1
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Xia X, Gao Y. Determining Reaction Paths by Evaluating Kinetic Isotopic Effects with Density Functional Theory: Example of Methane Thermogenesis. J Chem Inf Model 2023; 63:2742-2747. [PMID: 37094567 DOI: 10.1021/acs.jcim.3c00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
This study demonstrates the determination of reaction pathways by evaluating the carbon kinetic isotopic effect and interpreting isotopic fractionations based on quantum chemical calculations. The reaction under investigation is methane thermogenesis from the decomposition of kerogen, which is a geochemical reaction under temperatures below 150 °C and lasts for tens of millions of years. Investigating its mechanism requires theoretical simulations because lab experiments at practical time-lengths require elevated temperatures, which introduce unwanted side reactions. Density functional theory and kinetic simulations were conducted on isotopic fractionations with the use of two possible pathways (free-radical versus carbonium), and the results were compared to field data sets. Different molecular sizes of kerogen were investigated to account for the hindrance of translation and rotation in modeling a reactant in the solid phase. Both pathways have low reaction barriers, implying that the reaction rates are limited by the concentration of active species (hydrated protons and free radicals). The results support the carbonium pathway and rule out the free-radical pathway as the 13CH4 from the latter would be 30‰ more depleted than the observed data. Additionally, simulations were conducted on hydrocarbon isotope fractionation of the carbonium pathway with consideration of hydrogen exchange between methane and water, successively reproducing the observed abundances of deuterium-containing isotopologues (13CH3D, 13CH3D, and 12CH2D2).
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Affiliation(s)
- Xinyu Xia
- Department of Earth and Planetary Sciences, University of Texas at San Antonio, San Antonio, Texas 78249, United States
| | - Yongli Gao
- Department of Earth and Planetary Sciences, University of Texas at San Antonio, San Antonio, Texas 78249, United States
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2
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Exploring the Dynamical Nature of Intermolecular Hydrogen Bonds in Benzamide, Quinoline and Benzoic Acid Derivatives. Molecules 2022; 27:molecules27248847. [PMID: 36557978 PMCID: PMC9783803 DOI: 10.3390/molecules27248847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022] Open
Abstract
The hydrogen bonds properties of 2,6-difluorobenzamide, 5-hydroxyquinoline and 4-hydroxybenzoic acid were investigated by Car-Parrinello and path integral molecular dynamics (CPMD and PIMD), respectively. The computations were carried out in vacuo and in the crystalline phase. The studied complexes possess diverse networks of intermolecular hydrogen bonds (N-H…O, O-H…N and O-H…O). The time evolution of hydrogen bridges gave a deeper insight into bonds dynamics, showing that bridged protons are mostly localized on the donor side; however, the proton transfer phenomenon was registered as well. The vibrational features associated with O-H and N-H stretching were analyzed on the basis of the Fourier transform of the atomic velocity autocorrelation function. The spectroscopic effects of hydrogen bond formation were studied. The PIMD revealed quantum effects influencing the hydrogen bridges providing more accurate free energy sampling. It was found that the N…O or O…O interatomic distances decreased (reducing the length of the hydrogen bridge), while the O-H or N-H covalent bond was elongated, which led to the increase in the proton sharing. Furthermore, Quantum Theory of Atoms in Molecules (QTAIM) was used to give insight into electronic structure parameters. Finally, Symmetry-Adapted Perturbation Theory (SAPT) was employed to estimate the energy contributions to the interaction energy of the selected dimers.
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3
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Competitive nuclear quantum effect and H/D isotope effect on torsional motion of H2O2: An ab initio path integral molecular dynamics study. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2021.113542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Shenderovich IG. Editorial to the Special Issue "Gulliver in the Country of Lilliput: An Interplay of Noncovalent Interactions". Molecules 2020; 26:E158. [PMID: 33396433 PMCID: PMC7794748 DOI: 10.3390/molecules26010158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 12/30/2020] [Indexed: 11/18/2022] Open
Abstract
Noncovalent interactions allow our world to exist [...].
