Machine Learning Versus Clinicians

PubMed Central

Chen, Wei-Hsin; Hsu, Kai-Ping; Chen, Han-Ping; Su, Xing-Yu; Tseng, Yi-Ju; Chien, Yin-Hsiu; Hwu, Wuh-Liang; Lai, Feipei

2013-01-01

Background A hospital information system (HIS) that integrates screening data and interpretation of the data is routinely requested by hospitals and parents. However, the accuracy of disease classification may be low because of the disease characteristics and the analytes used for classification. Objective The objective of this study is to describe a system that enhanced the neonatal screening system of the Newborn Screening Center at the National Taiwan University Hospital. The system was designed and deployed according to a service-oriented architecture (SOA) framework under the Web services .NET environment. The system consists of sample collection, testing, diagnosis, evaluation, treatment, and follow-up services among collaborating hospitals. To improve the accuracy of newborn screening, machine learning and optimal feature selection mechanisms were investigated for screening newborns for inborn errors of metabolism. Methods The framework of the Newborn Screening Hospital Information System (NSHIS) used the embedded Health Level Seven (HL7) standards for data exchanges among heterogeneous platforms integrated by Web services in the C# language. In this study, machine learning classification was used to predict phenylketonuria (PKU), hypermethioninemia, and 3-methylcrotonyl-CoA-carboxylase (3-MCC) deficiency. The classification methods used 347,312 newborn dried blood samples collected at the Center between 2006 and 2011. Of these, 220 newborns had values over the diagnostic cutoffs (positive cases) and 1557 had values that were over the screening cutoffs but did not meet the diagnostic cutoffs (suspected cases). The original 35 analytes and the manifested features were ranked based on F score, then combinations of the top 20 ranked features were selected as input features to support vector machine (SVM) classifiers to obtain optimal feature sets. These feature sets were tested using 5-fold cross-validation and optimal models were generated. The datasets collected in year 2011 were used as predicting cases. Results The feature selection strategies were implemented and the optimal markers for PKU, hypermethioninemia, and 3-MCC deficiency were obtained. The results of the machine learning approach were compared with the cutoff scheme. The number of the false positive cases were reduced from 21 to 2 for PKU, from 30 to 10 for hypermethioninemia, and 209 to 46 for 3-MCC deficiency. Conclusions This SOA Web service–based newborn screening system can accelerate screening procedures effectively and efficiently. An SVM learning methodology for PKU, hypermethioninemia, and 3-MCC deficiency metabolic diseases classification, including optimal feature selection strategies, is presented. By adopting the results of this study, the number of suspected cases could be reduced dramatically. PMID:23702487

Prospective evaluation of cinefluoroscopy and chest radiography for Riata lead defects: implications for future lead screening.

PubMed

Lorvidhaya, Peem; Mendoza, Ivan; Sehli, Sharmila; Atalay, Michael K; Kim, Michael H

2013-11-01

Lead insulation defects with externalization of the conductors exist in Riata defibrillator leads. Cinefluoroscopy is currently the gold standard to detect such defects. Prospective evaluation of alternative screening options such as chest radiography (CXR), which has been recommended by the FDA, is not well described. Patients with Riata leads underwent cinefluoroscopy, CXR, and device interrogation. Leads were classified as abnormal (clear cable separation), borderline, or normal by independent evaluation of cinefluoroscopy and CXR. CXR evaluation was done in two ways as follows: (1) routine CXR read by daily staff radiologists for lead screening and (2) CXR evaluation by a radiologist educated about the lead defect. One hundred two patients were evaluated at our institution. Cinefluoroscopy showed externalized conductors in 33 patients (32 %). Twenty-five of 33 patients (76 %) who had abnormal cinefluoroscopic findings had abnormal CXR findings on blinded review by the educated radiologist. All 25 patients with abnormal CXR had abnormal findings on cinefluoroscopy. Daily staff radiologists without direct education other than prompts for lead screening detected CXR abnormalities in only 8 out of 102 (8 %) cases. Cinefluoroscopy appears to be more sensitive than CXR for the detection of Riata cable extrusion. Interpretation of CXR by a radiologist with education in lead defects correlates highly with cinefluoroscopy with very high specificity. Depending on available resources for screening, CXR may be a reasonable alternative to cinefluoroscopy. Multidisciplinary collaboration across specialties (radiology and electrophysiology) can lead to improved diagnostic capability and thus the potential for enhanced quality of care.

Design Principles for Fragment Libraries: Maximizing the Value of Learnings from Pharma Fragment-Based Drug Discovery (FBDD) Programs for Use in Academia.

PubMed

Keserű, György M; Erlanson, Daniel A; Ferenczy, György G; Hann, Michael M; Murray, Christopher W; Pickett, Stephen D

2016-09-22

Fragment-based drug discovery (FBDD) is well suited for discovering both drug leads and chemical probes of protein function; it can cover broad swaths of chemical space and allows the use of creative chemistry. FBDD is widely implemented for lead discovery in industry but is sometimes used less systematically in academia. Design principles and implementation approaches for fragment libraries are continually evolving, and the lack of up-to-date guidance may prevent more effective application of FBDD in academia. This Perspective explores many of the theoretical, practical, and strategic considerations that occur within FBDD programs, including the optimal size, complexity, physicochemical profile, and shape profile of fragments in FBDD libraries, as well as compound storage, evaluation, and screening technologies. This compilation of industry experience in FBDD will hopefully be useful for those pursuing FBDD in academia.

Machine-Learning Techniques Applied to Antibacterial Drug Discovery

PubMed Central

Durrant, Jacob D.; Amaro, Rommie E.

2014-01-01

The emergence of drug-resistant bacteria threatens to catapult humanity back to the pre-antibiotic era. Even now, multi-drug-resistant bacterial infections annually result in millions of hospital days, billions in healthcare costs, and, most importantly, tens of thousands of lives lost. As many pharmaceutical companies have abandoned antibiotic development in search of more lucrative therapeutics, academic researchers are uniquely positioned to fill the resulting vacuum. Traditional high-throughput screens and lead-optimization efforts are expensive and labor intensive. Computer-aided drug discovery techniques, which are cheaper and faster, can accelerate the identification of novel antibiotics in an academic setting, leading to improved hit rates and faster transitions to pre-clinical and clinical testing. The current review describes two machine-learning techniques, neural networks and decision trees, that have been used to identify experimentally validated antibiotics. We conclude by describing the future directions of this exciting field. PMID:25521642

Discovery of potent and selective rhodanine type IKKβ inhibitors by hit-to-lead strategy.

PubMed

Song, Hyeseung; Lee, Yun Suk; Roh, Eun Joo; Seo, Jae Hong; Oh, Kwang-Seok; Lee, Byung Ho; Han, Hogyu; Shin, Kye Jung

2012-09-01

Regulation of NF-κB activation through the inhibition of IKKβ has been identified as a promising target for the treatment of inflammatory and autoimmune disease such as rheumatoid arthritis. In order to develop novel IKKβ inhibitors, we performed high throughput screening toward around 8000 library compounds, and identified a hit compound containing rhodanine moiety. We modified the structure of hit compound to obtain potent and selective IKKβ inhibitors. Throughout hit-to-lead studies, we have discovered optimized compounds which possess blocking effect toward NF-κB activation and TNFα production in cell as well as inhibition activity against IKKβ. Among them, compound 3q showed the potent inhibitory activity against IKKβ, and excellent selectivity over other kinases such as p38α, p38β, JNK1, JNK2, and JNK3 as well as IKKα. Copyright © 2012 Elsevier Ltd. All rights reserved.

Fluorescence lifetime assays: current advances and applications in drug discovery.

PubMed

Pritz, Stephan; Doering, Klaus; Woelcke, Julian; Hassiepen, Ulrich

2011-06-01

Fluorescence lifetime assays complement the portfolio of established assay formats available in drug discovery, particularly with the recent advances in microplate readers and the commercial availability of novel fluorescent labels. Fluorescence lifetime assists in lowering complexity of compound screening assays, affording a modular, toolbox-like approach to assay development and yielding robust homogeneous assays. To date, materials and procedures have been reported for biochemical assays on proteases, as well as on protein kinases and phosphatases. This article gives an overview of two assay families, distinguished by the origin of the fluorescence signal modulation. The pharmaceutical industry demands techniques with a robust, integrated compound profiling process and short turnaround times. Fluorescence lifetime assays have already helped the drug discovery field, in this sense, by enhancing productivity during the hit-to-lead and lead optimization phases. Future work will focus on covering other biochemical molecular modifications by investigating the detailed photo-physical mechanisms underlying the fluorescence signal.

Metarrestin, a perinucleolar compartment inhibitor, effectively suppresses metastasis.

PubMed

Frankowski, Kevin J; Wang, Chen; Patnaik, Samarjit; Schoenen, Frank J; Southall, Noel; Li, Dandan; Teper, Yaroslav; Sun, Wei; Kandela, Irawati; Hu, Deqing; Dextras, Christopher; Knotts, Zachary; Bian, Yansong; Norton, John; Titus, Steve; Lewandowska, Marzena A; Wen, Yiping; Farley, Katherine I; Griner, Lesley Mathews; Sultan, Jamey; Meng, Zhaojing; Zhou, Ming; Vilimas, Tomas; Powers, Astin S; Kozlov, Serguei; Nagashima, Kunio; Quadri, Humair S; Fang, Min; Long, Charles; Khanolkar, Ojus; Chen, Warren; Kang, Jinsol; Huang, Helen; Chow, Eric; Goldberg, Esthermanya; Feldman, Coral; Xi, Romi; Kim, Hye Rim; Sahagian, Gary; Baserga, Susan J; Mazar, Andrew; Ferrer, Marc; Zheng, Wei; Shilatifard, Ali; Aubé, Jeffrey; Rudloff, Udo; Marugan, Juan Jose; Huang, Sui

2018-05-16

Metastasis remains a leading cause of cancer mortality due to the lack of specific inhibitors against this complex process. To identify compounds selectively targeting the metastatic state, we used the perinucleolar compartment (PNC), a complex nuclear structure associated with metastatic behaviors of cancer cells, as a phenotypic marker for a high-content screen of over 140,000 structurally diverse compounds. Metarrestin, obtained through optimization of a screening hit, disassembles PNCs in multiple cancer cell lines, inhibits invasion in vitro, suppresses metastatic development in three mouse models of human cancer, and extends survival of mice in a metastatic pancreatic cancer xenograft model with no organ toxicity or discernable adverse effects. Metarrestin disrupts the nucleolar structure and inhibits RNA polymerase (Pol) I transcription, at least in part by interacting with the translation elongation factor eEF1A2. Thus, metarrestin represents a potential therapeutic approach for the treatment of metastatic cancer. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Fragment-based discovery of potent inhibitors of the anti-apoptotic MCL-1 protein.

PubMed

Petros, Andrew M; Swann, Steven L; Song, Danying; Swinger, Kerren; Park, Chang; Zhang, Haichao; Wendt, Michael D; Kunzer, Aaron R; Souers, Andrew J; Sun, Chaohong

2014-03-15

Apoptosis is regulated by the BCL-2 family of proteins, which is comprised of both pro-death and pro-survival members. Evasion of apoptosis is a hallmark of malignant cells. One way in which cancer cells achieve this evasion is thru overexpression of the pro-survival members of the BCL-2 family. Overexpression of MCL-1, a pro-survival protein, has been shown to be a resistance factor for Navitoclax, a potent inhibitor of BCL-2 and BCL-XL. Here we describe the use of fragment screening methods and structural biology to drive the discovery of novel MCL-1 inhibitors from two distinct structural classes. Specifically, cores derived from a biphenyl sulfonamide and salicylic acid were uncovered in an NMR-based fragment screen and elaborated using high throughput analog synthesis. This culminated in the discovery of selective and potent inhibitors of MCL-1 that may serve as promising leads for medicinal chemistry optimization efforts. Copyright © 2014 Elsevier Ltd. All rights reserved.

Promiscuous 2-aminothiazoles (PrATs): a frequent hitting scaffold.

PubMed

Devine, Shane M; Mulcair, Mark D; Debono, Cael O; Leung, Eleanor W W; Nissink, J Willem M; Lim, San Sui; Chandrashekaran, Indu R; Vazirani, Mansha; Mohanty, Biswaranjan; Simpson, Jamie S; Baell, Jonathan B; Scammells, Peter J; Norton, Raymond S; Scanlon, Martin J

2015-02-12

We have identified a class of molecules, known as 2-aminothiazoles (2-ATs), as frequent-hitting fragments in biophysical binding assays. This was exemplified by 4-phenylthiazol-2-amine being identified as a hit in 14/14 screens against a diverse range of protein targets, suggesting that this scaffold is a poor starting point for fragment-based drug discovery. This prompted us to analyze this scaffold in the context of an academic fragment library used for fragment-based drug discovery (FBDD) and two larger compound libraries used for high-throughput screening (HTS). This analysis revealed that such "promiscuous 2-aminothiazoles" (PrATs) behaved as frequent hitters under both FBDD and HTS settings, although the problem was more pronounced in the fragment-based studies. As 2-ATs are present in known drugs, they cannot necessarily be deemed undesirable, but the combination of their promiscuity and difficulties associated with optimizing them into a lead compound makes them, in our opinion, poor scaffolds for fragment libraries.

Aminopyridine-based c-Jun N-terminal kinase inhibitors with cellular activity and minimal cross-kinase activity.

PubMed

Szczepankiewicz, Bruce G; Kosogof, Christi; Nelson, Lissa T J; Liu, Gang; Liu, Bo; Zhao, Hongyu; Serby, Michael D; Xin, Zhili; Liu, Mei; Gum, Rebecca J; Haasch, Deanna L; Wang, Sanyi; Clampit, Jill E; Johnson, Eric F; Lubben, Thomas H; Stashko, Michael A; Olejniczak, Edward T; Sun, Chaohong; Dorwin, Sarah A; Haskins, Kristi; Abad-Zapatero, Cele; Fry, Elizabeth H; Hutchins, Charles W; Sham, Hing L; Rondinone, Cristina M; Trevillyan, James M

2006-06-15

The c-Jun N-terminal kinases (JNK-1, -2, and -3) are members of the mitogen activated protein (MAP) kinase family of enzymes. They are activated in response to certain cytokines, as well as by cellular stresses including chemotoxins, peroxides, and irradiation. They have been implicated in the pathology of a variety of different diseases with an inflammatory component including asthma, stroke, Alzheimer's disease, and type 2 diabetes mellitus. In this work, high-throughput screening identified a JNK inhibitor with an excellent kinase selectivity profile. Using X-ray crystallography and biochemical screening to guide our lead optimization, we prepared compounds with inhibitory potencies in the low-double-digit nanomolar range, activity in whole cells, and pharmacokinetics suitable for in vivo use. The new compounds were over 1,000-fold selective for JNK-1 and -2 over other MAP kinases including ERK2, p38alpha, and p38delta and showed little inhibitory activity against a panel of 74 kinases.

Discovery of Novel Small-molecule Inhibitors of Nuclear Factor-κB Signaling with Anti-inflammatory and Anti-cancer Properties.

PubMed

Zhang, Lei; Shi, Lei; Soars, Shafer; Kamps, Joshua; Yin, Hang Hubert

2018-06-05

Excessive NF-κB activation contributes to the pathogenesis of numerous diseases. Small-molecule inhibitors of NF-κB signaling have significant therapeutic potential especially in treating inflammatory diseases and cancers. In this study, we performed a cell-based high-throughput screening to discover novel agents capable of inhibiting NF-κB signaling. Based on two hit scaffolds from the screening, we synthesized 69 derivatives to optimize the potency for inhibition of NF-κB activation, leading to successful discovery of the most potent compound Z9j with over 170-fold enhancement of inhibitory activity. Preliminary mechanistic studies revealed that Z9j inhibited NF-κB signaling via suppression of Src/Syk, PI3K/Akt and IKK/IκB pathways. This novel compound also demonstrated anti-inflammatory and anti-cancer activities, warranting its further development as a potential multifunctional agent to treat inflammatory diseases and cancers.

Newborn screening for congenital adrenal hyperplasia in Cuba: six years of experience.

PubMed

González, Ernesto Carlos; Carvajal, Frank; Frómeta, Amarilys; Arteaga, Ana Luisa; Castells, Elisa María; Espinosa, Tania; Coto, Remigio; Pérez, Pedro Lucio; Tejeda, Yileidis; Del Río, Lesley; Segura, Mary Triny; Almenares, Pedro; Robaina, René; Fernández, José Luis

2013-06-05

Since 2005, a newborn screening program for congenital adrenal hyperplasia (CAH) by measuring 17-alpha-hydroxyprogesterone (17OHP) in dried blood spots was introduced in Cuba. The hormone was measured by the 17OHP Neonatal UMELISA method, in samples collected on the 5th day as average. Confirmatory test was performed to those neonates with 17OHP values above 55 nmol/l. Some perinatal factors that can influence on 17OHP levels were studied. From January 2005 to December 2010, 621,303 newborns were screened and 39 CAH cases were detected. Coverage of the program reached 98%. The incidence of CAH in Cuba was 1:15,931, similar to that reported by other programs. A recall for suspected CAH was performed in 10,799 cases (1.74%). Therapy in classical CAH patients was started at the mean age of 22 days. 17OHP levels were significantly higher in newborns with lower birth-weight (BW) and/or gestational age (GA). In addition, 17OHP values were affected by the gender, twin status or mode of delivery. In Cuba, the nationwide newborn screening program has allowed the early detection of CAH. The use of an optimized cut-off level for BW or GA could lead to a reduction in the percentage of recalled babies. Copyright © 2013 Elsevier B.V. All rights reserved.

Virtual screening and optimization of Type II inhibitors of JAK2 from a natural product library.

PubMed

Ma, Dik-Lung; Chan, Daniel Shiu-Hin; Wei, Guo; Zhong, Hai-Jing; Yang, Hui; Leung, Lai To; Gullen, Elizabeth A; Chiu, Pauline; Cheng, Yung-Chi; Leung, Chung-Hang

2014-11-21

Amentoflavone has been identified as a JAK2 inhibitor by structure-based virtual screening of a natural product library. In silico optimization using the DOLPHIN model yielded analogues with enhanced potency against JAK2 activity and HCV activity in cellulo. Molecular modeling and kinetic experiments suggested that the analogues may function as Type II inhibitors of JAK2.

Optimal structure and parameter learning of Ising models

DOE PAGES

Lokhov, Andrey; Vuffray, Marc Denis; Misra, Sidhant; ...

2018-03-16

Reconstruction of the structure and parameters of an Ising model from binary samples is a problem of practical importance in a variety of disciplines, ranging from statistical physics and computational biology to image processing and machine learning. The focus of the research community shifted toward developing universal reconstruction algorithms that are both computationally efficient and require the minimal amount of expensive data. Here, we introduce a new method, interaction screening, which accurately estimates model parameters using local optimization problems. The algorithm provably achieves perfect graph structure recovery with an information-theoretically optimal number of samples, notably in the low-temperature regime, whichmore » is known to be the hardest for learning. Here, the efficacy of interaction screening is assessed through extensive numerical tests on synthetic Ising models of various topologies with different types of interactions, as well as on real data produced by a D-Wave quantum computer. Finally, this study shows that the interaction screening method is an exact, tractable, and optimal technique that universally solves the inverse Ising problem.« less

Optimal structure and parameter learning of Ising models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lokhov, Andrey; Vuffray, Marc Denis; Misra, Sidhant

Reconstruction of the structure and parameters of an Ising model from binary samples is a problem of practical importance in a variety of disciplines, ranging from statistical physics and computational biology to image processing and machine learning. The focus of the research community shifted toward developing universal reconstruction algorithms that are both computationally efficient and require the minimal amount of expensive data. Here, we introduce a new method, interaction screening, which accurately estimates model parameters using local optimization problems. The algorithm provably achieves perfect graph structure recovery with an information-theoretically optimal number of samples, notably in the low-temperature regime, whichmore » is known to be the hardest for learning. Here, the efficacy of interaction screening is assessed through extensive numerical tests on synthetic Ising models of various topologies with different types of interactions, as well as on real data produced by a D-Wave quantum computer. Finally, this study shows that the interaction screening method is an exact, tractable, and optimal technique that universally solves the inverse Ising problem.« less

Definitive screening design enables optimization of LC-ESI-MS/MS parameters in proteomics.

PubMed

Aburaya, Shunsuke; Aoki, Wataru; Minakuchi, Hiroyoshi; Ueda, Mitsuyoshi

2017-12-01

In proteomics, more than 100,000 peptides are generated from the digestion of human cell lysates. Proteome samples have a broad dynamic range in protein abundance; therefore, it is critical to optimize various parameters of LC-ESI-MS/MS to comprehensively identify these peptides. However, there are many parameters for LC-ESI-MS/MS analysis. In this study, we applied definitive screening design to simultaneously optimize 14 parameters in the operation of monolithic capillary LC-ESI-MS/MS to increase the number of identified proteins and/or the average peak area of MS1. The simultaneous optimization enabled the determination of two-factor interactions between LC and MS. Finally, we found two parameter sets of monolithic capillary LC-ESI-MS/MS that increased the number of identified proteins by 8.1% or the average peak area of MS1 by 67%. The definitive screening design would be highly useful for high-throughput analysis of the best parameter set in LC-ESI-MS/MS systems.

78 FR 12311 - FIFRA Scientific Advisory Panel; Notice of Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-22

... Screening Assays and Battery Performance. DATES: The meeting will be held on May 21-24, 2013, from... consideration to further optimize the Tier 1 screening battery. Tier 1 screening was recommended to include a... conducted as a battery. [[Page 12313

Taguchi's technique: an effective method for improving X-ray medical radiographic screen performance.

PubMed

Vlachogiannis, J G

2003-01-01

Taguchi's technique is a helpful tool to achieve experimental optimization of a large number of decision variables with a small number of off-line experiments. The technique appears to be an ideal tool for improving the performance of X-ray medical radiographic screens under a noise source. Currently there are very many guides available for improving the efficiency of X-ray medical radiographic screens. These guides can be refined using a second-stage parameter optimization. based on Taguchi's technique, selecting the optimum levels of controllable X-ray radiographic screen factors. A real example of the proposed technique is presented giving certain performance criteria. The present research proposes the reinforcement of X-ray radiography by Taguchi's technique as a novel hardware mechanism.

Complete genome-wide screening and subtractive genomic approach revealed new virulence factors, potential drug targets against bio-war pathogen Brucella melitensis 16M

PubMed Central

Pradeepkiran, Jangampalli Adi; Sainath, Sri Bhashyam; Kumar, Konidala Kranthi; Bhaskar, Matcha

2015-01-01

Brucella melitensis 16M is a Gram-negative coccobacillus that infects both animals and humans. It causes a disease known as brucellosis, which is characterized by acute febrile illness in humans and causes abortions in livestock. To prevent and control brucellosis, identification of putative drug targets is crucial. The present study aimed to identify drug targets in B. melitensis 16M by using a subtractive genomic approach. We used available database repositories (Database of Essential Genes, Kyoto Encyclopedia of Genes and Genomes Automatic Annotation Server, and Kyoto Encyclopedia of Genes and Genomes) to identify putative genes that are nonhomologous to humans and essential for pathogen B. melitensis 16M. The results revealed that among 3 Mb genome size of pathogen, 53 putative characterized and 13 uncharacterized hypothetical genes were identified; further, from Basic Local Alignment Search Tool protein analysis, one hypothetical protein showed a close resemblance (50%) to Silicibacter pomeroyi DUF1285 family protein (2RE3). A further homology model of the target was constructed using MODELLER 9.12 and optimized through variable target function method by molecular dynamics optimization with simulating annealing. The stereochemical quality of the restrained model was evaluated by PROCHECK, VERIFY-3D, ERRAT, and WHATIF servers. Furthermore, structure-based virtual screening was carried out against the predicted active site of the respective protein using the glycerol structural analogs from the PubChem database. We identified five best inhibitors with strong affinities, stable interactions, and also with reliable drug-like properties. Hence, these leads might be used as the most effective inhibitors of modeled protein. The outcome of the present work of virtual screening of putative gene targets might facilitate design of potential drugs for better treatment against brucellosis. PMID:25834405

Breast Cancer Screening in an Era of Personalized Regimens

PubMed Central

Onega, Tracy; Beaber, Elisabeth F.; Sprague, Brian L.; Barlow, William E.; Haas, Jennifer S.; Tosteson, Anna N.A.; Schnall, Mitchell D.; Armstrong, Katrina; Schapira, Marilyn M.; Geller, Berta; Weaver, Donald L.; Conant, Emily F.

2014-01-01

Breast cancer screening holds a prominent place in public health, health care delivery, policy, and women’s health care decisions. Several factors are driving shifts in how population-based breast cancer screening is approached, including advanced imaging technologies, health system performance measures, health care reform, concern for “overdiagnosis,” and improved understanding of risk. Maximizing benefits while minimizing the harms of screening requires moving from a “1-size-fits-all” guideline paradigm to more personalized strategies. A refined conceptual model for breast cancer screening is needed to align women’s risks and preferences with screening regimens. A conceptual model of personalized breast cancer screening is presented herein that emphasizes key domains and transitions throughout the screening process, as well as multilevel perspectives. The key domains of screening awareness, detection, diagnosis, and treatment and survivorship are conceptualized to function at the level of the patient, provider, facility, health care system, and population/policy arena. Personalized breast cancer screening can be assessed across these domains with both process and outcome measures. Identifying, evaluating, and monitoring process measures in screening is a focus of a National Cancer Institute initiative entitled PROSPR (Population-based Research Optimizing Screening through Personalized Regimens), which will provide generalizable evidence for a risk-based model of breast cancer screening, The model presented builds on prior breast cancer screening models and may serve to identify new measures to optimize benefits-to-harms tradeoffs in population-based screening, which is a timely goal in the era of health care reform. PMID:24830599

Retinopathy of prematurity: An update on screening and management

PubMed Central

Jefferies, Ann L

2016-01-01

Retinopathy of prematurity is a proliferative disorder of the developing retinal blood vessels in preterm infants. The present practice point reviews new information regarding screening and management for retinopathy of prematurity, including the role of risk factors in screening, optimal scheduling for screening examinations, pain management, digital retinal photography and antivascular endothelial growth factor therapy. PMID:27095887

Reliability and Validity of a Two-Question Alcohol Screen in the Pediatric Emergency Department.

PubMed

Spirito, Anthony; Bromberg, Julie R; Casper, T Charles; Chun, Thomas H; Mello, Michael J; Dean, J Michael; Linakis, James G

2016-12-01

A multisite study was conducted to determine the psychometric properties of the National Institute of Alcohol Abuse and Alcoholism (NIAAA) 2-question alcohol screen within pediatric emergency departments (PEDs). Participants (N = 4838) included 12- to 17-year-old subjects treated in 1 of the 16 participating PEDs across the United States. A criterion assessment battery (including the NIAAA 2-question alcohol screen and other measures of alcohol, drug use, and risk behaviors) was self-administered on a tablet computer. A subsample (n = 186) was re-administered the NIAAA 2-question screen 1 week later to assess test-retest reliability. Moderate to good test-retest reliability was demonstrated. A classification of moderate risk or higher on the screen had the best combined sensitivity and specificity for determining a diagnosis of alcohol use disorder (AUD) for all students. Any past year drinking among middle school students increased the odds of a diagnosis of an AUD according to Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition criteria, whereas the optimal cutoff for high school ages was ≥3 drinking days in the past year. The optimal cutoff for drinking days determining a positive Alcohol Use Disorders Identification Test score among middle school subjects was ≥1 drinking day, whereas the optimal cutoff for high school subjects was ≥2 drinking days. The NIAAA 2-question screen is a brief, valid approach for alcohol screening in PEDs. A positive screen suggests that referral for further evaluation is indicated to determine if an adolescent has an AUD. Copyright © 2016 by the American Academy of Pediatrics.

Reliability and Validity of a Two-Question Alcohol Screen in the Pediatric Emergency Department

PubMed Central

Spirito, Anthony; Bromberg, Julie R.; Casper, T. Charles; Chun, Thomas H.; Mello, Michael J.; Dean, J. Michael

2016-01-01

BACKGROUND AND OBJECTIVE: A multisite study was conducted to determine the psychometric properties of the National Institute of Alcohol Abuse and Alcoholism (NIAAA) 2-question alcohol screen within pediatric emergency departments (PEDs). METHODS: Participants (N = 4838) included 12- to 17-year-old subjects treated in 1 of the 16 participating PEDs across the United States. A criterion assessment battery (including the NIAAA 2-question alcohol screen and other measures of alcohol, drug use, and risk behaviors) was self-administered on a tablet computer. A subsample (n = 186) was re-administered the NIAAA 2-question screen 1 week later to assess test-retest reliability. RESULTS: Moderate to good test-retest reliability was demonstrated. A classification of moderate risk or higher on the screen had the best combined sensitivity and specificity for determining a diagnosis of alcohol use disorder (AUD) for all students. Any past year drinking among middle school students increased the odds of a diagnosis of an AUD according to Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition criteria, whereas the optimal cutoff for high school ages was ≥3 drinking days in the past year. The optimal cutoff for drinking days determining a positive Alcohol Use Disorders Identification Test score among middle school subjects was ≥1 drinking day, whereas the optimal cutoff for high school subjects was ≥2 drinking days. CONCLUSIONS: The NIAAA 2-question screen is a brief, valid approach for alcohol screening in PEDs. A positive screen suggests that referral for further evaluation is indicated to determine if an adolescent has an AUD. PMID:27940674

Framework for the rapid optimization of soluble protein expression in Escherichia coli combining microscale experiments and statistical experimental design.

PubMed

Islam, R S; Tisi, D; Levy, M S; Lye, G J

2007-01-01

A major bottleneck in drug discovery is the production of soluble human recombinant protein in sufficient quantities for analysis. This problem is compounded by the complex relationship between protein yield and the large number of variables which affect it. Here, we describe a generic framework for the rapid identification and optimization of factors affecting soluble protein yield in microwell plate fermentations as a prelude to the predictive and reliable scaleup of optimized culture conditions. Recombinant expression of firefly luciferase in Escherichia coli was used as a model system. Two rounds of statistical design of experiments (DoE) were employed to first screen (D-optimal design) and then optimize (central composite face design) the yield of soluble protein. Biological variables from the initial screening experiments included medium type and growth and induction conditions. To provide insight into the impact of the engineering environment on cell growth and expression, plate geometry, shaking speed, and liquid fill volume were included as factors since these strongly influence oxygen transfer into the wells. Compared to standard reference conditions, both the screening and optimization designs gave up to 3-fold increases in the soluble protein yield, i.e., a 9-fold increase overall. In general the highest protein yields were obtained when cells were induced at a relatively low biomass concentration and then allowed to grow slowly up to a high final biomass concentration, >8 g.L-1. Consideration and analysis of the model results showed 6 of the original 10 variables to be important at the screening stage and 3 after optimization. The latter included the microwell plate shaking speeds pre- and postinduction, indicating the importance of oxygen transfer into the microwells and identifying this as a critical parameter for subsequent scale translation studies. The optimization process, also known as response surface methodology (RSM), predicted there to be a distinct optimum set of conditions for protein expression which could be verified experimentally. This work provides a generic approach to protein expression optimization in which both biological and engineering variables are investigated from the initial screening stage. The application of DoE reduces the total number of experiments needed to be performed, while experimentation at the microwell scale increases experimental throughput and reduces cost.

Inhibitors of the Diadenosine Tetraphosphate Phosphorylase Rv2613c of Mycobacterium tuberculosis.

PubMed

Götz, Kathrin H; Hacker, Stephan M; Mayer, Daniel; Dürig, Jan-Niklas; Stenger, Steffen; Marx, Andreas

2017-10-20

The intracellular concentration of diadenosine tetraphospate (Ap 4 A) increases upon exposure to stress conditions. Despite being discovered over 50 years ago, the cellular functions of Ap 4 A are still enigmatic. If and how the varied Ap 4 A is a signal and involved in the signaling pathways leading to an appropriate cellular response remain to be discovered. Because the turnover of Ap 4 A by Ap 4 A cleaving enzymes is rapid, small molecule inhibitors for these enzymes would provide tools for the more detailed study of the role of Ap 4 A. Here, we describe the development of a high-throughput screening assay based on a fluorogenic Ap 4 A substrate for the identification and optimization of small molecule inhibitors for Ap 4 A cleaving enzymes. As proof-of-concept we screened a library of over 42 000 compounds toward their inhibitory activity against the Ap 4 A phosphorylase (Rv2613c) of Mycobacterium tuberculosis (Mtb). A sulfanylacrylonitril derivative with an IC 50 of 260 ± 50 nM in vitro was identified. Multiple derivatives were synthesized to further optimize their properties with respect to their in vitro IC 50 values and their cytotoxicity against human cells (HeLa). In addition, we selected two hits to study their antimycobacterial activity against virulent Mtb to show that they might be candidates for further development of antimycobacterial agents against multidrug-resistant Mtb.

