Archive for the ‘HT Screening’ Category
Nigeria: FG and Cost of Cancer Screening
Last Updated on Monday, 28 November 2011 02:03 Written by admin Monday, 28 November 2011 02:03
THE Federal Government’s recent directive to its hospitals to reduce the cost of cancer screening, though very commendable, is long overdue, considering that late diagnosis of the disease has resulted in the high rate of cancer related deaths in the country.
Cancer is one of the leading causes of deaths in the world, especially in developing countries, which carry about 80 per cent of the burden, globally. Unfortunately, in Nigeria with over 160 million people, going by the latest global report on population, detection of the killer non-communicable disease (NCD) is usually late.
Minister of Health, Prof. Onyebuchi Chukwu, who announced the reduction in the cost of screening for breast, cervical, prostate and colon cancers during the recent 17th Annual Conference of the Nigerian Association of Urological Surgeons (NAUS) in Abuja, said the directive to provide screening services at affordable prices is to ensure that the disease is detected early.
Other measures being taken by government to tackle the cancer scourge, he said, include equipping fully the University of Port Harcourt Teaching Hospital, the Federal Medical Centre, Gusau, Zamfara State and the Vesico Virginal Fistula (VVF) Centre, Abakaliki, Ebonyi State with mammography machines, cryoprobes, video culposcopes, ultrasound, loop electrosurgical excision procedure and enzyme-linked immunosorbent assay machines, so that these institutions can serve as referral centres for those who screen positive for pre-malignant lesions.
With the World Health Organisation (WHO) projecting that about 84 million people may die of cancer by 2015 if urgent steps are not taken to arrest the scourge, there is, indeed, need to facilitate a national policy on cancer management, starting with free or significantly reduced cost of cancer screening.
These moves by the Federal Government are steps in the right direction, considering that cancer is one disease that is no respecter of social status and one that has continued to deal devastating blows on the productive segments of the nation’s economy.
Among notable Nigerians whose lives were cut short by cancer are human rights activist and lawyer, Chief Gani Fawehinmi, who died in 2009 after a prolonged battle with lung cancer, Dr. Bekolari Ransome-Kuti, a medical doctor and human rights activist and Yemi Tella, coach of the Nigerian 2007 FIFA U-17 World Cup winning team.
Maryam, wife of former military president, Gen. Ibrahim Babangida, died of ovarian cancer on December 27, 2009 at California’s City Hope Hospital in the United States, aged 61, while the wife of Edo State Governor, Adams Oshiomhole, was swept away by cancer of the breast.
Presently, about two million cancer cases are said to be recorded in Nigeria with an estimated 350,000 new cases being diagnosed annually. Of the two million, only 10 per cent or about 200,000, have access to hospitals with radiotherapy facilities, while out of the number, only five per cent, about 10,000, have the resources to go abroad where they pay between $10,000 and $15,000 per patient for a three to five-weeks course of radiotherapy.
While about 27 per cent of the two million cases are suffering from breast cancer, about 25 per cent are cancer of the cervix cases. And of these two cancers that are devastating women in Nigeria, one has good prognosis, if detected early, while the other can be prevented. Yet they continue to cause untold hardships and deaths simply because of the dearth, and high cost, of facilities, especially for early detection, among other constraints.
Nigeria’s mortality and morbidity statistics for cancer are said to be high due to the late presentation syndrome involving 83-87 per cent of cancer patients, simply because the awareness level of Nigerians, especially women, is very low, even as this is dogged by superstition and cultural restraints.
As a matter of fact, some medical experts have argued that even the estimated 350,000 new cases of cancer diagnosed annually in Nigeria is far from the true figure of the cancer crisis in the country, insisting that a large number of cancers are not detected as majority of Nigerians are poor and live in rural areas, far removed from health facilities.
Lack of, or inadequate, research into this debilitating disease is also a major challenge. Nigeria, for instance, is said to contribute little or nothing to the global body of literature on cancers and most of these contributions are hospital based, perhaps representing the tip of the iceberg as majority of Nigerians live in rural areas, unable to access any health facilities.
As such, the cancer awareness efforts and screening methods to enhance early detection do not seem to have had much impact on the nation.
No doubt, the problems of lack of access to quality health care, ignorance, poverty and poor co-ordination of issues of health education complicate issues. For instance, facilities such as computerised tomography (CT) and Magnetic Resonance Imaging (MRI) are difficult to come by, and when available, the cost of accessing such facilities put them out of reach of the average citizen.
Of more concern is the fact that clinical services for cancer are grossly inadequate and poorly distributed. Only a few centers have functioning radiotherapy equipment, and though radiologic services are said to be generally available, access is seriously limited by high cost.
So, while the Federal Government’s move to reduce the cost of cancer screening in federal hospitals is commended, we call on the authorities to ensure that the screening equipment are available and more easily accessible, especially in the rural areas, while a more vigorous and better co-ordinated effort into cancer research must be encouraged in institutions across the country.
Source: http://allafrica.com/stories/201111241060.html
Posted under Africa, Cancer Research, Compound Screening, Genetics & Pharmacogenetics, HT Screening, Medicinal Chemistry, Oncology Research, Press Releases, R & D, Reports | Comments Off
NMR Fine-Tuned for High-Content Metabolomics Screening
Last Updated on Monday, 28 November 2011 01:48 Written by admin Monday, 28 November 2011 01:48
Scientists report on the development of a nuclear magnetic resonance (NMR)-based method forscreening the metabolomic response of drug-treated mammalian cells to drug therapy. TheSanford-Burnham Medical Research Institute, and Rady Children’s Hospital investigators, say the highly sensitive, fast, and simple method is carried out in 96-well format, and could have particular utility as a method for high-throughput primary screens. The preparation technique takes just five minutes to metabolically inactivate and lyse hundreds of drug-treated samples, and a metabolomic screening of around 100 samples can be carried out in 24 hours.
Giovanni Paternostro, M.D., and colleagues describe their approach, analyze the results of validation studies on drug-treated cancer cell lines, and evaluate the technique for screening a kinase inhibitor library. Their work is described in Nature Communications in a paper titled “Metabolomic high-content nuclear magnetic resonance-based drug screening of a kinase inhibitor library.”
High-throughput screening (HTS) is widely used as a tool in drug discovery, but most screens monitor a single variable, which is often related to activity on a single target, the researchers explain. Although high-content screening (HCS) approaches that provide multivariate readouts are gaining ground, these techniques generally rely on automated digital microscopy.
The technique developed by the Sanford-Burnham researchers involves seeding cells into a 96-well plate and treating them with several drugs. The cells’ metabolism is then quenched using sodium dodecyl sulphate (SDS), and the cells lysed using ultrasonication, in an overall process that takes just five minutes. The entire content of the well, including endo- and exo-metabolome, is then transferred into an NMR tube for analysis.
The team needed to address the relative contribution of the intracellular metabolome to the NMR spectrum acquired on the well content, including both medium and the lysed cell metabolomes. To answer this they generated NMR spectra on the entire content of the well (i.e., both endo- and exo-metabolomes), and also on the exometabolome, the endometabolome, and the medium. They found that major NMR signals arose from the extracellular metabolites, but several signals arising from the intracellular metabolites were also detected, for example glutamate, choline, and phosphocholine. Importantly, they found that spectra acquired on samples containing both endo- and extracellular metabolomes included signals resulting exclusively from the endometabolome—such as phosphocholine and glycerophosphocholine—which didn’t overlap with other extracellular resonances.
The researchers evaluated the sensitivity of the approach for monitoring metabolic changes induced by 24 hours of drug treatment, on both suspension (CCRF-CEM human leukemia cells) and adherent mammalian carcinoma cell lines (human SKOV-3 ovarian cancer cells). The cell lines were treated using either dexamethasone (Dex), rapamycin (Rap) dichloroacetate (DCA), vincristine (Vin), and different doses of L-asparaginase. The resulting spectra, generated using three different 1H NMR pulse sequences, showed that, as expected, the response to drug treatment by the more resistant SKOV-3 cells was far less pronounced compared with the CCRF-CEM cells. Encouragingly, the NMR screening approach could also be applied to detecting metabolic changes in response to forms of intervention, such as the transfection of HeLa cells the microRNAs mir-121 and mir-16. These results indicated that mir-16 induced a greater degree of metabolomic change than mir-121.
Because the developed technique requires just a small amount of cells, the investigators suggest in might have utility in studying drug response directly in primary cells, and so avoid phenotypic changes that can be induced by growth in culture. They evaluated metabolomic changes in cells isolated from bone marrow specimens of an untreated AML patient, in response to treatment with Rap and L-asparaginase, at different doses. In order to specifically highlight metabolic changes in the cells themselves, the NRM spectra acquired on unconditioned medium were compared to those acquired on AML primary cells with and without drug administraton. The resulting spectra clearly showed distinct changes in the metabolome of the primary cells as a result of drug treatment. Further analyses indicated these changes were more pronounced in response to L-asparaginase than for Rap therapy.
