1
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Mueller NPF, Carloni P, Alfonso-Prieto M. Molecular determinants of acrylamide neurotoxicity through covalent docking. Front Pharmacol 2023; 14:1125871. [PMID: 36937867 PMCID: PMC10018202 DOI: 10.3389/fphar.2023.1125871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/17/2023] [Indexed: 03/06/2023] Open
Abstract
Acrylamide (ACR) is formed during food processing by Maillard reaction between sugars and proteins at high temperatures. It is also used in many industries, from water waste treatment to manufacture of paper, fabrics, dyes and cosmetics. Unfortunately, cumulative exposure to acrylamide, either from diet or at the workplace, may result in neurotoxicity. Such adverse effects arise from covalent adducts formed between acrylamide and cysteine residues of several neuronal proteins via a Michael addition reaction. The molecular determinants of acrylamide reactivity and its impact on protein function are not completely understood. Here we have compiled a list of acrylamide protein targets reported so far in the literature in connection with neurotoxicity and performed a systematic covalent docking study. Our results indicate that acrylamide binding to cysteine is favored in the presence of nearby positively charged amino acids, such as lysines and arginines. For proteins with more than one reactive Cys, docking scores were able to discriminate between the primary ACR modification site and secondary sites modified only at high ACR concentrations. Therefore, docking scores emerge as a potential filter to predict Cys reactivity against acrylamide. Inspection of the ACR-protein complex structures provides insights into the putative functional consequences of ACR modification, especially for non-enzyme proteins. Based on our study, covalent docking is a promising computational tool to predict other potential protein targets mediating acrylamide neurotoxicity.
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Affiliation(s)
- Nicolas Pierre Friedrich Mueller
- Institute for Advanced Simulations IAS-5, Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Faculty of Mathematics and Natural Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Paolo Carloni
- Institute for Advanced Simulations IAS-5, Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Department of Physics, RWTH Aachen University, Aachen, Germany
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5, Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, Jülich, Germany
- Cécile and Oskar Vogt Institute for Brain Research, Medical Faculty, University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- *Correspondence: Mercedes Alfonso-Prieto,
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2
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Rahimi R, Solimannejad M. B3O3 monolayer with dual application in sensing of COVID-19 biomarkers and drug delivery for treatment purposes: A periodic DFT study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118855] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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3
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Why Monoamine Oxidase B Preferably Metabolizes N-Methylhistamine over Histamine: Evidence from the Multiscale Simulation of the Rate-Limiting Step. Int J Mol Sci 2022; 23:ijms23031910. [PMID: 35163835 PMCID: PMC8836602 DOI: 10.3390/ijms23031910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/04/2022] [Accepted: 02/05/2022] [Indexed: 11/18/2022] Open
Abstract
Histamine levels in the human brain are controlled by rather peculiar metabolic pathways. In the first step, histamine is enzymatically methylated at its imidazole Nτ atom, and the produced N-methylhistamine undergoes an oxidative deamination catalyzed by monoamine oxidase B (MAO-B), as is common with other monoaminergic neurotransmitters and neuromodulators of the central nervous system. The fact that histamine requires such a conversion prior to oxidative deamination is intriguing since MAO-B is known to be relatively promiscuous towards monoaminergic substrates; its in-vitro oxidation of N-methylhistamine is about 10 times faster than that for histamine, yet this rather subtle difference appears to be governing the decomposition pathway. This work clarifies the MAO-B selectivity toward histamine and N-methylhistamine by multiscale simulations of the rate-limiting hydride abstraction step for both compounds in the gas phase, in aqueous solution, and in the enzyme, using the established empirical valence bond methodology, assisted by gas-phase density functional theory (DFT) calculations. The computed barriers are in very good agreement with experimental kinetic data, especially for relative trends among systems, thereby reproducing the observed MAO-B selectivity. Simulations clearly demonstrate that solvation effects govern the reactivity, both in aqueous solution as well as in the enzyme although with an opposing effect on the free energy barrier. In the aqueous solution, the transition-state structure involving histamine is better solvated than its methylated analog, leading to a lower barrier for histamine oxidation. In the enzyme, the higher hydrophobicity of N-methylhistamine results in a decreased number of water molecules at the active side, leading to decreased dielectric shielding of the preorganized catalytic electrostatic environment provided by the enzyme. This renders the catalytic environment more efficient for N-methylhistamine, giving rise to a lower barrier relative to histamine. In addition, the transition state involving N-methylhistamine appears to be stabilized by the surrounding nonpolar residues to a larger extent than with unsubstituted histamine, contributing to a lower barrier with the former.
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4
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Zhang D, Jiang N, Li P, Zhang Y, Sun S, Mao J, Liu S, Wei W. Detection of monoamine oxidase B using dark-field light scattering imaging and colorimetry. Chem Commun (Camb) 2022; 58:12329-12332. [DOI: 10.1039/d2cc05139g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Detection of MAO-B using dark-field light scattering imaging and colorimetry based on localized surface plasmon resonance induced by silver deposited gold nanostars.
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Affiliation(s)
- Duoduo Zhang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, P. R. China
- School of Pharmacy, Changzhou University, Changzhou, 213164, P. R. China
| | - Nan Jiang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, P. R. China
| | - Peng Li
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, P. R. China
| | - Yusheng Zhang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, P. R. China
| | - Shihao Sun
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, P. R. China
| | - Jian Mao
- Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou, 450001, P. R. China
| | - Songqin Liu
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, P. R. China
| | - Wei Wei
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, P. R. China
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5
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Kotena ZM, Fattahi A. Computational insight into networking H‐bonds in open and cyclic forms of glucose. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | - Alireza Fattahi
- Department of Chemistry Sharif University of Technology Tehran Iran
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6
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Abstract
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).
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7
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Balasco N, Alba J, D'Abramo M, Vitagliano L. Quaternary Structure Transitions of Human Hemoglobin: An Atomic-Level View of the Functional Intermediate States. J Chem Inf Model 2021; 61:3988-3999. [PMID: 34375114 PMCID: PMC9473481 DOI: 10.1021/acs.jcim.1c00315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human hemoglobin (HbA) is one of the prototypal systems used to investigate structure-function relationships in proteins. Indeed, HbA has been used to develop the basic concepts of protein allostery, although the atomic-level mechanism underlying the HbA functionality is still highly debated. This is due to the fact that most of the three-dimensional structural information collected over the decades refers to the endpoints of HbA functional transition with little data available for the intermediate states. Here, we report molecular dynamics (MD) simulations by focusing on the relevance of the intermediate states of the protein functional transition unraveled by the crystallographic studies carried out on vertebrate Hbs. Fully atomistic simulations of the HbA T-state indicate that the protein undergoes a spontaneous transition toward the R-state. The inspection of the trajectory structures indicates that the protein significantly populates the intermediate HL-(C) state previously unraveled by crystallography. In the structural transition, it also assumes the intermediate states crystallographically detected in Antarctic fish Hbs. This finding suggests that HbA and Antarctic fish Hbs, in addition to the endpoints of the transitions, also share a similar deoxygenation pathway despite a distace of hundreds of millions of years in the evolution scale. Finally, using the essential dynamic sampling methodology, we gained some insights into the reverse R to T transition that is not spontaneously observed in classic MD simulations.
