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
• 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
• ~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

•
•
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”
• 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

OPS1
DrugBank ID DB07241
OPS4
OPS2
OPS3
OPS5 ops:OPS1 skos:exactMatch
<http://www4.wiwiss.fuberlin.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 .
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

Email : williamsa@rsc.org
ORCID : 0000-0002-2668-4821
Twitter : @ChemConnector
Personal Blog : www.chemconnector.com
SLIDES: www.slideshare.net/AntonyWilliams