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Price NJ, Nakamura A, Castagnoli N, Tanko JM. Why Does Monoamine Oxidase (MAO) Catalyze the Oxidation of Some Tetrahydropyridines? Chembiochem 2024; 25:e202400126. [PMID: 38602445 DOI: 10.1002/cbic.202400126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 03/18/2024] [Indexed: 04/12/2024]
Abstract
Results pertaining to the mechanism of the oxidation of the tertiary amine 1-methyl-4-(1-methyl-1-H-pyrrol-2-yl)-1,2,3,6-tetrahydropyridine (MMTP, a close analog of the Parkinsonism inducing compound MPTP) by 3-methyllumiflavin (3MLF), a chemical model for the FAD cofactor of monoamine oxidase, are reported. MMTP and related compounds are among the few tertiary amines that are monoamine oxidase B (MAO-B) substrates. The MMTP/3MLF reaction is catalytic in the presence of O2 and the results under anaerobic conditions strongly suggest the involvement of radical intermediates, consistent with a single electron transfer mechanism. These observations support a new hypothesis to explain the MAO-catalyzed oxidations of amines. In general, electron transfer is thermodynamically unfavorable, and as a result, most 1° and 2° amines react via one of the currently accepted polar pathways. Steric constraints prevent 3° amines from reacting via a polar pathway. Those select 3° amines that are MAO substrates possess certain structural features (e. g., a C-H bond that is α- both to nitrogen and a C=C) that dramatically lower the pKa of the corresponding radical cation. Consequently, the thermodynamically unfavorable electron transfer equilibrium is driven towards products by an extremely favorable deprotonation step in the context of Le Chatelier's principle.
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Affiliation(s)
- Nathan J Price
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Akiko Nakamura
- Department of Chemistry, Colorado State University, Fort Collins, CO, 80523, USA
| | - Neal Castagnoli
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, USA
| | - James M Tanko
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24061, USA
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2
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Yildiz I. Computational Mechanistic Study of l-Aspartate Oxidase by ONIOM Method. ACS OMEGA 2023; 8:19963-19968. [PMID: 37305300 PMCID: PMC10249383 DOI: 10.1021/acsomega.3c01949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023]
Abstract
l-Aspartate oxidase (Laspo) is responsible for the oxidation of l-aspartate into iminoaspartate using flavin as a cofactor. During this process flavin is reduced, and it can be reoxidized by either molecular oxygen or fumarate. The overall fold and the catalytic residues of Laspo are similar to succinate dehydrogenase and fumarate reductase. On the basis of deuterium kinetic isotope effects as well as other kinetic and structural data, it is proposed that the enzyme can catalyze the oxidation of l-aspartate through a mechanism similar to amino acid oxidases. It is suggested that a proton is removed from the α-amino group, while a hydride is transferred from C2 to flavin. It is also suggested that the hydride transfer is a rate-limiting step. However, there is still an ambiguity about the stepwise or concerted mechanism of hydride- and proton-transfer steps. In this study, we formulated some computational models to study the hydride-transfer mechanism using the crystal structure of Escherichia colil-aspartate oxidase in complexes with succinate. The calculations involved our own N-layered integrated molecular orbital and molecular mechanics method, and we evaluated the geometry and energetics of the hydride/proton-transfer processes while probing the roles of active site residues. Based on the calculations, it is concluded that proton- and hydride-transfer steps are decoupled, and a stepwise mechanism might be operative as opposed to the concerted one.
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3
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Sharma H, Raju B, Narendra G, Motiwale M, Sharma B, Verma H, Silakari O. QM/MM Studies on Enzyme Catalysis and Insight into Designing of New Inhibitors by ONIOM Approach: Recent Update. ChemistrySelect 2023. [DOI: 10.1002/slct.202203319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Himani Sharma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Baddipadige Raju
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Gera Narendra
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Mohit Motiwale
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Bhavna Sharma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Himanshu Verma
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
| | - Om Silakari
- Molecular Modeling Lab (MML) Department of Pharmaceutical Sciences and Drug Research Punjabi University Patiala Punjab 147002 India
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4
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Abstract
Proper elucidation of drug-target interaction is one of the most significant steps at the early stages of the drug development research. Computer-aided drug design tools have substantial contribution to this stage. In this chapter, we specifically concentrate on the computational methods widely used to develop reversible inhibitors for monoamine oxidase (MAO) isozymes. In this context, current computational techniques in identifying the best drug candidates showing high potency are discussed. The protocols of structure-based drug design methodologies, namely, molecular docking, in silico screening, and molecular dynamics simulations, are presented. Employing case studies of safinamide binding to MAO B, we demonstrate how to use AutoDock 4.2.6 and NAMD software packages.