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Affiliation(s)
- Ilya G Shenderovich
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitaetstrasse 31, 93053 Regensburg, Germany
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5
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Funahashi H, Tachikawa M, Udagawa T. Determining if Reaction Selectivity Can Be Controlled by the H/D Isotope Effect in CH···O Interactions. Org Lett 2020; 22:9439-9443. [PMID: 33167609 DOI: 10.1021/acs.orglett.0c03351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The H/D isotope effect in the CH···O interactions of several systems is systematically analyzed to determine whether it exerts control over reaction selectivity. Our theoretical study demonstrates that deuterium substitution has a negligible effect on CH···O interactions; thus, reaction selectivity likely cannot be controlled by the H/D isotope effect in these CH···O interactions.
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Affiliation(s)
- Haruki Funahashi
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
| | - Masanori Tachikawa
- Graduate School of NanobioScience, Yokohama City University, Yokohama 236-0027, Japan
| | - Taro Udagawa
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1-1, Gifu 501-1193, Japan
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6
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Prah A, Ogrin P, Mavri J, Stare J. Nuclear quantum effects in enzymatic reactions: simulation of the kinetic isotope effect of phenylethylamine oxidation catalyzed by monoamine oxidase A. Phys Chem Chem Phys 2020; 22:6838-6847. [DOI: 10.1039/d0cp00131g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
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.
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Affiliation(s)
- Alja Prah
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
- University of Ljubljana
| | - Peter Ogrin
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
- University of Ljubljana
| | - Janez Mavri
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
| | - Jernej Stare
- Theory Department
- National Institute of Chemistry
- Ljubljana
- Slovenia
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7
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How Important Is the Use of Cocaine and Amphetamines in the Development of Parkinson Disease? A Computational Study. Neurotox Res 2019; 37:724-731. [DOI: 10.1007/s12640-019-00149-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/18/2019] [Accepted: 11/29/2019] [Indexed: 11/25/2022]
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8
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Tandarić T, Vianello R. Computational Insight into the Mechanism of the Irreversible Inhibition of Monoamine Oxidase Enzymes by the Antiparkinsonian Propargylamine Inhibitors Rasagiline and Selegiline. ACS Chem Neurosci 2019; 10:3532-3542. [PMID: 31264403 DOI: 10.1021/acschemneuro.9b00147] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Monoamine oxidases (MAOs) are flavin adenine dinucleotide containing flavoenzymes that catalyze the degradation of a range of brain neurotransmitters, whose imbalance is extensively linked with the pathology of various neurological disorders. This is why MAOs have been the central pharmacological targets in treating neurodegeneration for more than 60 years. Still, despite this practical importance, the precise chemical mechanisms underlying the irreversible inhibition of the MAO B isoform with clinical drugs rasagiline (RAS) and selegiline (SEL) remained unknown. Here we employed a combination of MD simulations, MM-GBSA binding free energy evaluations, and QM cluster calculations to show the MAO inactivation proceeds in three steps, where, in the rate-limiting first step, FAD utilizes its N5 atom to abstracts a hydride anion from the inhibitor α-CH2 group to ultimately give the final inhibitor-FAD adduct matching crystallographic data. The obtained free energy profiles reveal a lower activation energy for SEL by 1.2 kcal mol-1 and a higher reaction exergonicity by 0.8 kcal mol-1, with the former being in excellent agreement with experimental ΔΔG‡EXP = 1.7 kcal mol-1, thus rationalizing its higher in vivo reactivity over RAS. The calculated ΔGBIND energies confirm SEL binds better due to its bigger size and flexibility allowing it to optimize hydrophobic C-H···π and π···π interactions with residues throughout both of enzyme's cavities, particularly with FAD, Gln206 and four active site tyrosines, thus overcoming a larger ability of RAS to form hydrogen bonds that only position it in less reactive orientations for the hydride abstraction. Offered results elucidate structural determinants affecting the affinity and rates of the inhibition reaction that should be considered to cooperate when designing more effective compounds devoid of untoward effects, which are of utmost significance and urgency with the growing prevalence of brain diseases.
