Subject: New Way to Develop High-Tech Drugs Monkeys With Darwin's Famed Theory Date: Published: 2/25/93 (157 lines) Source: Wall Street Journal. Copyright Dow Jones & Co. Inc. Biotechnology: New Way to Develop High-Tech Drugs Monkeys With Darwin's Famed Theory ---- By Jerry E. Bishop Staff Reporter of The Wall Street Journal Biotechnology has a new buzzword: evolution. In principle it is the same phenomenon that Charles Darwin wrote about after his voyage aboard HMS Beagle. But instead of survival of the fittest creatures in a species, the new human-directed evolution involves survival of the fittest molecules for use in high-tech drugs. Test-tube evolution starts with a molecule that does a somewhat useful job but doesn't do it well enough yet for medical or industrial purposes. Millions of variations of the molecule are created and subjected to a test of survival in the test tube. Those molecules that survive by doing the wanted task a bit better are reproduced by the millions and again put to a survival test. The procedure is repeated, generation after generation. Within a matter of weeks a few molecules evolve that can carry out the desired task with unprecedented efficiency. These molecules might have taken a human chemist decades to synthesize or nature millions of years to evolve. In the last several months, a half dozen new biotechnology companies have started up to exploit what some scientists are calling "directed" or "applied" molecular evolution. One Seattle-based start-up company is even calling itself Darwin Molecular Technologies Inc., because "we believe that the principles of evolution at the molecular level will speed up the development of new drugs," says its chief executive officer, Mark Pearson, a molecular biologist formerly with Du Pont Merck Pharmaceutical Co. "It's a whole new way of doing chemical synthesis," Gerald F. Joyce, a molecular biologist at the Scripps Research Institute in La Jolla, Calif., told a seminar sponsored last fall by the Council for the Advancement of Science Writing and the University of California, San Diego. New genes could even be "evolved" for insertion into cells to turn off deleterious genes or turn on beneficial genes, speculates one scientist. And, researchers add, applied molecular evolution could lead to powerful new enzymes and catalysts for industrial processes. Molecular evolution is far too new to have yielded any spectacular new medicines yet, and the small companies plunging into molecular evolution are reluctant to reveal exactly what drugs they are seeking. But a new drug that prevents blood clotting, now being tested in animals, offers an example of the power of the new technique. The anticlotting drug was evolved by Gilead Sciences Inc. in Foster City, Calif. and consists of a fragment of DNA, the stuff genes are made of. Ordinarily, DNA, a kind of molecular necklace of small beads called bases, serves only as a passive blueprint to guide a cell in making proteins. But John J. Toole and his colleagues at Gilead decided to make a DNA that actively seeks out and sticks to thrombin, a chemical in the body that triggers blood clotting. The goal was a piece of DNA that would neutralize thrombin and prevent blood clots, something important in treating heart disease. To begin the experiment they created 10 trillion variations of the DNA. All were tossed into a test tube with molecules of thrombin. A chemical bath then washed away all the DNA fragments that failed to latch on to a molecule of thrombin. This left about 0.01% of the DNA fragments that did stick to thrombin. These bound fragments were biochemically stripped off and copied by the millions. The researchers tossed the new copies into the test tube with thrombin, and repeated the process. By the fifth "generation," 40% of the DNA fragments were binding to thrombin molecules. More importantly, when scientists analyzed the bound DNA fragments, they found almost all contained the same short sequence of bases, or DNA building blocks. This short sequence has become the keystone of some new anticlotting drugs, in preclinical testing in animals, for preventing clots during open-heart surgery and other uses, says Gilead's chief executive officer, Michael Riordan. The feat contrasts sharply with the traditional approach to drug discovery, Dr. Riordan says. Traditionally, drug-company chemists tediously test substances that already exist in nature or on chemical laboratory shelves. The entire U. S. drug industry screens only 10,000 to 20,000 substances a year hoping to find a few useful drugs, Dr. Riordan notes. Gilead's screening of 10 trillion DNA molecules took only a matter of weeks. One of the first evolution-based companies to spring up, NeXagen Inc. in Boulder, Colo., has raised $17 million in venture capital since it was formed in March 1991, says its president and chief executive, Patrick J. Mahaffy, a financier who came to NeXagen from Warburg, Pincus Investors L. P., the venture capitalists who seeded the company. NeXagen was formed to exploit a test-tube evolution technique devised by its founder, molecular biologist Larry Gold of the University of Colorado. Gilead scientists used Dr. Gold's technique to evolve their anticlotting DNAs. NeXagen, however, is using it to evolve drugs from a sister genetic molecule, RNA. RNA, like DNA, is a long necklace made up of four kinds of bases, so the RNA molecule can also be mutated into an almost limitless number of variants, Dr. Gold says. This lets NeXagen researchers search for several drugs simultaneously. "You can take one test tube of 10 to the 18th fragments and divide it into 10 test tubes, each with its own target," Dr. Gold says. The targets the NeXagen researchers are using are proteins of medical interest. They are looking for RNA fragments that will grab hold and neutralize these proteins. So far, they have disclosed that they have found one RNA fragment that, in the test tube, glues itself to a protein that the AIDS virus uses to reproduce itself, thus blocking the virus's ability to proliferate. The trick is to figure how to use this RNA fragment in AIDS patients. They have found RNA variants that grab hold of nerve growth factor, a protein that may be involved in some nerve diseases. And they have found an RNA fragment that binds to thrombin, the clotting protein. But the biggest discovery, say the NeXagen scientists, is that variations of RNA can be created that can bind to almost any protein nature has ever made, and perhaps any chemical molecule. In Tucson, Ariz., another new company, Selectide Inc., founded by a group of University of Arizona biologists, is using test-tube evolution to create fragments of proteins, called peptides, that consist of only five amino acid beads, says Bruce Seligmann, vice president of research. The researchers can sift through a "library" of 3.2 million such peptide fragments in a matter of hours or a few days, for peptides that bind to selected targets such as proteins involved in arthritis. These fragments then become the starting points toward evolving new peptides that, it's hoped, will work even better against the target. Some established biotech companies are also plunging into test-tube evolution. Isis Pharmaceuticals Inc. in Carlsbad, Calif., has launched an evolution-type project it calls Osiris to screen millions of synthetic versions of RNA and DNA for potential drugs. One of the most ambitious efforts, however, is that of Darwin Molecular Technologies in Seattle. Darwin wants to analyze the huge volume of data on DNA base sequences that is flowing from the Human Genome Project. The company wants to be the first to find genes that produce proteins of medical importance. Once a protein of medical import is found, Darwin scientists hope to use test-tube evolution to evolve new drugs. But unlike others, they will try to evolve small organic molecules, instead of complex molecules like DNA and RNA, to block or enhance the action of these proteins, says Dr. Pearson, Darwin's chief executive. Test-tube evolution experiments ultimately may solve one of the great mysteries, the origin of life, suggests Dr. Joyce at the Scripps Institute. He and his colleagues are now putting RNA through test-tube evolution to see if they can move backward in time to the original versions of RNA that formed the first proteins, a step that had to precede the formation of living cells. --- Corrections & Amplifications GILEAD SCIENCES Inc. researchers used their own technique to "evolve" in the test tube a DNA drug to block the formation of blood clots, according to Gilead President Michael Riordan. A Feb. 25 article stated that Gilead scientists had used a "molecular evolution" technique developed by biologist Larry Gold of the University of Colorado. (WSJ March 16, 1993) [This article is made available here by Dow Jones Co. for the personal and non-commercial use of callers to this bbs, in the hope that it will be of some help to those who are suffering from the disease and others who are seeking to help them.]