# Inclusion of Enclosed Hydration Effects in the Binding Free Energy Estimation of Dopamine D3 Receptor Complexes

## TL;DR

This paper introduces a novel molecular dynamics-based method to accurately estimate binding free energies of dopamine D3 receptor antagonists by including the effects of enclosed hydration and conformational flexibility.

## Contribution

It presents a new approach that incorporates hydration site displacement effects into binding free energy calculations for G-protein coupled receptors.

## Key findings

- Hydration site displacement significantly impacts binding free energy estimates.
- The method improves understanding of receptor-ligand recognition mechanisms.
- Confined hydration effects are critical in dopamine D3 receptor binding.

## Abstract

Confined hydration and conformational flexibility are some of the challenges encountered for the rational design of selective antagonists of G-protein coupled receptors. We present a set of C3-substituted (-)-stepholidine derivatives as potent binders of the dopamine D3 receptor. The compounds are characterized biochemically, as well as by computer modeling using a novel molecular dynamics-based alchemical binding free energy approach which incorporates the effect of the displacement of enclosed water molecules from the binding site. The free energy of displacement of specific hydration sites is obtained using the Hydration Site Analysis method with explicit solvation. This work underscores the critical role of confined hydration and conformational reorganization in the molecular recognition mechanism of dopamine receptors and illustrates the potential of binding free energy models to represent these key phenomena.