Revealing the Target

HIV protease is a symmetrical molecule with two equal halves and an active site near its center. Molecular models of HIV protease in this chapter were generated by Alisa Zapp Machalek

Our story begins in 1989, when scientists determined the X-ray crystallographic structure of HIV protease, a viral enzyme critical in HIV's life cycle. Pharmaceutical scientists hoped that by blocking this enzyme, they could prevent the virus from spreading in the body.
With the structure of HIV protease at their fingertips, researchers were no longer working blindly. They could finally see their target enzyme—in exhilarating, color-coded detail. By feeding the structural information into a computer modeling program, they could spin a model of the enzyme around, zoom in on specific atoms, analyze its chemical properties, and even strip away or alter parts of it.

 

Knowing that HIV protease has two symmetrical halves, pharmaceutical researchers initially attempted to block the enzyme with symmetrical small molecules. They made these by chopping in half molecules of the natural substrate, then making a new molecule by fusing together two identical halves of the natural substrate.

Most importantly, they could use the computerized structure as a reference to determine the types of molecules that might block the enzyme. These molecules can be retrieved from chemical libraries or can be designed on a computer screen and then synthesized in a laboratory. Such structure-based drug design strategies have the potential to shave off years and millions of dollars from the traditional trial-and-error drug development process.
These strategies worked in the case of HIV protease inhibitors. "I think it's a remarkable success story," says Dale Kempf, a chemist involved in the HIV protease inhibitor program at Abbott Laboratories. "From the identification of HIV protease as a drug target in 1988 to early 1996, it took less than 8 years to have three drugs on the market." Typically, it takes 10 to 15 years and more than $800 million to develop a drug from scratch.
The structure of HIV protease revealed a crucial fact—like a butterfly, the enzyme is made up of two equal halves. For most such symmetrical molecules, both halves have a "business area," or active site, that carries out the enzyme's job. But HIV protease has only one such active site—in the center of the molecule where the two halves meet.
Pharmaceutical scientists knew they could take advantage of this feature. If they could plug this single active site with a small molecule, they could shut down the whole enzyme—and theoretically stop the virus' spread in the body.
Several pharmaceutical companies started out by using the enzyme's shape as a guide. "We designed drug candidate molecules that had the same two-fold symmetry as HIV protease," says Kempf. "Conceptually, we took some of the enzyme's natural substrate [the molecules it acts upon], chopped these molecules in half, rotated them 180 degrees, and glued two identical halves together."
To the researchers' delight, the first such molecule they synthesized fit perfectly into the active site of the enzyme. It was also an excellent inhibitor—it prevented HIV protease from functioning normally. But it wasn't water-soluble, meaning it couldn't be absorbed by the body and would never be effective as a drug.

A drug candidate molecule must pass many hurdles to earn the description "good medicine." It must have the best possible activity, solubility, bioavailability, half-life, and metabolic profile. Attempting to improve one of these factors often affects other factors. For example, if you structurally alter a lead compound to improve its activity, you may also decrease its solubility or shorten its half-life. The final result must always be the best possible compromise.

Abbott scientists continued to tweak the structure of the molecule to improve its properties. They eventually ended up with a nonsymmetrical molecule they called Norvir® (ritonavir).