Getting some of their own medicine: Leading pharmaceutical companies develop new drugs with X-ray research at Argonne

Eight of the world's largest pharmaceutical companies have banded together to run a beamline at Argonne's Advanced Photon Source (APS) dedicated to determining protein structures and developing new drugs. The discoveries that they and other biomedical researchers at the APS make today provide the foundation for life-saving drugs that doctors will prescribe tomorrow.

Imagine Mozart and Salieri teaming up to write a symphony, or Hemingway and Fitzgerald collaborating on the Great American Novel. Now imagine the most famous names in drug discovery joining forces to find new cures for the world's most widespread and serious diseases.

Although those masterpieces of music and literature will have to remain in the realm of fantasy, a collaboration of the biggest of the big drug companies has taken root at Argonne's Advanced Photon Source (APS). At the APS, eight of the 16 largest pharmaceutical giants – Abbott, Bristol Myers Squibb, Eli Lilly, Johnson and Johnson, Merck, Novartis, Pfizer and Schering Plough – currently team up to form the Industrial Macromolecular Crystallography Association (IMCA).

The creation of IMCA allowed all of these companies together to construct what none of them could separately afford: two beamlines at Argonne's Advanced Photon Source. The X-rays produced by the APS synchrotron and shot through IMCA's beamlines allow the researchers at these companies to scan thousands of proteins and inhibitor molecules for the next wonder drug.

The road of drug discovery is long and arduous. Once a drug company identifies what disease it wants to treat, it has to determine the protein responsible for causing its symptoms. Then, the company's chemists fashion scores of inhibitors, tiny molecules that can bind to the protein's surface and prevent it from carrying out its function.

Not every inhibitor, however, can form the core of a new drug. A molecule that binds to the target protein might also inhibit several others, wreaking havoc in other biological pathways. It can take years for the examination of thousands of potential candidates to yield a single ideal inhibitor. "Finding the right inhibitor is like trying to find a jigsaw puzzle piece in a 10,000-piece puzzle with two dozen sides," said Lisa Keefe, who directs the IMCA-Collaborative Access Team (IMCA-CAT) beamlines for the University of Chicago. "It has to fit exactly right, and almost always you have to make it yourself."

To determine protein structures – their grooves, curves, nooks and kinks – scientists use a process called X-ray crystallography. In this method, researchers manufacture small crystals of the pure protein-inhibitor combinations they want to study and take or ship them to the APS for analysis. The crystals are then robotically loaded onto a small arm and exposed to the APS's brilliant X-rays. IMCA-CAT offers on-site, mail-in and remote access through the Internet to the beamline for pharmaceutical researchers.

When the X-rays hit the protein crystal, the electrons in the atoms of the protein's structure scatter, or "diffract," them in all different directions. These diffracted X-rays then hit a detector on the other side of the crystal. By looking at the position and intensity of the scattered X-rays on the detector, biophysicists can calculate the positions of the atoms in the structure of a protein and its inhibitors.

Because of the enormous resources these companies invest in each new drug they create and the vast number of possible inhibitors they have to sort through, they need a fast machine to characterize and evaluate them. "To these companies, time truly is money," said Keefe. "Our mission is to take their hundreds and hundreds of crystals and analyze them as quickly as possible. By having an X-ray beamline dedicated to this work, these companies can radically reduce the time they need to plan and execute their research."

The most well-known drug to emerge from research at the APS, Kaletra®, has already saved thousands of lives by helping to prevent HIV-positive patients from developing full-blown AIDS.

In the mid-to-late 1990s, Abbott Laboratories, one of the founding partners of IMCA, used the APS's X-rays to examine a protein called HIV protease. Abbott's researchers hoped to find an inhibitor that would block the action of HIV protease, effectively thwarting the virus by preventing it from replicating.

After an exhaustive search, Abbott's scientists found an inhibitor that shut down the virus without harming other bodily functions. After months of animal and human testing, Kaletra gained FDA approval in 2000 and is now the most prescribed drug in its class for AIDS therapy.