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Affiliation(s)
- Kemal Yelekçi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Istanbul, Turkey.
| | - Safiye Sağ Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, Istanbul, Turkey
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5
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Fındık V, Varınca Gerçik BT, Sinek Ö, Erdem SS, Ruiz-López MF. Mechanistic Investigation of Lysine-Targeted Covalent Inhibition of PI3Kδ via ONIOM QM:QM Computations. J Chem Inf Model 2022; 62:6775-6787. [PMID: 35980989 DOI: 10.1021/acs.jcim.2c00569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Phosphoinositide 3-kinase (PI3K) enzymes are important drug targets, especially in oncology, and several inhibitors are currently under investigation in clinical trials for the treatment of lymphocytic leukemia, follicular lymphoma, breast, thyroid, colorectal, and lung cancer. Targeted covalent inhibitors hold significant promise for drug discovery research especially for kinases. Targeting the lysine residues attracts attention as a new strategy in designing targeted covalent inhibitors, since the lysine residue provides several advantages over the traditional cysteine residue. Recently, new highly selective covalent inhibitors of PI3Kδ with activated ester warheads, targeting the conserved Lys779 residue, were reported. Based on the observed kinetics, a covalent inhibition mechanism was proposed, but the atomistic details of the reaction are still not understood. Therefore, in the present work, we have conducted quantum chemical ONIOM M06-2X/6-31+G(d,p):PM6 calculations on the active site cluster structure of PI3Kδ to elucidate the microscopic details of the mechanism of the aminolysis reaction between Lys779 and the ester inhibitors. Our calculations clearly discriminate the noncovalent methyl ester inhibitor and the covalent inhibitors with activated phenolic esters. For the representative p-NO2, p-F, p-H, and p-OCH3 phenolic esters, the Gibbs free energy profiles of alternative mechanistic paths through either Asp782 or Asp911 demonstrate the modulatory role of active site aspartate residues. The most plausible path alters depending on the electron-withdrawing/donating nature of the p-substituted phenolate leaving group. Inhibitors with sufficiently strong electron-withdrawing group prefer direct dissociation of the leaving group from the tetrahedral zwitterion intermediate, while the ones with electron-donating group favor the formation of a neutral tetrahedral intermediate prior to the dissociation. The relative Gibbs free energy barriers of p-NO2 < p-F < p-H < p-OCH3 substituted phenyl esters display the same qualitative trend as the experimentally measured kinact/KI values. Our results provide in depth insight into the mechanism, which can pave the way for optimizing the inhibitor efficiency.
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Affiliation(s)
- Volkan Fındık
- LPCT, UMR 7019, University of Lorraine, CNRS, 54000, Nancy, France.,Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
| | | | - Öykü Sinek
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
| | - Safiye Sağ Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722, Istanbul, Turkey
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6
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In vitro and in silico investigation of inhibitory activities of 3-arylcoumarins and 3-phenylazo-4-hydroxycoumarin on MAO isoenzymes. Struct Chem 2022. [DOI: 10.1007/s11224-022-02092-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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7
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Prah A, Gavranić T, Perdih A, Sollner Dolenc M, Mavri J. Computational Insights into β-Carboline Inhibition of Monoamine Oxidase A. Molecules 2022; 27:molecules27196711. [PMID: 36235246 PMCID: PMC9571839 DOI: 10.3390/molecules27196711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 11/07/2022] Open
Abstract
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.
