A biophysical rationale for the selective inhibition of PTP1B over TCPTP by nonpolar terpenoids

Abstract

AbstractProtein tyrosine phosphatases (PTPs) are emerging drug targets for many diseases, including type 2 diabetes, obesity, and cancer. However, a high degree of structural similarity between the catalytic domains of these enzymes has made the development of selective pharmacological inhibitors an enormous challenge. Our previous research uncovered two unfunctionalized terpenoid inhibitors that selectively inhibit PTP1B over TCPTP, two PTPs with high sequence conservation. Here, we use molecular modeling with experimental validation to study the molecular basis of this unusual selectivity. Molecular dynamics (MD) simulations indicate that PTP1B and TCPTP contain a conserved h-bond network that connects the active site to a distal allosteric pocket; this network stabilizes the closed conformation of the catalytically influential WPD loop, which it links to the L–11 loop andα3 andα7 helices—the C-terminal side of the catalytic domain. Terpenoid binding to either of two proximal allosteric sites—anαsite and aβsite—can disrupt the allosteric network. Interestingly, binding to theαsite forms a stable complex with only PTP1B; in TCPTP, where two charged residues disfavor binding at theαsite, the terpenoids bind to theβsite, which is conserved between the two proteins. Our findings indicate that minor amino acid differences at the poorly conservedαsite enable selective binding, a property that might be enhanced with chemical elaboration, and illustrate, more broadly, how minor differences in the conservation of neighboring—yet functionally similar—allosteric sites can have very different implications for inhibitor selectivity.