Achieving efficient 3-D comparison models for discovering new therapeutic drugs

Discovering new drugs to treat diseases is often a lengthy and a costly process - we all know that. We may also know that the process involves a combination of lab-based and computational approaches.

Recently scientists have come up with a new virtual screening approach that involves using the 3D structural data of chemical compounds and use them to structurally dock-fit them against a target molecule. The findings appear in the recent issue of the Journal BMC Bioinformatics -an open access journal. The article is available for free download at http://www.biomedcentral.com/1471-2105/10/245.

Called 'LigCSRre', the new computational approach combines a 3D maximum common substructure search algorithm, with a tunable description of atomic compatabilities.

Using 47 experimentally validated active compounds across five protein targets having different specificities, the approach was able to recover about 52% of the co-actives in the top 1% of the ranked list, for a single compound search. The scientists claim this to be better than gold standards of the field while calling it a new efficient and generic approach to the 3D similarity screening of small compounds. Further the flexibility in the software program's structure is stated to open doors for many enhancements.

The program is freely available to the academics for non-profit research at http://bioserv.rpbs.univ-paris-diderot.fr/LigCSRre.html.

Can Mobile phone radiation damage DNA in the sperms?

Well... this is one touchy issue. The harm caused by mobile phone radiation has been debated for a long time and many scientific investigations have since been conducted. Though the debate is yet to settle, a recent finding by scientists that mobile phone radiation can cause harm to the DNA in human spermatozoa , is sure to raise many an eyebrow and make male readers wary of handling their mobile phones.

The paper appears in the recent issue of the Journal, PLoS ONE - July 2009 - PLoS ONE 4(7): e6446. doi:10.1371/journal.pone.0006446. The article is freely available for full download.

Cutting the long story short, the scientists exposed purified human spermatozoa to radio-frequency electromagentic radiation tuned to 1.8 GHz and covering a range of specific absorption rates. The findings shows significant reduction in the motility, vitality and other important features of the sperms health while increasing the generation of reactive oxygen species and DNA fragmentation. The conclusions leave no doubt that such levels of radiation directly reaching the spermatozoa are likely to cause the demostrated harm.

However, the findings are only likely to generate a fresh spark of scientific debate, not to say the semi-knowledgeable voices from the lobbying industry (whether, for or against).

1. For example, it could be pointed out that that the power of radiation decreases exponentially as the device is moved away from the target. Hence the levels of radiation reaching the target organs are likely to be negligible unless or otherwise when directly pointed at the target.
2. The next rebuttal could be that layers of protection surrounding the target organ being able to effectively ward of the radiation
3. Most importantly, it could be safely said that the findings are at the test-tube level i.e. in-vitro

I am just mentioning the points that come of the top of my head. It is entirely possible to argue this case at a biochemical level too.

1. For example, the 8-OH-dG assay may be a good biomarker for estimating the levels of DNA damage but what about about cellular repair mechanisms the effectively remove the adducts. Should not an assay be carried out to measure the inherent levels of expression of such repair mechanisms?
2. Since this experiment is carried in vitro, what additional gene assays need to be carried out when carrying out a population study?

Questions can raised at many levels and I hope the readers of this blog post will take an interest in reviewing the article and help in defining future directions to this research that is so relevant in the modern-tech world.