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Why There Needs to be Open Data for Ultra-Rare and Rare Disease
Drug Discovery
Sean Ekins1, Alex M. Clark2, Jill Wood3,4, Lori Sames5,6 and Allison Moore7
1Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay Varina, NC27526, USA.
2Molecular Materials Informatics, 1900 St. Jacques #302, Montreal, Quebec, Canada H3J 2S1
3Jonah's Just Begun, P.O. Box 150057, Brooklyn, NY 11215, USA.
4Phoenix Nest, P.O. BOX 150057, Brooklyn NY 11215, USA.
5Hannah's Hope Fund, P.O. Box 130, Rexford, NY 12148, USA.
6BioGAN Therapeutics, P.O. Box 130, Rexford, NY 12148, USA.
7Hereditary Neuropathy Foundation, 432 Park Avenue South – 4th floor,New York, NY 10016, USA.
• Very few researchers chasing
>7000 diseases
• NIH $3.5bn in rare diseases -
orphan drugs $749M 11.4%
budget in 2011 numbers
• Relatively easy to treat. At the
forefront of gene therapy
resurgence
• Only miniscule clinical trials
possible
Rare disease biology not well known
Affects 10s- 1000s per disease
Treatments need to be expensive $1M/yr pp
The Problem/ Opportunity
Examples of Rare Diseases
This is Jonah
• Parents founded
• He needs a cure for Sanfilippo
syndrome (MPS IIIC)
• Collaborates with global groups
• Researchers just developed a KO
mouse funded by Sanfilippo
foundations globally
• Searching for small molecule therapy,
study animal models (Dr. Alexey
Pshezhetsky, University of Montreal)
• Working on gene therapy (Dr. Brian
Bigger, University of Manchester)
• Natural History Study (Dr. Paul Levy,
Montefiore)
• Started registry
This is Hannah
• Parents founded
• She needs a cure for Giant Axonal
Neuropathy
• Searching for small molecule
therapy (funded postdoc with Dr.
Jim Inglese, NIH)
• Funded gene therapy - entering
clinical trial (Dr. Steven Gray, UNC)
• Funded - Natural history study (Dr.
Douglas Sproule, Columbia)
• Started Registry - GRIN
The Rare Disease Parent
Odyssey
• Diagnosis of child
• Try to find out about disease – papers behind paywall
• Try to connect with scientists
• Form not-for-profit
• Raise funds
• Fund Scientific research on disease
• Advocate for support from NIH, FDA etc
• Start a company
• Try to find a cure before its too late
Wood J et al., Drug Disc Today, 18: 1043–1051, 2013
Let me repeat….A Parent/ Patient
Advocate with no Ph.D. can do all this
• Start a foundation
• Raise funds
• Become an expert on their/childs disease
• Set up a scientific advisory board
• Fund scientific projects
• Submit NIH grants
• Start a company
• Leverage social media, traditional media
Why there needs to be open data for ultra-rare and rare disease drug discovery
Why there needs to be open data for ultra-rare and rare disease drug discovery
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? How do they fund it?
Just some of the many rare disease groups
Crowdfunding Science
Huffington Post The O’Neills raised > $1M through
crowdfunding to date
http://www.curesff.org/
www.SavingEliza.com
Funding gene therapy for Sanfilippo A
Jonny Lee Miller raised >$177,526 for
Sanfilippo C on Crowdrise
Crowdfunding Rare Disease Science
Disruption needed
• #1: NIH and other international scientific
funding bodies should mandate …open
accessibility for all data generated by
publicly funded research.
• #2: Reboot the pharmaceutical industry by
extending the notion of ‘‘precompetitive’’
collaboration to encompass later stages of
research to allow PPPs to flourish.
• #3: FDA takes a proactive role in making
relevant clinical data available that will help all
drug developers (as well as NCATS) to bridge
the valley of death and remove a bottleneck.
