CASD-NMR a boon to structure validation....

CASD-NMR(Critical Assessment of Automated Structure Determination) of Proteins is a rolling community-wide experiment involving developers of software tools / protocols for the automated calculation of protein structures from NMR data. The goal of CASD-NMR is to help advance the relevant methodology in order to reach the level of quality and reliability required for direct structure deposition in the PDB. CASD-NMR will also produce extensive data sets that will be useful to develop better methods for NMR structure validation. The more significance of this project is : In the future, automation in NMR will allow 'unsupervised' results to be accepted by the community as being correct and viable, ready for inclusion in the Protein Data Bank (PDB) straight away. The PDB is a database that stores macromolecular structural data that is freely and publicly available for further research.

Ref : http://www.e-nmr.eu/CASD-NMR

Novel Mass Spectrometry Application for drug discovery?

In one of my earlier blog, Dec., 28th 2008, ( FBDD- A New Approach Of Drug Discovery) I did mention about the use of a number of biophysical techniques as screening tools including high-throughput x-ray crystallography (the advantage of giving the best picture of how the fragment sits in the target) and when paired with NMR allows you to create a structure-based lead.

With different companies approaching this new route in different ways like :

1. high-throughput x-ray crystallography
2. NMR-fragment screening
3. fluorescence polarization assay and many other interesting ways like Protien-Protein interactions etc., this field I think have important role to play.

The drug discovery field got a momentum and has lead to a new direction.....

While reading Science Daily (Online issue, Sept 21, 2009), I found this interesting (article ) and really innovative finding , which I want to share...

Preliminary studies by the researchers (Dr. Ken & Dr.Rakesh )have shown that the new mass spectrometry tool—known as MALDI-QqQMS (matrix-assisted laser desorption ionization-triple quadruple mass spectrometer)—provides a superior means of measuring the enzyme reactions critical to drug discovery at speeds comparable to currently available high-throughput screening systems at significantly lower costs. As per the claim by the researchers, Dr. Ken Greis, "If introduced broadly, the new generation mass spectrometry-based method the researchers are proposing could significantly reduce the cost of running drug compound screening assays while also saving drug development teams substantial time by improving the accuracy of data collected. As per the claim by these researchers the above mentioned methods are costly.

Dr. Ken Greis and Dr. Rakesh Rathore have developed a custom high-throughput screening method using a generalized platform. Unlike the commercially available systems that analyze byproducts and coupled reactions, their system directly measures and quantifies the substrate and the end product of the reaction. They say using mass spectrometry to measure the mass and quantity of the product gives researchers a direct measure of the assay and more reliable compounds to explore, eliminating the chances for molecular interference common with chemiluminescence and fluorescence-based systems. Its a remarkable achievement and hope in the near future we will have an automated system for commercial use with least expense. Best of luck. For More....

Mode of action of curcumin establlished ?

In India, turmeric (Haldi-in Hindi, Arishin-in Kannada) has been used in food preparation. Curcumin (see the structure left side, is the principal curcuminoid). We used to read about its many properties like antitumour, antioxidant, antimyloid, antiarthritic and many others. Though scientific explanations were not established, still then our forefathers used turmeric for many centuries. Even it has been used in home remedies for cold, cough and as an antiseptic etc. But so for a little was known about the mode of action or how actually it works inside the body. Thanks to Dr.Rammoorthy, a professor of chemistry and biophysics at University of Michigan, has come up with explanation for this.

The authors claims that "curcumin acts as a disciplinarian, inserting itself into cell membranes and making them more orderly, a move that improves cells' resistance to infection and malignancy. More interesting is the technique they use is solid-state NMR spectroscopy(two-dimensional solid-state NMR technique). This technique which is unique helps to reveal atom-level details of these important molecules and the membranous milieu in which they operate.

In a related line of research, Ramamoorthy's team is using the same methods to investigate the effects of curcumin on the formation of amyloids---clumps of fibrous protein believed to be involved in type 2 diabetes, Alzheimer's disease, Parkinson's disease, and many other maladies. Congrats, Dr.Rammoorthy, for this achievement. If proven further details, hope something intersting and useful info for mankind. More..