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Affiliation(s)
- Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Josephine Alba
- Department of Chemistry, University of Rome Sapienza, P.le A.Moro 5, 00185 Rome, Italy
| | - Marco D'Abramo
- Department of Chemistry, University of Rome Sapienza, P.le A.Moro 5, 00185 Rome, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134 Naples, Italy
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8
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Haslak ZP, Zareb S, Dogan I, Aviyente V, Monard G. Using Atomic Charges to Describe the p Ka of Carboxylic Acids. J Chem Inf Model 2021; 61:2733-2743. [PMID: 34137248 DOI: 10.1021/acs.jcim.1c00059] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, we present an accurate protocol for the fast prediction of pKa's of carboxylic acids based on the linear relationship between computed atomic charges of the anionic form of the carboxylate fragment and their experimental pKa values. Five charge descriptors, three charge models, three solvent models, gas-phase calculations, several DFT methods (a combination of eight DFT functionals and fifteen basis sets), and four different semiempirical approaches were tested. Among those, the best combination to reproduce experimental pKa's is to compute the natural population analysis atomic charge using the solvation model based on density model at the M06L/6-311G(d,p) level of theory and selecting the maximum atomic charge on the carboxylic oxygen atoms (R2 = 0.955). The applicability of the suggested protocol and its stability along geometrical changes are verified by molecular dynamics simulations performed for a set of aspartate, glutamate, and alanine peptides. By reporting the calculated atomic charge of the carboxylate form into the linear relationship derived in this work, it should be possible to accurately estimate the amino acid's pKa's in a protein environment.
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Affiliation(s)
- Zeynep Pinar Haslak
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France.,Department of Chemistry, Boğaziçi University, 34342 Bebek, Istanbul, Turkey
| | - Sabrina Zareb
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Ilknur Dogan
- Department of Chemistry, Boğaziçi University, 34342 Bebek, Istanbul, Turkey
| | - Viktorya Aviyente
- Department of Chemistry, Boğaziçi University, 34342 Bebek, Istanbul, Turkey
| | - Gerald Monard
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
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9
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Wu X, Xu H, Luo F, Wang J, Zhao L, Zhou X, Yang Y, Cai H, Sun P, Zhou H. Sizes and ligands tuned gold nanocluster acting as a new type of monoamine oxidase B inhibitor. Biosens Bioelectron 2021; 189:113377. [PMID: 34090156 DOI: 10.1016/j.bios.2021.113377] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 05/10/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022]
Abstract
Monoamine oxidase inhibitors (MAOIs) are a class of drugs that can be used in the treatment of Parkinson's disease, clinical depression, and anxiety by targeting monoamine oxidase B (MAO). However, the side effects of MAOIs drive the requirement of a new framework of enzyme inhibitors development. In this context, a new type of MAOI has been built on the framework of gold nanoclusters (AuNCs), realizing the transformation from no function of small molecules to MAOI function of ligand-modified AuNCs. The MAOI activity of fabricated AuNCs can be achieved by size control and specific ligands modification. In this work, AuNCs modified with cysteamine or 4-aminothiophenol, about 1-3 nm in size, were found to have MAOI activity (MAOI-like AuNCs) and their characterization has been extensively described. Meanwhile, the possible mechanism behind this MAOI activity has been explored and it is believed that the proper size of AuNCs with ligands containing amino groups can bind tightly with the entrance to active sites of MAO, blocking the enzyme interacting with its substrates, thereby realizing the function of MAOI. Last, the antimicrobial activity and the performance of the MAOI-like AuNCs in the human blood sample were explored and suggested that MAOI-like AuNCs do not possess strong antimicrobial activity and have no visualized side effect on blood cells, although the by-product peroxide of MAO reaction may reshape the white blood cells. The research in this work may shed some light on the development of a new type of enzyme inhibitor based on the framework of nanomaterials.
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Affiliation(s)
- Xueqiang Wu
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China
| | - Heng Xu
- College of Life Sciences, Jiaying University, Meizhou, 514015, PR China
| | - Fazeng Luo
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China
| | - Jinhua Wang
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China
| | - Li Zhao
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China
| | - Xia Zhou
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China; First Affiliated Hospital of Jinan University, Guangzhou, 510632, PR China
| | - Ying Yang
- First Affiliated Hospital of Jinan University, Guangzhou, 510632, PR China
| | - Huaihong Cai
- College of Chemistry and Materials Science, Jinan University, Guangzhou, 510632, PR China.
| | - Pinghua Sun
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China; First Affiliated Hospital of Jinan University, Guangzhou, 510632, PR China.
| | - Haibo Zhou
- College of Pharmacy, Jinan University, Guangzhou, 510632, PR China; First Affiliated Hospital of Jinan University, Guangzhou, 510632, PR China.
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10
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Modeling of Solute-Solvent Interactions Using an External Electric Field-From Tautomeric Equilibrium in Nonpolar Solvents to the Dissociation of Alkali Metal Halides. Molecules 2021; 26:molecules26051283. [PMID: 33652943 PMCID: PMC7956811 DOI: 10.3390/molecules26051283] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/07/2021] [Accepted: 02/22/2021] [Indexed: 12/18/2022] Open
Abstract
An implicit account of the solvent effect can be carried out using traditional static quantum chemistry calculations by applying an external electric field to the studied molecular system. This approach allows one to distinguish between the effects of the macroscopic reaction field of the solvent and specific solute-solvent interactions. In this study, we report on the dependence of the simulation results on the use of the polarizable continuum approximation and on the importance of the solvent effect in nonpolar solvents. The latter was demonstrated using experimental data on tautomeric equilibria between the pyridone and hydroxypyridine forms of 2,6-di-tert-butyl-4-hydroxy-pyridine in cyclohexane and chloroform.
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11
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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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12
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Affiliation(s)
| | - Alireza Fattahi
- Department of Chemistry Sharif University of Technology Tehran Iran
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13
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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: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/26/2020] [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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14
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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. Int J Mol Sci 2020; 21:ijms21176151. [PMID: 32858935 PMCID: PMC7503497 DOI: 10.3390/ijms21176151] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/11/2020] [Accepted: 08/21/2020] [Indexed: 12/23/2022] Open
Abstract
Monoamine oxidases (MAOs) catalyze the degradation of a very broad range of biogenic and dietary amines including many neurotransmitters in the brain, whose imbalance is extensively linked with the biochemical pathology of various neurological disorders, and are, accordingly, used as primary pharmacological targets to treat these debilitating cognitive diseases. Still, despite this practical significance, the precise molecular mechanism underlying the irreversible MAO inhibition with clinically used propargylamine inhibitors rasagiline and selegiline is still not unambiguously determined, which hinders the rational design of improved inhibitors devoid of side effects current drugs are experiencing. To address this challenge, we present empirical valence bond QM/MM simulations of the rate-limiting step of the MAO inhibition involving the hydride anion transfer from the inhibitor α-carbon onto the N5 atom of the flavin adenin dinucleotide (FAD) cofactor. The proposed mechanism is strongly supported by the obtained free energy profiles, which confirm a higher reactivity of selegiline over rasagiline, while the calculated difference in the activation Gibbs energies of ΔΔG‡ = 3.1 kcal mol-1 is found to be in very good agreement with that from the measured literature kinact values that predict a 1.7 kcal mol-1 higher selegiline reactivity. Given the similarity with the hydride transfer mechanism during the MAO catalytic activity, these results verify that both rasagiline and selegiline are mechanism-based irreversible inhibitors and offer guidelines in designing new and improved inhibitors, which are all clinically employed in treating a variety of neuropsychiatric and neurodegenerative conditions.
