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Cambridge MedChem Consulting

Rare Diseases

There are between 5,000 and 8,000 rare diseases, and around 5 new rare diseases are described in the literature each week. There is no internationally recognised definition of a rare disease but they are defined by the European Union as one that affects less than 5 in 10,000 of the general population. Most rare diseases have a genetic component and if apparent in early life a significant number die before their 5th birthday. Reportedly only around 400 rare diseases have therapies and so I was interested to hear about The UK Strategy for Rare Diseases, if you have time it is an interesting read. The focus is more on the clinical side but the recognition of the need for robust epidemiological analysis and coordination of research activities of the major research funders is highlighted.

Useful sites:
Rare Diseases UK
National Organisation for Rare Diseases
Global Genes

EFMC Position Paper on Medicinal Chemistry

Changes in the Pharma industry have thrown into sharp focus the role of medicinal chemists, the European Federation for Medicinal Chemistry (EFMC) have now published a position paper defining the role of medicinal chemistry.

Medicinal chemistry is concerned with the design and synthesis of biologically active molecules. It aims at creating new chemical structures to better understand and influence physiological and/or pathological systems. Ultimately, it allows the discovery and optimization of novel drug candidates to address unmet medical needs, as exemplified by recent progress in the treatment of cancer, cardiovascular or infectious diseases.

You can read the full paper here.

Drug Discovery Resources Update

I spent the weekend updating the Drug Discovery Resources, in particular I added a page on Target Validation, updated the Hit Identification expanding the section on Published Fragment Hits, and updated the ADME section and Preclinical Checklist.

As ever any comments or suggestions are most welcome.

Acessing Open Source Malaria Data

The Open Source Malaria project is trying a different approach to curing malaria. Guided by open source principles, everything is open and anyone can contribute. To date a lot of people around the world have made contributions and the project is at a very exciting stage. Whilst everyone can see the compounds that have been made and the biological data, it is often spread over multiple web pages and can be tricky to link molecule with identifier with data. Over the last couple of months a significant effort has been put into populating a spreadsheet with all the information.

In addition to a Vortex script to access the information, there is now an iPython notebook that also shows how to import the data. Why not give it a try, do some analysis and build predictive models and then contribute your findings and suggestions to the Open Source Malaria project.

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Time Dependent Inhibition

I've just updated the Drug Discovery Resources page on CYP Interactions, included a section on Time Dependent Inhibition (TDI).

ResearchKit

An article on BuzzFeed suggests that Pharma companies are investigating the use of ResearchKit in clinical trial studies.

ResearchKit is an open source framework introduced by Apple that allows researchers and developers to create powerful apps for medical research. Easily create visual consent flows, real-time dynamic active tasks, and surveys using a variety of customizable modules that you can build upon and share with the community. And since ResearchKit works seamlessly with HealthKit, researchers can access even more relevant data for their studies — like daily step counts, calorie use, and heart rate

GlaxoSmithKline apparently is currently working on integrating (ResearchKit) into clinical trials and planning to start in coming months, whilst Purdue Pharma are in the early stages of exploring whether Apple’s new tool for research data collection can be used as part of its own drug R&D efforts.

So far, ResearchKit apps are being led by academic medical centers like the University of California, San Francisco, and nonprofits like Sage Bionetworks and the Michael J. Fox Foundation for Parkinson’s Research. LifeMap Solutions, a company that develops mobile health apps, helped create the asthma app in partnership with the Icahn School of Medicine at Mount Sinai. The first ResearchKit apps signed up more than 75,000 participants in just the first few months

Antibiotic Screening

A little while ago I mentioned The Community for Open Antimicrobial Drug Discovery effort to provide free compound screening against a variety of infective agents. I now have a few more details of what you might be able to access for a 1mg sample.

Primary Screening:- Test against key ESKAPE pathogens, E. coli, K. pneumoniae, A. baumannii, P. aeruginosa, S. aureus (MRSA), as well as the fungi C. neoformans and C. albicans, at a single concentration.
Hit Confirmation:- Confirm activity with minimum inhibitory concentration and counterscreen for cytotoxicity and membrane interaction.
Hit Validation:- Test the positive hit against a broader panel of microbes and evaluate the basic drug qualities of actives.

CO-ADD will screen your compounds for free and make no claim to IP

The linked flyer gives full details

Sounds like a great opportunity.

Metrabase

The Metabolism and Transport Database (Metrabase) is a cheminformatics and bioinformatics resource that contains curated data related to human small molecule metabolism and transport, Journal of Cheminformatics 2015, 7:31 DOI. Currently it includes interaction data on 20 transporters, 3438 molecules and 11649 interaction records manually abstracted from 1211 literature references and supplemented with data from other resources as shown in the image below taken from the original publication.

s13321-015-0083-5-1

I've added this and more details to the Transporters page of the Drug Discovery Resources

Importing Open Source Malaria Project data

The Open Source Malaria project is trying a different approach to curing malaria. Guided by open source principles, everything is open and anyone can contribute. To date a lot of people around the world have made contributions and the project is at a very exciting stage. Whilst everyone can see the compounds that have been made and the biological data, it is often spread over multiple web pages and can be tricky to link molecule with identifier with data. Over the last couple of months a significant effort has been put into populating a spreadsheet with all the information.

Whilst this is useful for viewing results it is not ideal for trying to build predictive models. Vortex is a chemically intelligent data analysis and visualisation platform. This vortex script provides a one-click access to the OSM data and creates a workspace containing all the data, and since it is linked to the live spreadsheet you will always have access to the latest data.

osmVortex

Why not give it a try and then contribute your findings and suggestions to the Open Source Malaria project.

Online Research Market for startups

A new research marketplace for biotech startups has been launched by One Nucleus, the life science membership guardian of the Cambridge life science cluster, and Californian partner organisation Assay Depot in San Diego -

Using the One Nucleus Marketplace, a biotech researcher can custom design and purchase any research service imaginable, including reagents (eg: antibodies, compounds, peptides, RNAi), biosamples (eg: tissues, cells, blood, serum), animal models (eg: patient derived xenografts, disease models) and any other preclinical study required by the EMA for drug candidate submission

More details here LINK