Volume 1, Issue 5
A Twist on Cancer DNA
Crammed inside every human cell are numerous strands of chromosomal DNA that, if laid end-to-end, would span a distance of about two meters. A special enzyme mechanically untangles the DNA, keeping our chromosomes from resembling a string of Christmas tree lights jammed into a box after the holiday. Someday, biochemist James Berger's efforts to understand the same enzyme in cancer cells could lead to new tumor-fighting drugs.
James Berger is also a faculty scientist in Lawrence Berkeley National Laboratory's Physical Biosciences Division and a faculty affiliate with the California Institute for Quantitative Biomedical Research (QB3).
"When an extension cord has tangles in it, you'd like to be able to cut it, specifically take out each knot, and put it back together again as opposed to threading the ends of cord through one another," says Berger, a professor of Molecular and Cell Biology. "Cells evolved an enzyme to do just that."
The enzyme is called a topoisomerase, so-named because it literally resolves topological dilemmas like knots and twists. Essential to the survival of many cells and viruses, topoisomerases have in recent years become prime targets for anticancer and antimicrobial drugs. Indeed, many traditional forms of chemotherapies are based on natural and synthetic compounds that inhibit the process. But Berger hopes his efforts to unveil the enzyme's subtle mechanics may inform the development of better drugs that throw a wrench in the cancer's topoisomerases while sparing healthy cells.
Think of a topoisomerase as a tiny multi-armed robot that clamps around a knot or twist in the DNA. One set of the arms grabs either side of the knot and pulls the strand apart while another uses a free segment of DNA to push through the break. After the strand is closed again, the DNA that was just transported through the break is expelled from the bottom of the enzyme.
"All of the components are coupled and coordinated so that the enzyme can remove two to three knots every second," Berger explains. "If it screws up though and doesn't paste the DNA back together correctly, the cell won't survive. That's the Achilles' Heel that many chemotherapeutics exploit."
"Classic" chemotherapeutics like Etoposide, Adriamycin and Mitoxantrone stop the enzyme in the middle of the reaction, preventing the gap from closing. Because tumor cells divide so rapidly, "jamming the enzymes just shreds the DNA," Berger says.
This model depicts the topoisomerase during one step of its unknotting reaction. The DNA (visible in green) has been cleaved and opened by the enzyme while the DNA being passed through the break is viewed end-on. (courtesy the researchers)
"Of course, these compounds hit the good cells as well as the bad cells, which is why the classic chemotherapy drugs from the last few decades make you sick," he adds. "On the other hand, the drugs achieve their goal remarkably well."
Most of those drugs, he explains, were discovered decades ago through trial-and-error methods. Since then, Berger and other researchers have produced detailed pictures of the topoisomerase reactions and deduced how certain drugs muck up the works. The biologists' technique, called X-ray crystallography, enables the position of every atom in a protein to be visualized, resulting in an "exploded view" of the molecule.
"It's like looking at a car engine that you've taken apart and put back together to get a much better idea of how it works," says Berger, who conducts his crystallography work at Lawrence Berkeley National Laboratory's Advanced Light Source.
Armed with the new physical information, Berger and his team are now studying a more recently-developed class of anti-cancer drugs called bisdioxopiperazines that inhibit the topoisomerase reaction in a different way than the classic compounds. Currently used to help alleviate the heart risk associated with chemotherapy, a bisdioxopiperazine may also be useful on its own, possibly with less impact on healthy cells.
It turns out that the drug works by acting similarly to a mortise-and-tenon joint in fine carpentry. It binds to one of the mechanical gates the enzyme uses to direct the transport of the DNA segments and locks it shut. Already, the Berkeley group's efforts have revealed how some cells develop mutations that increase their resistance to the drug.
"In the future, we'd like to tinker with it," Berger says. "Rational drug design is very difficult, but here we have something we already know is effective. So maybe it could be a good starting point to see if we can help make an even better drug."