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Updated: Jan 1, 2026
Real-Time Monitoring of Aurora kinase A Activation using Conformational FRET Biosensors in Live Cells
Published on: July 30, 2020
Structural Characterization of the Aurora Kinase B "DFG-flip" Using Metadynamics
Naga Rajiv Lakkaniga1, Meenakshisundaram Balasubramaniam2, Shuxing Zhang3
1Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas, 72205, USA.
Abstract:
Aurora kinase B (AKB), a Ser/Thr kinase that plays a crucial role in mitosis, is overexpressed in several cancers. Clinical inhibitors targeting AKB bind to the active DFG "in" conformation of the kinase. It would be beneficial, however, to understand if AKB is susceptible to type II kinase inhibitors that bind to the inactive, DFG "out" conformation, since type II inhibitors achieve higher kinome selectivity and higher potency in vivo. The DFG "out" conformation of AKB is not yet experimentally determined which makes the design of type II inhibitors exceedingly difficult. An alternate approach is to simulate the DFG "out" conformation from the experimentally determined DFG "in" conformation using atomistic molecular dynamics (MD) simulation. In this work, we employed metadynamics (MTD) approach to simulate the DFG "out" conformation of AKB by choosing the appropriate collective variables. We examined structural changes during the DFG-flip and determined the interactions crucial to stabilize the kinase in active and inactive states. Interestingly, the MTD approach also identified a unique transition state (DFG "up"), which can be targeted by small molecule inhibitors. Structural insights about these conformations is essential for structure-guided design of next-generation AKB inhibitors. This work also emphasizes the usefulness of MTD simulations in predicting macromolecular conformational changes at reduced computational costs.
Insights
We simulated the inactive DFG "out" conformation of Aurora kinase B (AKB) using molecular dynamics. This reveals new structural insights for designing more effective AKB inhibitors for cancer therapy.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Chemistry
Background:
- Aurora kinase B (AKB) is a key mitotic regulator overexpressed in cancers.
- Current AKB inhibitors target the active DFG "in" conformation.
- Type II inhibitors offer improved selectivity and potency but require the inactive DFG "out" conformation, which is uncharacterized for AKB.
Purpose of the Study:
- To computationally determine the inactive DFG "out" conformation of Aurora kinase B (AKB).
- To identify key interactions stabilizing active and inactive AKB states.
- To explore novel inhibitor design strategies targeting AKB conformations.
Main Methods:
- Atomistic molecular dynamics (MD) simulations, specifically using the metadynamics (MTD) approach.
- Simulation of the DFG "out" conformation from the experimentally determined DFG "in" state.
- Analysis of structural changes and stabilizing interactions during the DFG-flip.
Main Results:
- Successfully simulated the DFG "out" conformation of AKB, providing structural insights into its inactive state.
- Identified critical interactions responsible for stabilizing both active (DFG "in") and inactive (DFG "out") conformations.
- Discovered a unique "DFG up" transition state, a potential target for novel inhibitors.
Conclusions:
- Metadynamics simulations are effective for predicting macromolecular conformational changes at lower computational cost.
- Structural understanding of AKB's inactive and transition states is crucial for next-generation inhibitor design.
- This study provides a foundation for developing more selective and potent AKB-targeted cancer therapies.