• #4: Companies listen to the patients as they
generate data on social media, mine it for
indications and off target effects. Companies
and funding bodies will find the innovators to
exploit this information and use collaborative
tools to share data
Rare disease foundations
publishing their ideas and
recommendations
• New ways to do research
• Sharing data openly
Examples of Open Science and Tools to
Share Openly
Linked Open
data cloud
2011 (Wikipedia)
Insert disease of choice here
Learning from OSDD TB and Malaria efforts
Open Source Drug Discovery (OSDD) is the concept of drug discovery where all
data and ideas are shared in real time, and anyone may participate at any level.
This prior disclosure means that there will be no patents and that any
technology is both academically and commercially exploitable by whoever
wishes to do so.
Openness..can be confusing
• Open Access versus Free Access
• Open Data versus free to download
• Open Source and all of its “licenses”
Barriers
• Priority
• Ownership of data
• IP, patenting, How people make money
• Ethical
• Personal privacy
• Publishing, rewards and promotions – kudos
• Publishing open access has cost involved..
Benefits
• Other families and scientists can find your data
• Minimize repetition
• Lower costs of research, increase efficiency
• Analogy to Linux – open source can be
commercial success
• Some open scientists are notable
A Mobile App for Open Drug Discovery
A flipboard for science
#ODDT
iOS only
Embraced by rare disease
advocates
Getting people to share
data openly is a
challenge
NIH SBIR reviewers want
closed systems to
preserve IP
Developed with Alex Clark
Open Drug Discovery Teams – brings data from Twitter and the internet together
Ekins et al., Mol Informatics, 31: 585-597, 2012
http://goo.gl/r9NP7p
Uses of ODDT for Sanfilippo syndrome http://goo.gl/Zlpmyc
What is needed?
• “Helpers” to take the weight off the parent/patient
• How to manage the complex data?
• How to make sense of the literature?
• How to foster collaboration?
• How to leverage what is learnt from other diseases?
• How scientists find funding or projects to work on?
• How parents find scientists to solve their problems?
• How to accelerate the process of discovery?
• Find patients for registries and clinical studies
Support human Champions with
software and systems
• Parents need expert advice
• Drug Discovery advice
• Preclinical advice
• Awareness of research outside of their
disease
This could be you here
A mashup of..
• Crowdfunding
• Crowdsourcing
• Open Innovation
• Open Source
• Open Science
• Precompetitive Initiative
• Open Collaboration
Start a company
Enables you to apply for
SBIR /STTR grants
Fund research – help
academics and
commercialize their work
Then use NIH TRND and
NCATS programs
Getting the word out there – publish in open journals
Study using patient fibroblasts and
plasma showed TGF-B1 elevated
Published in closed journal
Knowns drugs that down regulate it
not tested
Losartan, statins, puromycin,
rimonabant, Aliskiren
http://goo.gl/Y2iBBF
Helping the researchers to help the patients
Finding Promiscuous Old Drugs for New Uses
everolimus
5-fluorouracil
ceftriaxone
Could In silico / in vitro repositioning find leads-drugs quicker?