The team then moved on to use the approach for carrying out screening of metabolomic response to a kinase inhibitor (KI) library. Multiple rounds of screening on KIs with well-characterized and less well-characterized effects on the metabolome confirmed the utility of the technique for identifying metabolic alterations resulting from inhibitor treatment. More specifically, four hits were validated from their action on the well-characterized lactate to pyruvate ratio parameter.
“We believe that this NMR-based assay might find an immediate relevant application for screening a large number of individual or combinatorial drug interventions, reducing the number of possible drugs to be studied in more detail,” the authors state. “In addition, it might find an immediate relevant application into clinical studies.”
They admit that the main drawback of NMR is the relatively limited number of compounds that can be detected. However, they stress, “although not comprehensive of all metabolites, the wealth of information obtained from the multivariate metabolic readout is of great advantage for drug screening purposes.” The method could therefore represent a valuable high-throughput primary screen, which could then be followed by secondary assays to analyze the exo- and endo-metabolomes of selected hits using combinations of different anaytical platforms.
“There are many other possible applications of this method, for example lactate production and substrate utilization in cancer versus noncancer cells, or gluconeogenesis from different substrates in hepatocytes, relevant to diabetes. Importantly, because the measurements are performed within a global metabolic profile, they can also provide a series of compounds with partially different mechanisms of actions, which can be explored for potential synergies.”
Source: http://www.genengnews.com/gen-news-highlights/nmr-fine-tuned-for-high-content-metabolomics-screening/81245988/
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University at Buffalo symposium on in silico methods, high throughput screening
Last Updated on Monday, 11 October 2010 09:55 Written by Editor Monday, 11 October 2010 09:55
BUFFALO, N.Y. — Twenty-first-century pharmaceutical breakthroughs require 21st-century drug discovery tools, such as computational or in silico molecular design and high-throughput screening of effective, new compounds. That’s the theme of a University at Buffalo symposium to be held Sept. 11 on “Twenty-first Century Bioscience: In Silico Methods and High-Throughput Screening,” which will feature a variety of cutting-edge advances in the field developed by researchers in Western New York and throughout the US.
The symposium will be held at the Hauptman-Woodward Medical Research Institute, 700 Ellicott St., Buffalo from 8:30 a.m. to 5 p.m.
Speakers will discuss techniques they are developing to treat cancer and other disorders, including such hereditary eye diseases as retinitis pigmentosa.
Symposium topics will range from using flow cytometry and combinatorial chemistry to screen new compounds, to overcoming the hurdles in RNA drug discovery and developing molecular regulators of gene expression.
Research into computational or in silico methods of designing potential new drug compounds and high throughput screening of them is especially strong in Western New York, according to Steven J. Fliesler, PhD (pronounced Fleece-ler), the Meyer H. Riwchun Endowed Chair Professor of Ophthalmology, and vice chair and director of research in the Department of Ophthalmology, Ross Eye Institute, in the UB School of Medicine and Biomedical Sciences. Fliesler is a health systems specialist at the Veterans Affairs Western New York Healthcare System; he organized the symposium and is one of the moderators.
“Western New York is fortunate to have a diversity of scientists working in these areas on specific applications to human disease,” Fliesler says. “So whether it’s in cancer, ophthalmology, cardiovascular disease or diabetes, these genetic approaches are going on in parallel, utilizing some of the same approaches but with diverse applications. The goal of this combination of methods is to give investigators more powerful tools with which to alter how the genome is expressed in cells and silence disease-causing genes.”
For example, Fliesler and his UB colleagues are conducting research on novel gene therapy applications to treat retinitis pigmentosa, a group of genetic eye conditions that can lead to incurable blindness and which Fliesler says underscores the importance of genomic research.
In retinitis pigmentosa, he says, there are well over a hundred known mutations in the gene that codes for the visual pigment rhodopsin alone, and there are dominant and recessive forms of the disease.
“If it was possible to just disable the disease-causing allele (one member of a pair of genes) early in development, then you’d get a normal individual,” Fliesler says.
Plenary lectures will be given by Larry A. Sklar, PhD, of the University of New Mexico, John S. Lazo, PhD, of the University of Pittsburgh, Bryan Roth, MD, PhD, of the University of North Carolina at Chapel Hill and Menghang Xia, PhD, of the National Institutes of Health.
Topics of other talks will include:
* Advances in genomic techniques that have allowed scientists to dissect how the cell responds to changes in the environment by modulating access to information encoded in the genome. The talk, by Michael J. Buck, PhD, UB assistant professor of biochemistry, will focus on a master regulator essential for cellular stress response and how it controls access to the genomic information.
* challenges in developing RNA drugs and ways that UB scientists and others are working to overcome them. Development of RNA drugs as novel gene-based therapies for retinitis pigmentosa and other retinal degenerations is a primary focus of the research program of Jack M. Sullivan, MD, PhD, UB associate professor of ophthalmology, who will discuss an experimental platform his group has developed to rapidly screen large sets of candidate RNA drugs to identify the most powerful treatments for retinitis pigmentosa and common age-related macular degeneration.
* A high-throughput functional genetic approach to anti-cancer drug targets developed by Andrei V. Gudkov, PhD, chair, Department of Cell Stress Biology at Roswell Park Cancer Institute.
* Computational methods developed by Rajendram V. Rajnarayanan, PhD, UB assistant professor of pharmacology and toxicology, who is using them to design small molecules that can alter RNA expression.
In addition to Fliesler, other moderators and speakers include Alexander N. Cartwright, PhD, interim vice president for research at UB, Norma J. Nowak, PhD, director of scientific planning at UB’s New York State Center of Excellence in Bioinformatics and Life Sciences, Eaton E. Lattman, PhD, chief executive officer of HWI and research professor in the UB Department of Structural Biology, and Jennifer A. Surtees, PhD, assistant professor of biochemistry at UB.
The symposium is sponsored by the UB 2020 Strategic Strength in Molecular Recognition in Biological Systems and Bioinformatics, a cross-disciplinary effort to foster new scientific ideas throughout different departments and schools at UB and its partner institutions. Co-sponsors are HWI, the UB departments of biochemistry and chemistry and the Ira G. Ross Eye Institute.
For more information and to register, contact Jennifer Hunt at jluck@buffalo.edu in the UB Department of Biochemistry.
The University at Buffalo is a premier research-intensive public university, a flagship institution in the State University of New York system and its largest and most comprehensive campus. UB’s more than 28,000 students pursue their academic interests through more than 300 undergraduate, graduate and professional degree programs. Founded in 1846, the University at Buffalo is a member of the Association of American Universities.
Source: molecularstation.com
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Practical Approach to Quantitative High Throughput Screening
Last Updated on Monday, 11 October 2010 09:50 Written by Editor Monday, 11 October 2010 09:50
Book: Chapter 18 Handbook of Drug Screening, Second Edition
Ramakrishna Seethala and Litao Zhang
Cover Image
Published
June 2009
ISBN
9781420061697
Edition
Second
Pages
504
Size
6 x 9 in
Format
Hardcover
142 illustrations
* Online Chapter
* Chapter PDF (431 KB)
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* Reprints
* Permissions
Chapter Opening
High throughput screening (HTS) has progressively evolved since the late 1980s as an important approach for new lead discovery and a chemistry starting point (1). The size of compound collections used in HTS campaigns has also increased significantly from under 100,000 to a few million in major pharmaceutical companies. In the 1990s, pooling approaches, in which 10 to 20 compounds were contained in one well, were widely used for compound screening due to the limited screening throughput (2). Frequent interference from compounds in pooled samples and time-consuming hit deconvolution from the primary screen impaired the ability of lead identification using early pooling strategies. In the late 1990s and early 2000s, single-compound screening became the main platform with the advances in HTS technology and increases in screening throughput. However, primary screening of compound collections is routinely performed at a single concentration, typically as a single replicate, due to the high cost and time requirement for screening such large compound collections (usually in millions of compounds). Screening at a single concentration provides only a limited window of opportunity to identify the useful lead compounds.
Source: informahealthcare.com
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Virtual Screening
Last Updated on Monday, 11 October 2010 09:46 Written by Editor Monday, 11 October 2010 09:46
1. Description
1.
Virtual screening (VS) can be a useful alternative to HTS, especially if the assay will only permit a relatively small number of compounds to be tested. Different methods can be used depending on the information available. For any virtual screening, the selection of the database is as important as the methods used.
2.
The number of compounds tested is also critical to the ability to identify hits. A typical HTS needs on the order of 5000 compounds to identify a single hit. Expecting virtual screening to reliably identify a hit in ~50 compounds is optimistic. This can usually only be successful when a great deal is known about the binding site, or a ligand series is already identified. A more reasonable expectation would be to test a few hundred compounds to identify (and confirm) a few good hits.
3.
Follow-up of VS hits typically follows a similar procedure to HTS follow-up as a great deal of additional information can be obtained by testing related compounds.
