Blogging the biotechnology revolution

Systems Biology is changing the way biology is done. Is it a fad or is it effective? This blog tracks current happenings and helps you stay on top of the field. You can find a list of relevant papers at systems biology paper watch Have you heard a talk or read a paper in bioinformatics / systems biology you would like to tell other people about? Email: and get the word out!

Friday, April 04, 2008

La Jolla Bioinformatics Conference 2008. This conference features a blend of speakers from both academia and industry with a focus on systems biology/bioinformatics. Because ive talked about most of the academic researchers speaking, ill focus on Industry in bioinformatics.

Steven Hofstadler, VP of research at Ibis Biosciences.
Presented the companies work in determining the identity of an unknown pathogen by primers in a conserved region around a variable region. Such as 23s ribosome which is conserved in many species. They use MS to determine base composition that they use as a signature of a species. The problem of determining base composition from mass measurements is made easier by base complementarity – you know the complement must have the same weight thus reducing your search space for possible bases compositions. From the data he presented this is enough information to distinguish most species of bacteria/pathogens. Using this they were able to identify multiple pathogens in a throat swab sample, which had multiple unknown pathogens. They also have applied this technology toward human and avian flus to determine their subtypes.

Coming away from this talk - someone asked how far do they think this MS-based approach will go. It would seem to me that the time for this is limited with the advent of fast and cheap sequencing technologies-- Its more likely that a hospital or first response site would have a sequencer rather than a mass spec..

Steven Burley, SGX pharmaceuticals
The company is based on Structure based drug discovery. The have a direct spot at the accelerator in Chicago which can run their whole library in 3 days. Their drugs are based on scaffolds that have attachable arms that can be interchanged—providing a modular design for drugs that can be customized using a liquid handler robot. Crystals are created in a pool of a large number of potential leads. Drugs that are tight binders would co-crystallize with the protein providing a potential drug hit. The compounds are optimized based on conformation prediction of drug variants with the known protein structure – a variant of combinatorial chemistry. One of the major boons of this approach is the selectivity, nearly 70% of their compounds only target a single kinase (rather than multiple kinases like many drugs). Showed beginnings of inhibitors targeted to BCR-ABL mutations (such as T315I) which are resistant to Gleevec. Also drugs targeted to MET receptor which activated various kinase cascades and mutations in which implicated in Hereditary papillary renal cell carcinoma.

This was a good talk with some very interesting insight into how drug discovery is done - from target identification to trails. The company was recently hit with some bad news about one of their prize BCR-ABL drug trials (apparently caused toxicity at high dose in trials), but Dr Burley didnt seem to worried about it, they had a couple of other drugs in the pipeline.

Overall it was an entertaining confernce that highlighted the great work done in the area around San Diego - Biotech Beach!