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15
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Bergant Loboda K, Janežič M, Štampar M, Žegura B, Filipič M, Perdih A. Substituted 4,5'-Bithiazoles as Catalytic Inhibitors of Human DNA Topoisomerase IIα. J Chem Inf Model 2020; 60:3662-3678. [PMID: 32484690 PMCID: PMC7469689 DOI: 10.1021/acs.jcim.0c00202] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human type II topoisomerases, molecular motors that alter the DNA topology, are a major target of modern chemotherapy. Groups of catalytic inhibitors represent a new approach to overcome the known limitations of topoisomerase II poisons such as cardiotoxicity and induction of secondary tumors. Here, we present a class of substituted 4,5'-bithiazoles as catalytic inhibitors targeting the human DNA topoisomerase IIα. Based on a structural comparison of the ATPase domains of human and bacterial type II topoisomerase, a focused chemical library of 4,5'-bithiazoles was assembled and screened to identify compounds that better fit the topology of the human topo IIα adenosine 5'-triphosphate (ATP) binding site. Selected compounds showed inhibition of human topo IIα comparable to that of the etoposide topo II drug, revealing a new class of inhibitors targeting this molecular motor. Further investigations showed that compounds act as catalytic inhibitors via competitive ATP inhibition. We also confirmed binding to the truncated ATPase domain of topo IIα and modeled the inhibitor molecular recognition with molecular simulations and dynophore models. The compounds also displayed promising cytotoxicity against HepG2 and MCF-7 cell lines comparable to that of etoposide. In a more detailed study with the HepG2 cell line, there was no induction of DNA double-strand breaks (DSBs), and the compounds were able to reduce cell proliferation and stop the cell cycle mainly in the G1 phase. This confirms the mechanism of action of these compounds, which differs from topo II poisons also at the cellular level. Substituted 4,5'-bithiazoles appear to be a promising class for further development toward efficient and potentially safer cancer therapies exploiting the alternative topo II inhibition paradigm.
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Affiliation(s)
- Kaja Bergant Loboda
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, SI-1000 Ljubljana, Slovenia
| | - Matej Janežič
- Laboratory for Structural Bioinformatics, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Martina Štampar
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Bojana Žegura
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Metka Filipič
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, Večna pot 111, SI-1000 Ljubljana, Slovenia
| | - Andrej Perdih
- National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia
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16
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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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17
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Ćehić M, Suć Sajko J, Karačić Z, Piotrowski P, Šmidlehner T, Jerić I, Schmuck C, Piantanida I, Tomić S. The guanidiniocarbonylpyrrole-fluorophore conjugates as theragnostic tools for dipeptidyl peptidase III monitoring and inhibition. J Biomol Struct Dyn 2019; 38:3790-3800. [PMID: 31496375 DOI: 10.1080/07391102.2019.1664936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Study of seven new guanidiniocarbonylpyrrole (GCP)-fluorophore conjugates interactions with dipeptidyl peptidase III (DPP III) showed that all compounds bind strongly (Ks ≈ µM) to enzyme active site, but with very different fluorimetric response (varying from quenching to strong increase), dependent on the fluorophore type and intramolecular pre-organisation of molecule. Positively charged lysine side chain improved significantly compound solubility but diminished fluorescence increase upon DPP III binding and completely abolished inhibitory effect on DPP III activity, whereas linker-neutral analogues showed stronger emission increase and were efficient enzyme inhibitors. By far the best fluorimetric response and inhibitive properties showed cyanine-GCP analogue, thus being promising lead compound for both enzyme sensing and bio-activity inhibiting (theragnostic) studies of DPP III in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | | | | | | | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, Essen, Germany
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18
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Tshepelevitsh S, Kütt A, Lõkov M, Kaljurand I, Saame J, Heering A, Plieger PG, Vianello R, Leito I. On the Basicity of Organic Bases in Different Media. European J Org Chem 2019. [DOI: 10.1002/ejoc.201900956] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Agnes Kütt
- Institute of Chemistry; University of Tartu; Ravila 14a 50411 Tartu Estonia
| | - Märt Lõkov
- Institute of Chemistry; University of Tartu; Ravila 14a 50411 Tartu Estonia
| | - Ivari Kaljurand
- Institute of Chemistry; University of Tartu; Ravila 14a 50411 Tartu Estonia
| | - Jaan Saame
- Institute of Chemistry; University of Tartu; Ravila 14a 50411 Tartu Estonia
| | - Agnes Heering
- Institute of Chemistry; University of Tartu; Ravila 14a 50411 Tartu Estonia
| | - Paul G. Plieger
- School of Fundamental Sciences; Massey University; Private Bag 11 222 Palmerston North New Zealand
| | - Robert Vianello
- Computational Organic Chemistry and Biochemistry Group; Ruđer Bošković Institute; Bijenička cesta 54 10000 Zagreb Croatia
| | - Ivo Leito
- Institute of Chemistry; University of Tartu; Ravila 14a 50411 Tartu Estonia
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19
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Jiang B, Meng L, Zou N, Wang H, Li S, Huang L, Cheng X, Wang Z, Chen W, Wang C. Mechanism-based pharmacokinetics-pharmacodynamics studies of harmine and harmaline on neurotransmitters regulatory effects in healthy rats: Challenge on monoamine oxidase and acetylcholinesterase inhibition. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2019; 62:152967. [PMID: 31154274 DOI: 10.1016/j.phymed.2019.152967] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/20/2019] [Accepted: 05/19/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND β-Carboline alkaloid harmine (HAR) and harmaline (HAL) are monoamine oxidase (MAO) and acetylcholinesterase (AChE) inhibitors. However, whether HAR and HAL inhibit MAO or AChE selectively and competitively is unclear. PURPOSE The purpose of this study was to investigate the potential competition inhibition of HAR and HAL on MAO and AChE in brain endothelial cells (RBE4) and in healthy rats to provide a basis for the application of the inhibitors in the treatment of patients with depression and with Parkinson's disease or Alzheimer's disease. STUDY DESIGN/METHODS The transport properties of HAR and HAL by using blood-brain barrier models constructed with RBE4 were systematically investigated. Then, the modulation effects of HAR and HAL on CNS neurotransmitters (NTs) in healthy rat brains were determined by a microdialysis method coupled with LC-MS/MS. The competition inhibition of HAR and HAL on MAO and AChE was evaluated through real time-PCR, Western blot analysis, and molecular docking experiments. RESULTS Results showed that HAL and HAR can be detected in the blood and striatum 300 min after intravenous injection (1 mg/kg). Choline (Ch), gamma-aminobutyric acid (GABA), glutamate (Glu), and phenylalanine (Phe) levels in the striatum decreased in a time-dependent manner after the HAL treatment, with average velocities of 1.41, 0.73, 3.86, and 1.10 (ng/ml)/min, respectively. The Ch and GABA levels in the striatum decreased after the HAR treatment, with average velocities of 1.16 and 0.22 ng/ml/min, respectively. The results of the cocktail experiment using the human liver enzyme indicated that the IC50 value of HAL on MAO-A was 0.10 ± 0.08 µm and that of HAR was 0.38 ± 0.21 µm. Their IC50 values on AChE were not obtained. These findings indicated that HAL and HAR selectively acted on MAO in vitro. However, RT-PCR and Western blot analysis results showed that the AChE mRNA and protein expression decreased in a time-dependent manner in RBE4 cells after the HAR and HAL treatments. CONCLUSION NT analysis results showed that HAL and HAR selectively affect AChE in vivo. HAL and HAR may be highly and suitably developed for the treatment of Alzheimer's disease.
