Prediction of the Drug–Target Binding Kinetics for Flexible Proteins by Comparative Binding Energy Analysis

There
is growing consensus that the optimization of the kinetic
parameters for drug–protein binding leads to improved drug
efficacy. Therefore, computational methods have been developed to
predict kinetic rates and to derive quantitative structure–kinetic
relationships (QSKRs). Many of these methods are based on crystal
structures of ligand–protein complexes. However, a drawback
is that each ligand–protein complex is usually treated as having
a single structure. Here, we present a modification of COMparative
BINding Energy (COMBINE) analysis, which uses the structures of ligand–protein
complexes to predict binding parameters. We introduce the option of
using multiple structures to describe each ligand–protein complex
in COMBINE analysis and apply this to study the effects of protein
flexibility on the derivation of dissociation rate constants (koff) for inhibitors of p38 mitogen-activated
protein (MAP) kinase, which has a flexible binding site. Multiple
structures were obtained for each ligand–protein complex by
performing docking to an ensemble of protein configurations obtained
from molecular dynamics simulations. Coefficients to scale ligand–protein
interaction energies determined from energy-minimized structures of
ligand–protein complexes were obtained by partial least squares
regression, and they allowed for the computation of koff values. The QSKR model obtained using single, energy-minimized
crystal structures for each ligand–protein complex had higher
predictive power than the QSKR model obtained with multiple structures
from ensemble docking. However, incorporation of ligand–protein
flexibility helped to highlight additional ligand–protein interactions
that lead to longer residence times, such as interactions with residues
Arg67 and Asp168, which are close to the ligand in many crystal structures.
These results show that COMBINE analysis is a promising method to
guide the design of compounds that bind to flexible proteins with
improved binding kinetics.