CDD News

Collaborative Drug Discovery, Inc. (CDD) today announced that it has received a grant for $1,896,923 from the Bill & Melinda Gates Foundation to develop a collaborative database that will enable scientists to archive, mine, and selectively collaborate around their research data to discover new cures for tuberculosis (TB). The TB bacillus infects approximately one third of the world’s population and the disease kills over 1.5 million people every year. The CDD TB database will integrate the efforts of academic, other non-profit, and corporate laboratories distributed across the globe and accelerate the discovery of new therapies against this deadly disease.

CDD also announced that it has hired Sean Ekins, PhD, as Director of Collaborations for the project. “The neglected disease research community needs new ways to integrate disjointed drug discovery efforts so that dispersed labs can form efficient virtual pharmaceutical organizations,” said Dr. Ekins. “This project will spark collaborative efforts to discover more effective drugs against TB that are less expensive and easier to administer.”

“This grant promotes our goal of developing more effective medicines for those in developing countries who need them most,” said Ken Duncan, Senior Program Officer at the Gates Foundation. “CDD’s technology will help the entire TB research community to collaborate more easily. We hope it will speed the scientific breakthroughs urgently needed to make effective therapies more accessible to the world’s poorest people, and confront the challenges of multidrug- and extensively drug-resistant TB strains.”

The two-year project will initially involve eight academic research groups and later expand to include other participants. “CDD has already established its software platform as an indispensable tool for many scientists studying neglected infectious diseases including TB,” said Professor Carl Nathan, MD, Chairman, Department of Microbiology and Immunology at Weill Medical College of Cornell University. “This grant from the Gates Foundation will encourage many more researchers to participate in the CDD community.”

“We are thrilled that the Gates Foundation is supporting this project,” said Barry Bunin, PhD, CEO & President of CDD. “Early on, CDD decided to focus on supporting humanitarian as well as commercial drug discovery. This grant validates that decision and provides a model for CDD to work with industry and other foundations targeting additional specific diseases.”

CDD is currently working with the Myelin Repair Foundation (MRF), which has pioneered a research paradigm that organizes diverse academic groups into highly-structured collaborations with a sharp focus on outcomes. “We are delighted to see more organizations and researchers endorse the emerging collaborative model for drug discovery,” said Scott Johnson, President and Founder of the Myelin Repair Foundation (MRF). The MRF and CDD recently partnered to customize CDD’s tools as part of a proof-of concept program to organize data from the MRF’s highly-structured myelin repair scientific collaboration.

About Collaborative Drug Discovery, Inc.

Collaborative Drug Discovery, Inc. (CDD) provides web-based software that organizes preclinical research data to help scientists advance new drug candidates more effectively. The CDD database enables scientists to “archive, mine, and collaborate”® around preclinical chemical and biological drug discovery data through a web-based interface. The software helps distributed research groups to safely store and intelligently analyze small molecule, enzyme, cell and animal bioactivity data accumulated from both low-throughput and high-throughput screens. Scientists can choose which datasets to keep completely private and which datasets, if any, to share securely with selected colleagues. Unique collaboration features and CDD’s community-oriented approach help unite globally dispersed humanitarian efforts against neglected infectious diseases. Similar collaborative strategies are also rapidly gaining prominence in the commercial arena. CDD offers its industrial-strength database software at a price affordable to academic laboratories, research foundations, and small companies. For more information, visit http://www.collaborativedrug.com.

For further information please contact:

Barry Bunin, Ph.D.
President & CEO
Collaborative Drug Discovery (CDD), Inc.
1818 Gilbreth Road, Suite 220
Burlingame, CA 94010
650-204-3084
info@collaborativedrug.com

TimTec LLC., the international distributor of synthetic organic and natural compounds, and Collaborative Drug Discovery, Inc. (CDD), the community based research information management enterprise, announced today that the CDD web-based software now hosts TimTec’s Natural Product Library and Natural Derivatives Library. The TimTec natural product and derivative compounds are now available as a structure searchable database in the CDD Web2.0 collaborative research information system.

Read the rest of this entry »

Collaborative Drug Discovery, Inc. (CDD), in partnership with the NIMH Psychoactive Drug Screening Program (PDSP) directed by Dr. Bryan L. Roth at the University of North Carolina Chapel Hill, announced today that CDD’s web-based software now hosts the largest open-access chemical sub-structure and similarity searchable G-Protein Coupled Receptor (GPCR) Ki database. The PDSP Ki database of 47,312 inhibitor equilibrium dissociation constants (Ki values) for 699 receptor targets is now available as a structure searchable database in the CDD Web 2.0 collaborative research information system.

