Accurate Prediction of Drug Resistance for Intrinsically Disordered Protein Regions

Area of Science:

• Computational chemistry
• Structural biology
• Biophysics

Background:

• Alchemical free energy calculations, such as free energy perturbation (FEP), are valuable for predicting how amino acid mutations impact ligand binding affinities.
• Established FEP protocols are not readily available for proteins featuring intrinsically disordered regions (IDRs), which are crucial for various biological processes.
• The N-terminal intrinsically disordered region (IDR) lid of MDM2 is known to undergo ligand-dependent folding, making it a challenging system for computational studies.

Purpose of the Study:

• To develop and validate robust FEP protocols for accurately predicting experimental binding affinities of MDM2 mutants against ligands AM-7209 and Nutlin-3a.
• To assess the performance of equilibrium and nonequilibrium alchemical FEP protocols, particularly for mutations involving slowly varying degrees of freedom in the IDR.
• To investigate the influence of protein force fields and water models on the simulation of flexible IDR regions.

Main Methods:

• Utilized relative alchemical binding free energy calculations, specifically free energy perturbation (FEP).
• Compared equilibrium and nonequilibrium alchemical FEP protocols for a panel of MDM2 mutants.
• Systematically evaluated the impact of different protein force fields and water models on FEP calculations for the IDR.

Main Results:

• The equilibrium FEP protocol demonstrated superior precision in free energy estimates compared to the nonequilibrium protocol.
• The study identified the significant effect of protein force field and water model choices on simulating the flexible IDR.
• The developed FEP protocol successfully reproduced experimental binding affinity trends for MDM2 mutants.

Conclusions:

• Developed an accurate FEP protocol applicable to intrinsically disordered protein regions.
• Demonstrated the effectiveness of equilibrium FEP for predicting mutational effects on ligand binding affinity in dynamic IDRs.
• Highlighted the importance of selecting appropriate force fields and water models for simulating flexible IDR systems.