How Ligand Protonation State Controls Water in Protein–Ligand Binding

Abstract

The role of water in protein-ligand binding has been an intensely studied topic in recent years; however, how ligand protonation state change perturbs water has not been considered. Here we show that water dynamics and interactions can be controlled by the protonation state of ligand using continuous constant pH molecular dynamics simulations of two closely related model systems, β-secretase 1 and 2 (BACE1 and BACE2), in complex with a small-molecule inhibitor. Simulations revealed that, upon binding, the inhibitor pyrimidine ring remains deprotonated in BACE1 but becomes protonated in BACE2. Pyrimidine protonation results in water displacement, rigidification of the binding pocket, and shift in the ligand binding mode from water-mediated to direct hydrogen bonding. These findings not only support but also rationalize the most recent structure-selectivity data in BACE1 drug design. Binding-induced protonation state changes are likely common; our work offers a glimpse at how modeling protein-ligand binding while allowing ligand titration can further advance the understanding of water and structure-based drug design.

Exploring the pH-dependent structure-dynamics-function relationship of human renin

“…In this work, we employed the hybrid-solvent continuous constant pH molecular dynamics (CpHMD) simulations with pH replica-exchange 26,27 to determine the catalytic dyad protonation states of renin and characterize the possibly pHdependent conformational dynamics of the flap. The replicaexchange hybrid-solvent CpHMD method has been previously applied to study several pepsin-like aspartyl proteases BACE I, 28,29 BACE II, 30 and CatD 29 and obtained dyad pK a order in agreement with experiments. These studies and another work that examined also other enzymes, 22 demonstrated that the general base or nucleophile forms more hydrogen bond than the general acid or proton donor and some of the hydrogen bonds are absent in the crystal structure and emerge during proton-coupled conformational sampling.…”

GPU-Accelerated Implementation of Continuous Constant pH Molecular Dynamics in Amber: pKa Predictions with Single-pH Simulations

“…Sometimes, structure-based pK a prediction tools, such as the empirical method Propka 3 and the Poisson-Boltzmann solver based methods APBS-PDB2PQR, 4 H++, 5 and DelPhiPKa, 6 are used to obtain estimates of the protonation states prior to running simulations; however, these tools do not directly account for the dynamic flexibility of the protein, which may lead to incorrect assignment of protonation states. Most importantly, even if the initial assignment is correct, protonation states may change in the course of conformational dynamics, as demonstrated in pH-dependent protein folding, 7,8 protein-ligand binding, [9][10][11] enzyme catalysis, 12 and ion/substrate transport across the membrane. 13,14 One solution to the above problems is to use constant pH molecular dynamics (CpHMD) methods to determine protonation states on the fly during the MD simulation.…”

Continuous constant pH Molecular Dynamics Simulations of Transmembrane Proteins

“…CpHMD methods have also been implemented in the popular Amber [8] and GROMACS [64] packages, including GBNeck2-CpHMD [35,28] in Amber and the all-atom CpHMD [18] in GROMACS [64]. Here we focus on the extensively validated [75,22,11,33,79,23,29,30,69] pH replica-exchange hybrid-solvent CpHMD method in CHARMM [73], which has been further developed to enable mechanistic studies of membrane proteins [33].…”