MAP: an iterative experimental design methodology for the optimization of catalytic search space structure modeling.

PubMed

Baumes, Laurent A

2006-01-01

One of the main problems in high-throughput research for materials is still the design of experiments. At early stages of discovery programs, purely exploratory methodologies coupled with fast screening tools should be employed. This should lead to opportunities to find unexpected catalytic results and identify the "groups" of catalyst outputs, providing well-defined boundaries for future optimizations. However, very few new papers deal with strategies that guide exploratory studies. Mostly, traditional designs, homogeneous covering, or simple random samplings are exploited. Typical catalytic output distributions exhibit unbalanced datasets for which an efficient learning is hardly carried out, and interesting but rare classes are usually unrecognized. Here is suggested a new iterative algorithm for the characterization of the search space structure, working independently of learning processes. It enhances recognition rates by transferring catalysts to be screened from "performance-stable" space zones to "unsteady" ones which necessitate more experiments to be well-modeled. The evaluation of new algorithm attempts through benchmarks is compulsory due to the lack of past proofs about their efficiency. The method is detailed and thoroughly tested with mathematical functions exhibiting different levels of complexity. The strategy is not only empirically evaluated, the effect or efficiency of sampling on future Machine Learning performances is also quantified. The minimum sample size required by the algorithm for being statistically discriminated from simple random sampling is investigated.

Longitudinal changes in blood lead level in children and their relationship to season, age, and exposure to paint or plaster.

PubMed Central

McCusker, J

1979-01-01

Children screened for lead poisoning in the Brownsville district of New York City in either summer or winter were followed with blood lead tests for approximately six months to one year from screening to measure longitudinal changes in blood lead level and to identify some determinants of the changes. Only minimal evidence was found of the hypothesized summer rise in blood lead level, while the predominant trend seemed to be for blood lead levels to display statistical regression to the mean. In children found to have low to intermediate blood lead levels (less than 55 microgram/100ml) at screening, variables which were found to predict a rise in blood lead level of 10 microgram/100ml or greater from winter to summer were under age three and/or exposure to paint or plaster. PMID:426160

Rational evolutionary design: the theory of in vitro protein evolution.

PubMed

Voigt, C A; Kauffman, S; Wang, Z G

2000-01-01

Directed evolution uses a combination of powerful search techniques to generate proteins with improved properties. Part of the success is due to the stochastic element of random mutagenesis; improvements can be made without a detailed description of the complex interactions that constitute function or stability. However, optimization is not a conglomeration of random processes. Rather, it requires both knowledge of the system that is being optimized and a logical series of techniques that best explores the pathways of evolution (Eigen et al., 1988). The weighing of parameters associated with mutation, recombination, and screening to achieve the maximum fitness improvement is the beginning of rational evolutionary design. The optimal mutation rate is strongly influenced by the finite number of mutants that can be screened. A smooth fitness landscape implies that many mutations can be accumulated without disrupting the fitness. This has the effect of lowering the required library size to sample a higher mutation rate. As the sequence ascends the fitness landscape, the optimal mutation rate decreases as the probability of discovering improved mutations also decreases. Highly coupled regions require that many mutations be simultaneously made to generate a positive mutant. Therefore, positive mutations are discovered at uncoupled positions as the fitness of the parent increases. The benefit of recombination is twofold: it combines good mutations and searches more sequence space in a meaningful way. Recombination is most beneficial when the number of mutants that can be screened is limited and the landscape is of an intermediate ruggedness. The structure of schema in proteins leads to the conclusion that many cut points are required. The number of parents and their sequence identity are determined by the balance between exploration and exploitation. Many disparate parents can explore more space, but at the risk of losing information. The required screening effort is related to the number of uphill paths, which decreases more rapidly for rugged landscapes. Noise in the fitness measurements causes a dramatic increase in the required mutant library size, thus implying a smaller optimal mutation rate. Because of strict limitations on the number of mutants that can be screened, there is motivation to optimize the content of the mutant library. By restricting mutations to regions of the gene that are expected to show improvement, a greater return can be made with the same number of mutants. Initial studies with subtilisin E have shown that structurally tolerant positions tend to be where positive activity mutants are made during directed evolution. Mutant fitness information is produced by the screening step that has the potential to provide insight into the structure of the fitness landscape, thus aiding the setting of experimental parameters. By analyzing the mutant fitness distribution and targeting specific regions of the sequence, in vitro evolution can be accelerated. However, when expediting the search, there is a trade-off between rapid improvement and the quality of the long-term solution. The benefit of neutrality has yet to be captured with in vitro protein evolution. Neutral theory predicts the punctuated emergence of novel structure and function, however, with current methods, the required time scale is not feasible. Utilizing neutral evolution to accelerate the discovery of new functional and structural solutions requires a theory that predicts the behavior of mutational pathways between networks. Because the transition from neutral to adaptive evolution requires a multi-mutational switch, increasing the mutation rate decreases the time required for a punctuated change to occur. By limiting the search to the less coupled region of the sequence (smooth portion of the fitness landscape), the required larger mutation rate can be tolerated. Advances in directed evolution will be achieved when the driving forces behind such proce

Heuristic lipophilicity potential for computer-aided rational drug design: Optimizations of screening functions and parameters

NASA Astrophysics Data System (ADS)

Du, Qishi; Mezey, Paul G.

1998-09-01

In this research we test and compare three possible atom-basedscreening functions used in the heuristic molecular lipophilicity potential(HMLP). Screening function 1 is a power distance-dependent function, b_{{i}} /| {R_{{i}}- r} |^γ, screening function 2is an exponential distance-dependent function, biexp(-| {R_i- r} |/d_0 , and screening function 3 is aweighted distance-dependent function, {{sign}}( {b_i } ){{exp}}ξ ( {| {R_i- r} |/| {b_i } |} )For every screening function, the parameters (γ ,d0, and ξ are optimized using 41 common organic molecules of 4 types of compounds:aliphatic alcohols, aliphatic carboxylic acids, aliphatic amines, andaliphatic alkanes. The results of calculations show that screening function3 cannot give chemically reasonable results, however, both the powerscreening function and the exponential screening function give chemicallysatisfactory results. There are two notable differences between screeningfunctions 1 and 2. First, the exponential screening function has largervalues in the short distance than the power screening function, thereforemore influence from the nearest neighbors is involved using screeningfunction 2 than screening function 1. Second, the power screening functionhas larger values in the long distance than the exponential screeningfunction, therefore screening function 1 is effected by atoms at longdistance more than screening function 2. For screening function 1, thesuitable range of parameter d0 is 1.5 < d0 < 3.0, and d0 = 2.0 is recommended. HMLP developed in this researchprovides a potential tool for computer-aided three-dimensional drugdesign.

Should the Centers for Disease Control and Prevention's childhood lead poisoning intervention level be lowered?

PubMed

Bernard, Susan M

2003-08-01

The US Centers for Disease Control and Prevention (CDC) in 1991 chose 10 micro g/dL as an initial screening level for lead in children's blood. Current data on health risks and intervention options do not support generally lowering that level, but federal lead poisoning prevention efforts can be improved by revising the follow-up testing schedule for infants aged 1 year or less with blood lead levels of 5 micro g/dL or higher; universal education about lead exposure risks; universal administration of improved, locally validated risk-screening questionnaires; enhanced compliance with targeted screening recommendations and federal health program requirements; and development by regulatory agencies of primary prevention criteria that do not use the CDC's intervention level as a target "safe" lead exposure.

Recommendations for newborn screening for galactokinase deficiency: A systematic review and evaluation of Dutch newborn screening data.

PubMed

Stroek, Kevin; Bouva, Marelle J; Schielen, Peter C J I; Vaz, Frédéric M; Heijboer, Annemieke C; de Jonge, Robert; Boelen, Anita; Bosch, Annet M

2018-03-21

Galactokinase (GALK) deficiency causes cataract leading to severe developmental consequences unless treated early. Because of the easy prevention and rapid reversibility of cataract with treatment, the Dutch Health Council advised to include GALK deficiency in the Dutch newborn screening program. The aim of this study is to establish the optimal screening method and cut-off value (COV) for GALK deficiency screening by performing a systematic review of the literature of screening strategies and total galactose (TGAL) values and by evaluating TGAL values in the first week of life in a cohort of screened newborns in the Netherlands. Systematic literature search strategies in OVID MEDLINE and OVID EMBASE were developed and study selection, data collection and analyses were performed by two independent investigators. A range of TGAL values measured by the Quantase Neonatal Total Galactose screening assay in a cohort of Dutch newborns in 2007 was evaluated. Eight publications were included in the systematic review. All four studies describing screening strategies used TGAL as the primary screening marker combined with galactose-1-phosphate uridyltransferase (GALT) measurement that is used for classical galactosemia screening. TGAL COVs of 2200 μmol/L, 1665 μmol/L and 1110 μmol/L blood resulted in positive predictive values (PPV) of 100%, 82% and 10% respectively. TGAL values measured in the newborn period were reported for 39 GALK deficiency patients with individual values ranging from 3963 to 8159 μmol/L blood and 2 group values with mean 8892 μmol/L blood (SD ± 5243) and 4856 μmol/L blood (SD ± 461). Dutch newborn screening data of 72,786 newborns from 2007 provided a median TGAL value of 110 μmol/L blood with a range of 30-2431 μmol/L blood. Based on TGAL values measured in GALK deficiency patients reported in the literature and TGAL measurements in the Dutch cohort by newborn screening we suggest to perform the GALK screening with TGAL as a primary marker with a COV of 2500 μmol/L blood, combined with GALT enzyme activity measurement as used in the classical galactosemia screening, to ensure detection of GALK deficiency patients and minimize false positive referrals. Copyright © 2018. Published by Elsevier Inc.

[Isolation, identification and fermentation optimization of Bacillus tequilensis PanD37 producing L-aspartate α- decarboxylase].

PubMed

Feng, Zhibin; Zhang, Juan; Chen, Guozhong; Cha, Yaping; Liu, Jinjie; Ge, Yihe; Cheng, Shiwei; Yu, Botao

2016-01-04

We screened bacteria producing L-aspartate α-decarboxylase from grapery soil and optimized the fermentation conditions. L-aspartate α-decarboxylase producing bacteria were screened by color-changing circle and liquid secondary screening culture media. Combination of morphological, physiological and biochemical characteristics and 16S rRNA sequence analysis were used to identify the bacteria. Fermentation conditions were optimized by single factor test and orthogonal experiment. Strain PanD37 showed high L-aspartate α-decarboxylase producing property and was identified as Bacillus tequilensis. The optimum fermentation conditions of PanD37 were liquid volume of 50 mL in 500 mL flask, 220 r/min at 35 °C, inoculation amount of 5% for 28 h with a medium of 22.5 g/L sucrose, 7.5 g/L fumaric acid, 20 g/L peptone, 6 g/L L-aspartic acid, 2 g/L Triton X-100, at initial pH of 7.0. Under the optimal fermentation conditions, the highest L-aspartate α-decarboxylase activity reached 44.57 U/mL, which was 2.57 folds higher than that obtained before optimization. Strain PanD37 was identified as Bacillus tequilensiswhich was capable of highly producing L-aspartate α-decarboxylase under the optimal fermentation conditions.

Optimization of Breast Tomosynthesis Imaging Systems for Computer-Aided Detection

DTIC Science & Technology

2011-05-01

R. Saunders, E. Samei, C. Badea, H. Yuan, K. Ghaghada, Y. Qi, L. Hedlund, and S. Mukundan, “Optimization of dual energy contrast enhanced breast...14 4 1 Introduction This is the final report for this body of research. Screen-film mammography and...digital mammography have been used for over 30 years in the early detection of cancer. The combination of screening and adjuvant therapies have led to

Optimal digital filtering for tremor suppression.

PubMed

Gonzalez, J G; Heredia, E A; Rahman, T; Barner, K E; Arce, G R

2000-05-01

Remote manually operated tasks such as those found in teleoperation, virtual reality, or joystick-based computer access, require the generation of an intermediate electrical signal which is transmitted to the controlled subsystem (robot arm, virtual environment, or a cursor in a computer screen). When human movements are distorted, for instance, by tremor, performance can be improved by digitally filtering the intermediate signal before it reaches the controlled device. This paper introduces a novel tremor filtering framework in which digital equalizers are optimally designed through pursuit tracking task experiments. Due to inherent properties of the man-machine system, the design of tremor suppression equalizers presents two serious problems: 1) performance criteria leading to optimizations that minimize mean-squared error are not efficient for tremor elimination and 2) movement signals show ill-conditioned autocorrelation matrices, which often result in useless or unstable solutions. To address these problems, a new performance indicator in the context of tremor is introduced, and the optimal equalizer according to this new criterion is developed. Ill-conditioning of the autocorrelation matrix is overcome using a novel method which we call pulled-optimization. Experiments performed with artificially induced vibrations and a subject with Parkinson's disease show significant improvement in performance. Additional results, along with MATLAB source code of the algorithms, and a customizable demo for PC joysticks, are available on the Internet at http:¿tremor-suppression.com.

Plate-based diversity subset screening generation 2: an improved paradigm for high-throughput screening of large compound files.

PubMed

Bell, Andrew S; Bradley, Joseph; Everett, Jeremy R; Loesel, Jens; McLoughlin, David; Mills, James; Peakman, Marie-Claire; Sharp, Robert E; Williams, Christine; Zhu, Hongyao

2016-11-01

High-throughput screening (HTS) is an effective method for lead and probe discovery that is widely used in industry and academia to identify novel chemical matter and to initiate the drug discovery process. However, HTS can be time consuming and costly and the use of subsets as an efficient alternative to screening entire compound collections has been investigated. Subsets may be selected on the basis of chemical diversity, molecular properties, biological activity diversity or biological target focus. Previously, we described a novel form of subset screening: plate-based diversity subset (PBDS) screening, in which the screening subset is constructed by plate selection (rather than individual compound cherry-picking), using algorithms that select for compound quality and chemical diversity on a plate basis. In this paper, we describe a second-generation approach to the construction of an updated subset: PBDS2, using both plate and individual compound selection, that has an improved coverage of the chemical space of the screening file, whilst only selecting the same number of plates for screening. We describe the validation of PBDS2 and its successful use in hit and lead discovery. PBDS2 screening became the default mode of singleton (one compound per well) HTS for lead discovery in Pfizer.

Prognostic Significance of Digital Rectal Examination and Prostate Specific Antigen in the Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Arm.

PubMed

Halpern, Joshua A; Shoag, Jonathan E; Mittal, Sameer; Oromendia, Clara; Ballman, Karla V; Hershman, Dawn L; Wright, Jason D; Shih, Ya-Chen Tina; Nguyen, Paul L; Hu, Jim C

2017-02-01

The absence of definitive data or explicit guidelines regarding the use of digital rectal examination for prostate cancer screening may lead to confusion for physicians and patients alike. We evaluated the prognostic value of abnormal digital rectal examination and prostate specific antigen following the widespread dissemination of prostate specific antigen testing in the U.S. Collectively, men comprising the screening arm of the PLCO cancer screening trial who underwent digital rectal examination screening (35,350) were followed for 314,033 person-years. Adjusted analyses with competing risks regression were performed to assess the association of suspicious (nodularity, induration, asymmetry) digital rectal examination and abnormal prostate specific antigen (4 ng/ml or greater) with the detection of clinically significant prostate cancer, prostate cancer specific mortality and overall mortality. Among all screening encounters with a suspicious digital rectal examination only 15.4% had a concurrently abnormal prostate specific antigen (McNemar's test p <0.001). During followup there were 1,612 clinically significant prostate cancers detected, 64 prostate cancer specific deaths and 4,600 deaths. On multivariable analysis suspicious digital rectal examination and abnormal prostate specific antigen were associated with a greater risk of clinically significant prostate cancer (HR 2.21, 95% CI 1.99-2.44 vs HR 5.48, 95% CI 5.05-5.96, p <0.001 and p <0.001) and prostate cancer specific mortality (HR 2.54, 95% CI 1.41-4.58 vs HR 5.23, 95% CI 3.08-8.88, p=0.002 and p <0.001), respectively. In a secondary analysis of a contemporary U.S. cohort, suspicious digital rectal examination and abnormal prostate specific antigen on routine screening were independently associated with clinically significant prostate cancer and prostate cancer specific mortality. However, additional research is needed to optimize screening protocols. Copyright © 2017 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Structure Guided Development of Novel Thymidine Mimetics targeting Pseudomonas aeruginosa Thymidylate Kinase: from Hit to Lead Generation

PubMed Central

Choi, Jun Yong; Plummer, Mark S.; Starr, Jeremy; Desbonnet, Charlene R.; Soutter, Holly; Chang, Jeanne; Miller, J. Richard; Dillman, Keith; Miller, Alita A.; Roush, William R.

2012-01-01

Thymidylate kinase (TMK) is a potential chemotherapeutic target because it is directly involved in the synthesis of an essential component, thymidine triphosphate, in DNA replication. All reported TMK inhibitors are thymidine analogs, which might retard their development as potent therapeutics due to cell permeability and off-target activity against human TMK. A small molecule hit (1, IC50 = 58 μM), which has reasonable inhibition potency against Pseudomonas aeruginosa TMK (PaTMK), was identified by the analysis of the binding mode of thymidine or TP5A in a PaTMK homology model. This hit (1) was co-crystallized with PaTMK, and several potent PaTMK inhibitors (leads, 46, 47, 48, and 56, IC50 = 100–200 nM) were synthesized using computer aided design approaches including virtual synthesis/screening, which was used to guide the design of inhibitors. The binding mode of the optimized leads in PaTMK overlaps with that of other bacterial TMKs, but not with human TMK which shares few common features with the bacterial enzymes. Therefore, the optimized TMK inhibitors described here should be useful for the development of antibacterial agents targeting TMK without undesired off-target effects. In addition, an inhibition mechanism associated with the LID loop, which mimics the process of phosphate transfer from ATP to dTMP, was proposed based on X-ray co-crystal structures, homology models, and SAR results. PMID:22243413

American Society for Enhanced Recovery and Perioperative Quality Initiative Joint Consensus Statement on Nutrition Screening and Therapy Within a Surgical Enhanced Recovery Pathway.

PubMed

Wischmeyer, Paul E; Carli, Franco; Evans, David C; Guilbert, Sarah; Kozar, Rosemary; Pryor, Aurora; Thiele, Robert H; Everett, Sotiria; Grocott, Mike; Gan, Tong J; Shaw, Andrew D; Thacker, Julie K M; Miller, Timothy E; Hedrick, Traci L; McEvoy, Matthew D; Mythen, Michael G; Bergamaschi, Roberto; Gupta, Ruchir; Holubar, Stefan D; Senagore, Anthony J; Abola, Ramon E; Bennett-Guerrero, Elliott; Kent, Michael L; Feldman, Liane S; Fiore, Julio F

2018-06-01

Perioperative malnutrition has proven to be challenging to define, diagnose, and treat. Despite these challenges, it is well known that suboptimal nutritional status is a strong independent predictor of poor postoperative outcomes. Although perioperative caregivers consistently express recognition of the importance of nutrition screening and optimization in the perioperative period, implementation of evidence-based perioperative nutrition guidelines and pathways in the United States has been quite limited and needs to be addressed in surgery-focused recommendations. The second Perioperative Quality Initiative brought together a group of international experts with the objective of providing consensus recommendations on this important topic with the goal of (1) developing guidelines for screening of nutritional status to identify patients at risk for adverse outcomes due to malnutrition; (2) address optimal methods of providing nutritional support and optimizing nutrition status preoperatively; and (3) identifying when and how to optimize nutrition delivery in the postoperative period. Discussion led to strong recommendations for implementation of routine preoperative nutrition screening to identify patients in need of preoperative nutrition optimization. Postoperatively, nutrition delivery should be restarted immediately after surgery. The key role of oral nutrition supplements, enteral nutrition, and parenteral nutrition (implemented in that order) in most perioperative patients was advocated for with protein delivery being more important than total calorie delivery. Finally, the role of often-inadequate nutrition intake in the posthospital setting was discussed, and the role of postdischarge oral nutrition supplements was emphasized.

Screening of Actinomycetes from mangrove ecosystem for L-asparaginase activity and optimization by response surface methodology.

PubMed

Usha, Rajamanickam; Mala, Krishnaswami Kanjana; Venil, Chidambaram Kulandaisamy; Palaniswamy, Muthusamy

2011-01-01

Marine actinomycetes were isolated from sediment samples collected from Pitchavaram mangrove ecosystem situated along the southeast coast of India. Maximum actinomycete population was noted in rhizosphere region. About 38% of the isolates produced L-asparaginase. One potential strain KUA106 produced higher level of enzyme using tryptone glucose yeast extract medium. Based on the studied phenotypic characteristics, strain KUA106 was identified as Streptomyces parvulus KUA106. The optimization method that combines the Plackett-Burman design, a factorial design and the response surface method, which were used to optimize the medium for the production of L-asparaginase by Streptomycetes parvulus. Four medium factors were screened from eleven medium factors by Plackett-Burman design experiments and subsequent optimization process to find out the optimum values of the selected parameters using central composite design was performed. Asparagine, tryptone, d) extrose and NaCl components were found to be the best medium for the L-asparaginase production. The combined optimization method described here is the effective method for screening medium factors as well as determining their optimum level for the production of L-asparaginase by Streptomycetes parvulus KUAP106.

Optimization of the protocols for the use of contrast agents in PET/CT studies.

PubMed

Pelegrí Martínez, L; Kohan, A A; Vercher Conejero, J L

The introduction of PET/CT scanners in clinical practice in 1998 has improved care for oncologic patients throughout the clinical pathway, from the initial diagnosis of disease through the evaluation of the response to treatment to screening for possible recurrence. The CT component of a PET/CT study is used to correct the attenuation of PET studies; CT also provides anatomic information about the distribution of the radiotracer. CT is especially useful in situations where PET alone can lead to false positives and false negatives, and CT thereby improves the diagnostic performance of PET. The use of intravenous or oral contrast agents and optimal CT protocols have improved the detection and characterization of lesions. However, there are circumstances in which the systematic use of contrast agents is not justified. The standard acquisition in PET/CT scanners is the whole body protocol, but this can lead to artifacts due to the position of patients and respiratory movements between the CT and PET acquisitions. This article discusses these aspects from a constructive perspective with the aim of maximizing the diagnostic potential of PET/CT and providing better care for patients. Copyright © 2016 SERAM. Publicado por Elsevier España, S.L.U. All rights reserved.

Three-Dimensional in Vitro Cell Culture Models in Drug Discovery and Drug Repositioning

PubMed Central

Langhans, Sigrid A.

2018-01-01

Drug development is a lengthy and costly process that proceeds through several stages from target identification to lead discovery and optimization, preclinical validation and clinical trials culminating in approval for clinical use. An important step in this process is high-throughput screening (HTS) of small compound libraries for lead identification. Currently, the majority of cell-based HTS is being carried out on cultured cells propagated in two-dimensions (2D) on plastic surfaces optimized for tissue culture. At the same time, compelling evidence suggests that cells cultured in these non-physiological conditions are not representative of cells residing in the complex microenvironment of a tissue. This discrepancy is thought to be a significant contributor to the high failure rate in drug discovery, where only a low percentage of drugs investigated ever make it through the gamut of testing and approval to the market. Thus, three-dimensional (3D) cell culture technologies that more closely resemble in vivo cell environments are now being pursued with intensity as they are expected to accommodate better precision in drug discovery. Here we will review common approaches to 3D culture, discuss the significance of 3D cultures in drug resistance and drug repositioning and address some of the challenges of applying 3D cell cultures to high-throughput drug discovery. PMID:29410625

Optimization of heavy metals total emission, case study: Bor (Serbia)

NASA Astrophysics Data System (ADS)

Ilić, Ivana; Bogdanović, Dejan; Živković, Dragana; Milošević, Novica; Todorović, Boban

2011-07-01

The town of Bor (Serbia) is one of the most polluted towns in southeastern Europe. The copper smelter which is situated in the centre of the town is the main pollutant, mostly because of its old technology, which leads to environmental pollution caused by higher concentrations of SO 2 and PM 10. These facts show that the word is about a very polluted region in Europe which, apart from harming human health in the region itself, poses a particular danger for wider area of southeastern Europe. Optimization of heavy metal's total emission was undertaken because years of long contamination of the soil with heavy metals of anthropogenic origin created a danger that those heavy metals may enter the food chains of animals and people, which can lead to disastrous consequences. This work represents the usage of Geographic Information System (GIS) for establishing a multifactor assessment model to quantitatively divide polluted zones and for selecting control sites in a linear programming model, combined with PROMETHEE/GAIA method, Screen View modeling system, and linear programming model. The results show that emissions at some control sites need to be cut for about 40%. In order to control the background of heavy metal pollution in Bor, the ecological environment must be improved.

Urban and Education Disparity for Autism Spectrum Disorders in Taiwan Birth Cohort Study.

PubMed

Lung, For-Wey; Chiang, Tung-Liang; Lin, Shio-Jean; Shu, Bih-Ching

2017-03-01

This study aimed to determine the optimal cut-off for autism spectrum disorder (ASD) screening in 66-month-old children, and to explore the distribution of ASD screening and diagnosis in Taiwan. The Taiwan Birth Cohort Study dataset was used (N = 20,095). The Modified Checklist for Autism in Toddlers (M-CHAT) cut-off point of 13/14 was considered optimal for screening of children at 66 months. More children were diagnosed with ASD in urban areas. Parents of children diagnosed with ASD had a higher level of education, but parents of children with a lower level of education were screened as being at higher risk of ASD. Urban disparity and parental level of education effected parental awareness of the illness and the rate of ASD diagnosis.

Virtual screening methods as tools for drug lead discovery from large chemical libraries.

PubMed

Ma, X H; Zhu, F; Liu, X; Shi, Z; Zhang, J X; Yang, S Y; Wei, Y Q; Chen, Y Z

2012-01-01

Virtual screening methods have been developed and explored as useful tools for searching drug lead compounds from chemical libraries, including large libraries that have become publically available. In this review, we discussed the new developments in exploring virtual screening methods for enhanced performance in searching large chemical libraries, their applications in screening libraries of ~ 1 million or more compounds in the last five years, the difficulties in their applications, and the strategies for further improving these methods.

Application of screened Coulomb potential in fitting DBV star PG 0112+104

NASA Astrophysics Data System (ADS)

Chen, Y. H.

2018-03-01

With 78.7 d of observations for PG 0112+104, a pulsating DB star, from Campaign 8 of Kepler 2 mission, Hermes et al. made a detailed mode identification. A reliable mode identification, with 5 l = 1 modes, 3 l = 2 modes, and 3 l = 1 or 2 modes, was identified. Grids of DBV star models are evolved by WDEC with element diffusion effect of pure Coulomb potential and screened Coulomb potential. Fitting the identified modes of PG 0112+104 by the calculated ones, we studied the difference of element diffusion effect between adopting pure Coulomb potential and screened Coulomb potential. Our aim is to reduce the fitting error by studying new input physics. The starting models including their chemical composition profile are from white dwarf models evolved by MESA. They were calculated following the stellar evolution from the main sequence to the start of the white dwarf cooling sequences. The optimal parameters are basically consistent with that of previous spectroscopic and asteroseismological studies. The pure and screened Coulomb potential lead to different composition profiles of the C/O-He interface area. High k modes are very sensitive to the area. However, most of the observed modes for PG 0112+104 are low k modes. The σRMS taking the screened Coulomb potential is reduced by 4 per cent compared with taking the pure Coulomb potential when fitting the identified low k modes of PG 0112+104. Fitting the Kepler 2 data with our models improved the σRMS of the fit by 27 per cent.

Simulation models in population breast cancer screening: A systematic review.

PubMed

Koleva-Kolarova, Rositsa G; Zhan, Zhuozhao; Greuter, Marcel J W; Feenstra, Talitha L; De Bock, Geertruida H

2015-08-01

The aim of this review was to critically evaluate published simulation models for breast cancer screening of the general population and provide a direction for future modeling. A systematic literature search was performed to identify simulation models with more than one application. A framework for qualitative assessment which incorporated model type; input parameters; modeling approach, transparency of input data sources/assumptions, sensitivity analyses and risk of bias; validation, and outcomes was developed. Predicted mortality reduction (MR) and cost-effectiveness (CE) were compared to estimates from meta-analyses of randomized control trials (RCTs) and acceptability thresholds. Seven original simulation models were distinguished, all sharing common input parameters. The modeling approach was based on tumor progression (except one model) with internal and cross validation of the resulting models, but without any external validation. Differences in lead times for invasive or non-invasive tumors, and the option for cancers not to progress were not explicitly modeled. The models tended to overestimate the MR (11-24%) due to screening as compared to optimal RCTs 10% (95% CI - 2-21%) MR. Only recently, potential harms due to regular breast cancer screening were reported. Most scenarios resulted in acceptable cost-effectiveness estimates given current thresholds. The selected models have been repeatedly applied in various settings to inform decision making and the critical analysis revealed high risk of bias in their outcomes. Given the importance of the models, there is a need for externally validated models which use systematical evidence for input data to allow for more critical evaluation of breast cancer screening. Copyright © 2015 Elsevier Ltd. All rights reserved.

Screening Technique for Lead and Cadmium in Toys and Other Materials Using Atomic Absorption Spectroscopy

ERIC Educational Resources Information Center

Brouwer, Henry

2005-01-01

A simple procedure to quickly screen different consumer products for the presence of lead, cadmium, and other metals is described. This screening technique avoids expending a lot of preparation time on samples known to contain low levels of hazardous metals where only samples testing positive for the desired elements need to be analyzed…

Automated Detection of Obstructive Sleep Apnea Events from a Single-Lead Electrocardiogram Using a Convolutional Neural Network.

PubMed

Urtnasan, Erdenebayar; Park, Jong-Uk; Joo, Eun-Yeon; Lee, Kyoung-Joung

2018-04-23

In this study, we propose a method for the automated detection of obstructive sleep apnea (OSA) from a single-lead electrocardiogram (ECG) using a convolutional neural network (CNN). A CNN model was designed with six optimized convolution layers including activation, pooling, and dropout layers. One-dimensional (1D) convolution, rectified linear units (ReLU), and max pooling were applied to the convolution, activation, and pooling layers, respectively. For training and evaluation of the CNN model, a single-lead ECG dataset was collected from 82 subjects with OSA and was divided into training (including data from 63 patients with 34,281 events) and testing (including data from 19 patients with 8571 events) datasets. Using this CNN model, a precision of 0.99%, a recall of 0.99%, and an F 1 -score of 0.99% were attained with the training dataset; these values were all 0.96% when the CNN was applied to the testing dataset. These results show that the proposed CNN model can be used to detect OSA accurately on the basis of a single-lead ECG. Ultimately, this CNN model may be used as a screening tool for those suspected to suffer from OSA.

Computational drug discovery

PubMed Central

Ou-Yang, Si-sheng; Lu, Jun-yan; Kong, Xiang-qian; Liang, Zhong-jie; Luo, Cheng; Jiang, Hualiang

2012-01-01

Computational drug discovery is an effective strategy for accelerating and economizing drug discovery and development process. Because of the dramatic increase in the availability of biological macromolecule and small molecule information, the applicability of computational drug discovery has been extended and broadly applied to nearly every stage in the drug discovery and development workflow, including target identification and validation, lead discovery and optimization and preclinical tests. Over the past decades, computational drug discovery methods such as molecular docking, pharmacophore modeling and mapping, de novo design, molecular similarity calculation and sequence-based virtual screening have been greatly improved. In this review, we present an overview of these important computational methods, platforms and successful applications in this field. PMID:22922346

Higher Throughput Calorimetry: Opportunities, Approaches and Challenges

PubMed Central

Recht, Michael I.; Coyle, Joseph E.; Bruce, Richard H.

2010-01-01

Higher throughput thermodynamic measurements can provide value in structure-based drug discovery during fragment screening, hit validation, and lead optimization. Enthalpy can be used to detect and characterize ligand binding, and changes that affect the interaction of protein and ligand can sometimes be detected more readily from changes in the enthalpy of binding than from the corresponding free-energy changes or from protein-ligand structures. Newer, higher throughput calorimeters are being incorporated into the drug discovery process. Improvements in titration calorimeters come from extensions of a mature technology and face limitations in scaling. Conversely, array calorimetry, an emerging technology, shows promise for substantial improvements in throughput and material utilization, but improved sensitivity is needed. PMID:20888754

Timing of definitive fixation of major long bone fractures: Can fat embolism syndrome be prevented?

