Please share your slides (or related materials) before your individual talk or give the link of the paper (or blog post) if you want to discuss in that session. One volunteer will reorganize the materials after each discussion.

Seminar Sep. 21, 2011

organizer--Bin Chen


PREDICT: a method for inferring novel drug indications with application to personalized medicine(nature molecular systems biology by Bin)

Improving Drug Candidates by Design: A Focus on Physicochemical Properties As a Means of Improving Compound Disposition and Safety (Chem. Res. Toxicol., 2011, 24 (9), pp 1420–1456 by Stefan)
Very interesting publication! Focus on the physicochemical properties, especially lipophilicity in drug design and implication on toxicity. Drug discovery is relying heavily on improving target affinity, while a more holistic approach on drug design would be neccessary. Structural fragments, with high dependence on aromatic rings are assembled into molecules with increased molecular weight and high overall lipophilicity – driving potency through “molecular obesity”. Trends in physicochemical properties of drugs launched over time are presented, highlighting the push to higher MW and cLogP. Impact of high cLogP on key ADME functions are described, like solubility, plasma protein binding or brain tissue binding to name a few – the higher the cLogP, the lower the solubility, the higher the binding. Concept of ligand efficiency (LE) – a measure of affinity per heavy atom and lipophilic ligand efficiency (LLE) – relating potency to lipophilicity are introduced and described on different examples.
Ligand efficiency LE = (pKi, pKd, pIC50) / # heavy atoms
Lipophilic ligand efficiency LLE = (pKi, pKd, pIC50) - cLogP

Seminar Oct. 5, 2011

Semantics Scales Up: Beyond Search in Web 3.0(from Amit Sheth blog by Bin)
Drug repurposing: Beta blockers 'may stop breast cancer spreading'(BBC news, by Bin)
It reports if blood pressure drugs could prevent the spreading of breast cancer.
Beta blockers 'may stop breast cancer spreading'Elemental composition determination based on MSn (from bioinformatics by Chuanyih)

Next Seminar

A web server for predicting inhibitors against bacterial target GlmU protein (Cheminformatics by Abhik)
ChemRobot: A Teaching and Research Assistant in Chemistry (Dr M Karthikeyan Blog By Abhik)
Seminar Nov 16 2011
Pharmacophore and Ftrees ABHIK

Next Seminar

PharmMapper : a web server for potential drug target identification using pharmacophore mapping approach (Abhik)

Feb 24th 2012

Kinnings et al. The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications. PLoS Computational Biology, 2010, 6, 11(Abhik)

March 2nd 2012

Predicting Adverse Drug Events Using Pharmacological Network Models .Aurel Cami etal. (Jae Hong)

The influence of the 'organizational factor' on compound quality in drug discovery .Paul D. Leeson & Stephen A. St-Gallay (Abhik)