4.
In the absence of a target protein crystal structure, VS can be done based on the ligand conformation, either through a pharmacophore search (if a series of ligands is known) or by a shape-based method if a single (or few) ligand is known. This method compared database ligands to the 3D shape of the surface of the query molecule. Those compounds that most closely match the query shape (and chemical nature) are the highest ranked. In cases where the ligand conformation is extracted from a crystal structure, this approach can be as good as docking to the protein directly.
5.
When a crystal structure of the target protein is available, VS is commonly done by high-throughput docking and scoring. The goal of this docking is not necessarily a highly accurate biding mode, but instead is a list of compounds that is likely to bind to the target. The docking algorithms used may therefore be different from those used for detailed docking and scoring. This approach is typically slower than ligand based VS methods.
2. Requirements
1.
•Ligand VS: single known ligand, ideally with known or predicted binding conformation
2.
•Pharmacophore: several ligands known to bind to the same target binding site
3.
•Structure VS: crystal structure, ideally with ligand or natural substrate bound
3. Limitations
1.
•Significant number of compounds must still be tested to obtain a hit
2.
•Choice of database often determines the quality of hits
4. Deliverables
1.
•Ranked list of compounds (available for purchase) for testing
2.
•Prediction of binding mode (if structure or pharmacophore is developed)
Source: biochem.wustl.edu
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The NIH Molecular Libraries Program: Identifying Chemical Probes for New Medicines
Last Updated on Saturday, 24 July 2010 04:24 Written by Editor Monday, 12 July 2010 02:12
Alice McCarthy
In 2003, several program leaders within the National Institutes of Health (NIH) recognized that the results from the recently completed Human Genome Project were a launching pad for further study. Now that scientists knew the genome, how could they determine gene function? In particular, how could scientists find specific biological pathways and targets that could lead to new advances in biology and new drug therapies?
MLP was founded to fund research spanning multiple NIH institutes, all with one goal: identify new chemical probes to explore new targets for drug therapies.
The Molecular Libraries Program (MLP), an NIH Roadmap Initiative first funded in 2004, has partially answered those questions. “At the time the term ‘chemical genomics’ was on the minds of NIH researchers,†explains Carson Loomis, Ph.D., Program Director, Molecular Libraries. “The human genome was available and it was agreed that the NIH should become more involved in screening new small molecules to get better targets.†The pharmaceutical industry had become frustrated by drug failures in development lacking the means to sufficiently validate potential targets. “They were at the breaking edge of science, yet when a new kinase was discovered and they developed a drug for it, it would often fail,†explains Loomis. “The feeling was that we needed more basic research and that the NIH needed to further this cause of validating targets.â€
The act of Congress creating the MLP now includes the efforts of nine Molecular Libraries Probe Production Centers. They include one intramural NIH site, the National Center for Chemical Genomics (NCGC), and eight extramural sequencing and screening centers: the Broad Institute, the Sanford-Burnham Medical Research Institute, Johns Hopkins University, Scripps Research Institute, the University of New Mexico, Southern Research Institute, the University of Kansas, and Vanderbilt University.
The common purpose of these probe production centers is to generate new small molecule chemical probes by performing high throughput screening, secondary screens, and medicinal chemistry. The biological assays for these probes are sourced from the scientific community at large.
MLP was founded to fund research spanning multiple NIH institutes, all with one goal: identify new chemical probes to explore new targets for drug therapies.
Screening Library
The workhorse of the MLP program is its 350,000-strong library of unique chemical structures of the NIH’s Molecular Libraries Small Molecule Repository (MLSMR). The MLSMR is screened with biological assays or bioactivity experiments looking for particular areas of biological activity.
Small molecule probes can be targeted to interact with extreme precision with a cell or cell byproduct. This specificity provides useful details about the steps in a cell’s function and ultimately to its disease pathway. A “true positive active†compound found to be active against a biological target is classified as a chemical probe.
As part of the MLP mandate, all identified probes are immediately reported to the National Library of Medicine’s PubChem, a chemical and biological activity repository. Full results may be withheld for up to year to allow investigators to publish their findings.
Though only 350,000 of the 26 million unique chemical structures found in PubChem derive from the MLP, they have generated a wealth of information when combined with the biological assays also deposited. Each participating MLP center receives the screening library and uses it to test a variety of biological questions. “The result is that over 90 million unique biological results have been placed in PubChem from the MLP sites, representing over 80% of the total,†explains Steve Bryant, Ph.D., Program Director, PubChem. “It’s the combination of the screening library with the unique bioassays that provide the information that lead to the designation of probe.â€
All of the centers deposit the entire screening experiment, even if most of the results showed no activity or low activity. “It’s important to know what doesn’t work as well as what does,†explains Bryant.
Before victory is proclaimed, however, a probe has to be validated. Enrique Michelotti, Ph.D., who oversees this process within the MLP, says, “The assays and the probes identified have to address a very specific problem in biology.†Assay providers need to supply the proposed assay to NIH for peer-review. The network runs the assay through high throughput screening against the 350,000 compound MLSMR collection. “Any new compound that is active in that assay is followed up by chemistry and has to be best in class in that it is addressing some particular issue in biology,†he says. “That is what we are looking for in a probe.â€
One hundred fifty validated probes have been created since the $70 million, 4 year production phase of the effort began in 2008, but only about 120 are publicly available due to the 1 year embargo. Full details on the available probes can be found at the MLP website (http://mli.nih.gov/mli/).
Screening, Et Al.
The data coming from the MLP includes information on the chemical structures as well as the assays and analytical tools regarding bioactivity.
“This lends real value to the program because each center in the MLP has a particular area of expertise regarding types of assays used or areas of research,†says Loomis.
But the MLP includes a bit more than small molecule screening. It also funds technology development encompassing new instrumentation, chemical diversity efforts including natural products methods, and pilot scale libraries to generate novel new compounds to put into the screening library. For example, researchers at the University of New Mexico, an MLP center, are adapting flow cytometry to high throughput screening.
Probe = Research Tool
MLP defines a probe as a compound that can be useful as a research tool. “It does not have to work in animals but ideally it will work in cells,†explains Loomis. “It could be a biochemical assay looking for a means to block a compound’s phosphorylation ability, or phenotypic assays.†The latter are of very high value to the MLP because these screens might point the way in finding a better target for a pathway.
The MLP emphasizes rare and neglected diseases, but they cover a large range of therapeutic areas including cancer, inflammation, infectious disease, and metabolic diseases. However, MLP funding is limited to the probe discovery process only. “If, with a little more study, some of these probes are found to be useful in animals and eventually becomes a lead for chemistry to develop a drug, that is a win/win for us, but our funding won’t go that far,†adds Loomis. If a probe discoverer believes it may represent a great opportunity for drug development, alternative funding is necessary.
“In my view, the most interesting and valuable part of the MLP program is the number of assays we have spanning multiple therapeutic areas or potential targets,†says Michelotti. In MLP, the assays are designed in a way to capture multiple levels of biological activity. “They also include information on potential roles of agonists, antagonists, partial agonists, etc., as the information we receive is denser, more rich, because it is not limited to one particular target.†And even within one target, Michelotti points out that the biological information is more comprehensive.
In the short time since full probe production began in September 2008, the MLP has become a go-to public resource in the burgeoning field of chemical probe production. With at least two more years of guaranteed funding, the number of new targets identified—and the probes to accompany them—will only rise in the hopes of quickening highly targeted drug discovery.
source: cell.com
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Speeding up drug screening
Last Updated on Saturday, 24 July 2010 04:24 Written by Editor Monday, 12 July 2010 10:28
Box 1: Speeding up drug screening
At the Swiss Tropical and Public Health Institute, Reto Brun provides a ‘gold standard’ screening centre for protozoan parasites for the World Health Organization (WHO)–Special Programme for Research and Training in Tropical Diseases (TDR) and the Drugs for Neglected Diseases Initiative (DNDi), as well as the Gates-funded Consortium for Parasitic Drug Development (CPDD). His in vitro system involves the cultivation of Trypanosoma cruzi-infected rat myoblasts in 96-well microtitre plates, using genetically modified parasites that express a bacterial enzyme that can be quantified by photometry. This allows the screening of up to 1,000 compounds a week.
At the Sandler Center, husband-and-wife team Juan Engel and Patricia Doyle have created a medium-to-high-throughput system using a robotic liquid handler dispensing into 96-well microtitre plates. This uses an automated microscope to detect DNA-stained parasite kinetoplasts in primary cell cultures from skin, muscle, liver and macrophages, and quantifies the number of T. cruzi per host cell. Screening capacity has risen from 100 compounds a month to 1,000 compounds a week in whole-cell assays, or tens of thousands a week in enzyme biochemical assays.