The PDSP Ki database is a unique resource in the public domain which provides information on the abilities of drugs to interact with an expanding number of molecular targets. The Ki database serves as a data warehouse for published and internally-derived Ki, or affinity, values for a large number of drugs and drug candidates at a growing number of G-protein coupled receptors, ion channels, transporters and enzymes.

“The PDSP Ki database web site, hosted by the University of North Carolina Medical Center, received about 1 million hits in the last year,” said Dr. Bryan Roth, PDSP Project Director and Professor of Pharmacology. This data is now available with chemical structure searching in the CDD system for everyone to view. Adds Dr. Roth, “The CDD Database is an extremely elegant platform. I highly recommend it for anyone generating drug discovery data.”

“It is a privilege to work with Dr. Bryan Roth to provide open access to the PDSP Ki data via the CDD platform,” said Dr. Barry Bunin, President of Collaborative Drug Discovery. “CDD provides the PDSP Ki data in a traditional structure/SAR mineable database combined with novel-to-the-world secure, collaborative public and private data integration capabilities. With ~40% of all small molecule drugs acting on GPCR targets, this will help the research community develop new drugs and better predict potential drug off target related side effects and likely drug-drug interferences.”

The PDSP Ki database joins 12 other publicly available data sources in the CDD system with chemical and biological data for over 40,000 compounds including:

• 1,700 FDA approved drugs with indications and sponsors
• Over 15,000 compounds with Malaria assay data from 5 public data sources
• More than 850 compounds with Tuberculosis antibacterial activity information
• A data set of almost 3,500 Natural Products and Derivatives
• 25,000+ compounds available for purchase

About the NIMH Psychoactive Drug Screening Program

The NIMH Psychoactive Drug Screening Program (PDSP) - http://pdsp.med.unc.edu - provides screening of novel psychoactive compounds for pharmacological and functional activity at cloned human or rodent CNS receptors, channels, and transporters as a contractor to National Institute of Mental Health (NIMH). Screening of compounds is provided to qualified academic investigators at no cost using assays for a large number of cloned human or rodent cDNAs for CNS receptors, channels and transporters, as well as functional assays to determine effects on second messenger systems, channel activity and transporter function. Ki values are calculated and registered to the PDSP database. Cloned receptors are also available at no cost to qualified investigators. For a list of current receptors/transporters go to http://pdsp.med.unc.edu/pdspw/clones.php.

For further information please contact:

Barry Bunin, PhD
President & CEO
Collaborative Drug Discovery (CDD)
1818 Gilbreth Road, Suite 220
Burlingame, CA 94010
Phone: 650-204-3084
info@collaborativedrug.com

Bryan Roth, M.D., Ph.D.
University of North Carolina Chapel Hill
Department of Pharmacology School of Medicine
CB 7365, 8032 Burnett-Womack Building
Chapel Hill, NC 27599
Phone: 919-966-7535
Fax: 919-843-5788
bryan_roth@med.unc.edu

The partnership provides InnoCentive Solvers with software needed to analyze and develop more effective solutions to scientific Challenges. For more details, please download the press release (PDF).

Collaborative Drug Discovery, Inc. (CDD) announced today that its web-based software, which organizes preclinical research data to help scientists advance new drug candidates, has been selected by the Myelin Repair Foundation (MRF) to enable the foundation’s sponsored researchers to collaborate more effectively.

MRF’s Accelerated Research Collaboration™ (ARC™) model creates a unique partnership between academic researchers, scientific and drug discovery advisors and a centralized management team to define and execute on an integrated research plan that will reduce the time to market for a wide range of patient treatments. Focused exclusively at this time on identifying myelin repair drug targets that will lead to treatments for multiple sclerosis by 2009, MRF provides the business infrastructure for a team of some 30 scientists, working together virtually, from different university laboratories in the U.S. By following best business practices, working on a common research plan, sharing their findings in real time, and piggybacking experiments that might otherwise have taken years to accomplish, the scientists have been able to considerably accelerate their research.

CDD enables scientists to collaborate easily across institutional and disciplinary boundaries and empowers new cooperative research strategies, such as MRF’s innovative ARC model. The database features the ability to share data with a spectrum of permissions—either selectively with just a few specific colleagues, openly with the entire scientific community, or not at all. This flexibility encourages data sharing where appropriate while protecting intellectual property, so promising approaches can be patented and commercialized.

