Type
Text
Type
Dissertation
Advisor
Seeliger, Markus A | Miller, W. Todd | Lin, Richard | Bowen, Mark | Rizzo, Robert.
Date
2015-05-01
Keywords
Allostery, Cooperativity, High throughput screening, Insulin Degrading Enzyme, Src Kinase | Biochemistry
Department
Department of Molecular and Cellular Biology.
Language
en_US
Source
This work is sponsored by the Stony Brook University Graduate School in compliance with the requirements for completion of degree.
Identifier
http://hdl.handle.net/11401/76478
Publisher
The Graduate School, Stony Brook University: Stony Brook, NY.
Format
application/pdf
Abstract
Protein kinases, as key cellular pathway regulators, are known drivers of cancer and have been successfully targeted with drugs to treat patients with certain types of cancers. However, the high sequence and structural conservation of the active site found in the multitude of protein kinases has created a challenge to developing specific inhibitors, which are necessary to prevent side effects caused by off target inhibition. Part of the mechanism through which protein kinases achieve precise regulation involves integration of many inter- and intramolecular signals via sites on the kinase that are considerably less well conserved in sequence and function. These sites therefore provide the opportunity for more specific therapeutic targeting, for example, through the development of allosteric inhibitors. However, it is challenging to identify such allosteric sites. The first part of my work identified an allosteric network of dynamically coupled amino acids in Src kinase that connects regulatory sites to the ATP- and substrate-binding sites. This work provides new insights into the regulation of protein tyrosine kinases and establishes a potential conduit by which resistance mutations to ATP-competitive kinase inhibitors can affect their activity. Secondly, I examined a site at the end of this allosteric network that was also identified by recent computational studies as a potential ligand binding site. By identifying a ligand that specifically binds to this allosteric site, I have provided a proof of principle that it is possible to predict allosteric binding sites and their ligands in the kinase domain, providing a route towards development of novel cancer therapeutics. Finally, I focused on another important enzyme whose targeting could lead to important future treatment options, Insulin Degrading Enzyme (IDE). Despite the identification of IDE as a diabetes susceptibility gene, the relationship between the activity of the protease IDE and glucose homeostasis remains unclear. My work explored the structural details of a newly discovered, physiologically active, IDE inhibitor identified from a DNA-templated macrocycle library. This inhibitor, which engages a binding pocket away from the catalytic site, demonstrates the feasibility of modulating IDE activity as a new therapeutic strategy to treat type-2 diabetes. These three examples provide a better understanding on how targeting disease relevant enzyme at distal sites could provide future breakthrough treatments. | 195 pages
Recommended Citation
Foda, Zachariah Hussein, "Structural studies on allosteric regulation and drug binding" (2015). Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions). 2393.
https://commons.library.stonybrook.edu/stony-brook-theses-and-dissertations-collection/2393