A new database of information on the properties and activities of drugs and drug-like small molecules and their targets, launched in January 2010 with data on more than 520,000 compounds.

The database is now hosted by the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) having been transferred from biotech firm Galapagos NV in July 2008 through a £4.7 million Strategic Award from the Wellcome Trust. ChEMBLdb is unique in focusing on drug discovery and because of its size; 520,000 small molecules and 2.4 million records of their effects on biological systems. The data include information about how small molecules bind to their targets, how these compounds affect cells and whole organisms, and information on the molecules’ absorption, distribution, metabolism, excretion and toxicity.

Alan Schafer of the Wellcome Trust said: “This unprecedented transfer of pharmaceutical data resources from the private sector to the public domain should have the greatest impact on researchers in academia and in small companies on limited budgets. ChEMBLdb will be a major resource of information for driving forward medicinal chemistry and drug development in the UK and internationally.”

ChEMBLdb can now be accessed here.

Kristin Williamson of Wolfram|Alpha got in touch with me today to highlight a blog post on the W|A site explaining how to us it as a resource for chemistry basics.

“From finding quick facts about elements and converting properties to exploring chemical qualities and solutions, our blog post walks you through some examples of how to use Wolfram|Alpha as a tool for fast and accurate chemistry-related computations,” she says.

This is a guest post by a good friend of the blog who wishes to remain anonymous.

Several months ago I was approached by a franchise owner from one of North America’s largest fast food chains. He was perplexed as to why he was paying $35.00 for a role of Quat (quaternary ammonium chloride) test paper from which he was getting at best 14 tests while we were selling a comparable product for $12.00 that did 100 tests…1/20 the cost!

We sent him a pack of our strips to test, which he reported worked fine except that the readings were exactly double. We thought it might be a special Quat formulation for which we needed to recalibrate our strips. So, we got a sample of his Quat solution (which turned out to be a well known brand called Oasis 146) as well as an unopened dispenser of the test paper he was using. Our lab discovered that not only were our strips dead-on but the competitive strips were consistently reading only 50% of the true value for both the sample solution as well as three other commercially available brands.

Armed with this information, I contacted the purchasing agent at the fast food chain who handles this. I had assumed the potential savings would interest him. Initially incredulous, he asked for supporting data which I provided. I even supplied him with the names of labs in his area he could go to for independent testing.

Within weeks, I was blown off. It dawned on me that I had overlooked the obvious. The fast food chain demands that its franchisees buy all their supplies from them. Each franchisee has to spend over $1800/year on test strips whereas if they bought ours, it would be around $80.00. The competitive test papers cost only about $0.25 a roll to make but sell for $35Cdn. (That’s three markups before it gets to the franchisee). Multiply that by 3000 stores in Canada & you have over $5 million being spent compared to $250,000 for ours. Someone is making a lot of money! And, at a bare minimum this is 1/20th of the North American market. So, at least $100 million worth of test paper is being foisted on fast food franchisees compared to $5 million of equally good test strips.

Interestingly, the competition sells their product as a long roll in a plastic dispenser, like Scotch tape. The fast food workers tear off much longer strips than they need to, hence only about 14 tests rolls. Ours come with a small pad glued to a plastic strip.

Moreover, each franchise uses up 1 US gallon of solution per week at roughly $15.00Cdn per jug. Since they are using double the amount they really need, that adds another $400 per franchisee or $1.2 million for the entire Canadian chain or ~$25 million for the North American market. Aside from the expense it begs the question as to the environmental impact.

To top it all off, the local health authorities who instruct restaurant owners in proper sanitation may be unknowing dupes. I contacted one such office who told me they got their strips free & I should report this problem to the supplier. However, I pointed out that it seemed a bit odd that if neither the chemical company that makes the solution nor the company that makes the strips hadn’t done the QA already, why would they start now?

If I were a suspicious individual, I would suggest that the fast food chain owners are in collusion with the chemical supplier who is in bed with the test paper maker…

ChemZoo Inc (the menagerie behind ChemSpider.com) and the UK’s Royal Society of Chemistry have joined forces to create an InChI Resolver. This unique, free service allows scientists to share chemical structures and data transparently using the standard linear chemical structure format (InChI).