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Affiliation(s)
- Tana Tandarić
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
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9
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Rekik N, Salman S, Suleiman J, Farooq U, Flakus HT. IR spectral density of the υS(Cl–H→) band in gaseous (CH3)2O…HCl complex: Phase decoherence due to the anharmonic coupling theory and the bending mode effects. Chem Phys 2019. [DOI: 10.1016/j.chemphys.2018.11.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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10
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Drake LR, Brooks AF, Mufarreh AJ, Pham JM, Koeppe RA, Shao X, Scott PJH, Kilbourn MR. Deuterium Kinetic Isotope Effect Studies of a Potential in Vivo Metabolic Trapping Agent for Monoamine Oxidase B. ACS Chem Neurosci 2018; 9:3024-3027. [PMID: 30074755 DOI: 10.1021/acschemneuro.8b00219] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Visualizing the in vivo activity of monoamine oxidase B (MAO-B) is a valuable tool in the ongoing investigation of astrogliosis in neurodegeneration. Existing strategies for imaging changes in MAO enzyme expression or activity have utilized the irreversible suicide inhibitors or high-affinity reversibly binding inhibitors as positron emission tomography (PET) ligands. As an alternative approach, we developed 4-methyl-7-[(1-[11C]methyl-1,2,3,6-tetrahydropyridin-4-yl)oxy]-2 H-chromen-2-one ([11C]Cou) as a metabolic trapping agent for MAO-B. Trapping of [11C]Cou in rhesus monkey brain demonstrated MAO-B selectivity. In this work, we have attempted to improve on the in vivo pharmacokinetics of [11C]Cou by using the deuterium kinetic isotope effect (KIE) to slow the MAO-B-mediated oxidation step and thus reduce the rate of trapping in brain tissues. However, in vitro assays of enzyme kinetics and in vivo PET imaging of pharmacokinetics in primate brain showed no effects of deuterium substitution on the tetrahydropyridine ring of [11C]Cou. The results are possibly due to masking of the KIE by a second step in the overall metabolism of the new imaging agent.
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Affiliation(s)
- Lindsey R. Drake
- The Interdepartmental Program in Medicinal Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
| | - Allen F. Brooks
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
| | - Anthony J. Mufarreh
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
| | - Jonathan M. Pham
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
| | - Robert A. Koeppe
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
| | - Xia Shao
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
| | - Peter J. H. Scott
- The Interdepartmental Program in Medicinal Chemistry, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109, United States
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
| | - Michael R. Kilbourn
- Department of Radiology, University of Michigan Medical School, 1301 Catherine Street, Ann Arbor, Michigan 48109, United States
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11
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Umek N, Geršak B, Vintar N, Šoštarič M, Mavri J. Dopamine Autoxidation Is Controlled by Acidic pH. Front Mol Neurosci 2018; 11:467. [PMID: 30618616 PMCID: PMC6305604 DOI: 10.3389/fnmol.2018.00467] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/03/2018] [Indexed: 11/16/2022] Open
Abstract
We studied the reaction mechanism of dopamine autoxidation using quantum chemical methods. Unlike other biogenic amines important in the central nervous system, dopamine and noradrenaline are capable of undergoing a non-enzymatic autoxidative reaction giving rise to a superoxide anion that further decomposes to reactive oxygen species. The reaction in question, which takes place in an aqueous solution, is as such not limited to the mitochondrial membrane where scavenging enzymes such as catalase and superoxide dismutase are located. With the experimental rate constant of 0.147 s−1, the dopamine autoxidation reaction is comparably as fast as the monoamine oxidase B catalyzed dopamine decomposition with a rate constant of 1 s−1. By using quantum chemical calculations, we demonstrated that the rate-limiting step is the formation of a hydroxide ion from a water molecule, which attacks the amino group that enters intramolecular Michael addition, giving rise to a pharmacologically inert aminochrome. We have shown that for dopamine stability on a time scale of days, it is essential that the pH value of the synaptic vesicle interior is acidic. The pathophysiologic correlates of the results are discussed in the context of Parkinson's disease as well as the pathology caused by long-term amphetamine and cocaine administration.
