A Synthetic Polyphosphoinositide Headgroup Surrogate in Complex with SHIP2 Provides a Rationale for Drug Discovery

Abstract

Phosphoinositides regulate many cellular processes, and cellular levels are controlled by kinases and phosphatases. SHIP2 (SH2 (Src homology 2)-domain-containing inositol-phosphatase-2) plays a critical role in phosphoinositide signaling, cleaving the 5-phosphate from phosphatidylinositol 3,4,5-trisphosphate. SHIP2 is thought to be involved in type-2 diabetes and obesity, conditions that could therefore be open to pharmacological modulation of the enzyme. However, rational design of SHIP2 inhibitors has been limited by the absence of a high-resolution structure. Here, we present a 2.1 Å resolution crystal structure of the phosphatase domain of SHIP2 bound to the synthetic ligand biphenyl 2,3′,4,5′,6-pentakisphosphate (BiPh(2,3′,4,5′,6)P5). BiPh(2,3′,4,5′,6)P5 is not a SHIP2 substrate but inhibits Ins(1,3,4,5)P4 hydrolysis with an IC50 of 24.8 ± 3.0 μM, (Km for Ins(1,3,4,5)P4 is 215 ± 28 μM). Molecular dynamics simulations suggest that when BiPh(2,3′,4,5′,6)P5 binds to SHIP2, a flexible loop folds over and encloses the ligand. Compounds targeting such a closed conformation might therefore deliver SHIP2-specific drugs.

The structure of phosphoinositide phosphatases: Insights into substrate specificity and catalysis

“…1). Crystal structures of 5-phosphatase catalytic domains from several members have been determined [59–61]. These structures provide insights into the molecular basis for catalysis, substrate recognition, membrane interaction, as well as human genetic diseases.…”

The “Other” Inositols and Their Phosphates: Synthesis, Biology, and Medicine (with Recent Advances inmyo‐Inositol Chemistry)

“…SHIP enzymes, for example, are linked to human diseases, particularly diabetes, cancer and obesity. The recent structure of a SHIP2:head group surrogate complex with a simple inositol polyphosphate surrogate identified an active site loop for targeting inhibition and specificity [251] and earlier work had demonstrated that a simple benzene tetrakisphosphate could be crystallized with the Akt-PKB PH domain.…”

Designer small molecules to target calcium signalling

“…Synthesis of biphenyl hexakisphosphate analogues illustrated that repositioning one phosphate group on the aromatic ring can induce an effective IP 3 R agonist/antagonist switch [27]. These compounds have also shown potential as templates for co-crystallization, facilitating the first high resolution structure of Src-homology 2 domain-containing inositol phosphatase 2 (SHIP2; Figure 1F) [28]. Future iterations of such simple analogues will need to focus on reducing polarity to improve permeability and specificity over the related 5-phosphatases.…”

“…J. Pharmacol. 161, 1070-1085; (D) 2-O-Modifed ligands such as 2-O-linked dimeric IP 3 are partial agonists of the IP 3 R;(E) Simple biphenyl polyphosphates can be easily synthesized and generate both antagonists and agonists of the IP3R; (F) Co-crystal structure of SHIP2 generated with lipid headgroup surrogate 2,3 ,4,5 ,6-pentakisphosphate[28].…”