By Martyn Williams, IDG News Service
January 12, 2004 | Researchers from Fujitsu Ltd. say they have developed a new software-calculation engine that increases accuracy and reduces the time taken during the initial stages of drug development.The new software uses a quantum chemistry computational method called local self-consistent field (SCF) to determine the binding energy for various candidate inhibitors in drug research, says Munetaka Sawada, director of Fujitsu's Bio IT Laboratory at its Advanced Scientific Group in Tokyo.Drug development typically begins by screening a database of hundreds of thousands of inhibitors. Measuring binding energy helps narrow down this field. At present, researchers have two main options: One is to use quantum chemistry calculations based on the Schrödinger equation that are highly accurate but time consuming, the other is to use classical chemistry and Newtonian physics, which is quicker but less precise.
Fujitsu's local SCF method delivers the accuracy of the quantum chemistry approach but in less time than the classical chemistry method. Says Sawada: "This product shortens that time and is cheaper than other experimental methods, because it runs on a standard computer."
The company worked with Japan's Tokai University to validate the software by using it to compare four HIV inhibitors. Confirming previous results, binding energy calculations showed that Saquinavir was most effective, followed by Ritonavir, Nelfinavir, and Indivair.
The calculations for each compound took just a few hours on a 2.8GHz desktop computer with a Pentium 4 chip and 2GB of memory. By contrast, the same calculation using Mozyme, an older program from Fujitsu, took 120 hours.
Local SCF also brings complex computations into the range of modest desktop computers, says Sawada. For example, a local SCF calculation for a chaperonin protein takes around 12 hours and requires 1.2 GB of memory. A similar desktop calculation using Mozyme is impossible -- it would require around 88 GB of memory and take an estimated 146 hours even if suitable hardware did exist.
The calculation engine is available as a plug-in for the Cache computer-aided chemistry modeling software and costs about $46,000 per copy, per machine. Fujitsu began worldwide sales in November and expects to sell around 200 copies of the software over the next two years.