Fred Buckner at the University of Washington Seattle in the United States has developed an HTS based on 384-well plates and recombinant T. cruzi expressing fluorescent β-galactosidase: “We’ve gone from an era where you could test a handful of compounds in a week to [one where it is possible to test] 250,000 in a few weeks. It’s helping everybody who’s interested in screening drugs — a much needed tool.†He has shared the system with laboratories in Brazil, Argentina, Panama, the United States and Europe.
LUCIO FREITAS-JUNIOR
One of the fastest HTS systems belongs to Lucio Freitas-Junior at the Institute Pasteur in Korea: a 384-well cell-culture system that combines an automated confocal microscope with an image analyser (pictured) to screen up to 30,000 compounds a week. Through DNA staining of wild-type rather than genetically modified T. cruzi, the system’s software can count the number of parasites per cell and the number of cells per well, measure the size and shape of each cell to give a read-out of viability and morphological change owing to parasite infection, and determine the effects of the would-be inhibitors. A second step selects compounds that interfere with replication of parasite kinetoplast DNA (which provides a specific set of targets that are relatively similar among T. cruzi, Trypanosoma brucei and Leishmania). Freitas-Junior and colleagues are now screening a Pfizer library of 150,000 compounds for leads against Leishmania and T. cruzi with a commission from the DNDi.
The HTS technology “has not been applied broadly in support of drug discovery for neglected diseases, so it presents a great opportunity to evaluate a large number of compounds to generate starting materials for further analysisâ€, says Solomon Nwaka of the WHO–TDR. Nonetheless, Nwaka is under no illusions about the difficulty of moving to the next state. “Just because you have a million compounds available to screen, doesn’t mean you will get a new drug. HTS just gets you to the next stepâ€.
source: nature.com
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NIH High-Throughput Screening Identifies Candidate Medicines for CMT
Last Updated on Saturday, 24 July 2010 04:24 Written by Editor Monday, 12 July 2010 09:55
The NIH has completed the high-throughput screening program.
Working with a chemical library of more than 350,000 compounds, the NIH screened each compound at approximately 7 different dosage levels-resulting in more than 2 million unique screens.
Out of the 4000 FDA approved drugs, 10 “hits” or candidate medicines were found. At this point in time, we are not able to divulge the names of these compounds.
Out of the non-FDA approved drugs, 800 “hits” were discovered.
These 800 hits proved to reduce the amount of PMP22 in the cells, without causing any damage to the cells.
A second cell assay, created by John Svaren, is being sent to the NIH this week. The 810 hits discovered from the initial screening will be tested on Svaren’s new assay over the summer and the final results should be released by the end of August.
At this point, we will know more about when the animal model testing will occur.
We are extremely excited about the progress made by the scientists involved in the STAR program. Never before has such a large portfolio of over 800 compounds been tested on a cell line in this fashion.
NIH Director Dr. Francis Collins Applauds the CMTA’s Research and Drug Development Collaboration with the National Chemical Genomics Center (NCGC) during Congressional Hearing
On June 15, 2010 the U.S. House of Representatives’ Committee on Energy and Commerce, Subcommittee on Health, held a hearing titled “NIH in the 21st Century: The Director’s Perspective.” Testifying before the Congressional Subcommittee was NIH-Director Dr. Francis Collins. During Dr. Collins’ testimony, the following exchange occurred with Representative Eliot Engel (D-NY) (watch video):
ENGEL: I’d like to ask you about Charcot-Marie-Tooth Disease. There is an innovative partnership between the NIH’s National Chemical Genomics Center and the Charcot-Marie-Tooth Association. I’ve worked with that association and I think that this could serve as a model of future rare disease research and drug development, and so I’m wondering if you could describe the program and offer some thoughts on it.
DR. COLLINS: I appreciate the question because I do agree this is a very exciting program. My father-in-law has Charcot-Marie-Tooth disease and so this is a disorder that is not only something from my clinic but also from my family’s experience, and this is an interesting disorder which causes a weakness of the legs particularly, but also the hands over the course of time and can be quite debilitating, but it is well-understand now what the cause of that is…the genetic abnormality has been now laid out in great clarity, but what could you do about it? Working with the NIH Genomic Center, which is this remarkable facility that has been mentioned already at least once in this hearing. It is…an effort is being made to identify a small molecule, which is sort of a drug that would basically compensate for the genetic problems that’s found in individuals with this type of Charcot-Marie-Tooth disease, so-called CMT1A, and that is an early stage effort but it’s a good example of this therapeutics for rare and neglected diseases effort that NIH is putting an increasing effort into. Charcot-Marie-Tooth is too rare for companies to generally see this as a good investment for them in terms of developing a therapy. But with the chemical genomic center working with academic investigators who know a lot about the disease…if they can push this forward to the point of identifying a promising compound, then you can imagine a company getting pretty interested in licensing it out and carrying it all the way through to a clinical trial.
The CMTA commends Representative Engel and the Subcommittee for their continued support of CMT research. The CMTA is honored to have the NCGC as a partner in our quest to find therapies and cures for CMT, and is greatly appreciative of Dr. Collins and his colleagues throughout the NIH for their commitment to rare disease research and drug development.
Additional information about the hearing, including a full transcript of Dr. Collins’ testimony can be found at http://energycommerce.house.gov.
source: zencaroline.blogspot.com
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Increased R&D Efforts Are Overcoming Obstacles and Showing Potential
Last Updated on Saturday, 24 July 2010 10:26 Written by Editor Monday, 12 July 2010 09:46
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Sanford-Burnham robots speed up path to discovery
Last Updated on Saturday, 24 July 2010 04:26 Written by admin Thursday, 8 July 2010 10:40
The work force at Lake Nona’s Sanford- Burnham Institute includes 90 scientific staffers, 60 administrators and support personnel — and a team of three robots. The robots are part of a $15 million investment from the National Institutes of Health and occupy a large, glass-enclosed room on the bottom floor of Burnham’s Lake Nona campus.
Although they resemble the robotic arms used in automobile assembly lines, these robots have a far different task: filling test tubes faster than a human being. And that, scientists say, will speed up the process of scientific discovery.
“The robots are from the automobile industry,” said Greg Roth, director of medicinal chemistry at Burnham’s Conrad Prebys Center for Chemical Genomics. “We use them because of the accuracy and precision of their movements.”
The robotic arms can fill miniature test-tube “wells” so tiny that 1,536 of them fit on a plate the size of an index card. Using such small test tubes allows researchers to save money on chemicals and compounds.
After filling the wells, the robotic arms take a plate of the tubes and subject them to numerous tests such as varying temperatures and pressures. The robots are connected to a main computer that compiles the data from the millions of tests.
Pharmaceutical companies developed the ultra-high throughput screening technology in the mid-1990s, but universities and nonprofit research institutions such as Burnham did not have access to the robots until recently.
Funded by NIH, the Burnham center and eight others around the country form the institute’s Molecular Libraries Production Centers Network. This resource library and network assists scientists in research and allows results to be shared across the public and private sectors.
The reason for the federal government’s interest? As the results of the Human Genome Project began pouring in, scientists found themselves with so many avenues to explore that they needed faster research procedures.
“My scientists like to say they can do more than a robot, but they can only do it for a day,” said Michelle Palmer, director of screening for the Broad Institute at Harvard and Massachusetts Institute of Technology.
“The humans can do it faster and better, but they can’t sustain it. We need to sustain this over months of effort and get it done exactly the same way every time,” Palmer said.
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Compound screening for drug development made simpler
Last Updated on Thursday, 13 May 2010 12:47 Written by Editor Thursday, 13 May 2010 12:47
The identification of compounds that could be promising candidates for drug development has become easier following research by the Walter and Eliza Hall Institute’s medicinal chemistry group.
Dr Jonathan Baell and Dr Georgina Holloway have developed a series of ‘filters’ that can be used to weed out those molecules likely to come up as false positives when screening a chemical library for compounds that could be useful in drug development.
High-throughput chemical screening (HTCS) seeks to identify chemical compounds that interact with a target protein and are therefore potential candidates for drug development. There can be from 30,000 to one million compounds in a screening library and thousands of compounds may be flagged as ‘positive’ for interaction with a protein of interest. These compounds then become the subject of time-consuming medicinal chemistry as scientists seek to refine them for entry into the drug development pipeline.
Dr Baell said about 10 per cent of compounds in any commercially available screening library might show up as false positives, potentially wasting hundreds of hours of scientists’ time as they undertake labour-intensive medicinal chemistry to optimise these molecules.
“We’re trying to remove molecules from the screening process that trick scientists into thinking they could be useful for being developed into drugs to treat disease but instead become a dead end,” Dr Baell said.
To this end, Dr Baell and Dr Holloway analysed data from previous chemical screens and developed a way of clearly identifying those molecules likely to show up as false positives.
“These pan assay interference compounds, or PAINS as I like to call them, caused us some grief not so many years ago. For that reason, Georgina and I have taken some effort to identify these PAINS.”
Dr Baell has made it possible for others to identify these troublesome molecules by developing ‘filters’, text files that can be incorporated into the software used to screen chemical libraries.
