Archive for the ‘HT Screening’ Category
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.
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.
All product and service names mentioned are the trademarks of their respective companies.
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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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High-Content Screening Surges Ahead
Last Updated on Tuesday, 1 December 2009 11:33 Written by Editor Tuesday, 1 December 2009 11:33
High-content screening (HCS) and the technology to do it faster, on more compounds in a shorter period of time, and to generate quantitative, multiparametric data took center stage at CHI’s “High Content East†meeting held in Boston last month. Presenters described how they are implementing enhanced screening systems, image-analysis methods, and data-management strategies to achieve daily HCS runs on tens of thousands of wells and screening campaigns totaling 200,000 to 3 million wells.
High throughput HCS—albeit not yet reaching the numbers common for conventional high-throughput screening (HTS) and with lingering limitations and challenges related to live-cell imaging over time—is making its mark and being used to probe the biological basis of disease and to detect even subtle phenotypic changes in response to experimental compounds.
Determining whether a cell looks like a cancer cell, for example, typically requires being able to detect subtle morphological changes, such as small alterations in size or structure, changes in the connections a cell makes with neighboring cells, or variations in the texture of staining. These have, historically, been mainly qualitative parameters detected by studying and comparing images of cells.
In her talk at the conference, Anne Carpenter, Ph.D., director of the imaging platform at the Broad Institute of Harvard University and MIT, presented her group’s work using HCS and image analysis to quantify difficult phenotypes and differentiate disease states such as leukemia.
Not only do HCS systems and image-analysis software automate the screening process, enabling theanalysis of many more cells in less time and increasing the chances of detecting even small numbers of altered cells, they can also utilize algorithms that evaluate defined combinations of parameters in a quantifiable manner and apply techniques to distinguish between clumping or closely juxtaposed cells. Relying on computer-based image analysis also standardizes the process, eliminating factors such as variability in human expertise and experience, consistency, and fatigue.
Dr. Carpenter’s group uses machine-learning methods to train image-analysis software to identify subtle phenotypic changes. Biologists work with the software in an iterative fashion in a process called supervised machine learning. They teach and correct the computers on a series of test images, refining the system’s knowledge base in a process that typically takes less than a day. The group developed the algorithms used by the biologists and has made them available as open-source software.
A recent paper published in PNAS by T. R. Jones, et al., documents the use of a trained image-analysis system to discriminate 15 different cellular phenotypes. Other projects involve teaching the software to discriminate leukemic from normal cells, to identify liver cells that are growing normally in culture—to aid in the development of physiologic models of liver function for use in drug testing—and training computers to detect subtle changes that signal the initiation of cell division for studying cell-cycle regulation in cancer.
Neil Carragher, Ph.D., senior scientist in the advanced science and technology laboratory at AstraZeneca, described how the company is applying high-content and live-cell imaging techniques and integrating the results with data derived from in vivo imaging and proteomic studies to improve clinical predictability.
Dr. Carragher’s group combines the results of high-content in vitro and in vivo assays to generate mechanistic information about phenotypic responses on candidate therapeutic compounds. The goal is to create a multiparametric fingerprint of a phenotype from images generated by HCS and to use this knowledge to enhance predictions of efficacy and toxicity early in drug discovery and reduce attrition later in development.
The phenotypic signatures are based on measurements of approximately 150 different parameters per cell for each assay. Data from multiple assays is collated for every test compound and compared with data obtained using well-characterized reference compounds to generate mechanistic hypotheses.
Only recently has open-source and commercial software become available “that allows you to quantitate more complex phenotypes, subtle changes, and heterogeneous responses from images,†Dr. Carragher said.
His group is employing two main approaches—each with different advantages and limitations. The first strategy relies on Definiens’ Cognition Network Technology™ software that allows users to develop algorithms that capture, computationally, what researchers can see visually. “It is very much context-based†and identifies objects based on how they are related to others in the image, rather than as individual pixels, explained Dr. Carragher. The in-house algorithm-development process depends on iterative programming steps. The other approach involves machine-learning tools using software such as the CellProfiler developed at the Broad Institute.
Redirecting Approved Drugs
| Identifying new applications for FDA-approved drugs using HCS and image-based systems biology is the focus of work being done by Stephen Wong, Ph.D., founding director of the bioinformatics and biomedical engineering program and the cellular and tissue microscopy core at the Methodist Hospital Research Institute and professor of radiology and neurosciences at Weill Cornell Medical College.