The software excels at capturing and organizing fragmented data that would otherwise remain dispersed across multiple laboratories. Foundations can easily set-up and manage collaborations involving multiple research groups located anywhere in the world and spanning multiple scientific disciplines. The central database maintains research continuity as participants change and ensures continued access to the results of sponsored research. CDD manages all the infrastructure and presents data to researchers through an intuitive web interface; contextually-aware hyperlinks steer scientists where they need to go without requiring them to master complex tools.

“By working together with CDD, we can fully exploit the value of the preclinical research data generated by our sponsored researchers and advance promising new therapies for multiple sclerosis more rapidly into clinical trials,” said MRF Chief Operating Officer Rusty Bromley. “CDD’s software perfectly complements MRF’s Accelerated Research Collaboration model which relies on multiple groups located throughout the country, each focusing on different aspects of the overall research challenge. Each group contributes different types of data to the collaboration depending on its distinct scientific specialty. CDD’s software integrates these efforts, so a virtual network of academic laboratories can drive toward developing new therapies with a degree of focus historically unavailable in academic laboratories.”

In addition to making its existing capabilities available to all MRF researchers, CDD will extend the software’s range to include target validation and customize the interface for MRF’s researchers. “We are delighted to enter into this partnership with MRF,” said CDD Founder and President Barry Bunin. “MRF has pioneered a research paradigm that organizes diverse academic groups into highly-structured collaborations with a sharp focus on outcomes. CDD’s software was designed specifically to encourage and support this type of research model, so we believe our database will significantly accelerate MRF’s efforts.”

MRF and CDD will also work together to help other disease research organizations realize the full potential of collaborative research. “While MRF is specifically focused on speeding myelin repair discoveries that will lead to treatments for multiple sclerosis, we believe that our ARC model has implications for research more broadly,” said Bromley. “Part of our mission is to enable others to reap the benefits of the ARC model for preclinical drug discovery R&D. A successful partnership with CDD will offer proof of concept to others seeking collaboration tools for similar research efforts.”

Also see other reports about CDD’s partnership with the MRF:

1. Biotech Transfer Week - “Myelin Repair Foundation Taps CDD Software To Support ‘Accelerated’ Academic Research”
2. Drug Discovery News - “One platform for MS research”

About Collaborative Drug Discovery, Inc.
Collaborative Drug Discovery, Inc. (CDD) - http://www.collaborativedrug.com - provides web-based software that organizes preclinical research data to help scientists advance new drug candidates more effectively. The CDD database enables scientists to “archive, mine, and collaborate”® around preclinical chemical and biological drug discovery data through a web-based interface. The software helps distributed research groups to safely store and intelligently analyze small molecule, enzyme, cell and animal bioactivity data accumulated from both low-throughput and high-throughput screens. Unique collaboration features and CDD’s community-oriented approach help unite globally dispersed humanitarian efforts against neglected infectious diseases. Similar collaborative strategies are also rapidly gaining prominence in the commercial arena. CDD offers its industrial-strength database software at a price affordable to academic laboratories, research foundations, and small companies.

About the Myelin Repair Foundation
The Myelin Repair Foundation (MRF) - http://www.myelinrepair.org - is a Northern California-based, not-for-profit research foundation created to provide a collaborative environment in which leading research scientists at multiple universities, and experienced business executives, can work together to execute a five-year research plan – with milestones, parallel experiments, collaboration, and, most important, a constant focus on developing effective treatments for multiple sclerosis. Many believe MRF’s Accelerated Research Collaboration model could change the way in which all medical research is conducted.

About Multiple Sclerosis (MS) and Myelin Repair
MS is a degenerative disease of the central nervous system that affects more than 2.5 million people worldwide. The destruction of myelin, the protective coating surrounding the nerve fibers of the brain and spinal cord, and the body’s inability to repair it, results in various types of disabilities including motor, sensory, cognitive and vision. By combining their research efforts, MRF scientists expect to develop viable treatment targets that restore the body’s natural ability to repair myelin, reversing the effects of MS.

ASINEX and Collaborative Drug Discovery (CDD), Inc. have formed a collaboration showcasing ASINEX high value compound libraries via the CDD Community Database. The first high value set offered is the ASINEX Lead Generation Library with additional libraries to follow. ASINEX and CDD have created special screening sets tailored to the specific needs of (and now available via the CDD Database to any) academic researchers. The combined information is being made available to the general public via CDD for the first time at https://www.collaborativedrug.com/register.