One family found another family with a child
with the disease by reading a blog
Increasing awareness – rare diseases go mainstream
..So lets make rare disease data open
PAPER ID: 22104 “Collaborative sharing of molecules and data in the mobile age” (final paper number: 43)
DIVISION: COMP; DAY & TIME OF PRESENTATION: August 10, 2014 from 4:45 pm to 5:15 pm
LOCATION: Moscone Center, West Bldg., Room: 2005
PAPER ID: 22094 “Expanding the metabolite mimic approach to identify hits for Mycobacterium tuberculosis ” (final paper number: 78)
DIVISION: COMP: DAY & TIME OF PRESENTATION: August 11, 2014 from 9:00 am to 9:30 am
LOCATION: Moscone Center, West Bldg., Room: 2005
PAPER ID: 22120 “Why there needs to be open data for ultrarare and rare disease drug discovery” (final paper number: 48)
DIVISION: CINF:SESSION DAY & TIME OF PRESENTATION: August 11, 2014 from 10:50 am to 11:20 am
LOCATION: Palace Hotel, Room: Marina
PAPER ID: 22183 “Progress in computational toxicology” (final paper number: 125)
DIVISION: TOXI: DAY & TIME OF PRESENTATION: August 12, 2014 from 6:30 pm to 10:30 pm
LOCATION: Moscone Center, North Bldg. , Room: 134
PAPER ID: 22091 “Examples of how to inspire the next generation to pursue computational chemistry/cheminformatics” (final paper
number: 100)
DIVISION: CINF: Division of Chemical Information DAY & TIME OF PRESENTATION: August 13, 2014 from 8:25 am to 8:50 am
LOCATION: Palace Hotel, Room: Presidio
PAPER ID: 22176 “Applying computational models for transporters to predict toxicity” (final paper number: 132)
DIVISION: TOXI: DAY & TIME OF PRESENTATION: August 13, 2014 from 9:45 am to 10:05 am
LOCATION: InterContinental San Francisco, Room: Grand Ballroom A
PAPER ID: 22186 “New target prediction and visualization tools incorporating open source molecular fingerprints for TB mobile version 2”
(final paper number: 123)
DIVISION: CINF: DAY & TIME OF PRESENTATION: August 13, 2014 from 1:35 pm to 2:05 pm
LOCATION: Palace Hotel, Room: California Parlor
You can find me @...
We gratefully acknowledge all the scientists who have worked on the rare
diseases described and shared their data
Lisa M. Jarvis for covering rare diseases at C&E News
Antony J. Williams for inspiring open research
 Email: ekinssean@yahoo.com
 Slideshare: http://www.slideshare.net/ekinssean
 Twitter: collabchem
 Blog: http://www.collabchem.com/
 Website: http://www.collaborations.com/CHEMISTRY.HTM

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Why there needs to be open data for ultra-rare and rare disease drug discovery

  • 1. Why There Needs to be Open Data for Ultra-Rare and Rare Disease Drug Discovery Sean Ekins1, Alex M. Clark2, Jill Wood3,4, Lori Sames5,6 and Allison Moore7 1Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay Varina, NC27526, USA. 2Molecular Materials Informatics, 1900 St. Jacques #302, Montreal, Quebec, Canada H3J 2S1 3Jonah's Just Begun, P.O. Box 150057, Brooklyn, NY 11215, USA. 4Phoenix Nest, P.O. BOX 150057, Brooklyn NY 11215, USA. 5Hannah's Hope Fund, P.O. Box 130, Rexford, NY 12148, USA. 6BioGAN Therapeutics, P.O. Box 130, Rexford, NY 12148, USA. 7Hereditary Neuropathy Foundation, 432 Park Avenue South – 4th floor,New York, NY 10016, USA.
