Crystal structure of human PIK3C3 in complex with 3-[4-(4-Morpholinyl)thieno[3,2-d]pyrimidin-2-yl]-phenol (Compound 15E)

About this structure

Phosphatidylinositol (PtdIns) 3-kinases (PI3K) are enzymes that catalyse phosphorylation of the 3′ hydroxyl position of myo-inositol lipids. The enzymes can be divided into three major classes depending on their substrate specificity and subunit organisation [1]. PIK3C3 also named Vps34 (vacuolar protein sorting 34) is the sole member of the class III PI3K and consists of an N-terminal C2 domain, an accessory helical domain and a catalytic domain in the C-terminus. The substrate specificity of PIK3C3 is restricted to phosphatidylinositol and is thus distinguished from the other family members which also use phosphorylated derivatives of this phospholipid as substrate [2]. PIK3C3 is involved in regulation of vesicular trafficking in the endosomal system where the phosphatidylinositol triphosphate (PtdIns3P) produced acts to recruiting proteins that contains PtdIns3P binding domain [3]. PIK3C3 also regulates autophagy [4] and is implicated in neurodegenerative disease and in tumor suppression by having a role in the clearance of pathological protein aggregations. Furthermore PIK3C3 is implicated to have a role in regulating cellular response to nutrient deprivation [5].

Although only weak homology exists and the substrate binding region is unique for PIK3C3, the overall structure bears striking similarities to other PI3 kinases. The accessory domain folds as an α-helical structure. The catalytic domain consists of an N-terminal lobe and a C-terminal lobe separated by a cleft that forms the catalytic site of the enzyme, representing the typical architecture of protein and lipid kinases.

We have previously solved and deposited the 2.8Å structure of apo-PIK3C3A (catalytic domain and accessory helical domain) (PDB-entry 3IHY). Here we present the 2.25Å structure of the same fragment of PIK3C3A complexed with the inhibitor called "compound 15e" (C15e).

The thieno[3,2-d]pyrimidine derivative (C15e) was obtained by structural modifications of phenyl quinazoline that was identified by high throughput screening as a PI3Kα inhibitor. The modification that resulted in compound 15e increased both potency (PI3Kα IC50 = 2nM) and selectivity (10-fold selectivity for PI3Kα over –β and over 100-fold selectivity for –γ and –δ) [6]. This compound has shown significant antiproliferative activity in vitro but has a poor pharmacokinetic profile due to a short half-life of less than 10 min. Further modifications of C15e have led to the discovery of GDC-0941 which is an orally bioavailable potent and selective inhibitor of Class I PI3K currently in human clinical trials for cancer [7].

C15e appeared to bind PIK3C3 in a hydrophobic pocket located between N- and C-lobe of the kinase domain. Positioning of compound 15e in its binding site is maintained mainly by three H-bonds: i) one involves the oxygen of the morpholinic moiety of C15e and backbone NH of Ile685 and ii) one bidentate H-bond whose participating members are the hydroxyl group of Tyr670, the hydroxyl of the phenolic ring of C15e and side-chain carboxylate of Asp644. C15e conformations as well as bonding networks are identical between the two PIK3C3 monomers present in the asymmetric unit.

No specific Class III PI3K inhibitor has been reported to date and the structure of PIK3C3 in complex with compound 15e may facilitate the design of PIK3C3 selective compounds.

References

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