An InChI is an IUPAC standard identifier for compounds and provides a neat way to share chemical information when a 2D or 3D molecular structure cannot be transmitted. It has the advantage of being nothing but an alphanumeric string, which means it can be Googled from any web resource.

According to the press blurb: “The RSC/ChemSpider InChI Resolver will give researchers the tools to create standard InChI data for their own compounds, create and use search engine-friendly InChIKeys to search for compounds, and deposit their data for others to use in the future.”

Thanks to Chemspiderman, Tony Williams, for alerting us to the source.

ACS Publications has recently launched a dynamic new web delivery system, hosting 34 ACS peer-reviewed research journals on a fully integrated web platform rich with new features and functionality. The new website provides a state-of-the-art online experience for information discovery, interactivity and research productivity for scientists and professionals worldwide. A Flash-based demonstration available at http://pubs.acs.org/flashdemo showcases many of the features and benefits of the new site.

That’s all well and good, but boy do they make you jump through digital hoops to get registered and up and running. First off, I had several duplicate emails making the announcement and telling me to login at pubs.acs.org to set my e-alerts (I only want ASAPs but I seem to be getting ToCs now as well). You cannot then just login with your membership number, you have to register as a user, but that happens on www.acs.org which is announced via a popup dialog box that has to be closed before you can then re-enter the new URL instead of simply redirecting.

There are several more steps but once you’re in, correcting errors in your work address seems to involve starting entry from scratch so I abandoned that update with my old zipcode intact. Just as I thought I’d got through the last hoop and clicked the link in the confirmation email, I get a “network error” on attempting to login. Not a fun experience, I have to say, but at least they’ve got a nice flash video, and once you’re in it should be well worth the effort…

Defining chemical definitions – Chemists Catherine Castillo-Colaux and Alain Krief of the University Notre-Dame de la Paix, Namur, Belgium, describe the different stages involved in the collaborative construction of an organic chemical ontology – a glossary of definitions and relationships – by chemists. Writing in the International Journal of Knowledge and Learning, they reveal their experiences, as chemists as opposed to computer scientists, in learning how to build a collaborative ontology and how to use the ontology software to do so. In so doing they show how chemists can work together on essentially computer science projects that benefit the chemistry community.

The chemists were working on building EnCOrE, a freely accessible net-based encyclopaedia of organic chemistry. They had selected what they thought to be adequate tools and strategies for transferring chemical knowledge into an electronic format but the whole process proved to be “far from easy”.

“The initial expectation that selected hypertext links would solve the problem proved to be inaccurate,” the researchers explain, “since those links were too numerous and too static. We also found that even the more elaborated XML language was inadequate, since we had too many interconnected contexts related to a single paragraph.”

The way forward was to adopt an ontological approach. An ontology, in the informatics and computing, as opposed to philosophical sense, is a formal explicit description of all the concepts in a given field. So an organic chemical ontology would include details of carbon, compounds, reactions, bonds, etc. An ontology contains Classes, or concepts, Slots, roles or properties, and Facets, role restrictions and together with a set of individual instances of classes, represents the sum of knowledge for the subject in question. It is the complete dictionary, taxonomy and semantics of the field formalised so that it is machine readable.

“We have been attracted by their efficiency to organise the inherent concepts within a domain or a subdomain and to ensure consistency between the different modules of our encyclopaedia,” the researchers explain.

The researchers outline the aches and pains they experienced in developing their ontology using various collaborative and Grid tools and ultimately the successes.

It took us quite a lot of time to become acquainted with and to understand ontology building. Our goal, as ‘chemists who are neophytes in ontology’ was not only to create an ontology of organic chemistry but also to find the important steps to enable ourselves as well as other chemists to be able to do so. It implies finding the best way to learn this new field.

Given the failures of certain approaches to ontology building, the team carefully analysed the different problems encountered and have devised a new protocol they say will help other chemists develop ontologies for their own purposes and in their own fields.

“This way, we believe, the chemist or the expert in general can work at his/her own rhythm and find the right support at the right moment,” the researchers say, “The success of this protocol indeed deals with its capacity to allow the participant to learn and at the same time to work. Use of the appropriate tool seems to be essential for success.”