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Affiliation(s)
- Bo Jiang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines; Shanghai R&D Centre for Standardization of Chinese Medicines, Shanghai 201203, China; Department of Pharmacy, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
| | - Liyuan Meng
- Department of Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Nan Zou
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines; Shanghai R&D Centre for Standardization of Chinese Medicines, Shanghai 201203, China
| | - Hanxue Wang
- Shanghai TCM-integrated Hospital, Shanghai University of Traditional Chinese Medicine, 230 Baoding Road, Shanghai 200082, China
| | - Shuping Li
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines; Shanghai R&D Centre for Standardization of Chinese Medicines, Shanghai 201203, China
| | - Lifeng Huang
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Xuemei Cheng
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines; Shanghai R&D Centre for Standardization of Chinese Medicines, Shanghai 201203, China
| | - Zhengtao Wang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines; Shanghai R&D Centre for Standardization of Chinese Medicines, Shanghai 201203, China
| | - Wansheng Chen
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Changhong Wang
- Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, The MOE Key Laboratory for Standardization of Chinese Medicines and the SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines; Shanghai R&D Centre for Standardization of Chinese Medicines, Shanghai 201203, China.
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20
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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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21
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Bilić L, Barić D, Banhatti RD, Smith DM, Kovačević B. Computational Study of Glycerol Binding within the Active Site of Coenzyme B12-Dependent Diol Dehydratase. J Phys Chem B 2019; 123:6178-6187. [DOI: 10.1021/acs.jpcb.9b04071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Luka Bilić
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Danijela Barić
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Radha Dilip Banhatti
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - David M. Smith
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
| | - Borislav Kovačević
- Division of Physical Chemistry, Rud̵er Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia
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22
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DNA/RNA recognition controlled by the glycine linker and the guanidine moiety of phenanthridine peptides. Int J Biol Macromol 2019; 134:422-434. [PMID: 31082420 DOI: 10.1016/j.ijbiomac.2019.05.063] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/09/2019] [Accepted: 05/09/2019] [Indexed: 12/27/2022]
Abstract
The binding of four phenanthridine-guanidine peptides to DNA/RNA was evaluated via spectrophotometric/microcalorimetric methods and computations. The minor structural modifications-the type of the guanidine group (pyrrole guanidine (GCP) and arginine) and the linker length (presence or absence of glycine)-greatly affected the conformation of compounds and consequently the binding to double- (ds-) and single-stranded (ss-) polynucleotides. GCP peptide with shorter linker was able to distinguish between RNA (A-helix) and DNA (B-helix) by different circular dichroism response at 295 nm and thus can be used as a chiral probe. Opposed to the dominant stretched conformation of GCP peptide with shorter linker, the more flexible and longer linker of its analogue enabled the molecule to adopt the intramolecularly stacked form which resulted in weaker yet selective binding to DNA. Beside efficient organization of ss-polynucleotide structures, GCP peptide with shorter linker bound stronger to ss-DNA/RNA compared to arginine peptides which emphasize the importance of GCP unit.
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23
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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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24
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Ahmad S, Raza S, Abbasi SW, Azam SS. Identification of natural inhibitors against Acinetobacter baumannii d-alanine-d-alanine ligase enzyme: A multi-spectrum in silico approach. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.04.124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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25
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Albreht A, Vovk I, Mavri J, Marco-Contelles J, Ramsay RR. Evidence for a Cyanine Link Between Propargylamine Drugs and Monoamine Oxidase Clarifies the Inactivation Mechanism. Front Chem 2018; 6:169. [PMID: 29892597 PMCID: PMC5985292 DOI: 10.3389/fchem.2018.00169] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/27/2018] [Indexed: 01/06/2023] Open
Abstract
Successful propargylamine drugs such as deprenyl inactivate monoamine oxidase (MAO), a target in multi-faceted approaches to prevent neurodegeneration in the aging population, but the chemical structure and mechanism of the irreversible inhibition are still debated. We characterized the covalent cyanine structure linking the multi-target propargylamine inhibitor ASS234 and the flavin adenine dinucleotide in MAO-A using a combination of ultra-high performance liquid chromatography, spectroscopy, mass spectrometry, and computational methods. The partial double bond character of the cyanine chain gives rise to 4 interconverting geometric isomers of the adduct which were chromatographically separated at low temperatures. The configuration of the cyanine linker governs adduct stability with segments of much higher flexibility and rigidity than previously hypothesized. The findings indicate the importance of intramolecular electrostatic interactions in the MAO binding site and provide key information relevant to incorporation of the propargyl moiety into novel multi-target drugs. Based on the structure, we propose a mechanism of MAO inactivation applicable to all propargylamine inhibitors.
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Affiliation(s)
- Alen Albreht
- Department of Food Chemistry, National Institute of Chemistry, Ljubljana, Slovenia
| | - Irena Vovk
- Department of Food Chemistry, National Institute of Chemistry, Ljubljana, Slovenia
| | - Janez Mavri
- Laboratory of Computational Biochemistry and Drug Design, Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Jose Marco-Contelles
- Laboratorio de Química Médica, Instituto de Química Orgánica General (CSIC), Madrid, Spain
| | - Rona R Ramsay
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
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26
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Maršavelski A, Petrović D, Bauer P, Vianello R, Kamerlin SCL. Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase. ACS OMEGA 2018; 3:3665-3674. [PMID: 30023875 PMCID: PMC6044848 DOI: 10.1021/acsomega.8b00346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
Diamine oxidase (DAO) is an enzyme involved in the regulation of cell proliferation and the immune response. This enzyme performs oxidative deamination in the catabolism of biogenic amines, including, among others, histamine, putrescine, spermidine, and spermine. The mechanistic details underlying the reductive half-reaction of the DAO-catalyzed oxidative deamination which leads to the reduced enzyme cofactor and the aldehyde product are, however, still under debate. The catalytic mechanism was proposed to involve a prototropic shift from the substrate-Schiff base to the product-Schiff base, which includes the rate-limiting cleavage of the Cα-H bond by the conserved catalytic aspartate. Our detailed mechanistic study, performed using a combined quantum chemical cluster approach with empirical valence bond simulations, suggests that the rate-limiting cleavage of the Cα-H bond involves direct hydride transfer to the topaquinone cofactor-a mechanism that does not involve the formation of a Schiff base. Additional investigation of the D373E and D373N variants supported the hypothesis that the conserved catalytic aspartate is indeed essential for the reaction; however, it does not appear to serve as the catalytic base, as previously suggested. Rather, the electrostatic contributions of the most significant residues (including D373), together with the proximity of the Cu2+ cation to the reaction site, lower the activation barrier to drive the chemical reaction.
