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Makhaeva GF, Kovaleva NV, Rudakova EV, Boltneva NP, Lushchekina SV, Astakhova TY, Timokhina EN, Serebryakova OG, Shchepochkin AV, Averkov MA, Utepova IA, Demina NS, Radchenko EV, Palyulin VA, Fisenko VP, Bachurin SO, Chupakhin ON, Charushin VN, Richardson RJ. Derivatives of 9-phosphorylated acridine as butyrylcholinesterase inhibitors with antioxidant activity and the ability to inhibit β-amyloid self-aggregation: potential therapeutic agents for Alzheimer's disease. Front Pharmacol 2023; 14:1219980. [PMID: 37654616 PMCID: PMC10466253 DOI: 10.3389/fphar.2023.1219980] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/18/2023] [Indexed: 09/02/2023] Open
Abstract
We investigated the inhibitory activities of novel 9-phosphoryl-9,10-dihydroacridines and 9-phosphorylacridines against acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and carboxylesterase (CES). We also studied the abilities of the new compounds to interfere with the self-aggregation of β-amyloid (Aβ42) in the thioflavin test as well as their antioxidant activities in the ABTS and FRAP assays. We used molecular docking, molecular dynamics simulations, and quantum-chemical calculations to explain experimental results. All new compounds weakly inhibited AChE and off-target CES. Dihydroacridines with aryl substituents in the phosphoryl moiety inhibited BChE; the most active were the dibenzyloxy derivative 1d and its diphenethyl bioisostere 1e (IC50 = 2.90 ± 0.23 µM and 3.22 ± 0.25 µM, respectively). Only one acridine, 2d, an analog of dihydroacridine, 1d, was an effective BChE inhibitor (IC50 = 6.90 ± 0.55 μM), consistent with docking results. Dihydroacridines inhibited Aβ42 self-aggregation; 1d and 1e were the most active (58.9% ± 4.7% and 46.9% ± 4.2%, respectively). All dihydroacridines 1 demonstrated high ABTS•+-scavenging and iron-reducing activities comparable to Trolox, but acridines 2 were almost inactive. Observed features were well explained by quantum-chemical calculations. ADMET parameters calculated for all compounds predicted favorable intestinal absorption, good blood-brain barrier permeability, and low cardiac toxicity. Overall, the best results were obtained for two dihydroacridine derivatives 1d and 1e with dibenzyloxy and diphenethyl substituents in the phosphoryl moiety. These compounds displayed high inhibition of BChE activity and Aβ42 self-aggregation, high antioxidant activity, and favorable predicted ADMET profiles. Therefore, we consider 1d and 1e as lead compounds for further in-depth studies as potential anti-AD preparations.
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Affiliation(s)
- Galina F. Makhaeva
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, Russia
| | - Nadezhda V. Kovaleva
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, Russia
| | - Elena V. Rudakova
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, Russia
| | - Natalia P. Boltneva
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, Russia
| | - Sofya V. Lushchekina
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Yu Astakhova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Elena N. Timokhina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Olga G. Serebryakova
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, Russia
| | - Alexander V. Shchepochkin
- Institute of Organic Synthesis, Russian Academy of Sciences, Yekaterinburg, Russia
- Department of Organic and Biomolecular Chemistry, Ural Federal University, Yekaterinburg, Russia
| | - Maxim A. Averkov
- Institute of Organic Synthesis, Russian Academy of Sciences, Yekaterinburg, Russia
- Department of Organic and Biomolecular Chemistry, Ural Federal University, Yekaterinburg, Russia
| | - Irina A. Utepova
- Institute of Organic Synthesis, Russian Academy of Sciences, Yekaterinburg, Russia
- Department of Organic and Biomolecular Chemistry, Ural Federal University, Yekaterinburg, Russia
| | - Nadezhda S. Demina
- Institute of Organic Synthesis, Russian Academy of Sciences, Yekaterinburg, Russia
| | - Eugene V. Radchenko
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir A. Palyulin
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, Russia
- Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir P. Fisenko
- Department of Pharmacology of the Institute of Biodesign and Complex System Modeling of Biomedical Science & Technology Park of Sechenov I.M., First Moscow State Medical University, Moscow, Russia
