Molecular Dynamics Simulation and QM/MM Calculation Reveals the Selectivity Mechanism of Type I 1/2 Kinase Inhibitors: The Effect of Intramolecular H-bonds and Conformational Restriction for Improved Selectivity

Understanding the selectivity mechanisms of inhibitors towards highly similar protein kinases is extremely important for discovering new selective candidates with satisfactory safety profile. Here, we aim to reveal the selectivity mechanisms of type I 1/2 kinase inhibitors towards two highly similar protein kinases, p21-activated kinase (PAK4) and mitogen-activated protein kinase kinase kinase 14 (MAP3K14, NIK). PAK4 belongs to serine/threonine protein kinases that involves in cell signaling pathways, controls cellular functions and has received attention as an attractive drug target. Sharing highly similar structure with PAK4, NIK is a lymphotoxin beta-activated kinase mediating noncanonical NF-κB pathway, which is associated with proinflammatory genes expression and carcinoma, and mediates the activation of TNF receptor superfamily members. The high sequence identity between PAK4 and NIK makes it challenging to design selective PAK4 inhibitors. In this work, computational methods including protein comparison, molecular docking, QM/MM, molecular dynamics simulations, density function theory (DFT) calculation were employed to explore the binding mechanisms of selective inhibitors against NIK and PAK4. The simulation results revealed the crucial factors accounting for selective inhibition of PAK4 over NIK including essential features between protein-ligand interactions like intramolecular H-bond, the positions and conformations of key residues and the ligand flexibility. This study will shed lights on understanding the selectivity mechanisms of PAK4 and NIK inhibitors.