Medicinal Herb Analysis with Grid Technology

The use of medicinal herb in curing the disease is part of Thai’s way of life since the ancient time. This is especially true in the remote rural area where the drug is expensive and the ancient wisdom still has a effect on people life. Anyway, most of the information collected about this medicinal herb is about how it can be used to cure various kinds of diseases. This is mostly based on the experimental results and conventional believe. In order to improve the understanding about how the medicinal herb can be used a more scientific approach that can be used to verify the results can be substantially useful. In order to do so , a more complete information about the molecular structure of these herbs and a massive analysis infrastructure is needed.In order to reach that goal, Dr. Chak Sangma and his team from Cheminformatics Research Unit, Department of Chemistry, Faculty of science, Kasetsart University has been busy working on developing the databases of the three-dimensional molecular structure of medicinal herbs for the past few years. The goal is to enable Thai Researchers to have a centralized access to various molecular structures and use them to study how these medicines will interact with the diseases. The information his team collected in the database is a vital key to the scientific study of the medicinal herb.

Dr. Chak reveals that “Thailand has a large number of medicinal herbs and many drugs are produced base on medicinal herb can the conventional method. However, many drugs being produced that way may not be tested at the chemical level. Hence, it is not very certain that which drug really contains which chemical substances and how it actually cures the disease. Therefore, there should be an extensive study of each medicinal herb by collecting their property and molecular structure and apply computer method to pre-test them. Then, a small number of active substances can be further experiment in the lab. This scientific approach will lead to a much safer medicinal herb drug for Thailand.”. Currently, his team has built a database of more than 100,000 3D molecular structures by collecting all the test data and model the molecular structure into computer using software such as corina. Dr. Chak and his team rely on the Grid infrastructure for the work. The Autodock, FRED (from openeyes software), and many open sources tools has been installed and use on the Grid. SGE and Gridway is employed to manage the available resources on the Grid.

Dr. Chak and his team also work  on buillding a virtual screening portal on the Grid so that researchers can choose from the database of more than 100,000 3D molecular structure collected. Researchers can directly experiment with them using the power of the Grid to do the molecular docking experiment with selected molecule. This, in fact, will let to a more effective way from researchers to conduct the research on diseases such as avian flu and HIV. So far, more than 30 positive substances has been found and the test are being conduct in the experimental lab to verify the results.

Dr. Chak concludes that “With the power of the Grid, the work that we do finish much faster. This allows us to do more work and more extensive study of the active substances. In addition, by providing the access through portal, the data and computing power available will help driving the medicinal herb research into another level. I hope that the use of scientific approach to medicinal herb based drug design will be widely adopted in Thailand and lead to a cost-effective, safer, and better drug for Thai People in the future. We hope to make a life for poor people or people in the remote rural area a little bit better”