Category: Chemspy

I’m a bit confused, I had assumed that the complete stereochemistry of the anticancer drug Taxol (paclitaxel) had been assigned years ago, presumably at the point when its first total synthesis was performed if not before. I’ve written about the compound several times, in particular reporting that first total synthesis of the compound in the UK paper, The Daily Telegraph.

However, it seems there is ambiguity spreading across the net. Most notably, ChemSpider’s Tony Williams tells me (and has blogged about it), there is a potential discrepancy in the structure of Taxol given in Wikipedia.

Now, I know for a fact that Wikipedian chemist Martin Walker (see my recent interview with him in Reactive Reports) who is a member of the ChemSpider advisory board will already be on the case to double check and check again the structure in Wikipedia.

Aside from the politics of open access information and data, it is crucial that services like ChemSpider and Wikipedia give their users the correct structure for any given compound. There must be dozens of synthetic organic chemists who have carried out full stereochemical assignments on Taxol and know for certain the correct structure. Perhaps it’s time we had a referendum so that the winning structure could be posted to Wikipedia and other information repositories.

Earlier this month, I hinted at how InChIKeys might be used in Googling for chemical information, well, I missed a trick. In 2006, at the BioIT World Life Sciences Conference and Expo, Microsoft announced the formation of the BioIT Alliance. The Alliance is a group of organizations working together to realize the potential of personalized medicine. Now, the Institute of Pure and Applied Chemistry (IUPAC) has joined the club. IUPAC’s contribution to the enterprise will lie primarily in being responsible for establishing standards in chemical information transmission. In this regard the InChI/InChIKey system will be critical to success.

IUPAC representative Stephen Heller says: The InChI/InChIKey is the first publicly available unique chemical identifier, which allows scientists to link and exchange information and data across the chemosphere and in the life sciences. The InChI/InChIKey is the molecular equivalent of a Digital Object Identifier (DOI), the journal article tracking code. “The InChI/InChIKey is an agent of change and an agent of the future for linking the chemical, biochemical, and biomedical information and data on the web,” says Heller. It will now provide the Microsoft BioIT Alliance with a much simpler, and free, way to work with chemical information.

A new project that combines work from two distinct cheminformatics groups will form a new system for the delivery of modeling and identification of commercially available compounds for biological testing.

The North Carolina State University Exploratory Center for Cheminformatics Research group, developed ChemModLab to compute quantitative structure-activity relationship (QSAR) models and this will be pulled together with the almost 18million structures currently in the ChemSpider database. These structures are sourced from the scientific literature, chemistry database providers and commercial chemical vendors and screening library providers.

“This data collection provides an ideal basis for combing the QSAR capabilities of ChemModLab with the compound collection and indexing of ChemSpider to allow identification of virtual hit compounds via in silico screening, says ChemSpider boss Antony Williams.

What it is to be an InChI – at once unique and representative of so much and yet meandering and potentially far too long. Now, IUPAC has launched a new version – InChIKey – a condensed version of the InChI chemical identifier that will be a fixed 25-characters long.

This new format will make searching for molecules on the web much simpler by preventing unpredictable breaks that happen with the conventional seemingly endless InChI strings for some of the more complex compounds. It will thus facilitate a web-based InChI lookup service and allow InChI to be stored in fixed length database fields and so make chemical structure database indexing far easier. One of the most important aspects of this new approach to the InChI is that it will allow verification of InChI strings across networks. Imagine the woe, for instance, if the tail of your Viagra InChI were cropped short in transmission…

IUPAC admits that there is a finite, but very small probability of finding two structures with the same InChIKey. The odds are of the order of billions to one against, but chemists are making more and more new substances as we speak so you never know when there might be a data collision. It is very, very unlikely, however.

The new release can be downloaded from the IUPAC web site (www.iupac.org/inchi). What effect this will have on my passwords for chemists idea, I simply don’t know!

ChemAxon recently announced version 2 of its Instant JChem, a desktop application for working with chemical and
other data on local and remote databases. Version 2 adds forms and form building, relational data support, advanced query
building and multiuser access.

Instant JChem is a software application for all major operating systems which bundles ChemAxon’s Marvin and JChem enterprise cheminformatics toolkits with a local database engine to give an ‘out of the box’ solution for research informatics. Personal use is free, although if you want to go “enterprise” you will have to check out their price list.

antibodies-online launched in April 2006 and calls itself the marketplace for research antibodies providing scientists in Germany, Austria, and Switzerland with invaluable assistance in finding antibodies quickly and easily, a task that was once very time-consuming when predominantly paper-based catalogues were the only resource for searching available.

The company also acts as a kind of immunological broker allowing antibody distributors and producers to ply their trade online at low costs and no risks. The reason I mentioned it on ChemSpy.com is that the their site provides access to information on some 60,000 antibodies in a database, with that number growing every day. Such a resource could prove invaluable to many researchers working in silico let alone in vitro and in vivo. antibodies-online.com claims to be one of the largest vendor-independent platform for research antibodies in that region and plans to increase its product portfolio to more than 100,000 antibodies by Spring 2008, which could make it an even more useful resource.

The American Chemical Society is following up the success of its preliminary reports publication Nano Letters with a full-blown journal – ACS Nano. Penn State’s Paul Weiss will be Editor and the journal will publish monthly in print and online.

The inaugural issue features work from David Allara, Hongjie Dai, Prashant Kamat, and Frank Caruso, as well as a conversation with Nobel Laureate Heinrich Rohrer, and an editorial from Weiss. A news ection, NanoFocus, will also feature.

If you’re an institutional subscriber you can access Nano at no extra charge for the remainder of 2007 at www.acsnano.org.

American Biotechnology Magazine – ABL is one of the leading editorial publications for the life sciences research community for the last twenty years. The magazine is free to readers in North America and will help you keep abreast of the latest developments in life science instrumentation and apparatus, bioanalytical chemistry, kits, and biologicals. Just click the link and fill in the form to qualify for a free subscription for qualified professionals.