Taking a Coffee Break Could Help Find Cures for Cancer Or Aids. Katrina

Community computing Idle cures Taking a coffee break could help find cures for cancer or Aids. Katrina Megget looks at the future of research that harnesses the computing power of the World Community Grid It’s not every day that just twiddling Institute in Hawthorne, US. ‘It’s like diseases, time and money is of the your thumbs might solve some of In short that with humans and the same holds essence in medical research. humanity’s biggest health problems. The World Community true for computers.’ This is exactly where the grid But while you are off having your Grid uses volunteers’ PCs comes in. ‘For example,’ says Jasinski, caffeine fix or gossiping over the to run simulations during Together we’re stronger ‘if we have a million molecules we water cooler, behind the scenes your inactive periods Since their conception, computers want to test to see if they will be computer could be helping to find The vast number of have always had a strong role in effective as new drugs, we need the cure for cancer or Aids. In fact, computers involved can research, performing complex to do one computation for each 1.6 million personal computers in slash computation times algorithms and the like. However, molecule. If I only have one idle mode are currently chugging from years to weeks it has only been in recent years that computer and each calculation through a plethora of virtual Projects range computing power has been granted takes one minute, it will take me a simulations, from protein folding to from drug discovery to the average worker. This has led to million minutes or about two years drug–target interactions, as part of the to simulating the way a notable improvement in research to complete my task. On the other world’s largest public humanitarian proteins fold, but – multiple processors can work hand, if I have one million computers supercomputer known as the World could be applied to together to perform computations at a I can complete the task in about one Community Grid (WCG). any computationally faster pace. This allows them to cope minute by having each computer Now in its sixth year, the IBM demanding problem with more sophisticated models and perform one calculation.’ initiative represents a network of graphics-heavy simulations. The individual computers belonging to ‘Until grid technology came reality 530 000 volunteers in more than 80 along, scientists tended to rely on of this is countries around the world. This ‘grid’ stand-alone computers that were already works by harnessing an individual not connected to the outside world evident. For computer’s down time. Rather than and to each other,’ says Jasinski. the ‘Help fight an amusing animated screensaver, ‘This began to change with the childhood PCs run various computations using internet, where computational jobs cancer specially developed software. When could be controlled remotely or project,’ completed, the results are sent back to sent to a colleague. Then peer-to- some 8000 the main server to provide scientists peer networking, the falling cost years of with research information in their of processors and the advent of research quest for disease cures. multiprocessor PCs began to make should be It might seem like a hands-off grid computing feasible.’ cut by using the grid, approach, but the beauty of the grid In many ways the WCG is says Akira Nakagawara, president is the accelerated pace of research revolutionary, combining technology of the Chiba Cancer Centre at Chiba – what could take years in a costly and the collective power of linked University in Japan. ‘In the ordinary time-consuming lab takes just months PCs with the spirit of community to lab, it is absolutely impossible to via the relatively inexpensive and eco- provide cheap, speedy and promising do this kind of research,’ he notes. friendly World Community Grid. The results. But Jasinski denies it is a The project is screening three grid receives seven computational futurist technology, even though million small compounds against results from volunteers’ PCs every decades ago grid computing may have six targets in the hope of finding second of the day. And when the been envisioned as science fiction. about 30 chemicals that could number of computations performed ‘The World Community Grid is a great potentially treat the childhood by the grid each day is equivalent example of how the world can be cancer neuroblastoma. Already to one PC computing continuously made smarter by pooling the goodwill, seven chemicals that specifically kill for over 180 years, the genius of grid ideas and resources of people without the neuroblastoma cells have been computing becomes apparent. demanding an excessive amount of finalised for the first target. ‘There is strength in numbers – two money or time,’ he says. And when Likewise, the separate ‘Help heads are better than one,’ explains the world is faced with an ageing conquer cancer’ project – which Joseph Jasinski, programme director population, increasing chronic disease is analysing 86 million x-ray THINKSTOCK of IBM’s Healthcare and Lifesciences burden and poorly treated infectious crystallography images to aid 52 | Chemistry World | February 2011 www.chemistryworld.org www.chemistryworld.org Chemistry World | February 2011 | 53 Community computing understanding of cancer-related proteins – has been able to dramatically slash research times. ‘It is a long project even on the grid,’ says Igor Jurisica from the Ontario Cancer Institute in Canada. ‘But without WCG we would not be able to make this comprehensive analysis in our lifetime.’ The computation helps the team to identify characteristic gene or protein expression ‘signatures’ that can assist in diagnosing and monitoring diseases, or predicting how well patients will respond to certain treatments. Three of the lung cancer signatures are in preclinical stage already, while similar signatures in leukaemia, ovarian and head and neck cancer are in the pipeline. Number crunchers For Stan Watowich at the University of Texas Medical Branch in Galveston, US, doing research in this LIBRARY PHOTO SCIENCE / PHANTATOMIX way is a no-brainer – particularly in disease areas considered high risk or One grid project is completing accurate free energy says there are very few things in life financially unattractive. Watowich’s modelling the binding of of binding calculations on highly that are infallible. While there are team is using the WCG to find 300 000 potential HIV distributed computer resources. advantages to electronic simulations, treatment cures for dengue fever and protease inhibitors ‘If successful, our grid-based drug they are, in the end, only as good as West Nile virus and has been able to discovery approach can be applied the accuracy of the computational cut research times from an estimated to almost any disease with defined model, he says. False positives do 25 years on traditional laboratory molecular triggers,’ he adds. exist, and it requires additional multiprocessor computers to just research to eliminate these. weeks via the WCG. The end of experiments? In the case of finding new drugs, In the first phase of the project, the So does this all point to grid-based Watowich adds that the candidates team investigated about 15 different computer simulations trumping from grid-based research are proteins that could be potential drug traditional lab-based work? Jasinski really no different to leads that targets because of the role each plays says it is important to see the have entered the pipeline through in disease pathogenesis. Some 2.5 two as complementary. ‘Today’s more conventional paths. They will million small drug-like molecules science demands both approaches. still require significant medicinal were screened against these 15 A computer can certainly offer chemistry effort to be developed into proteins, resulting in over 35 million certain efficiencies that reduce drug candidates. However, he says, docking simulations. Now in the time and expense dramatically. the greater number of grid-generated second phase, this number has been At some point though, it becomes leads does mean an increased whittled down to 5000 promising necessary to perform experiments probability that at least one will candidate molecules and the team with physical matter.’ Likewise, he become an approved treatment. is running free energy calculations for each protein target. From these calculations, 50 of the best binding compounds for each target protein will be tested in biochemical assays to confirm the computer predictions. Active compounds will then be evaluated in cell culture assays and other preclinical tests with the ultimate goal of moving promising new drug candidates into clinical trials in humans with regulatory drug approval as the end result, says Watowich. Not only does this research aim to attack the high attrition rate for compounds moving through the development process by providing more promising drug candidates that should have an improved probability Volunteers can monitor of regulatory approval, Watowich their contributions using says it also aims to show it is possible screen savers and get to accelerate drug discovery by ‘points’ for work done NAMAZU-TRON 54 | Chemistry World | February 2011 www.chemistryworld.org Modelling limitations aside, Jurisica believes that computation is going to ‘revolutionise’ medicine. He points out that it was exactly this kind of ‘brute force computing’ that enabled the identification of thousands of prognostic signatures in lung cancer. Indeed, this success has led to Jurisica’s

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