| | - Sergey O. Bachurin
- Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry, Russian Academy of Sciences, Chernogolovka, Russia
| | - Oleg N. Chupakhin
- Institute of Organic Synthesis, Russian Academy of Sciences, Yekaterinburg, Russia
- Department of Organic and Biomolecular Chemistry, Ural Federal University, Yekaterinburg, Russia
| | - Valery N. Charushin
- Institute of Organic Synthesis, Russian Academy of Sciences, Yekaterinburg, Russia
- Department of Organic and Biomolecular Chemistry, Ural Federal University, Yekaterinburg, Russia
| | - Rudy J. Richardson
- Department of Pharmacology of the Institute of Biodesign and Complex System Modeling of Biomedical Science & Technology Park of Sechenov I.M., First Moscow State Medical University, Moscow, Russia
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
- Department of Neurology, University of Michigan, Ann Arbor, MI, United States
- Center of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
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2
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Mlakić M, Fodor L, Odak I, Horváth O, Lovrić MJ, Barić D, Milašinović V, Molčanov K, Marinić Ž, Lasić Z, Škorić I. Resveratrol–Maltol and Resveratrol–Thiophene Hybrids as Cholinesterase Inhibitors and Antioxidants: Synthesis, Biometal Chelating Capability and Crystal Structure. Molecules 2022; 27:molecules27196379. [PMID: 36234916 PMCID: PMC9573353 DOI: 10.3390/molecules27196379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 12/02/2022] Open
Abstract
New resveratrol–thiophene and resveratrol–maltol hybrids were synthesized as cholinesterase inhibitors and antioxidants. As with photostability experiments, biological tests also found remarkable differences in the properties and behavior of thiophene and maltol hybrids. While resveratrol–thiophene hybrids have excellent inhibitory and antioxidant properties (similar to the activity of reference drug galantamine), maltols have been proven to be weaker inhibitors and antioxidants. The molecular docking of selected active ligands gave insight into the structures of docked enzymes. It enabled the identification of interactions between the ligand and the active site of both cholinesterases. The maltols that proved to be active cholinesterase inhibitors were able to coordinate Fe3+ ion, forming complexes of 1:1 composition. Their formation constants, determined by spectrophotometry, are very similar, lgK = 11.6–12.6, suggesting that Fe3+ binds to the common hydroxy-pyranone moiety and is hardly affected by the other aromatic part of the ligand. Accordingly, the characteristic bands in their individual absorption spectra are uniformly red-shifted relative to those of the free ligands. The crystal structures of two new resveratrol–maltol hybrids were recorded, giving additional information on the molecules’ intermolecular hydrogen bonds and packing. In this way, several functionalities of these new resveratrol hybrids were examined as a necessary approach to finding more effective drugs for complicated neurodegenerative diseases.
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Affiliation(s)
- Milena Mlakić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia
| | - Lajos Fodor
- Department of General and Inorganic Chemistry, Institute of Chemistry, Faculty of Engineering, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Ilijana Odak
- Department of Chemistry, Faculty of Science and Education, University of Mostar, Matice hrvatske bb, 88000 Mostar, Bosnia and Herzegovina
- Correspondence: (I.O.); (I.Š.)
| | - Ottó Horváth
- Department of General and Inorganic Chemistry, Institute of Chemistry, Faculty of Engineering, University of Pannonia, P.O. Box 158, H-8201 Veszprém, Hungary
| | - Marija Jelena Lovrić
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Danijela Barić
- Group for Computational Life Sciences, Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Valentina Milašinović
- Division of Physical Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Krešimir Molčanov
- Division of Physical Chemistry, Rudjer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Željko Marinić
- NMR Center, Rudjer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
| | - Zlata Lasić
- Teva api Analytical R&D, Pliva, Prilaz Baruna Filipovića 25, HR-10000 Zagreb, Croatia
| | - Irena Škorić
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 19, HR-10000 Zagreb, Croatia
- Correspondence: (I.O.); (I.Š.)
