CDD News

Last October, Collaborative Drug Discovery (CDD) and TimTec established a collaboration in which CDD’s web-based data management system would host two TimTec Natural Products libraries on their free community Public Access site.  Through this partnership, researchers would be able to register for a free account with CDD allowing them to chemically mine the contents of these TimTec compound libraries using CDD’s powerful, intuitive web-based database software.

TimTec has now published three additional compound collections distinct in screening approach and design for CDD research community access: 1) Diversity Set, screening library of 10,000 cmpds, 2) ActiTarg-K, Kinase Modulators Library of over 6,000 cmpds, and 3) OTG-Inhibitors Analogs SET, 300 cmpds. Total number of TimTec molecules is now about 20,000 including previously published two collections of Natural Products.

Resourceful Diversity Set is a general screening collection of drug-like compounds that present most diversified selection from TimTec stock. ActiTarg-K is diverse targeted library of kinase modulators. Smaller compound set of O-GlcNAc Transferase inhibitors analogs selection is further narrowed down in design to structural characteristics of only few known and potent molecules.

TimTec’s five databases are joined with more than 25 other databases containing chemical and biological data hosted on CDD Public Access, including:

• 47,000 Ki values for 20,000 compounds against 699 GPCR targets from the NIMH Psychoactive Drug Screening Program at the University of North Carolina
• Over 15,000 compounds with Malaria assay data from 5 public data sources
• 48,818 compounds from the Distributed Drug Discovery (D3) at Indiana University – Purdue University Indianapolis (IUPUI)
• Almost 7,500 compounds with Tuberculosis antibacterial and cell viability information from 4 public data sets and growing thanks to their collaboration with the Bill & Melinda Gates Foundation
• Over 200,000 compounds collected by Molecular Libraries Small Molecule Repository (MLSMR) for testing against Mtb H37Rv.

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 TimTec LLC:
TimTec LLC. - http://www.timtec.net - is a privately held company located in Newark Delaware, USA. It was founded in 1995 and began its work in the areas of acquisition and distribution of synthetic organic and natural compounds, custom synthesis, and laboratory equipment to become a full service partner for drug discovery. TimTec has established a global network of thousands of scientists from research centers around the world. The company has developed strong in-house expertise assembling general and targeted library collections for variety of research purposes. International customers include major pharmaceutical, biotech, agricultural, and educational companies and institutions, which use TimTec products for research and development programs.

For further information please contact:

Barry Bunin, Ph.D.
President & CEO
Collaborative Drug Discovery (CDD)
1633 Bayshore Hwy, Suite 342
Burlingame, CA 94010
info@collaborativedrug.com

Kay Denisova
Business Development
TimTec LLC.
Harmony Business Park Building 301-A
Newark, DE 19711
Tel 302 292 8500
Fax 302 292 8520
info@timtec.net
http://www.timtec.net

Collaborative Drug Discovery, Inc. (CDD) is proud to announce that CDD’s Web 2.0 collaborative research information system now hosts over 1 million structure searchable compounds. The accelerated adoption of CDD by academic, non-profit and corporate customers for securely storing focused chemical and biological research data validates CDD’s new paradigm in online research information management.

“The 1 millionth structure is a key milestone for CDD, the culmination of large compound contributions from several customers, including the University of Texas Austin Screening Center,” said Dr. Barry Bunin, CEO and President of Collaborative Drug Discovery. “More importantly, it demonstrates that CDD capabilities and performance scales - searches are very rapid, a substructure search of even a molecule as common as (-) Epinephrine will generate all the hits in just seconds.”

“It has been great to work with the CDD database and wonderful customer support team,” said Dr. Eun Jeong Cho at the TI3D Screening at the University of Texas Austin. “We are impressed with the CDD system which is accurate, fast, and identified data inconsistencies that we might not have seen in our quality control reports.”

Notes Sean Ekins, PhD, CDD Collaborations Director, “The 1 millionth structure, (4-chlorophenyl) N-benzylcarbamate, is from Maybridge’s HitFinder screening compound library which is part of the University of Texas TI3D Screening Center’s private CDD data set. CDD allows secure searching of both private data and the CDD Public Access data. Searching the CDD public data shows this Maybridge compound is 68% similar to rivastigmine which is used to treat Alzheimer’s and Parkinson’s disease. In addition to the maximum dosing information for rivastigmine in the CDD public data, integrated linking to ChemSpider finds further useful properties and references.”

CDD’s hosted compounds include several publicly available data sources with chemical and biological data for 140,000 chemical structures only available via CDD, including:

• 47,000 Ki values for 20,000 compounds against 699 GPCR targets from the NIMH Psychoactive Drug Screening Program at the University of North Carolina
• 48,818 compounds from the Distributed Drug Discovery (D3) at Indiana University - Purdue University Indianapolis (IUPUI)
• Unique compounds from ASINEX’s Synergy, Focused & Building Blocks Libraries
• TimTec’s databases of Natural Products and Derivatives
• Over 15,000 compounds with Malaria assay data from 5 public data sources
• Almost 7,500 compounds with Tuberculosis antibacterial and cell viability information from 4 public data sets and growing thanks to our collaboration with the Bill & Melinda Gates Foundation

Plus much more…

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.

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

Two articles were recently published covering CDD’s new effort for the tuberculosis research community and our collaboration with TBDB. To read more, see Bioinform’s article, “Collaborative Drug Discovery to Use Gates Foundation Grant for Tuberculosis Database”, and the article in Drug Discovery News, “Tuberculosis portal”.

Important note regarding BioInform: Reading the BioInform article once straight through is free. If you visit the article again or hit the back button, you must have a subscription to access the text.

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.