Why does the Y326I mutant of monoamine oxidase B decompose an endogenous amphetamine at a slower rate than the wild type enzyme? Reaction step elucidated by multiscale molecular simulations

Abstract

This work investigates the Y326I point mutation effect on the kinetics of oxidative deamination of phenylethylamine (PEA) catalyzed by the monoamine oxidase B (MAO B) enzyme. PEA is a neuromodulator capable of affecting the plasticity of the brain and is responsible for the mood enhancing effect caused by physical exercise. Due to a similar functionality, PEA is often regarded as an endogenous amphetamine. The rate limiting step of the deamination was simulated at the multiscale level, employing the Empirical Valence Bond approach for the quantum treatment of the involved valence states, whereas the environment (solvated protein) was represented with a classical force field. A comparison of the reaction free energy profiles delivered by simulation of the reaction in the wild type MAO B and its Y326I mutant yields an increase in the barrier by 1.06 kcal mol upon mutation, corresponding to a roughly 6-fold decrease in the reaction rate. This is in excellent agreement with the experimental kinetic studies. Inspection of simulation trajectories reveals possible sources of the point mutation effect, namely vanishing favorable electrostatic interactions between PEA and a Tyr326 side chain and an increased amount of water molecules at the active site due to the replacement of tyrosine by a less spacious isoleucine residue, thereby increasing the dielectric shielding of the catalytic environment provided by the enzyme.

Hydride Abstraction as the Rate-Limiting Step of the Irreversible Inhibition of Monoamine Oxidase B by Rasagiline and Selegiline: A Computational Empirical Valence Bond Study

“…Once placed within such a hydrophobic environment, the amino groups within investigated inhibitors will likely experience a reduced basicity making their unionized analogues the predominant protonation forms prior to reacting with the FAD cofactor. Even if that would not be the case, such a deprotonation can easily be achieved by the active site water molecules with a cost of only a few kcal mol −1 [ 69 , 70 ]. In this context, we utilized neutral SEL and RAS in all subsequent calculations, and our DFT results with implicit SMD solvation for their aqueous phase reactivity are presented in Table 1 .…”

“…The simulations were built around the OPLS-AA force field [ 79 ], with the ligand parameters acquired by the ffld_server utility and assisted by the Maestro v. 11.7 graphical interface [ 80 ]. The charges of the ligand atoms were determined by fitting to the electrostatic potential computed by QM calculations on the HF/6–31G(d) level of theory according to the RESP scheme, as implemented in AmberTools18 [ 81 ]—all in line with our previous reports [ 56 , 57 , 58 , 69 , 70 , 74 , 75 , 76 , 82 , 83 ].…”

Monoamine oxidase‐B inhibitors as potential neurotherapeutic agents: An overview and update

“…Additionally, slightly large water molecules were found to be present near the reacting moiety in the mutant, which resulted in the increase in the dielectric shielding of the catalytic environment of the enzyme. Further, the results revealed that the methodology appeared to correctly predict the sign and magnitude of the changed performance of MAO‐B for PEA decomposition, thus supporting the hydride transfer mechanism …”

“…Recently, Pregeljc et al investigated the Y326I point mutation effect on the kinetics of oxidative deamination of PEA catalyzed by MAO‐B. The rate‐limiting step of the deamination was simulated at the multiscale level, employing the EVB approach for the quantum treatment of the involved valence states, whereas the environment (solvated protein) was represented with a classical force field.…”

“…Further, the results revealed that the methodology appeared to correctly predict the sign and magnitude of the changed performance of MAO-B for PEA decomposition, thus supporting the hydride transfer mechanism. 277 Thus, molecular modeling techniques including various QSAR and hybrid QM/MM approaches have been useful in rational alteration of the MAO-B reactivity to fling opportunities to exploit this enzyme in biotechnology and extended the dig into its application in alternative therapies such as cardiovascular damage, hair growth, obesity, sexual dysfunction, epilepsy, and so forth, unraveling further mysteries of this enzyme. 278 NDDs epitomize a stink for drug discovery owing to their eminent preponderance and exiguity of mechanism-based treatments.…”