Royal Society of Chemistry developments to support open drug discovery

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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 worlds 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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As host of chemistry databases

• 30 million chemicals and growing
• Data sourced from gt500 different sources
• Crowdsourced curation and annotation
• Ongoing deposition of data from our journals and
  our collaborators
• Structure centric hub for web-searching

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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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Importance of Natural Products

• Over half of all drugs introduced between 1940
  and 2006 were of natural origin or inspired by
  natural compounds

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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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• 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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OPS2
opsOPS1 skosexactMatch lthttp//www4.wiwiss.fu-be
rlin.de/drugbank/resource/drugs/DB07241gt
. opsOPS2 skosrelatedMatch opsOPS1
. opsOPS3 skosrelatedMatch opsOPS1
. opsOPS3 skoscloseMatch opsOPS4 . opsOPS3
skoscloseMatch opsOPS5 . opsOPS4
skoscloseMatch opsOPS6 . opsOPS5
skoscloseMatch opsOPS6 .
OPS3
OPS1
DrugBank ID DB07241
OPS4
OPS5
OPS6
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Quality Assurance
ChemSpider Validation Standardization Platform
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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 itwe will do more

• Royal Society of Chemistry developments to
  support open drug discovery

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Thank you Email williamsa_at_rsc.org ORCID
0000-0002-2668-4821 Twitter _at_ChemConnector Pers
onal Blog www.chemconnector.com SLIDES
www.slideshare.net/AntonyWilliams