The goggle-wearing scientists sat staring at a movie screen as 3-D images danced before their eyes. One munched on popcorn, another on a candy bar. Unmindful of movie theater etiquette, they chattered excitedly among themselves. "What if we put a carbon atom here?" one suggested. "How about an oxygen there?" said another.
This was not Friday night at the movies. Nor were the scientists watching videos of those wildly popular 3-D movies of the 1950s. Rather, the subject of their rapt attention was a molecule they had created that might someday become a potent weapon against a currently incurable disease.The scientists, a chemist, two biochemists and a physicist-biologist at Cornell University in Ithaca, hope to develop new drugs more systematically than the traditional approaches that involve either luck or the laborious screening of tens of thousands of compounds.
As one of the scientists, Steven E. Ealick, put it: "The trial-and-error method of drug development is simply too inefficient. It's like collecting everyone's office keys from the Empire State Building and trying to find the one key that will open a particular door. But if you called a locksmith, you'd be in the door in a matter of minutes."
The approach, known as rational - or, more precisely, structure-based - drug design, has been hotly pursued for at least a decade by scientific teams both in research institutions and in drug companies. The Cornell team is a relative newcomer to the field, having plunged in about five years ago.
Its interest was spurred by a $3.3 million grant from the National Institutes of Health and ready access to what Cornell describes as the world's most powerful X-ray machine and computer.
Although no team has yet produced a clinically useful drug, the Cornell group describes the progress to date as "surprisingly successful" in producing the fundamental data about protein structures needed to design potent new medications.
Like others working on structure-based drug design, Ealick and his colleagues try to be molecular locksmiths: they devise chemical keys, but ones designed to fit and jam locks, not to open them. The locks are usually the enzymes needed by disease organisms, like those of AIDS, malaria and African sleeping sickness.
"Within five years, a lot of protein structures were determined and several potential inhibitors have been designed," said Ealick, a biochemist at Cornell's New York State College of Agriculture and Life Sciences. So far, though, the AIDS virus has managed to outwit them all by undergoing mutations that change it just enough to render it resistant to the specially designed drugs.
But the approach continues to hold great promise, if not for AIDS - an effort still being vigorously pursued - then for other diseases that have defied usual methods of drug development, including many cancers against which chemotherapy has been ineffective.
"This is still a field in progress," Ealick said. "On a scale of one to 10, we're at about five. It's one of those things that makes so much sense. We know we can do it, but we're just learning the rules."
One project involves an enzyme critical to the health of T cells, the cells of the immune system involved in rejecting foreign tissue, like cancers and transplanted organs.
The enzyme, purine nucleoside phosphorylase, or PNP, cleans up metabolic debris that would otherwise build up inside the T cells and shut them down. Sometimes, Ealick explained, T-cell inactivation is just what is needed, for example, to prevent rejection of transplanted organs or suppress the attack on body tissues that occurs in autoimmune diseases like rheumatoid arthritis and type I diabetes.
"If we could make an inhibitor to this enzyme, we should be able to suppress T-cell response without totally eliminating it," he said. He and his colleagues have analyzed the molecular structure of the enzyme's active site that allows it to pick up metabolic debris. Next they will try to design a substance similar enough to slip right into the spot but so tight fitting that it will jam the enzyme's operation.
Three assets have made Cornell a unique center for a more systematic approach to drug development. Buried beneath a field on the university's sprawling campus is the world's most powerful X-ray machine, the Cornell High-Energy Synchrotron Source, or Chess. The device makes it possible to see easily and rapidly the structure of crystallized molecules, including the proteins involved in disease.
Second, Cornell's Theory Center is home to one of the world's fastest supercomputers, which enables researchers to analyze quickly the vast amounts of data generated by X-ray crystallography and produce three-dimensional computer images of molecules under study.
The third attraction that prompted Ealick to join Cornell's faculty in 1991 was the "constellation" of people who had the interest and skills needed to pursue structure-based drug design. They include P. Andrew Karplus, a biochemist, Bruce Ganem, a chemist, and David Shalloway, a physicist turned biologist.
Ealick, a professor of biochemistry and molecular and cell biology, is one of about 100 X-ray crystallographers in the world now studying large molecules.
Ganem and Karplus have been focusing their drug-designing efforts on a parasitic enzyme, trypanothione reductase. The enzyme is crucial to the survival of a group of parasites, the trypanosomes, that causes diseases like African sleeping sickness.
"The trypanosome's Achilles' heel," Ganem explained, "is its susceptibility to oxidation by molecules like superoxide and hydrogen peroxide."
An antioxidant, trypanothione, defends the parasite against attacks from oxygen by converting it to water. The enzyme, trypano- thione reductase, then promptly rearms the antioxidant, enabling it to resume its protective role. If this enzyme was knocked out of commission, all the trypanothione would soon be used and the parasite would die from oxygen damage.
People, too, contain a similar antioxidant, glutathione, and its restorative enzyme, glutathione reductase. But, Ganem said, there are just enough differences between the parasitic enzyme and the one in people to make it possible to design a drug that would incapacitate the parasite without harming the person who harbors it.
To achieve such a goal, the scientists must first produce large quantities of the protein molecule in question, a step greatly eased by modern cloning techniques in which segments of DNA are used to dictate unlimited production of a particular molecule. Next, the protein must be rendered as pristine as Ivory soap, 99.44 percent pure. Then the purified protein must be crystallized.
A solution of the protein is suspended over a precipitating agent for a day to as long as a few months until crystals of adequate size form, much like what happens when a solution of sugar or salt is evaporated. It can be a real trick to find the right precipitating agent, a process Ealick described as "currently entirely by trial and error."
Once crystals of at least 300 microns in diameter are obtained, it is then bombarded with extremely powerful X-rays. Most pass right through the crystal, but some are defracted by atoms in the molecule, producing scatter patterns that enable the scientists to identify the exact position of every atom in the molecule.