Dr. Wong gave examples of screening campaigns to decipher targets in the pathways responsible for the metastasis of breast cancer to the brain in his talk. He specifically described the computational tools his group is developing for high-content and network analysis, and the animal-imaging techniques being used to evaluate combinations of small molecule chemotherapeutic agents for their ability to cross the blood-brain barrier and to have an effect against central nervous system metastases in breast cancer. Dr. Wong’s group has also developed a series of quantitative image-analysis tools, including zebrafish image quantifier (ZFIQ), as well as software for studying neuronal spines (NeuronIQ), neurites (Neurite IQ), and time-lapse mitotic events in cells (DCellIQ). Dr. Wong’s HCS/systems biology research is funded by the NCI, NIA, and NLM. Because the compounds being studied are already approved drugs, Phase I trials are not needed. The quantitative data generated from HCS provides the evidence necessary for moving into Phase II studies, shortening the drug-development cycle to a year or less. The types of studies essential to Dr. Wong’s efforts, such as assays to monitor cell-cycle regulation or dendritic spine dynamics, require time-lapse, live-cell imaging. Looking at fixed cells provides only an artificial snapshot of where cells are at a particular point in time, explained Dr. Wong. “We want to look at a 384-well plate of continuously growing cells over five to six days,†he said, and in his view none of the instrument manufacturers competing in the HCS market has yet to provide a robust, incubator-based, environmentally controlled system that can achieve this. Vendors have tended to view HCS as just another type of high-throughput screening, but live-cell imaging done in as natural an environment as possible has quite different requirements, contended Dr. Wong. “Vendors are going in the wrong direction. The power of HCS is in the ability to visualize things in action and to extract lots more quantitative information from the images. If you, instead, retrofit HCS to HTS, you are losing its advantages,†such as the ability to see cells or spines change over time, to visualize cell-cell interactions, and to sync cell populations and study cell-cycle events in time-lapse, said Dr. Wong. In any experiment, “if you generate enough data you will get hits, but how many will be real hits versus false positives?†asked Dr. Wong. “We need to push the quality upfront on the biology side†and screen out, earlier in the discovery process, compounds that are destined to fail. Researchers at Pfizer are using HCS to study the genetic variation and physiologic interactions that underlie hepatic insulin resistance in type 2 diabetes and the prediabetic state. Diabetes is a complex, multigenic disease, and while advances in genomic and SNP-based technologies have led to the identification of at least 30 genes that contribute to the diabetic phenotype, much work remains to understand their role in cell biology and disease and how they interact. “If you are careful about the cell models you choose, you can use HCS to characterize these genes and monitor their effects on biochemical pathways,†said Steven Haney, Ph.D., associate fellow in biological profiling at Pfizer’s biotherapeutics and bioinnovation center. The company has invested heavily in developing cell models that are representative of human physiology, including hepatocytes that faithfully mimic liver function when grown in culture. The other main aspect of this research effort involves identifying changes that affect the diabetic phenotype, specifically glucose storage and utilization pathways, and distinguishing between effects that involve the insulin-signaling pathway from more general phenomena related to activation of toxicologic or stress pathways. “HCS can alert us to things we don’t necessarily know to look for, in a mechanism-independent way,†said Dr. Haney. “The increasing throughput of HCS allows us to look at a lot of cells and determine whether subtle phenotypic changes are significant or spurious.†Vendors Roll Out Image-Analysis SolutionsVersatility across application areas, from microscope-based imaging for detecting intracellular phenomena to high-speed scans at the cellular level to whole organism screening, is the focal point of instrument development at MDS Analytical Technologies. “With the options in our Complete Solution and the right infrastructure, you can use image-based assays for primary screening. We have tackled all the common bottlenecks,†said Michael Sjaastad, Ph.D., director of marketing for cellular imaging at MDS. The IsoCyte® DL laser-scanning cytometer complements the company’s ImageXpress® instrument platform as part of its overall HCS solution. MDS offers a high-throughput option that can screen and do image analysis on a 1,536-well plate in two to five minutes, according to Dr. Sjaastad. The instrument can image whole wells for accurate cell counting in cell-viability measurements, scan a microscope slide, or produce and analyze images of organisms such as zebrafish or worms when used in conjunction with the MetaXpress image-analysis software. For now, current systems “have the image resolution and acquisition speed researchers need,†and in Dr. Sjaastad’s view, future improvements will focus on “streamlining the data-analysis workflow and bringing the costs down per data point.