PubMed

Blokhuis, Taco J; Pape, Hans-Christoph; Frölke, Jan-Paul

2017-06-01

Fat embolism is common in patients with major fractures, but leads to devastating consequences, named fat embolism syndrome (FES) in some. Despite advances in treatment strategies regarding the timing of definitive fixation of major fractures, FES still occurs in patients. In this overview, current literature is reviewed and optimal treatment strategies for patients with multiple traumatic injuries, including major fractures, are discussed. Considering the multifactorial etiology of FES, including mechanical and biochemical pathways, FES cannot be prevented in all patients. However, screening for symptoms of FES should be standard in the pre-operative work-up of these patients, prior to definitive fixation of major fractures. Copyright © 2017. Published by Elsevier Ltd.

Identification of effective screening strategies for cardiovascular disease prevention in a developing country: using cardiovascular risk-estimation and risk-reduction tools for policy recommendations.

PubMed

Selvarajah, Sharmini; Haniff, Jamaiyah; Kaur, Gurpreet; Guat Hiong, Tee; Bujang, Adam; Chee Cheong, Kee; Bots, Michiel L

2013-02-25

Recent increases in cardiovascular risk-factor prevalences have led to new national policy recommendations of universal screening for primary prevention of cardiovascular disease in Malaysia. This study assessed whether the current national policy recommendation of universal screening was optimal, by comparing the effectiveness and impact of various cardiovascular screening strategies. Data from a national population based survey of 24 270 participants aged 30 to 74 was used. Five screening strategies were modelled for the overall population and by gender; universal and targeted screening (four age cut-off points). Screening strategies were assessed based on the ability to detect high cardiovascular risk populations (effectiveness), incremental effectiveness, impact on cardiovascular event prevention and cost of screening. 26.7% (95% confidence limits 25.7, 27.7) were at high cardiovascular risk, men 34.7% (33.6, 35.8) and women 18.9% (17.8, 20). Universal screening identified all those at high-risk and resulted in one high-risk individual detected for every 3.7 people screened, with an estimated cost of USD60. However, universal screening resulted in screening an additional 7169 persons, with an incremental cost of USD115,033 for detection of one additional high-risk individual in comparison to targeted screening of those aged ≥35 years. The cost, incremental cost and impact of detection of high-risk individuals were more for women than men for all screening strategies. The impact of screening women aged ≥45 years was similar to universal screening in men. Targeted gender- and age-specific screening strategies would ensure more optimal utilisation of scarce resources compared to the current policy recommendations of universal screening.

Identification of effective screening strategies for cardiovascular disease prevention in a developing country: using cardiovascular risk-estimation and risk-reduction tools for policy recommendations

PubMed Central

2013-01-01

Background Recent increases in cardiovascular risk-factor prevalences have led to new national policy recommendations of universal screening for primary prevention of cardiovascular disease in Malaysia. This study assessed whether the current national policy recommendation of universal screening was optimal, by comparing the effectiveness and impact of various cardiovascular screening strategies. Methods Data from a national population based survey of 24 270 participants aged 30 to 74 was used. Five screening strategies were modelled for the overall population and by gender; universal and targeted screening (four age cut-off points). Screening strategies were assessed based on the ability to detect high cardiovascular risk populations (effectiveness), incremental effectiveness, impact on cardiovascular event prevention and cost of screening. Results 26.7% (95% confidence limits 25.7, 27.7) were at high cardiovascular risk, men 34.7% (33.6, 35.8) and women 18.9% (17.8, 20). Universal screening identified all those at high-risk and resulted in one high-risk individual detected for every 3.7 people screened, with an estimated cost of USD60. However, universal screening resulted in screening an additional 7169 persons, with an incremental cost of USD115,033 for detection of one additional high-risk individual in comparison to targeted screening of those aged ≥35 years. The cost, incremental cost and impact of detection of high-risk individuals were more for women than men for all screening strategies. The impact of screening women aged ≥45 years was similar to universal screening in men. Conclusions Targeted gender- and age-specific screening strategies would ensure more optimal utilisation of scarce resources compared to the current policy recommendations of universal screening. PMID:23442728

Breast cancer screening in an era of personalized regimens: a conceptual model and National Cancer Institute initiative for risk-based and preference-based approaches at a population level.

PubMed

Onega, Tracy; Beaber, Elisabeth F; Sprague, Brian L; Barlow, William E; Haas, Jennifer S; Tosteson, Anna N A; D Schnall, Mitchell; Armstrong, Katrina; Schapira, Marilyn M; Geller, Berta; Weaver, Donald L; Conant, Emily F

2014-10-01

Breast cancer screening holds a prominent place in public health, health care delivery, policy, and women's health care decisions. Several factors are driving shifts in how population-based breast cancer screening is approached, including advanced imaging technologies, health system performance measures, health care reform, concern for "overdiagnosis," and improved understanding of risk. Maximizing benefits while minimizing the harms of screening requires moving from a "1-size-fits-all" guideline paradigm to more personalized strategies. A refined conceptual model for breast cancer screening is needed to align women's risks and preferences with screening regimens. A conceptual model of personalized breast cancer screening is presented herein that emphasizes key domains and transitions throughout the screening process, as well as multilevel perspectives. The key domains of screening awareness, detection, diagnosis, and treatment and survivorship are conceptualized to function at the level of the patient, provider, facility, health care system, and population/policy arena. Personalized breast cancer screening can be assessed across these domains with both process and outcome measures. Identifying, evaluating, and monitoring process measures in screening is a focus of a National Cancer Institute initiative entitled PROSPR (Population-based Research Optimizing Screening through Personalized Regimens), which will provide generalizable evidence for a risk-based model of breast cancer screening, The model presented builds on prior breast cancer screening models and may serve to identify new measures to optimize benefits-to-harms tradeoffs in population-based screening, which is a timely goal in the era of health care reform. © 2014 American Cancer Society.

Optically Based Rapid Screening Method for Proven Optimal Treatment Strategies Before Treatment Begins

DTIC Science & Technology

to rapidly test /screen breast cancer therapeutics as a strategy to streamline drug development and provide individualized treatment. The results...system can therefore be used to streamline pre-clinical drug development, by reducing the number of animals , cost, and time required to screen new drugs

Quantum chemical approaches in structure-based virtual screening and lead optimization

NASA Astrophysics Data System (ADS)

Cavasotto, Claudio N.; Adler, Natalia S.; Aucar, Maria G.

2018-05-01

Today computational chemistry is a consolidated tool in drug lead discovery endeavors. Due to methodological developments and to the enormous advance in computer hardware, methods based on quantum mechanics (QM) have gained great attention in the last 10 years, and calculations on biomacromolecules are becoming increasingly explored, aiming to provide better accuracy in the description of protein-ligand interactions and the prediction of binding affinities. In principle, the QM formulation includes all contributions to the energy, accounting for terms usually missing in molecular mechanics force-fields, such as electronic polarization effects, metal coordination, and covalent binding; moreover, QM methods are systematically improvable, and provide a greater degree of transferability. In this mini-review we present recent applications of explicit QM-based methods in small-molecule docking and scoring, and in the calculation of binding free-energy in protein-ligand systems. Although the routine use of QM-based approaches in an industrial drug lead discovery setting remains a formidable challenging task, it is likely they will increasingly become active players within the drug discovery pipeline.

A collaborative vendor-buyer production-inventory systems with imperfect quality items, inspection errors, and stochastic demand under budget capacity constraint: a Karush-Kuhn-Tucker conditions approach

NASA Astrophysics Data System (ADS)

Kurdhi, N. A.; Nurhayati, R. A.; Wiyono, S. B.; Handajani, S. S.; Martini, T. S.

2017-01-01

In this paper, we develop an integrated inventory model considering the imperfect quality items, inspection error, controllable lead time, and budget capacity constraint. The imperfect items were uniformly distributed and detected on the screening process. However there are two types of possibilities. The first is type I of inspection error (when a non-defective item classified as defective) and the second is type II of inspection error (when a defective item classified as non-defective). The demand during the lead time is unknown, and it follows the normal distribution. The lead time can be controlled by adding the crashing cost. Furthermore, the existence of the budget capacity constraint is caused by the limited purchasing cost. The purposes of this research are: to modify the integrated vendor and buyer inventory model, to establish the optimal solution using Kuhn-Tucker’s conditions, and to apply the models. Based on the result of application and the sensitivity analysis, it can be obtained minimum integrated inventory total cost rather than separated inventory.

Should the Centers for Disease Control and Prevention’s Childhood Lead Poisoning Intervention Level Be Lowered?

PubMed Central

Bernard, Susan M.

2003-01-01

The US Centers for Disease Control and Prevention (CDC) in 1991 chose 10 μg/dL as an initial screening level for lead in children’s blood. Current data on health risks and intervention options do not support generally lowering that level, but federal lead poisoning prevention efforts can be improved by revising the follow-up testing schedule for infants aged 1 year or less with blood lead levels of 5 μg/dL or higher; universal education about lead exposure risks; universal administration of improved, locally validated risk-screening questionnaires; enhanced compliance with targeted screening recommendations and federal health program requirements; and development by regulatory agencies of primary prevention criteria that do not use the CDC’s intervention level as a target “safe” lead exposure. PMID:12893607

USASOC Injury Prevention/Performance Optimization Musculoskeletal Screening Initiative

DTIC Science & Technology

2016-10-29

Initiative " PRINCIPAL INVESTIGATOR: Kim Beals RECIPIENT: Dr. Christie Vu REPORT DATE: October 2016 TYPE OF REPORT: Annual PREPARED FOR: U.S...Injury Prevention/Performance Optimization Musculoskeletal Screening Initiative 5a. CONTRACT NUMBER W81XWH-15-C-0179 " 5b. GRANT NUMBER 5c... initiate work on the Phase 3 and 4 research aims b) IRB & DoD Regulatory Approvals i) University of Pittsburgh IRB approved May 23, 2016 ii) HRPO USAMRMC

Hit identification and optimization in virtual screening: practical recommendations based on a critical literature analysis.

PubMed

Zhu, Tian; Cao, Shuyi; Su, Pin-Chih; Patel, Ram; Shah, Darshan; Chokshi, Heta B; Szukala, Richard; Johnson, Michael E; Hevener, Kirk E

2013-09-12

A critical analysis of virtual screening results published between 2007 and 2011 was performed. The activity of reported hit compounds from over 400 studies was compared to their hit identification criteria. Hit rates and ligand efficiencies were calculated to assist in these analyses, and the results were compared with factors such as the size of the virtual library and the number of compounds tested. A series of promiscuity, druglike, and ADMET filters were applied to the reported hits to assess the quality of compounds reported, and a careful analysis of a subset of the studies that presented hit optimization was performed. These data allowed us to make several practical recommendations with respect to selection of compounds for experimental testing, definition of hit identification criteria, and general virtual screening hit criteria to allow for realistic hit optimization. A key recommendation is the use of size-targeted ligand efficiency values as hit identification criteria.

Rationally reduced libraries for combinatorial pathway optimization minimizing experimental effort.

PubMed

Jeschek, Markus; Gerngross, Daniel; Panke, Sven

2016-03-31

Rational flux design in metabolic engineering approaches remains difficult since important pathway information is frequently not available. Therefore empirical methods are applied that randomly change absolute and relative pathway enzyme levels and subsequently screen for variants with improved performance. However, screening is often limited on the analytical side, generating a strong incentive to construct small but smart libraries. Here we introduce RedLibs (Reduced Libraries), an algorithm that allows for the rational design of smart combinatorial libraries for pathway optimization thereby minimizing the use of experimental resources. We demonstrate the utility of RedLibs for the design of ribosome-binding site libraries by in silico and in vivo screening with fluorescent proteins and perform a simple two-step optimization of the product selectivity in the branched multistep pathway for violacein biosynthesis, indicating a general applicability for the algorithm and the proposed heuristics. We expect that RedLibs will substantially simplify the refactoring of synthetic metabolic pathways.

Quantifying Overdiagnosis in Cancer Screening: A Systematic Review to Evaluate the Methodology.

PubMed

Ripping, Theodora M; Ten Haaf, Kevin; Verbeek, André L M; van Ravesteyn, Nicolien T; Broeders, Mireille J M

2017-10-01

Overdiagnosis is the main harm of cancer screening programs but is difficult to quantify. This review aims to evaluate existing approaches to estimate the magnitude of overdiagnosis in cancer screening in order to gain insight into the strengths and limitations of these approaches and to provide researchers with guidance to obtain reliable estimates of overdiagnosis in cancer screening. A systematic review was done of primary research studies in PubMed that were published before January 1, 2016, and quantified overdiagnosis in breast cancer screening. The studies meeting inclusion criteria were then categorized by their methods to adjust for lead time and to obtain an unscreened reference population. For each approach, we provide an overview of the data required, assumptions made, limitations, and strengths. A total of 442 studies were identified in the initial search. Forty studies met the inclusion criteria for the qualitative review. We grouped the approaches to adjust for lead time in two main categories: the lead time approach and the excess incidence approach. The lead time approach was further subdivided into the mean lead time approach, lead time distribution approach, and natural history modeling. The excess incidence approach was subdivided into the cumulative incidence approach and early vs late-stage cancer approach. The approaches used to obtain an unscreened reference population were grouped into the following categories: control group of a randomized controlled trial, nonattenders, control region, extrapolation of a prescreening trend, uninvited groups, adjustment for the effect of screening, and natural history modeling. Each approach to adjust for lead time and obtain an unscreened reference population has its own strengths and limitations, which should be taken into consideration when estimating overdiagnosis. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Promoter library-based module combination (PLMC) technology for optimization of threonine biosynthesis in Corynebacterium glutamicum.

PubMed

Wei, Liang; Xu, Ning; Wang, Yiran; Zhou, Wei; Han, Guoqiang; Ma, Yanhe; Liu, Jun

2018-05-01

Due to the lack of efficient control elements and tools, the fine-tuning of gene expression in the multi-gene metabolic pathways is still a great challenge for engineering microbial cell factories, especially for the important industrial microorganism Corynebacterium glutamicum. In this study, the promoter library-based module combination (PLMC) technology was developed to efficiently optimize the expression of genes in C. glutamicum. A random promoter library was designed to contain the putative - 10 (NNTANANT) and - 35 (NNGNCN) consensus motifs, and refined through a three-step screening procedure to achieve numerous genetic control elements with different strength levels, including fluorescence-activated cell sorting (FACS) screening, agar plate screening, and 96-well plate screening. Multiple conventional strategies were employed for further precise characterizations of the promoter library, such as real-time quantitative PCR, sodium dodecyl sulfate polyacrylamide gel electrophoresis, FACS analysis, and the lacZ reporter system. These results suggested that the established promoter elements effectively regulated gene expression and showed varying strengths over a wide range. Subsequently, a multi-module combination technology was created based on the efficient promoter elements for combination and optimization of modules in the multi-gene pathways. Using this technology, the threonine biosynthesis pathway was reconstructed and optimized by predictable tuning expression of five modules in C. glutamicum. The threonine titer of the optimized strain was significantly improved to 12.8 g/L, an approximate 6.1-fold higher than that of the control strain. Overall, the PLMC technology presented in this study provides a rapid and effective method for combination and optimization of multi-gene pathways in C. glutamicum.

A simple method to determine IgG light chain to heavy chain polypeptide ratios expressed by CHO cells.

PubMed

Gerster, Anja; Wodarczyk, Claas; Reichenbächer, Britta; Köhler, Janet; Schulze, Andreas; Krause, Felix; Müller, Dethardt

2016-12-01

To establish a high-throughput method for determination of antibodies intra- and extracellular light chain (LC) to heavy chain (HC) polypeptide ratio as screening parameter during cell line development. Chinese Hamster Ovary (CHO) TurboCell pools containing different designed vectors supposed to result in different LC:HC polypeptide ratios were generated by targeted integration. Cell culture supernatants and cell lysates of a fed batch experiment were purified by combined Protein A and anti-kappa affinity batch purification in 96-well format. Capture of all antibodies and their fragments allowed the determination of the intra- and extracellular LC:HC peptide ratios by reduced SDS capillary electrophoresis. Results demonstrate that the method is suitable to show the significant impact of the vector design on the intra- and extracellular LC:HC polypeptide ratios. Determination of LC:HC polypeptide ratios can give important information in vector design optimization leading to CHO cell lines with optimized antibody assembly and preferred product quality.

Discovery and Development of ATP-Competitive mTOR Inhibitors Using Computational Approaches.

PubMed

Luo, Yao; Wang, Ling

2017-11-16

The mammalian target of rapamycin (mTOR) is a central controller of cell growth, proliferation, metabolism, and angiogenesis. This protein is an attractive target for new anticancer drug development. Significant progress has been made in hit discovery, lead optimization, drug candidate development and determination of the three-dimensional (3D) structure of mTOR. Computational methods have been applied to accelerate the discovery and development of mTOR inhibitors helping to model the structure of mTOR, screen compound databases, uncover structure-activity relationship (SAR) and optimize the hits, mine the privileged fragments and design focused libraries. Besides, computational approaches were also applied to study protein-ligand interactions mechanisms and in natural product-driven drug discovery. Herein, we survey the most recent progress on the application of computational approaches to advance the discovery and development of compounds targeting mTOR. Future directions in the discovery of new mTOR inhibitors using computational methods are also discussed. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Optimization of isolation and cultivation of bacterial endophytes through addition of plant extract to nutrient media

PubMed Central

Eevers, N; Gielen, M; Sánchez-López, A; Jaspers, S; White, J C; Vangronsveld, J; Weyens, N

2015-01-01

Many endophytes have beneficial effects on plants and can be exploited in biotechnological applications. Studies hypothesize that only 0.001–1% of all plant-associated bacteria are cultivable. Moreover, even after successful isolations, many endophytic bacteria often show reduced regrowth capacity. This research aimed to optimize isolation processes and culturing these bacteria afterwards. We compared several minimal and complex media in a screening. Beside the media themselves, two gelling agents and adding plant extract to media were investigated to enhance the number and diversity of endophytes as well as the growth capacity when regrown after isolation. In this work, 869 medium delivered the highest numbers of cultivable bacteria, as well as the highest diversity. When comparing gelling agents, no differences were observed in the numbers of bacteria. Adding plant extract to the media lead to a slight increase in diversity. However, when adding plant extract to improve the regrowth capacity, sharp increases of viable bacteria occurred in both rich and minimal media. PMID:25997013

Applying operations research to optimize a novel population management system for cancer screening.

PubMed

Zai, Adrian H; Kim, Seokjin; Kamis, Arnold; Hung, Ken; Ronquillo, Jeremiah G; Chueh, Henry C; Atlas, Steven J

2014-02-01

To optimize a new visit-independent, population-based cancer screening system (TopCare) by using operations research techniques to simulate changes in patient outreach staffing levels (delegates, navigators), modifications to user workflow within the information technology (IT) system, and changes in cancer screening recommendations. TopCare was modeled as a multiserver, multiphase queueing system. Simulation experiments implemented the queueing network model following a next-event time-advance mechanism, in which systematic adjustments were made to staffing levels, IT workflow settings, and cancer screening frequency in order to assess their impact on overdue screenings per patient. TopCare reduced the average number of overdue screenings per patient from 1.17 at inception to 0.86 during simulation to 0.23 at steady state. Increases in the workforce improved the effectiveness of TopCare. In particular, increasing the delegate or navigator staff level by one person improved screening completion rates by 1.3% or 12.2%, respectively. In contrast, changes in the amount of time a patient entry stays on delegate and navigator lists had little impact on overdue screenings. Finally, lengthening the screening interval increased efficiency within TopCare by decreasing overdue screenings at the patient level, resulting in a smaller number of overdue patients needing delegates for screening and a higher fraction of screenings completed by delegates. Simulating the impact of changes in staffing, system parameters, and clinical inputs on the effectiveness and efficiency of care can inform the allocation of limited resources in population management.

Screening for increased cardiometabolic risk in primary care: a systematic review

PubMed Central

den Engelsen, Corine; Koekkoek, Paula S; Godefrooij, Merijn B; Spigt, Mark G; Rutten, Guy E

2014-01-01

Background Many programmes to detect and prevent cardiovascular disease (CVD) have been performed, but the optimal strategy is not yet clear. Aim To present a systematic review of cardiometabolic screening programmes performed among apparently healthy people (not yet known to have CVD, diabetes, or cardiometabolic risk factors) and mixed populations (apparently healthy people and people diagnosed with risk factor or disease) to define the optimal screening strategy. Design and setting Systematic review of studies performed in primary care in Western countries. Method MEDLINE, Embase, and CINAHL databases were searched for studies screening for increased cardiometabolic risk. Exclusion criteria were studies designed to assess prevalence of risk factors without follow-up or treatment; without involving a GP; when fewer than two risk factors were considered as the primary outcome; and studies constrained to ethnic minorities. Results The search strategy yielded 11 445 hits; 26 met the inclusion criteria. Five studies (1995–2012) were conducted in apparently healthy populations: three used a stepwise method. Response rates varied from 24% to 79%. Twenty-one studies (1967–2012) were performed in mixed populations; one used a stepwise method. Response rates varied from 50% to 75%. Prevalence rates could not be compared because of heterogeneity of used thresholds and eligible populations. Observed time trends were a shift from mixed to apparently healthy populations, increasing use of risk scores, and increasing use of stepwise screening methods. Conclusion The optimal screening strategy in primary care is likely stepwise, in apparently healthy people, with the use of risk scores. Increasing public awareness and actively involving GPs might facilitate screening efficiency and uptake. PMID:25267047

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens

PubMed Central

Hart, Traver; Tong, Amy Hin Yan; Chan, Katie; Van Leeuwen, Jolanda; Seetharaman, Ashwin; Aregger, Michael; Chandrashekhar, Megha; Hustedt, Nicole; Seth, Sahil; Noonan, Avery; Habsid, Andrea; Sizova, Olga; Nedyalkova, Lyudmila; Climie, Ryan; Tworzyanski, Leanne; Lawson, Keith; Sartori, Maria Augusta; Alibeh, Sabriyeh; Tieu, David; Masud, Sanna; Mero, Patricia; Weiss, Alexander; Brown, Kevin R.; Usaj, Matej; Billmann, Maximilian; Rahman, Mahfuzur; Costanzo, Michael; Myers, Chad L.; Andrews, Brenda J.; Boone, Charles; Durocher, Daniel; Moffat, Jason

2017-01-01

The adaptation of CRISPR/SpCas9 technology to mammalian cell lines is transforming the study of human functional genomics. Pooled libraries of CRISPR guide RNAs (gRNAs) targeting human protein-coding genes and encoded in viral vectors have been used to systematically create gene knockouts in a variety of human cancer and immortalized cell lines, in an effort to identify whether these knockouts cause cellular fitness defects. Previous work has shown that CRISPR screens are more sensitive and specific than pooled-library shRNA screens in similar assays, but currently there exists significant variability across CRISPR library designs and experimental protocols. In this study, we reanalyze 17 genome-scale knockout screens in human cell lines from three research groups, using three different genome-scale gRNA libraries. Using the Bayesian Analysis of Gene Essentiality algorithm to identify essential genes, we refine and expand our previously defined set of human core essential genes from 360 to 684 genes. We use this expanded set of reference core essential genes, CEG2, plus empirical data from six CRISPR knockout screens to guide the design of a sequence-optimized gRNA library, the Toronto KnockOut version 3.0 (TKOv3) library. We then demonstrate the high effectiveness of the library relative to reference sets of essential and nonessential genes, as well as other screens using similar approaches. The optimized TKOv3 library, combined with the CEG2 reference set, provide an efficient, highly optimized platform for performing and assessing gene knockout screens in human cell lines. PMID:28655737

Factors associated with psychological distress amongst outpatient chemotherapy patients: An analysis of depression, anxiety and stress using the DASS-21.

PubMed

McMullen, Michelle; Lau, Peter K H; Taylor, Scott; McTigue, Joseph; Cook, Angus; Bamblett, Marion; Hasani, Arman; Johnson, Claire E

2018-04-01

This study sought to identify clinical, demographic and service-related factors associated with psychological distress amongst outpatient chemotherapy patients. Distress in cancer patients leads to increased risk of psychological comorbidity, contributing to sub-optimal treatment adherence and potentially leading to poorer health outcomes. Screening and recognition of distress and risk factors is an important aspect of holistic care within a multidisciplinary team environment. Data were obtained via survey and chart review of ambulatory chemotherapy patients at three public tertiary referral hospitals in Perth, Western Australia. The DASS-21 was used to screen for psychological distress. Regression analyses were used to assess the relationship between distress and a range of cancer, socioeconomic and treatment factors. Patients with a Karnofsky Performance Score≤80 (OR 3.8, 95% CI [1.7, 78.7]) and average waiting time (between oncology outpatient appointment and commencement of chemotherapy infusion) >60min (OR 2.4, 95% CI [1.04, 5.5]) were at increased risk of moderate-severe distress. Patients with a household income between $AU 50-75,000 p.a. had a lower risk of distress compared to <$25,000 p.a. (OR 0.05, 95% CI [0.01, 0.52]). On sub-scale analysis, depression and anxiety contributed more to overall distress than the stress subscales. Performance status, waiting times and household income were key predictors of distress. Findings could assist clinicians to identify higher-risk population subsets that could benefit from targeted screening and additional psychological and social work support. Findings could also assist administrators to consider the contribution of modifiable factors such as waiting times to patient distress. Copyright © 2017 Elsevier Inc. All rights reserved.

Screening of Natural Product Derivatives Identifies Two Structurally Related Flavonoids as Potent Quorum Sensing Inhibitors against Gram-Negative Bacteria.

PubMed

Manner, Suvi; Fallarero, Adyary

2018-05-03

Owing to the failure of conventional antibiotics in biofilm control, alternative approaches are urgently needed. Inhibition of quorum sensing (QS) represents an attractive target since it is involved in several processes essential for biofilm formation. In this study, a compound library of natural product derivatives ( n = 3040) was screened for anti-quorum sensing activity using Chromobacterium violaceum as reporter bacteria. Screening assays, based on QS-mediated violacein production and viability, were performed in parallel to identify non-bactericidal QS inhibitors (QSIs). Nine highly active QSIs were identified, while 328 compounds were classified as moderately actives and 2062 compounds as inactives. Re-testing of the highly actives at a lower concentration against C. violaceum , complemented by a literature search, led to the identification of two flavonoid derivatives as the most potent QSIs, and their impact on biofilm maturation in Escherichia coli and Pseudomonas aeruginosa was further investigated. Finally, effects of these leads on swimming and swarming motility of P. aeruginosa were quantified. The identified flavonoids affected all the studied QS-related functions at micromolar concentrations. These compounds can serve as starting points for further optimization and development of more potent QSIs as adjunctive agents used with antibiotics in the treatment of biofilms.

Colorectal cancer screening with virtual colonoscopy

NASA Astrophysics Data System (ADS)

Ge, Yaorong; Vining, David J.; Ahn, David K.; Stelts, David R.

1999-05-01

Early detection and removal of colorectal polyps have been proven to reduce mortality from colorectal carcinoma (CRC), the second leading cause of cancer deaths in the United States. Unfortunately, traditional techniques for CRC examination (i.e., barium enema, sigmoidoscopy, and colonoscopy) are unsuitable for mass screening because of either low accuracy or poor public acceptance, costs, and risks. Virtual colonoscopy (VC) is a minimally invasive alternative that is based on tomographic scanning of the colon. After a patient's bowel is optimally cleansed and distended with gas, a fast tomographic scan, typically helical computed tomography (CT), of the abdomen is performed during a single breath-hold acquisition. Two-dimensional (2D) slices and three-dimensional (3D) rendered views of the colon lumen generated from the tomographic data are then examined for colorectal polyps. Recent clinical studies conducted at several institutions including ours have shown great potential for this technology to be an effective CRC screening tool. In this paper, we describe new methods to improve bowel preparation, colon lumen visualization, colon segmentation, and polyp detection. Our initial results show that VC with the new bowel preparation and imaging protocol is capable of achieving accuracy comparable to conventional colonoscopy and our new algorithms for image analysis contribute to increased accuracy and efficiency in VC examinations.

Developing Hypothetical Inhibition Mechanism of Novel Urea Transporter B Inhibitor

NASA Astrophysics Data System (ADS)

Li, Min; Tou, Weng Ieong; Zhou, Hong; Li, Fei; Ren, Huiwen; Chen, Calvin Yu-Chian; Yang, Baoxue

2014-07-01

Urea transporter B (UT-B) is a membrane channel protein that specifically transports urea. UT-B null mouse exhibited urea selective urine concentrating ability deficiency, which suggests the potential clinical applications of the UT-B inhibitors as novel diuretics. Primary high-throughput virtual screening (HTVS) of 50000 small-molecular drug-like compounds identified 2319 hit compounds. These 2319 compounds were screened by high-throughput screening using an erythrocyte osmotic lysis assay. Based on the pharmacological data, putative UT-B binding sites were identified by structure-based drug design and validated by ligand-based and QSAR model. Additionally, UT-B structural and functional characteristics under inhibitors treated and untreated conditions were simulated by molecular dynamics (MD). As the result, we identified four classes of compounds with UT-B inhibitory activity and predicted a human UT-B model, based on which computative binding sites were identified and validated. A novel potential mechanism of UT-B inhibitory activity was discovered by comparing UT-B from different species. Results suggest residue PHE198 in rat and mouse UT-B might block the inhibitor migration pathway. Inhibitory mechanisms of UT-B inhibitors and the functions of key residues in UT-B were proposed. The binding site analysis provides a structural basis for lead identification and optimization of UT-B inhibitors.

High-Performance Screen-Printed Thermoelectric Films on Fabrics.

PubMed

Shin, Sunmi; Kumar, Rajan; Roh, Jong Wook; Ko, Dong-Su; Kim, Hyun-Sik; Kim, Sang Il; Yin, Lu; Schlossberg, Sarah M; Cui, Shuang; You, Jung-Min; Kwon, Soonshin; Zheng, Jianlin; Wang, Joseph; Chen, Renkun

2017-08-04

Printing techniques could offer a scalable approach to fabricate thermoelectric (TE) devices on flexible substrates for power generation used in wearable devices and personalized thermo-regulation. However, typical printing processes need a large concentration of binder additives, which often render a detrimental effect on electrical transport of the printed TE layers. Here, we report scalable screen-printing of TE layers on flexible fiber glass fabrics, by rationally optimizing the printing inks consisting of TE particles (p-type Bi 0.5 Sb 1.5 Te 3 or n-type Bi 2 Te 2.7 Se 0.3 ), binders, and organic solvents. We identified a suitable binder additive, methyl cellulose, which offers suitable viscosity for printability at a very small concentration (0.45-0.60 wt.%), thus minimizing its negative impact on electrical transport. Following printing, the binders were subsequently burnt off via sintering and hot pressing. We found that the nanoscale defects left behind after the binder burnt off became effective phonon scattering centers, leading to low lattice thermal conductivity in the printed n-type material. With the high electrical conductivity and low thermal conductivity, the screen-printed TE layers showed high room-temperature ZT values of 0.65 and 0.81 for p-type and n-type, respectively.

Optimization of a resazurin-based microplate assay for large-scale compound screenings against Klebsiella pneumoniae.

PubMed

Kim, Hyung Jun; Jang, Soojin

2018-01-01

A new resazurin-based assay was evaluated and optimized using a microplate (384-well) format for high-throughput screening of antibacterial molecules against Klebsiella pneumoniae . Growth of the bacteria in 384-well plates was more effectively measured and had a > sixfold higher signal-to-background ratio using the resazurin-based assay compared with absorbance measurements at 600 nm. Determination of minimum inhibitory concentrations of the antibiotics revealed that the optimized assay quantitatively measured antibacterial activity of various antibiotics. An edge effect observed in the initial assay was significantly reduced using a 1-h incubation of the bacteria-containing plates at room temperature. There was an approximately 10% decrease in signal variability between the edge and the middle wells along with improvement in the assay robustness ( Z ' = 0.99). This optimized resazurin-based assay is an efficient, inexpensive, and robust assay that can quantitatively measure antibacterial activity using a high-throughput screening system to assess a large number of compounds for discovery of new antibiotics against K. pneumoniae .

Addressing decreasing blood lead screening rates in young children in Broken Hill, NSW.

