I’ve just updated the online chemical databases page.

Several companies have kindly sent me updated copies of the structure files for their fragment collections.

I’ve updated the analysis of the collections and added a couple more properties, by calculating the most acid/basic pKa I’ve catagorised the fragments into acid/base/neutral/zwitterion. I’ve also calculated the fraction of aromatic atoms (number of aromatic/number heavy atoms), one comment I’ve heard about some collections is that they contain too many aromatic compounds and have issues with solubility.

Full details are on the Fragment Collection Profiles page.

I’ve just updated the page on fragment collection profiles

Full details are on the Fragment Collection Profiles page.

I’ve just completed an addition to the Drug Discovery Resources, since fragment-based screening has increased in popularity I thought I’d have a look at available fragment collections. In particular, I looked at the overlap between collections, the physicochemical profiles and their diversity.

Full details are on the Fragment Collection Profiles page.

Just completed a project to help design a fragment library for Selcia to be used with their proprietary fragment screening technology CEFrag.

A poster will be presented at the FBLD2010 meeting in Philadelphia in October

The first circular for the 16th RSC-SCI Medicinal Chemistry Symposium, 11-14 September 2011, Churchill College, Cambridge, UK is now available here.

Scientifc Program includes:-

• Strategies to success - H-PGDS inhibitors for the treatment of inflamatory disorders, Sukanthini Thurauratnam, Sanofi -Aventis

• Discovery on next generation glucokinase activators, Mike Waring, AstraZeneca

• Inhalation by design, Paul Glosson, Pfizer

• Bromodomains a new class of epigenetic targets for small molecule drug discovery, Jason Witherington, GSK

• GPCR Structure based drug design using stabilised receptors(StaRs), Miles Congreve, Heptares

• GS-9350: a novel pharmacoenhancer, Lianhong Xu, Gilead Sciences

If like me you regularly come across drugs mentioned on web pages that you are unfamiliar with then this Safari Extension will be of interest. If a page contains a drug name (this page describes AOX1 substrates), select the name and right click (or control click) and an option appears to search for the highlighted drug on ChemSpider.

Click on Search for “Loratidine” on ChemSpider option and the structure appears in a small window.

The new version of the extension has a few extra options, the small window that pops up containing the structure now has a number of additional options highlighted below, if you click on the “3D” button the display changes to a 3D rendering using the Java applet JMOL. If you now click on the “Zoom” button.

If you then click on the “view” option a new page opens showing the full details in ChemSpider.

Recently two groups have reported the results of screening campaigns, GlaxoSmithKline (GSK) published ( doi:10.1038/nature09107 ) the results of screening nearly 2 million compounds from their chemical library for inhibitors of P. falciparum, of which 13,533 were confirmed to inhibit parasite growth by at least 80% at 2 uM. The chemical structures and associated data were made public to encourage additional drug lead identification efforts and further research into this disease. In a second paper ( doi:10.1038/nature09099 ) a library containing 309,474 unique compounds, “designed at the scaffold level to provide diverse, comprehensive coverage of bioactive space”, was screened against Plasmodium falciparum strain 3D7 at a fixed concentration of 7 uM and afforded 1536 hits.

I thought I'd contribute to this generous effort by calculating a number of descriptors and properties for the molecules and then cluster the molecules in a variety of ways to help analysis and provide the data for download. You can read about it here.

Added the RSS feed for MedChemComm the new journal from the RSC

I’ve added a section on Aldehyde Oxidase (AOX1), an enzyme involved in the metabolism of many nitrogen containing heterocycles.

Updated Essential Reading

Updated the section on Bioisosteres.

Added a page of privileged structures.

I’ve added a page on Computational Chemistry Books.

Updated the Chemical Databases and Physicochemical Properties pages of the Drug Discovery Resources.

Updated the list of commercially available fragment libraries.

I’ve just added a new section to the Drug Discovery Resources describing :-

Frequent Hitters, False Positives, Promiscuous Compounds

I’ve just updated the HERG activity page. Adding new data from the literature.