†In a workshop at the meeting, Oliver Leven, Ph.D., head of screener professional services at Genedata, identified several ongoing challenges in HCS, including managing the volume and complexity of the data, improving the efficiency of data analysis, and creating an audit trail of results interpretation. As the throughput and scale of HCS increases, so too, do the difficulty and scope of these challenges. As researchers scale up an assay for high-throughput HCS, they need to select a defined set of parameters that represent the phenotype of interest and that allow them to assess the quality of both the assay and the data output. They also need to identify threshold values above or below which a result signifies a change in phenotype. The typical HCS image-analysis software that drives HCS systems routinely quantifies the cell images to yield a numerical description of the phenotypes. For large experiments, however, Dr. Leven described the researcher’s need to go back and view an image associated with an interesting or suspicious measurement as a persistent bottleneck. “The image is the experiment,†said Dr. Leven. A hit should signify a change in the cells, but it could also be an anecdotal finding or the result of an image out of focus. Distinguishing true hits from false positive results remains a challenge. Dr. Leven recounted the HCS projects that Genedata has performed for its pharma customers emphasizing the ability of the company’s High Content Analyzer—a new addition to the Genedata Screener® enterprise solution—to retrieve immediately any desired image. The high-throughput HCS projects described by Dr. Leven were able to analyze 40,000 compounds on a daily basis, for a total campaign of more than two million compounds, generating multifeatured data sets for each well. PerkinElmer’s high-content screening portfolio includes the Opera confocal microplate image reader and Acapellaâ„¢ image-analysis software, the compact Operetta HCS system, driven by Harmonyâ„¢ software, and the Columbusâ„¢ data-management system and new Columbus 2.0 for use with the Opera platform. Gabriele Gradl, Ph.D., global product leader for HCS at PerkinElmer Cellular Technologies, emphasized the complexity involved in deriving robust, quantitative data from cellular measurements derived on image analysis of high-content screens. Whereas, fluorescence-based analysis typically relies on identifying objects in cells and measuring their fluorescence intensities, PerkinElmer has developed a computational strategy that is independent of absolute fluorescence intensity. It relies on texture analysis and quantitative pattern analysis for data generation. Texture-analysis tools can detect patterns and effects that would not be apparent on routine visual analysis, according to Dr. Gradl. Threshold adjacency statistics is one example of such a tool. It searches for differences in fluorescence intensity values between adjacent pixels over a defined distance. Dr. Gradl described the particular advantages of applying texture analysis for detecting subtle morphologic changes associated with cell viability or toxicity assays and in stem cell research. It can detect differences not visible to the eye and identify changes that the user might not even have known to look for in the data. She presented, as an example, the use of texture analysis to assess mitochondrial integrity, as loss of mitochondrial activity and enhanced mitochondrial biogenesis are early markers of cytotoxicity. Dr. Gradl also described the use of texture analysis in brightfield imaging and the ability to assess segmentation based on granularity, enabling label-free proliferation assays and analysis of cell differentiation in real time. The algorithms developed by PerkinElmer can apply texture analysis to whole cells or to specific intracellular compartments depending on the design of the assay. The company is exploring a range of applications for its texture-analysis software tools, including stem cell differentiation analysis, quality control of stem cells produced for therapeutic use, live-cell imaging over time, and 3-D tissue sample analysis. Earlier this year, GE Healthcare introduced the IN Cell Analyzer 2000 cell-imaging system, which incorporates several new features: preview scoring of a selected area of a sample before an acquisition run; a large chip CCD camera coupled with a widefield illumination source for twice the brightness of a conventional xenon lamp, according to GE; whole-well imaging; an objectives range from 2x–100x; six imaging restoration modes; and a manual microscope mode. Fred Koller, Ph.D., president and CEO of Cyntellect, launched the company’s new Celigoâ„¢ cytometer at the “High Content East†meeting, emphasizing the system’s ability to image “every cell in every well,â€Â from edge to edge without edge effects using both brightfield and fluorescence imaging. Cyntellect’s optical technology achieves high-quality large field imaging using a set of mirrors to capture each well in its entirety without moving the plate and without the need to refocus, allowing for rapid, full-plate imaging. Celigo provides “uniform illumination with no gradient across the well,†said Dr. Koller, and allows for a combination of label-free imaging and three-color fluorescence. He described the instrument’s capabilities for performing cell-counting assays, cell growth tracking, and confluency studies, for example, and for noninvasive imaging of stem cell cultures without disrupting their three-dimensional colony structures. Celigo can switch from single-cell to colony-counting mode. The company has also developed a secretion assay for use on the Celigo that measures the amount of protein secreted by individual cells. The assay can distinguish between high and low secretors and is useful for detecting heterogeneity and instability in cell cultures early in process development, such as for antibody manufacturing. The Cellular Imaging and Analysis group at Thermo Fisher Scientific introduced the Cellomics iDevâ„¢ intelligent assay development workflow for HCS image analysis at “High Content Eastâ€. Users work training image sets of positive and negative biology, applying imaging and analytical algorithms that allow for real-time interaction with the images. The software employs the biological data generated to optimize assay protocols. Source: genengnews.com |
Posted under Compound Screening, Drug Development, HT Screening, Press Releases, Research Projects | No Comments
Researchers find candidates for new HIV drugs
Last Updated on Tuesday, 1 December 2009 11:26 Written by Editor Tuesday, 1 December 2009 11:26
While studying an HIV protein that plays an essential role in AIDS progression, researchers at the University of Pittsburgh School of Medicine have discovered compounds that show promise as novel treatments for the disease.