The filters were made publically available on 4 February through online publication in the Journal of Medicinal Chemistry.
High-throughput chemical screening has been used by large pharmaceutical companies for more than 20 years. In the past decade scientists at universities and research institutes and in small biotechnology companies have had increasing access to HTCS. “Many of them have spent vast amounts of time and money optimising and patenting molecules that were never going to amount to anything,” Dr Baell said.
“We were in a position where we had all the data, we had the software, and we had the expertise to identify these molecules. Importantly, we also had the ability to publish our data.
“Pharmaceutical companies, which have used high-throughput chemical screening for many years, would know about many compounds that turn up as false positives. But they also operate in a competitive environment where publishing this data could compromise their competitive edge. For this particular situation, we didn’t have such constraints.”
Dr Baell said that within 48 hours of publishing the filters he was contacted by a number of pharmaceutical companies wishing to use them to assess their impact on their own high throughput screening libraries.”
source: eurekalert.org
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High Throughput Screening 2010 Study Finds HTS Laboratories Using Effective Screening Strategies and Innovative Technologies to Increase Drug Discovery Success
Last Updated on Thursday, 13 May 2010 11:31 Written by Editor Thursday, 13 May 2010 11:31
HTS laboratories are essential contributors to drug discovery, participating extensively in assay development and lead optimization as well as in primary and secondary screening of compound libraries. Effective screening strategies adopted by HTS laboratories include the use of more complex biological systems: more membrane-bound targets, more cell-based high content assays, and increased use of stem cells and primary cells.Fifty-two directors from HTS laboratories and thirty-three executives from suppliers of HTS products and services in Asia, Europe and North America were extensively interviewed in a recently published study, High Throughput Screening 2010: Effective Strategies, Innovative Technologies, and Use of Better Assays, described technology and strategies that are evolving to increase success in drug discovery.
HTS laboratories are exploring novel targets and strategically expanding compound libraries to include more diverse backbones, more target-focused compounds, natural products, and biologics. The directors at HTS laboratories also plan to employ improved technologies, including further adoption of HCS and label-free technologies and more accurate liquid handling dispensers.
HTS laboratories funded through NIH or other private foundations have an increased presence, as more universities and institutes initiate translational research. This new report includes analysis and data from interviews with HTS laboratory directors at these centers to better understand their impact on the high throughput screening market.
William Downey, President of HighTech Business Decisions, explains, “High throughput screening is established as a critical activity in drug discovery. In the past two years, challenging targets have yielded to advances in assay and detection technologies. High content and label-free assays and new interest in stem cells as promising disease models are leading the way to improved drug discovery.â€
The findings and analysis are in this 1050–page industry report, with over 300 charts and tables, High Throughput Screening 2010: Effective Strategies, Innovative Technologies, and Use of Better Assays. This new study was published in February 2010, and it is available from HighTech Business Decisions.
About HighTech Business Decisions
HighTech Business Decisions is a market research and consulting firm specializing in the areas of pharmaceutical drug discovery and biopharmaceutical contract manufacturing. The company has been producing in-depth public reports and customized benchmarking, market analysis and customer loyalty programs for over ten years. Visit us at www.hightechdecisions.com
source: businesswire.com
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Evotec Signs High Throughput Screening Agreement With Active Biotech
Last Updated on Thursday, 13 May 2010 11:06 Written by Editor Thursday, 13 May 2010 11:06
Evotec AG (Frankfurt:EVT) (TecDAX) today announced that it has entered into a collaboration with Active Biotech AB (Stockholm:ACTI) to identify small molecule modulators of a priority biological target, selected by Active Biotech, involved in immune disorders and cancer.
Evotec will use its expertise and technologies in assay development, high throughput screening (HTS) and surface plasmon resonance (SPR) screening for the identification and validation of novel hits. In order to maximise the probability of finding high quality medicinal chemistry starting points, Evotec will screen its Lead Discovery Library, a small molecule collection designed for diversity, novelty and quality.
Dorthe da Graça Thrige, Director of Development of Active Biotech, commented: “We have a high regard for Evotec’s expertise and capabilities in assay development and compound screening. In addition, we are impressed with the excellent quality of Evotec’s Lead Discovery Library, which we believe will enable us to generate high quality hits, ensuring a smooth transition to medicinal chemistry activities. Importantly, the hits identified in the HTS will complement the ongoing lead optimisation of compounds identified in-house.”
Dr. Mark Ashton, Executive Vice President, Business Development of Evotec stated: “We are proud to have been selected by Active Biotech, a leading biotechnology company with advanced drug candidates in the area of immune modulation, to carry out hit identification activities on this important biological target. We look forward to supporting them in their quest to find novel treatments to address immune disorders and cancer.”
Evotec has a unique assay development and screening platform built around proprietary and the latest commercial technologies providing a flexible and high quality approach to lead identification. Evotec has successfully developed assays and high throughput screens for all of the major target classes including GPCR’s, kinases and other enzymes, ion channel and protein::protein interactions.
No financial details are disclosed.
About Evotec AG
Evotec is a leader in the discovery and development of novel small molecule drugs with operational sites in Europe and Asia. The Company has built substantial drug discovery expertise and an industrialised platform that can drive new innovative small molecule compounds into the clinic. In addition, Evotec has built a deep internal knowledge base in the treatment of diseases related to neuroscience, pain, and inflammation. Leveraging these skills and expertise the Company intends to develop best-in-class differentiated therapeutics and deliver superior science-driven discovery alliances with pharmaceutical and biotechnology companies. Evotec has long-term discovery alliances with partners including Boehringer Ingelheim, CHDI, Novartis, Ono Pharmaceutical and Roche. Evotec has product candidates in clinical development and a series of preclinical compounds and development partnerships, including for example a strategic alliance with Roche for the EVT 100 compound family, subtype selective NMDA receptor antagonists for use in treatment-resistant depression. For additional information please go to www.evotec.com.
About Active Biotech AB
Active Biotech AB (Stockholm:ACTI) is a biotechnology company with focus on autoimmune/inflammatory diseases and cancer. Projects in pivotal phase are laquinimod, an orally administered small molecule with unique immunomodulatory properties for the treatment of multiple sclerosis, as well as ANYARA for use in cancer targeted therapy, primarily of renal cancer. Further key projects in clinical development comprise the three orally administered compounds TASQ for prostate cancer, 57-57 for SLE and RhuDexTM for RA. Please visit www.activebiotech.com for more information.
Forward-looking statements
Information set forth in this press release contains forward-looking statements, which involve a number of risks and uncertainties. Such forward-looking statements include, but are not limited to, statements about our expectations and assumptions concerning our strategic collaborations, our regulatory, clinical and business strategies, the progress of our clinical development programmes and management’s plans, objectives and strategies. These statements are neither promises nor guarantees, but are subject to a variety of risks and uncertainties, many of which are beyond our control, and which could cause actual results to differ materially from those contemplated in these forward-looking statements. In particular, the risks and uncertainties include, among other things: risks that product candidates may fail in the clinic or may not be successfully marketed or manufactured; the risk that we will not achieve the anticipated benefits of our collaborations, partnerships and acquisitions in the timeframes expected, or at all; risks relating to our ability to advance the development of product candidates currently in the pipeline or in clinical trials; our inability to further identify, develop and achieve commercial success for new products and technologies; the risk that competing products may be more successful; our inability to interest potential partners in our technologies and products; our inability to achieve commercial success for our products and technologies; our inability to protect our intellectual property and the cost of enforcing or defending our intellectual property rights; our failure to comply with regulations relating to our products and product candidates, including FDA requirements; the risk that the FDA may interpret the results of our studies differently than we have; the risk that clinical trials may not result in marketable products; the risk that we may be unable to successfully secure regulatory approval of and market our drug candidates; and risks of new, changing and competitive technologies and regulations in the U.S. and internationally.
The list of risks above is not exhaustive. Our most recent Annual Report on Form 20-F, filed with the Securities and Exchange Commission, and other documents filed with, or furnished to the Securities and Exchange Commission, contain additional factors that could impact our businesses and financial performance. We expressly disclaim any obligation or undertaking to release publicly any updates or revisions to any such statements to reflect any change in our expectations or any change in events, conditions or circumstances on which any such statement is based.
This news release was distributed by GlobeNewswire, www.globenewswire.com
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Genentech and UCSF’s Small Molecule Discovery Center Ink Deal Targeting Neurodegenerative Diseases
Last Updated on Wednesday, 12 May 2010 02:26 Written by Editor Wednesday, 12 May 2010 02:26
The University of California, San Francisco and Genentech are partnering to discover and develop drug candidates for neurodegenerative diseases. The company will support the work of several researchers at the UCSF Small Molecule Discovery Center (SMDC) to progress prior SMDC research and Genentech discoveries.
In addition to receiving financial support for its research function, UCSF has the potential for further funding in excess of $13 million if certain development and commercial milestones are met. UCSF will also earn royalties on sales of any resulting products.