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Affiliation(s)
- Aleksandra Maršavelski
- Computational
Organic Chemistry and Biochemistry Group, Division of Organic Chemistry
and Biochemistry, Ruđer Bošković
Institute, Bijenička
cesta 54, 10000 Zagreb, Croatia
- Department
of Chemistry, Faculty of Science, University
of Zagreb, Horvatovac
102a, 10000 Zagreb, Croatia
- Department
of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Dušan Petrović
- Department
of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Paul Bauer
- Department
of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
- Department
of Biophysics, SciLifeLab, KTH Royal Institute
of Technology, S-10691 Stockholm, Sweden
| | - Robert Vianello
- Computational
Organic Chemistry and Biochemistry Group, Division of Organic Chemistry
and Biochemistry, Ruđer Bošković
Institute, Bijenička
cesta 54, 10000 Zagreb, Croatia
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27
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Dasgupta S, Mukherjee S, Mukhopadhyay BP. Recognition of trans and gauche phenylethylamine conformers in the active site of human monoamine oxidase B: A MD-simulation and DFT studies. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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28
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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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29
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Timucin E, Sezerman OU. Thermostability of the PYL–PP2C Heterodimer Is Dependent on Magnesium: In Silico Insights into the Link between Heat Stress Response and Magnesium Deficiency in Plants. J Chem Inf Model 2018; 58:661-672. [DOI: 10.1021/acs.jcim.7b00655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir, 34752, Istanbul Turkey
| | - Osman Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir, 34752, Istanbul Turkey
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30
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Nucleobase-Guanidiniocarbonyl-Pyrrole Conjugates as Novel Fluorimetric Sensors for Single Stranded RNA. Molecules 2017; 22:molecules22122213. [PMID: 29236076 PMCID: PMC6149679 DOI: 10.3390/molecules22122213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/04/2017] [Accepted: 12/09/2017] [Indexed: 01/13/2023] Open
Abstract
We demonstrate here for the first time that a guanidiniocarbonyl-pyrrole (GCP) unit can be applied for the fine recognition of single stranded RNA sequences—an intuitively unexpected result since so far binding of the GCP unit to ds-DNA or ds-RNA relied strongly on minor or major groove interactions, as shown in previous work. Two novel nucleobase–GCP isosteric conjugates differing in the flexibility of GCP unit revealed a fluorimetric recognition of various single stranded RNA, which could be additionally regulated by pH. The more rigid conjugate showed a specific fluorescence increase for poly A only at pH 7, whereby this response could be reversibly switched-off at pH 5. The more flexible derivative revealed selective fluorescence quenching by poly G at pH 7 but no change for poly A, whereas its recognition of poly AH+ can be switched-on at pH 5. The computational analysis confirmed the important role of the GCP fragment and its protonation states in the sensing of polynucleotides and revealed that it is affected by the intrinsic dynamical features of conjugates themselves. Both conjugates showed a negligible response to uracil and cytosine ss-RNA as well as ds-RNA at pH 7, and only weak interactions with ds-DNA. Thus, nucleobase–GCP conjugates can be considered as novel lead compounds for the design of ss-RNA or ss-DNA selective fluorimetric probes.
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31
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Lee YV, Choi SB, Wahab HA, Choong YS. Active Site Flexibility of Mycobacterium tuberculosis Isocitrate Lyase in Dimer Form. J Chem Inf Model 2017; 57:2351-2357. [PMID: 28820943 DOI: 10.1021/acs.jcim.7b00265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tuberculosis (TB) still remains a global threat due to the emergence of a drug-resistant strain. Instead of focusing on the drug target of active stage TB, we are highlighting the isocitrate lyase (ICL) at the dormant stage TB. ICL is one of the persistent factors for Mycobacterium tuberculosis (MTB) to survive during the dormant phase. In addition, the absence of ICL in human has made ICL a potential drug target for TB therapy. However, the dynamic details of ICL which could give insights to the ICL-ligand interaction have yet to be solved. Therefore, a series of ICL dimer dynamics studies through molecular dynamics simulation were performed in this work. The ICL active site entrance gate closure is contributed to by hydrogen bonding and electrostatic interactions with the C-terminal. Analysis suggested that the open-closed behavior of the ICL active site entrance depends on the type of ligand present in the active site. We also observed four residues (Ser91, Asp108, Asp153, and Cys191) which could possibly be the nucleophiles for nucleophilic attack on the cleavage of isocitrate at the C2-C3 bond. We hope that the elucidation of ICL dynamics can benefit future works such as lead identification or antibody design against ICL for TB therapeutics.
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Affiliation(s)
- Yie-Vern Lee
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia , 11800 Minden, Penang, Malaysia
| | - Sy Bing Choi
- Pharmaceutical Design and Simulation Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia , 11800 Minden, Penang, Malaysia
| | - Habibah A Wahab
- Pharmaceutical Design and Simulation Laboratory, School of Pharmaceutical Sciences, Universiti Sains Malaysia , 11800 Minden, Penang, Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia , 11800 Minden, Penang, Malaysia
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32
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The design of target specific antibodies (scFv) by applying de novo workflow: Case study on BmR1 antigen from Brugia malayi. J Mol Graph Model 2017; 76:543-550. [DOI: 10.1016/j.jmgm.2017.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 06/02/2017] [Accepted: 07/05/2017] [Indexed: 11/24/2022]
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Oanca G, Stare J, Mavri J. How fast monoamine oxidases decompose adrenaline? Kinetics of isoenzymes A and B evaluated by empirical valence bond simulation. Proteins 2017; 85:2170-2178. [PMID: 28836294 DOI: 10.1002/prot.25374] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/18/2017] [Accepted: 08/21/2017] [Indexed: 12/22/2022]
Abstract
This work scrutinizes kinetics of decomposition of adrenaline catalyzed by monoamine oxidase (MAO) A and B enzymes, a process controlling the levels of adrenaline in the central nervous system and other tissues. Experimental kinetic data for MAO A and B catalyzed decomposition of adrenaline are reported only in the form of the maximum reaction rate. Therefore, we estimated the experimental free energy barriers form the kinetic data of closely related systems using regression method, as was done in our previous study. By using multiscale simulation on the Empirical Valence Bond (EVB) level, we studied the chemical reactivity of the MAO A catalyzed decomposition of adrenaline and we obtained a value of activation free energy of 17.3 ± 0.4 kcal/mol. The corresponding value for MAO B is 15.7 ± 0.7 kcal/mol. Both values are in good agreement with the estimated experimental barriers of 16.6 and 16.0 kcal/mol for MAO A and MAO B, respectively. The fact that we reproduced the kinetic data and preferential catalytic effect of MAO B over MAO A gives additional support to the validity of the proposed hydride transfer mechanism. Furthermore, we demonstrate that adrenaline is preferably involved in the reaction in a neutral rather than in a protonated form due to considerably higher barriers computed for the protonated adrenaline substrate. The results are discussed in the context of chemical mechanism of MAO enzymes and possible applications of multiscale simulation to rationalize the effects of MAO activity on adrenaline level.
