Regulatory Mechanisms and Novel Therapeutic Targeting Strategies for Protein Tyrosine Phosphatases

Abstract

An appropriate level of protein phosphorylation on tyrosine is essential for cells to react to extracellular stimuli and maintain cellular homeostasis. Faulty operation of signal pathways mediated by protein tyrosine phosphorylation causes numerous human diseases, which presents enormous opportunities for therapeutic intervention. While the importance of protein tyrosine kinases in orchestrating the tyrosine phosphorylation networks and in target-based drug discovery has long been recognized, the significance of protein tyrosine phosphatases (PTPs) in cellular signaling and disease biology has historically been underappreciated, due to a large extent to an erroneous assumption that they are largely constitutive and housekeeping enzymes. Here, we provide a comprehensive examination of a number of regulatory mechanisms, including redox modulation, allosteric regulation, and protein oligomerization, that control PTP activity. These regulatory mechanisms are integral to the myriad PTP-mediated biochemical events and reinforce the concept that PTPs are indispensable and specific modulators of cellular signaling. We also discuss how disruption of these PTP regulatory mechanisms can cause human diseases and how these diverse regulatory mechanisms can be exploited for novel therapeutic development.

Figure 1

Classification and schematic representation of the PTP superfamily.

Figure 2

Key structure features of PTPs depicted on the crystal structure of PTP1B. (A) Overall structure of PTP1B catalytic domain in ribbon mode. All α-helix and β-sheet are labeled, and the four loop fragments (i.e. P-loop, WPD-loop, Q-loop and pTyr-loop) constituting active site pocket are highlighted. Essential residues for catalysis are shown in stick and labeled. (B) The representation of active site pocket on the surface of PTP1B. The surface contributed by the P-loop, WPD-loop, Q-loop and pTyr-recognition loop are colored in red, green, magenta and blue.

Figure 3

The catalytic mechanism for PTP-mediated dephosphorylation reaction. The gray dash lines indicate H-bonds which position the phosphate group and nucleophilic water, the blue dash lines show broken/formed bond in the transition state, and the blue solid line represent newly formed bond.

Figure 4

Redox regulation of PTP activity by ROS. Intracellular ROS, including H₂O₂, O₂^·−, •OH and peroxidized lipids, converts PTP catalytic Cys to sulfenic acid and inactivates the PTPs. The sulfenic acid form could be further irreversibly oxidized to the sulfinic or sulfonic acid forms, or reversibly converted to a cyclic sulfenyl amide or intramolecular disulfide form.

Figure 5

Allosteric activation of MKP3 by MKP3-ERK2 interaction. (A) Distorted MKP3 active site in the X-ray crystal structure of the MKP3 phosphatase domain. (B) Key interaction elements presented in a structural model of MKP3-ERK2 complex. (C) Crystal structure revealed that a peptide from KIM sequence of MKP3 binds at the common docking site of ERK2, which consists of an acidic patch and a hydrophobic groove.

Figure 6

Allosteric regulation of SHP2. (A) The schematic representation of SHP2 structure and allosteric regulation. (B) The comparison of N-SH2 domain conformation at I (gray) and A (cyan) state. (C) The pY peptide binding surface in N-SH2 domain at I and A state. BG- and EF-loop are depicted in purple and yellow, respectively. (D) The N-SH2/PTP interaction surface in the N-SH2 domain at the I and A state.

Figure 7

Disease associated SHP2 mutations. (A) NS/cancer-associated SHP2 mutations mainly reside at the interface of N-SH2 and PTP domains. (B) LS-associated SHP2 mutations only appear within the PTP domain.

Figure 8

LS SHP2 mutations reduce SHP2 phosphatase activity by disturbing different step(s) in the catalytic process. In this figure, SHP2 wild-type (gray) and mutant (green) were superimposed onto PTP1B (cyan) structure representing transition state 1 or 2 to show mutation-induced disturbance at each specific step. Residue numbers are shown in blue for PTP1B and black for SHP2. Red dash lines represent mutation induced steric conflicts.

Figure 9

Dimeric structure of PTPα D1 domain. The N-terminal helix-turn-helix ‘wedge’ and catalytic Cys are highlighted in green and red respectively.

Figure 10

Dimeric structures of (A) VH1, (B) laforin, and (C) MTMR2. In the MTMR2 dimer presentation, the coiled-coil domain is not observed in the crystal structure and delineated as a cylinder to show its relative location.

Figure 11

Trimeric arrangement of PRL1 in the crystal structure. (A) Overall structure of the PRL1 trimer in two orientations. In each monomer, the secondary structures are labeled; the P-loop and C-terminal tail are highlighted in red and blue, respectively. (B) Surface representation of the PRL1 trimer. Two dimer interfaces in monomer b are highlighted in purple (ba-interface) and yellow (bc-interface), and all residues involved in these interfaces in monomer b are listed accordingly. The close-up view of key interactions are respectively shown in (C) and (D) for ba- and bc-interface.

Figure 12

Structures of small molecule PTP inhibitors discussed in this review, which target the regulatory mechanisms unique to each PTP.

Figure 13

The binding modes for two allosteric PTP inhibitors. (A) SHP099 binds at the inter-domain interfaces of SHP2 to stabilize the autoinhibited conformation. (B) Analog 3 binds at the trimer interfaces of PRL1 to prevent trimer formation.