More recently, another IMCA member has taken up the fight against another notoriously deadly disease. Merck scientists used the IMCA beamline to determine the structure of platensimycin, a member of a previously unknown class of antibiotics that scientists have successfully synthesized only within the past two years. According to Keefe, Merck hopes to use the information gained from the APS to tailor platensimycin to treat infections against which conventional antibiotics have little effect. The most infamous of these, Multidrug-Resistant Staphylococcus aureus (MRSA), killed more than 18,000 nationwide in 2005. Merck also used their time on IMCA-CAT to determine the structure of proteins involved in Type II Diabetes, which aided their development of the drug Januvia®.

The idea of a dedicated beamline attracted the IMCA consortium because the companies themselves would retain the rights to all of the discoveries made by scientists at IMCA-CAT. Under this kind of arrangement, called proprietary research, the drug companies pay for all the costs of construction and operation of the beamline, as well as a proprietary fee to the APS, and in return are able to develop their research for an eventual patent instead of making their results public. Without proprietary research, Keefe said, few if any medications would ever reach the hands of those who need them the most.

Proprietary research, however, is not the only method by which scientists can work towards new cures and treatments. At least a quarter of the beam-time at IMCA-CAT and the other APS beamlines is reserved for use by unaffiliated researchers at universities, laboratories and other scientific agencies from around the world. The collected structural knowledge that these general users gain goes into a shared protein "library," to which researchers constantly add new knowledge about disease chemistry. This "Protein Data Bank" is available to the public and can be accessed online at www.rcsb.org.

Aside from IMCA-CAT, Argonne offers several other beamlines for groundbreaking medical discoveries. One of these, SGX-CAT, is operated by SGX Pharmaceuticals, Inc., a company recently acquired by Eli Lilly. Another beamline represents part of Argonne's Structural Biology Center (SBC), where researchers have determined more protein structures than at any other facility in the world, according to SBC Director Andrzej Joachimiak. Thirteen other beamlines at the APS also house X-ray crystallography experiments.

Work at the SGX-CAT beamline focuses on the discovery, development and commercialization of innovative cancer drug therapies. In one experiment, scientists at SGX-CAT are targeting abnormal proteins that result from a genetic abnormality known as the " Philadelphia translocation," a molecular mistake in which two different chromosomes inadvertently swap small segments of DNA.

Scientists have ascertained that these anomalous proteins trigger uncontrolled cell growth that results in a bone-marrow cancer called chronic myelogenous leukemia, Joachimiak said. "The most effective treatment of this disease relies on finding inhibitors for these rogue proteins," he added.

SGX-CAT offers a number of non-profit and for-profit crystallography services to the biology community.  In addition to a mail-in crystallography service, SGX developed several new approaches and technologies for drug discovery.

One of these new approaches, an algorithm called "Fragments of Active Structures (FAST)," draws on a diverse library of approximately 1,000 small molecular fragments. By using FAST, scientists increase the likelihood of developing a successful drug candidate by focusing their research on a small number of fragments that can then form the backbone of a range of novel and potent pharmaceutical candidates.

Unlike those owned by IMCA and SGX, the majority of the SBC beamline's users on the come from academic institutions. Although they do not have as large a financial stake in their discoveries as IMCA's scientists, these scientists also tackle some of medicine's biggest challenges.

In one project currently underway, SBC biologists are trying to determine the structure of the aldose reductase enzyme, a protein that breaks down glucose into a sugar alcohol called sorbitol. In diabetics, an accumulation of sorbitol in the bloodstream often causes nerve and eye damage. A successful inhibitor of aldose reductase could form the core of a new drug that would dramatically improve the lives of more than 20 million American diabetics.

"Drug discovery is an incredibly expensive and time-consuming process," Joachimiak said. "The facilities we have here at Argonne speed it up considerably, allowing these drugs to get to the people who need them more quickly, cheaply and safely." — by Jared Sagoff

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For more information, please contact Jared Sagoff (630/252-5549 or jsagoff@anl.gov) at Argonne.