FAU researchers seek to improve drug design
The effects of millions of natural biological compounds are now known to modern health and pharmaceutical research. If, for instance, the body’s levels of protein A are too low or too high, reaction B or C can occur. Pharmacists use this knowledge to produce new drugs. They develop synthetic materials that imitate the therapeutic effects of known natural compounds in a process known as “drug design”. Computers are now routinely used in this process, helping researchers to find the best combination of active substances, most suitable for synthetic production, from among the millions of available compounds. However, so far, computer hit ratios have been very low. This is where the research project “High-performance Computer-aided Drug Design”, led by Prof. Dr. Tim Clark from the Computer Chemistry Centre at Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU) comes in. Clark and his research team intend to replace conventional computers with a new high-performance version. The German Federal Ministry for Education and Research has also decided to support the project with 1.5 million euros over three years. Around 1.1 million of this financing will come to FAU.
In addition to the Computer Chemistry Centre (CCC), FAU’s Prof. Dr. Dirk Zahn from the Department for Theoretical Chemistry and Prof. Dr. Gerhard Wellein, holder of a professorship in high-performance computing, will also be involved in the project. Further project partners include the Department for Theoretical Chemistry at the Technical University of Dortmund and Sanofi Aventis Deutschland GmbH.
“Databases contain information on the therapeutic effects of millions of molecules,” says Prof. Dr. Tim Clark. “Drug manufacturers are, however, often faced with the problem that these compounds do not have the desired effect, or are not suitable as active ingredients for oral use, for example, as tablets.” Computers will be used to go through the vast quantities of data sets to look for further compounds which will then be tested to ascertain whether they have the same effect as natural compounds and whether they would be suitable for pharmaceutical purposes.
“Using current programs and computers, a maximum of between one and two per cent of the filtered compounds are actually suitable for pharmaceutical production,” says Prof. Clark. As such, he intends to use high-performance computers, devices that only a few years ago did not even exist. Prof. Clark and his research team’s task is to develop new algorithms that make it possible for high-performance computers to simultaneously execute millions of computing processes. Their goal is to make drug production more efficient and to increase the hit ratio.
The Erlangen Regional Computing Centre already has a “super computer” that Prof. Clark’s research team will use for their work. The LIMA Cluster, as it is known, is currently ranked 196 among the 500 fastest computers in the world.
Prof. Dr. Tim Clark
uni | media service research | news No. 39/2011 on 22.7.2011