News tips from UC Santa Cruz American Chemical Society meeting --
April 13-17, 1997 San Francisco, CA
For more information, contact
Robert Irion: (408) 459-2495 or [email protected]
Chemists squeeze potpourri of compounds from marine sponges
Oligosaccharides, Cell-Surface Molecules, and Peptides, paper #485 Wednesday, April 16, 4:40 p.m. Moscone Center, room 103 Speaker: William D. Clark (408) 459-4280 or [email protected]
Earth's natural pharmacy is stocked with medicines derived from microbes, plants, and other denizens of the land. The ocean's waves may conceal an equally rich supply of potential drugs, some chemists believe. Although marine organisms haven't yet yielded an approved drug, promising compounds continue to surface--including an intriguing new toxin from a grape-sized sponge found in Papua New Guinea.
Chemist Phillip Crews and his team at UC Santa Cruz collected the purplish-green sponge, Psammocinia, in 1993. The sponge's major metabolic products didn't display notable toxic activity against cells. However, graduate student William Clark persevered. Clark separated the sponge's minor constituents with a bioassay-guided isolation that probes for toxicity to brine shrimp. These shrimp, the National Cancer Institute has found, are sensitive to compounds that also kill cancer cells. After many purifications, Clark isolated an especially potent product, called "cyclocinamide A."
Cyclocinamide A packs some chemical surprises, Clark discovered. The molecule is a "hexapeptide" of six amino acids, including one complex with chlorine that chemists have never seen in a marine product. Indeed, Clark suspects that cyclocinamide A comes not from the sponge, but from symbiotic cyanobacteria that colonize the sponge like low-rent houseguests.
Biologists Thomas Corbett and Frederick Valeriote of Wayne State University worked with the Crews group to test cyclocinamide A against cancer cell lines. Their promising results, combined with the brine-shrimp assay, convinced the researchers that the compound deserves in vivo testing in living animals. However, such testing requires 100 milligrams of material. Cyclocinamide A was such a minor ingredient that Clark only isolated about 6.7 milligrams-- roughly 0.5 milligrams of which remain. Further, UCSC divers haven't yet found large numbers of the same sponge again in Papua New Guinea's reefs.
So, chemist Paul Grieco of Indiana University is working on synthesizing the molecule in his lab. If he succeeds, the in vivo testing could proceed with a manufactured substance identical to the one found in the sea.
Clark, who will earn his Ph.D. in June, emphasizes that cyclocinamide A--and all marine natural products--face steep odds against reaching the pharmacy shelf. For him, the main lesson is that diving deeply into the chemistry of each new marine organism may bring up hidden treasures.
"This was a minor constituent, and it was very hard to isolate," he said. "We probably will find new and interesting compounds if we look hard enough, even in sponges studied 10 or 15 years ago. Mother Nature isn't going to give away all of her secrets at once."
Partially folded proteins yield clues about how they aggregate
Biophysical Studies of Protein Stability and Aggregation, paper #296 Thursday, April 17, 2:30 p.m. Moscone Center, room 238 Speaker: Anthony Fink (408) 459-2744 or [email protected]
Proteins are the cell's dependable workhorses. Sometimes, though, they behave like old wire hangars in the back of your closet, snarling into useless tangles. Such aggregates can trigger debilitating diseases, such as Alzheimer's and primary amyloidosis. Now, UC Santa Cruz chemists are helping to unravel how those microscopic messes arise.
Newly born proteins emerge from their cellular factories as long strings of amino acids, which can take up to a minute to fold into their proper shapes. However, it seems that neither the unfolded strings nor the fully folded proteins are the precursors to protein clumps. Rather, specific stages in the middle of the folding process appear most susceptible to entangling with their neighbors.
Scientists in UCSC biochemist Anthony Fink's lab used detailed spectroscopic techniques to probe troublesome protein knots, known as "inclusion bodies," in living cells. Their structures, the team found, looked much like those of certain aggregates created in laboratory vials. They also resembled other harmful clumps of misfolded proteins called "amyloid deposits."