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Affiliation(s)
- Nejc Umek
- Department of Anesthesiology and Surgical Intensive Therapy, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Institute of Anatomy, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Blaž Geršak
- Department of Anesthesiology and Surgical Intensive Therapy, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Neli Vintar
- Department of Anesthesiology and Surgical Intensive Therapy, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Department of Anesthesiology and Reanimatology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Šoštarič
- Department of Anesthesiology and Surgical Intensive Therapy, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Department of Anesthesiology and Reanimatology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Janez Mavri
- National Institute of Chemistry, Ljubljana, Slovenia
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12
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Tupikina E, Denisov G, Melikova S, Kucherov S, Tolstoy P. New look at the Badger-Bauer rule: Correlations of spectroscopic IR and NMR parameters with hydrogen bond energy and geometry. FHF complexes. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Rekik N, Suleiman J, Blaise P, Wojcik MJ. Equivalence between the Classical and Quantum IR Spectral Density Approaches of Weak H-Bonds in the Absence of Damping. J Phys Chem A 2018; 122:2108-2115. [PMID: 29436830 DOI: 10.1021/acs.jpca.8b00269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The aim of this paper is to overhaul the quantum elucidation of the spectral density (SD) of weak H-bonds treated without taking into account any of the damping mechanisms. The reconsideration of the SD is performed within the framework the linear response theory. Working in the setting of the strong anharmonic coupling theory and the adiabatic approximation, the simplified expression of the classical SD, in the absence of dampings, is equated to be ICl(ω) = Re[∫0∞GCl(t)e-iΩt dt] in which the classical-like autocorrelation function (ACF), GCl(t), is given by GCl(t) = tr{ρ(β){μ(0)}{μ(t)}†}. With this consideration, we have shown that the classical SD is equivalent to the line shape obtained by F(ω) = ΩICl(ω), which in turn is equivalent to the quantum SD given by IQu(ω) = Re[∫0∞GQu(t)e-iΩt dt], where GQu(t) is the corresponding quantum ACF having for expression GQu(t) = (1/β) tr{ρ∫0β[μ(0)}{μ(t + iλℏ)}† dλ}. Thus, we have shown that for weak H-bonds dealt without dampings, the SDs obtained by the quantum approaches are equivalent to the SDs geted by the classical approach in which the incepation ACF is, however, of quantum nature and where the line shape is the Fourier transform of the ACF times the angular frequency. It is further shown that the classical approach dealing with the SD of weak H-bonds leads identically to the result found by Maréchal and Witkowski in their pioneering quantum treatment where they ignored the linear response theory and dampings.
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Affiliation(s)
- Najeh Rekik
- Physics Department, Faculty of Science, University of Ha'il , Kingdom of Saudi Arabia.,Department of Chemistry, University of Alberta , Edmonton, Alberta T6G 2G2, Canada
| | - Jamal Suleiman
- Physics Department, College of Science, King Faisal University , Al Ahsa 31982, Kingdom of Saudi Arabia
| | - Paul Blaise
- Laboratoire de Mathématiques et Physique (LAMPS), Université de Perpignan Via Domitia (UPVD) , 52 Av. Paul Alduy, 66860 Perpignan Cedex, France
| | - Marek J Wojcik
- Laboratory of Molecular Spectroscopy, Faculty of Chemistry, Jagiellonian University , Gronostajowa 2, 30-387 Krakow, Poland
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14
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Pregeljc D, Jug U, Mavri J, Stare J. 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. Phys Chem Chem Phys 2018; 20:4181-4188. [PMID: 29360121 DOI: 10.1039/c7cp07069a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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-1 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.
