Meet CDD at these Upcoming Conferences

CDD will be attending a number of upcoming conferences this year. If you would like to meet with us while at any of these conferences, please contact us at info@collaborativedrug.com to schedule a time.

Barry Bunin Ph.D., our CEO, will be attending the following conferences:

  • Gordon Research Conferences: Biology Of Host-Parasite Interactions
    June 22-27, 2008
    Salve Regina University
    Newport, RI
    Poster:

    • “Malaria and Neglected Infectious Disease Collaborative Drug Discovery Case Studies in Academia”
    • Authors: B. Bunin, Ph.D., M. Hohman, PhD, S. Ernst, PhD, K. Gregory

    More info

  • Ninth Tetrahedron Symposium, “Challenges in Organic and Bioorganic Chemistry”
    July 22-25 (Tuesday - Friday)
    Claremont Resort and Hotel
    Berkeley, California, USA
    Poster:

    • “Community-based approach to research on infectious diseases of the developing world and global health”
    • Authors: B. Bunin, Ph.D., M. Hohman, PhD, S. Ernst, PhD, K. Gregory

    More info

  • 236th ACS National Meeting & Exposition
    August 17-21, 2008
    Philadelphia, Pennsylvania, USA
    Poster:

    • “Community-based collaborative drug discovery for neglected infectious diseases and cancer”
    • Authors: B. Bunin, Ph.D., M. Hohman, PhD, S. Ernst, PhD, K. Gregory
    • Division: Division of Medicinal Chemistry
    • Session: General Poster Session
    • Day & Time: Sunday, August 17, 2008 from 7:00 PM to 9:00 PM
    • Location: Pennsylvania Convention Center, Room: Hall C

    More info

  • ASTMH 57th Annual Meeting
    December 7-11, 2008
    Sheraton New Orleans
    New Orleans, Louisiana, USA
    More info

Sean Ekins, Ph.D., our computational chemist, will be attending the following conference:

  • Drug Discovery & Development of Innovative Therapeutics 2008
    August 04 - 07, 2008
    World Trade Center
    Boston, Boston, MA
    More info
Posted June 5th, 2008, in Events | No Comments »

Collaborative Drug Discovery and Myelin Repair Foundation Announce Partnership

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.”

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.

Posted May 27th, 2008, in Press | No Comments »

ASINEX and CDD Team up for Open Access Data for the Scientific Community

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

Posted May 20th, 2008, in Data Publication | No Comments »

Meet us in April at the ACS Meeting or at the Bio IT Conference

CDD will be at two conferences this spring: The ACS meeting in New Orleans (April 6th -10th) and the Bio IT meeting in Boston (April 28th -30th). If you would like to meet directly with our founder Barry Bunin, Ph.D. while at either conference, we will be happy to arrange. Please contact us at info@collaborativedrug.com for scheduling.

ACS National meeting, April 6-10, New Orleans, LA:
Talk: speaker Barry Bunin, Ph.D., CEO, Collaborative Drug Discovery, Inc.
Title: “Community-based collaborative drug discovery for neglected infectious diseases”
Division: Division of Chemical Information
Session: Cheminformatics Implications of Collaborations between Academia and
Industry
Day & Time: Monday, April 7, 2008 from 2:00 PM to 2:30 PM
Location: Marriott Convention Center, Room: Blaine Kern C

Poster:
Paper ID: 1128437
Title: “Community-based collaborative drug discovery for neglected infectious diseases”
Division: Division of Chemical Information
Session: Sci-Mix
Day & Time: Monday, April 7, 2008 from 8:00 PM to 10:00 PM
Location: Morial Convention Center, Room: Hall A

Bio IT World conference, April 28th – 30th, Boston, MA:
Talk: speaker Barry Bunin, Ph.D., CEO, Collaborative Drug Discovery, Inc.
Title: “A Community-Based Collaborative Drug Discovery Platform for Neglected Infectious Diseases and Cancer”
Session: Platform and Storage Design
Day & Time: Wednesday April 30th, 2:00 pm
Location: World Trade Center • Boston, MA

Posted March 13th, 2008, in Events | No Comments »

Drug Discovery News Article on CDD

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.

