Slides for rare disorders meeting

Translational Overiew: Generalized Approach What can I do to Help? Sean Ekins Collaborations in Chemistry, Fuquay Varina, NC. Collaborative Drug Discovery, Burlingame, CA. Department of Pharmacology, University of Medicine & Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, NJ. School of Pharmacy, Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD.

Abigail Alliance for Better Access to Developmental Drugs Addi & Cassi Fund American Behcet's Disease Association Amschwand Sarcoma Cancer Foundation BDSRA (Batten Disease Support and Research Association) Beyond Batten Disease Foundation Blake’s Purpose Foundation Breakthrough Cancer Coalition Canadian PKU & Allied Disorders Center for Orphan Disease Research and Therapy, University of Pennsylvania Children’s Cardiomyopathy Foundation Cooley's Anemia Foundation Dani’s Foundation Drew’s Hope Research Foundation EveryLife Foundation for Rare Diseases GIST Cancer Awareness Foundation Hannah's Hope Fund Hope4Bridget Foundation Hypertrophic Cardiomyopathy Association - HCMA I Have IIH ISRMD (International Society for Mannosidosis and Related Diseases) Jacob’s Cure Jain Foundation Jonah's Just Begun-Foundation to Cure Sanfilippo Inc. Kids V Cancer Kurt+Peter Foundation LGMD2I Research Fund Lymphangiomatosis & Gorham's Disease Alliance MAGIC Foundation Manton Center for Orphan Disease Research MarbleRoad Mary Payton's Miracle Foundation Midwest Asian Health Association (MAHA) MPD Support National Gaucher Foundation National MPS Society National Organization Against Rare Cancers National PKU Alliance National Tay-Sachs & Allied Diseases Association New Hope Research Foundation NextGEN Policy Noah's Hope - Batten disease research fund Our Promise to Nicholas Foundation Oxalosis and Hyperoxaluria Foundation Partnership for Cures Periodic Paralysis Association RARE Project Ryan Foundation for MPS Children Sanfilippo Foundation for Children Sarcoma Foundation of America Solving Kids' Cancer Taylor's Tale: Fighting Batten Disease Team Sanfilippo Foundation The Alliance Against Alveolar Soft Part Sarcoma The Life Raft Group The NOMID Alliance The Transverse Myelitis Association The XLH Network, Inc. United Pompe Foundation Many of these groups are doing R&D on a shoestring how can we help? Why am I here? Why are we here?

Jonah’s mum, Jill Wood started a foundation, raises money, awareness, funds ground breaking research happening globally. Willing to sell her house to fund research to save Jonah. She is in a race against time – what can we do to translate ideas from bench to patient faster? How do we get more ideas tested, who funds the research How can we help parents and families ? One example of why Pharmaceutical R&D needs disrupting

How to do it better? What can we do with software to facilitate it ? The future is more collaborative We have tools but need integration
Groups involved traverse the spectrum from pharma, academia, not for profit and government
More free, open technologies to enable biomedical research
Precompetitive organizations, consortia..
How can it help orphan and rare diseases?
A starting point is collaboration; software may help A core root of the current inefficiencies in drug discovery are due to organizations’ and individual’s barriers to collaborate effectively Bunin & Ekins DDT 16: 643-645, 2011

Example ; Collaborative Drug Discovery Platform
CDD Vault – Secure web-based place for private data – private by default
CDD Collaborate – Selectively share subsets of data
CDD Public – public data sets - Over 3 Million compounds, with molecular properties, similarity and substructure searching, data plotting etc
will host datasets from companies, foundations etc
vendor libraries (Asinex, TimTec, ChemBridge)
Unique to CDD – simultaneously query your private data, collaborators’ data, & public data, Easy GUI
www.collaborativedrug.com