Mark Parisi, the Executive Director at ASINEX stated, “CDD has an impressive group of collaborators and ASINEX looks forward to helping this group with its early drug discovery efforts.”

Barry Bunin, the President of CDD commented, “This begins a qualitatively different phase of the CDD platform by bringing quality industry products and services to the growing community — and vice-versa.”

Every compound uploaded from ASINEX can be viewed within the context of your own private, secure data for scaffold jumping via substructure or Tanimoto similarity search within the merged data for lead identification and optimization. The main premise is for new screens, fewer compounds of higher quality are often required. This means more different scaffolds with fewer compounds per scaffold for greater coverage of novel chemical space (novel IP) without creating compounds so lipophilic that they violate the more traditional rule of 5 (which ASINEX has further refined to a rule of 4.5).

CDD has included other complementary data sets including a list of FDA/Ophran approved drugs courtesy of Dr. Christopher Lipinski, a set of known aggregators likely to cause false positives courtesy of Dr. Brian Shoichet, a set of toxicity profiles on known compounds courtesy of Dr. Sean Ekins, and numerous sets of Malaria and Tuberculosis SAR data which can now be compared with commercial compounds from ASINEX in personal, secure private groups.

From a purely economical perspective, a strong argument can be made that it makes sense to screen fewer, high-quality compounds resulting in higher quality leads at lower overall cost. ASINEX has a strong reputation for quality, especially in Europe. This collaboration with CDD will help bring awareness of these compounds to academic laboratories and smaller startup companies who require a more cost-effective mechanism for collaborative drug discovery.

About ASINEX: With more than a fourteen year history, ASINEX is a world leader in supplying compound libraries, focused libraries, custom libraries, and building blocks for early drug discovery. ASINEX also has a growing list of partners who have decided to utilize its computational, custom synthesis, and biology services for lead optimization projects. The company has a total of 151 chemists (54 Ph.D.), 9 computational chemists (7 Ph.D.) and 38 biologists / biochemists (24 Ph.D.). For more info please contact:

ASINEX Corporation
Mark Parisi
Executive Director
Toll Free Tel.: 1-877-ASINEX1 (1-877-274-6391)
Email: MParisi@asinex.com

About CDD: CDD is the world’s first platform for selectively sharing collaborative drug discovery data. Scientists working with the CDD community platform can pool their research in order to more effectively develop new drug candidates for commercial and humanitarian markets. Conceived in 2003, and formally launched in 2004, Collaborative Drug Discovery (CDD) has been serving the collaborative data needs of researchers for years. The CDD global community includes hundreds of scientists from leading research foundations, academia and industry. A subset of the data is available openly to the public at no cost. For more information, please visit http://www.collaborativedrug.com or contact:

Collaborative Drug Discovery, Inc. (CDD, Inc.)
Barry Bunin, PhD
President
info@collaborativedrug.com
Tel: (650) 204-3084

Drug Discovery news has published an article on CDD’s work with the St. Jude Children’s Research Hospital. From the article:

A collaboration to identify and develop drugs for resistant strains of malaria draws on an unusual combination of resources: U.S. Army research from 1946 plus 21st century informatics and lab technology.

The joint work on malaria began about two years ago between Collaborative Drug Discovery Inc., (CDD) and the Department of Chemical Biology and Therapeutics at St. Jude Children’s Research Hospital. CDD created a database of over 12,000 molecules from the 61-year-old, two-volume “A Survey of Malaria Drugs,” edited by Frederick Y. Wiselogle.

Read the entire article here.

CDD updated our core database software today with the initial release of our collaboration technology and a number of security updates. Some of the highlights of the release:

• Community data, including the list of FDA approved drug structures, is now available to all user.
• Over 27 separate security enhancement to make sure that your data is more secure.
• New collaboration technology allows you to share data across all group, if so desired.

To try out the application, please register now for a free trial account.

Collaborative Drug Discovery has captured extensive literature data from six years of recent publications focused on the fight against Chagas’ disease. Now, for the first time, these data are available to researchers free of charge, via the CDD Database.

Sources include the Journal of Medicinal Chemistry, Bioorganic & Medicinal Chemistry, the Journal of American Chemical Society, Journal of Ethnopharmacology, Proceedings of the National Academy of Sciences (PNAS), International Journal of Antimicrobial Agents, Bioorganic & Medicinal Chemistry Letters, European Journal of Medicinal Chemistry, Molecular and Biochemical Parasitology, Journal of Inorganic Biochemistry, Acta Topical,
and Experimental Parasitology.