PubMed

Kardamanidis, Katina; Lyle, David M; Boreland, Frances

2008-01-01

This paper outlines the findings of a review commissioned in response to concerns about declining attendance of young children for blood lead screening in Broken Hill, NSW. A review of the literature and feedback from the local community revealed that reasons for reduced screening attendance elsewhere can be applied here, but that any proposed response should take account of local conditions.

Screening Young Children for Lead Poisoning: Guidance for State and Local Public Health Officials.

ERIC Educational Resources Information Center

Centers for Disease Control and Prevention (DHHS/PHS), Atlanta, GA.

Noting that too many children with elevated lead levels are not being identified in the United States, this report presents policy guidelines for increasing screening and follow-up care of children who most need these services, and for helping communities pursue the most appropriate approach to preventing childhood lead poisoning. Following an…

Parallel screening of drug-like natural compounds using Caco-2 cell permeability QSAR model with applicability domain, lipophilic ligand efficiency index and shape property: A case study of HIV-1 reverse transcriptase inhibitors

NASA Astrophysics Data System (ADS)

Patel, Rikin D.; Kumar, Sivakumar Prasanth; Patel, Chirag N.; Shankar, Shetty Shilpa; Pandya, Himanshu A.; Solanki, Hitesh A.

2017-10-01

The traditional drug design strategy centrally focuses on optimizing binding affinity with the receptor target and evaluates pharmacokinetic properties at a later stage which causes high rate of attrition in clinical trials. Alternatively, parallel screening allows evaluation of these properties and affinity simultaneously. In a case study to identify leads from natural compounds with experimental HIV-1 reverse transcriptase (RT) inhibition, we integrated various computational approaches including Caco-2 cell permeability QSAR model with applicability domain (AD) to recognize drug-like natural compounds, molecular docking to study HIV-1 RT interactions and shape similarity analysis with known crystal inhibitors having characteristic butterfly-like model. Further, the lipophilic properties of the compounds refined from the process with best scores were examined using lipophilic ligand efficiency (LLE) index. Seven natural compound hits viz. baicalien, (+)-calanolide A, mniopetal F, fagaronine chloride, 3,5,8-trihydroxy-4-quinolone methyl ether derivative, nitidine chloride and palmatine, were prioritized based on LLE score which demonstrated Caco-2 well absorption labeling, encompassment in AD structural coverage, better receptor affinity, shape adaptation and permissible AlogP value. We showed that this integrative approach is successful in lead exploration of natural compounds targeted against HIV-1 RT enzyme.

Cost-effectiveness of prostate cancer screening: a simulation study based on ERSPC data.

PubMed

Heijnsdijk, E A M; de Carvalho, T M; Auvinen, A; Zappa, M; Nelen, V; Kwiatkowski, M; Villers, A; Páez, A; Moss, S M; Tammela, T L J; Recker, F; Denis, L; Carlsson, S V; Wever, E M; Bangma, C H; Schröder, F H; Roobol, M J; Hugosson, J; de Koning, H J

2015-01-01

The results of the European Randomized Study of Screening for Prostate Cancer (ERSPC) trial showed a statistically significant 29% prostate cancer mortality reduction for the men screened in the intervention arm and a 23% negative impact on the life-years gained because of quality of life. However, alternative prostate-specific antigen (PSA) screening strategies for the population may exist, optimizing the effects on mortality reduction, quality of life, overdiagnosis, and costs. Based on data of the ERSPC trial, we predicted the numbers of prostate cancers diagnosed, prostate cancer deaths averted, life-years and quality-adjusted life-years (QALY) gained, and cost-effectiveness of 68 screening strategies starting at age 55 years, with a PSA threshold of 3, using microsimulation modeling. The screening strategies varied by age to stop screening and screening interval (one to 14 years or once in a lifetime screens), and therefore number of tests. Screening at short intervals of three years or less was more cost-effective than using longer intervals. Screening at ages 55 to 59 years with two-year intervals had an incremental cost-effectiveness ratio of $73000 per QALY gained and was considered optimal. With this strategy, lifetime prostate cancer mortality reduction was predicted as 13%, and 33% of the screen-detected cancers were overdiagnosed. When better quality of life for the post-treatment period could be achieved, an older age of 65 to 72 years for ending screening was obtained. Prostate cancer screening can be cost-effective when it is limited to two or three screens between ages 55 to 59 years. Screening above age 63 years is less cost-effective because of loss of QALYs because of overdiagnosis. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Do Men and Women Need to Be Screened Differently with Fecal Immunochemical Testing? A Cost-Effectiveness Analysis.

PubMed

Meulen, Miriam P van der; Kapidzic, Atija; Leerdam, Monique E van; van der Steen, Alex; Kuipers, Ernst J; Spaander, Manon C W; de Koning, Harry J; Hol, Lieke; Lansdorp-Vogelaar, Iris

2017-08-01

Background: Several studies suggest that test characteristics for the fecal immunochemical test (FIT) differ by gender, triggering a debate on whether men and women should be screened differently. We used the microsimulation model MISCAN-Colon to evaluate whether screening stratified by gender is cost-effective. Methods: We estimated gender-specific FIT characteristics based on first-round positivity and detection rates observed in a FIT screening pilot (CORERO-1). Subsequently, we used the model to estimate harms, benefits, and costs of 480 gender-specific FIT screening strategies and compared them with uniform screening. Results: Biennial FIT screening from ages 50 to 75 was less effective in women than men [35.7 vs. 49.0 quality-adjusted life years (QALY) gained, respectively] at higher costs (€42,161 vs. -€5,471, respectively). However, the incremental QALYs gained and costs of annual screening compared with biennial screening were more similar for both genders (8.7 QALYs gained and €26,394 for women vs. 6.7 QALYs gained and €20,863 for men). Considering all evaluated screening strategies, optimal gender-based screening yielded at most 7% more QALYs gained than optimal uniform screening and even resulted in equal costs and QALYs gained from a willingness-to-pay threshold of €1,300. Conclusions: FIT screening is less effective in women, but the incremental cost-effectiveness is similar in men and women. Consequently, screening stratified by gender is not more cost-effective than uniform FIT screening. Impact: Our conclusions support the current policy of uniform FIT screening. Cancer Epidemiol Biomarkers Prev; 26(8); 1328-36. ©2017 AACR . ©2017 American Association for Cancer Research.

Optimizing bowel preparation for colonoscopy: a guide to enhance quality of visualization

PubMed Central

Bechtold, Matthew L.; Mir, Fazia; Puli, Srinivas R.; Nguyen, Douglas L.

2016-01-01

Colonoscopy is an important screening and therapeutic modality for colorectal cancer. Unlike other screening tests, colonoscopy is dependent on pre-procedure bowel preparation. If the bowel preparation is poor, significant pathology may be missed. Many factors are known to improve bowel preparation. This review will highlight those factors that may optimize the bowel preparation, including choice of bowel preparation, grading or scoring of the bowel preparation, special factors that influence preparation, and diet prior to colonoscopy that affects bowel preparation. The aim of the review is to offer suggestions and guide endoscopists on how to optimize the bowel preparation for the patients undergoing colonoscopy. PMID:27065725

Fabrication of aluminum-carbon composites

NASA Technical Reports Server (NTRS)

Novak, R. C.

1973-01-01

A screening, optimization, and evaluation program is reported of unidirectional carbon-aluminum composites. During the screening phase both large diameter monofilament and small diameter multifilament reinforcements were utilized to determine optimum precursor tape making and consolidation techniques. Difficulty was encountered in impregnating and consolidating the multifiber reinforcements. Large diameter monofilament reinforcement was found easier to fabricate into composites and was selected to carry into the optimization phase in which the hot pressing parameters were refined and the size of the fabricated panels was scaled up. After process optimization the mechanical properties of the carbon-aluminum composites were characterized in tension, stress-rupture and creep, mechanical fatigue, thermal fatigue, thermal aging, thermal expansion, and impact.

Understanding and Creating Accessible Touch Screen Interactions for Blind People

ERIC Educational Resources Information Center

Kane, Shaun K.

2011-01-01

Using touch screens presents a number of usability and accessibility challenges for blind people. Most touch screen-based user interfaces are optimized for visual interaction, and are therefore difficult or impossible to use without vision. This dissertation presents an approach to redesigning gesture-based user interfaces to enable blind people…

Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge

PubMed Central

Gallicchio, Emilio; Deng, Nanjie; He, Peng; Wickstrom, Lauren; Perryman, Alexander L.; Santiago, Daniel N.; Forli, Stefano; Olson, Arthur J.; Levy, Ronald M.

2014-01-01

As part of the SAMPL4 blind challenge, filtered AutoDock Vina ligand docking predictions and large scale binding energy distribution analysis method binding free energy calculations have been applied to the virtual screening of a focused library of candidate binders to the LEDGF site of the HIV integrase protein. The computational protocol leveraged docking and high level atomistic models to improve enrichment. The enrichment factor of our blind predictions ranked best among all of the computational submissions, and second best overall. This work represents to our knowledge the first example of the application of an all-atom physics-based binding free energy model to large scale virtual screening. A total of 285 parallel Hamiltonian replica exchange molecular dynamics absolute protein-ligand binding free energy simulations were conducted starting from docked poses. The setup of the simulations was fully automated, calculations were distributed on multiple computing resources and were completed in a 6-weeks period. The accuracy of the docked poses and the inclusion of intramolecular strain and entropic losses in the binding free energy estimates were the major factors behind the success of the method. Lack of sufficient time and computing resources to investigate additional protonation states of the ligands was a major cause of mispredictions. The experiment demonstrated the applicability of binding free energy modeling to improve hit rates in challenging virtual screening of focused ligand libraries during lead optimization. PMID:24504704

Screening and identification of genetic loci involved in producing more/denser inclusion bodies in Escherichia coli

PubMed Central

2013-01-01

Background Many proteins and peptides have been used in therapeutic or industrial applications. They are often produced in microbial production hosts by fermentation. Robust protein production in the hosts and efficient downstream purification are two critical factors that could significantly reduce cost for microbial protein production by fermentation. Producing proteins/peptides as inclusion bodies in the hosts has the potential to achieve both high titers in fermentation and cost-effective downstream purification. Manipulation of the host cells such as overexpression/deletion of certain genes could lead to producing more and/or denser inclusion bodies. However, there are limited screening methods to help to identify beneficial genetic changes rendering more protein production and/or denser inclusion bodies. Results We report development and optimization of a simple density gradient method that can be used for distinguishing and sorting E. coli cells with different buoyant densities. We demonstrate utilization of the method to screen genetic libraries to identify a) expression of glyQS loci on plasmid that increased expression of a peptide of interest as well as the buoyant density of inclusion body producing E. coli cells; and b) deletion of a host gltA gene that increased the buoyant density of the inclusion body produced in the E. coli cells. Conclusion A novel density gradient sorting method was developed to screen genetic libraries. Beneficial host genetic changes could be exploited to improve recombinant protein expression as well as downstream protein purification. PMID:23638724

Screening and identification of genetic loci involved in producing more/denser inclusion bodies in Escherichia coli.

PubMed

Pandey, Neeraj; Sachan, Annapurna; Chen, Qi; Ruebling-Jass, Kristin; Bhalla, Ritu; Panguluri, Kiran Kumar; Rouviere, Pierre E; Cheng, Qiong

2013-05-02

Many proteins and peptides have been used in therapeutic or industrial applications. They are often produced in microbial production hosts by fermentation. Robust protein production in the hosts and efficient downstream purification are two critical factors that could significantly reduce cost for microbial protein production by fermentation. Producing proteins/peptides as inclusion bodies in the hosts has the potential to achieve both high titers in fermentation and cost-effective downstream purification. Manipulation of the host cells such as overexpression/deletion of certain genes could lead to producing more and/or denser inclusion bodies. However, there are limited screening methods to help to identify beneficial genetic changes rendering more protein production and/or denser inclusion bodies. We report development and optimization of a simple density gradient method that can be used for distinguishing and sorting E. coli cells with different buoyant densities. We demonstrate utilization of the method to screen genetic libraries to identify a) expression of glyQS loci on plasmid that increased expression of a peptide of interest as well as the buoyant density of inclusion body producing E. coli cells; and b) deletion of a host gltA gene that increased the buoyant density of the inclusion body produced in the E. coli cells. A novel density gradient sorting method was developed to screen genetic libraries. Beneficial host genetic changes could be exploited to improve recombinant protein expression as well as downstream protein purification.

Identification of novel drug scaffolds for inhibition of SARS-CoV 3-Chymotrypsin-like protease using virtual and high-throughput screenings.

PubMed

Lee, Hyun; Mittal, Anuradha; Patel, Kavankumar; Gatuz, Joseph L; Truong, Lena; Torres, Jaime; Mulhearn, Debbie C; Johnson, Michael E

2014-01-01

We have used a combination of virtual screening (VS) and high-throughput screening (HTS) techniques to identify novel, non-peptidic small molecule inhibitors against human SARS-CoV 3CLpro. A structure-based VS approach integrating docking and pharmacophore based methods was employed to computationally screen 621,000 compounds from the ZINC library. The screening protocol was validated using known 3CLpro inhibitors and was optimized for speed, improved selectivity, and for accommodating receptor flexibility. Subsequently, a fluorescence-based enzymatic HTS assay was developed and optimized to experimentally screen approximately 41,000 compounds from four structurally diverse libraries chosen mainly based on the VS results. False positives from initial HTS hits were eliminated by a secondary orthogonal binding analysis using surface plasmon resonance (SPR). The campaign identified a reversible small molecule inhibitor exhibiting mixed-type inhibition with a K(i) value of 11.1 μM. Together, these results validate our protocols as suitable approaches to screen virtual and chemical libraries, and the newly identified compound reported in our study represents a promising structural scaffold to pursue for further SARS-CoV 3CLpro inhibitor development. Copyright © 2013. Published by Elsevier Ltd.

Unifying Screening Processes Within the PROSPR Consortium: A Conceptual Model for Breast, Cervical, and Colorectal Cancer Screening

PubMed Central

Kim, Jane J.; Schapira, Marilyn M.; Tosteson, Anna N. A.; Zauber, Ann G.; Geiger, Ann M.; Kamineni, Aruna; Weaver, Donald L.; Tiro, Jasmin A.

2015-01-01

General frameworks of the cancer screening process are available, but none directly compare the process in detail across different organ sites. This limits the ability of medical and public health professionals to develop and evaluate coordinated screening programs that apply resources and population management strategies available for one cancer site to other sites. We present a trans-organ conceptual model that incorporates a single screening episode for breast, cervical, and colorectal cancers into a unified framework based on clinical guidelines and protocols; the model concepts could be expanded to other organ sites. The model covers four types of care in the screening process: risk assessment, detection, diagnosis, and treatment. Interfaces between different provider teams (eg, primary care and specialty care), including communication and transfer of responsibility, may occur when transitioning between types of care. Our model highlights across each organ site similarities and differences in steps, interfaces, and transitions in the screening process and documents the conclusion of a screening episode. This model was developed within the National Cancer Institute–funded consortium Population-based Research Optimizing Screening through Personalized Regimens (PROSPR). PROSPR aims to optimize the screening process for breast, cervical, and colorectal cancer and includes seven research centers and a statistical coordinating center. Given current health care reform initiatives in the United States, this conceptual model can facilitate the development of comprehensive quality metrics for cancer screening and promote trans-organ comparative cancer screening research. PROSPR findings will support the design of interventions that improve screening outcomes across multiple cancer sites. PMID:25957378

Early Detection and Screening for Breast Cancer.

PubMed

Coleman, Cathy

2017-05-01

To review the history, current status, and future trends related to breast cancer screening. Peer-reviewed articles, web sites, and textbooks. Breast cancer remains a complex, heterogeneous disease. Serial screening with mammography is the most effective method to detect early stage disease and decrease mortality. Although politics and economics may inhibit organized mammography screening programs in many countries, the judicious use of proficient clinical and self-breast examination can also identify small tumors leading to reduced morbidity. Oncology nurses have exciting opportunities to lead, facilitate, and advocate for delivery of high-quality screening services targeting individuals and communities. A practical approach is needed to translate the complexities and controversies surrounding breast cancer screening into improved care outcomes. Copyright © 2017 Elsevier Inc. All rights reserved.

Identification and statistical optimization of fermentation conditions for a newly isolated extracellular cholesterol oxidase-producing Streptomyces cavourensis strain NEAE-42.

PubMed

El-Naggar, Noura El-Ahmady; El-Shweihy, Nancy M; El-Ewasy, Sara M

2016-09-20

Due to broad range of clinical and industrial applications of cholesterol oxidase, isolation and screening of bacterial strains producing extracellular form of cholesterol oxidase is of great importance. One hundred and thirty actinomycete isolates were screened for their cholesterol oxidase activity. Among them, a potential culture, strain NEAE-42 is displayed the highest extracellular cholesterol oxidase activity. It was selected and identified as Streptomyces cavourensis strain NEAE-42. The optimization of different process parameters for cholesterol oxidase production by Streptomyces cavourensis strain NEAE-42 using Plackett-Burman experimental design and response surface methodology was carried out. Fifteen variables were screened using Plackett-Burman experimental design. Cholesterol, initial pH and (NH4)2SO4 were the most significant positive independent variables affecting cholesterol oxidase production. Central composite design was chosen to elucidate the optimal concentrations of the selected process variables on cholesterol oxidase production. It was found that, cholesterol oxidase production by Streptomyces cavourensis strain NEAE-42 after optimization process was 20.521U/mL which is higher than result obtained from the basal medium before screening process using Plackett-Burman (3.31 U/mL) with a fold of increase 6.19. The cholesterol oxidase level production obtained in this study (20.521U/mL) by the statistical method is higher than many of the reported values.

2D/ 3D Quantitative Ultrasound of the Breast

NASA Astrophysics Data System (ADS)

Nasief, Haidy Gerges

Breast cancer is the second leading cause of cancer death of women in the United States, so breast cancer screening for early detection is common. The purpose of this dissertation is to optimize quantitative ultrasound (QUS) methods to improve the specificity and objectivity of breast ultrasound. To pursue this goal, the dissertation is divided into two parts: 1) to optimize 2D QUS, and 2) to introduce and validate 3D QUS. Previous studies had validated these methods in phantoms. Applying our QUS analysis on subcutaneous breast fat demonstrated that QUS parameter estimates for subcutaneous fat were consistent among different human subjects. This validated our in vivo data acquisition methods and supported the use of breast fat as a clinical reference tissue for ultrasound BI-RADSRTM assessments. Although current QUS methods perform well for straightforward cases when assumptions of stationarity and diffuse scattering are well-founded, these conditions often are not present due to the complicated nature of in vivo breast tissue. Key improvements in QUS algorithms to address these challenges were: 1) applying a "modified least squares method (MLSM)" to account for the heterogeneous tissue path between the transducer and the region of interest, ROI; 2) detecting anisotropy in acoustic parameters; and 3) detecting and removing the echo sources that depart from diffuse and stationary scattering conditions. The results showed that a Bayesian classifier combining three QUS parameters in a biased pool of high-quality breast ultrasound data successfully differentiated all fibroadenomas from all carcinomas. Given promising initial results in 2D, extension to 3D acquisitions in QUS provided a unique capability to test QUS for the entire breast volume. QUS parameter estimates using 3D data were consistent with those found in 2D for phantoms and in vivo data. Extensions of QUS technology from 2D to 3D can improve the specificity of breast ultrasound, and thus, could lead to improved screening with this modality.

Virtual Screening with AutoDock: Theory and Practice

PubMed Central

Cosconati, Sandro; Forli, Stefano; Perryman, Alex L.; Harris, Rodney; Goodsell, David S.; Olson, Arthur J.

2011-01-01

Importance to the field Virtual screening is a computer-based technique for identifying promising compounds to bind to a target molecule of known structure. Given the rapidly increasing number of protein and nucleic acid structures, virtual screening continues to grow as an effective method for the discovery of new inhibitors and drug molecules. Areas covered in this review We describe virtual screening methods that are available in the AutoDock suite of programs, and several of our successes in using AutoDock virtual screening in pharmaceutical lead discovery. What the reader will gain A general overview of the challenges of virtual screening is presented, along with the tools available in the AutoDock suite of programs for addressing these challenges. Take home message Virtual screening is an effective tool for the discovery of compounds for use as leads in drug discovery, and the free, open source program AutoDock is an effective tool for virtual screening. PMID:21532931

An Efficient Variable Screening Method for Effective Surrogate Models for Reliability-Based Design Optimization

DTIC Science & Technology

2014-04-01

surrogate model generation is difficult for high -dimensional problems, due to the curse of dimensionality. Variable screening methods have been...a variable screening model was developed for the quasi-molecular treatment of ion-atom collision [16]. In engineering, a confidence interval of...for high -level radioactive waste [18]. Moreover, the design sensitivity method can be extended to the variable screening method because vital

Optimization of electrostatic dual-grid beam-deflection system

NASA Technical Reports Server (NTRS)

Hudson, W. R.; Lathem, W. C.; Power, J. L.; Banks, B. A.

1972-01-01

Tests were performed to minimize accelerator grid erosion of a 5-cm diameter Kaufman ion thruster due to direct beam impingement. Several different screen hole diameters, pillow-shape-square screen holes, and dished screen grids were tried. The optimization was accomplished by copper plating the accelerator grid before testing each grid configuration on a thruster for a 2-hour run. The thruster beam sputtered copper and molybdenum from the accelerator grid where the beam impinged. The observed erosion patterns and measured accelerator currents were used to determine how to modify the accelerator system. The lowest erosion was obtained for a 50-percent open area pillow-shape-square-aperture screen grid, dished 0.043 centimeter convex toward the accelerator grid, which was positioned with the center of the screen grid 0.084 centimeter from the accelerator grid. During this investigation the accelerator current was reduced from 120 to 55 microamperes and was also more uniformly distributed over the area of the accelerator grid.

The interdependence between screening methods and screening libraries.

PubMed

Shelat, Anang A; Guy, R Kiplin

2007-06-01

The most common methods for discovery of chemical compounds capable of manipulating biological function involves some form of screening. The success of such screens is highly dependent on the chemical materials - commonly referred to as libraries - that are assayed. Classic methods for the design of screening libraries have depended on knowledge of target structure and relevant pharmacophores for target focus, and on simple count-based measures to assess other properties. The recent proliferation of two novel screening paradigms, structure-based screening and high-content screening, prompts a profound rethink about the ideal composition of small-molecule screening libraries. We suggest that currently utilized libraries are not optimal for addressing new targets by high-throughput screening, or complex phenotypes by high-content screening.

Heuristic lipophilicity potential for computer-aided rational drug design: optimizations of screening functions and parameters.

PubMed

Du, Q; Mezey, P G

1998-09-01

In this research we test and compare three possible atom-based screening functions used in the heuristic molecular lipophilicity potential (HMLP). Screening function 1 is a power distance-dependent function, bi/[formula: see text] Ri-r [formula: see text] gamma, screening function 2 is an exponential distance-dependent function, bi exp(-[formula: see text] Ri-r [formula: see text]/d0), and screening function 3 is a weighted distance-dependent function, sign(bi) exp[-xi [formula: see text] Ri-r [formula: see text]/magnitude of bi)]. For every screening function, the parameters (gamma, d0, and xi) are optimized using 41 common organic molecules of 4 types of compounds: aliphatic alcohols, aliphatic carboxylic acids, aliphatic amines, and aliphatic alkanes. The results of calculations show that screening function 3 cannot give chemically reasonable results, however, both the power screening function and the exponential screening function give chemically satisfactory results. There are two notable differences between screening functions 1 and 2. First, the exponential screening function has larger values in the short distance than the power screening function, therefore more influence from the nearest neighbors is involved using screening function 2 than screening function 1. Second, the power screening function has larger values in the long distance than the exponential screening function, therefore screening function 1 is effected by atoms at long distance more than screening function 2. For screening function 1, the suitable range of parameter gamma is 1.0 < gamma < 3.0, gamma = 2.3 is recommended, and gamma = 2.0 is the nearest integral value. For screening function 2, the suitable range of parameter d0 is 1.5 < d0 < 3.0, and d0 = 2.0 is recommended. HMLP developed in this research provides a potential tool for computer-aided three-dimensional drug design.

Fragment-Based Phenotypic Lead Discovery: Cell-Based Assay to Target Leishmaniasis.

PubMed

Ayotte, Yann; Bilodeau, François; Descoteaux, Albert; LaPlante, Steven R

2018-05-02

A rapid and practical approach for the discovery of new chemical matter for targeting pathogens and diseases is described. Fragment-based phenotypic lead discovery (FPLD) combines aspects of traditional fragment-based lead discovery (FBLD), which involves the screening of small-molecule fragment libraries to target specific proteins, with phenotypic lead discovery (PLD), which typically involves the screening of drug-like compounds in cell-based assays. To enable FPLD, a diverse library of fragments was first designed, assembled, and curated. This library of soluble, low-molecular-weight compounds was then pooled to expedite screening. Axenic cultures of Leishmania promastigotes were screened, and single hits were then tested for leishmanicidal activity against intracellular amastigote forms in infected murine bone-marrow-derived macrophages without evidence of toxicity toward mammalian cells. These studies demonstrate that FPLD can be a rapid and effective means to discover hits that can serve as leads for further medicinal chemistry purposes or as tool compounds for identifying known or novel targets. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integration of Lead Discovery Tactics and the Evolution of the Lead Discovery Toolbox.

PubMed

Leveridge, Melanie; Chung, Chun-Wa; Gross, Jeffrey W; Phelps, Christopher B; Green, Darren

2018-06-01

There has been much debate around the success rates of various screening strategies to identify starting points for drug discovery. Although high-throughput target-based and phenotypic screening has been the focus of this debate, techniques such as fragment screening, virtual screening, and DNA-encoded library screening are also increasingly reported as a source of new chemical equity. Here, we provide examples in which integration of more than one screening approach has improved the campaign outcome and discuss how strengths and weaknesses of various methods can be used to build a complementary toolbox of approaches, giving researchers the greatest probability of successfully identifying leads. Among others, we highlight case studies for receptor-interacting serine/threonine-protein kinase 1 and the bromo- and extra-terminal domain family of bromodomains. In each example, the unique insight or chemistries individual approaches provided are described, emphasizing the synergy of information obtained from the various tactics employed and the particular question each tactic was employed to answer. We conclude with a short prospective discussing how screening strategies are evolving, what this screening toolbox might look like in the future, how to maximize success through integration of multiple tactics, and scenarios that drive selection of one combination of tactics over another.

Cost-effectiveness of cervical cancer screening with primary human papillomavirus testing in Norway.

PubMed

Burger, E A; Ortendahl, J D; Sy, S; Kristiansen, I S; Kim, J J

2012-04-24

New screening technologies and vaccination against human papillomavirus (HPV), the necessary cause of cervical cancer, may impact optimal approaches to prevent cervical cancer. We evaluated the cost-effectiveness of alternative screening strategies to inform cervical cancer prevention guidelines in Norway. We leveraged the primary epidemiologic and economic data from Norway to contextualise a simulation model of HPV-induced cervical cancer. The current cytology-only screening was compared with strategies involving cytology at younger ages and primary HPV-based screening at older ages (31/34+ years), an option being actively deliberated by the Norwegian government. We varied the switch-age, screening interval, and triage strategies for women with HPV-positive results. Uncertainty was evaluated in sensitivity analysis. Current cytology-only screening was less effective and more costly than strategies that involve switching to primary HPV testing in older ages. For unvaccinated women, switching at age 34 years to primary HPV testing every 4 years was optimal given the Norwegian cost-effectiveness threshold ($83,000 per year of life saved). For vaccinated women, a 6-year screening interval was cost-effective. When we considered a wider range of strategies, we found that an earlier switch to HPV testing (at age 31 years) may be preferred. Strategies involving a switch to HPV testing for primary screening in older women is expected to be cost-effective compared with current recommendations in Norway.

An optimized, fast-to-perform mouse lung infection model with the human pathogen Chlamydia trachomatis for in vivo screening of antibiotics, vaccine candidates and modified host-pathogen interactions.

PubMed

Dutow, Pavel; Wask, Lea; Bothe, Miriam; Fehlhaber, Beate; Laudeley, Robert; Rheinheimer, Claudia; Yang, Zhangsheng; Zhong, Guangming; Glage, Silke; Klos, Andreas

2016-03-01

Chlamydia trachomatis causes sexually transmitted diseases with infertility, pelvic inflammatory disease and neonatal pneumonia as complications. The duration of urogenital mouse models with the strict mouse pathogen C. muridarum addressing vaginal shedding, pathological changes of the upper genital tract or infertility is rather long. Moreover, vaginal C. trachomatis application usually does not lead to the complications feared in women. A fast-to-perform mouse model is urgently needed to analyze new antibiotics, vaccine candidates, immune responses (in gene knockout animals) or mutants of C. trachomatis. To complement the valuable urogenital model with a much faster and quantifiable screening method, we established an optimized lung infection model for the human intracellular bacterium C. trachomatis serovar D (and L2) in immunocompetent C57BL/6J mice. We demonstrated its usefulness by sensitive determination of antibiotic effects characterizing advantages and limitations achievable by early or delayed short tetracycline treatment and single-dose azithromycin application. Moreover, we achieved partial acquired protection in reinfection with serovar D indicating usability for vaccine studies, and showed a different course of disease in absence of complement factor C3. Sensitive monitoring parameters were survival rate, body weight, clinical score, bacterial load, histological score, the granulocyte marker myeloperoxidase, IFN-γ, TNF-α, MCP-1 and IL-6. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Breast health in developing countries.

PubMed

Yip, C H; Taib, N A

2014-12-01

Breast cancer is one of the leading cancers world-wide. While the incidence in developing countries is lower than in developed countries, the mortality is much higher. Of the estimated 1 600 000 new cases of breast cancer globally in 2012, 794 000 were in the more developed world compared to 883 000 in the less developed world; however, there were 198 000 deaths in the more developed world compared to 324 000 in the less developed world (data from Globocan 2012, IARC). Survival from breast cancer depends on two main factors--early detection and optimal treatment. In developing countries, women present with late stages of disease. The barriers to early detection are physical, such as geographical isolation, financial as well as psychosocial, including lack of education, belief in traditional medicine and lack of autonomous decision-making in the male-dominated societies that prevail in the developing world. There are virtually no population-based breast cancer screening programs in developing countries. However, before any screening program can be implemented, there must be facilities to treat the cancers that are detected. Inadequate access to optimal treatment of breast cancer remains a problem. Lack of specialist manpower, facilities and anticancer drugs contribute to the suboptimal care that a woman with breast cancer in a low-income country receives. International groups such as the Breast Health Global Initiative were set up to develop economically feasible, clinical practice guidelines for breast cancer management to improve breast health outcomes in countries with limited resources.

Lead Poison Detection

NASA Technical Reports Server (NTRS)

1976-01-01

With NASA contracts, Whittaker Corporations Space Science division has developed an electro-optical instrument to mass screen for lead poisoning. Device is portable and detects protoporphyrin in whole blood. Free corpuscular porphyrins occur as an early effect of lead ingestion. Also detects lead in urine used to confirm blood tests. Test is inexpensive and can be applied by relatively unskilled personnel. Similar Whittaker fluorometry device called "drug screen" can measure morphine and quinine in urine much faster and cheaper than other methods.

Breast Cancer Screening in the Precision Medicine Era: Risk-Based Screening in a Population-Based Trial.