3 Academia/ Govt lab – Industry screening partnerships
CDD used for data sharing / collaboration – along with cheminformatics expertise
Previously supported larger groups of labs – many continued as customers
How CDD software has been used: BMGF CDD is a partner on a 5 year project supporting >20 labs and proving cheminformatics support www.mm4tb.org More Medicines for Tuberculosis

Ekins et al, Trends in Microbiology 19: 65-74, 2011 Fitting into the drug discovery process Insert your disease here…

Searching for TB molecular mimics; collaboration Lamichhane G, et al Mbio, 2: e00301-10, 2011 Modeling – CDD Biology – Johns Hopkins Chemistry – Texas A&M

Combining cheminformatics methods and pathway analysis
Identified essential TB targets that had not been exploited
Used resources available to both to identify targets and molecules that mimic substrates
Computationally searched >80,000 molecules - tested 23 compounds in vitro (3 picked as inactives), lead to 2 proposed as mimics of D-fructose 1,6 bisphosphate, (MIC of 20 and 40 ug/ml)
POC took < 6mths - - Submitted phase II STTR, Submitted manuscript
Still need to test vs target - verify hits vs suggested target
Ekins et al, Trends in Microbiology Feb 2011 Phase I STTR - NIAID funded collaboration with Stanford Research International Sarker et al, submitted 2011

Finding Promiscuous Old Drugs for New Uses
Research published in the last six years - 34 studies - Screened libraries of FDA approved drugs against various whole cell or target assays.
1 or more compounds with a suggested new bioactivity
13 drugs were active against more than one additional disease in vitro
Perhaps screen these first?
Ekins and Williams, Pharm Res 28(8):1785-91, 2011

Finding Promiscuous Old Drugs for New Uses
109 molecules were identified by screening in vitro
Statistically more hydrophobic (log P) and higher MWT than orphan-designated products with at least one marketing approval for a common disease indication or one marketing approval for a rare disease from the FDA’s rare disease research database.
Created multiple structure searchable databases in CDD
This work was unfunded
Data in publications is increasing but who is tracking it?
FDA databases for rare disease research are XL files!!
After this paper published NCGC released NPC browser….but

Government Databases Should Come With a Health Warning Openness Can Bring Serious Quality Issues NPC Browser http://tripod.nih.gov/npc/ Database released and within days 100’s of errors found in structures Williams and Ekins, DDT, 16: 747-750 (2011) Science Translational Medicine 2011 This work was unfunded Science Translational Medicine 2011

2D Similarity search with “hit” from screening Export database and use for 3D searching with a pharmacophore or other model Suggest approved drugs for testing - may also indicate other uses if it is present in more than one database Suggest in silico hits for in vitro screening Key databases of structures and bioactivity data FDA drugs database Repurpose FDA drugs in silico Ekins S, Williams AJ, Krasowski MD and Freundlich JS, Drug Disc Today, 16: 298-310, 2011

Crowdsourcing Project “Off the Shelf R&D” All pharmas have assets on shelf that reached clinic “ Off the Shelf R&D” Get the crowd to help in repurposing / repositioning these assets How can software help? - Create communities to test - Provide informatics tools that are accessible to the crowd - enlarge user base - Data storage on cloud – integration with public data - Crowd becomes virtual pharma-CROs and the “customer” for enabling services

Massive models – using open tools Gupta RR, et al., Drug Metab Dispos, 38: 2083-2090, 2010 Can we get pharmas to share models rather than data – precompetitive? What can be developed with very large training and test sets? training 194,000 and testing 39,000 Open molecular descriptors / models vs commercial descriptors Potential to share models selectively with collaborators e.g. academics, rare & neglected disease researchers Lundbeck Pfizer Merck GSK Novartis Lilly BMS Allergan Bayer AZ Roche BI Merk KGaA

Future Drug Discovery Could our Pharma R&D look like this – a big network I think we are seeing something like this with all the orphan disease networks Massive collaboration networks – software enabled. We are in “Generation App” Crowdsourcing will have a role in R&D. Drug discovery possible by anyone with “app access” Ekins & Williams, Pharm Res, 27: 393-395, 2010.