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Affiliation(s)
- Gabriel Oanca
- Department of Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana, Slovenia.,Faculty of Physics, Alexandru Ioan Cuza University of Iasi, Iasi, Romania
| | - Jernej Stare
- Department of Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana, Slovenia
| | - Janez Mavri
- Department of Computational Biochemistry and Drug Design, National Institute of Chemistry, Ljubljana, Slovenia
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Multiscale simulation of monoamine oxidase catalyzed decomposition of phenylethylamine analogs. Eur J Pharmacol 2017; 817:46-50. [PMID: 28583428 DOI: 10.1016/j.ejphar.2017.05.061] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 03/31/2017] [Accepted: 05/31/2017] [Indexed: 01/01/2023]
Abstract
Phenylethylamine (PEA) is an endogenous amphetamine and its levels are increased by physical activity. As other biogenic monoamines, it is decomposed by monoamine oxidase (MAO) enzymes. The chemical mechanism of MAO, and flavoenzymes in general, is a subject of heated debate. We have previously shown that the rate-limiting step of MAO catalysis involves a hydride transfer from the substrate methylene group vicinal to the amino group to the N5 atom of the lumiflavin co-factor moiety. By using multiscale simulation on the Empirical Valence Bond (EVB) level, we studied the chemical reactivity of the monoamine oxidase B catalyzed decomposition of PEA and its two derivatives: p-chloro-β-methylphenylamine (p-CMP) and p-methoxy-β-methylphenethylamine (p-MMP). We calculated activation free energies of 17.1kcal/mol (PEA), 18.4kcal/mol (p-MMP) and 20.0kcal/mol (p-CMP), which are in excellent agreement with the experimental values of 16.7kcal/mol for PEA and 18.3kcal/mol for p-MMP, while the experimental value for p-CMP is not available. This gives strong support to the validity of our hydride transfer mechanism for both MAO A and B isoforms. The results are discussed in the context of the interplay between MAO point mutations and neuropsychiatric disorders.
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35
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Dasgupta S, Mukherjee S, Mukhopadhyay BP, Banerjee A, Mishra DK. Recognition dynamics of dopamine to human Monoamine oxidase B: role of Leu171/Gln206 and conserved water molecules in the active site cavity. J Biomol Struct Dyn 2017; 36:1439-1462. [PMID: 28460566 DOI: 10.1080/07391102.2017.1325405] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Subrata Dasgupta
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur 713209, West Bengal, India
| | - Soumita Mukherjee
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur 713209, West Bengal, India
| | - Bishnu P Mukhopadhyay
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur 713209, West Bengal, India
| | - Avik Banerjee
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur 713209, West Bengal, India
| | - Deepak K Mishra
- Department of Chemistry, National Institute of Technology-Durgapur, Durgapur 713209, West Bengal, India
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36
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Khan MKA, Akhtar S, Arif JM. Development of In Silico Protocols to Predict Structural Insights into the Metabolic Activation Pathways of Xenobiotics. Interdiscip Sci 2017; 10:329-345. [PMID: 28527150 DOI: 10.1007/s12539-017-0237-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 11/26/2022]
Abstract
To establish in silico model to predict the structural insight into the metabolic bioactivation pathway of xenobiotics, we considered two specific and one non-specific mammary procarcinogen [e.g., dibenzo[a,l]pyrene (DBP), 7,12-dimethylbenz[a]anthracene (DMBA), and benzo[a]pyrene (BP)]. The CYP1A1, 1B1, 2C9, 1A2 and 2B6 reported in wet-lab studies to actively metabolize DBP also showed strong binding energies (kcal/mol) of -11.50, -10.67, -10.37, -9.76 and -9.72, respectively, with inhibition constants ranging between 0.01 and 0.08 µM. The CYP3A4 depicted minimum binding energy (-9.51 kcal/mol) which is in agreement with the wet-lab reports. Further, relatively better affinity of CYP1A1 and CYP1B1 with the dibenzo[a,l]pyrene-11,12-diol (DBPD) might be indicative of their involvement in carcinogenicity of parent compound. Like DBP, BP (-10.13 kcal/mol, Ki: 0.04 µM) and BP-diols (BPD) (-9.01 kcal/mol, Ki: 0.25 µM) observed plausible binding with CYP1A1 supporting to the reported data that emphasize the major contribution of CYP1A1 in the activation of similar procarcinogens and mutagens. Likewise, in silico results further highlighted the CYP1A1 as key player in bioactivation of DMBA to its carcinogenic metabolites. In case of PhIP metabolism, strong binding interaction predicted with CYP1A1 (-9.63 kcal/mol) rather than CYP1A2 (-8.84 kcal/mol). Dissimilarity in the binding affinity of PhIP might be due to its basic scaffold. Further, molecular dynamics (MD) simulation of 10 ns has been revealed that docked complexes of CYP1A1 with DBP, DMBA and BP are comparatively more stable than the complex of PhIP. Moreover, the current findings might be valuable as reference model in prediction and elucidation of the approximate metabolic pathway of xenobiotics.
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Affiliation(s)
- M Kalim A Khan
- Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow, 226026, India
| | - Salman Akhtar
- Department of Bioengineering, Faculty of Engineering, Integral University, Lucknow, 226026, India
| | - Jamal M Arif
- Department of Biosciences, Faculty of Applied Sciences, Integral University, Kursi Road, P.O. Box Basha, Lucknow, 226026, India.
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37
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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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38
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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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39
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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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41
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Kržan M, Vianello R, Maršavelski A, Repič M, Zakšek M, Kotnik K, Fijan E, Mavri J. The Quantum Nature of Drug-Receptor Interactions: Deuteration Changes Binding Affinities for Histamine Receptor Ligands. PLoS One 2016; 11:e0154002. [PMID: 27159606 PMCID: PMC4861267 DOI: 10.1371/journal.pone.0154002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/21/2016] [Indexed: 11/19/2022] Open
Abstract
In this article we report a combined experimental and computational study concerning the effects of deuteration on the binding of histamine and two other histaminergic agonists to 3H-tiotidine-labeled histamine H2 receptor in neonatal rat astrocytes. Binding affinities were measured by displacing radiolabeled tiotidine from H2 receptor binding sites present on cultured neonatal rat astrocytes. Quantum-chemical calculations were performed by employing the empirical quantization of nuclear motion within a cluster model of the receptor binding site extracted from the homology model of the entire H2 receptor. Structure of H2 receptor built by homology modelling is attached in the supporting information (S1 Table) Experiments clearly demonstrate that deuteration affects the binding by increasing the affinity for histamine and reducing it for 2-methylhistamine, while basically leaving it unchanged for 4-methylhistamine. Ab initio quantum-chemical calculations on the cluster system extracted from the homology H2 model along with the implicit quantization of the acidic N-H and O-H bonds demonstrate that these changes in the binding can be rationalized by the altered strength of the hydrogen bonding upon deuteration known as the Ubbelohde effect. Our computational analysis also reveals a new mechanism of histamine binding, which underlines an important role of Tyr250 residue. The present work is, to our best knowledge, the first study of nuclear quantum effects on ligand receptor binding. The ligand H/D substitution is relevant for therapy in the context of perdeuterated and thus more stable drugs that are expected to enter therapeutic practice in the near future. Moreover, presented approach may contribute towards understanding receptor activation, while a distant goal remains in silico discrimination between agonists and antagonists based on the receptor structure.