Posted December 1st, 2007, in Press | No Comments »

Collaboration and Security Release

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.

Posted October 26th, 2007, in Releases | No Comments »

Free Access to Literature Data on Chagas’ Disease Offered Online

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.

Posted October 17th, 2007, in Data Publication | No Comments »

Army Malaria Data Released to the CDD Community

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.

Posted October 11th, 2007, in Data Publication, Press | No Comments »

Collaborative Drug Discovery Releases Next Generation Database for Both Private Collaborations and Public Open Access

Collaborative Drug Discovery (CDD, Inc) is pleased to announce the introduction of its next generation database technology. Collaborative Drug Discovery’s Web-based database enables scientists to collaborate in novel, global efforts to more effectively develop new drug candidates for commercial and humanitarian markets. The technology enables novel community-based research efforts that become more and more useful as additional participants contribute data. Publicly available data sets currently in the system include the FDA orphan and approved drugs and small molecule drug discovery data dating back over half a century. These data sets pertain to a diverse group of neglected diseases, including malaria, tuberculosis, African Sleeping Sickness, Chagas Disease and Leishmania.

Customers can also securely archive, mine, and collaborate around their small molecule preclinical drug discovery data in invitation-only, username-password protected groups.

The CDD Database is one of the easiest to use drug discovery informatics platforms available today. In designing the product, CDD has focused on making it easy enough for first year graduate students to use, yet powerful enough to satisfy the needs of experienced drug discovery scientists. In the July 2007 release of the Database, CDD has completely overhauled the user interface to make it easier to navigate and comprehend, has simplified the batch uploading of molecule and assay data, and has made the entire application more robust and secure.

Researchers can choose to keep their data private or share any or all of it with other research groups in the community. By default, labs using the CDD database only share their imported data privately with fellow lab members. A subset of the data is available openly to the public at no cost (please contact register@collaborativedrug.com for access).

Using the CDD technology, researchers can:

• Permanently archive their drug-centric data
• Mine chemical and biological data for lead optimization
• Access data instantaneously and securely
• Connect with multidisciplinary experts, yielding new insights
• Avoid duplication of research effort
• Optimize the use of valuable research resources
• Facilitate current and future collaborations
• Accelerate target validation and drug discovery
• Leverage a practical mechanism to maximize the benefit of collaborative data while minimizing intellectual property protection costs

For more information please visit: http://www.collaborativedrug.com/

Posted July 5th, 2007, in Press, Releases | No Comments »

First Annual CDD Community Meeting

The meeting provided new perspectives on collaborative research,
scientific community development and global health, with a focus on
infectious diseases of the developing world.

We had 114 people register, 10 posters presented and many great speakers.

Presentation Videos and Slides (PDF):

  • Developing drugs for neglected parasitic diseases in an academic incubator
    James McKerrow, PhD,
    Sandler Center/QB3, UCSF
    video | slides
  • Mining Small Molecule Probes of Human Parasite Proteases from Libraries of Covalent Inhibitors
    Matt Bogyo, PhD,
    Stanford University Medical School
    video | slides
  • Charting the Past and Proposing the Future Course of Antimalarial Discovery in Chemical Space
    Anang Shelat, PhD,
    St. Jude Children’s Research Hospital
    video | slides
  • Modeling and Determining the Structures of Proteins and Macromolecular Assemblies
    Andrej Sali, PhD
    UCSF/QB3
    video | slides
  • Academic drug discovery: the chemistry challenges of target choice and screening library selection
    Christopher Lipinski, PhD,
    Melior Discovery
    video | slides
  • Panel, Technical community roadmap for open collaborations and global health
    Barry Bunin, PhD,
    Collaborative Drug Discovery
    intro video | intro slides | video

Thanks to our other speakers and panel members.

The Community Meeting Program is now available for download and presented posters abstracts are available online.

Posted March 5th, 2007, in Events | No Comments »