HIV drug discovery efforts have met with little success in finding compounds that interact with an important HIV virulence factor, called Nef, because it lacks biochemical activity that can be directly measured, explained Thomas E. Smithgall, Ph.D., William S. McEllroy Professor and Chair, Department of Microbiology and Molecular Genetics, and senior author of the paper, which was published last week in the early, online version of ACS Chemical Biology.
To get around that problem, Dr. Smithgall’s team developed an assay to measure Nef function indirectly by coupling it to another protein, called Hck, which Nef activates in HIV-infected cells. Because Hck activity can be easily measured, the investigators were able to use it as a reporter for Nef activity in an automated high-throughput screening process. In collaboration with the University of Pittsburgh Drug Discovery Institute, they screened a library of 10,000 chemical compounds against the coupled proteins to see which ones influenced Nef-induced activation of Hck.
After further testing, they confirmed that three compounds inhibited the activity of the Nef-Hck complex and, more importantly, all of them also interfered with HIV replication. One compound was so effective that it suppressed HIV replication to undetectable levels in cell culture experiments.
“So we now have a way to rapidly and efficiently screen for inhibitors of Nef signaling through Hck,” Dr. Smithgall said. “But the surprise was that some of those inhibitors also showed strong antiviral activity in cell culture models.”
There is evidence that people infected with HIV variants that have mutations in the Nef gene take substantially longer to develop disease symptoms or AIDS, he said. In animal models, disrupting the production of Nef from the virus or its interaction with Hck also delays or prevents disease symptoms. The next challenge for the researchers will be to determine whether these compounds also interfere with progression of AIDS-like disease in animal models by blocking Nef function.
“Most current therapies for HIV infection use drugs that interfere with the function of viral enzymes such as reverse transcriptase or with the interaction of the virus and the host cell,” Dr. Smithgall said. “Targeting Nef represents an entirely new approach that could be useful to deal with issues such as drug-resistant HIV strains, and may slow the progression to AIDS.”
He added that Nef is just one of several so-called “accessory proteins” encoded by HIV which are important virulence factors in AIDS. Inhibitory compounds against some of the others might be revealed using a similar coupled protein approach for high throughput screening.
Source: labspaces.net
MALDI-Based Method May Reduce Cost of Rx-Screening Assays, Speed Drug Development
Last Updated on Tuesday, 20 October 2009 09:44 Written by Editor Tuesday, 20 October 2009 09:44
This story originally ran on Oct. 6.
By Tony Fong
Researchers from the University of Cincinnati and MDS Analytical Technologies have used mass spectrometry to develop a high-throughput screening method for drug discovery they say can be more precise and cost-effective than existing techniques.
The technique is based on a MALDI triple-quadrupole platform and exploits the selective multiple-reaction monitoring transition features of the platform. By doing so, the new method is able to lower the cost of high-throughput screening for drug compounds to pennies per well from as much as $1 per well currently, Ken Greis, associate professor of cancer and cell biology and director of proteomics and mass spectrometry at the University of Cincinnati College of Medicine, told ProteoMonitor recently.
A study detailing the method was published Sep. 15 in the online edition of Rapid Communications in Mass Spectrometry.
In the paper, Greis and his co-authors said that drug discovery typically begins with a validated target enzyme “with the initial goal of finding appropriate molecular scaffolds with inhibitory activity via high-throughput screening.” The scaffolds are then subsequently used for lead compound optimization, and “ideally for the development of a safe and effective therapeutic compound.”