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Affiliation(s)
- Mojca Kržan
- Department of Pharmacology and Experimental Toxicology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Robert Vianello
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute, Zagreb, Croatia
| | - Aleksandra Maršavelski
- Computational Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute, Zagreb, Croatia
| | - Matej Repič
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Ljubljana, Slovenia
| | - Maja Zakšek
- Department of Pharmacology and Experimental Toxicology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Kristina Kotnik
- Department of Pharmacology and Experimental Toxicology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Estera Fijan
- Department of Pharmacology and Experimental Toxicology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Janez Mavri
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Ljubljana, Slovenia
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42
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Oanca G, Purg M, Mavri J, Shih JC, Stare J. Insights into enzyme point mutation effect by molecular simulation: phenylethylamine oxidation catalyzed by monoamine oxidase A. Phys Chem Chem Phys 2016; 18:13346-56. [PMID: 27121693 DOI: 10.1039/c6cp00098c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The I335Y point mutation effect on the kinetics of phenylethylamine decomposition catalyzed by monoamine oxidase A was elucidated by means of molecular simulation. The established empirical valence bond methodology was used in conjunction with the free energy perturbation sampling technique and a classical force field representing the state of reactants and products. The methodology allows for the simulation of chemical reactions, in the present case the breaking of the α-C-H bond in a phenylethylamine substrate and the subsequent hydrogen transfer to the flavin cofactor, resulting in the formation of the N-H bond on flavin. The empirical parameters were calibrated against the experimental data for the simulated reaction in a wild type protein and then used for the calculation of the reaction free energy profile in the I335Y mutant. In very good agreement with the measured kinetic data, mutation increases the free energy barrier for the rate limiting step by slightly more than 1 kcal mol(-1) and consequently decreases the rate constant by about an order of magnitude. The magnitude of the computed effect slightly varies with simulation settings, but always remains in reasonable agreement with the experiment. Analysis of trajectories reveals a major change in the interaction between phenyl rings of the substrate and the neighboring Phe352 residue upon the I335Y mutation due to the increased local polarity, leading to an attenuated quadrupole interaction between the rings and destabilization of the transition state. Additionally, the increased local polarity in the mutant allows for a larger number of water molecules to be present near the active site, effectively shielding the catalytic effect of the enzyme and contributing to the increased barrier.
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Affiliation(s)
- Gabriel Oanca
- Laboratory of Biocomputing and Bioinformatics, National Institute of Chemistry, Ljubljana, Slovenia.
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43
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Mavri J, Matute RA, Chu ZT, Vianello R. Path Integral Simulation of the H/D Kinetic Isotope Effect in Monoamine Oxidase B Catalyzed Decomposition of Dopamine. J Phys Chem B 2016; 120:3488-92. [DOI: 10.1021/acs.jpcb.6b00894] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Janez Mavri
- Laboratory
for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI−1000 Ljubljana, Slovenia
| | - Ricardo A. Matute
- University of Southern California, Department of Chemistry
SGM 418, 3620 McClintock
Avenue Los Angeles, California 90089-1062, United States
| | - Zhen T. Chu
- University of Southern California, Department of Chemistry
SGM 418, 3620 McClintock
Avenue Los Angeles, California 90089-1062, United States
| | - Robert Vianello
- Computational
Organic Chemistry and Biochemistry Group, Ruđer Bošković Institute, Bijenička 54, HR−10000 Zagreb, Croatia
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44
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Mazzone G, Galano A, Alvarez-Idaboy JR, Russo N. Coumarin-Chalcone Hybrids as Peroxyl Radical Scavengers: Kinetics and Mechanisms. J Chem Inf Model 2016; 56:662-70. [PMID: 26998844 DOI: 10.1021/acs.jcim.6b00006] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The primary antioxidant activity of coumarin-chalcone hybrids has been investigated using the density functional and the conventional transition state theories. Their peroxyl radical scavenging ability was studied in solvents of different polarity and taking into account different reaction mechanisms. It was found that the activity of the hybrids increases with the polarity of the environment and the number of phenolic sites. In addition, their peroxyl radical scavenging activity is larger than those of the corresponding nonhybrid coumarin and chalcone molecules. This finding is in line with previous experimental evidence. All the investigated molecules were found to react faster than Trolox with (•)OOH, regardless of the polarity of the environment. The role of deprotonation on the overall activity of the studied compounds was assessed. The rate constants and branching ratios for the reactions of all the studied compounds with (•)OOH are reported for the first time.
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Affiliation(s)
- Gloria Mazzone
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria , I-87036 Arcavacata di Rende, Italy
| | - Annia Galano
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa , San Rafael Atlixco 186, Col. Vicentina. Iztapalapa, C. P. 09340 México, D. F. México
| | - Juan R Alvarez-Idaboy
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México , México DF 04510, México
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria , I-87036 Arcavacata di Rende, Italy
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45
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Ashwinder K, Kho MT, Chee PM, Lim WZ, Yap IKS, Choi SB, Yam WK. Targeting Heat Shock Proteins 60 and 70 of Toxoplasma gondii as a Potential Drug Target: In Silico Approach. Interdiscip Sci 2015; 8:374-387. [PMID: 26297309 DOI: 10.1007/s12539-015-0107-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/27/2015] [Accepted: 06/04/2015] [Indexed: 11/26/2022]
Abstract
Heat shock proteins (Hsps) 60 and 70 are postulated as a potential drug target for toxoplasmosis due to its importance in the developmental and survival of Toxoplasma gondii (T. gondii). As of today, there have been no reports on three-dimensional (3D) structure of Hsp60 and Hsp70 deposited in the Brookhaven Protein Data Bank. Hence, this study was conducted to predict 3D structures for Hsp60 and Hsp70 in T. gondii by homology modeling. Selection of the best predicted model was done based on multiple scoring functions. In addition, virtual screening was performed to short-list chemical compounds from the National Cancer Institute (NCI) Diversity Set III in search of potential inhibitor against Hsp60 and Hsp70 in T. gondii. Prior to virtual screening, binding sites of Hsp60 and Hsp70 were predicted using various servers and were used as the center in docking studies. The Hsps were docked against known natural ligands to validate the method used in estimating free energy of binding (FEB) and possible interactions between ligand and protein. Virtual screening was performed with a total of 1560 compounds from the NCI Diversity Set III. The compounds were ranked subsequently according to their FEB. Molecular basis of interactions of the top five ranked compounds was investigated using Ligplot+. The major interactions exhibited were hydrogen bonding and hydrophobic interactions in binding to Hsp60 and Hsp70. The results obtained provided information and guidelines for the development of inhibitors for Hsp60 and Hsp70 in T. gondii.
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Affiliation(s)
- Kaur Ashwinder
- School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Mee Teck Kho
- School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Phui Mun Chee
- School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Wui Zhuan Lim
- School of Health Sciences, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Ivan K S Yap
- Life Sciences Department, School of Pharmacy, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Sy Bing Choi
- Natural Product and Drug Discovery Centre, Malaysian Institutes of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Ministry of Science, Technology and Innovation, Block 5-A, Halaman Bukit Gambir, 11700, Penang, Malaysia
| | - Wai Keat Yam
- Life Sciences Department, School of Pharmacy, International Medical University, 126 Jalan Jalil Perkasa 19, Bukit Jalil, 57000, Kuala Lumpur, Malaysia.
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46
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Pieńko T, Taciak PP, Mazurek AP. On the Basicity of 8-Phenylsulfanyl Quipazine Derivatives: New Potential Serotonergic Agents. J Phys Chem A 2015; 119:6989-99. [PMID: 25928251 DOI: 10.1021/acs.jpca.5b02908] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A protonation state of serotonergic ligands plays a crucial role in their pharmacological activity. In this research, the basicity of 8-phenylsulfanyl quipazine derivatives as new potential serotonergic agents was studied. The most favorable protonation sites were determined in the gas and aqueous phases. In water, a solvation effect promoting the protonation of the N3 atom overcomes a positive charge delocalization phenomenon favoring a N1 atom protonation. The most stable conformations of neutral and protonated molecules in gas and water were found. It was demonstrated that a diprotonation reaction may occur. The most favorable among the diprotonated structures is the molecule with the N1 and N3 atoms protonated. A calculation of the pKa and pKa2 in water of a set of monosubstituted 8-phenylsulfanyl quipazine derivatives was performed using B3LYP/6-31G(d) and the SMD continuum solvation model. Enthalpic and entropic contributions to the pKa and pKa2 in gas and water were separated for a rationalization of a substituent effect on values of the pKa and pKa2. The relationship of the proton affinity and the solvation enthalpy in water with some reactivity descriptors, such as the Fukui function, the molecular electrostatic potential (MEP), and the global softness, was investigated. The order of the pKa values is the most controlled by the entropy. The diprotonation reaction, despite having an unfavorable enthalpy in water, is driven entropically. Final state effects in the diprotonated species were analyzed with the triadic formula. Results of a calculation of the theoretical basicity of the 8-phenylsulfanyl quipazines indicate that they should be monoprotonated on the N3 atom in the CNS environment. Diprotonation of the studied compounds may occur in very acidic body fluids such as the gastric juice.