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Affiliation(s)
- Domen Pregeljc
- Theory Department, National Institute of Chemistry, Ljubljana, Slovenia.
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15
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Mori Y. Reaction pathway and H/D kinetic isotope effects of the triple proton transfer in a 7-hydroxyquinoline-methanol complex in the ground state: A computational approach. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Yukie Mori
- Department of Chemistry, Faculty of Science; Ochanomizu University; Tokyo Japan
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16
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Dixit VA, Lal LA, Agrawal SR. Recent advances in the prediction of non‐
CYP450
‐mediated drug metabolism. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1323] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmaceutical Chemistry, School of Pharmacy & Technology Management (SPTM)Shri Vile Parle Kelavani Mandal's (SVKM's), Narsee Monjee Institute of Management Studies (NMIMS)ShirpurIndia
| | - L. Arun Lal
- Department of Pharmaceutical Chemistry, School of Pharmacy & Technology Management (SPTM)Shri Vile Parle Kelavani Mandal's (SVKM's), Narsee Monjee Institute of Management Studies (NMIMS)ShirpurIndia
| | - Simran R. Agrawal
- Department of Pharmaceutical Chemistry, School of Pharmacy & Technology Management (SPTM)Shri Vile Parle Kelavani Mandal's (SVKM's), Narsee Monjee Institute of Management Studies (NMIMS)ShirpurIndia
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17
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Rekik N, Alshammari MF. Electrical anharmonicity and dampings contributions to Cl- H→ stretching band in gaseous (CH 3 ) 2 O…HCl complex: Quantum dynamic study and prediction of the temperature effects. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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18
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Rekik N. Signature of Congregated Effects of Mechanical and Electrical Anharmonicities, Fermi Resonances, and Dampings on the IR Spectra of Hydrogen Bonded Systems: Quantum Dynamic Study. J Phys Chem A 2017; 121:3555-3566. [DOI: 10.1021/acs.jpca.7b01616] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Najeh Rekik
- Physics
Department, Faculty of Science, University of Ha’il, Ha’il, 81451, Kingdom of Saudi Arabia
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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19
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Flakus HT, Hachuła B, Hołaj-Krzak JT, Al-Agel FA, Rekik N. "Long-distance" H/D isotopic self-organization phenomena in scope of the infrared spectra of hydrogen-bonded terephthalic and phthalic acid crystals. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:65-74. [PMID: 27599190 DOI: 10.1016/j.saa.2016.08.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/23/2016] [Accepted: 08/25/2016] [Indexed: 06/06/2023]
Abstract
This paper deals with the experimental and theoretical studies of abnormal properties of terephthalic acid (TAC) and phthalic acid (PAC) crystals manifested in the H/D isotopic exchange. The widely utilized deuteration routine appeared to be insufficiently effective in the case of the h6-TAC isotopomer. In the case of the d4-TAC derivative the isotopic exchange process occurred noticeably more effectively. In contrast, both isotopomers of PAC, h6 and d4, appeared much more susceptible for deuteration. A theoretical model was elaborated describing "long-distance" dynamical co-operative interactions involving hydrogen bonds in TAC and PAC crystals. The model assumes extremely strong dynamical co-operative interactions of hydrogen bonds from the adjacent (COOH)2 cycles. This leads to an additional stabilization of h6-TAC molecular chains. The interaction energies affect the chemical equilibrium of the H/D isotopic exchange. The model predicts a differentiated influence of the H and D atoms linked to the aromatic rings on to the process. In this approach the totally-symmetric CH bond stretching vibrations and the proton stretching totally symmetric vibrations couple with the π-electronic motions. It was also shown that identical hydrogen isotope atoms, H or D, in whole TAC molecules, noticeably enlarge the energy of the dynamical co-operative interactions in the crystals, in contrast to the case of different hydrogen isotopes present in the carboxyl groups and linked to the aromatic rings. The "long-distance" dynamical co-operative interactions in PAC crystals were found of a minor importance due to the electronic properties of PAC molecules.
