The Chemistry of Life Processes program supports this EAGER grant to Professor Neville R. Kallenbach of the Department of Chemistry, New York University. Proteins are the most vital active agents in living matter, responsible for the shape, structure and function of cells and tissues. One key role of protein molecules is to recognize and interact specifically with other proteins. The ability to control these interactions among protein molecules affords a means of intervening in almost any vital process, including cell growth, development, signaling and transformation. Many currently important drugs are small molecules that interfere with the surfaces of proteins that make contacts with other proteins. A critical problem facing modern drug development centers on our inability to control the large number of protein-protein interacting surfaces that do not present favorable features (such as binding pockets) that make small molecule intervention possible. This project develops a general strategy to exert chemical control over a wide range of featureless, extended helical protein-protein interfaces. The approach is designed to produce biologically active peptides, fragments of proteins, rather than traditional small molecules. First, the team will elaborate short peptides that can be structurally locked-in by clamps to enhance their stability and binding affinity. Next, they will synthesize random "libraries" of 10- 12 amino acid peptides with thousands of different sequences, each containing the reactive clamps. Finally, they will use the selective "stickiness" of the peptides to specific target proteins to promote clamping of only the tightest binding compounds. Instead of selecting individual targets by freezing-in precisely positioned linkers, this strategy enables a global attack on an exceptional range of extended and previously "undruggable" interfaces that cannot be approached by small molecule inhibition. While intact proteins, biologics, can also selectively inhibit protein-protein interfaces, these are expensive, unstable and not bioavailable. The products of this research will be more stable and economical to produce than biologics, as well as more versatile, selective and less likely to encounter mutational resistance than small molecules. The initial target of the project is the protein-protein interface that is crucial for formation of microtubules, structures essential for cell division. Small molecules that block microtubule assembly include important antitumor agents. A successful outcome would identify a new route to discover inhibitors of a wide range of currently "undruggable" protein interfaces, a class of new reagents and therapeutics with exceptional selectivity and affinity relative to existing small molecule alternatives.
This project will allow the investigator to train undergraduates, a graduate student, and a postdoctoral fellow in modern chemical biology, a valuable educational experience. In addition the results of the project will be disseminated at conferences and meetings and by means of journal publications. Kallenbach has organized and directed science workshops for faculty from a group of colleges and universities (including 10 HBCUs and 11 campuses of the University of Puerto Rico) that promote faculty development. A future chemical biology workshop will be offered that centers on high throughput approaches in modern pharmacology, and the products of this research will be presented to science faculty from a diverse set of institutions.
Proteins are the most important class of large molecules in living matter, responsible for a host of vital functions. In any cell, thousands of protein molecules interact with other proteins to control processes such as gene expression, development, and repair of DNA. Certain protein interactions play a key role in disease, and selectively blocking these offers an attractive diagnostic or therapeutic avenue. This EAGER project aimed to devise a new way to generate molecules that can specifically target an undesired protein-protein interface. The present day arsenal of drugs can inhibit many interfaces, but are limited to structures that offer suitable "pockets" or cavities into which a small molecule can fit. The agents we propose bypass this limitation, since they are themselves protein fragments, called peptides. Peptides are much larger and can access more extended, featureless interfaces than any small molecule. In addition, our scheme would identify self-selecting peptides that organize themselves around their target protein surfaces. The experiments supported by this grant allowed us to demonstrate that the concept is feasible: we can design and synthesize agents that organize themselves around a target and then block that protein from interacting with others. We believe that the next generation of pharmaceuticals will include larger molecules than the current drugs, but which are smaller, more stable and economical than antibodies for example. The agents we have produced have potential to function as probes of important biological reactions and ultimately therapeutics if they can be taken up into cells.