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3
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Hasanvand Z, Motahari R, Nadri H, Moghimi S, Foroumadi R, Ayati A, Akbarzadeh T, Bukhari SNA, Foroumadi A. Novel 3-aminobenzofuran derivatives as multifunctional agents for the treatment of Alzheimer’s disease. Front Chem 2022; 10:882191. [PMID: 36017161 PMCID: PMC9395670 DOI: 10.3389/fchem.2022.882191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/05/2022] [Indexed: 11/13/2022] Open
Abstract
A novel multifunctional series of 3-aminobenzofuran derivatives 5a-p were designed and synthesized as potent inhibitors of acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). The target compounds 5a-p were prepared via a three-step reaction, starting from 2-hydroxy benzonitrile. In vitro anti-cholinesterase activity exhibited that most of the compounds had potent acetyl- and butyrylcholinesterase inhibitory activity. In particular, compound 5f containing 2-fluorobenzyl moiety showed the best inhibitory activity. Furthermore, this compound showed activity on self- and AChE-induced Aβ-aggregation and MTT assay against PC12 cells. The kinetic study revealed that compound 5f showed mixed-type inhibition on AChE. Based on these results, compound 5f can be considered as a novel multifunctional structural unit against Alzheimer’s disease.
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Affiliation(s)
- Zaman Hasanvand
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Rasoul Motahari
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Nadri
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Setareh Moghimi
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Roham Foroumadi
- Department of Pharmacology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Adileh Ayati
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Tahmineh Akbarzadeh
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Syed Nasir Abbas Bukhari
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Drug Design and Development Research Center, The Institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
- *Correspondence: Alireza Foroumadi,
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Martínez-Herrera M, Figueroa-Gerstenmaier S, López-Camacho PY, Millan-Pacheco C, Balderas-Altamirano MA, Mendoza-Franco G, García-Sierra F, Zavala-Ocampo LM, Basurto-Islas G. Multiadducts of C60 Modulate Amyloid-β Fibrillation with Dual Acetylcholinesterase Inhibition and Antioxidant Properties: In Vitro and In Silico Studies. J Alzheimers Dis 2022; 87:741-759. [DOI: 10.3233/jad-215412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background: Amyloid-β (Aβ) fibrils induce cognitive impairment and neuronal loss, leading to onset of Alzheimer’s disease (AD). The inhibition of Aβ aggregation has been proposed as a therapeutic strategy for AD. Pristine C60 has shown the capacity to interact with the Aβ peptide and interfere with fibril formation but induces significant toxic effects in vitro and in vivo. Objective: To evaluate the potential of a series of C60 multiadducts to inhibit the Aβ fibrillization. Methods: A series of C60 multiadducts with four to six diethyl malonyl and their corresponding disodium-malonyl substituents were synthesized as individual isomers. Their potential on Aβ fibrillization inhibition was evaluated in vitro, in cellulo, and silico. Antioxidant activity, acetylcholinesterase inhibition capacity, and toxicity were assessed in vitro. Results: The multiadducts modulate Aβ fibrils formation without inducing cell toxicity, and that the number and polarity of the substituents play a significant role in the adducts efficacy to modulate Aβ aggregation. The molecular mechanism of fullerene-Aβ interaction and modulation was identified. Furthermore, the fullerene derivatives exhibited antioxidant capacity and reduction of acetylcholinesterase activity. Conclusion: Multiadducts of C60 are novel multi-target-directed ligand molecules that could hold considerable promise as the starting point for the development of AD therapies.
