Sengent's D2OL uses idle computing time to find a cure for SARS

Boca Raton 29 April 2003About a year ago, Sengent Inc., a provider of technology that allows organisations to unify Web services via the Service Grid, was chosen by the Rothberg Institute for Childhood Diseases, a non-profit research organisation, to power the institute's current and ongoing scientific research to find a cure for tuberous sclerosis complex (TSC). Based on the technology behind Sengent's first initiative for life sciences, the Drug Design and Optimization Lab (D2OL), every company and household across the globe is able to contribute to the search for a cure for TSC by simply downloading the non-intrusive software application. The software company has now released a distributed computing agent that harnesses the spare processor cycles of PCs all over the world to come up with a possible cure for the Severe Acute Respiratory Syndrome (SARS) virus.

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D2OL is a client application that models potential drug molecules attacking disease-causing germs. When installed on a PC, the D2OL runs in the system tray, and sends results back to D2OL when an Internet link is established. Sengent's Drug Design and Optimization Lab was successfully deployed in 2001 to combat the threat of biological weapons through a worldwide volunteer community. More than 25.000 users downloaded Sengent's CommunityOS software application, which enabled them to contribute the idle time available on their computers to participate in the drug discovery efforts of the nation's scientific research community.

The CommunityOS software framework leverages grid to locate idle computing resources and services, and organise them into a Service Grid. Sengent's framework represents a quick and efficient path to integrate new and existing Web-based applications with legacy systems regardless of platform or development language. A security model is woven throughout the entire framework that provides enterprise-strength authentication and authorisation capabilities while localising policy management and streamlining system administration.

The D2OL programme is similar to other distributed computing projects, the most famous one being the search interstellar radio waves for signs of intelligent life, the SETI@home or Search for Extra-Terrestrial Intelligence project. D2OL began life as a bid to harness distributed computing for diseases such as anthrax, ebola and smallpox. SARS has just been added to the list. CommunityOS ties thousands of computers into a single machine able to rival or beat with more volunteers the world's largest supercomputers. D2OL is the software programme that is downloaded to the computer and used to evaluate drug candidates for SARS.

When the project comes up with a promising lead, collaborating scientists in Shanghai take the molecules into the lab for testing. Researchers there use petri dishes to grow samples of the SARS virus that were taken from patients. Many people who had volunteered their computers to find a treatment for tubular sclerosis have temporarily switched to supporting the SARS effort, according to Tian Xu. Tian Xu, a professor of genetics at Yale University as well as a scientific adviser at the Rothberg Institute, is also a visiting professor at the Fudan University in Shanghai, where the research is going on.

"It is absolutely essential that we test our compounds against varieties of SARS that can cause disease in patients", stated Bonnie Gould Rothberg, medical director of the Rothberg Institute for Childhood Diseases. "Our collaboration with the Fudan University will allow us to accomplish this goal." Professor Xu is working with the Fudan researchers to test potential SARS treatments, including drugs that are already approved for other diseases as well as Chinese herbs.

The D2OL project hasn't come up with any leads yet, but the professor said many molecules remain to be tested. "We need to screen many more compounds in order to find an effective one", noted Tian Xu. "We would like to screen 1 million compounds." After promising compounds are pinpointed, they'll be ranked in order of how likely they are to work, and the Shanghai researchers will test them in that order.

A previously unrecognised coronavirus has been detected in patients with SARS. While the new coronavirus is the leading hypothesis for the cause of SARS, other viruses are still under investigation as potential causes. Coronaviruses are a group of viruses that have a halo or crown-like (corona) appearance when viewed under a microscope. These viruses are a common cause of mild to moderate upper-respiratory illness in humans and are associated with respiratory, gastro-intestinal, liver and neurologic disease in animals. Coronaviruses can survive in the environment for as long as three hours.

The new virus diverges by 50 to 60 percent from the three known groups of coronavirus. Because of the variation between coronavirus, scientists working with D2OL have selected a coronavirus protein target that has high conservation between human and animal strains. Three-dimensional structure is actually more resistant to change than primary "sequence", and hence "SARS Target 1" is expected to have the same functionality and active site across all strains, and potentially allow for selection of compounds with broad activity against all coronavirus strains.

Several treatment regimens have been used for patients with SARS, but there is insufficient information at this time to determine if they have had a beneficial effect. D2OL's target is also believed to be critical in the life cycle of the coronavirus and drugs selected against it are expected to be viralcydal.


Leslie Versweyveld

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