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Affiliation(s)
- Henryk T Flakus
- Institute of Chemistry, University of Silesia, Katowice 40-006, Poland.
| | - Barbara Hachuła
- Institute of Chemistry, University of Silesia, Katowice 40-006, Poland.
| | | | - Faisal A Al-Agel
- Physics Department, College of Science, Aljouf University, P. O. Box 2014, Sakaka, Saudi Arabia
| | - Najeh Rekik
- Physics Department, Faculty of Science, Ha'il University, P. O. Box 2440, 81451 Ha'il, Saudi Arabia; Laboratoire de Physique Quantique, Faculté des Sciences de Monastir, 5019 Monastir, Tunisia.
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20
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Maršavelski A, Vianello R. What a Difference a Methyl Group Makes: The Selectivity of Monoamine Oxidase B Towards Histamine and N-Methylhistamine. Chemistry 2017; 23:2915-2925. [PMID: 28052533 DOI: 10.1002/chem.201605430] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Indexed: 12/17/2022]
Abstract
Monoamine oxidase (MAO) enzymes 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. Although sharing around 70 % sequence identity, both MAO A and B isoforms differ in substrate affinities and inhibitor sensitivities. Inhibitors that act on MAO A are used to treat depression, due to their ability to raise serotonin concentrations, whereas MAO B inhibitors decrease dopamine degradation and improve motor control in patients with Parkinson disease. Despite this functional importance, the factors affecting MAO selectivity are poorly understood. Here, we used a combination of molecular dynamics (MD) simulations, molecular mechanics with Poisson-Boltzmann and surface area solvation (MM-PBSA) binding free energy evaluations, and quantum mechanical (QM) cluster calculations to address the unexpected, yet challenging MAO B selectivity for N-methylhistamine (NMH) over histamine (HIS), differing only in a single methyl group distant from the reactive ethylamino center. This study shows that a dominant selectivity contribution is offered by a lower activation free energy for NMH by 2.6 kcal mol-1 , in excellent agreement with the experimental ΔΔG≠EXP =1.4 kcal mol-1 , together with a more favorable reaction exergonicity and active-site binding. This study also confirms the hydrophobic nature of the MAO B active site and underlines the important role of Ile199, Leu171, and Leu328 in properly orienting substrates for the reaction.
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Affiliation(s)
- Aleksandra Maršavelski
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
| | - Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute, Bijenička cesta 54, 10000, Zagreb, Croatia
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Poberžnik M, Purg M, Repič M, Mavri J, Vianello R. Empirical Valence Bond Simulations of the Hydride-Transfer Step in the Monoamine Oxidase A Catalyzed Metabolism of Noradrenaline. J Phys Chem B 2016; 120:11419-11427. [PMID: 27734680 DOI: 10.1021/acs.jpcb.6b09011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Monoamine oxidases (MAOs) A and B are flavoenzymes responsible for the metabolism of biogenic amines, such as dopamine, serotonin, and noradrenaline (NA), which is why they have been extensively implicated in the etiology and course of various neurodegenerative disorders and, accordingly, used as primary pharmacological targets to treat these debilitating cognitive diseases. The precise chemical mechanism through which MAOs regulate the amine concentration, which is vital for the development of novel inhibitors, is still not unambiguously determined in the literature. In this work, we present atomistic empirical valence bond simulations of the rate-limiting step of the MAO-A-catalyzed NA (norepinephrine) degradation, involving hydride transfer from the substrate α-methylene group to the flavin moiety of the flavin adenine dinucleotide prosthetic group, employing the full dimensionality and thermal fluctuations of the hydrated enzyme, with extensive configurational sampling. We show that MAO-A lowers the free energy of activation by 14.3 kcal mol-1 relative to that of the same reaction in aqueous solution, whereas the calculated activation free energy of ΔG‡ = 20.3 ± 1.6 kcal mol-1 is found to be in reasonable agreement with the correlated experimental value of 16.5 kcal mol-1. The results presented here strongly support the fact that both MAO-A and MAO-B isoforms function by the same hydride-transfer mechanism. We also considered a few point mutations of the "aromatic cage" tyrosine residue (Tyr444Phe, Tyr444Leu, Tyr444Trp, Tyr444His, and Tyr444Glu), and the calculated changes in the reaction barriers are in agreement with the experimental values, thus providing further support to the proposed mechanism.