Catherine Castillo Colaux, Alain Krief (2008). Protocols for building an organic chemical ontology International Journal of Knowledge and Learning, 4 (2/3) DOI: 10.1504/IJKL.2008.020652

A $2 egg-beater could save lives in developing countries, according to a report from the UK’s Royal Society of Chemistry. A piece of inexpensive plastic tubing taped to a handheld egg-whisk could be used as an ad hoc centrifuge for separating out blood plasma in a matter of minutes and allow life-saving diagnostic medical tests to be carried out much faster and at far less cost than with conventional lab-based centrifuge equipment.

George Whitesides and colleagues at Harvard University, USA, say the plasma obtained is easily good enough to use in tests to detect diseases such as Hepatitis B and cysticercosis, a parasitic infection of the nervous system.

“The object was to separate serum [plasma] from blood using readily-obtained materials in a resource-constrained environment,” explains Whitesides. The equipment can be bought from shops for around two dollars. It needs no special training to use, no electricity or maintenance, and can be sterilised with boiling water and reused. The user can even prepare several samples at once – just by taping more lengths of tubing to the beater.

This simple DIY approach to diagnostics contrasts starkly with the bulky, and fragile commercial centrifuges, that cost thousands of dollars and require extensive operator training. Given that it is Blog Action Day on poverty, it is rather timely that this new, simple technology is announced today.

“This technique is simple and works remarkably well,” says Doug Weibel, an expert in microbiology at the University of Wisconsin-Madison, US. “This technique complements several other ’simple solutions’ that the Whitesides group has developed to tackle point-of-care diagnostics in resource-poor settings.”

Amy P. Wong, Malancha Gupta, Sergey S. Shevkoplyas, George M. Whitesides (2008). Egg beater as centrifuge: isolating human blood plasma from whole blood in resource-poor settings Lab on a Chip DOI: 10.1039/b809830c

My latest feature article was published recently in Nature Reviews Drug Discovery. In it I discuss the issues surrounding the next phase of the US National Institutes of Health roadmap in which the Molecular Libraries Initiative (MLI) becomes the Molecular Libraries Program (MLP) with what appears to be a deficit of cheminformatics.

You can subscribe to the print edition of Nature Reviews Drug Discovery, which I can, of course, highly recommend, courtesy of Chemspy. It’s free to qualifying professionals in North America and some selected international readers. There’s a quick form to fill in but free if you make the effort to do that.
(2008). Dealing with a data dilemma. Nature Reviews Drug Discovery, 7(8), 632-633. DOI: 10.1038/nrd2649

As of October, the UK Department of Health is updating the health warnings and information taglines it includes on packets of cigarettes and other tobacco products because, despite a nationwide ban on smoking in the workplace (buildings and vehicles), smoking remains an incredibly popular pastime. As of October 1, 2008, they are also going to force tobacco manufacturers to include graphic images of cadavers and diseased body parts to be printed on packaging.

Anyway, in case you couldn’t think of a reason not to stop smoking, here are the fifteen top warnings:

1. Smokers die younger
2. Smoking clogs the arteries and causes heart attacks and strokes
3. Smoking causes fatal lung cancer
4. Smoking is highly addictive, don’t start
5. Stopping smoking reduces the risk of fatal heart and lung diseases
6. Smoking can cause a slow and painful death
7. Smoking causes aging of the skin
8. Smoking can damage sperm and decreases fertility
9. Smoking may reduce the blood flow and cause impotence
10. Smoking contains benzene, nitrosamines, formaldehyde and hydrogen cyanide
11. Smoking when pregnant harms your baby
12. Protect children, don’t make them breathe your smoke
13. Smoking costs a packet

Actually #13 is one I added to the list of warnings. #14 would have to be smoking causes global warming, but that is perhaps laboring the point a little too much. More information here.

(Imperial College London) A new type of drug could alleviate pain in a similar way to cannabis without affecting the brain, according to a new study. The research demonstrates for the first time that cannabinoid receptors called CB2, which can be activated by cannabis use, are present in human sensory nerves in the peripheral nervous system, but are not present in a normal human brain.