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Affiliation(s)
- Alja Prah
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Tanja Gavranić
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | | | - Janez Mavri
- National Institute of Chemistry, SI-1000 Ljubljana, Slovenia
- Correspondence:
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8
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In silico study to identify new monoamine oxidase type a (MAO-A) selective inhibitors from natural source by virtual screening and molecular dynamics simulation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.132244] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Prah A, Mavri J, Stare J. An electrostatic duel: subtle differences in the catalytic performance of monoamine oxidase A and B isoenzymes elucidated at the residue level using quantum computations. Phys Chem Chem Phys 2021; 23:26459-26467. [PMID: 34806105 DOI: 10.1039/d1cp03993h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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.
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Affiliation(s)
- Alja Prah
- Theory Department, National Institute of Chemistry, Slovenia. .,University of Ljubljana, Faculty of Pharmacy, Slovenia
| | - Janez Mavri
- Theory Department, National Institute of Chemistry, Slovenia.
| | - Jernej Stare
- Theory Department, National Institute of Chemistry, Slovenia.
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10
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Yildiz I. Computational Analysis of the Nicotine Oxidoreductase Mechanism by the ONIOM Method. ACS OMEGA 2021; 6:22422-22428. [PMID: 34497931 PMCID: PMC8412962 DOI: 10.1021/acsomega.1c03357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Nicotine oxidoreductase (NicA2) is a monoamine oxidase (MAO)-based flavoenzyme that catalyzes the oxidation of S-nicotine into N-methylmyosmine. Due to its nanomolar binding affinity toward nicotine, it is seen as an ideal candidate for the treatment of nicotine addiction. Based on the crystal structure of the substrate-bound enzyme, hydrophobic interactions mainly govern the binding of the substrate in the active site through Trp108, Trp364, Trp427, and Leu217 residues. In addition, Tyr308 forms H-bonding with the pyridyl nitrogen of the substrate. Experimental and computational studies support the hydride transfer mechanism for MAO-based enzymes. In this mechanism, a hydride ion transfers from the substrate to the flavin cofactor. In this study, computational models involving the ONIOM method were formulated to study the hydride transfer mechanism based on the crystal structure of the enzyme-substrate complex. The geometry and energetics of the hydride transfer mechanism were analyzed, and the roles of active site residues were highlighted.
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Affiliation(s)
- Ibrahim Yildiz
- Chemistry Department, Khalifa
University, P.O. Box 127788 Abu Dhabi, United Arab Emirates
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11
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Yildiz I, Yildiz BS. Mechanistic study of L-6-hydroxynicotine oxidase by DFT and ONIOM methods. J Mol Model 2021; 27:53. [PMID: 33507404 DOI: 10.1007/s00894-020-04646-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/10/2020] [Indexed: 10/22/2022]
Abstract
L-6-Hydroxynicotine oxidase (LHNO) is a member of monoamine oxidase (MAO) family and catalyzes conversion of (S)-6-hydroxynicotine to 6-hydroxypseudooxynicotine during bacterial degradation of nicotine. Recent studies indicated that the enzyme catalyzes oxidation of carbon-nitrogen bond instead of previously proposed carbon-carbon bond. Based on kinetics and mutagenesis studies, Asn166, Tyr311, and Lys287 as well as an active site water molecule have roles in the catalysis of the enzyme. A number of studies including experimental and computational methods support hydride transfer mechanism in MAO family as a common mechanism in which a hydride ion transfer from amine substrate to flavin cofactor is the rate-limiting step. In this study, we formulated computational models to study the hydride transfer mechanism using crystal structure of enzyme-substrate complex. The calculations involved ONIOM and DFT methods, and we evaluated the geometry and energetics of the hydride transfer process while probing the roles of active site residues. Based on the calculations involving hydride, radical, and polar mechanisms, it was concluded that hydride transfer mechanism is the only viable mechanism for LHNO.
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Affiliation(s)
- Ibrahim Yildiz
- Chemistry Department, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates.
| | - Banu Sizirici Yildiz
- CIVE Department, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates
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12
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Kubicskó K, Farkas Ö. Quantum chemical (QM:MM) investigation of the mechanism of enzymatic reaction of tryptamine and N,N-dimethyltryptamine with monoamine oxidase A. Org Biomol Chem 2020; 18:9660-9674. [PMID: 33215182 DOI: 10.1039/d0ob01118e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
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.
