Insight into the mechanism of molecular recognition between human Integrin-Linked Kinase and Cpd22 and its implication at atomic level

Abstract

AbsractPseudokinases have received increasing attention over the past decade because of their role in different physiological phenomena. Although pseudokinases lack several active-site residues, thereby hindering their catalytic activity, recent discoveries have shown that these proteins can play a role in intracellular signaling thanks to their non-catalytic functions. Integrin-linked kinase (ILK) was discovered more than two decades ago and was subsequently validated as a promising target for neoplastic diseases. Since then, only a few small-molecule inhibitors have been described, with the V-shaped pyrazole Cpd22 being the most interesting and characterized. However, little is known about its detailed mechanism of action at atomic level. In this study, using a combination of computational chemistry methods including PELE calculations, docking, molecular dynamics and experimental surface plasmon resonance, we were able to prove the direct binding of this molecule to ILK, thus providing the basis of its molecular recognition by the protein and the effect over its architecture. Our breakthroughs show that Cpd22 binding stabilizes the ILK domain by binding to the pseudo-active site in a similar way to the ATP, possibly modulating its scaffolding properties as pseudokinase. Moreover, our results explain the experimental observations obtained during Cpd22 development, thus paving the way to the development of new chemical probes and potential drugs. Graphical abstract

Molecular dynamics simulations reveal the impact of NUTD15 variants in structural conformation and dynamics

“…This effect has been previously observed in other computational studies which consider this metric to study the effect of direct ligand binding when a molecule acts towards the active site of the enzyme (García-Marín, Rodríguez-Puyol, and Vaquero 2022; Makurat, Cournia, and Rak 2022; Ge and others 2017). This tendency is also in accordance with Tm values when the inhibitor is present in the assay, confirming the ability of the substrate to stabilize protein structure (Rehling and others 2021; Man and others 2019).…”