  • 2. • Very few researchers chasing >7000 diseases • NIH $3.5bn in rare diseases - orphan drugs $749M 11.4% budget in 2011 numbers • Relatively easy to treat. At the forefront of gene therapy resurgence • Only miniscule clinical trials possible Rare disease biology not well known Affects 10s- 1000s per disease Treatments need to be expensive $1M/yr pp The Problem/ Opportunity
  • 3. Examples of Rare Diseases
  • 4. This is Jonah • Parents founded • He needs a cure for Sanfilippo syndrome (MPS IIIC) • Collaborates with global groups • Researchers just developed a KO mouse funded by Sanfilippo foundations globally • Searching for small molecule therapy, study animal models (Dr. Alexey Pshezhetsky, University of Montreal) • Working on gene therapy (Dr. Brian Bigger, University of Manchester) • Natural History Study (Dr. Paul Levy, Montefiore) • Started registry
  • 5. This is Hannah • Parents founded • She needs a cure for Giant Axonal Neuropathy • Searching for small molecule therapy (funded postdoc with Dr. Jim Inglese, NIH) • Funded gene therapy - entering clinical trial (Dr. Steven Gray, UNC) • Funded - Natural history study (Dr. Douglas Sproule, Columbia) • Started Registry - GRIN
  • 6. The Rare Disease Parent Odyssey • Diagnosis of child • Try to find out about disease – papers behind paywall • Try to connect with scientists • Form not-for-profit • Raise funds • Fund Scientific research on disease • Advocate for support from NIH, FDA etc • Start a company • Try to find a cure before its too late Wood J et al., Drug Disc Today, 18: 1043–1051, 2013
  • 7. Let me repeat….A Parent/ Patient Advocate with no Ph.D. can do all this • Start a foundation • Raise funds • Become an expert on their/childs disease • Set up a scientific advisory board • Fund scientific projects • Submit NIH grants • Start a company • Leverage social media, traditional media
  • 10. 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? How do they fund it? Just some of the many rare disease groups
  • 12. Huffington Post The O’Neills raised > $1M through crowdfunding to date http://www.curesff.org/ www.SavingEliza.com Funding gene therapy for Sanfilippo A Jonny Lee Miller raised >$177,526 for Sanfilippo C on Crowdrise Crowdfunding Rare Disease Science
  • 13. Disruption needed • #1: NIH and other international scientific funding bodies should mandate …open accessibility for all data generated by publicly funded research. • #2: Reboot the pharmaceutical industry by extending the notion of ‘‘precompetitive’’ collaboration to encompass later stages of research to allow PPPs to flourish. • #3: FDA takes a proactive role in making relevant clinical data available that will help all drug developers (as well as NCATS) to bridge the valley of death and remove a bottleneck. • #4: Companies listen to the patients as they generate data on social media, mine it for indications and off target effects. Companies and funding bodies will find the innovators to exploit this information and use collaborative tools to share data
  • 14. Rare disease foundations publishing their ideas and recommendations
  • 15. • New ways to do research • Sharing data openly
  • 16. Examples of Open Science and Tools to Share Openly Linked Open data cloud 2011 (Wikipedia)
  • 17. Insert disease of choice here Learning from OSDD TB and Malaria efforts Open Source Drug Discovery (OSDD) is the concept of drug discovery where all data and ideas are shared in real time, and anyone may participate at any level. This prior disclosure means that there will be no patents and that any technology is both academically and commercially exploitable by whoever wishes to do so.
  • 18. Openness..can be confusing • Open Access versus Free Access • Open Data versus free to download • Open Source and all of its “licenses”
  • 19. Barriers • Priority • Ownership of data • IP, patenting, How people make money • Ethical • Personal privacy • Publishing, rewards and promotions – kudos • Publishing open access has cost involved..
  • 20. Benefits • Other families and scientists can find your data • Minimize repetition • Lower costs of research, increase efficiency • Analogy to Linux – open source can be commercial success • Some open scientists are notable
  • 21. A Mobile App for Open Drug Discovery A flipboard for science #ODDT iOS only Embraced by rare disease advocates Getting people to share data openly is a challenge NIH SBIR reviewers want closed systems to preserve IP Developed with Alex Clark Open Drug Discovery Teams – brings data from Twitter and the internet together Ekins et al., Mol Informatics, 31: 585-597, 2012 http://goo.gl/r9NP7p
  • 22. Uses of ODDT for Sanfilippo syndrome http://goo.gl/Zlpmyc
  • 23. What is needed? • “Helpers” to take the weight off the parent/patient • How to manage the complex data? • How to make sense of the literature? • How to foster collaboration? • How to leverage what is learnt from other diseases? • How scientists find funding or projects to work on? • How parents find scientists to solve their problems? • How to accelerate the process of discovery? • Find patients for registries and clinical studies
  • 24. Support human Champions with software and systems • Parents need expert advice • Drug Discovery advice • Preclinical advice • Awareness of research outside of their disease This could be you here
  • 25. A mashup of.. • Crowdfunding • Crowdsourcing • Open Innovation • Open Source • Open Science • Precompetitive Initiative • Open Collaboration
  • 26. Start a company Enables you to apply for SBIR /STTR grants Fund research – help academics and commercialize their work Then use NIH TRND and NCATS programs
  • 27. Getting the word out there – publish in open journals
  • 28. Study using patient fibroblasts and plasma showed TGF-B1 elevated Published in closed journal Knowns drugs that down regulate it not tested Losartan, statins, puromycin, rimonabant, Aliskiren http://goo.gl/Y2iBBF Helping the researchers to help the patients
  • 29. Finding Promiscuous Old Drugs for New Uses everolimus 5-fluorouracil ceftriaxone Could In silico / in vitro repositioning find leads-drugs quicker?