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Affiliation(s)
- Károly Kubicskó
- Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary.
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13
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Jian C, Yan J, Zhang H, Zhu J. Recent advances of small molecule fluorescent probes for distinguishing monoamine oxidase-A and monoamine oxidase-B in vitro and in vivo. Mol Cell Probes 2020; 55:101686. [PMID: 33279529 DOI: 10.1016/j.mcp.2020.101686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023]
Abstract
Monoamine oxidases (MAO-A and MAO-B) are the two flavin adenine dinucleotide (FAD) enzymes that play an important role in neurotransmitter homeostasis and in protection against biogenic amines. The two MAO enzymes are related to various diseases such as neurological disorders, cancer or other systemic diseases. It is crucial to distinguish these two subtypes in order to explore the pathogenesis and pathophysiology of different diseases. In this review, the relationship between MAOs and related diseases is briefly introduced. Additionally, we summarize the recent advances in small molecule fluorescent probes for specific detection of MAO-A and MAO-B.
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Affiliation(s)
- Chang'e Jian
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University, Nanjing, 211800, China
| | - Jiaxu Yan
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University, Nanjing, 211800, China
| | - Hang Zhang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University, Nanjing, 211800, China.
| | - Jianwei Zhu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Nanjing Tech University, Nanjing, 211800, China; College of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211800, China.
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14
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Yildiz I, Sizirici Yildiz B. Computational mechanistic study of human liver glycerol 3‐phosphate dehydrogenase using ONIOM method. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Prah A, Purg M, Stare J, Vianello R, Mavri J. How Monoamine Oxidase A Decomposes Serotonin: An Empirical Valence Bond Simulation of the Reactive Step. J Phys Chem B 2020; 124:8259-8265. [PMID: 32845149 PMCID: PMC7520887 DOI: 10.1021/acs.jpcb.0c06502] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
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.
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Affiliation(s)
- Alja Prah
- Laboratory for Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana 1001, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Ljubljana 1001, Slovenia
| | - Miha Purg
- Department of Cell and Molecular Biology, Uppsala University, Uppsala SE-751 24, Sweden
| | - Jernej Stare
- Laboratory for Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana 1001, Slovenia
| | - Robert Vianello
- Division of Organic Chemistry and Biochemistry, Rud̵er Bošković Institute, Zagreb 10002, Croatia
| | - Janez Mavri
- Laboratory for Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana 1001, Slovenia
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16
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Fang H, Zhang H, Li L, Ni Y, Shi R, Li Z, Yang X, Ma B, Zhang C, Wu Q, Yu C, Yang N, Yao SQ, Huang W. Rational Design of a Two‐Photon Fluorogenic Probe for Visualizing Monoamine Oxidase A Activity in Human Glioma Tissues. Angew Chem Int Ed Engl 2020; 59:7536-7541. [DOI: 10.1002/anie.202000059] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 02/06/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Haixiao Fang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Hang Zhang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Yun Ni
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Riri Shi
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Zheng Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Xuekang Yang
- Department of Burns and Cutaneous SurgeryXijing HospitalThe Fourth Military Medical University Xi'an 710032 P. R. China
| | - Bo Ma
- School of Pharmaceutical SciencesNanjing Tech University Nanjing 210023 P. R. China
| | - Chengwu Zhang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Changmin Yu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Naidi Yang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Shao Q. Yao
- Department of ChemistryNational University of Singapore 3 Science Drive 3 117543 Singapore Singapore
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
- Shaanxi Institute of Flexible Electronics (SIFE) & Institute of Biomedical Materials & Engineering (IBME)Northwestern Polytechnical University (NPU) 127 West Youyi Road Xi'an 710072 P. R. China
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17
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Fang H, Zhang H, Li L, Ni Y, Shi R, Li Z, Yang X, Ma B, Zhang C, Wu Q, Yu C, Yang N, Yao SQ, Huang W. Rational Design of a Two‐Photon Fluorogenic Probe for Visualizing Monoamine Oxidase A Activity in Human Glioma Tissues. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Haixiao Fang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Hang Zhang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Yun Ni
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Riri Shi
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Zheng Li
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Xuekang Yang
- Department of Burns and Cutaneous SurgeryXijing HospitalThe Fourth Military Medical University Xi'an 710032 P. R. China
| | - Bo Ma
- School of Pharmaceutical SciencesNanjing Tech University Nanjing 210023 P. R. China