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Affiliation(s)
- T Pieńko
- †Department of Drug Chemistry, Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, Banacha 1 Street, 02-097 Warsaw, Poland
| | - P P Taciak
- †Department of Drug Chemistry, Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, Banacha 1 Street, 02-097 Warsaw, Poland
| | - A P Mazurek
- †Department of Drug Chemistry, Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, Banacha 1 Street, 02-097 Warsaw, Poland.,‡National Medicines Institute, 30/34 Chełmska Street, 00-725 Warsaw, Poland
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Zapata-Torres G, Fierro A, Barriga-González G, Salgado JC, Celis-Barros C. Revealing Monoamine Oxidase B Catalytic Mechanisms by Means of the Quantum Chemical Cluster Approach. J Chem Inf Model 2015; 55:1349-60. [PMID: 26091526 DOI: 10.1021/acs.jcim.5b00140] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Two of the possible catalytic mechanisms for neurotransmitter oxidative deamination by monoamine oxidase B (MAO B), namely, polar nucleophilic and hydride transfer, were addressed in order to comprehend the nature of their rate-determining step. The Quantum Chemical Cluster Approach was used to obtain transition states of MAO B complexed with phenylethylamine (PEA), benzylamine (BA), and p-nitrobenzylamine (NBA). The choice of these amines relies on their importance to address MAO B catalytic mechanisms so as to help us to answer questions such as why BA is a better substrate than NBA or how para-substitution affects substrate's reactivity. Transition states were later validated by comparison with the experimental free energy barriers. From a theoretical point of view, and according to the our reported transition states, their calculated barriers and structural and orbital differences obtained by us among these compounds, we propose that good substrates such as BA and PEA might follow the hydride transfer pathway while poor substrates such as NBA prefer the polar nucleophilic mechanism, which might suggest that MAO B can act by both mechanisms. The low free energy barriers for BA and PEA reflect the preference that MAO B has for hydride transfer over the polar nucleophilic mechanism when catalyzing the oxidative deamination of neurotransmitters.
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Affiliation(s)
- Gerald Zapata-Torres
- †Molecular Graphics Suite, Department of Inorganic and Analytical Chemistry, Faculty of Chemical and Pharmaceutical Sciences, University of Chile, Santiago, Chile
| | - Angélica Fierro
- ‡Facultad de Química, Departamento de Química Orgánica, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - German Barriga-González
- §Universidad Andres Bello, Facultad de Ciencias Exactas, Departamento de Ciencias Quimicas, Avenida República 275, 8370146 Santiago, Chile
| | - J Cristian Salgado
- ∥Laboratory of Process Modeling and Distributed Computing, Department of Chemical Engineering and Biotechnology, University of Chile, Beauchef 850, Santiago, Chile
| | - Cristian Celis-Barros
- §Universidad Andres Bello, Facultad de Ciencias Exactas, Departamento de Ciencias Quimicas, Avenida República 275, 8370146 Santiago, Chile
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Wang J, Li Y, Yang Y, Zhang J, Du J, Zhang S, Yang L. Profiling the interaction mechanism of indole-based derivatives targeting the HIV-1 gp120 receptor. RSC Adv 2015. [DOI: 10.1039/c5ra04299b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A glycoprotein exposed on a viral surface, human immunodeficiency virus type 1 (HIV-1) gp120 is essential for virus entry into cells as it plays a vital role in seeking out specific cell surface receptors for entry.
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Affiliation(s)
- Jinghui Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Department of Materials Sciences and Chemical Engineering
- Dalian University of Technology
- Dalian
- China
| | - Yan Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Department of Materials Sciences and Chemical Engineering
- Dalian University of Technology
- Dalian
- China
| | - Yinfeng Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Department of Materials Sciences and Chemical Engineering
- Dalian University of Technology
- Dalian
- China
| | - Jingxiao Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Department of Materials Sciences and Chemical Engineering
- Dalian University of Technology
- Dalian
- China
| | - Jian Du
- Institute of Chemical Process Systems Engineering
- Dalian University of Technology
- Dalian 116024
- China
| | - Shuwei Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE)
- Department of Materials Sciences and Chemical Engineering
- Dalian University of Technology
- Dalian
- China
| | - Ling Yang
- Laboratory of Pharmaceutical Resource Discovery
- Dalian Institute of Chemical Physics
- Graduate School of the Chinese Academy of Sciences
- Dalian
- China
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Sharir-Ivry A, Varatharaj R, Shurki A. Challenges within the Linear Response Approximation When Studying Enzyme Catalysis and Effects of Mutations. J Chem Theory Comput 2014; 11:293-302. [DOI: 10.1021/ct500751f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Avital Sharir-Ivry
- Institute for Drug Design,
School of Pharmacy, The Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Rajapandian Varatharaj
- Institute for Drug Design,
School of Pharmacy, The Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Avital Shurki
- Institute for Drug Design,
School of Pharmacy, The Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
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50
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Repič M, Vianello R, Purg M, Duarte F, Bauer P, Kamerlin SCL, Mavri J. Empirical valence bond simulations of the hydride transfer step in the monoamine oxidase B catalyzed metabolism of dopamine. Proteins 2014; 82:3347-55. [PMID: 25220264 DOI: 10.1002/prot.24690] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 09/10/2014] [Indexed: 01/05/2023]
Abstract
Monoamine oxidases (MAOs) A and B are flavoenzymes responsible for the metabolism of biogenic amines such as dopamine, serotonin and noradrenaline. In this work, we present a comprehensive study of the rate-limiting step of dopamine degradation by MAO B, which consists in the hydride transfer from the methylene group of the substrate to the flavin moiety of the FAD prosthetic group. This article builds on our previous quantum chemical study of the same reaction using a cluster model (Vianello et al., Eur J Org Chem 2012; 7057), but now considering the full dimensionality of the hydrated enzyme with extensive configurational sampling. We show that MAO B is specifically tuned to catalyze the hydride transfer step from the substrate to the flavin moiety of the FAD prosthetic group and that it lowers the activation barrier by 12.3 kcal mol⁻¹ compared to the same reaction in aqueous solution, a rate enhancement of more than nine orders of magnitude. Taking into account the deprotonation of the substrate prior to the hydride transfer reaction, the activation barrier in the enzyme is calculated to be 16.1 kcal mol⁻¹, in excellent agreement with the experimental value of 16.5 kcal mol⁻¹. Additionally, we demonstrate that the protonation state of the active site residue Lys296 does not have an influence on the hydride transfer reaction.
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Affiliation(s)
- Matej Repič
- Laboratory for Biocomputing and Bioinformatics, National Institute of Chemistry, Hajdrihova 19, SI-1000, Ljubljana, Slovenia
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