Crystal structure of human vaccinia‐related kinase 1 in complex with AMP‐PNP, a non‐hydrolyzable ATP analog

Abstract

Vaccinia‐related kinase 1 (VRK1), a serine/threonine mitotic kinase, is widely over‐expressed in dividing cells and regarded as a cancer drug target primarily due to its function as an early response gene in cell proliferation. However, the mechanism of VRK1 phosphorylation and substrate activation is not well understood. More importantly even the molecular basis of VRK1 interaction with its cofactor, adenosine triphosphate (ATP), is unavailable to‐date. As designing specific inhibitors remains to be the major challenge in kinase research, such a molecular understanding will enable us to design ATP‐competitive specific inhibitors of VRK1. Here we report the molecular characterization of VRK1 in complex with AMP‐PNP, a non‐hydrolyzable ATP‐analog, using NMR titration followed by the co‐crystal structure determined upto 2.07 Å resolution. We also carried out the structural comparison of the AMP‐PNP bound‐form with its apo and inhibitor‐bound counterparts, which has enabled us to present our rationale toward designing VRK1‐specific inhibitors.

VRK1 functional insufficiency due to alterations in protein stability or kinase activity of human VRK1 pathogenic variants implicated in neuromotor syndromes

“…Gly135 interacts with ATP and is required for the kinase activity 30 , and the variant G135R has lost most of its activity, and is also unstable. These two residues, R133 and G135 undergo chemical shift perturbations and affect the DRF motif 53 . It is known that the loss of VRK1 kinase activity by itself makes this protein unstable 13 .…”

“…Modelling of the human VRK1 pathogenic variant proteins was performed using as reference the published structures 2RSV 29 and 2LAV 30,53 available from the Protein Data Bank. FoldX program 81 (http://foldxsuite.crg.eu/) was used to predict the effect of missense mutations in the structural stability of the VRK kinase (PDB identifier 2LAV).…”

FragExplorer: GRID-Based Fragment Growing and Replacement

“…Vaccinia-related kinase 1 (VRK1) is a serine/threonine mitotic nuclear kinase that is linked to cell proliferation and regarded as a cancer drug target. , Starting from the bound substrate analogue structure (PDB: 6ac9), we decided to apply our approach toward designing a potential ligand inhibitor. First, we removed the ribose phosphate tail and predicted a fragment to replace it; interestingly, the top solution was an aminotetrahydrofuran ring, with the oxygen atom of the tetrahydrofuran interacting with Lys71 and the charged amino group interacting with Asp197 and Asn182.…”