Supporting 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
Supporting Open Drug Discovery
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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
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
As host of chemistry databases
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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
ChemSpider
ChemSpider
Properties – ACD/Labs
Properties – EPI Suite
Properties - ChemAxon
Literature references
Patents references
Books
Chemical vendors and data sources
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
ChemSpider SyntheticPages
ChemSpider SyntheticPages
ChemSpider Reactions
ChemSpider Spectra
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
Open Source Drug Discovery
India
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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
OSDD Collaboration
Recently sponsored
cheminformatics
jamboree – training
by skilled specialists
in the applications of
cheminformatics to
medicinal chemistry
and drug design
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
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)
Antibiotic resistance
Discovery Curve Decay
Focus on Marine Natural Products
• RSC cheminformatics support to include:
• Provide access to natural products subset
(make available on ChemSpider)
• Develop “dereplication techniques”
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Searching NMR features against database
Develop advanced searches for MS data
• Host Open Data from the PharmaSea project
and make available to the community
Marinlit
• RSC acquired Marinlit. Goes online in April
• All Marinlit chemical compounds in ChemSpider
• Marinlit developers are dereplication experts
Cancer Deaths Worldwide
Top Treatments for Cancer
Importance of Natural Products
• Over half of all drugs introduced between
1940 and 2006 were of natural origin or
inspired by natural compounds
Natural Products for all of us!
Natural Products Data Availability
• 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…
The Open PHACTS community ecosystem
• New Chemical Registration System
• Utilizes ChemSpider Validation and
Standardization platform
• Utilizes FDA rule set as basis for
standardizations
• Generate Open PHACTS identifier
(OPS ID)
Chemistry
Registration
Normalisation
& Q/C
OPS2
ops:OPS1 skos:exactMatch
<http://www4.wiwiss.fuberlin.de/drugbank/resource/drugs/DB07241> .
ops:OPS2 skos:relatedMatch ops:OPS1 .
OPS3
ops:OPS3 skos:relatedMatch ops:OPS1 .
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 .
DrugBank ID DB07241
OPS4
OPS5
OPS6
Quality Assurance
ChemSpider Validation & Standardization Platform
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)
Enabling Academic Researchers
UK National Chemical Database
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!
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
We are doing it…we will do more
Royal Society of Chemistry
developments to support
open drug discovery
Thank you
Email: [email protected]
ORCID: 0000-0002-2668-4821
Twitter: @ChemConnector
Personal Blog: www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams
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