Structure-based drug designers identify and optimize small molecules that affect the activity of target proteins, such as kinases, by understanding and modeling 3-D molecular interactions. Techniques have improved significantly, and those like x-ray crystallography, NMR, and computational modeling are now considered indispensable tools for all stages of drug discovery.
Novartis (www.novartis.com) Gleevec, an inhibitor of wild-type Bcr-Abl kinase, was a breakthrough discovery, according to Tomi K. Sawyer, Ph.D., senior vp, drug discovery, Ariad Pharmaceuticals (www.ariad.com). It established and validated the fact that you can make a small molecule inhibitor of a protein kinase and that it can work, in fact, quite dramatically.
Although Gleevec is a blockbuster drug for chronic myelogenous leukemia, clinical resistance can occur because the drug is ineffective against mutant forms of Bcr-Abl that patients may develop. Ariad is one of the few companies using structure-based drug design to identify next-generation Gleevec drugs that can inhibit these mutants.
It has been most challenging for companies to find small molecule inhibitors of a particular Bcr-Abl mutant, T315I, according to Dr. Sawyer. Threonine-315 resides near the ATP binding site and is thought of as a gateway residue that sits next to a fairly well-sized hydrophobic pocket, he explains. The change to isoleucine is just enough to compromise the ability of many inhibitors to optimally exploit their functional group binding in the hydrophobic pocket.
Ariad uses 3-D structural information, including x-ray crystallography and computational chemistry methodologies to identify clinically relevant inhibitors of Bcr-Abl. An early lead molecule, AP23464, showed potent inhibition of both oncogenic protein kinases Src and Bcr-Abl with the exception of the T315I mutation. A subsequent analog, AP23846, demonstrated improved pharmacology relative to AP23464.
W. Patrick Walters, Ph.D., senior research fellow, computational chemistry and molecular modeling, takes an integrated approach to library design at Vertex Pharmaceuticals (www.vrtx.com). While docking programs are essential, finding a small molecule that fits inside the active site is only 10% of the solution, he stresses. At the end of the day, you dont want just an inhibitor that fits in an active site, you want a drug that has an appropriate set of physical properties.
Vertex leverages its knowledge base to identify new molecules with desirable properties, says Dr. Walters. For example, scientists can probe hundreds of crystal structures available in company databases. The crystal structure of one or more lead compound, co-complexed with a protein of interest, can then be used to guide the placement of new molecules within the same active site. The company has developed software that utilizes this structure-guided docking approach to evaluate and prioritize large compound libraries.
Dr. Walters believes that combining its internally developed docking software with chemistry-based enumeration, filtering, and structure-based evaluations sets Vertex apart. The integrated software platform at Vertex allows chemists to go very rapidly from a chemical reaction to a model of a small molecule library in a protein active site.
Starting with a chemical reaction and a set of reagents, the software enumerates and filters the library based on a set of physical properties, such as the presence of reactive or potentially toxic functionality, aqueous solubility, or potential metabolic problems. The program generates 3-D structures for molecules surviving the filters and flexibly fits them into the protein active site for binding affinity prediction. Chemists then select a set of compounds to synthesize and test in biological assays, and the process is repeated until a compound with the desired property and activity profile is obtained.