While
the function of enzymes has been well-known to researchers
for decades, the driving force behind it is still a hotly debated
topic. Herein, we report significant evidence for electrostatics being
that driving force, using a simple, computationally inexpensive, multiscale
model of monoamine oxidase A and phenylethylamine. We found that electrostatics
provided by the enzyme substantially enhances the reaction by all
the considered criteria (lowering the energy barrier, increasing charge
transfer, decreasing the highest occupied molecular orbital–lowest
unoccupied molecular orbital (HOMO–LUMO) gap, increasing the
dipole moment). The catalytic effect can be rationalized by the stabilizing
interaction between the dipole moment of the reacting moiety and the
electric field exerted by the charged environment. Both the dipole
moment and the electric field are perceivably larger in the transition
state as compared to the state of reactants; hence the transition
state is stabilized to a larger extent and better solvated than the
state of reactants, thereby lowering the barrier. Our findings support
the view that catalysis in enzymes originates from preorganized electrostatics.
The enzyme-catalyzed
degradation of the biogenic amine serotonin
is an essential regulatory mechanism of its level in the human organism.
In particular, monoamine oxidase A (MAO A) is an important flavoenzyme
involved in the metabolism of monoamine neurotransmitters. Despite
extensive research efforts, neither the catalytic nor the inhibition
mechanisms of MAO enzymes are currently fully understood. In this
article, we present the quantum mechanics/molecular mechanics simulation
of the rate-limiting step for the serotonin decomposition, which consists
of hydride transfer from the serotonin methylene group to the N5 atom
of the flavin moiety. Free-energy profiles of the reaction were computed
by the empirical valence bond method. Apart from the enzymatic environment,
the reference reaction in the gas phase was also simulated, facilitating
the estimation of the catalytic effect of the enzyme. The calculated
barrier for the enzyme-catalyzed reaction of 14.82 ± 0.81 kcal
mol
–1
is in good agreement with the experimental
value of 16.0 kcal mol
–1
, which provides strong
evidence for the validity of the proposed hydride-transfer mechanism.
Together with additional experimental and computational work, the
results presented herein contribute to a deeper understanding of the
catalytic mechanism of MAO A and flavoenzymes in general, and in the
long run, they should pave the way toward applications in neuropsychiatry.
Electrostatic interactions not only represent the main source of catalytic function of enzymes, but are also responsible for the fine tuning of their performance. We presently demonstrate this on the example of two related enzymes, MAO A and MAO B.
Monoamine oxidases (MAOs) catalyze the degradation of a very broad range of biogenic and dietary amines including many neurotransmitters in the brain, whose imbalance is extensively linked with the biochemical pathology of various neurological disorders, and are, accordingly, used as primary pharmacological targets to treat these debilitating cognitive diseases. Still, despite this practical significance, the precise molecular mechanism underlying the irreversible MAO inhibition with clinically used propargylamine inhibitors rasagiline and selegiline is still not unambiguously determined, which hinders the rational design of improved inhibitors devoid of side effects current drugs are experiencing. To address this challenge, we present empirical valence bond QM/MM simulations of the rate-limiting step of the MAO inhibition involving the hydride anion transfer from the inhibitor α-carbon onto the N5 atom of the flavin adenin dinucleotide (FAD) cofactor. The proposed mechanism is strongly supported by the obtained free energy profiles, which confirm a higher reactivity of selegiline over rasagiline, while the calculated difference in the activation Gibbs energies of ΔΔG‡ = 3.1 kcal mol−1 is found to be in very good agreement with that from the measured literature kinact values that predict a 1.7 kcal mol−1 higher selegiline reactivity. Given the similarity with the hydride transfer mechanism during the MAO catalytic activity, these results verify that both rasagiline and selegiline are mechanism-based irreversible inhibitors and offer guidelines in designing new and improved inhibitors, which are all clinically employed in treating a variety of neuropsychiatric and neurodegenerative conditions.
Monoamine oxidase A (MAO A) is a well-known enzyme responsible for the oxidative deamination of several important monoaminergic neurotransmitters. The rate-limiting step of amine decomposition is hydride anion transfer from the substrate α–CH2 group to the N5 atom of the flavin cofactor moiety. In this work, we focus on MAO A-catalyzed benzylamine decomposition in order to elucidate nuclear quantum effects through the calculation of the hydrogen/deuterium (H/D) kinetic isotope effect. The rate-limiting step of the reaction was simulated using a multiscale approach at the empirical valence bond (EVB) level. We applied path integral quantization using the quantum classical path method (QCP) for the substrate benzylamine as well as the MAO cofactor flavin adenine dinucleotide. The calculated H/D kinetic isotope effect of 6.5 ± 1.4 is in reasonable agreement with the available experimental values.
By using computational techniques for quantizing nuclear motion one can accurately reproduce kinetic isotope effect of enzymatic reactions, as demonstrated for phenylethylamine oxidation catalyzed by the monoamine oxidase A enzyme.
Monoamine oxidases (MAOs) are an important group of enzymes involved in the degradation of neurotransmitters and their imbalanced mode of action may lead to the development of various neuropsychiatric or neurodegenerative disorders. In this work, we report the results of an in-depth computational study in which we performed a static and a dynamic analysis of a series of substituted β-carboline natural products, found mainly in roasted coffee and tobacco smoke, that bind to the active site of the MAO‑A isoform. By applying molecular docking in conjunction with structure-based pharmacophores and molecular dynamics simulations coupled with dynamic pharmacophores, we extensively investigated the geometric aspects of MAO-A binding. To gain insight into the energetics of binding, we used the linear interaction energy (LIE) method and determined the key anchors that allow productive β-carboline binding to MAO-A. The results presented herein could be applied in the rational structure-based design and optimization of β-carbolines towards preclinical candidates that would target the MAO-A enzyme and would be applicable especially in the treatment of mental disorders such as depression.
Brunner syndrome is a disorder characterized by intellectual disability and impulsive, aggressive behavior associated with deficient function of the monoamine oxidase A (MAO-A) enzyme. These symptoms (along with particularly high serotonin levels) have been reported in patients with two missense variants in MAO-A (p.R45W and p.E446K). Herein, we report molecular simulations of the rate-limiting step of MAO-A-catalyzed serotonin degradation for these variants. We found that the R45W mutation causes a 6000-fold slowdown of enzymatic function, whereas the E446K mutation causes a 450-fold reduction of serotonin degradation rate, both of which are practically equivalent to a gene knockout. In addition, we thoroughly compared the influence of enzyme electrostatics on the catalytic function of both the wild type MAO-A and the p.R45W variant relative to the wild type enzyme, revealing that the mutation represents a significant electrostatic perturbation that contributes to the barrier increase. Understanding genetic disorders is closely linked to understanding the associated chemical mechanisms, and our research represents a novel attempt to bridge the gap between clinical genetics and the underlying chemical physics.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.