  • 30. One family found another family with a child with the disease by reading a blog Increasing awareness – rare diseases go mainstream
  • 31. ..So lets make rare disease data open
  • 32. PAPER ID: 22104 “Collaborative sharing of molecules and data in the mobile age” (final paper number: 43) DIVISION: COMP; DAY & TIME OF PRESENTATION: August 10, 2014 from 4:45 pm to 5:15 pm LOCATION: Moscone Center, West Bldg., Room: 2005 PAPER ID: 22094 “Expanding the metabolite mimic approach to identify hits for Mycobacterium tuberculosis ” (final paper number: 78) DIVISION: COMP: DAY & TIME OF PRESENTATION: August 11, 2014 from 9:00 am to 9:30 am LOCATION: Moscone Center, West Bldg., Room: 2005 PAPER ID: 22120 “Why there needs to be open data for ultrarare and rare disease drug discovery” (final paper number: 48) DIVISION: CINF:SESSION DAY & TIME OF PRESENTATION: August 11, 2014 from 10:50 am to 11:20 am LOCATION: Palace Hotel, Room: Marina PAPER ID: 22183 “Progress in computational toxicology” (final paper number: 125) DIVISION: TOXI: DAY & TIME OF PRESENTATION: August 12, 2014 from 6:30 pm to 10:30 pm LOCATION: Moscone Center, North Bldg. , Room: 134 PAPER ID: 22091 “Examples of how to inspire the next generation to pursue computational chemistry/cheminformatics” (final paper number: 100) DIVISION: CINF: Division of Chemical Information DAY & TIME OF PRESENTATION: August 13, 2014 from 8:25 am to 8:50 am LOCATION: Palace Hotel, Room: Presidio PAPER ID: 22176 “Applying computational models for transporters to predict toxicity” (final paper number: 132) DIVISION: TOXI: DAY & TIME OF PRESENTATION: August 13, 2014 from 9:45 am to 10:05 am LOCATION: InterContinental San Francisco, Room: Grand Ballroom A PAPER ID: 22186 “New target prediction and visualization tools incorporating open source molecular fingerprints for TB mobile version 2” (final paper number: 123) DIVISION: CINF: DAY & TIME OF PRESENTATION: August 13, 2014 from 1:35 pm to 2:05 pm LOCATION: Palace Hotel, Room: California Parlor You can find me @...
  • 33. We gratefully acknowledge all the scientists who have worked on the rare diseases described and shared their data Lisa M. Jarvis for covering rare diseases at C&E News Antony J. Williams for inspiring open research
  • 34.  Email: ekinssean@yahoo.com  Slideshare: http://www.slideshare.net/ekinssean  Twitter: collabchem  Blog: http://www.collabchem.com/  Website: http://www.collaborations.com/CHEMISTRY.HTM

Notas del editor

  1. Imagine a future Where we help cure rare diseases Where we help tailor medicines to overcome variability and side effects Where most academics use CDD Where all scientists collaborate securely