Make science more accessible = >communication
Mobile – take a phone into field /lab and do science more readily than on a laptop
MolSync + DropBox + MMDS = Share molecules as SDF files on the cloud = collaborate
How could orphan disease research leverage apps?
Mobile Apps for Drug Discovery Williams et al DDT 16:928-939, 2011

http://www.slideshare.net/ekinssean Ekins S and Williams AJ, MedChemComm, 1: 325-330, 2010. Need to learn from neglected disease research Do we really need to screen massive libraries of compounds as we have for TB and malaria?

The Evolving Pfizer R&D Ecosystem
Evolving paradigm for the discovery of medicines (Collaborative)
A vision that points towards open innovation and collaborations
Open research model to collectively share scientific expertise
Enhance speed of drug discovery beyond individual resource capabilities (Speed)
Limited research budgets and capabilities driving greater shared resources
Goal to see all partners succeed by accelerating the SCIENCE
Synergize Pfizer’s strengths with Research Partners (Knowledge)
Pair Pfizer’s design, cutting edge tools, synthetic excellence with research partners (academics, not-for-profits, venture capitalists, or biotechs) to develop break through science, novel targets, and indications of unmet medical need
Current example of academic and not-for-profits partners (Discover and Publish)
Drive to publish in top journal with science receiving high visibility and interest
Contacts:
Travis Wager ( [email_address] )
Paul Galatsis ( [email_address] )
a few months ago we entered into a collaboration with the giant pharmaceutical industry Pfizer to test some of their leading molecules for potential relevance to HD. Found on the internet http://dl.dropbox.com/u/14511423/VRU.pptx Body clock mouse study suggests new drug potential Mon, Aug 23 2010 By Kate Kelland LONDON (Reuters) - Scientists have used experimental drugs being developed by Pfizer to reset and restart the body clock of mice in a lab and say their work may offer clues on a range of human disorders, from jetlag to bipolar disorder.

The newest reality Gone full circle Pharma now becoming more like rare disease groups Working on a shoestring, limited resources, leverages academics, partners with disease foundations, funded by them – open innovation Collaboration is a core element If Jill Wood can become a virtual pharma, Pfizer and other pharmas can be more like Jill and other parent entrepreneurs, smaller, leaner, working on many more diseases as collaborators

1. Write grants to fund researchers to develop products. 2. Write papers about rare disease to draw attention to urgency. 3. Organize special Journal issues on rare disease research. 4. Leverage my collaborative network to do preclinical research. 5. Use virtual screening to narrow down FDA and GRAS molecules to be repurposed. 6. Use computational models to predict potential toxicities for compounds for rare diseases. 7. Lobby funding agencies to support rare disease research. 8. Leverage as much open software, data and free resources as possible. 9. Maximally collaborative, results driven, no IP, socially networked. 10. Create a template for more disruptive research. 2012 my goals – Open research, focused on rare diseases, Fundable?

Acknowledgments
Antony J. Williams (RSC)
Rishi Gupta, Eric Gifford, Ted Liston, Chris Waller (Pfizer)
Joel Freundlich (Texas A&M), Gyanu Lamichhane (Johns Hopkins)
Carolyn Talcott, Malabika Sarker , Peter Madrid, Sidharth Chopra (SRI International)
MM4TB colleagues
Matthew D. Krasowski (University of Iowa)
Alex Clark (Molecular Materials Informatics, Inc)
Accelrys
CDD – Barry Bunin
Funding BMGF, NIAID.
Everyone that has shared data in CDD..
Email: ekinssean@yahoo.com
Slideshare: http://www.slideshare.net/ekinssean
Twitter: collabchem
Blog: http://www.collabchem.com/
Website: http://www.collaborations.com/CHEMISTRY.HTM

Slides for rare disorders meeting

by Sean Ekins on Dec 01, 2011

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