13lz
Crystal Structure of Human Inositol 1,3,4-Trisphosphate 5/6-kinase (ITPK1) in Complex with an Inhibitor NCGC00879727
Structural highlights
FunctionITPK1_HUMAN Kinase that can phosphorylate various inositol polyphosphate such as Ins(3,4,5,6)P4 or Ins(1,3,4)P3. Phosphorylates Ins(3,4,5,6)P4 at position 1 to form Ins(1,3,4,5,6)P5. This reaction is thought to have regulatory importance, since Ins(3,4,5,6)P4 is an inhibitor of plasma membrane Ca(2+)-activated Cl(-) channels, while Ins(1,3,4,5,6)P5 is not. Also phosphorylates Ins(1,3,4)P3 on O-5 and O-6 to form Ins(1,3,4,6)P4, an essential molecule in the hexakisphosphate (InsP6) pathway. Also acts as an inositol polyphosphate phosphatase that dephosphorylate Ins(1,3,4,5)P4 and Ins(1,3,4,6)P4 to Ins(1,3,4)P3, and Ins(1,3,4,5,6)P5 to Ins(3,4,5,6)P4. May also act as an isomerase that interconverts the inositol tetrakisphosphate isomers Ins(1,3,4,5)P4 and Ins(1,3,4,6)P4 in the presence of ADP and magnesium. Probably acts as the rate-limiting enzyme of the InsP6 pathway. Modifies TNF-alpha-induced apoptosis by interfering with the activation of TNFRSF1A-associated death domain.[1] [2] [3] [4] Publication Abstract from PubMedInositol-tetrakisphosphate 1-kinase (ITPK1) is a pivotal enzyme in the inositol phosphate signaling pathway that functions to maintain the balance of inositol phosphate (IP) species. Dysregulation of this pathway has been linked to human disease, making ITPK1 an attractive therapeutic target. While high-throughput screening (HTS) is a traditional strategy for identifying small molecule inhibitors, integrating computational approaches can significantly speed up and enhance hit rates. Here, we developed a hybrid experimental and virtual approach towards the identification of ITPK1 chemical probe candidates. We first miniaturized an ITPK1 enzymatic assay to 1,536-well format and screened approximately 19,000 annotated and chemically diverse compounds. We then utilized the resulting dataset to develop Machine Learning (ML) and Pharmacophore (PH4) models to virtually screen a larger library of 120,000 compounds to expand the chemical diversity of the screening set. Importantly, our screening platform included a selectivity assay against PPIP5K2, the closest structural relative of ITPK1. The identified hits were evaluated for ITPK1 binding, including via a novel high-throughput Structure Dynamic Response (SDR) target engagement assay. Hits underwent further confirmation through orthogonal assays and mechanistic investigation, including obtaining a co-crystal structure for one of the hits. This integrated workflow-combining physical HTS with computational modeling-led to the identification of two novel candidate inhibitors. This study demonstrates an efficient, scalable strategy for targeting ITPK1 and offers a promising platform for drug discovery efforts in diseases linked to perturbed inositol phosphate pathways. A Hybrid Experimental and in silico Platform for ITPK1 Chemical Probe Discovery.,Yasgar A, Jain S, Wang H, Lee CS, Zong G, Zhang H, Lindberg E, Woodroofe C, Lane K, Blackman B, Crook D, Lin H, Baljinnyam B, Ronzetti M, Simeonov A, Rana S, Rai G, Shears S, Stanley RE, Zakharov AV, Luo J, Martinez NJ SLAS Discov. 2026 Jun 23:100323. doi: 10.1016/j.slasd.2026.100323. PMID:42336208[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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