PubMed

Shieh, Yiwey; Eklund, Martin; Madlensky, Lisa; Sawyer, Sarah D; Thompson, Carlie K; Stover Fiscalini, Allison; Ziv, Elad; Van't Veer, Laura J; Esserman, Laura J; Tice, Jeffrey A

2017-01-01

Ongoing controversy over the optimal approach to breast cancer screening has led to discordant professional society recommendations, particularly in women age 40 to 49 years. One potential solution is risk-based screening, where decisions around the starting age, stopping age, frequency, and modality of screening are based on individual risk to maximize the early detection of aggressive cancers and minimize the harms of screening through optimal resource utilization. We present a novel approach to risk-based screening that integrates clinical risk factors, breast density, a polygenic risk score representing the cumulative effects of genetic variants, and sequencing for moderate- and high-penetrance germline mutations. We demonstrate how thresholds of absolute risk estimates generated by our prediction tools can be used to stratify women into different screening strategies (biennial mammography, annual mammography, annual mammography with adjunctive magnetic resonance imaging, defer screening at this time) while informing the starting age of screening for women age 40 to 49 years. Our risk thresholds and corresponding screening strategies are based on current evidence but need to be tested in clinical trials. The Women Informed to Screen Depending On Measures of risk (WISDOM) Study, a pragmatic, preference-tolerant randomized controlled trial of annual vs personalized screening, will study our proposed approach. WISDOM will evaluate the efficacy, safety, and acceptability of risk-based screening beginning in the fall of 2016. The adaptive design of this trial allows continued refinement of our risk thresholds as the trial progresses, and we discuss areas where we anticipate emerging evidence will impact our approach. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Applying operations research to optimize a novel population management system for cancer screening

PubMed Central

Zai, Adrian H; Kim, Seokjin; Kamis, Arnold; Hung, Ken; Ronquillo, Jeremiah G; Chueh, Henry C; Atlas, Steven J

2014-01-01

Objective To optimize a new visit-independent, population-based cancer screening system (TopCare) by using operations research techniques to simulate changes in patient outreach staffing levels (delegates, navigators), modifications to user workflow within the information technology (IT) system, and changes in cancer screening recommendations. Materials and methods TopCare was modeled as a multiserver, multiphase queueing system. Simulation experiments implemented the queueing network model following a next-event time-advance mechanism, in which systematic adjustments were made to staffing levels, IT workflow settings, and cancer screening frequency in order to assess their impact on overdue screenings per patient. Results TopCare reduced the average number of overdue screenings per patient from 1.17 at inception to 0.86 during simulation to 0.23 at steady state. Increases in the workforce improved the effectiveness of TopCare. In particular, increasing the delegate or navigator staff level by one person improved screening completion rates by 1.3% or 12.2%, respectively. In contrast, changes in the amount of time a patient entry stays on delegate and navigator lists had little impact on overdue screenings. Finally, lengthening the screening interval increased efficiency within TopCare by decreasing overdue screenings at the patient level, resulting in a smaller number of overdue patients needing delegates for screening and a higher fraction of screenings completed by delegates. Conclusions Simulating the impact of changes in staffing, system parameters, and clinical inputs on the effectiveness and efficiency of care can inform the allocation of limited resources in population management. PMID:24043318

Identification of compounds protective against G93A-SOD1 toxicity for the treatment of amyotrophic lateral sclerosis.

PubMed

Benmohamed, Radhia; Arvanites, Anthony C; Kim, Jinho; Ferrante, Robert J; Silverman, Richard B; Morimoto, Richard I; Kirsch, Donald R

2011-03-01

The underlying cause of amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disorder, remains unknown. However, there is strong evidence that one pathophysiological mechanism, toxic protein misfolding and/or aggregation, may trigger motor neuron dysfunction and loss. Since the clinical and pathological features of sporadic and familial ALS are indistinguishable, all forms of the disease may be better understood and ultimately treated by studying pathogenesis and therapy in models expressing mutant forms of SOD1. We developed a cellular model in which cell death depended on the expression of G93A-SOD1, a mutant form of superoxide dismutase found in familial ALS patients that produces toxic protein aggregates. This cellular model was optimized for high throughput screening to identify protective compounds from a >50,000 member chemical library. Three novel chemical scaffolds were selected for further study following screen implementation, counter-screening and secondary testing, including studies with purchased analogs. All three scaffolds blocked SOD1 aggregation in high content screening assays and data on the optimization and further characterization of these compounds will be reported separately. These data suggest that optimization of these chemicals scaffolds may produce therapeutic candidates for ALS patients.

Generation of ligand-based pharmacophore model and virtual screening for identification of novel tubulin inhibitors with potent anticancer activity.

PubMed

Chiang, Yi-Kun; Kuo, Ching-Chuan; Wu, Yu-Shan; Chen, Chung-Tong; Coumar, Mohane Selvaraj; Wu, Jian-Sung; Hsieh, Hsing-Pang; Chang, Chi-Yen; Jseng, Huan-Yi; Wu, Ming-Hsine; Leou, Jiun-Shyang; Song, Jen-Shin; Chang, Jang-Yang; Lyu, Ping-Chiang; Chao, Yu-Sheng; Wu, Su-Ying

2009-07-23

A pharmacophore model, Hypo1, was built on the basis of 21 training-set indole compounds with varying levels of antiproliferative activity. Hypo1 possessed important chemical features required for the inhibitors and demonstrated good predictive ability for biological activity, with high correlation coefficients of 0.96 and 0.89 for the training-set and test-set compounds, respectively. Further utilization of the Hypo1 pharmacophore model to screen chemical database in silico led to the identification of four compounds with antiproliferative activity. Among these four compounds, 43 showed potent antiproliferative activity against various cancer cell lines with the strongest inhibition on the proliferation of KB cells (IC(50) = 187 nM). Further biological characterization revealed that 43 effectively inhibited tubulin polymerization and significantly induced cell cycle arrest in G(2)-M phase. In addition, 43 also showed the in vivo-like anticancer effects. To our knowledge, 43 is the most potent antiproliferative compound with antitubulin activity discovered by computer-aided drug design. The chemical novelty of 43 and its anticancer activities make this compound worthy of further lead optimization.

Rapid discovery and structure-activity profiling of novel inhibitors of human immunodeficiency virus type 1 protease enabled by the copper(I)-catalyzed synthesis of 1,2,3-triazoles and their further functionalization.

PubMed

Whiting, Matthew; Tripp, Jonathan C; Lin, Ying-Chuan; Lindstrom, William; Olson, Arthur J; Elder, John H; Sharpless, K Barry; Fokin, Valery V

2006-12-28

Building from the results of a computational screen of a range of triazole-containing compounds for binding efficiency to human immunodeficiency virus type 1 protease (HIV-1-Pr), a novel series of potent inhibitors has been developed. The copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC), which provides ready access to 1,4-disubstituted-1,2,3-triazoles, was used to unite a focused library of azide-containing fragments with a diverse array of functionalized alkyne-containing building blocks. In combination with direct screening of the crude reaction products, this method led to the rapid identification of a lead structure and readily enabled optimization of both azide and alkyne fragments. Replacement of the triazole with a range of alternative linkers led to greatly reduced protease inhibition; however, further functionalization of the triazoles at the 5-position gave a series of compounds with increased activity, exhibiting Ki values as low as 8 nM.

In- and Ga-based inorganic double perovskites with direct bandgaps for photovoltaic applications.

PubMed

Dai, Jun; Ma, Liang; Ju, Minggang; Huang, Jinsong; Zeng, Xiao Cheng

2017-08-16

Double perovskites in the form of A 2 B'B''X 6 (A = Cs, B' = Ag, B'' = Bi) have been reported as potential alternatives to lead-containing organometal trihalide perovskites. However, all double perovskites synthesized to date exhibit indirect bandgaps >1.95 eV, which are undesirable for photovoltaic and optoelectronic applications. Herein, we report a comprehensive computer-aided screening of In- and Ga-based double perovskites for potential photovoltaic applications. To this end, several preconditions are implemented for the screening of optimal candidates, which include structural stability, electronic bandgaps, and optical absorption. Importantly, four In- and Ga-based double perovskites are identified to possess direct bandgaps within the desirable range of 0.9-1.6 eV for photovoltaic applications. Dominant optical absorption of the four double perovskites is found to be in the UV range. The structural and thermal stability of the four double perovskites are examined using both the empirical Goldschmidt ratio and convex-hull calculations. Only Cs 2 AgInBr 6 is predicted to be thermodynamically stable.

Rapid Parallel Screening for Strain Optimization

DTIC Science & Technology

2013-08-16

fermentation yields of industrially relevant biological compounds. Screening of the desired chemicals was completed previously. Microbes that can...reporter, and, 2) a yeast TAR cloning shuttle vector for transferring catabolic clusters to E. coli. 15. SUBJECT TERMS NA 16. SECURITY CLASSIFICATION OF... fermentation yields of industrially relevant biological compounds. Screening of the desired chemicals was completed previously. Microbes that can utilize

Rapid Parallel Screening for Strain Optimization

DTIC Science & Technology

2013-05-16

fermentation yields of industrially relevant biological compounds. Screening of the desired chemicals was completed previously. Microbes that can...reporter, and, 2) a yeast TAR cloning shuttle vector for transferring catabolic clusters to E. coli. 15. SUBJECT TERMS NA 16. SECURITY CLASSIFICATION OF... fermentation yields of industrially relevant biological compounds. Screening of the desired chemicals was completed previously. Microbes that can utilize

Optimizing the Use of the AUDIT for Alcohol Screening in College Students

ERIC Educational Resources Information Center

DeMartini, Kelly S.; Carey, Kate B.

2012-01-01

The screening and brief intervention modality of treatment for at-risk college drinking is becoming increasingly popular. A key to effective implementation is use of validated screening tools. Although the Alcohol Use Disorders Identification Test (AUDIT) has been validated in adult samples and is often used with college students, research has not…

Behavioral economics: "nudging" underserved populations to be screened for cancer.

PubMed

Purnell, Jason Q; Thompson, Tess; Kreuter, Matthew W; McBride, Timothy D

2015-01-15

Persistent disparities in cancer screening by race/ethnicity and socioeconomic status require innovative prevention tools and techniques. Behavioral economics provides tools to potentially reduce disparities by informing strategies and systems to increase prevention of breast, cervical, and colorectal cancers. With an emphasis on the predictable, but sometimes flawed, mental shortcuts (heuristics) people use to make decisions, behavioral economics offers insights that practitioners can use to enhance evidence-based cancer screening interventions that rely on judgments about the probability of developing and detecting cancer, decisions about competing screening options, and the optimal presentation of complex choices (choice architecture). In the area of judgment, we describe ways practitioners can use the availability and representativeness of heuristics and the tendency toward unrealistic optimism to increase perceptions of risk and highlight benefits of screening. We describe how several behavioral economic principles involved in decision-making can influence screening attitudes, including how framing and context effects can be manipulated to highlight personally salient features of cancer screening tests. Finally, we offer suggestions about ways practitioners can apply principles related to choice architecture to health care systems in which cancer screening takes place. These recommendations include the use of incentives to increase screening, introduction of default options, appropriate feedback throughout the decision-making and behavior completion process, and clear presentation of complex choices, particularly in the context of colorectal cancer screening. We conclude by noting gaps in knowledge and propose future research questions to guide this promising area of research and practice.

Behavioral Economics: “Nudging” Underserved Populations to Be Screened for Cancer

PubMed Central

Thompson, Tess; Kreuter, Matthew W.; McBride, Timothy D.

2015-01-01

Persistent disparities in cancer screening by race/ethnicity and socioeconomic status require innovative prevention tools and techniques. Behavioral economics provides tools to potentially reduce disparities by informing strategies and systems to increase prevention of breast, cervical, and colorectal cancers. With an emphasis on the predictable, but sometimes flawed, mental shortcuts (heuristics) people use to make decisions, behavioral economics offers insights that practitioners can use to enhance evidence-based cancer screening interventions that rely on judgments about the probability of developing and detecting cancer, decisions about competing screening options, and the optimal presentation of complex choices (choice architecture). In the area of judgment, we describe ways practitioners can use the availability and representativeness of heuristics and the tendency toward unrealistic optimism to increase perceptions of risk and highlight benefits of screening. We describe how several behavioral economic principles involved in decision-making can influence screening attitudes, including how framing and context effects can be manipulated to highlight personally salient features of cancer screening tests. Finally, we offer suggestions about ways practitioners can apply principles related to choice architecture to health care systems in which cancer screening takes place. These recommendations include the use of incentives to increase screening, introduction of default options, appropriate feedback throughout the decision-making and behavior completion process, and clear presentation of complex choices, particularly in the context of colorectal cancer screening. We conclude by noting gaps in knowledge and propose future research questions to guide this promising area of research and practice. PMID:25590600

Pointing Device Performance in Steering Tasks.

PubMed

Senanayake, Ransalu; Goonetilleke, Ravindra S

2016-06-01

Use of touch-screen-based interactions is growing rapidly. Hence, knowing the maneuvering efficacy of touch screens relative to other pointing devices is of great importance in the context of graphical user interfaces. Movement time, accuracy, and user preferences of four pointing device settings were evaluated on a computer with 14 participants aged 20.1 ± 3.13 years. It was found that, depending on the difficulty of the task, the optimal settings differ for ballistic and visual control tasks. With a touch screen, resting the arm increased movement time for steering tasks. When both performance and comfort are considered, whether to use a mouse or a touch screen for person-computer interaction depends on the steering difficulty. Hence, a input device should be chosen based on the application, and should be optimized to match the graphical user interface. © The Author(s) 2016.

From Protein Structure to Small-Molecules: Recent Advances and Applications to Fragment-Based Drug Discovery.

PubMed

Ferreira, Leonardo G; Andricopulo, Adriano D

2017-01-01

Fragment-based drug discovery (FBDD) is a broadly used strategy in structure-guided ligand design, whereby low-molecular weight hits move from lead-like to drug-like compounds. Over the past 15 years, an increasingly important role of the integration of these strategies into industrial and academic research platforms has been successfully established, allowing outstanding contributions to drug discovery. One important factor for the current prominence of FBDD is the better coverage of the chemical space provided by fragment-like libraries. The development of the field relies on two features: (i) the growing number of structurally characterized drug targets and (ii) the enormous chemical diversity available for experimental and virtual screenings. Indeed, fragment-based campaigns have contributed to address major challenges in lead optimization, such as the appropriate physicochemical profile of clinical candidates. This perspective paper outlines the usefulness and applications of FBDD approaches in medicinal chemistry and drug design. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Antitrypanosomal lead discovery: Identification of a ligand-efficient inhibitor of Trypanosoma cruzi CYP51 and parasite growth

PubMed Central

Andriani, Grasiella; Amata, Emanuele; Beatty, Joel; Clements, Zeke; Coffey, Brian J.; Courtemanche, Gilles; Devine, William; Erath, Jessey; Juda, Cristin E.; Wawrzak, Zdzislaw; Wood, JodiAnne T.; Lepesheva, Galina I.; Rodriguez, Ana; Pollastri, Michael P.

2013-01-01

Chagas disease is caused by the intracellular protozoan parasite Trypanosomal cruzi, and current drugs are lacking in terms of desired safety and efficacy profiles. Following on a recently reported high-throughput screening campaign, we have explored initial structure-activity relationships around a class of imidazole-based compounds. This profiling has uncovered compounds 4c (NEU321) and 4j (NEU704), which are potent against in vitro cultures of T. cruzi and are greater than 160-fold selective over host cells. We report in vitro drug metabolism and properties profiling of 4c and show that this chemotype inhibits the T cruzi CYP51 enzyme, an observation confirmed by X-ray crystallographic analysis. We compare the binding orientation of 4c to that of other, previously reported inhibitors. We show that 4c displays a significantly better ligand efficiency and a shorter synthetic route over previously disclosed CYP51 inhibitors, and should therefore be considered a promising lead compound for further optimization. PMID:23448316

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ghosh, Arun K.; Takayama, Jun; Rao, Kalapala Venkateswar

The design, synthesis, X-ray crystal structure, molecular modeling, and biological evaluation of a series of new generation SARS-CoV PLpro inhibitors are described. A new lead compound 3 (6577871) was identified via high-throughput screening of a diverse chemical library. Subsequently, we carried out lead optimization and structure-activity studies to provide a series of improved inhibitors that show potent PLpro inhibition and antiviral activity against SARS-CoV infected Vero E6 cells. Interestingly, the (S)-Me inhibitor 15h (enzyme IC{sub 50} = 0.56 {mu}M; antiviral EC{sub 50} = 9.1 {mu}M) and the corresponding (R)-Me 15g (IC{sub 50} = 0.32 {mu}M; antiviral EC{sub 50} = 9.1more » {mu}M) are the most potent compounds in this series, with nearly equivalent enzymatic inhibition and antiviral activity. A protein-ligand X-ray structure of 15g-bound SARS-CoV PLpro and a corresponding model of 15h docked to PLpro provide intriguing molecular insight into the ligand-binding site interactions.« less

Automated processing of the single-lead electrocardiogram for the detection of obstructive sleep apnoea.

PubMed

de Chazal, Philip; Heneghan, Conor; Sheridan, Elaine; Reilly, Richard; Nolan, Philip; O'Malley, Mark

2003-06-01

A method for the automatic processing of the electrocardiogram (ECG) for the detection of obstructive apnoea is presented. The method screens nighttime single-lead ECG recordings for the presence of major sleep apnoea and provides a minute-by-minute analysis of disordered breathing. A large independently validated database of 70 ECG recordings acquired from normal subjects and subjects with obstructive and mixed sleep apnoea, each of approximately eight hours in duration, was used throughout the study. Thirty-five of these recordings were used for training and 35 retained for independent testing. A wide variety of features based on heartbeat intervals and an ECG-derived respiratory signal were considered. Classifiers based on linear and quadratic discriminants were compared. Feature selection and regularization of classifier parameters were used to optimize classifier performance. Results show that the normal recordings could be separated from the apnoea recordings with a 100% success rate and a minute-by-minute classification accuracy of over 90% is achievable.

Lead iodide perovskite light-emitting field-effect transistor

PubMed Central

Chin, Xin Yu; Cortecchia, Daniele; Yin, Jun; Bruno, Annalisa; Soci, Cesare

2015-01-01

Despite the widespread use of solution-processable hybrid organic–inorganic perovskites in photovoltaic and light-emitting applications, determination of their intrinsic charge transport parameters has been elusive due to the variability of film preparation and history-dependent device performance. Here we show that screening effects associated to ionic transport can be effectively eliminated by lowering the operating temperature of methylammonium lead iodide perovskite (CH3NH3PbI3) field-effect transistors. Field-effect carrier mobility is found to increase by almost two orders of magnitude below 200 K, consistent with phonon scattering-limited transport. Under balanced ambipolar carrier injection, gate-dependent electroluminescence is also observed from the transistor channel, with spectra revealing the tetragonal to orthorhombic phase transition. This demonstration of CH3NH3PbI3 light-emitting field-effect transistors provides intrinsic transport parameters to guide materials and solar cell optimization, and will drive the development of new electro-optic device concepts, such as gated light-emitting diodes and lasers operating at room temperature. PMID:26108967

Using Decision-Analytic Modeling to Isolate Interventions That Are Feasible, Efficient and Optimal: An Application from the Norwegian Cervical Cancer Screening Program.

PubMed

Pedersen, Kine; Sørbye, Sveinung Wergeland; Burger, Emily Annika; Lönnberg, Stefan; Kristiansen, Ivar Sønbø

2015-12-01

Decision makers often need to simultaneously consider multiple criteria or outcomes when deciding whether to adopt new health interventions. Using decision analysis within the context of cervical cancer screening in Norway, we aimed to aid decision makers in identifying a subset of relevant strategies that are simultaneously efficient, feasible, and optimal. We developed an age-stratified probabilistic decision tree model following a cohort of women attending primary screening through one screening round. We enumerated detected precancers (i.e., cervical intraepithelial neoplasia of grade 2 or more severe (CIN2+)), colposcopies performed, and monetary costs associated with 10 alternative triage algorithms for women with abnormal cytology results. As efficiency metrics, we calculated incremental cost-effectiveness, and harm-benefit, ratios, defined as the additional costs, or the additional number of colposcopies, per additional CIN2+ detected. We estimated capacity requirements and uncertainty surrounding which strategy is optimal according to the decision rule, involving willingness to pay (monetary or resources consumed per added benefit). For ages 25 to 33 years, we eliminated four strategies that did not fall on either efficiency frontier, while one strategy was efficient with respect to both efficiency metrics. Compared with current practice in Norway, two strategies detected more precancers at lower monetary costs, but some required more colposcopies. Similar results were found for women aged 34 to 69 years. Improving the effectiveness and efficiency of cervical cancer screening may necessitate additional resources. Although efficient and feasible, both society and individuals must specify their willingness to accept the additional resources and perceived harms required to increase effectiveness before a strategy can be considered optimal. Copyright © 2015. Published by Elsevier Inc.

Hierarchical virtual screening of the dual MMP-2/HDAC-6 inhibitors from natural products based on pharmacophore models and molecular docking.

PubMed

Wang, Yijun; Yang, Limei; Hou, Jiaying; Zou, Qing; Gao, Qi; Yao, Wenhui; Yao, Qizheng; Zhang, Ji

2018-02-12

The dual-target inhibitors tend to improve the response rate in treating tumors, comparing with the single-target inhibitors. Matrix metalloproteinase-2 (MMP-2) and histone deacetylase-6 (HDAC-6) are attractive targets for cancer therapy. In this study, the hierarchical virtual screening of dual MMP-2/HDAC-6 inhibitors from natural products is investigated. The pharmacophore model of MMP-2 inhibitors is built based on ligands, but the pharmacophore model of HDAC-6 inhibitors is built based on the experimental crystal structures of multiple receptor-ligand complexes. The reliability of these two pharmacophore models is validated subsequently. The hierarchical virtual screening, combining these two different pharmacophore models of MMP-2 and HDAC-6 inhibitors with molecular docking, is carried out to identify the dual MMP-2/HDAC-6 inhibitors from a database of natural products. The four potential dual MMP-2/HDAC-6 inhibitors of natural products, STOCK1 N-46177, STOCK1 N-52245, STOCK1 N-55477, and STOCK1 N-69706, are found. The studies of binding modes show that the screened four natural products can simultaneously well bind with the MMP-2 and HDAC-6 active sites by different kinds of interactions, to inhibit the MMP-2 and HDAC-6 activities. In addition, the ADMET properties of screened four natural products are assessed. These found dual MMP-2/HDAC-6 inhibitors of natural products could serve as the lead compounds for designing the new dual MMP-2/HDAC-6 inhibitors having higher biological activities by carrying out structural modifications and optimizations in the future studies.

Evolutions in fragment-based drug design: the deconstruction–reconstruction approach

PubMed Central

Chen, Haijun; Zhou, Xiaobin; Wang, Ailan; Zheng, Yunquan; Gao, Yu; Zhou, Jia

2014-01-01

Recent advances in the understanding of molecular recognition and protein–ligand interactions have facilitated rapid development of potent and selective ligands for therapeutically relevant targets. Over the past two decades, a variety of useful approaches and emerging techniques have been developed to promote the identification and optimization of leads that have high potential for generating new therapeutic agents. Intriguingly, the innovation of a fragment-based drug design (FBDD) approach has enabled rapid and efficient progress in drug discovery. In this critical review, we focus on the construction of fragment libraries and the advantages and disadvantages of various fragment-based screening (FBS) for constructing such libraries. We also highlight the deconstruction–reconstruction strategy by utilizing privileged fragments of reported ligands. PMID:25263697

Genetics of Hearing Loss – Syndromic

PubMed Central

Koffler, Tal; Ushakov, Kathy; Avraham, Karen B.

2015-01-01

Synopsis Hearing loss (HL) is one of the most common birth defects in developed countries and is a diverse pathology with different classifications. One of these is based on the association with other clinical features, defined as syndromic hearing loss (SHL). Determining the etiology of the HL in these patients is extremely beneficial as it enables a personalized approach to caring for the individual. Early screening can further aid in optimal rehabilitation for a child’s development and growth. Pathogenic variants in forty-five genes, encoding proteins functioning as ion channels, transcription factors, molecular motors and more, are known to lead to eleven forms of SHL. The development of high-throughput sequencing technology is facilitating rapid and low-cost diagnostics for patients with SHL. PMID:26443487

The Changing Landscape of Genetic Testing for Inherited Breast Cancer Predisposition.

PubMed

Afghahi, Anosheh; Kurian, Allison W

2017-05-01

The advent of multiple-gene germline panel testing has led to significant advances in hereditary breast and ovarian cancer risk assessment. These include guideline-specific cancer risk management recommendations for patients and their families, such as screening with breast magnetic resonance imaging and risk-reducing surgeries, which have the potential to reduce substantially the morbidity and mortality associated with a hereditary cancer predisposition. However, controversy remains about the clinical validity and actionability of genetic testing in a broader patient population. We discuss events leading to the wider availability of commercialized multiple-gene germline panel testing, the recent data that support using this powerful tool to improve cancer risk assessment and reduction strategies, and remaining challenges to clinical optimization of this new genetic technology.

Small Molecule Fluoride Toxicity Agonists

PubMed Central

Nelson1, James W.; Plummer, Mark S.; Blount, Kenneth F.; Ames, Tyler D.; Breaker, Ronald R.

2015-01-01

SUMMARY Fluoride is a ubiquitous anion that inhibits a wide variety of metabolic processes. Here we report the identification of a series of compounds that enhance fluoride toxicity in Escherichia coli and Streptococcus mutans. These molecules were isolated by using a high-throughput screen (HTS) for compounds that increase intracellular fluoride levels as determined via a fluoride riboswitch-reporter fusion construct. A series of derivatives were synthesized to examine structure-activity relationships, leading to the identification of compounds with improved activity. Thus, we demonstrate that small molecule fluoride toxicity agonists can be identified by HTS from existing chemical libraries by exploiting a natural fluoride riboswitch. In addition, our findings suggest that some molecules might be further optimized to function as binary antibacterial agents when combined with fluoride. PMID:25910244

Breast cancer screening controversies: who, when, why, and how?

PubMed

Chetlen, Alison; Mack, Julie; Chan, Tiffany

2016-01-01

Mammographic screening is effective in reducing mortality from breast cancer. The issue is not whether mammography is effective, but whether the false positive rate and false negative rates can be reduced. This review will discuss controversies including the reduction in breast cancer mortality, overdiagnosis, the ideal screening candidate, and the optimal imaging modality for breast cancer screening. The article will compare and contrast screening mammography, tomosynthesis, whole-breast screening ultrasound, magnetic resonance imaging, and molecular breast imaging. Though supplemental imaging modalities are being utilized to improve breast cancer diagnosis, mammography still remains the gold standard for breast cancer screening. Copyright © 2015 Elsevier Inc. All rights reserved.

Universal Versus Targeted Screening for Lynch Syndrome: Comparing Ascertainment and Costs Based on Clinical Experience.

PubMed

Erten, Mujde Z; Fernandez, Luca P; Ng, Hank K; McKinnon, Wendy C; Heald, Brandie; Koliba, Christopher J; Greenblatt, Marc S

2016-10-01

Strategies to screen colorectal cancers (CRCs) for Lynch syndrome are evolving rapidly; the optimal strategy remains uncertain. We compared targeted versus universal screening of CRCs for Lynch syndrome. In 2010-2011, we employed targeted screening (age < 60 and/or Bethesda criteria). From 2012 to 2014, we screened all CRCs. Immunohistochemistry for the four mismatch repair proteins was done in all cases, followed by other diagnostic studies as indicated. We modeled the diagnostic costs of detecting Lynch syndrome and estimated the 5-year costs of preventing CRC by colonoscopy screening, using a system dynamics model. Using targeted screening, 51/175 (29 %) cancers fit criteria and were tested by immunohistochemistry; 15/51 (29 %, or 8.6 % of all CRCs) showed suspicious loss of ≥1 mismatch repair protein. Germline mismatch repair gene mutations were found in 4/4 cases sequenced (11 suspected cases did not have germline testing). Using universal screening, 17/292 (5.8 %) screened cancers had abnormal immunohistochemistry suspicious for Lynch syndrome. Germline mismatch repair mutations were found in only 3/10 cases sequenced (7 suspected cases did not have germline testing). The mean cost to identify Lynch syndrome probands was ~$23,333/case for targeted screening and ~$175,916/case for universal screening at our institution. Estimated costs to identify and screen probands and relatives were: targeted, $9798/case and universal, $38,452/case. In real-world Lynch syndrome management, incomplete clinical follow-up was the major barrier to do genetic testing. Targeted screening costs 2- to 7.5-fold less than universal and rarely misses Lynch syndrome cases. Future changes in testing costs will likely change the optimal algorithm.

Unifying screening processes within the PROSPR consortium: a conceptual model for breast, cervical, and colorectal cancer screening.

PubMed

Beaber, Elisabeth F; Kim, Jane J; Schapira, Marilyn M; Tosteson, Anna N A; Zauber, Ann G; Geiger, Ann M; Kamineni, Aruna; Weaver, Donald L; Tiro, Jasmin A

2015-06-01

General frameworks of the cancer screening process are available, but none directly compare the process in detail across different organ sites. This limits the ability of medical and public health professionals to develop and evaluate coordinated screening programs that apply resources and population management strategies available for one cancer site to other sites. We present a trans-organ conceptual model that incorporates a single screening episode for breast, cervical, and colorectal cancers into a unified framework based on clinical guidelines and protocols; the model concepts could be expanded to other organ sites. The model covers four types of care in the screening process: risk assessment, detection, diagnosis, and treatment. Interfaces between different provider teams (eg, primary care and specialty care), including communication and transfer of responsibility, may occur when transitioning between types of care. Our model highlights across each organ site similarities and differences in steps, interfaces, and transitions in the screening process and documents the conclusion of a screening episode. This model was developed within the National Cancer Institute-funded consortium Population-based Research Optimizing Screening through Personalized Regimens (PROSPR). PROSPR aims to optimize the screening process for breast, cervical, and colorectal cancer and includes seven research centers and a statistical coordinating center. Given current health care reform initiatives in the United States, this conceptual model can facilitate the development of comprehensive quality metrics for cancer screening and promote trans-organ comparative cancer screening research. PROSPR findings will support the design of interventions that improve screening outcomes across multiple cancer sites. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The importance of hydration thermodynamics in fragment-to-lead optimization.

PubMed

Ichihara, Osamu; Shimada, Yuzo; Yoshidome, Daisuke

2014-12-01

Using a computational approach to assess changes in solvation thermodynamics upon ligand binding, we investigated the effects of water molecules on the binding energetics of over 20 fragment hits and their corresponding optimized lead compounds. Binding activity and X-ray crystallographic data of published fragment-to-lead optimization studies from various therapeutically relevant targets were studied. The analysis reveals a distinct difference between the thermodynamic profile of water molecules displaced by fragment hits and those displaced by the corresponding optimized lead compounds. Specifically, fragment hits tend to displace water molecules with notably unfavorable excess entropies-configurationally constrained water molecules-relative to those displaced by the newly added moieties of the lead compound during the course of fragment-to-lead optimization. Herein we describe the details of this analysis with the goal of providing practical guidelines for exploiting thermodynamic signatures of binding site water molecules in the context of fragment-to-lead optimization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development and Optimization of a High-Throughput Assay To Measure Neutralizing Antibodies against Clostridium difficile Binary Toxin

PubMed Central

Xie, Jinfu; Horton, Melanie; Zorman, Julie; Antonello, Joseph M.; Zhang, Yuhua; Arnold, Beth A.; Secore, Susan; Xoconostle, Rachel; Miezeiewski, Matthew; Wang, Su; Price, Colleen E.; Thiriot, David; Goerke, Aaron; Gentile, Marie-Pierre; Skinner, Julie M.

2014-01-01

Clostridium difficile strains producing binary toxin, in addition to toxin A (TcdA) and toxin B (TcdB), have been associated with more severe disease and increased recurrence of C. difficile infection in recent outbreaks. Binary toxin comprises two subunits (CDTa and CDTb) and catalyzes the ADP-ribosylation of globular actin (G-actin), which leads to the depolymerization of filamentous actin (F-actin) filaments. A robust assay is highly desirable for detecting the cytotoxic effect of the toxin and the presence of neutralizing antibodies in animal and human sera to evaluate vaccine efficacy. We describe here the optimization, using design-of-experiment (DOE) methodology, of a high-throughput assay to measure the toxin potency and neutralizing antibodies (NAb) against binary toxin. Vero cells were chosen from a panel of cells screened for sensitivity and specificity. We have successfully optimized the CDTa-to-CDTb molar ratio, toxin concentration, cell-seeding density, and sera-toxin preincubation time in the NAb assay using DOE methodology. This assay is robust, produces linear results across serial dilutions of hyperimmune serum, and can be used to quantify neutralizing antibodies in sera from hamsters and monkeys immunized with C. difficile binary toxin-containing vaccines. The assay will be useful for C. difficile diagnosis, for epidemiology studies, and for selecting and optimizing vaccine candidates. PMID:24623624

Hit Identification and Optimization in Virtual Screening: Practical Recommendations Based Upon a Critical Literature Analysis

PubMed Central

Zhu, Tian; Cao, Shuyi; Su, Pin-Chih; Patel, Ram; Shah, Darshan; Chokshi, Heta B.; Szukala, Richard; Johnson, Michael E.; Hevener, Kirk E.

