Protein-Ligand Binding Enthalpies from Near-Millisecond Simulations: Analysis of a Preorganization Paradox

Abstract

Calorimetric studies of protein-ligand binding often yield thermodynamic data that are difficult to explain in physical terms. Today, explicit solvent molecular dynamics simulations are fast enough that we can begin to use them to look for explanations of such thermodynamic puzzles. Additionally, when such simulations generate results that do not agree well with experiment, this may motivate further development of computational methods and force fields. Here, we apply near-millisecond duration simulations to compute and analyze the binding of four peptidic ligands with the Grb2 SH2 domain, focusing on relative binding enthalpies. The ligands fall into matched pairs, which differ only in the presence or absence of a conformationally constraining bond, which preorganizes two of the ligands for binding. Prior experimental work had revealed, unexpectedly, that binding of the constrained ligands is favored enthalpically, rather than entropically, relative to their flexible<br>analogs. However, the present calculations yield the opposite trend. On further analysis, the computed relative binding enthalpies are found to be small balances of much larger underlying differences in the mean energies of structural components, such as the ligand and the binding site residues. As a consequence, the deviations from experiment in the relative binding enthalpies represent small differences between these large numbers. We also computed first order estimates of changes in configurational entropy on binding. These suggest that the more rigid constrained ligands reduce the entropy of binding site residues more than their flexible analogs do. The implications of these calculations for the use of simulations to understand the thermodynamics of molecular recognition, and for the computational analysis of binding thermodynamics, are discussed.

The current impact of water thermodynamics for small-molecule drug discovery

“…The effect would thus not be visible in most standard procedure studies where one tends to focus entirely on the bound protein/ligand/water complex. This effect is different from the one observed in the study by Li and Gilson [15], where more flexible ligands displayed a larger entropy contribution to the binding dominated by conformational effects on protein residues. MD simulations can be used to investigate water-networks [16].…”

Biophysics of Nucleic Acids Celebrating the 75th Birthday of Professor Kenneth J. Breslauer

“…In contrast, the EE metric requires rigorous determination of complete thermodynamic binding parameters [i.e., free energy (∆G), enthalpy (∆H), and entropy (T∆S)] via model-independent analytical techniques, such as isothermal titration calorimetry (ITC). An alternative approach is to employ model-dependent van't Hoff optical measurements or robust computational methods [117] as substitutes for the more precise calorimetric instrumentation.…”

“…This prompted serious re-evaluation of available data to corroborate the assumption that enthalpy-driven binders are favored in drug development [7]. Additional concerns and queries regarding method protocols, the role of solvation, and impact of ligand conformational constraints [182,210], must be addressed and reassessed [117,211]. Following a period of relative euphoria with the prospect of achieving a successful structural-energetics consensus, a certain level of skepticism has surfaced as drug design laboratories seeking rapid and straightforward decision criteria often face the realization that critical data are lacking for a complete interpretation [7].…”

“…These findings suggest a counterproductive outcome when attempting to improve ligand potency by purposely avoiding entropic penalties due to binding-induced conformational strain. A plausible explanation for this apparent discrepancy has been offered by assessing the conformational energetics computationally [117]. Specifically, the conformationallyconstrained ligands might further reduce binding site residue entropies, thereby offering a counterargument to the expected improvement in overall binding entropy upon ligand pre-organization.…”

Evaluating the Performance of Water Models with Host–Guest Force Fields in Binding Enthalpy Calculations for Cucurbit[7]uril–Guest Systems

“…15 Their simple structures overcome setup problems in MD simulations, and their small sizes make it possible to reach numerical convergence faster than protein-ligand systems in explicit-solvent for binding free energy calculations. [17][18] Host-guest systems as tiny models are alternative for informative testing and improving forcefields before using them in protein-ligand systems. 19 It may be complicated to choose which force field to use in MD simulations for protein-ligand systems, as new options are continually being offered.…”