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

L-DOPA Autoxidation: An Empirical Valence Bond Simulation of the Reactive Step

L-DOPA, or levodopa, plays an important role in the treatment of Parkinson's disease, a debilitating neurological disorder. It acts as a precursor to dopamine, a neurotransmitter crucial for the regulation of motor functions. Administered orally, L-DOPA easily crosses the blood-brain barrier and converts into dopamine in the brain, relieving symptoms such as tremors and rigidity. However, its prolonged use can lead to complications. A significant concern with L-DOPA is its conversion to dopaquinone, a quinone metabolite that enters the redox cycle and continuously produces hydrogen peroxide. In addition, L-DOPA, which resembles tyrosine with an additional hydroxyl group, can randomly incorporate into the proteins of dopaminergic neurons and thus become an additional source of oxidative stress in Parkinson's patients. In this study, we scrutinized the rate-limiting step of L-DOPA autoxidation in aqueous solution. The reaction we studied is an intramolecular Michael addition concerted with a proton transfer from the amino group. Using the Empirical Valence Bond (EVB) method, we computed the free energy profiles of the reaction in water. The calculated barrier of 30.93 ± 1.12 kcal/mol is in reasonable agreement with the experimental barrier of 27.55 kcal/mol. This agreement confirms the validity of the studied mechanism and demonstrates the applicability of our simulation methodology for studying the autoxidation kinetics of L-DOPA within proteins.

Hypertensive Emergency Secondary to Combining Psilocybin Mushrooms, Extended Release Dextroamphetamine-Amphetamine, and Tranylcypromine

Data on medication interactions with psychedelics are limited. Here we present what may be the first published report of a hypertensive emergency following the combination of psilocybin mushrooms with a monoamine oxidase inhibitor (MAOI). A 42-year-old man with treatment-resistant major depressive disorder took 1 g of Psilocybe cubensis mushrooms, while prescribed tranylcypromine, extended-release dextroamphetamine-amphetamine, and other medications. Approximately half an hour later, he developed severe hypertension with chest pain, palpitations, and headache. Upon hospital presentation, the electrocardiogram demonstrated ST-elevation. The patient was diagnosed with a myocardial infarction and treated with lorazepam, nitroglycerin, and aspirin. He subsequently underwent emergency cardiac catheterization, which revealed no significant cardiac abnormalities. Following overnight hospitalization, he was discharged home with no lasting physical sequelae. Though data are few, past studies suggest that classic serotonergic psychedelics (5HT-2A receptor agonists) such as dimethyltryptamine (DMT), lysergic acid (LSD), and synthetic psilocybin should not produce hypertensive emergency when combined with MAOIs. We suspect phenylethylamine, found in Psilocybe cubensis and other species of psilocybin mushrooms, interacted with tranylcypromine and dextroamphetamine-amphetamine to produce this hypertensive emergency. Patients prescribed MAOIs should be warned of the potential for hypertensive emergency when consuming psilocybin mushrooms, particularly when also prescribed norepinephrine releasers such as dextroamphetamine-amphetamine.

Brunner syndrome caused by point mutation explained by multiscale simulation of enzyme reaction

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.

An electrostatic duel: subtle differences in the catalytic performance of monoamine oxidase A and B isoenzymes elucidated at the residue level using quantum computations

The origin of the immense catalytic power of enzymes remains one of the biggest unresolved questions in biochemistry, with electrostatics being one of the main contenders. Herein, we report results that not only confirm that electrostatics is the driving force behind enzyme catalysis, but also that it is capable of tuning subtle differences in the catalytic performance between structurally similar enzymes, as demonstrated using the example of isoenzymes, monoamine oxidases A and B. Using our own computationally efficient multiscale model [A. Prah, et al., ACS Catal., 2019, 9, 1231] we analyzed the rate-limiting step of the reaction between phenylethylamine and both isoenzymes and deduced that the electrostatic environment provided by isoenzyme B has a perceivably higher catalytic influence on all the considered parameters of the reaction (energy barrier, charge transfer, dipole moment, and HOMO-LUMO gap). This is in full agreement with the available experimental kinetic data and with our own simulations of the reaction in question. In-depth analysis of individual amino acid contributions of both isoenzymes to the barrier (based on the interaction between the electric field provided by the enzyme and the dipole moment of the reacting moiety) shows that the majority of the difference between the isoenzymes can be attributed to a small number of sizable differences between the aligned amino acid pairs, whereas in most of the pairs the difference in contribution to the barrier is vanishingly small. These results suggest that electrostatics largely controls the substrate selectivity of enzymes and validates our approach as being capable of discerning fine nuances in the selectivity of structurally related isoenzymes.

Questions in the Chemical Enzymology of MAO

We have structure, a wealth of kinetic data, thousands of chemical ligands and clinical information for the effects of a range of drugs on monoamine oxidase activity in vivo. We have comparative information from various species and mutations on kinetics and effects of inhibition. Nevertheless, there are what seem like simple questions still to be answered. This article presents a brief summary of existing experimental evidence the background and poses questions that remain intriguing for chemists and biochemists researching the chemical enzymology of and drug design for monoamine oxidases (FAD-containing EC 4.1.3.4).