2013-01-01

A critical analysis of virtual screening results published between 2007 and 2011 was performed. The activity of reported hit compounds from over 400 studies was compared to their hit identification criteria. Hit rates and ligand efficiencies were calculated to assist in these analyses and the results were compared with factors such as the size of the virtual library and the number of compounds tested. A series of promiscuity, drug-like, and ADMET filters were applied to the reported hits to assess the quality of compounds reported and a careful analysis of a subset of the studies which presented hit optimization was performed. This data allowed us to make several practical recommendations with respect to selection of compounds for experimental testing, defining hit identification criteria, and general virtual screening hit criteria to allow for realistic hit optimization. A key recommendation is the use of size-targeted ligand efficiency values as hit identification criteria. PMID:23688234

The economics of screening infants at risk of hearing impairment: an international analysis.

PubMed

Burke, Martyn J; Shenton, Ruth C; Taylor, Matthew J

2012-02-01

Hearing impairment in children across the world constitutes a particularly serious obstacle to their optimal development and education, including language acquisition. Around 0.5-6 in every 1000 neonates and infants have congenital or early childhood onset sensorineural deafness or severe-to-profound hearing impairment, with significant consequences. Therefore, early detection is a vitally important element in providing appropriate support for deaf and hearing-impaired babies that will help them enjoy equal opportunities in society alongside all other children. This analysis estimates the costs and effectiveness of various interventions to screen infants at risk of hearing impairment. The economic analysis used a decision tree approach to determine the cost-effectiveness of newborn hearing screening strategies. Two unique models were built to capture different strategic screening decisions. Firstly, the cost-effectiveness of universal newborn hearing screening (UNHS) was compared to selective screening of newborns with risk factors. Secondly, the cost-effectiveness of providing a one-stage screening process vs. a two-stage screening process was investigated. Two countries, the United Kingdom and India, were used as case studies to illustrate the likely cost outcomes associated with the various strategies to diagnose hearing loss in infants. In the UK, the universal strategy incurs a further cost of approximately £2.3 million but detected an extra 63 cases. An incremental cost per case detected of £36,181 was estimated. The estimated economic burden was substantially higher in India when adopting a universal strategy due to the higher baseline prevalence of hearing loss. The one-stage screening strategy accumulated an additional 13,480 and 13,432 extra cases of false-positives, in the UK and India respectively when compared to a two-stage screening strategy. This represented increased costs by approximately £1.3 million and INR 34.6 million. The cost-effectiveness of a screening intervention was largely dependent upon two key factors. As would be expected, the cost (per patient) of the intervention drives the model substantially, with higher costs leading to higher cost-effectiveness ratios. Likewise, the baseline prevalence (risk) of hearing impairment also affected the results. In scenarios where the baseline risk was low, the intervention was less likely to be cost-effective compared to when the baseline risk was high. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

[Use the Markov-decision tree model to optimize vaccination strategies of hepatitis E among women aged 15 to 49].

PubMed

Chen, Z M; Ji, S B; Shi, X L; Zhao, Y Y; Zhang, X F; Jin, H

2017-02-10

Objective: To evaluate the cost-utility of different hepatitis E vaccination strategies in women aged 15 to 49. Methods: The Markov-decision tree model was constructed to evaluate the cost-utility of three hepatitis E virus vaccination strategies. Parameters of the models were estimated on the basis of published studies and experience of experts. Both methods on sensitivity and threshold analysis were used to evaluate the uncertainties of the model. Results: Compared with non-vaccination group, strategy on post-screening vaccination with rate as 100%, could save 0.10 quality-adjusted life years per capital in the women from the societal perspectives. After implementation of screening program and with the vaccination rate reaching 100%, the incremental cost utility ratio (ICUR) of vaccination appeared as 5 651.89 and 6 385.33 Yuan/QALY, respectively. Vaccination post to the implementation of a screening program, the result showed better benefit than the vaccination rate of 100%. Results from the sensitivity analysis showed that both the cost of hepatitis E vaccine and the inoculation compliance rate presented significant effects. If the cost were lower than 191.56 Yuan (RMB) or the inoculation compliance rate lower than 0.23, the vaccination rate of 100% strategy was better than the post-screening vaccination strategy, otherwise the post-screening vaccination strategy appeared the optimal strategy. Conclusion: Post-screening vaccination for women aged 15 to 49 from social perspectives seemed the optimal one but it had to depend on the change of vaccine cost and the rate of inoculation compliance.

Internationally comparable screening tests for listening in noise in several European languages: the German digit triplet test as an optimization prototype.

PubMed

Zokoll, Melanie A; Wagener, Kirsten C; Brand, Thomas; Buschermöhle, Michael; Kollmeier, Birger

2012-09-01

A review is given of internationally comparable speech-in-noise tests for hearing screening purposes that were part of the European HearCom project. This report describes the development, optimization, and evaluation of such tests for headphone and telephone presentation, using the example of the German digit triplet test. In order to achieve the highest possible comparability, language- and speaker-dependent factors in speech intelligibility should be compensated for. The tests comprise spoken numbers in background noise and estimate the speech reception threshold (SRT), i.e. the signal-to-noise ratio (SNR) yielding 50% speech intelligibility. The respective reference speech intelligibility functions for headphone and telephone presentation of the German version for 15 and 10 normal-hearing listeners are described by a SRT of -9.3 ± 0.2 and -6.5 ± 0.4 dB SNR, and slopes of 19.6 and 17.9%/dB, respectively. Reference speech intelligibility functions of all digit triplet tests optimized within the HearCom project allow for investigation of the comparability due to language specificities. The optimization criteria established here should be used for similar screening tests in other languages.

Elevated blood lead levels in refugee children--New Hampshire, 2003-2004.

PubMed

2005-01-21

As a result of reductions in lead hazards and improved screening practices, blood lead levels (BLLs) in children aged 1-5 years are decreasing in the United States. However, the risk for elevated BLLs (> or =10 microg/dL) remains high for certain populations, including refugees. After the death of a Sudanese refugee child from lead poisoning in New Hampshire in 2000, the New Hampshire Department of Health and Human Services (NHDHHS) developed lead testing guidelines to screen and monitor refugee children. These guidelines recommend 1) capillary blood lead testing for refugee children aged 6 months-15 years within 3 months after arrival in New Hampshire, 2) follow-up venous testing of children aged <6 years within 3-6 months after initial screening, and 3) notation of refugee status on laboratory slips for first tests. In 2004, routine laboratory telephone reports of elevated BLLs to the New Hampshire Childhood Lead Poisoning Prevention Program (NHCLPPP) called attention to a pattern of elevated BLLs among refugee children. To develop prevention strategies, NHDHHS analyzed NHCLPPP and Manchester Health Department (MHD) data, focusing on the 37 African refugee children with elevated BLLs on follow-up for whom complete data were available. This report describes the results of that analysis, which indicated that 1) follow-up blood lead testing is useful to identify lead exposure that occurs after resettlement and 2) refugee children in New Hampshire older than those routinely tested might have elevated BLLs. Refugee children in all states should be tested for lead poisoning on arrival and several months after initial screening to assess exposure after resettlement.

USASOC Injury Prevention/Performance Optimization Musculoskeletal Screening Initiative

DTIC Science & Technology

2011-11-01

Tactical Human Optimization , Rapid Rehabilitation , and Reconditioning (THOR3) program to identify the...Special Operations Command (USASOC) to support development of USASOC’s Tactical Human Optimization , Rapid Rehabilitation , and Reconditioning (THOR3...biomechanical, musculoskeletal, physiological, tactical , and injury data and refine its current human performance program to address the

Computationally optimized deimmunization libraries yield highly mutated enzymes with low immunogenicity and enhanced activity.

PubMed

Salvat, Regina S; Verma, Deeptak; Parker, Andrew S; Kirsch, Jack R; Brooks, Seth A; Bailey-Kellogg, Chris; Griswold, Karl E

2017-06-27

Therapeutic proteins of wide-ranging function hold great promise for treating disease, but immune surveillance of these macromolecules can drive an antidrug immune response that compromises efficacy and even undermines safety. To eliminate widespread T-cell epitopes in any biotherapeutic and thereby mitigate this key source of detrimental immune recognition, we developed a Pareto optimal deimmunization library design algorithm that optimizes protein libraries to account for the simultaneous effects of combinations of mutations on both molecular function and epitope content. Active variants identified by high-throughput screening are thus inherently likely to be deimmunized. Functional screening of an optimized 10-site library (1,536 variants) of P99 β-lactamase (P99βL), a component of ADEPT cancer therapies, revealed that the population possessed high overall fitness, and comprehensive analysis of peptide-MHC II immunoreactivity showed the population possessed lower average immunogenic potential than the wild-type enzyme. Although similar functional screening of an optimized 30-site library (2.15 × 10 9 variants) revealed reduced population-wide fitness, numerous individual variants were found to have activity and stability better than the wild type despite bearing 13 or more deimmunizing mutations per enzyme. The immunogenic potential of one highly active and stable 14-mutation variant was assessed further using ex vivo cellular immunoassays, and the variant was found to silence T-cell activation in seven of the eight blood donors who responded strongly to wild-type P99βL. In summary, our multiobjective library-design process readily identified large and mutually compatible sets of epitope-deleting mutations and produced highly active but aggressively deimmunized constructs in only one round of library screening.

Screening And Optimizing Antimicrobial Peptides By Using SPOT-Synthesis

NASA Astrophysics Data System (ADS)

López-Pérez, Paula M.; Grimsey, Elizabeth; Bourne, Luc; Mikut, Ralf; Hilpert, Kai

2017-04-01

Peptide arrays on cellulose are a powerful tool to investigate peptide interactions with a number of different molecules, for examples antibodies, receptors or enzymes. Such peptide arrays can also be used to study interactions with whole cells. In this review, we focus on the interaction of small antimicrobial peptides with bacteria. Antimicrobial peptides (AMPs) can kill multidrug-resistant (MDR) human pathogenic bacteria and therefore could be next generation antibiotics targeting MDR bacteria. We describe the screen and the result of different optimization strategies of peptides cleaved from the membrane. In addition, screening of antibacterial activity of peptides that are tethered to the surface is discussed. Surface-active peptides can be used to protect surfaces from bacterial infections, for example implants.

Taguchi-generalized regression neural network micro-screening for physical and sensory characteristics of bread.

PubMed

Besseris, George J

2018-03-01

Generalized regression neural networks (GRNN) may act as crowdsourcing cognitive agents to screen small, dense and complex datasets. The concurrent screening and optimization of several complex physical and sensory traits of bread is developed using a structured Taguchi-type micro-mining technique. A novel product outlook is offered to industrial operations to cover separate aspects of smart product design, engineering and marketing. Four controlling factors were selected to be modulated directly on a modern production line: 1) the dough weight, 2) the proofing time, 3) the baking time, and 4) the oven zone temperatures. Concentrated experimental recipes were programmed using the Taguchi-type L 9 (3 4 ) OA-sampler to detect potentially non-linear multi-response tendencies. The fused behavior of the master-ranked bread characteristics behavior was smart sampled with GRNN-crowdsourcing and robust analysis. It was found that the combination of the oven zone temperatures to play a highly influential role in all investigated scenarios. Moreover, the oven zone temperatures and the dough weight appeared to be instrumental when attempting to synchronously adjusting all four physical characteristics. The optimal oven-zone temperature setting for concurrent screening-and-optimization was found to be 270-240 °C. The optimized (median) responses for loaf weight, moisture, height, width, color, flavor, crumb structure, softness, and elasticity are: 782 g, 34.8 %, 9.36 cm, 10.41 cm, 6.6, 7.2, 7.6, 7.3, and 7.0, respectively.

Fast Optimization of LiMgMnOx/La2O3 Catalysts for the Oxidative Coupling of Methane.

PubMed

Li, Zhinian; He, Lei; Wang, Shenliang; Yi, Wuzhong; Zou, Shihui; Xiao, Liping; Fan, Jie

2017-01-09

The development of efficient catalyst for oxidative coupling of methane (OCM) reaction represents a grand challenge in direct conversion of methane into other useful products. Here, we reported that a newly developed combinatorial approach can be used for ultrafast optimization of La 2 O 3 -based multicomponent metal oxide catalysts in OCM reaction. This new approach integrated inkjet printing assisted synthesis (IJP-A) with multidimensional group testing strategy (m-GT) tactfully takes the place of conventionally high-throughput synthesis-and-screen experiment. Just within a week, 2048 formulated LiMgMnO x -La 2 O 3 catalysts in a 64·8·8·8·8 = 262 144 compositional space were fabricated by IJP-A in a four-round synthesis-and-screen process, and an optimized formulation has been successfully identified through only 4·8 = 32 times of tests via m-GT screening strategy. The screening process identifies the most promising ternary composition region is Li 0-0.48 Mg 0-6.54 Mn 0-0.62 -La 100 O x with an external C 2 yield of 10.87% at 700 °C. The yield of C 2 is two times as high as the pure nano-La 2 O 3 . The good performance of the optimized catalyst formulation has been validated by the manual preparation, which further prove the effectiveness of the new combinatorial methodology in fast discovery of heterogeneous catalyst.

The synergistic use of computation, chemistry and biology to discover novel peptide-based drugs: the time is right.

PubMed

Audie, J; Boyd, C

2010-01-01

The case for peptide-based drugs is compelling. Due to their chemical, physical and conformational diversity, and relatively unproblematic toxicity and immunogenicity, peptides represent excellent starting material for drug discovery. Nature has solved many physiological and pharmacological problems through the use of peptides, polypeptides and proteins. If nature could solve such a diversity of challenging biological problems through the use of peptides, it seems reasonable to infer that human ingenuity will prove even more successful. And this, indeed, appears to be the case, as a number of scientific and methodological advances are making peptides and peptide-based compounds ever more promising pharmacological agents. Chief among these advances are powerful chemical and biological screening technologies for lead identification and optimization, methods for enhancing peptide in vivo stability, bioavailability and cell-permeability, and new delivery technologies. Other advances include the development and experimental validation of robust computational methods for peptide lead identification and optimization. Finally, scientific analysis, biology and chemistry indicate the prospect of designing relatively small peptides to therapeutically modulate so-called 'undruggable' protein-protein interactions. Taken together a clear picture is emerging: through the synergistic use of the scientific imagination and the computational, chemical and biological methods that are currently available, effective peptide therapeutics for novel targets can be designed that surpass even the proven peptidic designs of nature.

Quantitative structure-activity relationship: promising advances in drug discovery platforms.

PubMed

Wang, Tao; Wu, Mian-Bin; Lin, Jian-Ping; Yang, Li-Rong

2015-12-01

Quantitative structure-activity relationship (QSAR) modeling is one of the most popular computer-aided tools employed in medicinal chemistry for drug discovery and lead optimization. It is especially powerful in the absence of 3D structures of specific drug targets. QSAR methods have been shown to draw public attention since they were first introduced. In this review, the authors provide a brief discussion of the basic principles of QSAR, model development and model validation. They also highlight the current applications of QSAR in different fields, particularly in virtual screening, rational drug design and multi-target QSAR. Finally, in view of recent controversies, the authors detail the challenges faced by QSAR modeling and the relevant solutions. The aim of this review is to show how QSAR modeling can be applied in novel drug discovery, design and lead optimization. QSAR should intentionally be used as a powerful tool for fragment-based drug design platforms in the field of drug discovery and design. Although there have been an increasing number of experimentally determined protein structures in recent years, a great number of protein structures cannot be easily obtained (i.e., membrane transport proteins and G-protein coupled receptors). Fragment-based drug discovery, such as QSAR, could be applied further and have a significant role in dealing with these problems. Moreover, along with the development of computer software and hardware, it is believed that QSAR will be increasingly important.

Urinary metallomics as a novel biomarker discovery platform: Breast cancer as a case study.

PubMed

Burton, Casey; Dan, Yongbo; Donovan, Ariel; Liu, Kun; Shi, Honglan; Ma, Yinfa; Bosnak, Cynthia P

2016-01-15

Urinary metallomics is presented here as a new "omics" approach that aims to facilitate personalized cancer screening and prevention by improving our understanding of urinary metals in disease. Twenty-two urinary metals were examined with inductively-coupled plasma-mass spectrometry in 138 women newly diagnosed with breast cancer and benign conditions. Urinary metals from spot urine samples were adjusted to renal dilution using urine specific gravity. Two urinary metals, copper (P-value=0.036) and lead (P-value=0.003), were significantly increased in the urine of breast cancer patients. A multivariate model that comprised copper, lead, and patient age afforded encouraging discriminatory power (AUC: 0.728, P-value<0.0005), while univariate models of copper (61.7% sensitivity, 50.0% specificity) and lead (76.6% sensitivity, 51.2% specificity) at optimized cutoff thresholds compared favorably with other breast cancer diagnostic modalities such as mammography. Correlations found among various metals suggested potential geographic and dietary influences on the urine metallome that warrant further investigation. This proof-of-concept work introduces urinary metallomics as a noninvasive, potentially transformative "omics" approach to early cancer detection. Urinary copper and lead have also been preliminarily identified as potential breast cancer biomarkers. Copyright © 2015 Elsevier B.V. All rights reserved.

Disposable electrochemical sensor to evaluate the phytoremediation of the aquatic plant Lemna minor L. toward Pb(2+) and/or Cd(2+).

PubMed

Neagu, Daniela; Arduini, Fabiana; Quintana, Josefina Calvo; Di Cori, Patrizia; Forni, Cinzia; Moscone, Danila

2014-07-01

In this work a miniaturized and disposable electrochemical sensor was developed to evaluate the cadmium and lead ion phytoremediation potential by the floating aquatic macrophyte Lemna minor L. The sensor is based on a screen-printed electrode modified "in-situ" with bismuth film, which is more environmentally friendly than the mercury-based sensor usually adopted for lead and cadmium ion detection. The sensor was coupled with a portable potentiostat for the simultaneous measurement of cadmium and lead ions by stripping analysis. The optimized analytical system allows the simultaneous detection of both heavy metals at the ppb level (LOD equal to 0.3 and 2 ppb for lead and cadmium ions, respectively) with the advantage of using a miniaturized and cost-effective system. The sensor was then applied for the evaluation of Pb(2+) or/and Cd(2+) uptake by measuring the amount of the heavy metals both in growth medium and in plant tissues during 1 week experiments. In this way, the use of Lemna minor coupled with a portable electrochemical sensor allows the set up of a model system able both to remove the heavy metals and to measure "in-situ" the magnitude of heavy metal removal.

A rapid quantification method for the screening indicator for β-thalassemia with near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Chen, Jiemei; Peng, Lijun; Han, Yun; Yao, Lijun; Zhang, Jing; Pan, Tao

2018-03-01

Near-infrared (NIR) spectroscopy combined with chemometrics was applied to rapidly analyse haemoglobin A2 (HbA2) for β-thalassemia screening in human haemolysate samples. The relative content indicator HbA2 was indirectly quantified by simultaneous analysis of two absolute content indicators (Hb and Hb • HbA2). According to the comprehensive prediction effect of the multiple partitioning of calibration and prediction sets, the parameters were optimized to achieve modelling stability, and the preferred models were validated using the samples not involved in modelling. Savitzky-Golay smoothing was firstly used for the spectral pretreatment. The absorbance optimization partial least squares (AO-PLS) was used to eliminate high-absorption wave-bands appropriately. The equidistant combination PLS (EC-PLS) was further used to optimize wavelength models. The selected optimal models were I = 856 nm, N = 16, G = 1 and F = 6 for Hb and I = 988 nm, N = 12, G = 2 and F = 5 for Hb • HbA2. Through independent validation, the root-mean-square errors and correlation coefficients for prediction (RMSEP, RP) were 3.50 g L- 1 and 0.977 for Hb and 0.38 g L- 1 and 0.917 for Hb • HbA2, respectively. The predicted values of relative percentage HbA2 were further calculated, and the calculated RMSEP and RP were 0.31% and 0.965, respectively. The sensitivity and specificity for β-thalassemia both reached 100%. Therefore, the prediction of HbA2 achieved high accuracy for distinguishing β-thalassemia. The local optimal models for single parameter and the optimal equivalent model sets were proposed, providing more models to match possible constraints in practical applications. The NIR analysis method for the screening indicator of β-thalassemia was successfully established. The proposed method was rapid, simple and promising for thalassemia screening in a large population.

Cost-effectiveness of cervical cancer screening with primary human papillomavirus testing in Norway

PubMed Central

Burger, E A; Ortendahl, J D; Sy, S; Kristiansen, I S; Kim, J J

2012-01-01

Background: New screening technologies and vaccination against human papillomavirus (HPV), the necessary cause of cervical cancer, may impact optimal approaches to prevent cervical cancer. We evaluated the cost-effectiveness of alternative screening strategies to inform cervical cancer prevention guidelines in Norway. Methods: We leveraged the primary epidemiologic and economic data from Norway to contextualise a simulation model of HPV-induced cervical cancer. The current cytology-only screening was compared with strategies involving cytology at younger ages and primary HPV-based screening at older ages (31/34+ years), an option being actively deliberated by the Norwegian government. We varied the switch-age, screening interval, and triage strategies for women with HPV-positive results. Uncertainty was evaluated in sensitivity analysis. Results: Current cytology-only screening was less effective and more costly than strategies that involve switching to primary HPV testing in older ages. For unvaccinated women, switching at age 34 years to primary HPV testing every 4 years was optimal given the Norwegian cost-effectiveness threshold ($83 000 per year of life saved). For vaccinated women, a 6-year screening interval was cost-effective. When we considered a wider range of strategies, we found that an earlier switch to HPV testing (at age 31 years) may be preferred. Conclusions: Strategies involving a switch to HPV testing for primary screening in older women is expected to be cost-effective compared with current recommendations in Norway. PMID:22441643

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahn, J. -W.; Briesemester, A. R.; Kobayashi, M.

Enhanced perpendicular heat and momentum transport induces parallel pressure loss leading to divertor detachment, which can be produced by the increase of density in 2D tokamaks. However, in the 3D configurations such as tokamaks with 3D fields and stellarators, the fraction of perpendicular transport can be higher even in a lower density regime, which could lead to the early transition to detachment without passing through the high-recycling regime. 3D fields applied to the limiter tokamak plasmas produce edge stochastic layers close to the last closed flux surface (LCFS), which can allow for enhanced perpendicular transport and indeed the absence ofmore » high recycling regime and early detachment have been observed in TEXTOR and Tore Supra. However, in the X-point divertor tokamaks with the applied 3D fields, the parallel transport is still dominant and the detachment facilitation has not been observed yet. Rather, 3D fields affected detachment adversely under certain conditions, either by preventing detachment onset as seen in DIII-D or by re-attaching the existing detached plasma as shown in NSTX. The possible way for strong 3D effects to induce access to the early detachment in divertor tokamaks appears to be via significant perpendicular loss of parallel momentum by frictional force for the counter-streaming flows between neighboring flow channels in the divertor. In principle, the adjacent lobes in the 3D divertor tokamak may generate the counter-streaming flow channels. However, an EMC3-EIRENE simulation for ITER H-mode plasmas demonstrated that screened RMP leads to significantly reduced counter-flows near the divertor target, therefore the momentum loss effect leading to detachment facilitation is expected to be small. This is consistent with the observation in LHD, which showed screening (amplification) of RMP fields in the attachment (stable detachment) case. In conclusion, work for optimal parameter window for best divertor operation scenario is needed particularly for the 3D divertor tokamak configuration.« less

Automated detection of ventricular pre-excitation in pediatric 12-lead ECG.

PubMed

Gregg, Richard E; Zhou, Sophia H; Dubin, Anne M

2016-01-01

With increased interest in screening of young people for potential causes of sudden death, accurate automated detection of ventricular pre-excitation (VPE) or Wolff-Parkinson-White syndrome (WPW) in the pediatric resting ECG is important. Several recent studies have shown interobserver variability when reading screening ECGs and thus an accurate automated reading for this potential cause of sudden death is critical. We designed and tested an automated algorithm to detect pediatric VPE optimized for low prevalence. Digital ECGs with 12 leads or 15 leads (12-lead plus V3R, V4R and V7) were selected from multiple hospitals and separated into a testing and training database. Inclusion criterion was age less than 16 years. The reference for algorithm detection of VPE was cardiologist annotation of VPE for each ECG. The training database (n=772) consisted of VPE ECGs (n=37), normal ECGs (n=492) and a high concentration of conduction defects, RBBB (n=232) and LBBB (n=11). The testing database was a random sample (n=763). All ECGs were analyzed with the Philips DXL ECG Analysis algorithm for basic waveform measurements. Additional ECG features specific to VPE, mainly delta wave scoring, were calculated from the basic measurements and the average beat. A classifier based on decision tree bootstrap aggregation (tree bagger) was trained in multiple steps to select the number of decision trees and the 10 best features. The classifier accuracy was measured on the test database. The new algorithm detected pediatric VPE with a sensitivity of 78%, a specificity of 99.9%, a positive predictive value of 88% and negative predictive value of 99.7%. This new algorithm for detection of pediatric VPE performs well with a reasonable positive and negative predictive value despite the low prevalence in the general population. Copyright © 2016 Elsevier Inc. All rights reserved.

Effect of 3D magnetic perturbations on divertor conditions and detachment in tokamak and stellarator

DOE PAGES

Ahn, J. -W.; Briesemester, A. R.; Kobayashi, M.; ...

2017-06-22

Enhanced perpendicular heat and momentum transport induces parallel pressure loss leading to divertor detachment, which can be produced by the increase of density in 2D tokamaks. However, in the 3D configurations such as tokamaks with 3D fields and stellarators, the fraction of perpendicular transport can be higher even in a lower density regime, which could lead to the early transition to detachment without passing through the high-recycling regime. 3D fields applied to the limiter tokamak plasmas produce edge stochastic layers close to the last closed flux surface (LCFS), which can allow for enhanced perpendicular transport and indeed the absence ofmore » high recycling regime and early detachment have been observed in TEXTOR and Tore Supra. However, in the X-point divertor tokamaks with the applied 3D fields, the parallel transport is still dominant and the detachment facilitation has not been observed yet. Rather, 3D fields affected detachment adversely under certain conditions, either by preventing detachment onset as seen in DIII-D or by re-attaching the existing detached plasma as shown in NSTX. The possible way for strong 3D effects to induce access to the early detachment in divertor tokamaks appears to be via significant perpendicular loss of parallel momentum by frictional force for the counter-streaming flows between neighboring flow channels in the divertor. In principle, the adjacent lobes in the 3D divertor tokamak may generate the counter-streaming flow channels. However, an EMC3-EIRENE simulation for ITER H-mode plasmas demonstrated that screened RMP leads to significantly reduced counter-flows near the divertor target, therefore the momentum loss effect leading to detachment facilitation is expected to be small. This is consistent with the observation in LHD, which showed screening (amplification) of RMP fields in the attachment (stable detachment) case. In conclusion, work for optimal parameter window for best divertor operation scenario is needed particularly for the 3D divertor tokamak configuration.« less

Effect of 3D magnetic perturbations on divertor conditions and detachment in tokamak and stellarator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahn, J. -W.; Briesemester, A. R.; Kobayashi, M.

Enhanced perpendicular heat and momentum transport induces parallel pressure loss leading to divertor detachment, which can be produced by the increase of density in 2D tokamaks. However, in the 3D configurations such as tokamaks with 3D fields and stellarators, the fraction of perpendicular transport can be higher even in a lower density regime, which could lead to the early transition to detachment without passing through the high-recycling regime. 3D fields applied to the limiter tokamak plasmas produce edge stochastic layers close to the last closed flux surface (LCFS), which can allow for enhanced perpendicular transport and indeed the absence ofmore » high recycling regime and early detachment have been observed in TEXTOR and Tore Supra. However, in the X-point divertor tokamaks with the applied 3D fields, the parallel transport is still dominant and the detachment facilitation has not been observed yet. Rather, 3D fields affected detachment adversely under certain conditions, either by preventing detachment onset as seen in DIII-D or by re-attaching the existing detached plasma as shown in NSTX. The possible way for strong 3D effects to induce access to the early detachment in divertor tokamaks appears to be via significant perpendicular loss of parallel momentum by frictional force for the counter-streaming flows between neighboring flow channels in the divertor. In principle, the adjacent lobes in the 3D divertor tokamak may generate the counter-streaming flow channels. However, an EMC3-EIRENE simulation for ITER H-mode plasmas demonstrated that screened RMP leads to significantly reduced counter-flows near the divertor target, therefore the momentum loss effect leading to detachment facilitation is expected to be small. This is consistent with the observation in LHD, which showed screening (amplification) of RMP fields in the attachment (stable detachment) case. In conclusion, work for optimal parameter window for best divertor operation scenario is needed particularly for the 3D divertor tokamak configuration.« less

Strategies for the Optimization of Natural Leads to Anticancer Drugs or Drug Candidates

PubMed Central

Xiao, Zhiyan; Morris-Natschke, Susan L.; Lee, Kuo-Hsiung

2015-01-01

Natural products have made significant contribution to cancer chemotherapy over the past decades and remain an indispensable source of molecular and mechanistic diversity for anticancer drug discovery. More often than not, natural products may serve as leads for further drug development rather than as effective anticancer drugs by themselves. Generally, optimization of natural leads into anticancer drugs or drug candidates should not only address drug efficacy, but also improve ADMET profiles and chemical accessibility associated with the natural leads. Optimization strategies involve direct chemical manipulation of functional groups, structure-activity relationship-directed optimization and pharmacophore-oriented molecular design based on the natural templates. Both fundamental medicinal chemistry principles (e.g., bio-isosterism) and state-of-the-art computer-aided drug design techniques (e.g., structure-based design) can be applied to facilitate optimization efforts. In this review, the strategies to optimize natural leads to anticancer drugs or drug candidates are illustrated with examples and described according to their purposes. Furthermore, successful case studies on lead optimization of bioactive compounds performed in the Natural Products Research Laboratories at UNC are highlighted. PMID:26359649

Development of α-glucosidase inhibitors by room temperature C-C cross couplings of quinazolinones.

PubMed

Garlapati, Ramesh; Pottabathini, Narender; Gurram, Venkateshwarlu; Kasani, Kumara Swamy; Gundla, Rambabu; Thulluri, Chiranjeevi; Machiraju, Pavan Kumar; Chaudhary, Avinash B; Addepally, Uma; Dayam, Raveendra; Chunduri, Venkata Rao; Patro, Balaram

2013-08-07

Novel quinazolinone based α-glucosidase inhibitors have been developed. For this purpose a virtual screening model has been generated and validated utilizing acarbose as a α-glucosidase inhibitor. Homology modeling, docking, and virtual screening were successfully employed to discover a set of structurally diverse compounds active against α-glucosidase. A search of a 3D database containing 22,500 small molecules using the structure based virtual model yielded ten possible candidates. All ten candidates were N-3-pyridyl-2-cyclopropyl quinazolinone-4-one derivatives, varying at the 6 position. This position was modified by Suzuki-Miyaura cross coupling with aryl, heteroaryl, and alkyl boronic acids. A catalyst screen was performed, and using the best optimal conditions, a series of twenty five compounds was synthesized. Notably, the C-C cross coupling reactions of the 6-bromo-2-cyclopropyl-3-(pyridyl-3-ylmethyl)quinazolin-4(3H)-one precursor have been accomplished at room temperature. A comparison of the relative reactivities of 6-bromo and 6-chloro-2,3-disubstituted quinazolinones with phenyl boronic acid was conducted. An investigation of pre-catalyst loading for the reaction of the 6-bromo-2-cyclopropyl-3-(pyridyl-3-ylmethyl)quinazolin-4(3H)-one substrate was also carried out. Finally, we submitted our compounds to biological assays against α-glucosidase inhibitors. Of these, three hits (compounds 4a, 4t and 4r) were potentially active as α-glucosidase inhibitors and showed activity with IC50 values <20 μM. Based on structural novelty and desirable drug-like properties, 4a was selected for structure-activity relationship study, and thirteen analogs were synthesized. Nine out of thirteen analogs acted as α-glucosidase inhibitors with IC50 values <10 μM. These lead compounds have desirable physicochemical properties and are excellent candidates for further optimization.

Multiclass classification of obstructive sleep apnea/hypopnea based on a convolutional neural network from a single-lead electrocardiogram.

PubMed

Urtnasan, Erdenebayar; Park, Jong-Uk; Lee, Kyoung-Joung

2018-05-24

In this paper, we propose a convolutional neural network (CNN)-based deep learning architecture for multiclass classification of obstructive sleep apnea and hypopnea (OSAH) using single-lead electrocardiogram (ECG) recordings. OSAH is the most common sleep-related breathing disorder. Many subjects who suffer from OSAH remain undiagnosed; thus, early detection of OSAH is important. In this study, automatic classification of three classes-normal, hypopnea, and apnea-based on a CNN is performed. An optimal six-layer CNN model is trained on a training dataset (45,096 events) and evaluated on a test dataset (11,274 events). The training set (69 subjects) and test set (17 subjects) were collected from 86 subjects with length of approximately 6 h and segmented into 10 s durations. The proposed CNN model reaches a mean -score of 93.0 for the training dataset and 87.0 for the test dataset. Thus, proposed deep learning architecture achieved a high performance for multiclass classification of OSAH using single-lead ECG recordings. The proposed method can be employed in screening of patients suspected of having OSAH. © 2018 Institute of Physics and Engineering in Medicine.

