Free Energies and Entropies of Water Molecules at the Inhibitor−Protein Interface of DNA Gyrase

Abstract

Complexes of the antibiotics novobiocin and clorobiocin with DNA gyrase are illustrative of the importance of bound water to binding thermodynamics. Mutants resistant to novobiocin as well as those with a decreased affinity for novobiocin over clorobiocin both involve a less favorable entropy of binding, which more than compensates for a more favorable enthalpy, and additional water molecules at the protein-ligand interface. Free energy, enthalpy, and entropy for these water molecules were calculated by thermodynamic integration computer simulations. The calculations show that addition of the water molecules is entropically unfavorable, with values that are comparable to the measured entropy differences. The free energies and entropies correlate with the change in the number of hydrogen bonds due to the addition of water molecules.

Exploring the conformational changes of the ATP binding site of gyrase B from Escherichia coli complexed with different established inhibitors by using molecular dynamics simulation

“…Waters 1 and 11, (PDB numbering), were expected to be located between the nitrogen atom of the carbamate group attached to the sugar ring on novobiocin and polar atoms of Val43. A hydrogen bond between Asp73 and carboxylate of the novobiocin has been described as well [15]. However, water 11 was exchanged by water 10 after the equilibration in both systems 1AJ6(R136H)-NOV and 1AJ6-NOV and during the simulation water 1 and 10 swapped their position while water 7 was stable.…”

“…This can be explained by the absence of water 12 (PDB code) interacting with His136 and the novobiocin ligand, which could not be included in the energy calculations. Yu and Rick [15] predicted this entropic contribution correctly by a more accurate alchemical free energy calculation approach. In our simulation, we use a significant amount of approximations intrinsic in the two end-points MM/PB(GB)SA approach [49].…”

“…Na + ions were added to obtain electrostatic neutrality. The assignment of the protonation state of the histidine residues in the active site was done based on the pKa calculations for the wild type protein reported by Schechner et al [10], which also has been used by Yu and Rick [15]. The resulting systems to start simulations with added Na + and water molecules are depicted in Table 2, as well as the charged residues present in the protein subunit.…”

“…According to descriptions found in the literature, DNA GyrB is one of those proteins with ordered water molecules (relative to the liquid) located at the protein-ligand interface that affect the binding affinity for the ligands because of the entropic cost [15,46]. The stability of these water molecules in the active site were analyzed along the simulation trajectory to identify the ones that were stable enough to be included as explicit molecules in the binding free energy calculations.…”

“…Strong correlations between the thermodynamic parameters ( G, H and S) and the change in the hydrogen bonds made when a water molecule is added were found. One of the most important conclusions drawn by the authors was the advantage of designing new drugs for this target modifying the ligands so that, water molecules are removed from the site or the number of hydrogen bonds they can make is reduced [15].…”