Insights into Resistance Mechanisms of Inhibitors to Mps1 C604Y Mutation via a Comprehensive Molecular Modeling Study

Abstract

Mono-polar spindle 1 (Mps1/TTK) represents a protein kinase reported to be vital for cell division processes and is generally regarded as an attractive target for the treatment of hepatocellular carcinoma, breast carcinoma, and colon cancer. However, the C604Y mutation has been linked to acquired resistance. Recently, three potential small-molecule inhibitors of Mps1 (i.e., reversine, NMS-P715, and its derivative Cpd-5) were reported for the C604Y mutation that exhibit significant resistance to NMS-P715 and Cpd-5, but retain affinity for reversine. In this study, classical molecular dynamic (MD) simulations, accelerated MD (aMD) simulations, and umbrella sampling (US) simulations were performed to illustrate the resistance mechanisms of inhibitors to Mps1. The classical MD simulations combined with free energy calculations revealed that reversine features similar binding affinity characteristics to both Mps1WT and Mps1C604Y, but both NMS-P715 and Cpd-5 feature much higher binding affinities to Mps1WT than to Mps1C604Y. The major variations were shown to be controlled by electrostatic energy and the conformational change of A-loop-induced entropy increased. The large conformational changes of Mps1C604Y bound to NMS-P715 and Cpd-5 were also observed in aMD simulations. The US simulation results further suggest that reversine and Cpd-5 both exhibit similar dissociation processes from both Mps1WT and Mps1C604Y, but Cpd-5 and NMS-P715 were found to dissociate more easily from Mps1C604Y than from Mps1WT, thus a reduced residence time was responsible for the inhibitors resistance to the C604Y mutation. The physical principles provided by the present study may provide important clues for the discovery and rational design of novel inhibitors to combat the C604Y mutation of Mps1.

Molecular mechanism of point mutation-induced Monopolar spindle 1 (Mps1/TTK) inhibitor resistance revealed by a comprehensive molecular modeling study

“…This finding was also consistent with the previous study that when Mps1 binds with Cpd-5, the A-loop region of Mps1 C604Y changes into an outward-moving conformation, but not the Mps1 WT (Chen et al, 2018). Compared with the previous results, we also found that the P-loop had a slight conformational change (Chen et al, 2018), particularly in Mps1 I598F and Mps1 C604Y systems. Overall, these results indicated that mutation-induced conformational change might be the main driving force for the redistributed energies.…”

“…Cpd-5 (N-(2,6-diethylphenyl)-8-((2-methoxy-4-(4-methylpiperazin-1-yl)phenyl)amino)-1-methyl-4,5-dihydro-1H-pyrazolo[4,3h] quinazoline-3 carboxamide), a derivative of NMS-P715, has been reported to display higher potency toward Mps1 than NMS-P715, reversine, MPI-0479605 (Koch et al, 2016). Recently, Chen et al (2018) reported resistance mechanisms of inhibitors to Mps1 C604Y Mutation, however, it is not clear from the structures why other mutations (I531M, I598F, S611R) would cause resistance. Molecular dynamics (MD) simulations may be helpful to explain these resistance mutations by monitoring the dynamics of the protein and its interactions with bound inhibitors.…”

Peer Review #2 of "Molecular mechanism of point mutation-induced Monopolar spindle 1 (Mps1/TTK) inhibitor resistance revealed by a comprehensive molecular modeling study (v0.1)"

“…The A-loop region of mutant systems showed an outward-moving conformation ( Figure 5A-5D). This finding was also consistent with the previous study that when Mps1 binds with Cpd-5, the A-loop region of Mps1 C604Y changes into an outward-moving conformation, but not the Mps1 WT (Chen et al 2018). Compared with the previous results, we also found that P-loop had a slight conformational change (Chen et al 2018), particularly in Mps1 I598F and Mps1 C604Y systems.…”

“…Recently, Chen et al (Chen et al 2018) reported resistance mechanisms of inhibitors to Mps1 C604Y Mutation, however, it is not clear from the structures why other mutations (I531M, I598F, S611R) would cause resistance. Molecular dynamics (MD) simulations may be helpful to explain these resistance mutations by monitoring the dynamics of the protein and its interactions with bound inhibitors.…”

Discovery of the First Examples of Threonine Tyrosine Kinase PROTAC Degraders

“…Despite the promising progress in the development of highly selective and potent TTK inhibitors, their clinical efficacy and/or safety results have not been disclosed yet. Additionally, several “laboratory-generated” mutations, e.g., Ile 531 → Met 531 (I531M), Ile 598 → Phe 598 (I598F), Cys 604 → Tyr 604 (C604Y), and Ser 611 → Gly/Arg 611 (S611G/R), were reported to mediate resistance against the current TTK inhibitors, although no such mutant was detected from clinical samples yet. − This might not be strange because the “occupancy-driven” action mode of a kinase inhibitor would unavoidably result in drug-induced mutations in the kinase domain.…”