Enhancing Drug Residence Time by Shielding of Intra-Protein Hydrogen Bonds: A Case Study on CCR2 Antagonists

Abstract

The target residence time (RT) for a given ligand is one of the important parameters that have to be optimized during drug design. It is well established that shielding the receptor-ligand hydrogen bond (H-bond) interactions from water has been one of the factors in increasing ligand RT. Building on this foundation, here we report that shielding an intra-protein H-bond, which confers rigidity to the binding pocket and which is not directly involved in drug-receptor interactions, can strongly influence RT for CCR2 antagonists. Based on our recently solved CCR2 structure with MK-0812 and molecular dynamics (MD) simulations, we show that the RT for this and structurally related ligands is directly dependent on the shielding of the Tyr120-Glu291 H-bond from the water. If solvated this H-bond is often broken, making the binding pocket flexible and leading to shorter RT.

Figure 1

(A) Thermodynamic and kinetic parameters of MK-0812, 8, and 15a (Vilums et al.,) as well as a simplified energy barrier defining the free energy differences of the ligand bound state ΔG_BS as well as the free energy differences of the transition state ΔG_TS. (B) Structures of the molecules under investigation (X = N for MK-0812 and X = C for 8 and 15a) as well as quantification of the free energy differences in comparison to MK-0812.

Figure 2

(A) Overlay of ligands (simulation snapshot). MK-0812 (in red), 15a (in yellow), and 8 (in blue) in CCR2 binding pocket. (B) Overlay of water density mesh of MK-0812 (red) and 15a (yellow); the “extra-water” density region for MK-0812 is shown in the green circle. (C) Overlay of water density mesh of MK-0812 (red) and 8 (blue); the “extra-water” density is shown in the green circle. (D) Water network in the protein binding site for MK-0812 and (E) for 15a.

Figure 3

H-bond interactions in the CCR2 binding pocket. (A) Schematic showing broken H-bond between Glu291-Tyr120 due to insertion of water molecules in between for MK-0812. Water molecule highlighted by the green circle denotes the extra water density region identified for MK-0812. (B) H-bond between Glu291-Tyr120 vs time for MK-0812, 15a, and 8.

Figure 4

Tyr120-Glu291 interactions: (A) Schematic representation of Glu291 and Tyr120 heavy atoms showing conformational space explored by these residues from 1 μs long MD simulations. (B) RMSF showing the flexibility of heavy atoms of Glu291 and Ty120 for MK-0812, 15a, and 8.