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Royal Society of Chemistry developments to support open drug discovery
Antony Williams, Ken Karapetyan, Valery Tkachenko, Colin Batchelor Alexey Pshenichnov and Jon Steele
ACS Dallas
March 2014
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Supporting Open Drug Discovery
• As a publisher
• As a host of chemistry databases
• As a charity and community support
• As a provider of grant-based services
• As an innovator in cheminformatics
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RSC as a Publisher• One of the world’s top publishers for chemistry
– journals, books and databases
• High quality, high impact journals – direct journals of relevance for drug discovery
• Databases to support drug discovery – Merck Index, ChemSpider, Natural Product Updates…
• Innovative publisher – semantic markup, mobile developments
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• ~30 million chemicals and growing
• Data sourced from >500 different sources
• Crowdsourced curation and annotation
• Ongoing deposition of data from our journals and our collaborators
• Structure centric hub for web-searching
As host of chemistry databases
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ChemSpider
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ChemSpider
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Properties – ACD/Labs
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Properties – EPI Suite
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Properties - ChemAxon
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Literature references
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Patents references
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Books
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Chemical vendors and data sources
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ChemSpider
• Ongoing expansion of integrated services of value to open drug discovery• Integration to Mcule online docking and
toxicity checker – in development• New grant to integrate to improved patent
service with Cambridge IP (UK)• Integration to enhance MedChemComm
journal articles for property extraction and data management
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ChemSpider SyntheticPages
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ChemSpider SyntheticPages
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ChemSpider Reactions
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ChemSpider Spectra
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RSC as a Charity
• Acts as host and funder for networking meetings
• Funds trainings and onsite participation
• Provides funding for RSC cheminformatics team to work on open drug discovery projects
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Open Source Drug DiscoveryIndia
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• Tuberculosis kills 1.6-1.7 million people every year (~1 every 8 seconds)
• 1/3 of the worlds population is infected
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OSDD Collaboration
Recently sponsored cheminformatics jamboree – training by skilled specialists in the applications of cheminformatics to medicinal chemistry and drug design
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OSDD Collaboration
• We will provide access and support to the ChemSpider API to integrate to their OSDD cheminformatics platform
• We will extend our data model to support their Open Data – compounds, pharmacology data
• Synthetic reactions will be published to ChemSpider SyntheticPages and Reactions
• Analytical Data to be published to ChemSpider Spectra
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As a provider of grant-based services
• RSC cheminformatics participates in multiple European consortium-based grants• PharmaSea (FP7 funded)• Open PHACTS (IMI funded)
• RSC hosts the UK National Chemical Database Service (http://cds.rsc.org)
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Antibiotic resistance
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Discovery Curve Decay
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Focus on Marine Natural Products
• RSC cheminformatics support to include:• Provide access to natural products subset
(make available on ChemSpider)• Develop “dereplication techniques”
• Searching NMR features against database• Develop advanced searches for MS data
• Host Open Data from the PharmaSea project and make available to the community
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Marinlit
• RSC acquired Marinlit. Goes online in April
• All Marinlit chemical compounds in ChemSpider
• Marinlit developers are dereplication experts
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Cancer Deaths Worldwide
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Top Treatments for Cancer
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• Over half of all drugs introduced between 1940 and 2006 were of natural origin or inspired by natural compounds
Importance of Natural Products
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Natural Products for all of us!
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Natural Products Data Availability
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• 3-year Innovative Medicines Initiative project
• Integrating chemistry and biology data using semantic web technologies
• Open source code, open data and open standards
• Academics, Pharmas, Publishers…• To put medicines in the pipeline…
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The Open PHACTS community ecosystem
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Chemistry RegistrationNormalisation & Q/C
• New Chemical Registration System• Utilizes ChemSpider Validation
and Standardization platform• Utilizes FDA rule set as basis for
standardizations • Generate Open PHACTS identifier
(OPS ID)
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O H
O
O H
O
O–
O
Na+
Na+
O
O–
O
O–
OPS1
O–
ONa
+
DrugBank ID DB07241
OPS5OPS4
OPS3
OPS2
OPS6
ops:OPS1 skos:exactMatch <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB07241> .
ops:OPS2 skos:relatedMatch ops:OPS1 .
ops:OPS3 skos:relatedMatch ops:OPS1 .
ops:OPS3 skos:closeMatch ops:OPS4 .
ops:OPS3 skos:closeMatch ops:OPS5 .
ops:OPS4 skos:closeMatch ops:OPS6 .
ops:OPS5 skos:closeMatch ops:OPS6 .
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ChemSpider Validation & Standardization Platform
Quality Assurance
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Open Sourcing Data and Code
• All Open PHACTS data is licensed as Open Data and available from Open PHACTS website – ca. 2 Million chemicals
• The Chemical Registration Service, including Chemical Validation and Standardization Platform will be released as Open Source code to the community (from Open PHACTS github site)
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Enabling Academic ResearchersUK National Chemical Database
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Data for the Community
• Data on ChemSpider is curated in an ongoing fashion - take what you need!
• Used a lot for accessing the “dictionary of chemicals” to build models – right Sean?
• Pharmacalogy data will increasingly be available – from PharmaSea and OSDD
• All Open PHACTS data already available!
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As Innovator in Cheminformatics
• Hopefully self-evident by now?• ChemSpider• Support of Open PHACTS, PharmaSea and
Chemical Database Service• Releasing Open Source code to community
• To come:• Chemical Data Repository in development• Hosting models for the community
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We are doing it…we will do more
Royal Society of Chemistry developments to support
open drug discovery
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Thank you
Email: [email protected]: 0000-0002-2668-4821 Twitter: @ChemConnectorPersonal Blog: www.chemconnector.com SLIDES: www.slideshare.net/AntonyWilliams