Cocaine Esterase–Cocaine Binding Process and the Free Energy Profiles by Molecular Dynamics and Potential of Mean Force Simulations

Abstract

The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profiles for the binding process of (−)-cocaine interacting with wild-type cocaine esterase (CocE) and its mutants (T172R/G173Q and L119A/L169K/G173Q). According to the MD simulations, the general protein-(−)-cocaine binding mode is not affected by the mutations, e.g. the benzoyl group of (−)-cocaine is always bound in a sub-site composed of aromatic residues W151, W166, F261, and F408 and hydrophobic residue L407, while the carbonyl oxygen on the benzoyl group of (−)-cocaine is hydrogen-bonded with the oxyanion-hole residues Y44 and Y118. According to the PMF-calculated free energy profiles for the binding process, the binding free energies for (−)-cocaine with the wild-type, T172R/G173Q, and L119A/L169K/G173Q CocEs are predicted to be −6.4, −6.2, and −5.0 kcal/mol, respectively. The computational predictions are supported by experimental kinetic data, as the calculated binding free energies are in good agreement with the experimentally-derived binding free energies, i.e. −7.2, −6.7, and −4.8 kcal/mol for the wild-type, T172R/G173Q, and L119A/L169K/G173Q, respectively. The reasonable agreement between the computational and experimental data suggests that the PMF simulations may be used as a valuable tool in new CocE mutant design that aims to decrease the Michaelis-Menten constant of the enzyme for (−)-cocaine.

Binding Modes of Three Inhibitors 8CA, F8A and I4A to A-FABP Studied Based on Molecular Dynamics Simulation

“…In order to quantificationally estimate the strength of the hydrogen bonds, the contributions of the hydrogen bonds to the binding free energy of 8CA to A-FABP was calculated using the following equation [58], [59], and the results were listed in Table 2.where is the H atom-acceptor distance for the i th hydrogen bond. The calibrated parameters and were set to 5.571 and 668.580, respectively [58], [59]. As seen from Table 2, the strengths of the hydrogen bond O1…R126HH21 and O1…R128HH21 are −2.50 and −1.81 kcal·mol −1 , respectively, while the another two hydrogen bonds are weaker than the two previous hydrogen bonds.…”

Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations

“…It has been known that the T172R/G173Q mutations can significantly stabilize the CocE structure without changing the catalytic activity. The same T172R/G173Q mutant CocE was also used to study the CocE-(−)-cocaine binding process [33]. For convenience, below we simply refer CocE to the T172R/G173Q mutant CocE, unless indicated explicitly otherwise.…”

“…For convenience, below we simply refer CocE to the T172R/G173Q mutant CocE, unless indicated explicitly otherwise. Initial structure of the CocE-(+)-cocaine binding complex was prepared based on the available X-ray crystal structure [34] of CocE (PDB code 3I2F for the T172R/G173Q mutant CocE) and the results of our previous molecular docking and MD simulations on CocE binding with (−)-cocaine [14, 33]. The initial CocE-(+)-cocaine binding structure was energy-minimized by using the Sander module of Amber 12 program [35] via a combined use of the steepest descent/conjugate gradient algorithms, with a convergence criterion of 0.01 kcal mol -1 Å -1 , and the non-bonded cutoff distance was set to 10.0 Å. MD simulation was performed by using the Sander module of the Amber 12 program package.…”

“…It has also been known that the CocE-(−)-cocaine binding process [33] is remarkably different from the BChE-(−)-cocaine binding process [23]. BChE-(−)-cocaine binding process is associated with a very high energy barrier [22, 23], whereas the CocE-(−)-cocaine binding process is barrier-less [33].…”

“…BChE-(−)-cocaine binding process is associated with a very high energy barrier [22, 23], whereas the CocE-(−)-cocaine binding process is barrier-less [33]. For the remaining mechanistic question to be addressed, it is unknown whether the CocE-(+)-cocaine binding process is also different from the CocE-(−)-cocaine binding process, because no computational study has been reported on the CocE-(+)-cocaine binding process.…”