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Dr. Wong's Group Develops Computer Program to Aid in the Synthesis of Oligosaccharides

ligosaccharides -- biomolecules made up of chains of sugar groups -- play an important role in the body, from the ability of immune cells to recognize their targets to the spread of cancer cells, for example. Synthesizing them, however, has been a complicated and painstaking endeavor.

Now, Chi-Huey Wong, Ph.D., Professor, The Skaggs Institute for Chemical Biology and Department of Chemistry, has devised a computer program for creating a range of oligosaccharides in one simple reaction, a "one-pot" operation. Scientists believe that speeding up the process of synthesizing these sugar chains can help them delineate their precise roles.

"This is the first time that a personal computer has been used in a systematic manner to guide the synthesis of carbohydrates by researchers who may or may not know that much about carbohydrate synthesis," according to Wong. "We simplified the synthesis of carbohydrates by developing a program called OptiMer. You can create a library of oligosaccharides one-by-one, as individual compounds, or you can synthesize a specific target for study," he continued. Wong notes that while the technique initially will be used to facilitate the reactions used in oligosaccharide synthesis to link sugar groups together, it may be applicable to other types of organic reactions as well.

"It is very important work," says Samuel Danishefsky, Ph.D., an organic chemist at the Sloan-Kettering Institute for Cancer Research and Columbia University. And Carolyn Bertozzi, Ph.D., a chemist at the University of California, Berkeley, commented, "We spend 95 percent of our time making the compounds. This new work could help us turn that around" and spend 95 percent of the time on the biology, she says.

While it is relatively straightforward to synthesize peptides­ short protein chains whose building blocks are linked with the same bond­oligosaccharides are more complex and can form a multiplicity of three-dimensional shapes. With OptiMer, all of the requisite reagents and carbohydrate building blocks necessary to create the desired oligosaccharide are preselected.

Then they are mixed in the same vessel and react to form the desired product. By using different patterns of protecting groups to adjust the reactivity of the building blocks, they can be joined together in the correct order.

TSRI has applied for a patent on the technology and Wong believes it will be commercialized.