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Affiliation(s)
- Melchor Martínez-Herrera
- Departamento de Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Cuajimalpa, Ciudad de México, México
| | | | - Perla Y. López-Camacho
- Departamento de Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Cuajimalpa, Ciudad de México, México
| | - Cesar Millan-Pacheco
- Facultad de Farmacia, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | | | - Graciela Mendoza-Franco
- Departamento de Biología Celular, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Franciscos García-Sierra
- Departamento de Biología Celular, Centro de Investigación y Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, México
| | - Lizeth M. Zavala-Ocampo
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Cuajimalpa, Ciudad de México, México
| | - Gustavo Basurto-Islas
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Campus León, León, Gto., Mexico
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5
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Bagri K, Kumar A, Manisha, Kumar P. Computational Studies on Acetylcholinesterase Inhibitors: From Biochemistry to Chemistry. Mini Rev Med Chem 2021; 20:1403-1435. [PMID: 31884928 DOI: 10.2174/1389557520666191224144346] [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: 09/10/2019] [Revised: 10/23/2019] [Accepted: 10/28/2019] [Indexed: 11/22/2022]
Abstract
Acetylcholinesterase inhibitors are the most promising therapeutics for Alzheimer's disease treatment as these prevent the loss of acetylcholine and slows the progression of the disease. The drugs approved for the management of Alzheimer's disease by the FDA are acetylcholinesterase inhibitors but are associated with side effects. Consistent and stringent efforts by the researchers with the help of computational methods opened new ways of developing novel molecules with good acetylcholinesterase inhibitory activity. In this manuscript, we reviewed the studies that identified the essential structural features of acetylcholinesterase inhibitors at the molecular level as well as the techniques like molecular docking, molecular dynamics, quantitative structure-activity relationship, virtual screening, and pharmacophore modelling that were used in designing these inhibitors.
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Affiliation(s)
- Kiran Bagri
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Ashwani Kumar
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Manisha
- Department of Pharmaceutical Sciences, Guru Jambheshwar University of Science & Technology, Hisar 125001, India
| | - Parvin Kumar
- Department of Chemistry, Kurukshetra University, Kurukshetra, India
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De Boer D, Nguyen N, Mao J, Moore J, Sorin EJ. A Comprehensive Review of Cholinesterase Modeling and Simulation. Biomolecules 2021; 11:580. [PMID: 33920972 PMCID: PMC8071298 DOI: 10.3390/biom11040580] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/08/2021] [Accepted: 04/11/2021] [Indexed: 01/18/2023] Open
Abstract
The present article reviews published efforts to study acetylcholinesterase and butyrylcholinesterase structure and function using computer-based modeling and simulation techniques. Structures and models of both enzymes from various organisms, including rays, mice, and humans, are discussed to highlight key structural similarities in the active site gorges of the two enzymes, such as flexibility, binding site location, and function, as well as differences, such as gorge volume and binding site residue composition. Catalytic studies are also described, with an emphasis on the mechanism of acetylcholine hydrolysis by each enzyme and novel mutants that increase catalytic efficiency. The inhibitory activities of myriad compounds have been computationally assessed, primarily through Monte Carlo-based docking calculations and molecular dynamics simulations. Pharmaceutical compounds examined herein include FDA-approved therapeutics and their derivatives, as well as several other prescription drug derivatives. Cholinesterase interactions with both narcotics and organophosphate compounds are discussed, with the latter focusing primarily on molecular recognition studies of potential therapeutic value and on improving our understanding of the reactivation of cholinesterases that are bound to toxins. This review also explores the inhibitory properties of several other organic and biological moieties, as well as advancements in virtual screening methodologies with respect to these enzymes.
