When you pop a pill or receive an injection, the molecules of healing disperse into the body and suddenly find themselves lost in a universe of strangers. But not for long: although they may bump and jostle through a veritable China of potential mates, the wandering molecules eventually find their intended targets on cells in that aching shoulder, infected wound, or misfiring heart muscle.
This process of searching and binding is called molecular recognition, and computational chemist Carol Venanzi is bringing the Alliance's supercomputing resources to bear on it. The insights she is gaining may someday help in the design of pharmaceuticals and chemical reagents that can seek out their targets with bloodhound-like accuracy.
Venanzi, a professor of chemistry at the New Jersey Institute of Technology in Newark, has a long track record in computational studies of molecular recognition. Some of her recent efforts have included research to develop inhalation anesthetics with fewer side effects and molecules to block cell receptors in the brain responsible for cocaine's euphoria. But right now she's focused on the binding of DNA--the stuff of genes--and a molecule called amiloride.
Venanzi first came across amiloride a few years ago, when she did some research for the Campbell Research Institute in Camden, NJ. The Campbell Soup Company was sponsoring research to find a substance that would enhance the salty taste of low-sodium soups. Scientists on the project were using amiloride to sort out different kinds of ion channels, the passageways that conduct various substances into and out of cells. Amiloride blocks the action of channels that ferry sodium into the cell but does not block other types of channels.
As part of the project, Venanzi did some computational studies on amiloride's molecular structure and properties. While searching the scientific literature on the molecule, she came across some research by Michael Waring, a pharmacologist at Cambridge University in England. Waring, an expert in the molecular mechanisms of anticancer drugs, had discovered that amiloride has a very strong affinity for certain regions of the DNA molecule but shuns others. Venanzi thought computational chemistry might help her to figure out what was behind amiloride's discriminating taste in DNA.