This is the first major collaboration that the SMDC has formed with an industry partner, according to Jim Wells, Ph.D., who founded the center in 2005 and serves as its director. Dr. Wells and the center’s associate directors Adam Renslo, Ph.D., and Michelle Arkin, Ph.D., will lead the project.
“What is transformative about this agreement from the university’s perspective is that it is a true collaboration between UCSF and Genentech scientists with the intent to generate drug candidates,†Dr. Wells comments. “This is different from a standard out-license or simple research collaboration.
“Finding targeted compounds is a major obstacle in the drug discovery process in part because most academic researchers don’t have access to this type of facility,†Dr. Wells adds. “This collaboration shows how a center like the SMDC can help support the path from new biology into therapeutic products to help improve patients’ lives.â€
The center is based on high-throughput screening, medicinal chemistry, and fragment-based screening, including a novel approach called tethering, which Dr. Wells pioneered in his previous role as founder, president, and CSO at Sunesis Pharmaceuticals. SMDC offers all UC biomedical researchers access to high-throughput screening and follow-up medicinal chemistry technologies. The center performs biochemical and cell-based assays using liquid-handling robots and a screening library of more than 180,000 compounds. Over the past four years, the center has grown to 18 biologists and chemists, many reportedly with pharmaceutical experience.
SMDC’s arrangement with Genentech builds on the existing master agreement between the company and UCSF, which allows the two to collaborate in a streamlined manner. “To date we have entered into more than 15 research collaborations with UCSF across several therapeutic areas,†comments Marc Tessier-Lavigne, Ph.D., evp, research and CSO of Genentech.
source: genengnews.com
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An Emerald in the Rough
Last Updated on Thursday, 6 May 2010 03:10 Written by Editor Thursday, 6 May 2010 03:10
Late last year, scientists at Emerald BioStructures, located on Bainbridge Island just across the Puget Sound from downtown Seattle, experienced the bittersweet ride that so often characterizes the drug discovery business. In August 2009, a team led by CEO Lance Stewart published a major paper outlining the application of a Fragments of Life (FOL) drug discovery approach to help identify an exciting small-molecule drug candidate, DG051, in the Journal of Medicinal Chemistry. But publication came just a few months before Emerald severed ties with deCODE genetics after the Icelandic firm filed for bankruptcy in November (the company was formerly deCODE biostructures) and was acquired by Beryllium LLC.
Newly independent, Stewart has the goal of expanding its drug discovery services in the field of gene-to-structure research. Emerald bills itself as “the largest gene-to-structure CRO in the U.S.†One of its success stories was the development of DG051, one of two drug candidates it helped deCODE to identify. DG051 has completed Phase IIa studies, and the second drug candidate, DG071, is approved for entry into Phase I safety studies.
The DG051 story is remarkable for the speed with which deCODE’s biologists and chemists and Emerald’s structural biologists sped from target identification to IND in just 2.5 years, which might be a record. Yes, there were some fortuitous bounces along the way, but Stewart believes his high-throughput crystallography approach provides an attractive alternative to conventional high-throughput screening (HTS) techniques. It is, to his knowledge, “the first example of a human genomics target discovery that was followed up by a gene-to-clinic paradigm enabled by a fragment-based drug discovery effort.â€
deCODE’s strength was using genetic mapping studies to identify at-risk haplotypes for a host of common diseases. Several years ago, studies identified two genes in the leukotriene biosynthetic pathway that were incriminated in myocardial infarction. In January 2006, deCODE published a report that markers in the gene for LTA4H (leukotriene A4 hydrolase) were associated with increased risk of myocardial infarction, particularly in African Americans. After deCODE confirmed that those at-risk haplotypes were associated with higher levels of leukotriene B4, it targeted LTA4H as a viable drug target, bringing to bear the full capabilities of structure-based drug design (SBDD) and fragment lead identification, in a full-force effort to identify leads as quickly as possible.
By August 2006, DG051 was in Phase I clinical trials. “As far as we know, this molecule is the furthest along in a true genetic-underpinning, SBDD approach,†says Stewart. As of the end of 2009, DG051 had finished Phase 2A. Presently, the DG051 asset is tied up in deCODE’s bankruptcy proceedings.
Among the keys to identifying and developing DG051 so quickly was a fully integrated organization that saved a lot of time and money with integrated process chemistry, analytical chemistry and ADME-tox efforts. It wasn’t exactly under one roof—deCODE’s facilities were split between Seattle (now Emerald BioStructures) and Chicago (deCODE chemistry)—but that was a minor inconvenience. Stewart’s high-throughput crystallography operation dovetailed neatly with deCODE chemistry’s structure-based drug design, managed by president Alex Kiselyov.
When work began, there was little crystal structure data on LTA4H and only a few known inhibitors (from Searle). In all, Stewart’s group solved about 50 crystal structures, focusing on higher resolution, improved crystallization conditions, and structures with bound ligands. The goal, said Stewart, was “to make 100% sure we understood how fragments would interact with the target. We wanted to identify new chemotypes that could inspire chemistry on LTA4H.â€
An important in-house advantage for the crystallization work was software called Gene Composer, which is used to design and optimize the codon usage in the gene depending on the nucleotide bias of the expression system. “When you’re doing X-ray crystallography, you’re doing a lot of protein engineering, and so you’re better off synthesizing the gene,†says Stewart. “So you may as well tweak and engineer the overall molecule.â€
Synthesize This
While Stewart’s team was crystallizing the target, Kiselyov was leading the effort to identify the lead. “We were living the paradigm of moving therapeutic discoveries from gene to clinic,†says Kiselyov. Seeing DG051 finally reach the market would be “the key validation of this approach.†DG051 is actually 4-[(2S)-2-{[4-(4-Chlorophenoxy)phenoxy]methyl}-1-pyrrolidinyl]butanoic acid (See, Journal of Medicinal Chemistry. 2009 Dec 1).
Emerald used its FOL library of ~1,500 small molecules to initiate discovery of the DG051 drug candidate using high-throughput crystallography, rather than use the traditional funnel of HTS to screen large multi-million compound libraries. “It’s a bit like a Lego kit; every component makes sense and fits this selection.â€
Emerald gets “the biggest bang by doing structural biology and in parallel, doing the small-molecule chemistry. If they’re timed right, then like a Reese’s peanut butter cup, they come together.†The key to successful crystallography, he adds, is to feed the protein a well designed ligand, which aids the visualization of the enzyme-ligand complex.
Stewart’s iterative crystallization process produced a much more dynamic picture of the protein target in the presence of candidate small molecules. That enabled Kiselyov to do both docking and optimization studies. “Small molecule fragments bound to the target provided us with critical structural information for the design. Think of them as tiny pieces of clay, a molecular 3-D imprint of a specific protein sites. Previous art in the field, for example research done at Berlex and Searle, was also considered in a final assembly of these fragments into the ultimate clinical candidate, DG051.â€
“Instead of making thousands of compounds guiding us through the optimization process, synthesizing a matrix of about 500 molecules across four chemotypes was sufficient to identify a winner,†says Kiselyov. Notably, the deCODE team identified multiple chemotypes that occupied the buried active site of the target LTA4H enzyme. Fragments had to be lined up within three critical areas within the binding pocket—the catalytic zinc atom, a hydrophobic region, and a transitional kink or linker. “Since we identified the mode of binding and simultaneously optimized physiochemical and PKPD/tox parameters for our lead candidate, we didn’t even have to go to our backup. DG051 was good enough to push instantly from bench to a GMP production and clinic.†It took about 12 months from the initial structural biology efforts to finally settle on DG051.
One of the key observations was that the catalytic zinc atom liked to bind acetate, thus providing a hint regarding pharmacophore requirements for this portion of the enzyme. A rigid, prolinol derivative provided for a linker to combine a biaryl fragment with the acetate fragment culminating in DG051. Kiselyov’s team attempted various medicinal chemistry modifications, but most of them worsened the toxicology or metabolic properties of the molecule. “It’s almost like nature itself guided us and told us do not do silly things with this molecule,†he said. DG051 had outstanding specificity, with no HERG triggered toxicity. The molecule has very favorable drug-like properties including molecular weight, and production scaled nicely. Bioavailability was excellent in animal models and in human. The half-life was 9 hours, favoring a single daily clinical administration. There was also good evidence that DG051 affected levels of the key biomarker associated with the acute myocardial infarction and stroke.
From Genes 2 Drugs
DG051 is currently held up in Phase II trials. “We don’t know too many people who get molecules from scratch into the clinic in a safe way. Of course, efficacy is to be shown still, but we’d love to see them tried in phase 3,†said Stewart.
Another drug, DG071, did not progress as swiftly through development because it required some “heavy lifting†in structural biology, chemistry and enzymology. Additional crystallography information was required to picture the regulatory domains.