The most common methods of high-throughput screening have been fluorescence- and chemiluminescence-based approaches. Such approaches, Greis said, have been “very successful” because the same reagents can be used for many different enzymes.
But that same characteristic also creates a risk for interference.
“When one’s evaluating a compound repository for inhibitors, you often have a series of compounds that will fluoresce themselves,” Greis said. “If they fluoresce, they’re going to give you a false signal. Alternatively … there are compounds that inhibit the fluorescent properties, or what’s called quenching fluorescence, [that] also give false read-outs.”
Another problem is in the way the assays get generalized so that the reagents work for a wide range of enzymes. Such assays are called coupled assays: “You have a product being formed from your enzyme reaction but that’s not what actually triggers the fluorescence,” Greis said. “That product gets converted to another enzyme to another product through another enzyme to another product that then can be fluoresced.â€
This series of enzyme step, or coupled assays, ultimately results in a read-out. “The problem is any compound that interferes with any of those steps along the way also gives you false read-outs,” which tend to be false positives, he added.
But by using mass spectrometry to measure enzyme activity, Greis and his colleagues are able to get a direct read-out, “so a mass spectrometer effectively can give you a quantitation and a mass of a compound.”
By taking a ratio of the substrate being converted to a product — the essence of an enzyme assay, Greis said — and measuring that directly on a mass spec, there is no interference either from quenching or auto-fluorescence.
“And what we’ve found thus far is we’ve not seen any false positive read-outs. If we get a compound that shows that it’s active, even in single-point assays, it’s been demonstrated that it’s a dose-dependent inhibitor.”
And because the method uses native peptides or small-molecule substrates, the method can be done for “at most, pennies per sample well,” Greis said. By comparison, fluorescent and chemiluminescence reagents cost between 50 cents to $1 per well.
“So if you run a million compounds, you can run up a half-million dollars of reagents costs right away, whereas the label-free read-out is going to cost you maybe a couple thousand dollars for the reagents,” he said. “That’s a mass spec advantage.”
A prior study by researchers in China had demonstrated the utility of a MALDI-Fourier transform mass spectrometer for high-throughput screening of small-molecule substrate/product conversion.
The researchers chose AChE because of its long history of enzyme assay development, including colorimetric assays, pH-change assays, and most recently aggregation-induced fluorescence assays and mass-spec assays.
Speed is of the Essence
They also chose a MALDI platform, rather than an electrospray platform, because of the higher speed that can be achieved on the MALDI. Most enzymatic reactions contain salts that can interfere with mass spectrometry. An ESI platform requires a desalting step, which limits the throughput to five to 10 seconds per sample. A MALDI-based approach skips the desalting step, however, because the technology is less sensitive to salts.
“Essentially all that we do is run the enzyme reaction on a 384-well format,” Greis said. “We transfer all at once into a matrix plate mix and onto our MALDI target plate.”
Because there are no cleanup steps on the MALDI triple-quad, samples can be scanned at up to three samples per second, he said.
Greis acknowledged that the MALDI technology, especially the MALDI triple-quad, is not a popular tool for drug discovery. In his opinion, that’s because drug-discovery researchers were trained on electrospray mass specs and are comfortable with them.
“To then move them into a MALDI platform that they don’t understand, they’ve got a bias that it can’t be quantitative, and all these sorts of things from earlier studies using MALDI-based approaches that have been demonstrated time and time again to not be true anymore — I think there’s a cultural thing,” he said.
A criticism of a MALDI approach is that while it works well for peptide substrate screening, it doesn’t for small-molecule substrate products because of matrix interference in the low mass range.
“And we show very directly … that by taking advantage of the transition,” a chemical fragmentation that is diagnostic of a substrate or product “that one can do in a triple-quad, that matrix interference completely goes away,” Greis said.
The researchers tested their method by screening a library of 1,008 structurally diverse compounds across 384-well microtiter plates as an example of a single-dose primary screen, and reported that all known AChE inhibitors resulted in complete inhibition of enzyme activity, as expected. The hits were then validated “by demonstrating concentration-dependent inhibition and the rank order of inhibitory potency in hit follow-up assays,” they said in their study.
The technique they’ve developed can also be used on a simple MALDI instrument, though it works best for peptide substrate enzymes. With low molecular-weight enzymes, sensitivity can be an order of magnitude lower on a simple MALDI “because you’d have to be using enough enzyme substrate product to see your substrate products down in those low mass ranges in amongst all of the matrix peaks,” Greis said.