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Affiliation(s)
- Matic Poberžnik
- Department of Physical and Organic Chemistry, Jožef Stefan Institute , Jamova cesta 39, SI-1000 Ljubljana, Slovenia
| | - Miha Purg
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre , Husargatan 3, S-75124 Uppsala, Sweden
| | - Matej Repič
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry , Hajdrihova ulica 19, SI-1000 Ljubljana, Slovenia
| | - Janez Mavri
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry , Hajdrihova ulica 19, SI-1000 Ljubljana, Slovenia
| | - Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute , Bijenička cesta 54, HR-10000 Zagreb, Croatia
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Vianello R, Domene C, Mavri J. The Use of Multiscale Molecular Simulations in Understanding a Relationship between the Structure and Function of Biological Systems of the Brain: The Application to Monoamine Oxidase Enzymes. Front Neurosci 2016; 10:327. [PMID: 27471444 PMCID: PMC4945635 DOI: 10.3389/fnins.2016.00327] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 06/28/2016] [Indexed: 01/17/2023] Open
Abstract
HIGHLIGHTS Computational techniques provide accurate descriptions of the structure and dynamics of biological systems, contributing to their understanding at an atomic level.Classical MD simulations are a precious computational tool for the processes where no chemical reactions take place.QM calculations provide valuable information about the enzyme activity, being able to distinguish among several mechanistic pathways, provided a carefully selected cluster model of the enzyme is considered.Multiscale QM/MM simulation is the method of choice for the computational treatment of enzyme reactions offering quantitative agreement with experimentally determined reaction parameters.Molecular simulation provide insight into the mechanism of both the catalytic activity and inhibition of monoamine oxidases, thus aiding in the rational design of their inhibitors that are all employed and antidepressants and antiparkinsonian drugs. Aging society and therewith associated neurodegenerative and neuropsychiatric diseases, including depression, Alzheimer's disease, obsessive disorders, and Parkinson's disease, urgently require novel drug candidates. Targets include monoamine oxidases A and B (MAOs), acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and various receptors and transporters. For rational drug design it is particularly important to combine experimental synthetic, kinetic, toxicological, and pharmacological information with structural and computational work. This paper describes the application of various modern computational biochemistry methods in order to improve the understanding of a relationship between the structure and function of large biological systems including ion channels, transporters, receptors, and metabolic enzymes. The methods covered stem from classical molecular dynamics simulations to understand the physical basis and the time evolution of the structures, to combined QM, and QM/MM approaches to probe the chemical mechanisms of enzymatic activities and their inhibition. As an illustrative example, the later will focus on the monoamine oxidase family of enzymes, which catalyze the degradation of amine neurotransmitters in various parts of the brain, the imbalance of which is associated with the development and progression of a range of neurodegenerative disorders. Inhibitors that act mainly on MAO A are used in the treatment of depression, due to their ability to raise serotonin concentrations, while MAO B inhibitors decrease dopamine degradation and improve motor control in patients with Parkinson disease. Our results give strong support that both MAO isoforms, A and B, operate through the hydride transfer mechanism. Relevance of MAO catalyzed reactions and MAO inhibition in the context of neurodegeneration will be discussed.
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Affiliation(s)
- Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković InstituteZagreb, Croatia
| | - Carmen Domene
- Department of Chemistry, King's College LondonLondon, UK
- Chemistry Research Laboratory, University of OxfordOxford, UK
| | - Janez Mavri
- Department of Computational Biochemistry and Drug Design, National Institute of ChemistryLjubljana, Slovenia
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