Stewart has seen upheavals in the market before. The predecessor to Emerald was a company called Medichem which acquired Emerald in 2000 and completed the last life science IPO as Medichem Life Sciences just before the 2001 market crash. In 2002, deCODE acquired Medichem and Emerald to run a hybrid business model, running contract research for multiple clients while executing a handful of drug discovery projects for itself.
So why was the development of DG051 so successful? Part of the answer was in the way the project was managed. Stewart says his group was driven by milestones and specified timelines. He says deCODE had a “gene to IND capability. We have goals and set timelines. We wanted an IND in two years… We wanted to meet those goals. When you put a number of shots on goal, in an integrated way, you don’t know when but you’ll catch a break somewhere.†Emerald did indeed catch a break—the acetate binding to catalytic zinc was deemed too good. “We still did more and more chemistry, thinking we could do better, but we didn’t need to do all that work.â€
Another critical factor at deCODE chemistry, says Kiselyov, was having the process chemists working closely with the medicinal chemists to jump into large-scale production. That helps rule out building blocks that are too expensive or commercially unavailable, and avoid the possibility of toxic impurities. In the event, deCODE chemistry was able to do just a 4-step synthesis from commercially available building blocks, and scale up production before the IND.
Stewart says the FOL collection creates new IP and the ability to identify new druggable sites, which in turn leads to selectivity. And with so many constructs, he could look at the same lead molecule in different protein environments as he considered the medicinal chemistry.
“I’m way too humble to say we’re the best in the field,†says Kiselyov. He quotes a phrase from Fiddler on the Roof: “We’re just trying to scratch a simple tune here.†It’s still the early stages of using fragment based crystallography for SBDD. “Whatever our fate, we’re somewhat monolithic,†says Kiselyov. “If we can take an IND, that would be ideal. deCODE has a drug candidate in DG051 that has completed Phase2A. That is what pharma is or will be looking for.â€
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BellBrook Labs Launches a New Transcreener HTS Enzyme Assay
Last Updated on Thursday, 6 May 2010 11:26 Written by Editor Thursday, 6 May 2010 11:26
Madison, Wis. (PRWEB) January 11, 2010 — BellBrook Labs today announced that it has launched a new product in their proprietary Transcreener HTS Assay platform. The Transcreener GDP FI Assay was developed for detection of GTPases, a large family of enzymes that play diverse roles in normal and disease-related cell processes. The new assay overcomes a longstanding problem in GTPase detection in that it relies on direct detection of GDP rather than phosphate. Phosphate is a component of many biomolecules and commonly used reagents, and its ubiquitous presence in biological samples causes high background and false positives in the current GTPase enzyme assays. BellBrook’s new assay detects GDP – a much more specific product of GTPase enzymes – eliminating the background problems associated with phosphate detection.
Transcreener is a universal, high throughput biochemical assay platform based on detection of nucleotides, which are formed by thousands of cellular enzymes, many of which catalyze the covalent regulatory reactions that are central to cell signaling and represent new opportunities for therapeutic intervention. It relies on highly specific antibodies that detect nucleotides coupled with homogenous fluorescent detection formats suitable for automated HTS applications. A single Transcreener assay can be used with any enzyme that produces a given nucleotide, allowing detection of hundreds of different drug targets. It is the only enzyme assay method that allows direct detection of nucleotide enzyme products without the use of additional coupling or reporter enzymes, which are a common source of interference by chemical library compounds. BellBrook currently holds three patents on the Transcreener technology and the company is pursuing additional patent applications. In addition to BellBrook’s own Transcreener line, a number of other companies in the Life Science sector including Invitrogen, CisBio and Evotec have licensed the Transcreener technology for their own HTS assay products and/or screening services.
The new GDP assay is similar to BellBrook’s flagship product, the Transcreener ADP Assay, which was introduced in 2006, and has since been validated by pharmaceutical companies worldwide in tens of millions of HTS assays. The company launched a fluorescence polarization GDP assay in 2009, and developed the new fluorescence intensity assay to target academic laboratories that may not have access to an expensive multimode plate reader. The assay incorporates a novel non-fluorescent quencher licensed from Li-Cor Biosciences in addition to BellBrook’s antibody technology. Binding of GDP to the antibody displaces a red tracer, which relieves quenching and results in a fluorescence increase. The positive fluorescent signal is another unique feature of the assay and makes it attractive to new users who are not familiar with competitive immunoassay formats such as TR-FRET and FP.
About BellBrook Labs. BellBrook Labs, LLC was founded in 2002 and currently employs 21 people. The company develops detection reagents and microfluidic devices that accelerate the discovery of more effective therapies for cancer and other debilitating diseases. Transcreener® is a patented high throughput screening assay platform that was introduced in 2005 and is used to identify inhibitors for kinases and other types of protein drug targets. The iuvo™ Microconduit Array technology is a line of unique microscale devices for miniaturization and automation of advanced cell models that are more representative of human physiology. Visit BellBrook’s website for more information: www.bellbrooklabs.com.
source: prweb.com
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Genedata at HCA Announces Banner Year for Genedata Screener at Leading Pharmaceutical Companies
Last Updated on Thursday, 6 May 2010 11:14 Written by Editor Thursday, 6 May 2010 11:14
7 out of the 25 top pharmas now use Genedata Screener for High Content Screening analysis.
San Francisco, CA (PRWEB) January 11, 2010 — Genedata, a leading provider of advanced software solutions for drug discovery and life science research, today announced that over the past 12 months Genedata Screener has experienced unprecedented industry adoption with 7 out of the 25 leading pharmaceutical companies using Screener for High Content Screening (HCS) analysis. Screener’s HCS capabilities support complex multiplexed assay formats, enable comparative visualization of HCS images and help standardize processes from a centrally managed platform. The announcement was made at the 7th Annual High Content Analysis Conference where Genedata is presenting and exhibiting (January 11 – 15; Fairmont Hotel – Booth # 27).
“HCS analysis within a high throughput screening infrastructure is evolving and 2009 proved to be the year in which we saw leading pharmaceutical companies understand how they can use Screener’s HCS capabilities in conjunction with their high throughput screening workflows,” said Dr. Othmar Pfannes, CEO of Genedata. “These companies have quickly transitioned from the learning – enlightenment phase to actual production in which data analysis is no longer a bottleneck in high content screening.”
 leading pharmaceutical companies understand how they can use Screener’s HCS capabilities in conjunction with their high throughput screening workflows  |
Genedata customers, who rely on Screener for high content confirmation and secondary screens, are beginning to use Screener for HCS at high throughputs. Several customers report that Screener HCS enables them to easily process 1,000,000 compounds or more per screen. This is a result of Screener’s ability to leverage this information within a scalable framework, which features automated data processing and intelligent management functions – all of which can be reviewed by scientists at any stage in the process. “2009 was a banner year for HCS adoption,” continued Pfannes, “and I project that 2010 will be the year in which we see HCS in far more rigorous production settings as well as continued adoption by customers looking for a scalable HCS technology.”Screener standardizes and automates in-depth analysis of high content screens passing from single-cell data to hit selection in a highly efficient workflow. The increased throughput of Screener HCS and user-friendly interface for visualization, management, and review allows researchers and scientists to review more cellular images in less time and quickly identify subtle variances. While Screener is fully compatible with the Thermo Scientific Cellomics Store image management system, it has also been integrated with other in-house and commercial HCS image storage solutions.
Note to Editors: Genedata will deliver a presentation on how to establish a routine application of HCS in high throughput screening at HCA on January 13th at 1:00 p.m. To schedule an editorial briefing, email Jackie.Thrasivoulos@genedata.com.
About Genedata
Genedata transforms data into intelligence with a portfolio of advanced software solutions for drug discovery and life science research, which spans target, lead and biomarker discovery. Used by a majority of the world’s top 50 pharmaceutical companies and leading research organizations, Genedata Phylosopher®, Genedata Screener®, and Genedata Expressionist® make research data accessible and understandable, enabling scientific discovery that fights disease and improves health worldwide. Founded in 1997, Genedata is privately held, with headquarters in Basel, Switzerland, and offices in Japan, Germany and the US. www.genedata.com
Disclaimer
The statements in this press release that relate to future plans, events or performance are forward-looking statements that involve risks and uncertainties, including risks associated with uncertainties related to contract cancellations, developing risks, competitive factors, uncertainties pertaining to customer orders, demand for products and services, development of markets for the Company’s products and services. Readers are cautioned not to place undue reliance on these forward-looking statements, which speak only as of the date hereof. The Company undertakes no obligation to release publicly the result of any revisions to these forward-looking statements that may be made to reflect events or circumstances after the date hereof or to reflect the occurrence of unanticipated events.