Carbon dioxide sequestration by chemolithotrophic oleaginous bacteria for production and optimization of polyhydroxyalkanoate.

PubMed

Kumar, Manish; Gupta, Asmita; Thakur, Indu Shekhar

2016-08-01

The present work involved screening of a previously reported carbon concentrating oleaginous bacterial strain Serratia sp. ISTD04 for production of PHA and optimization of process parameters for enhanced PHA and biomass generation. The selected bacterial strain was screened for PHA production based on Nile red staining followed by visualization under fluorescence microscope. Spectrofluorometric measurement of Nile red fluorescence of the bacterial culture was also done. Confirmatory analysis of PHA accumulation by GC-MS revealed the presence of 3-hydroxyvalerate. Detection of characteristic peaks in the FT-IR spectrum further confirmed the production of PHA by the bacterium. Response Surface Methodology was used for optimization of pH and carbon sources' concentrations for higher PHA production. There was almost a 2 fold increase in the production of PHA following optimization as compared to un-optimized condition. The study thus establishes the production of PHA by Serratia sp. ISTD04. Copyright © 2016 Elsevier Ltd. All rights reserved.

Information Engineering and Workflow Design in a Clinical Decision Support System for Colorectal Cancer Screening in Iran.

PubMed

Maserat, Elham; Seied Farajollah, Seiede Sedigheh; Safdari, Reza; Ghazisaeedi, Marjan; Aghdaei, Hamid Asadzadeh; Zali, Mohammad Reza

2015-01-01

Colorectal cancer is a major cause of morbidity and mortality throughout the world. Colorectal cancer screening is an optimal way for reducing of morbidity and mortality and a clinical decision support system (CDSS) plays an important role in predicting success of screening processes. DSS is a computer-based information system that improves the delivery of preventive care services. The aim of this article was to detail engineering of information requirements and work flow design of CDSS for a colorectal cancer screening program. In the first stage a screening minimum data set was determined. Developed and developing countries were analyzed for identifying this data set. Then information deficiencies and gaps were determined by check list. The second stage was a qualitative survey with a semi-structured interview as the study tool. A total of 15 users and stakeholders' perspectives about workflow of CDSS were studied. Finally workflow of DSS of control program was designed by standard clinical practice guidelines and perspectives. Screening minimum data set of national colorectal cancer screening program was defined in five sections, including colonoscopy data set, surgery, pathology, genetics and pedigree data set. Deficiencies and information gaps were analyzed. Then we designed a work process standard of screening. Finally workflow of DSS and entry stage were determined. A CDSS facilitates complex decision making for screening and has key roles in designing optimal interactions between colonoscopy, pathology and laboratory departments. Also workflow analysis is useful to identify data reconciliation strategies to address documentation gaps. Following recommendations of CDSS should improve quality of colorectal cancer screening.

Development of a quantitative assay amenable for high-throughput screening to target the type II secretion system for new treatments against plant-pathogenic bacteria.

PubMed

Tran, Nini; Zielke, Ryszard A; Vining, Oliver B; Azevedo, Mark D; Armstrong, Donald J; Banowetz, Gary M; McPhail, Kerry L; Sikora, Aleksandra E

2013-09-01

Plant-pathogenic bacteria are the causative agents of diseases in important agricultural crops and ornamental plants. The severe economic burden of these diseases requires seeking new approaches for their control, particularly because phytopathogenic bacteria are often resistant to available treatments. The type II secretion (T2S) system is a key virulence factor used by major groups of phytopathogenic bacteria. The T2S machinery transports many hydrolytic enzymes responsible for degradation of the plant cell wall, thus enabling successful colonization and dissemination of the bacteria in the plant host. The genetic inactivation of the T2S system leads to loss of virulence, which strongly suggests that targeting the T2S could enable new treatments against plant-pathogenic bacteria. Accordingly, we have designed and optimized an assay to identify small-molecule inhibitors of the T2S system. This assay uses a double parametric output: measurement of bacterial growth and the enzymatic activity of cellulase, which is secreted via the T2S pathway in our model organism Dickeya dadantii. The assay was evaluated by screening natural extracts, culture filtrates isolated from rhizosphere bacteria, and a collection of pharmaceutically active compounds in LOPAC(1280). The calculated Z' values of 0.63, 0.63, and 0.58, respectively, strongly suggest that the assay is applicable for a high-throughput screening platform.

Making the cut: Depression screening in urban general hospital clinics for culturally diverse Latino populations.

PubMed

Gutnick, Damara; Siegel, Carole; Laska, Eugene; Wanderling, Joseph; Wagner, Ellen Cogen; Haugland, Gary; Conlon, Mary K

We examined whether the cut-point 10 for the Patient Health Questionnaire-9 (PHQ9) depression screen used in primary care populations is equally valid for Mexicans (M), Ecuadorians (E), Puerto Ricans (PR) and non-Hispanic whites (W) from inner-city hospital-based primary care clinics; and whether stressful life events elevate scores and the probability of major depressive disorder (MDD). Over 18-months, a sample of persons from hospital clinics with a positive initial PHQ2 and a subsequent PHQ9 were administered a stressful life event questionnaire and a Structured Clinical Interview to establish an MDD diagnosis, with oversampling of those between 8 and 12: (n=261: 75 E, 71 M, 51 PR, 64 W). For analysis, the sample was weighted using chart review (n=368) to represent a typical clinic population. Receiver Operating Characteristics analysis selected cut-points maximizing sensitivity (Sn) plus specificity (Sp). The optimal cut-point for all groups was 13 with the corresponding Sn and Sp estimates for E=(Sn 73%, Sp 71%), M=(76%, 81%), PR=(81%, 63%) and W=(80%, 74%). Stressful life events impacted screen scores and MDD diagnosis. Elevating the PHQ9 cut-point for inner-city Latinos as well as whites is suggested to avoid high false positive rates leading to improper treatment with clinical and economic consequences. Copyright © 2016 Elsevier Inc. All rights reserved.

A systematic approach to prioritize drug targets using machine learning, a molecular descriptor-based classification model, and high-throughput screening of plant derived molecules: a case study in oral cancer.

PubMed

Randhawa, Vinay; Kumar Singh, Anil; Acharya, Vishal

2015-12-01

Systems-biology inspired identification of drug targets and machine learning-based screening of small molecules which modulate their activity have the potential to revolutionize modern drug discovery by complementing conventional methods. To utilize the effectiveness of such pipelines, we first analyzed the dysregulated gene pairs between control and tumor samples and then implemented an ensemble-based feature selection approach to prioritize targets in oral squamous cell carcinoma (OSCC) for therapeutic exploration. Based on the structural information of known inhibitors of CXCR4-one of the best targets identified in this study-a feature selection was implemented for the identification of optimal structural features (molecular descriptor) based on which a classification model was generated. Furthermore, the CXCR4-centered descriptor-based classification model was finally utilized to screen a repository of plant derived small-molecules to obtain potential inhibitors. The application of our methodology may assist effective selection of the best targets which may have previously been overlooked, that in turn will lead to the development of new oral cancer medications. The small molecules identified in this study can be ideal candidates for trials as potential novel anti-oral cancer agents. Importantly, distinct steps of this whole study may provide reference for the analysis of other complex human diseases.

Improving the delivery of brief interventions for heavy drinking in primary health care: outcome results of the Optimizing Delivery of Health Care Intervention (ODHIN) five-country cluster randomized factorial trial.

PubMed

Anderson, Peter; Bendtsen, Preben; Spak, Fredrik; Reynolds, Jillian; Drummond, Colin; Segura, Lidia; Keurhorst, Myrna N; Palacio-Vieira, Jorge; Wojnar, Marcin; Parkinson, Kathryn; Colom, Joan; Kłoda, Karolina; Deluca, Paolo; Baena, Begoña; Newbury-Birch, Dorothy; Wallace, Paul; Heinen, Maud; Wolstenholme, Amy; van Steenkiste, Ben; Mierzecki, Artur; Okulicz-Kozaryn, Katarzyna; Ronda, Gaby; Kaner, Eileen; Laurant, Miranda G H; Coulton, Simon; Gual, Toni

2016-11-01

To test if training and support, financial reimbursement and option of referring screen-positive patients to an internet-based method of giving advice (eBI) can increase primary health-care providers' delivery of Alcohol Use Disorders Identification Test (AUDIT)-C-based screening and advice to heavy drinkers. Cluster randomized factorial trial with 12-week implementation and measurement period. Primary health-care units (PHCU) in different locations throughout Catalonia, England, the Netherlands, Poland and Sweden. A total of 120 PHCU, 24 in each of Catalonia, England, the Netherlands, Poland and Sweden. PHCUs were randomized to one of eight groups: care as usual, training and support (TS), financial reimbursement (FR) and eBI; paired combinations of TS, FR and eBI, and all of FR, TS and eBI. The primary outcome measure was the proportion of eligible adult (age 18+ years) patients screened during a 12-week implementation period. Secondary outcome measures were proportion of screen-positive patients advised; and proportion of consulting adult patients given an intervention (screening and advice to screen-positives) during the same 12-week implementation period. During a 4-week baseline measurement period, the proportion of consulting adult patients who were screened for their alcohol consumption was 0.059 per PHCU (95% CI 0.034 to 0.084). Based on the factorial design, the ratio of the logged proportion screened during the 12-week implementation period was 1.48 (95% CI = 1.13-1.95) in PHCU that received TS versus PHCU that did not receive TS; for FR, the ratio was 2.00 (95% CI = 1.56-2.56). The option of referral to eBI did not lead to a higher proportion of patients screened. The ratio for TS plus FR was 2.34 (95% CI = 1.77-3.10), and the ratio for TS plus FR plus eBI was1.68 (95% CI = 1.11-2.53). Providing primary health-care units with training, support and financial reimbursement for delivering Alcohol Use Disorders Identification Test-C-based screening and advice to heavy drinkers increases screening for alcohol consumption. Providing primary health-care units with the option of referring screen-positive patients to an internet-based method of giving advice does not appear to increase screening for alcohol consumption. © 2016 Society for the Study of Addiction.

Diabetes screening in overweight and obese children and adolescents: choosing the right test.

PubMed

Ehehalt, Stefan; Wiegand, Susanna; Körner, Antje; Schweizer, Roland; Liesenkötter, Klaus-Peter; Partsch, Carl-Joachim; Blumenstock, Gunnar; Spielau, Ulrike; Denzer, Christian; Ranke, Michael B; Neu, Andreas; Binder, Gerhard; Wabitsch, Martin; Kiess, Wieland; Reinehr, Thomas

2017-01-01

Type 2 diabetes can occur without any symptoms, and health problems associated with the disease are serious. Screening tests allowing an early diagnosis are desirable. However, optimal screening tests for diabetes in obese youth are discussed controversially. We performed an observational multicenter analysis including 4848 (2668 female) overweight and obese children aged 7 to 17 years without previously known diabetes. Using HbA1c and OGTT as diagnostic criteria, 2.4% (n = 115, 55 female) could be classified as having diabetes. Within this group, 68.7% had HbA1c levels ≥48 mmol/mol (≥6.5%). FPG ≥126 mg/dl (≥7.0 mmol/l) and/or 2-h glucose levels ≥200 mg/dl (≥11.1 mmol/l) were found in 46.1%. Out of the 115 cases fulfilling the OGTT and/or HbA1c criteria for diabetes, diabetes was confirmed in 43.5%. For FPG, the ROC analysis revealed an optimal threshold of 98 mg/dl (5.4 mmol/l) (sensitivity 70%, specificity 88%). For HbA1c, the best cut-off value was 42 mmol/mol (6.0%) (sensitivity 94%, specificity 93%). HbA1c seems to be more reliable than OGTT for diabetes screening in overweight and obese children and adolescents. The optimal HbA1c threshold for identifying patients with diabetes was found to be 42 mmol/mol (6.0%). What is Known: • The prevalence of obesity is increasing and health problems related to type 2 DM can be serious. However, an optimal screening test for diabetes in obese youth seems to be controversial in the literature. What is New: • In our study, the ROC analysis revealed for FPG an optimal threshold of 98 mg/dl (5.4 mmol/l, sensitivity 70%, specificity 88%) and for HbA1c a best cut-off value of 42 mmol/mol (6.0%, sensitivity 94%, specificity 93%) to detect diabetes. Thus, in overweight and obese children and adolescents, HbA1c seems to be a more reliable screening tool than OGTT.

Identification of translational activators of glial glutamate transporter EAAT2 through cell-based high-throughput screening: an approach to prevent excitotoxicity.

PubMed

Colton, Craig K; Kong, Qiongman; Lai, Liching; Zhu, Michael X; Seyb, Kathleen I; Cuny, Gregory D; Xian, Jun; Glicksman, Marcie A; Lin, Chien-Liang Glenn

2010-07-01

Excitotoxicity has been implicated as the mechanism of neuronal damage resulting from acute insults such as stroke, epilepsy, and trauma, as well as during the progression of adult-onset neurodegenerative disorders such as Alzheimer's disease and amyotrophic lateral sclerosis (ALS). Excitotoxicity is defined as excessive exposure to the neurotransmitter glutamate or overstimulation of its membrane receptors, leading to neuronal injury or death. One potential approach to protect against excitotoxic neuronal damage is enhanced glutamate reuptake. The glial glutamate transporter EAAT2 is the quantitatively dominant glutamate transporter and plays a major role in clearance of glutamate. Expression of EAAT2 protein is highly regulated at the translational level. In an effort to identify compounds that can induce translation of EAAT2 transcripts, a cell-based enzyme-linked immunosorbent assay was developed using a primary astrocyte line stably transfected with a vector designed to identify modulators of EAAT2 translation. This assay was optimized for high-throughput screening, and a library of approximately 140,000 compounds was tested. In the initial screen, 293 compounds were identified as hits. These 293 hits were retested at 3 concentrations, and a total of 61 compounds showed a dose-dependent increase in EAAT2 protein levels. Selected compounds were tested in full 12-point dose-response experiments in the screening assay to assess potency as well as confirmed by Western blot, immunohistochemistry, and glutamate uptake assays to evaluate the localization and function of the elevated EAAT2 protein. These hits provide excellent starting points for developing therapeutic agents to prevent excitotoxicity.

Diagnostic performance and optimal cut-off scores of the Massachusetts youth screening instrument-second version in a sample of Swiss youths in welfare and juvenile justice institutions.

PubMed

Dölitzsch, Claudia; Leenarts, Laura E W; Schmeck, Klaus; Fegert, Jorg M; Grisso, Thomas; Schmid, Marc

2017-02-08

There is a growing consensus about the importance of mental health screening of youths in welfare and juvenile justice institutions. The Massachusetts Youth Screening Instrument-second version (MAYSI-2) was specifically designed, normed and validated to assist juvenile justice facilities in the United States of America (USA), in identifying youths with potential emotional or behavioral problems. However, it is not known if the USA norm-based cut-off scores can be used in Switzerland. Therefore, the primary purpose of the current study was to estimate the diagnostic performance and optimal cut-off scores of the MAYSI-2 in a sample of Swiss youths in welfare and juvenile justice institutions. As the sample was drawn from the French-, German- and Italian-speaking parts of Switzerland, the three languages were represented in the total sample of the current study and consequently we could estimate the diagnostic performance and the optimal cut-off scores of the MAYSI-2 for the language regions separately. The other main purpose of the current study was to identify potential gender differences in the diagnostic performance and optimal cut-off scores. Participants were 297 boys and 149 girls (mean age = 16.2, SD = 2.5) recruited from 64 youth welfare and juvenile justice institutions (drawn from the French-, German- and Italian-speaking parts of Switzerland). The MAYSI-2 was used to screen for mental health or behavioral problems that could require further evaluation. Psychiatric classification was based on the Schedule for Affective Disorders and Schizophrenia for School-Age Children, Present and Lifetime version (K-SADS-PL). The MAYSI-2 scores were submitted into Receiver-Operating Characteristic (ROC) analyses to estimate the diagnostic performance and optimal 'caution' cut-off scores of the MAYSI-2. The ROC analyses revealed that nearly all homotypic mappings of MAYSI-2 scales onto (cluster of) psychiatric disorders revealed above chance level accuracy. The optimal 'caution' cut-off scores derived from the ROC curve for predicting (cluster of) psychiatric disorders were, for several MAYSI-2 scales, comparable to the USA norm-based 'caution' cut-off scores. For some MAYSI-2 scales, however, higher optimal 'caution' cut-off scores were found. With adjusted optimal 'caution' cut-off scores, the MAYSI-2 screens potential emotional or behavioral problems well in a sample of Swiss youths in welfare and juvenile justice institutions. However, as for choosing the optimal 'caution' cut off score for the MAYSI-2, both language as well as gender seems to be of importance. The results of this study point to a compelling need to test the diagnostic performance and optimal 'caution' cut-off scores of the MAYSI-2 more elaborately in larger differentiated language samples in Europe.

Cancer risk estimation in Digital Breast Tomosynthesis using GEANT4 Monte Carlo simulations and voxel phantoms.

PubMed

Ferreira, P; Baptista, M; Di Maria, S; Vaz, P

2016-05-01

The aim of this work was to estimate the risk of radiation induced cancer following the Portuguese breast screening recommendations for Digital Mammography (DM) when applied to Digital Breast Tomosynthesis (DBT) and to evaluate how the risk to induce cancer could influence the energy used in breast diagnostic exams. The organ doses were calculated by Monte Carlo simulations using a female voxel phantom and considering the acquisition of 25 projection images. Single organ cancer incidence risks were calculated in order to assess the total effective radiation induced cancer risk. The screening strategy techniques considered were: DBT in Cranio-Caudal (CC) view and two-view DM (CC and Mediolateral Oblique (MLO)). The risk of cancer incidence following the Portuguese screening guidelines (screening every two years in the age range of 50-80years) was calculated by assuming a single CC DBT acquisition view as standalone screening strategy and compared with two-view DM. The difference in the total effective risk between DBT and DM is quite low. Nevertheless in DBT an increase of risk for the lung is observed with respect to DM. The lung is also the organ that is mainly affected when non-optimal beam energy (in terms of image quality and absorbed dose) is used instead of an optimal one. The use of non-optimal energies could increase the risk of lung cancer incidence by a factor of about 2. Copyright © 2016 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Novel high-resolution computed tomography-based radiomic classifier for screen-identified pulmonary nodules in the National Lung Screening Trial.

PubMed

Peikert, Tobias; Duan, Fenghai; Rajagopalan, Srinivasan; Karwoski, Ronald A; Clay, Ryan; Robb, Richard A; Qin, Ziling; Sicks, JoRean; Bartholmai, Brian J; Maldonado, Fabien

2018-01-01

Optimization of the clinical management of screen-detected lung nodules is needed to avoid unnecessary diagnostic interventions. Herein we demonstrate the potential value of a novel radiomics-based approach for the classification of screen-detected indeterminate nodules. Independent quantitative variables assessing various radiologic nodule features such as sphericity, flatness, elongation, spiculation, lobulation and curvature were developed from the NLST dataset using 726 indeterminate nodules (all ≥ 7 mm, benign, n = 318 and malignant, n = 408). Multivariate analysis was performed using least absolute shrinkage and selection operator (LASSO) method for variable selection and regularization in order to enhance the prediction accuracy and interpretability of the multivariate model. The bootstrapping method was then applied for the internal validation and the optimism-corrected AUC was reported for the final model. Eight of the originally considered 57 quantitative radiologic features were selected by LASSO multivariate modeling. These 8 features include variables capturing Location: vertical location (Offset carina centroid z), Size: volume estimate (Minimum enclosing brick), Shape: flatness, Density: texture analysis (Score Indicative of Lesion/Lung Aggression/Abnormality (SILA) texture), and surface characteristics: surface complexity (Maximum shape index and Average shape index), and estimates of surface curvature (Average positive mean curvature and Minimum mean curvature), all with P<0.01. The optimism-corrected AUC for these 8 features is 0.939. Our novel radiomic LDCT-based approach for indeterminate screen-detected nodule characterization appears extremely promising however independent external validation is needed.

Optimizing the Use of the AUDIT for Alcohol Screening in College Students

PubMed Central

DeMartini, Kelly S.; Carey, Kate B.

2013-01-01

The screening and brief intervention (SBI) modality of treatment for at-risk college drinking is becoming increasingly popular. A key to effective implementation is use of validated screening tools. While the Alcohol Use Disorder Identification Test (AUDIT) has been validated in adult samples and is often used with college students, research has not yet established optimal cut-off scores to screen for at-risk drinking. A total of 401 current drinkers completed computerized assessments of demographics, family history of alcohol use disorders, alcohol use history, alcohol-related problems, and general health. Of the 401 drinkers, 207 met criteria for at-risk drinking. Receiver-operating characteristic (ROC) curve analysis revealed that the AUROC of the AUDIT was 0.86 (95% CI = 0.83-0.90). The AUDIT-C (AUROC = 0.89, 95% CI = 0.86--.92) performed significantly better than the AUDIT in the detection of at-risk drinking in the whole sample, and specifically for females. Gender differences emerged in the optimal cut-off scores for the AUDIT-C. A total score of 7 should be used for males and a score of 5 should be used for females. These empirical guidelines may enhance identification of at-risk drinkers in college settings. PMID:22612646

Optimizing the use of the AUDIT for alcohol screening in college students.

PubMed

Demartini, Kelly S; Carey, Kate B

2012-12-01

The screening and brief intervention modality of treatment for at-risk college drinking is becoming increasingly popular. A key to effective implementation is use of validated screening tools. Although the Alcohol Use Disorders Identification Test (AUDIT) has been validated in adult samples and is often used with college students, research has not yet established optimal cutoff scores to screen for at-risk drinking. Four hundred and one current drinkers completed computerized assessments of demographics, family history of alcohol use disorders, alcohol use history, alcohol-related problems, and general health. Of the 401 drinkers, 207 met criteria for at-risk drinking. Receiver operating characteristic (ROC) curve analysis revealed that the area under the ROC (AUROC) of the AUDIT was .86 (95% CI [.83, .90]). The first 3 consumption items of the AUDIT (AUDIT-C; AUROC = .89, 95% CI [.86, .92]) performed significantly better than the AUDIT in the detection of at-risk drinking in the whole sample, and specifically for females. Gender differences emerged in the optimal cutoff scores for the AUDIT-C. A total score of 7 should be used for males, and a score of 5 should be used for females. These empirical guidelines may enhance identification of at-risk drinkers in college settings.

Predictive simulations and optimization of nanowire field-effect PSA sensors including screening

NASA Astrophysics Data System (ADS)

Baumgartner, Stefan; Heitzinger, Clemens; Vacic, Aleksandar; Reed, Mark A.

2013-06-01

We apply our self-consistent PDE model for the electrical response of field-effect sensors to the 3D simulation of nanowire PSA (prostate-specific antigen) sensors. The charge concentration in the biofunctionalized boundary layer at the semiconductor-electrolyte interface is calculated using the propka algorithm, and the screening of the biomolecules by the free ions in the liquid is modeled by a sensitivity factor. This comprehensive approach yields excellent agreement with experimental current-voltage characteristics without any fitting parameters. Having verified the numerical model in this manner, we study the sensitivity of nanowire PSA sensors by changing device parameters, making it possible to optimize the devices and revealing the attributes of the optimal field-effect sensor.

A reliable computational workflow for the selection of optimal screening libraries.

PubMed

Gilad, Yocheved; Nadassy, Katalin; Senderowitz, Hanoch

2015-01-01

The experimental screening of compound collections is a common starting point in many drug discovery projects. Successes of such screening campaigns critically depend on the quality of the screened library. Many libraries are currently available from different vendors yet the selection of the optimal screening library for a specific project is challenging. We have devised a novel workflow for the rational selection of project-specific screening libraries. The workflow accepts as input a set of virtual candidate libraries and applies the following steps to each library: (1) data curation; (2) assessment of ADME/T profile; (3) assessment of the number of promiscuous binders/frequent HTS hitters; (4) assessment of internal diversity; (5) assessment of similarity to known active compound(s) (optional); (6) assessment of similarity to in-house or otherwise accessible compound collections (optional). For ADME/T profiling, Lipinski's and Veber's rule-based filters were implemented and a new blood brain barrier permeation model was developed and validated (85 and 74 % success rate for training set and test set, respectively). Diversity and similarity descriptors which demonstrated best performances in terms of their ability to select either diverse or focused sets of compounds from three databases (Drug Bank, CMC and CHEMBL) were identified and used for diversity and similarity assessments. The workflow was used to analyze nine common screening libraries available from six vendors. The results of this analysis are reported for each library providing an assessment of its quality. Furthermore, a consensus approach was developed to combine the results of these analyses into a single score for selecting the optimal library under different scenarios. We have devised and tested a new workflow for the rational selection of screening libraries under different scenarios. The current workflow was implemented using the Pipeline Pilot software yet due to the usage of generic components, it can be easily adapted and reproduced by computational groups interested in rational selection of screening libraries. Furthermore, the workflow could be readily modified to include additional components. This workflow has been routinely used in our laboratory for the selection of libraries in multiple projects and consistently selects libraries which are well balanced across multiple parameters.Graphical abstract.

Identification and characterization of highly versatile peptide-vectors that bind non-competitively to the low-density lipoprotein receptor for in vivo targeting and delivery of small molecules and protein cargos

PubMed Central

David, Marion; Lécorché, Pascaline; Masse, Maxime; Faucon, Aude; Abouzid, Karima; Gaudin, Nicolas; Varini, Karine; Gassiot, Fanny; Ferracci, Géraldine; Jacquot, Guillaume; Vlieghe, Patrick

2018-01-01

Insufficient membrane penetration of drugs, in particular biotherapeutics and/or low target specificity remain a major drawback in their efficacy. We propose here the rational characterization and optimization of peptides to be developed as vectors that target cells expressing specific receptors involved in endocytosis or transcytosis. Among receptors involved in receptor-mediated transport is the LDL receptor. Screening complex phage-displayed peptide libraries on the human LDLR (hLDLR) stably expressed in cell lines led to the characterization of a family of cyclic and linear peptides that specifically bind the hLDLR. The VH411 lead cyclic peptide allowed endocytosis of payloads such as the S-Tag peptide or antibodies into cells expressing the hLDLR. Size reduction and chemical optimization of this lead peptide-vector led to improved receptor affinity. The optimized peptide-vectors were successfully conjugated to cargos of different nature and size including small organic molecules, siRNAs, peptides or a protein moiety such as an Fc fragment. We show that in all cases, the peptide-vectors retain their binding affinity to the hLDLR and potential for endocytosis. Following i.v. administration in wild type or ldlr-/- mice, an Fc fragment chemically conjugated or fused in C-terminal to peptide-vectors showed significant biodistribution in LDLR-enriched organs. We have thus developed highly versatile peptide-vectors endowed with good affinity for the LDLR as a target receptor. These peptide-vectors have the potential to be further developed for efficient transport of therapeutic or imaging agents into cells -including pathological cells—or organs that express the LDLR. PMID:29485998

TSH Receptor Signaling Abrogation by a Novel Small Molecule

PubMed Central

Latif, Rauf; Realubit, Ronald B.; Karan, Charles; Mezei, Mihaly; Davies, Terry F.

2016-01-01

Pathological activation of the thyroid-stimulating hormone receptor (TSHR) is caused by thyroid-stimulating antibodies in patients with Graves’ disease (GD) or by somatic and rare genomic mutations that enhance constitutive activation of the receptor influencing both G protein and non-G protein signaling. Potential selective small molecule antagonists represent novel therapeutic compounds for abrogation of such abnormal TSHR signaling. In this study, we describe the identification and in vitro characterization of a novel small molecule antagonist by high-throughput screening (HTS). The identification of the TSHR antagonist was performed using a transcription-based TSH-inhibition bioassay. TSHR-expressing CHO cells, which also expressed a luciferase-tagged CRE response element, were optimized using bovine TSH as the activator, in a 384 well plate format, which had a Z score of 0.3–0.6. Using this HTS assay, we screened a diverse library of ~80,000 compounds at a final concentration of 16.7 μM. The selection criteria for a positive hit were based on a mean signal threshold of ≥50% inhibition of control TSH stimulation. The screening resulted in 450 positive hits giving a hit ratio of 0.56%. A secondary confirmation screen against TSH and forskolin – a post receptor activator of adenylyl cyclase – confirmed one TSHR-specific candidate antagonist molecule (named VA-K-14). This lead molecule had an IC50 of 12.3 μM and a unique chemical structure. A parallel analysis for cell viability indicated that the lead inhibitor was non-cytotoxic at its effective concentrations. In silico docking studies performed using a TSHR transmembrane model showed the hydrophobic contact locations and the possible mode of inhibition of TSHR signaling. Furthermore, this molecule was capable of inhibiting TSHR stimulation by GD patient sera and monoclonal-stimulating TSHR antibodies. In conclusion, we report the identification of a novel small molecule TSHR inhibitor, which has the potential to be developed as a therapeutic antagonist for abrogation of TSHR signaling by TSHR autoantibodies in GD. PMID:27729899

WISDOM-II: screening against multiple targets implicated in malaria using computational grid infrastructures.

PubMed

Kasam, Vinod; Salzemann, Jean; Botha, Marli; Dacosta, Ana; Degliesposti, Gianluca; Isea, Raul; Kim, Doman; Maass, Astrid; Kenyon, Colin; Rastelli, Giulio; Hofmann-Apitius, Martin; Breton, Vincent

2009-05-01

Despite continuous efforts of the international community to reduce the impact of malaria on developing countries, no significant progress has been made in the recent years and the discovery of new drugs is more than ever needed. Out of the many proteins involved in the metabolic activities of the Plasmodium parasite, some are promising targets to carry out rational drug discovery. Recent years have witnessed the emergence of grids, which are highly distributed computing infrastructures particularly well fitted for embarrassingly parallel computations like docking. In 2005, a first attempt at using grids for large-scale virtual screening focused on plasmepsins and ended up in the identification of previously unknown scaffolds, which were confirmed in vitro to be active plasmepsin inhibitors. Following this success, a second deployment took place in the fall of 2006 focussing on one well known target, dihydrofolate reductase (DHFR), and on a new promising one, glutathione-S-transferase. In silico drug design, especially vHTS is a widely and well-accepted technology in lead identification and lead optimization. This approach, therefore builds, upon the progress made in computational chemistry to achieve more accurate in silico docking and in information technology to design and operate large scale grid infrastructures. On the computational side, a sustained infrastructure has been developed: docking at large scale, using different strategies in result analysis, storing of the results on the fly into MySQL databases and application of molecular dynamics refinement are MM-PBSA and MM-GBSA rescoring. The modeling results obtained are very promising. Based on the modeling results, In vitro results are underway for all the targets against which screening is performed. The current paper describes the rational drug discovery activity at large scale, especially molecular docking using FlexX software on computational grids in finding hits against three different targets (PfGST, PfDHFR, PvDHFR (wild type and mutant forms) implicated in malaria. Grid-enabled virtual screening approach is proposed to produce focus compound libraries for other biological targets relevant to fight the infectious diseases of the developing world.

Production, statistical optimization and application of endoglucanase from Rhizopus stolonifer utilizing coffee husk.

PubMed

Navya, P N; Pushpa, S Murthy

2013-08-01

Coffee cherry husk (CH) is one of the major by-products obtained from coffee processing industry and accounts to 43 ± 5.9% of cellulose. Screening of fungal organism for cellulase production was carried out and the potential organism was identified as Rhizopus stolonifer by internal transcribed spacer's (ITS)-5.8S rDNA analysis. A systematic study with response surface methodology (RSM) based on CCRD was used to study the interactions among the variables such as pH (3-7), moisture (40-80%) and progression duration (72-168 h) of the fermentation process to maximize the enzyme production. Under the optimized cultivation condition, R. stolonifer synthesized 22,109 U/gds. Model validations at optimum operating conditions showed excellent agreement between the experimental results and the predicted responses with a confidence level of 95%. Endoglucanase thus produced was utilized for ethanol production by simultaneous saccharification and fermentation and maximum of 65.5 g/L of ethanol was obtained. This fungal cellulase has also reported to be efficient detergent additives and promising for commercial use. The present study demonstrates coffee husk as a significant bioprocess substrate. Statistical optimization with major parameters for cellulase production can be highly applicable for industrial scale. Furthermore, value addition to coffee husk with sustainable waste management leading to environment conservation can be achieved.