All of these protein agglomerations were rich in "beta sheets," sets of amino acids that link up in flat, broad patterns. Beta sheets are common in many normal, fully folded proteins; indeed, they often are vital to preserving a protein's overall shape. But if too many of them form in some intermediate stage of the protein-folding process, the proteins may become too sticky--almost as if the beta sheets act like swaths of Velcro.
"For a given protein, it seems that one partially folded intermediate is particularly prone to aggregate," Fink said. "The contacts between the molecules that lead to this aggregation appear to involve increased beta-sheet interactions."
Fink's group hopes to develop a clearer picture of why the clumps form and which cellular conditions seem to favor their growth. With that knowledge, researchers might design ways to prevent or reverse the entanglements. For instance, an engineered protein fragment that complements part of a beta-sheet assembly could inhibit anything else from binding to it--like sealing off the sticky hooks of Velcro with a strip of felt.
Fink will chair a 1997 FASEB Summer Research Conference at which chemists will discuss progress on many of these issues. The conference, "Amyloid and Other Abnormal Protein Assembly Processes," is scheduled for July 13-18 in Copper Mountain, CO.
Former graduate student Sangita Seshadri, now at Inhale Therapeutics in Palo Alto, conducted most of the research reported at the ACS meeting. Other contributors were current graduate student Anupam Talapatra and former graduate student Keith Oberg.
Biochemists unveil molecular dance of antibiotics and bacterial RNA
Aminoglycoside-RNA Interactions, paper #72 Wednesday, April 16, 10:20 a.m. Moscone Center, room 123 Speaker: Joseph Puglisi (408) 459-3961 or [email protected]
Scientists at UC Santa Cruz have exposed the precise interactions between a common class of antibiotics and the vital machinery in bacteria that they disable, setting the stage for targeted efforts by researchers to design new and more effective drugs.
A team led by biochemist Joseph Puglisi solved the puzzle of how the antibiotics grab a bacterium's ribosomes--the factories in every cell that make the proteins an organism needs to survive. The answers, mapped out atom by painstaking atom, shed light on why the antibiotics kill bacteria but not people, as well as how bacteria manage an end run around the drugs by developing resistance to their crippling tactics.
Puglisi's group focused first on paromomycin, one of the naturally occurring antibiotics called "aminoglycosides." Doctors have used aminoglycosides for decades to treat bacterial infections, but they have become less effective as antibiotic resistance has spread. Further, the details of how aminoglycosides work in the cell were poorly understood. Researchers knew only that the drugs latched directly onto bacterial ribosomes and somehow disrupted their protein assembly lines.
The UCSC team solved the structure of the drug attached to a short bit of RNA from the most critical part of the bacterial ribosome. Other scientists had probed how antibiotics link to proteins, but none had deciphered an antibiotic-RNA complex.
"There's a big rebirth in the idea of targeting RNA in cells by using small molecules," Puglisi said. "This is an example of how these 'lock-and-key' systems work. Manipulating the details of this system suggests a strategy for a whole new field of RNA-drug interactions."
Puglisi's lab published its paromomycin research in the November 22 issue of Science. At the ACS meeting, Puglisi also will report on the solutions of other aminoglycoside-RNA complexes.
In three dimensions, the structures reveal that the ribosome forms a small pocket into which the L-shaped antibiotic molecules fit precisely. Chemical groups at several spots interact to "glue" the two units together. The group's research exposes in detail where those atomic attachments occur.
This level of scrutiny has allowed Puglisi and his coworkers to address why the antibiotics act selectively on bacteria. A tiny evolutionary switch between a stretch of RNA in bacteria and in higher organisms, it turns out, is enough to disrupt the pocket into which the antibiotic molecule clicks. Thus, the fit isn't as tight in people as it is in bacteria.
However, resistance arises easily. A single change in either the RNA sequence of the bacterial ribosome or the structure of the antibiotic molecule can prevent them from fitting snugly. "Our research shows exactly which parts of the structure are important to the functions of these drugs," Puglisi said. "So, we can try to vary the other parts to come up with versions that are less toxic to humans and less prone to resistance."
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