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Affiliation(s)
- Danna De Boer
- Department of Chemistry & Biochemistry, California State University, Long Beach, CA 90840, USA;
| | - Nguyet Nguyen
- Department of Chemical Engineering, California State University, Long Beach, CA 90840, USA; (N.N.); (J.M.)
| | - Jia Mao
- Department of Chemical Engineering, California State University, Long Beach, CA 90840, USA; (N.N.); (J.M.)
| | - Jessica Moore
- Department of Biomedical Engineering, California State University, Long Beach, CA 90840, USA;
| | - Eric J. Sorin
- Department of Chemistry & Biochemistry, California State University, Long Beach, CA 90840, USA;
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7
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Silman I, Shnyrov VL, Ashani Y, Roth E, Nicolas A, Sussman JL, Weiner L. Torpedo californica acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif. Protein Sci 2021; 30:966-981. [PMID: 33686648 PMCID: PMC8040873 DOI: 10.1002/pro.4061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/05/2021] [Accepted: 03/05/2021] [Indexed: 11/07/2022]
Abstract
Stabilization of Torpedo californica acetylcholinesterase by the divalent cations Ca+2, Mg+2, and Mn+2 was investigated. All three substantially protect the enzyme from thermal inactivation. Electron paramagnetic resonance revealed one high‐affinity binding site for Mn+2 and several much weaker sites. Differential scanning calorimetry showed a single irreversible thermal transition. All three cations raise both the temperature of the transition and the activation energy, with the transition becoming more cooperative. The crystal structures of the Ca+2 and Mg+2 complexes with Torpedo acetylcholinesterase were solved. A principal binding site was identified. In both cases, it consists of four aspartates (a 4D motif), within which the divalent ion is embedded, together with several water molecules. It makes direct contact with two of the aspartates, and indirect contact, via waters, with the other two. The 4D motif has been identified in 31 acetylcholinesterase sequences and 28 butyrylcholinesterase sequences. Zebrafish acetylcholinesterase also contains the 4D motif; it, too, is stabilized by divalent metal ions. The ASSAM server retrieved 200 other proteins that display the 4D motif, in many of which it is occupied by a divalent cation. It is a very versatile motif, since, even though tightly conserved in terms of RMSD values, it can contain from one to as many as three divalent metal ions, together with a variable number of waters. This novel motif, which binds primarily divalent metal ions, is shared by a broad repertoire of proteins. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Protein_Science:3. PDB‐ID(s): 7B38, 7B8E and 7B2W;
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Affiliation(s)
- Israel Silman
- Department of NeurobiologyWeizmann Institute of ScienceRehovotIsrael
| | - Valery L. Shnyrov
- Department of Biochemistry and Molecular BiologyUniversidad de SalamancaSalamancaSpain
| | - Yacov Ashani
- Department of Biomolecular SciencesWeizmann Institute of ScienceRehovotIsrael
| | - Esther Roth
- Department of NeurobiologyWeizmann Institute of ScienceRehovotIsrael
| | - Anne Nicolas
- Department of NeurobiologyWeizmann Institute of ScienceRehovotIsrael
- Department of Chemical and Structural BiologyWeizmann Institute of ScienceRehovotIsrael
| | - Joel L. Sussman
- Department of Chemical and Structural BiologyWeizmann Institute of ScienceRehovotIsrael
- Structural Proteomics UnitWeizmann Institute of ScienceRehovotIsrael
| | - Lev Weiner
- Department of NeurobiologyWeizmann Institute of ScienceRehovotIsrael
- Department of Chemical Research SupportWeizmann Institute of ScienceRehovotIsrael
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8
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Molecular modeling-guided optimization of acetylcholinesterase reactivators: A proof for reactivation of covalently inhibited targets. Eur J Med Chem 2021; 215:113286. [PMID: 33611189 PMCID: PMC7877871 DOI: 10.1016/j.ejmech.2021.113286] [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: 10/15/2020] [Revised: 12/23/2020] [Accepted: 02/03/2021] [Indexed: 11/23/2022]
Abstract
Covalent drugs have been intensively studied in some very important fields such as anti-tumor and anti-virus, including the currently global-spread SARS-CoV-2. However, these drugs may interact with a variety of biological macromolecules and cause serious toxicology, so how to reactivate the inhibited targets seems to be imperative in the near future. Organophosphate was an extreme example, which could form a covalent bound easily with acetylcholinesterase and irreversibly inhibited the enzyme, causing high toxicology. Some nucleophilic oxime reactivators for organophosphate poisoned acetylcholinesterase had been developed, but the reactivation process was still less understanding. Herein, we proposed there should be a pre-reactivated pose during the reactivating process and compounds whose binding pose was easy to transfer to the pre-reactivated pose might be efficient reactivators. Then we refined the previous reactivators based on the molecular dynamic simulation results, the resulting compounds L7R3 and L7R5 were proven as much more efficient reactivators for organophosphate inhibited acetylcholinesterase than currently used oximes. This work might provide some insights for constructing reactivators of covalently inhibited targets by using computational methods.