Discovery, Synthesis, And Structure-Based Optimization of a Series of N-(tert-Butyl)-2-(N-arylamido)-2-(pyridin-3-yl) Acetamides (ML188) as Potent Noncovalent Small Molecule Inhibitors of the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) 3CL Protease

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jacobs, Jon; Grum-Tokars, Valerie; Zhou, Ya

A high-throughput screen of the NIH molecular libraries sample collection and subsequent optimization of a lead dipeptide-like series of severe acute respiratory syndrome (SARS) main protease (3CLpro) inhibitors led to the identification of probe compound ML188 (16-(R), (R)-N-(4-(tert-butyl)phenyl)-N-(2-(tert-butylamino)-2-oxo-1-(pyridin-3-yl)ethyl)furan-2-carboxamide, Pubchem CID: 46897844). But, unlike the majority of reported coronavirus 3CLpro inhibitors that act via covalent modification of the enzyme, 16-(R) is a noncovalent SARS-CoV 3CLpro inhibitor with moderate MW and good enzyme and antiviral inhibitory activity. A multicomponent Ugi reaction was utilized to rapidly explore structure–activity relationships within S1', S1, and S2enzyme binding pockets. Moreover, the X-ray structure of SARS-CoV 3CLpromore » bound with 16-(R) was instrumental in guiding subsequent rounds of chemistry optimization. 16-(R) provides an excellent starting point for the further design and refinement of 3CLpro inhibitors that act by a noncovalent mechanism of action.« less

40 CFR 421.36 - Pretreatment standards for new sources.

Code of Federal Regulations, 2011 CFR

2011-07-01

... dried Lead .000 .000 Zinc .000 .000 Ammonia (as N) .000 .000 (b) Subpart C—Scrap Screening and Milling... per million pounds) of aluminum scrap screened and milled Lead .000 .000 Zinc .000 .000 Ammonia (as N... .000 Ammonia (as N) .000 .000 (d) Subpart C—Demagging Wet Air Pollution Control. PSNS Pollutant or...

40 CFR 421.36 - Pretreatment standards for new sources.

Code of Federal Regulations, 2014 CFR

2014-07-01

... dried Lead .000 .000 Zinc .000 .000 Ammonia (as N) .000 .000 (b) Subpart C—Scrap Screening and Milling... per million pounds) of aluminum scrap screened and milled Lead .000 .000 Zinc .000 .000 Ammonia (as N... .000 Ammonia (as N) .000 .000 (d) Subpart C—Demagging Wet Air Pollution Control. PSNS Pollutant or...

40 CFR 421.36 - Pretreatment standards for new sources.

Code of Federal Regulations, 2013 CFR

2013-07-01

... dried Lead .000 .000 Zinc .000 .000 Ammonia (as N) .000 .000 (b) Subpart C—Scrap Screening and Milling... per million pounds) of aluminum scrap screened and milled Lead .000 .000 Zinc .000 .000 Ammonia (as N... .000 Ammonia (as N) .000 .000 (d) Subpart C—Demagging Wet Air Pollution Control. PSNS Pollutant or...

40 CFR 421.36 - Pretreatment standards for new sources.

Code of Federal Regulations, 2010 CFR

2010-07-01

... dried Lead .000 .000 Zinc .000 .000 Ammonia (as N) .000 .000 (b) Subpart C—Scrap Screening and Milling... per million pounds) of aluminum scrap screened and milled Lead .000 .000 Zinc .000 .000 Ammonia (as N... .000 Ammonia (as N) .000 .000 (d) Subpart C—Demagging Wet Air Pollution Control. PSNS Pollutant or...

40 CFR 421.36 - Pretreatment standards for new sources.

Code of Federal Regulations, 2012 CFR

2012-07-01

... dried Lead .000 .000 Zinc .000 .000 Ammonia (as N) .000 .000 (b) Subpart C—Scrap Screening and Milling... per million pounds) of aluminum scrap screened and milled Lead .000 .000 Zinc .000 .000 Ammonia (as N... .000 Ammonia (as N) .000 .000 (d) Subpart C—Demagging Wet Air Pollution Control. PSNS Pollutant or...

Putting a New Filter On Cancer Screening.

PubMed

Huff, Charlotte

2016-10-01

Experts are rethinking routine cancer screening. Genetic tests could be the answer. They may add upfront expense, but might eventually lead to savings by winnowing out unnecessary screening. Concern about false positives helps push this movement along.

Neuroblastoma Screening (PDQ®)—Health Professional Version

Cancer.gov

Neuroblastoma screening, according to solid evidence, does not lead to decreased mortality and exposes infants to potential serious harms. Get detailed information about neuroblastoma and the potential benefits and harms of screening in this summary for clinicians.

Colorectal cancer development and advances in screening.

PubMed

Simon, Karen

2016-01-01

Most colon tumors develop via a multistep process involving a series of histological, morphological, and genetic changes that accumulate over time. This has allowed for screening and detection of early-stage precancerous polyps before they become cancerous in individuals at average risk for colorectal cancer (CRC), which may lead to substantial decreases in the incidence of CRC. Despite the known benefits of early screening, CRC remains the second leading cause of cancer-related deaths in the United States. Hence, it is important for health care providers to have an understanding of the risk factors for CRC and various stages of disease development in order to recommend appropriate screening strategies. This article provides an overview of the histological/molecular changes that characterize the development of CRC. It describes the available CRC screening methods and their advantages and limitations and highlights the stages of CRC development in which each screening method is most effective.

Real-time 3-D X-ray and gamma-ray viewer

NASA Technical Reports Server (NTRS)

Yin, L. I. (Inventor)

1983-01-01

A multi-pinhole aperture lead screen forms an equal plurality of invisible mini-images having dissimilar perspectives of an X-ray and gamma-ray emitting object (ABC) onto a near-earth phosphor layer. This layer provides visible light mini-images directly into a visible light image intensifier. A viewing screen having an equal number of dissimilar perspective apertures distributed across its face in a geometric pattern identical to the lead screen, provides a viewer with a real, pseudoscopic image (A'B'C') of the object with full horizontal and vertical parallax. Alternatively, a third screen identical to viewing screen and spaced apart from a second visible light image intensifier, may be positioned between the first image intensifier and the viewing screen, thereby providing the viewer with a virtual, orthoscopic image (A"B"C") of the object (ABC) with full horizontal and vertical parallax.

Colorectal cancer development and advances in screening

PubMed Central

Simon, Karen

2016-01-01

Most colon tumors develop via a multistep process involving a series of histological, morphological, and genetic changes that accumulate over time. This has allowed for screening and detection of early-stage precancerous polyps before they become cancerous in individuals at average risk for colorectal cancer (CRC), which may lead to substantial decreases in the incidence of CRC. Despite the known benefits of early screening, CRC remains the second leading cause of cancer-related deaths in the United States. Hence, it is important for health care providers to have an understanding of the risk factors for CRC and various stages of disease development in order to recommend appropriate screening strategies. This article provides an overview of the histological/molecular changes that characterize the development of CRC. It describes the available CRC screening methods and their advantages and limitations and highlights the stages of CRC development in which each screening method is most effective. PMID:27486317

Screen printing technology applied to silicon solar cell fabrication

NASA Technical Reports Server (NTRS)

Thornhill, J. W.; Sipperly, W. E.

1980-01-01

The process for producing space qualified solar cells in both the conventional and wraparound configuration using screen printing techniques was investigated. Process modifications were chosen that could be easily automated or mechanized. Work was accomplished to optimize the tradeoffs associated with gridline spacing, gridline definition and junction depth. An extensive search for possible front contact metallization was completed. The back surface field structures along with the screen printed back contacts were optimized to produce open circuit voltages of at least an average of 600 millivolts. After all intended modifications on the process sequence were accomplished, the cells were exhaustively tested. Electrical tests at AMO and 28 C were made before and after boiling water immersion, thermal shock, and storage under conditions of high temperature and high humidity.

The application and use of chemical space mapping to interpret crystallization screening results

PubMed Central

Snell, Edward H.; Nagel, Ray M.; Wojtaszcyk, Ann; O’Neill, Hugh; Wolfley, Jennifer L.; Luft, Joseph R.

2008-01-01

Macromolecular crystallization screening is an empirical process. It often begins by setting up experiments with a number of chemically diverse cocktails designed to sample chemical space known to promote crystallization. Where a potential crystal is seen a refined screen is set up, optimizing around that condition. By using an incomplete factorial sampling of chemical space to formulate the cocktails and presenting the results graphically, it is possible to readily identify trends relevant to crystallization, coarsely sample the phase diagram and help guide the optimization process. In this paper, chemical space mapping is applied to both single macromolecules and to a diverse set of macromolecules in order to illustrate how visual information is more readily understood and assimilated than the same information presented textually. PMID:19018100

The application and use of chemical space mapping to interpret crystallization screening results.

PubMed

Snell, Edward H; Nagel, Ray M; Wojtaszcyk, Ann; O'Neill, Hugh; Wolfley, Jennifer L; Luft, Joseph R

2008-12-01

Macromolecular crystallization screening is an empirical process. It often begins by setting up experiments with a number of chemically diverse cocktails designed to sample chemical space known to promote crystallization. Where a potential crystal is seen a refined screen is set up, optimizing around that condition. By using an incomplete factorial sampling of chemical space to formulate the cocktails and presenting the results graphically, it is possible to readily identify trends relevant to crystallization, coarsely sample the phase diagram and help guide the optimization process. In this paper, chemical space mapping is applied to both single macromolecules and to a diverse set of macromolecules in order to illustrate how visual information is more readily understood and assimilated than the same information presented textually.

Optimizing Bone Health in Duchenne Muscular Dystrophy.

PubMed

Buckner, Jason L; Bowden, Sasigarn A; Mahan, John D

2015-01-01

Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder characterized by progressive muscle weakness, with eventual loss of ambulation and premature death. The approved therapy with corticosteroids improves muscle strength, prolongs ambulation, and maintains pulmonary function. However, the osteoporotic impact of chronic corticosteroid use further impairs the underlying reduced bone mass seen in DMD, leading to increased fragility fractures of long bones and vertebrae. These serious sequelae adversely affect quality of life and can impact survival. The current clinical issues relating to bone health and bone health screening methods in DMD are presented in this review. Diagnostic studies, including biochemical markers of bone turnover and bone mineral density by dual energy X-ray absorptiometry (DXA), as well as spinal imaging using densitometric lateral spinal imaging, and treatment to optimize bone health in patients with DMD are discussed. Treatment with bisphosphonates offers a method to increase bone mass in these children; oral and intravenous bisphosphonates have been used successfully although treatment is typically reserved for children with fractures and/or bone pain with low bone mass by DXA.

Breast ultrasound image segmentation: an optimization approach based on super-pixels and high-level descriptors

NASA Astrophysics Data System (ADS)

Massich, Joan; Lemaître, Guillaume; Martí, Joan; Mériaudeau, Fabrice

2015-04-01

Breast cancer is the second most common cancer and the leading cause of cancer death among women. Medical imaging has become an indispensable tool for its diagnosis and follow up. During the last decade, the medical community has promoted to incorporate Ultra-Sound (US) screening as part of the standard routine. The main reason for using US imaging is its capability to differentiate benign from malignant masses, when compared to other imaging techniques. The increasing usage of US imaging encourages the development of Computer Aided Diagnosis (CAD) systems applied to Breast Ultra-Sound (BUS) images. However accurate delineations of the lesions and structures of the breast are essential for CAD systems in order to extract information needed to perform diagnosis. This article proposes a highly modular and flexible framework for segmenting lesions and tissues present in BUS images. The proposal takes advantage of optimization strategies using super-pixels and high-level descriptors, which are analogous to the visual cues used by radiologists. Qualitative and quantitative results are provided stating a performance within the range of the state-of-the-art.

Automation in biological crystallization.

PubMed

Stewart, Patrick Shaw; Mueller-Dieckmann, Jochen

2014-06-01

Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given.

Automation in biological crystallization

PubMed Central

Shaw Stewart, Patrick; Mueller-Dieckmann, Jochen

2014-01-01

Crystallization remains the bottleneck in the crystallographic process leading from a gene to a three-dimensional model of the encoded protein or RNA. Automation of the individual steps of a crystallization experiment, from the preparation of crystallization cocktails for initial or optimization screens to the imaging of the experiments, has been the response to address this issue. Today, large high-throughput crystallization facilities, many of them open to the general user community, are capable of setting up thousands of crystallization trials per day. It is thus possible to test multiple constructs of each target for their ability to form crystals on a production-line basis. This has improved success rates and made crystallization much more convenient. High-throughput crystallization, however, cannot relieve users of the task of producing samples of high quality. Moreover, the time gained from eliminating manual preparations must now be invested in the careful evaluation of the increased number of experiments. The latter requires a sophisticated data and laboratory information-management system. A review of the current state of automation at the individual steps of crystallization with specific attention to the automation of optimization is given. PMID:24915074

Discovery and Optimization of Benzotriazine Di-N-Oxides Targeting Replicating and Non-replicating Mycobacterium tuberculosis

PubMed Central

Chopra, Sidharth; Koolpe, Gary A.; Tambo-ong, Arlyn A.; Matsuyama, Karen N.; Ryan, Kenneth J.; Tran, Tran B.; Doppalapudi, Rupa S.; Riccio, Edward S.; Iyer, Lalitha V.; Green, Carol E.; Wan, Baojie; Franzblau, Scott G.; Madrid, Peter B.

2012-01-01

Compounds bactericidal against both replicating and non-replicating Mtb may shorten the length of TB treatment regimens by eliminating infections more rapidly. Screening of a panel of antimicrobial and anticancer drug classes that are bioreduced into cytotoxic species revealed that 1,2,4-benzotriazine di-N-oxides (BTOs) are potently bactericidal against replicating and non-replicating Mtb. Medicinal chemistry optimization, guided by semi-empirical molecular orbital calculations, identified a new lead compound (20q) from this series with an MIC of 0.31 μg/mL against H37Rv and a cytotoxicity (CC50) against Vero cells of 25 μg/mL. 20q also had equivalent potency against a panel of single-drug resistant strains of Mtb and remarkably selective activity for Mtb over a panel of other pathogenic bacterial strains. 20q was also negative in a L5178Y MOLY assay, indicating low potential for genetic toxicity. These data along with measurements of the physiochemical properties and pharmacokinetic profile demonstrate that BTOs have the potential to be developed into a new class of antitubercular drugs. PMID:22691154

Discovery of 4-aryl-N-arylcarbonyl-2-aminothiazoles as Hec1/Nek2 inhibitors. Part I: optimization of in vitro potencies and pharmacokinetic properties.

PubMed

Lee, Ying-Shuan E; Chuang, Shih-Hsien; Huang, Lynn Y L; Lai, Chun-Liang; Lin, Yu-Hsiang; Yang, Ju-Ying; Liu, Chia-Wei; Yang, Sheng-chuan; Lin, Her-Sheng; Chang, Chia-chi; Lai, Jun-Yu; Jian, Pei-Shiou; Lam, King; Chang, Jia-Ming; Lau, Johnson Y N; Huang, Jiann-Jyh

2014-05-22

A series of 4-aryl-N-arylcarbonyl-2-aminothiazoles of scaffold 4 was designed and synthesized as Hec1/Nek2 inhibitors. Structural optimization of 4 led to compound 32 bearing C-4' 4-methoxyphenoxy and 4-(o-fluoropyridyl)carbonyl groups that showed low nanomolar in vitro antiproliferative activity (IC50: 16.3-42.7 nM), high intravenous AUC (64.9 μM·h, 2.0 mg/kg) in SD rats, and significant in vivo antitumor activity (T/C = 32%, 20 mg/kg, IV) in mice bearing human MDA-MB-231 xenografts. Cell responses resulting from Hec1/Nek2 inhibition were observed in cells treated with 32, including a reduced level of Hec1 coimmunoprecipitated with Nek2, degradation of Nek2, mitotic abnormalities, and apoptosis. Compound 32 showed selectivity toward cancer cells over normal phenotype cells and was inactive in a [(3)H]astemizole competitive binding assay for hERG liability screening. Therefore, 32 is as a good lead toward the discovery of a preclinical candidate targeting Hec1/Nek2 interaction.

Discovery and Synthesis of a Phosphoramidate Prodrug of a Pyrrolo[2,1-f][triazin-4-amino] Adenine C-Nucleoside (GS-5734) for the Treatment of Ebola and Emerging Viruses.

PubMed

Siegel, Dustin; Hui, Hon C; Doerffler, Edward; Clarke, Michael O; Chun, Kwon; Zhang, Lijun; Neville, Sean; Carra, Ernest; Lew, Willard; Ross, Bruce; Wang, Queenie; Wolfe, Lydia; Jordan, Robert; Soloveva, Veronica; Knox, John; Perry, Jason; Perron, Michel; Stray, Kirsten M; Barauskas, Ona; Feng, Joy Y; Xu, Yili; Lee, Gary; Rheingold, Arnold L; Ray, Adrian S; Bannister, Roy; Strickley, Robert; Swaminathan, Swami; Lee, William A; Bavari, Sina; Cihlar, Tomas; Lo, Michael K; Warren, Travis K; Mackman, Richard L

2017-03-09

The recent Ebola virus (EBOV) outbreak in West Africa was the largest recorded in history with over 28,000 cases, resulting in >11,000 deaths including >500 healthcare workers. A focused screening and lead optimization effort identified 4b (GS-5734) with anti-EBOV EC 50 = 86 nM in macrophages as the clinical candidate. Structure activity relationships established that the 1'-CN group and C-linked nucleobase were critical for optimal anti-EBOV potency and selectivity against host polymerases. A robust diastereoselective synthesis provided sufficient quantities of 4b to enable preclinical efficacy in a non-human-primate EBOV challenge model. Once-daily 10 mg/kg iv treatment on days 3-14 postinfection had a significant effect on viremia and mortality, resulting in 100% survival of infected treated animals [ Nature 2016 , 531 , 381 - 385 ]. A phase 2 study (PREVAIL IV) is currently enrolling and will evaluate the effect of 4b on viral shedding from sanctuary sites in EBOV survivors.

Barriers to optimal diabetes care in Trinidad and Tobago: a health care Professionals' perspective.

PubMed

Roopnarinesingh, Nira; Brennan, Nancyellen; Khan, Claude; Ladenson, Paul W; Hill-Briggs, Felicia; Kalyani, Rita Rastogi

2015-09-19

The republic of Trinidad and Tobago (T&T) is a middle income country with a comparatively high prevalence of diabetes mellitus (DM) compared to others in the Caribbean. To date, there have been no studies on health care professionals' (HCP) perspectives regarding the barriers to achieving optimal care of patients with DM in this country and few previous studies in the Caribbean, yet such perspectives are imperative to develop strategies that reduce the global burden of this disease. An electronic invitation was sent to prospective HCP in T&T inviting them to attend a symposium on DM and cardiovascular disease. A total of 198 HCP participants attended of whom approximately 100 participants completed an Audience Response Survey at the completion of the conference. The Audience Response Survey included questions regarding access to resources, need for prevention and education, and coordination of care for to diabetes care in T&T. Responses were analyzed in aggregate. The 198 HCP participants attending the symposium included mostly nurses (40 %) and physicians (43 %). The most common specialty indicated by the 198 HCP participants was Internal and Family Medicine (28 %), followed by Anesthesiology (7 %), Emergency Medicine (6 %), Endocrinology and Diabetes (5 %) and Cardiology (3 %). Among the ~100 HCP who completed the Audience Response Survey, multiple barriers to achieving optimal care of patients with diabetes were reported such as: limited access to blood testing (75 %), ophthalmological evaluations (96 %), ECGs (69 %), and cardiac stress tests (92 %); inadequate time to screen and evaluate DM complications (95 %); poor access to consultants for referral of difficult cases (77 %); and lack of provider education regarding cardiovascular complications of DM (57 %). HCP agreed that nurses could potentially be considered to have a more active role in the care and prevention of cardiovascular disease and diabetes through leading patient education efforts (98 %), screening patients for complications (91 %), coordinating care efforts (99 %) and educating family members (98 %). The HCP in our study reported significant barriers to achieving optimal diabetes care in T&T. In the future, such barriers to care will need to be addressed in order to respond to the projected growth of diabetes in developing countries both within the Caribbean and globally.

Application of QSAR and shape pharmacophore modeling approaches for targeted chemical library design.

PubMed

Ebalunode, Jerry O; Zheng, Weifan; Tropsha, Alexander

2011-01-01

Optimization of chemical library composition affords more efficient identification of hits from biological screening experiments. The optimization could be achieved through rational selection of reagents used in combinatorial library synthesis. However, with a rapid advent of parallel synthesis methods and availability of millions of compounds synthesized by many vendors, it may be more efficient to design targeted libraries by means of virtual screening of commercial compound collections. This chapter reviews the application of advanced cheminformatics approaches such as quantitative structure-activity relationships (QSAR) and pharmacophore modeling (both ligand and structure based) for virtual screening. Both approaches rely on empirical SAR data to build models; thus, the emphasis is placed on achieving models of the highest rigor and external predictive power. We present several examples of successful applications of both approaches for virtual screening to illustrate their utility. We suggest that the expert use of both QSAR and pharmacophore models, either independently or in combination, enables users to achieve targeted libraries enriched with experimentally confirmed hit compounds.

Validity of the AUDIT-C screen for at-risk drinking among students utilizing university primary care.

PubMed

Campbell, Clare E; Maisto, Stephen A

2018-03-22

Research is needed to establish the psychometric properties of brief screens in university primary care settings. This study aimed to assess the construct validity of one such screen, the Alcohol Use Disorders Identification Test-Consumption (AUDIT-C), for detecting at-risk drinking among students who have utilized on-campus primary care. 389 students recently seen in university primary care completed a confidential online survey in December 2014. Bivariate correlations between the AUDIT-C and measures of alcohol consumption and negative drinking consequences provided concurrent evidence for construct validity. Receiver Operating Characteristic curve analyses determined optimal cut-off scores for at-risk drinking. The AUDIT-C significantly correlated with measures of alcohol consumption and negative drinking consequences (p < .001). Analyses support optimal AUDIT-C cut-off scores of 5 for females and 7 for males. The AUDIT-C is a valid screen for at-risk drinking among students who utilize university primary care.

The plug-based nanovolume Microcapillary Protein Crystallization System (MPCS)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gerdts, Cory J.; Elliott, Mark; Lovell, Scott

2012-02-08

The Microcapillary Protein Crystallization System (MPCS) embodies a new semi-automated plug-based crystallization technology which enables nanolitre-volume screening of crystallization conditions in a plasticware format that allows crystals to be easily removed for traditional cryoprotection and X-ray diffraction data collection. Protein crystals grown in these plastic devices can be directly subjected to in situ X-ray diffraction studies. The MPCS integrates the formulation of crystallization cocktails with the preparation of the crystallization experiments. Within microfluidic Teflon tubing or the microfluidic circuitry of a plastic CrystalCard, {approx}10-20 nl volume droplets are generated, each representing a microbatch-style crystallization experiment with a different chemical composition.more » The entire protein sample is utilized in crystallization experiments. Sparse-matrix screening and chemical gradient screening can be combined in one comprehensive 'hybrid' crystallization trial. The technology lends itself well to optimization by high-granularity gradient screening using optimization reagents such as precipitation agents, ligands or cryoprotectants.« less

High throughput ADME screening: practical considerations, impact on the portfolio and enabler of in silico ADME models.

PubMed

Hop, Cornelis E C A; Cole, Mark J; Davidson, Ralph E; Duignan, David B; Federico, James; Janiszewski, John S; Jenkins, Kelly; Krueger, Suzanne; Lebowitz, Rebecca; Liston, Theodore E; Mitchell, Walter; Snyder, Mark; Steyn, Stefan J; Soglia, John R; Taylor, Christine; Troutman, Matt D; Umland, John; West, Michael; Whalen, Kevin M; Zelesky, Veronica; Zhao, Sabrina X

2008-11-01

Evaluation and optimization of drug metabolism and pharmacokinetic data plays an important role in drug discovery and development and several reliable in vitro ADME models are available. Recently higher throughput in vitro ADME screening facilities have been established in order to be able to evaluate an appreciable fraction of synthesized compounds. The ADME screening process can be dissected in five distinct steps: (1) plate management of compounds in need of in vitro ADME data, (2) optimization of the MS/MS method for the compounds, (3) in vitro ADME experiments and sample clean up, (4) collection and reduction of the raw LC-MS/MS data and (5) archival of the processed ADME data. All steps will be described in detail and the value of the data on drug discovery projects will be discussed as well. Finally, in vitro ADME screening can generate large quantities of data obtained under identical conditions to allow building of reliable in silico models.

Siemens Immulite Aspergillus-specific IgG assay for chronic pulmonary aspergillosis diagnosis.

PubMed

Page, Iain D; Richardson, Malcolm D; Denning, David W

2018-05-14

Chronic pulmonary aspergillosis (CPA) complicates underlying lung disease, including treated tuberculosis. Measurement of Aspergillus-specific immunoglobulin G (IgG) is a key diagnostic step. Cutoffs have been proposed based on receiver operating characteristic (ROC) curve analyses comparing CPA cases to healthy controls, but performance in at-risk populations with underlying lung disease is unclear. We evaluated optimal cutoffs for the Siemens Immulite Aspergillus-specific IgG assay for CPA diagnosis in relation to large groups of healthy and diseased controls with treated pulmonary tuberculosis. Sera from 241 patients with CPA attending the UK National Aspergillosis Centre, 299 Ugandan blood donors (healthy controls), and 398 Ugandans with treated pulmonary tuberculosis (diseased controls) were tested. Radiological screening removed potential CPA cases from diseased controls (234 screened diseased controls). ROC curve analyses were performed and optimal cutoffs identified by Youden J statistic. CPA versus control ROC area under curve (AUC) results were: healthy controls 0.984 (95% confidence interval 0.972-0.997), diseased controls 0.972 (0.959-0.985), screened diseased controls 0.979 (0.967-0.992). Optimal cutoffs were: healthy controls 15 mg/l (94.6% sensitivity, 98% specificity), unscreened diseased controls 15 mg/l (94.6% sensitivity, 94.5% specificity), screened diseased controls 25 mg/l (92.9% sensitivity, 98.7% specificity). Results were similar in healthy and diseased controls. We advocate a cutoff of 20 mg/l as this is the midpoint of the range of optimal cutoffs. Cutoffs calculated in relation to healthy controls for other assays are likely to remain valid for use in a treated tuberculosis population.

Minimal invasive epicardial lead implantation: optimizing cardiac resynchronization with a new mapping device for epicardial lead placement.

PubMed

Maessen, J G; Phelps, B; Dekker, A L A J; Dijkman, B

2004-05-01

To optimize resynchronization in biventricular pacing with epicardial leads, mapping to determine the best pacing site, is a prerequisite. A port access surgical mapping technique was developed that allowed multiple pace site selection and reproducible lead evaluation and implantation. Pressure-volume loops analysis was used for real time guidance in targeting epicardial lead placement. Even the smallest changes in lead position revealed significantly different functional results. Optimizing the pacing site with this technique allowed functional improvement up to 40% versus random pace site selection.

Hydraulische Optimierung des Reaktionsraumes um einen Infiltrationsbrunnen zur unterirdischen Enteisenung. Feldversuche und numerische Simulation zur Planung der optimalen Verfahrensergiebigkeit (Teil 1/2) Hydraulic optimization of the reaction zone around an injection well during subsurface iron removal

NASA Astrophysics Data System (ADS)

Ahrns, Johannes; Bartak, Rico; Grischek, Thomas; Pörschke, Richard

2017-11-01

In subsurface iron removal (SIR), oxygen-enriched water is injected into an aquifer to create a reaction zone. Aside from the hydraulic properties of the aquifer, groundwater quality often varies with depth so that in vertical wells the dissolved oxygen distribution (reaction zone) may not correspond to the dissolved iron concentration which may result in a lower efficiency coefficient. Therefore, measures to hydraulically optimize the formation of the reaction zone through a non-conventional injection were investigated. A high-resolution groundwater flow model was calibrated based on tracer and pump tests and used to plan the optimized injection for a SIR-pilot well with two screen segments. An optimized injection appears to be possible through the inactivation of well screen sections using packers. A doubling of the efficiency coefficient in comparison to a conventional injection was predicted when a packer, which remains evacuated inside the well while pumping, was used to seal 4/5 of the upper well screen length during injection. This scenario was used to plan the operating regime for a SIR field test, which is presented in Part 2.

Factors Accounting for a Missed Diagnosis of Cystic Fibrosis After Newborn Screening

PubMed Central

Rock, Michael J.; Levy, Hara; Zaleski, Christina; Farrell, Philip M.

2015-01-01

Summary Newborn screening is a public health policy program involving the centralized testing laboratory, infant and their family, primary care provider, and subspecialist for confirmatory testing and follow-up of abnormal results. Cystic fibrosis (CF) newborn screening has now been enacted in all 50 states and the District of Columbia and throughout many countries in the world. Although CF neonatal screening will identify the vast majority of infants with CF, there are many factors in the newborn screening system that can lead to a missed diagnosis of CF. To inform clinicians, this article summarizes the CF newborn screening system and highlights 14 factors that can account for a missed diagnosis of CF. Care providers should maintain a high suspicion for CF if there are compatible symptoms, regardless of the results of the newborn screening test. These factors in newborn screening programs leading to a missed diagnosis of CF present opportunities for quality improvement in specimen collection, laboratory analysis of immunoreactive tryspinogen (IRT) and CF mutation testing, communication, and sweat testing. PMID:22081556

Mesoionic Pyrido[1,2-a]pyrimidinone Insecticides: From Discovery to Triflumezopyrim and Dicloromezotiaz.

PubMed

Zhang, Wenming

2017-09-19

One of the greatest global challenges is to feed the ever-increasing world population. The agrochemical tools growers currently utilize are also under continuous pressure, due to a number of factors that contribute to the loss of existing products. Mesoionic pyrido[1,2-a]pyrimidinones are an unusual yet very intriguing class of compounds. Known for several decades, this class of compounds had not been systemically studied until we started our insecticide discovery program. This Account provides an overview of the efforts on mesoionic pyrido[1,2-a]pyridinone insecticide discovery, beginning from the initial high throughput screen (HTS) discovery to ultimate identification of triflumezopyrim (4, DuPont Pyraxalt) and dicloromezotiaz (5) for commercialization as novel insecticides. Mesoionic pyrido[1,2-a]pyrimidinones with a n-propyl group at the 1-position, such as compound 1, were initially isolated as undesired byproducts from reactions for a fungicide discovery program at DuPont Crop Protection. Such compounds showed interesting insecticidal activity in a follow-up screen and against an expanded insect species list. The area became an insecticide hit for exploration and then a lead area for optimization. At the lead optimization stage, variations at three regions of compound 1, i.e., side-chain (n-propyl group), substituents on the 3-phenyl group, and substitutions on the pyrido- moiety, were explored with many analogues prepared and evaluated. Breakthrough discoveries included replacing the n-propyl group with a 2,2,2-trifluoroethyl group to generate compound 2, and then with a 2-chlorothiazol-5-ylmethyl group to form compound 3. 3 possesses potent insecticidal activity not only against a group of hopper species, including corn planthopper (Peregrinus maidis (Ashmead), CPH) and potato leafhopper (Empoasca fabae (Harris), PLH), as well as two key rice hopper species, namely, brown planthopper (Nilaparvata lugens (Stål), BPH) and rice green leafhopper (Nephotettix virescens (Distant), GLH), but also against representative lepidoptera species Diamondback moth (Plutella xylostella (Linnaeus), DBM) and fall armyworm (Spodoptera frugiperda (J.E. Smith), FAW). Further optimization based on 3 led to discovery of triflumezopyrim (4), with a 5-pyrimidinylmethyl group, as a potent hopper insecticide for rice usage. Optimization of the substituents on the pyrido- moiety of 3 resulted in discovery of dicloromezotiaz (5) as a lepidoptera insecticide. In this Account, we present the discovery and optimization of mesoionic pyrido[1,2-a]pyrimidinone insecticides toward the identification of triflumezopyrim (4) and dicloromezotiaz (5). We hope that knowledge and lessons derived from this discovery program will provide valuable information for future agrochemical and drug discovery. Our successful discovery and commercialization development of two novel insecticides based on meosoionic pyrido[1,2-a]pyridiminones may also stimulate interests of scientists from other disciplines to adopt this uncommon yet intriguing heterocycle ring system in pharmaceutical and other material science discovery research.