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Product Focus: Ultra-High-Throughput Screening
Last Updated on Wednesday, 5 May 2010 05:14 Written by Editor Wednesday, 5 May 2010 05:14
Ultra-high-throughput screening (uHTS) is an automation-based methodology for conducting hundreds of thousands of biological or chemical screening tests per day. The cutoff between high-throughput screening (HTS) and ultra-high-throughput is somewhat arbitrary. “There is no fixed boundary,†says Simon Sheard, Ph.D., business development manager at RTS Life Science (Manchester, UK), which supplies automated sample management equipment used in uHTS. The generally accepted crossover point today is 100,000 tests per day.uHTS is conducted in microtiter plates. To provide numerical perspective, 100,000 tests per day require 1,450 96-well plates (by far the most commonly used type), 261 384-well plates, or 65 1536-well plates. uHTS programs that exceed 1 million screens per day use ten times as many plates.
Equipment for conducting uHTS is indistinguishable from a standard microplate handling system, consisting of a robotic microplate handler, a liquid dispenser, and a plate reader. Additional components for washing, agitation, bar code reading and incubation are also possible.
uHTS achieves its speed through a combination of higher-density microtiter plates and multichannel (384 and higher) liquid dispensing. Equally important in achieving high throughput, however, is assay simplicity. Most ultrafast screens involve simple binding and rapid reading of results. For this reason, uHTS lends itself most readily to drug screening where, classically, tens of thousands or hundreds of thousands of wells are plated with entries from a large compound library, and the assay reagents (protein, enzyme, cell, or receptor, plus reporting reagent) remain constant in every well. Depending on the nature of the detection event, the interaction between compound and target is read as fluorescence or luminescence.
It is possible to “cheat†in HTS/uHTS by utilizing unpurified compounds, mixtures of compounds, or even multiple targets, a technique known as high-content screening because a multiple of the information normally available is collected. Wells that “light up†are examined more closely, for example by purifying mixtures or plating components individually.
The pharmaceutical connection
Parallel screening methods have been used for decades in the pharmaceutical industry. The advent of automated plate-handling and reading instrumentation, and the replacement of radiolabeling assays with luminescence- and fluorescence-based screens, created the opportunity for the several-hundredfold improvement in throughput represented by uHTS. Original equipment was expensive, but over the past decade instrumentation prices have fallen in terms of cost per assay per day, to the point where uHTS is now accessible to small drug discovery firms and academic groups. Numerous service providers also conduct uHTS services for organizations that lack this capability or whose own systems are overcommitted.
Wei Zheng, Ph.D., a group leader at the NIH Chemical Genomics Center (Rockville, Md.) learned the HTS and uHTS trades while screening drug candidates at Merck and Amgen. One of the instruments in use at the NIH Center is a plate-handling robotic system, codeveloped by Zheng at Merck, that processes hundreds of thousands of wells per day and has 1,536-well capability. “It runs between half a million and a million screens per day, depending on the assay,†Zheng told Lab Manager Magazine. The system uses plate readers from PerkinElmer and GE, and core robotics from Kalypsys Systems.
Zheng’s group uses 1,536-well plates almost exclusively, as do most pharmaceutical labs. “Miniaturization saves time and enables higher throughput at reduced cost,†he notes. However, minuscule assay volumes sometimes create difficulties for cell-based assays. “It’s often difficult to deliver the number of cells you need for an assay at such low volumes. In these circumstances the screens cannot be run at 1,536-well density.â€
Recently, researchers from the Chemical Genomics Center, in collaboration with scientists at Trinity College (Dublin, Ireland) reported on a screen of 17,143 FDA-approved and experimental drugs. The biological target in this case was a panel of human liver enzymes that metabolize drugs, and hence are critical to a medicine’s effectiveness.
uHTS received a bad reputation around the beginning of the decade, based on a perceived low success rate in identifying new drugs. The fault, says Zheng, was not with uHTS methods but with the drug companies’ choice of screening targets.
Simon Sheard agrees. “We hear comments about the failure of the ‘law of big numbers’ regularly. That’s a generalization, and the approach of cranking the handle faster has not completely fallen out of use. Nevertheless, what we have seen during the last few years is a shift away from uHTS to automated screening of smaller compound sets through assays that provide more information per well, or higher-quality data.â€
HTS and uHTS systems don’t differ much in terms of instrumentation. What changes is the trend towards modularity. “Both systems employ a collection of instruments linked by software and robotics,†Sheard observes. As assay strategies become more sophisticated and screens more numerous, the number of components increases. uHTS is greatly facilitated, for example, by dedicated compound management systems that store compounds directly in readyto- test plates. At some point, Sheard notes, “It may not be sensible to have a single robot feeding plates to numerous instruments.†And all this added functionality necessitates software products that tie everything together seamlessly.
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Focus on collagen: in vitro systems to study fibrogenesis and antifibrosis — state of the art
Last Updated on Wednesday, 5 May 2010 10:25 Written by Editor Wednesday, 5 May 2010 10:25
Fibrosis represents a major global disease burden, yet a potent antifibrotic compound is still not in sight. Part of the explanation for this situation is the difficulties that both academic laboratories and research and development departments in the pharmaceutical industry have been facing in re-enacting the fibrotic process in vitro for screening procedures prior to animal testing.
Effective in vitro characterization of antifibrotic compounds has been hampered by cell culture settings that are lacking crucial cofactors or are not holistic representations of the biosynthetic and depositional pathway leading to the formation of an insoluble pericellular collagen matrix. In order to appreciate the task which in vitro screening of antifibrotics is up against, we will first review the fibrotic process by categorizing it into events that are upstream of collagen biosynthesis and the actual biosynthetic and depositional cascade of collagen I.
We point out oversights such as the omission of vitamin C, a vital cofactor for the production of stable procollagen molecules, as well as the little known in vitro tardy procollagen processing by collagen C-proteinase/BMP-1, another reason for minimal collagen deposition in cell culture. We review current methods of cell culture and collagen quantitation vis-a-vis the high content options and requirements for normalization against cell number for meaningful data retrieval.
Only when collagen has formed a fibrillar matrix that becomes cross-linked, invested with ligands, and can be remodelled and resorbed, the complete picture of fibrogenesis can be reflected in vitro. We show here how this can be achieved.
A well thought-out in vitro fibrogenesis system represents the missing link between brute force chemical library screens and rational animal experimentation, thus providing both cost-effectiveness and streamlined procedures towards the development of better antifibrotic drugs.
Author: Clarice ChenMichael Raghunath
Credits/Source: Fibrogenesis &Tissue Repair 2009, 2:7
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Enzyme binds both sides of the mirror
Last Updated on Monday, 28 December 2009 11:30 Written by Editor Monday, 28 December 2009 11:30
European chemists have discovered that both mirror-image forms of a particular compound can bind at the same time in the same site of an enzyme, a phenomenon that has never been seen before. The finding has significance for drug discovery screening and studies of how small molecules interact with proteins.
Rolf Breinbauer from Graz University of Technology, Austria, and Wulf Blankenfeldt from the Max Planck Institute of Molecular Physiology in Dortmund, Germany, were studying a metabolic enzyme from a species of the bacterium Burkholderia cepacia, using racemic mixtures of chiral probe molecules to find ones that bound in the enzyme’s active site. In most cases only one form of a chiral (or ‘handed’) molecule would bind at once, but they found that in one instance both enantiomeric forms occupied the binding site at the same time.
‘If you read the textbooks about enantiomers,’ says Breinbauer, ‘there’s a simplified notion that one enantiomer is good and the other is either bad or just idle.’ He explains that for most proteins (apart from certain enzymes that have evolved to cope with wide ranges of substrate molecules) either only one enantiomer will bind, or both can bind individually - with the assumption that one form will be significantly more active than the other. ‘Our findings show that the world is more complicated,’ he adds.
While each individual enantiomer can bind to the enzyme seperately, Breinbauer notes that the arrangement of the molecules within the binding site is quite different when both bind together. This could lead to cooperative effects, producing either an enhanced or diminished response relative to the individual enantiomers.
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The three ways enantiomers can bind in enzymes: only one enantiomer binds (top); each binds individually (middle); both bind together (bottom)
© Angewandte Chemie
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He adds that this could have relevance in drug discovery screening, where mixtures of both enantiomers of chiral compounds are routinely screened together to find initial hits. ‘People need to consider more options when interpreting binding data from racemic mixtures.’
Dafydd Owen of Pfizer Research Chemistry in Sandwich, UK, agrees that the finding is an important reminder that chemists need to be open-minded about interpreting screening data. It also highlights the inherent trade-offs made when screening mixtures - particularly in high-throughput screens when mixtures of several compounds are tested at once.
Owen sees most interest in the discovery in the area of fragment-based drug discovery, where small ‘fragment’ molecules found to bind to a drug target are linked together to make potential drug molecules. ‘As a medicinal chemist,’ he adds, ‘my immediate thought was to join the two structures together to incorporate the best of each and make a hybrid.’ He points out, however, that from a fragment point of view it is almost irrelevant to the enzyme that the two molecules happen to be mirror images of each other, ‘despite their apparent similarity, nature views enantiomers as very different molecules’.
Phillip Broadwith
Source: rsc.org
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