Hydration Properties of Ligands and Drugs in Protein Binding Sites: Tightly-Bound, Bridging Water Molecules and Their Effects and Consequences on Molecular Design Strategies

Abstract

Some water molecules in binding sites are important for intermolecular interactions and stability. The way binding site explicit water molecules are dealt with affects the diversity and nature of designed ligand chemical structures and properties. The strategies commonly employed frequently assume that a gain in binding affinity will be achieved by their targeting or neglect. However, in the present work, 2332 high-resolution X-ray crystal structures of hydrated and nonhydrated, drug and nondrug compounds in biomolecular complexes with reported Ki or Kd show that compounds that use tightly bound, bridging water molecules are as potent as those that do not. The distribution of their energies, physicochemical properties, and ligand efficiency indices were compared for statistical significance, and the results were confirmed using 2000 permutation runs. Ligand cases were also split into agonists and antagonists, and crystal structure pairs with differing tightly bound water molecules were also compared. In addition, agonists and antagonists that use tightly bound water bridges are smaller, less lipophilic, and less planar; have deeper ligand efficiency indices; and in general, possess better physicochemical properties for further development. Therefore, tightly bound, bridging water molecules may in some cases be replaced and targeted as a strategy, though sometimes keeping them as bridges may be better from a pharmacodynamic perspective. The results suggest general indications on tightly hydrated and nontightly hydrated compounds in binding sites and practical considerations to adopt a strategy in drug and molecular design when faced with this special type of water molecules. There are also benefits of lower log P and better developability for tightly hydrated compounds, while stronger potency is not always required or beneficial. The hydrated binding site may be one of the many structure conformations available to the receptor, and different ligands will have a different ability to select either hydrated or nonhydrated receptor binding site conformations. Compounds may thus be designed, and if a tightly bound, bridging water molecule is observed in the binding site, attempts to replace it should only be made if the subsequent ligand modification would improve also its ligand efficiency, enthalpy, specificity, and pharmacokinetic properties. If the modification does succeed in replacing the tightly bound, bridging water molecule, it will have at least achieved benefits for ligand optimization and development independently of either positive or negative change in binding affinity outcome.

Water Sites, Networks, And Free Energies with Grand Canonical Monte Carlo

“…23 Instead, more approximate methods, such as Poisson-Boltzmann surface area techniques, 24 cellular automata models, 25 and grid cell theory 26 are typically employed. There is an unmet need for a technique that can rigorously and efficiently calculate the hydration free energy of protein binding sites using atomistic models, as such a method could facilitate investigations on the driving forces of biomolecular association, [27][28][29] help validate faster and more approximate techniques, as well as indicate forcefield inadequacies in projects where the length of simulation is not a constraint.…”

Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description

“…Unfortunately, there is no general rule to predict whether a water molecule will be retained within a protein-complex formation, or will be removed [22]. Trying to replace bridging waters led, also, to some unfavorable consequences in binding [244,245], highlighting how challenging is binding energy prediction, and the identification of the different contributions when water molecules are present.…”

“…It has been recently reported that compounds interacting with tightly bound bridging waters are as potent as those interacting only with binding site residues [22]. Ligands not stabilized by waters are generally bulkier, more hydrophobic, more complex, and have larger steric effects than those making interactions with structurally conserved water molecules within the target binding site.…”

“…Overall, promoting enthalpic with respect to pre-supposed entropic gain could represent the winning strategy. In this perspective, designing or removing a bridging water should be done only if the subsequent ligand modifications would also improve ligand efficiency, enthalpy, entropy, specificity and pharmacokinetic properties, which will at least have benefits on ligand optimization and development [22].…”

“…The plasticity of proteins and, in particular, of binding sites is even increased by the possible presence of water molecules mediating catalytic reactions and/or protein-ligand recognition processes. In this perspective, algorithms able to rationalize water contribution, and to simulate multi-part interactions could provide better and more reliable results in a structure-based drug design scenario [21][22][23] (cf. section "Modeling waters within the active site").…”