Also, Greis said there will be enzymes — such as fatty acids and long-chain hydrocarbons —that will not be amenable to a MALDI-based approach.
“The fact of the matter is that any mass spectrometry-based technique is only as good as the molecule that it’s trying to evaluate,” he said. “We have to be able to ionize the substrate and/or the product to be able to measure and quantify it.”
In ongoing work, he and his team members are developing multiplex assays. The typical screening approach is to take a target enzyme and pass the whole repository across it to look for inhibitors, and then validate the inhibitors. The next therapeutic target is then set up and the process is repeated.
With a mass spec-based approach, “as long as your enzymes reactions are compatible … you can run multiple enzymes in one pot and pass your repository against it once and get hits for all those different enzymes,” Greis said.
In conferences, Greis and his colleagues have presented proof-of-concept studies that show that “this in fact works quite well using a kinase and acetylcholinesterase or a kinase with a protease all in the same part,” he said. “We’ve shown that we can get selective inhibitors for each of them individually without interference in the multiplex format.”
Source: genomeweb.com
Posted under Compound Screening, HT Screening, Industry News, Press Releases | No Comments
Structure-based substrate screening for an enzyme
Last Updated on Wednesday, 26 August 2009 11:20 Written by Editor Wednesday, 26 August 2009 11:20
Nowadays, more and more novel enzymes can be easily found in the whole enzyme pool with the rapid development of genetic operation. However, experimental work for substrate screening of a new enzyme is laborious, time consuming and costly.
On the other hand, many computational methods have been widely used in lead screening of drug design. Seeing that the ligand-target protein system in drug design and the substrate-enzyme system in enzyme applications share the similar molecular recognition mechanism, we aim to fulfill the goal of substrate screening by in silico means in the present study.
Results: A computer-aided substrate screening (CASS) system which was based on the enzyme structure was designed and employed successfully to help screen substrates of Candida antarctica lipase B (CALB).
In this system, restricted molecular docking which was derived from the mechanism of the enzyme was applied to predict the energetically favorable poses of substrate-enzyme complexes. Thereafter, substrate conformation, distance between the oxygen atom of the alcohol part of the ester (in some compounds, this oxygen atom was replaced by nitrogen atom of the amine part of acid amine or sulfur atom of the thioester) and the hydrogen atom of imidazole of His224, distance between the carbon atom of the carbonyl group of the compound and the oxygen atom of hydroxyl group of Ser105 were used sequentially as the criteria to screen the binding poses.
223 out of 233 compounds were identified correctly for the enzyme by this screening system. Such high accuracy guaranteed the feasibility and reliability of the CASS system.
Conclusions: The idea of computer-aided substrate screening is a creative combination of computational skills and enzymology.
Although the case studied in this paper is tentative, high accuracy of the CASS system sheds light on the field of computer-aided substrate screening.
Author: Tao XuLujia ZhangXuedong WangDongzhi WeiTianbi Li
Credits/Source: BMC Bioinformatics 2009, 10:257
Source: 7thspace.com
GTCbio Announces 4th Annual Assay Development and Screening Conference taking place June 8-9, 2009.
Last Updated on Friday, 27 March 2009 09:40 Written by admin Friday, 27 March 2009 09:40
San Francisco, CA – GTCbio Announces its 4th Annual Assay Development and Screening Conference taking place June 8-9, 2009. As compounds derived from high throughput screening increasingly find their way into clinical trials, drug screening has become widely accepted as a critical step in the drug discovery process. After more than a decade of rapid growth, tremendous progress has been made in assay technology, laboratory automation, and informatics. These technological developments have not only facilitated a drastic increase in throughput and efficiency in drug screening, but have also provided novel solutions in other areas of drug discovery and development. As screening has also become prominent in biological research, screening facilities have become increasingly popular in academic institutions.
As the pharmaceutical industry continues to face the challenges of developing more new chemical entities and reducing the cost of R&D, the demand for novel technologies and creative approaches for improving the efficiency of screening has intensified. Cell-based assays used in compound screening and high-content screening technologies have gained popularity in the industry. Years of intensive research have finally resulted in label-free technologies in the drug screening market place. These technologies provide new ways of interrogating cellular and molecular binding events and enable orthogonal screening approaches to drug targets.
The goal of the 4th annual Assay and Screening Technologies Conference is to provide a forum for academics and professionals in the drug discovery industry to stay abreast of exciting new developments in assay technologies while exchanging ideas and developing more efficient approaches to the drug discovery and development process.
For more information, visit http://gtcbio.com/conferenceDetails.aspx?id=123