The data sets captured include 574 compound structures and just over 350 different enzyme, cell, animal, and toxicity based protocols. The data are conveniently organized so scientists can easily mine for hits, sub-structural motifs or keywords and obtain the original literature reference for more detailed analysis.

These data sets will help researchers better prioritize compounds to test experimentally and
build superior models to guide experiments.

This project is the first of a series literature data capture projects focused on drug discovery research into neglected infectious diseases. In addition to literature data, community members also provide open access to some of their experimental results either pre- or post-publication. The CDD global community includes leading researchers from four continents.

To access this data set, please register for a free account.

Collaborative Drug Discovery, Inc. (CDD, Inc.) and St. Jude Children’s Research Hospital have joined together for a project aimed at speeding the development of new drugs to overcome resistant strains of malaria.

The collaboration combines the malaria drug data and informatics technology of CDD with the drug discovery expertise of the St. Jude Department of Chemical Biology and Therapeutics. Informatics is the use of computer hardware and software to extract and manage knowledge from large databases.

“CDD’s databases will probably help us reduce the number of potential molecules we’ll need to analyze from tens of millions down to hundreds of thousands,” said Kip Guy, Ph.D., chair of the St. Jude Department of Chemical Biology and Therapeutics. “Our own screening capability will significantly reduce that to a much smaller number of promising compounds.
This will be a widely used database. We are already making the data freely available through CDD so that other researchers can use different analytical strategies to identify potential new anti-malarial drugs.”

The collaboration is designed to help scientists quickly screen millions of chemicals, based on their structure and their chemical and biological properties, to find those that are most likely to make effective anti-malaria drugs. The key to this quest to find the drug “needle in the haystack” is the enormous two-volume collection of data from studies on malarial drugs published by the U.S. Army in 1946.

This 61-year-old publication, “A Survey of Malaria Drugs,” was originally edited by Frederick Y. Wiselogle and had contributions from a number of leading researchers of the time. The two-volume set was designed to help researchers develop effective anti-malarial drugs; and to serve as a model for how scientists could develop drugs for other infections,
according to the authors of that publication. The collection presents the structures of many compounds and the results of studies on their biochemical activity in animals, data on how they work in the body, how long they last, and other pharmacological data, in addition to their level of toxicity. The results of the animal studies represent one of the largest sets of published data on the structure-activity relationship (SAR) of molecules against a single disease, Guy said. SAR refers to the link between a molecule’s specific structure and the biological effect it has because of that structure.

CDD scanned the information from the original publication into a computer database and organized it into a format that can be read, searched and shared. This more convenient format will enable St. Jude scientists to use the information to develop models of new anti-malaria drugs and predict their efficacy, toxicity, and how the body will respond to them.

Based on such models, St. Jude researchers are conducting a comprehensive analysis of “relevant chemical space” of these molecules, something that has never before been done for malarial drug research, Guy said. Relevant chemical space refers to the study of individual families of molecules whose members all share a similar structure that holds promise for a
specific therapeutic use. Concentrating on only certain families of molecules likely to have the desired effect saves time and speeds the discovery of the few molecules most likely to have all the characteristics needed for an effective anti-malaria drug, he said.

The anti-malarial drug study is the first of several planned by CDD to help the research community discover drugs for orphan infectious diseases—disorders for which there is little commercial interest in developing drugs. Future CDD communities are planned in other more commercial areas, such as cancer research and selected gene families.

To access this historical set of Malaria Animal SAR data for the first time, either visit http://www.collaborativedrug.com/register or e-mail info@collaborativedrug.com for the username and password to the open data sets.

About Collaborative Drug Discovery: CDD is the world’s first platform for selectively sharing collaborative drug discovery data. Scientists working with the CDD community platform can pool their research in order to more effectively develop new drug candidates for commercial and humanitarian markets. Conceived in 2003, and formally launched in 2004,
Collaborative Drug Discovery (CDD) has been serving the collaborative data needs of researchers for years. The CDD global community includes hundreds of scientists from leading research foundations, academia and industry. A subset of the data is available openly to the public at no cost.

About St. Jude Children’s Research Hospital
St. Jude Children’s Research Hospital is internationally recognized for its pioneering work in finding cures and saving children with cancer and other catastrophic diseases. Founded by late entertainer Danny Thomas and based in Memphis, Tenn., St. Jude freely shares its discoveries with scientific and medical communities around the world. No family ever pays for treatments not covered by insurance, and families without insurance are never asked to pay. St. Jude is
financially supported by ALSAC, its fundraising organization. For more information, please visit www.stjude.org.