| | - Chengwu Zhang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Changmin Yu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Naidi Yang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
| | - Shao Q. Yao
- Department of ChemistryNational University of Singapore 3 Science Drive 3 117543 Singapore Singapore
| | - Wei Huang
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM)Nanjing Tech University (NanjingTech) 30 South Puzhu Road Nanjing 211816 P. R. China
- Shaanxi Institute of Flexible Electronics (SIFE) & Institute of Biomedical Materials & Engineering (IBME)Northwestern Polytechnical University (NPU) 127 West Youyi Road Xi'an 710072 P. R. China
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18
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Nakamura A, Latif MA, Deck PA, Castagnoli N, Tanko JM. Evidence for a Proton-Coupled Electron Transfer Mechanism in a Biomimetic System for Monoamine Oxidase B Catalysis. Chemistry 2020; 26:823-829. [PMID: 31658386 DOI: 10.1002/chem.201904634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Indexed: 11/11/2022]
Abstract
Mechanistic studies with 5-ethyl-3-methyllumiflavinium (Fl+ ) perchlorate, a biomimetic model for flavoenzyme monoamine oxidase B (MAO-B) catalysis, and the tertiary, allyl amine 1-methyl-4-(1-methyl-1 H-pyrrol-2-yl)-1,2,3,6-tetrahydropyridine (MMTP) reveal that proton-coupled electron transfer (PCET) may be an important pathway for MAO catalysis. The first step involves a single-electron transfer (SET) leading to the free radicals Fl. and MMTP. , the latter produced by deprotonation of the initially formed and highly acidic MMTP.+ . Molecular oxygen (O2 ) is found to play a hitherto unrecognized role in the early steps of the oxidation. MMTP and several structurally similar tertiary amines are the only tertiary amines oxidized by MAO, and their structural/electronic properties provide the key to understanding this behavior. A general hypothesis about the role of SET in MAO catalysis, and the recognition that PCET occurs with appropriately substituted substrates is presented.
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Affiliation(s)
- Akiko Nakamura
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24060, USA
| | | | - Paul A Deck
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24060, USA
| | - Neal Castagnoli
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24060, USA
| | - James M Tanko
- Department of Chemistry, Virginia Tech, Blacksburg, VA, 24060, USA
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19
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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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20
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Mechanistic study of the role of hydrogen bond donors in the two-component organocatalysis of the ring-opening reaction of epoxides. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2019.110425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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21
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Dulger H, Sari O, Demirel N, Erdem SS. Computational Insight Into the Enantioselectivity of Homoboroproline Catalyzed Asymmetric Aldol Reaction. ChemistrySelect 2019. [DOI: 10.1002/slct.201901737] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Habibe Dulger
- Department of Chemistry, Faculty of Arts and SciencesMarmara University, Goztepe Campus 34722 Istanbul Turkey
- Department of ChemistryKirsehir Ahi Evran University 40100 Kirsehir Turkey
| | - Ozlem Sari
- Department of ChemistryKirsehir Ahi Evran University 40100 Kirsehir Turkey
| | - Nadir Demirel
- Department of ChemistryKirsehir Ahi Evran University 40100 Kirsehir Turkey
| | - Safiye S. Erdem
- Department of Chemistry, Faculty of Arts and SciencesMarmara University, Goztepe Campus 34722 Istanbul Turkey
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22
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A three-component, one-pot synthesis of 1,8-naphthyridine and isoxazole derivatives and computational elucidation of the mechanism. RESEARCH ON CHEMICAL INTERMEDIATES 2019. [DOI: 10.1007/s11164-018-03721-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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23
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Khoshnevisan K, Maleki H, Honarvarfard E, Baharifar H, Gholami M, Faridbod F, Larijani B, Faridi Majidi R, Khorramizadeh MR. Nanomaterial based electrochemical sensing of the biomarker serotonin: a comprehensive review. Mikrochim Acta 2019; 186:49. [PMID: 30610391 DOI: 10.1007/s00604-018-3069-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Accepted: 10/20/2018] [Indexed: 02/06/2023]
Abstract
This review (with 131 references) summarizes the progress made in the past years in the field of nanomaterial based sensing of serotonin (5-HT). An introduction summarizes the significant role of 5-HT as a biomarker for several major diseases, methods for its determination and the various kinds of nanomaterials for use in electrochemical sensing process relies principally on a precise choice of electrodes. The next main section covers nanomaterial based methods for sensing 5-HT, with subsections on electrodes modified with carbon nanotubes, graphene related materials, gold nanomaterials, and by other nanomaterials. A concluding section discusses future perspectives and current challenges of 5-HT determination. Graphical abstract Conceptual design of electrochemical sensing process of the biomarker serotonin by using nanomaterials and the role of 5-HTas biomarker in the body from preclinical to clincal.
