Date of Award

Spring 2022

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Chemistry

First Advisor

Bennett, Anton

Abstract

Protein tyrosine phosphatases (PTPs), while important regulatory enzymes, have proven a challenge to elucidate their mechanisms of actions, distinct functions, as well as their potential inhibition. These enzymes, responsible for the removal of phosphate groups from tyrosine residues, share high domain and sequence homology and a charged active site. Two factors that increase the difficulty in using small molecules, either as activators or inhibitors, to investigate their functions in cells. A subclass of the PTPs is the mitogen-activated protein kinases (MAPKs) phosphatases (MKPs), responsible for the dephosphorylation and inactivation of the three groups of MAPKs: ERK, p38 MAPK, and JNK. These kinases trigger major cell functions including apoptosis, migration, and differentiation as a response to external stimuli such as cellular stress and growth factors. Thus, aberrant signaling of proteins in the MAPK pathway, such as the MKPs, have been implicated in a host of diseases including cancer, diabetes, fibrosis, and autoimmune diseases. Several MAPK inhibitors have been successfully established while MKP inhibition has remained a challenge. The MKPs share high sequence and domain homology, a charged active site, and target the same three groups of MAPKs. All factors that often contribute to small molecules that have weak potency, poor cell permeability, and non-specificity for one MKP over the other. As such, small molecule regulation of the MKPs requires a combination of techniques and creativity in approach. One way to circumvent poor small molecule hits is to develop small molecule targets that attack/bind to the MKPs outside of their active site, i.e., allosteric inhibitors. My thesis focuses on current progress in the field of MKP small molecule inhibition, including a highly-selective small molecule inhibitor of one of the MKPs known as MKP5. Additionally, a co-crystal structure of MKP5 with this small molecule, revealed that the molecule bound to a site on MKP5 8 Å away from the active site, revealing a novel binding site. Interestingly, sequence alignment of the MKPs demonstrate that this binding site is somewhat conserved amongst the MKPs. Here, I delve into the importance of this novel region, particularly a key tyrosine residue within this site that is required for compound binding, and MKP5 functionality. Additionally, I explore this site in one of the closest family members to MKP5, MKP7, and compare the ways in which this pocket mediates both MKPs’ activity. The data presented here suggests that this tyrosine residue is critical for substrate recognition and inactivation in both MKP5 and MKP7. This new information on the tyrosine residue within the allosteric site, paired with the knowledge from our previously published work, that there are other residues within this pocket that can confer MKP inhibitor specificity, opens the door for development of selective inhibitors of the MKPs. Thus, this thesis provides a small piece to the puzzle of therapeutic targeting of the MKPs in many diseases.

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