Binding mechanism of naringenin with monoamine oxidase - B enzyme: QM/MM and molecular dynamics perspective

The reduced level of dopamine at midbrain (substantia nigra) leads to Parkinson disease by the influence of monoamine oxidation process of monoamine oxidase B (MAO-B) enzyme. This disease mostly affects the aged people. Reports outline that the naringenin molecule acts as an inhibitor of MAO-B enzyme and it potentially prevents the development of PD. To elucidate the binding mechanism of naringenin with MAO-B, we performed the molecular docking, QM/MM and molecular dynamics (MD) simulations. The molecular docking results confirm that the naringenin strongly binds with the substrate binding site of MAO-B enzyme (-12.0 kcal/mol). The low values of RMSD, RMSF and Rg indicate that the naringenin - MAO-B complex is stable over the entire period of MD simulation. Naringenin forms strong interaction with the orient keeper residue Tyr326 and other binding site residues Leu171, Glu206 and these interactions were maintained throughout the MD simulation. It is also important to block the function of MAO-B enzyme. The QM/MM study coupled with the charge density analysis reveals the charge density distribution and the strength of intermolecular interactions of naringenin-MAO-B complex. The above results suggest that this molecule is a potential inhibitor of MAO-B enzyme.

Quantum chemical (QM:MM) investigation of the mechanism of enzymatic reaction of tryptamine and N,N-dimethyltryptamine with monoamine oxidase A

The endogenous psychedelic (mind-altering) N,N-dimethyltryptamine (DMT) molecule has an important role in tissue protection, regeneration, and immunity via sigma-1 receptor activation as its natural ligand. The immunologic properties of DMT suggest this biogenic compound should be investigated thoroughly in other aspects as well. In our in silico project, we examined the metabolism of DMT and its primary analogue, the tryptamine (T), by the monoamine oxidase (MAO) flavoenzyme. MAO has two isoforms, MAO-A and MAO-B. MAOs perform the oxidation of various monoamines by their flavin adenine dinucleotide (FAD) cofactor. Two-layer QM:MM calculations at the ONIOM(M06-2X/6-31++G(d,p):UFF=QEq) level were performed including the whole enzyme to explore the potential energy surface (PES) of the reactions. Our findings reinforced that a hybrid mechanism, a mixture of pure H+ and H- transfer pathways, describes precisely the rate-determining step of amine oxidation as suggested by earlier works. Additionally, our results show that the oxidation of tertiary amine DMT requires a lower activation barrier than the primary amine T. This may reflect a general rule, thus we recommend further investigations. Furthermore, we demonstrated that at pH 7.4 the protonated form of these substrates enter the enzyme. As the deprotonation of substrates is crucial, we presumed protonated cofactor, FADH+, may form. Surprisingly, the activation barriers are much lower compared to FAD with both substrates. Therefore, we suggest further investigations in this direction.

How Monoamine Oxidase A Decomposes Serotonin: An Empirical Valence Bond Simulation of the Reactive Step

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.

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

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 k_inact 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.

Adduct under Field-A Qualitative Approach to Account for Solvent Effect on Hydrogen Bonding

The location of a mobile proton in acid-base complexes in aprotic solvents can be predicted using a simplified Adduct under Field (AuF) approach, where solute–solvent effects on the geometry of hydrogen bond are simulated using a fictitious external electric field. The parameters of the field have been estimated using experimental data on acid-base complexes in CDF₃/CDClF₂. With some limitations, they can be applied to the chemically similar CHCl₃ and CH₂Cl₂. The obtained data indicate that the solute–solvent effects are critically important regardless of the type of complexes. The temperature dependences of the strength and fluctuation rate of the field explain the behavior of experimentally measured parameters.

Nuclear quantum effects in enzymatic reactions: simulation of the kinetic isotope effect of phenylethylamine oxidation catalyzed by monoamine oxidase A

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.

Insight into the Highly Conserved and Differentiated Cofactor-Binding Sites of meso-Diaminopimelate Dehydrogenase StDAPDH

meso-Diaminopimelate dehydrogenase ( meso-DAPDH) is a good candidate for one-step synthesis of d-amino acid from 2-keto acids. Our previous research revealed the classification of meso-DAPDH family and showed that type II meso-DAPDH, such as the meso-DAPDH from Symbiobacterium thermophilum (StDAPDH), could catalyze reductive amination. In this article, seven residues of StDAPDH, which are highly conserved in each subfamily but are different between two subfamilies, were targeted to explore the relationships between structure and function. Determination of kinetic parameters showed that the amino acid residues, including P69, K159, V68, S90, V14, and V156, played very important roles in the catalytic function of StDAPDH. Molecular dynamics simulation revealed that these point mutations reduced the productive conformations by the newly formed or eliminated interactions between the residues and ligands. These results strengthen our understanding of the catalytic mechanism and evolution of meso-DAPDH and can aid future endeavors in enzyme engineering.

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

Monoamine oxidase (MAO) inhibitors have made significant contributions and remain an indispensable approach of molecular and mechanistic diversity for the discovery of antineurodegenerative drugs. However, their usage has been hampered by nonselective and/or irreversible action which resulted in drawbacks like liver toxicity, cheese effect, and so forth. Hence, the search for selective MAO inhibitors (MAOIs) has become a substantial focus in current drug discovery. This review summarizes our current understanding on MAO-A/MAO-B including their structure, catalytic mechanism, and biological functions with emphases on the role of MAO-B as a potential therapeutic target for the development of medications treating neurodegenerative disorders. It also highlights the recent developments in the discovery of potential MAO-B inhibitors (MAO-BIs) belonging to diverse chemical scaffolds, arising from intensive chemical-mechanistic and computational studies documented during past 3 years (2015-2018), with emphases on their potency and selectivity. Importantly, readers will gain knowledge of various newly established MAO-BI scaffolds and their development potentials. The comprehensive information provided herein will hopefully accelerate ideas for designing novel selective MAO-BIs with superior activity profiles and critical discussions will inflict more caution in the decision-making process in the MAOIs discovery.