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Affiliation(s)
- Kamyar Khoshnevisan
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, 1411713137, Iran.,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, 1411713137, Iran
| | - Hassan Maleki
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, 1417755354, Iran
| | - Elham Honarvarfard
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, 13699-5810, USA
| | - Hadi Baharifar
- Department of Medical Nanotechnology, Applied Biophotonics Research Center, Science and Research Branch, Islamic Azad University, Tehran, 1477893855, Iran
| | - Morteza Gholami
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Molecular -Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, 1411713137, Iran
| | - Farnoush Faridbod
- Center of Excellence in Electrochemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran.
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, 1411713137, Iran.
| | - Reza Faridi Majidi
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, 1417755354, Iran
| | - Mohammad Reza Khorramizadeh
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, 1411713137, Iran. .,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, 1411713137, Iran.
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24
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Tripathi RKP, Ayyannan SR. Monoamine oxidase-B inhibitors as potential neurotherapeutic agents: An overview and update. Med Res Rev 2019; 39:1603-1706. [PMID: 30604512 DOI: 10.1002/med.21561] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 12/13/2018] [Accepted: 12/15/2018] [Indexed: 12/23/2022]
Abstract
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.
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Affiliation(s)
- Rati Kailash Prasad Tripathi
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India.,Department of Pharmaceutical Chemistry, Parul Institute of Pharmacy, Parul University, Vadodara, India
| | - Senthil Raja Ayyannan
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering and Technology, Indian Institute of Technology, Banaras Hindu University, Varanasi, India
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25
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Batista VF, Galman JL, G. A. Pinto DC, Silva AMS, Turner NJ. Monoamine Oxidase: Tunable Activity for Amine Resolution and Functionalization. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03525] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Vasco F. Batista
- Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - James L. Galman
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
| | - Diana C. G. A. Pinto
- Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Artur M. S. Silva
- Department of Chemistry & QOPNA, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Nicholas J. Turner
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, U.K
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26
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Asymmetric synthesis, molecular modeling and biological evaluation of 5-methyl-3-aryloxazolidine-2,4-dione enantiomers as monoamine oxidase (MAO) inhibitors. Bioorg Chem 2018; 77:608-618. [DOI: 10.1016/j.bioorg.2018.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/05/2018] [Accepted: 02/09/2018] [Indexed: 11/15/2022]
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28
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Kaya AA, Salamci E, Menzek A, Erdem SS, Şahin E, Ecer K. Reaction of 9-oxabicyclo[4.2.1]non-7-ene-1-ol with tetrazine: An unusually facile intramolecular rearrangement. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.07.040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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29
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Stare J. Complete sampling of an enzyme reaction pathway: a lesson from gas phase simulations. RSC Adv 2017. [DOI: 10.1039/c6ra27894a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
With proper sampling strategy, convergence of free energy profiles of biomolecular reactions in the gas phase can be achieved in microseconds of simulation.
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Affiliation(s)
- Jernej Stare
- Department of Computational Biochemistry and Drug Design
- National Institute of Chemistry
- SI-1000 Ljubljana
- Slovenia
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