Ultrafast Sequencing Boosts Target Identification in Diarylquinoline Drug Research

The ultrafast Genome Sequencer 20 System from Roche Diagnostics finds its application in ever-increasing fields of life science research.

In a recent publication (1), K. Andries et al. reported on the antimycobacterial prop­erties of the diarylquinolines (DARQs). The lead compound, R207910, not only has several properties that may improve the treatment of tuberkulosis, but also appears to act at a new target, providing an antimycobacterial spectrum different from those of current drugs. The researchers used the Genome Sequencer 20 technology (GS 20 System) for target identification, thus saving some months of time in finishing their work.

Andries et al. found the target and mechanism of action of R207910 different from those of other anti-TB agents. Inhibition of ATP synthase function may lead to ATP depletion and imbalance in pH homeostasis, both contributing to decreased survival (2, 3). In comparing the ATP synthases sequences of different bacteria and of eukaryotic ATP synthase the researchers found a rationale for the specificity of the antibacterial spectrum, and - to a lesser extent - the safety profile of R207910. A further finding was that the distinct target of R207910 indicates the lack of crossresistance with existing anti-TB drugs. The studies verified that R207910 is as effective against MDR strains as it is against fully antibiotic-susceptible strains.

The DARQ R207910 belongs to a new chemical class of antimycobacterial agents and has a MIC equal to or lower than that of reference compounds. Its spectrum is unique in its specificity to mycobacteria, including typical species important in humans such as MAC, M. kansasii, and the fast growers M. fortuitum and M. abscessus. According to Andries et al.´s paper, the clinical use of R207910 will be highly targeted to the treatment of TB and mycobacterial infections.

Since 1980, when Gilbert and Sanger received the Nobel Prize for chemistry for DNA-sequencing, the shotgun sequencing method according to Sanger developed to the the most popular sequencing technology (4). Some 280 microbial genomes have been completely sequenced to date with this electrophoresis-based technique (5).

Since end of last year, a new approach is available on the market, setting new standards in velocitiy and cost-effectiveness. The Genome Sequencer 20 System from Roche Applied Science, a business unit of Roche Diagnostics basing on a technology developed by the US company 454 Life Sciences (6), can perform sequencing runs up to 100 times faster than conventional commercially available platforms. For preparation of a whole genome, only one single preparation step, without extensive robots for colony picking and handling of the microtiter plates, is needed. One single instrument can produce dozens of megabases of sequence data within a few hours, thanks to parallel-processing, the latest imaging techniques and unique data analysis. The resulting substantial reductions in both time and costs will offer the prospect of new applications for sequencing, which particularly maybe suitable for the following tasks:

• production of high-quality drafts of hitherto unsequenced genomes, for identification of ORFs (open reading frame), comparison with other organisms, and generation of an overview of genome structure,
• production of high-quality drafts of strain variants, to identify preserved sections, mutation hotspots, and inserted or deleted genes,
• searching for rare mutations in genomes

After AIDS, tuberculosis (TB) is the leading cause of infectious disease mortality in the world, with 2 to 3 million deaths per year. The TB and HIV epidemics fuel one another in coinfected people, and at least 11 million adults are infected with both pathogens. Consequently, one of the factors contributing to the TB burden is the recent increase in the number of HIV-infected individuals. Although current first-line anti-TB drug regimens can achieve more than 99% effica­cy, this is often reduced because of drug resistance. New drugs that could shorten or simplify effective treatment of TB would substantially improve TB control programs.

(1) K. Andries, P. Verhasselt, J. Guillemont, H. W. H. Göhlmann, J.-M. Neefs, H. Winkler, J. van Gestel, P.Timmerman, M. Zhu, E. Lee, P. Williams, D. de Chaffoy, E. Huitric, S. Hoffner, E. Cambau, C. Truffot-Pernot, N. Lounis, V. Jarlier, SCIENCE Vol. 307, 223-227 (2005).
(2) M. Rao, T. L. Streur, F. E. Aldwell, G. M. Cook, Microbiology 147, 1017 (2001).
(3) G. Deckers-Hebestreit, K. Altendorf, Annu. Rev. Microbiol. 50, 791 (1996).
(4) http://www.jgi.doe.gov/education/how/index.html
(5) http://www.genomesonline.org/
(6) Margulies, M. et al., Nature online publication. Doi:10,1038/nature 03959 (2005).