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9
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Computational studies on cholinesterases: Strengthening our understanding of the integration of structure, dynamics and function. Neuropharmacology 2020; 179:108265. [DOI: 10.1016/j.neuropharm.2020.108265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/21/2020] [Accepted: 07/27/2020] [Indexed: 12/17/2022]
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10
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Vitorović-Todorović M, Cvijetić I, Zloh M, Perdih A. Molecular recognition of acetylcholinesterase and its subnanomolar reversible inhibitor: a molecular simulations study. J Biomol Struct Dyn 2020; 40:1671-1691. [DOI: 10.1080/07391102.2020.1831960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
| | - Ilija Cvijetić
- Innovation Center of the Faculty of Chemistry, University of Belgrade, Serbia
| | - Mire Zloh
- Faculty of Pharmacy, University Business Academy, Novi Sad, Serbia
- Nanopuzzle Medicines Design Ltd, Stevenage, UK
| | - Andrej Perdih
- National Institute of Chemistry, Ljubljana, Slovenia
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11
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Setny P. Conserved internal hydration motifs in protein kinases. Proteins 2020; 88:1578-1591. [DOI: 10.1002/prot.25977] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 05/18/2020] [Accepted: 07/05/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Piotr Setny
- Centre of New Technologies University of Warsaw Warsaw Poland
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12
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Catto M, Pisani L, de la Mora E, Belviso BD, Mangiatordi GF, Pinto A, Palma AD, Denora N, Caliandro R, Colletier JP, Silman I, Nicolotti O, Altomare CD. Chiral Separation, X-ray Structure, and Biological Evaluation of a Potent and Reversible Dual Binding Site AChE Inhibitor. ACS Med Chem Lett 2020; 11:869-876. [PMID: 32435398 DOI: 10.1021/acsmedchemlett.9b00656] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 02/07/2020] [Indexed: 11/30/2022] Open
Abstract
Acetylcholinesterase (AChE) inhibitors (AChEIs) still remain the leading therapeutic options for the symptomatic treatment of cognitive deficits associated with mild-to-moderate Alzheimer's disease. The search for new AChEIs benefits from well-established knowledge of the molecular interactions of selective AChEIs, such as donepezil and related dual binding site inhibitors. Starting from a previously disclosed coumarin-based inhibitor (±)-cis-1, active as racemate in the nanomolar range toward AChE, we proceeded on a double track by (i) achieving chiral resolution of the enantiomers of 1 by HPLC and (ii) preparing two close achiral analogues of 1, i.e., compounds 4 and 6. An eudismic ratio as high as 20 was observed for the (-) enantiomer of cis-1. The X-ray crystal structure of the complex between the (-)-cis-1 eutomer (coded as MC1420) and T. californica AChE was determined at 2.8 Å, and docking calculation results suggested that the eutomer in (1R,3S) absolute configuration should be energetically more favored in binding the enzyme than the eutomer in (1S,3R) configuration. The achiral analogues 4 and 6 were less effective in inhibiting AChE compared to (±)-cis-1, but interestingly butylamide 4 emerged as a potent inhibitor of butyrylcholinesterase (BChE).
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Affiliation(s)
- Marco Catto
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Leonardo Pisani
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Eugenio de la Mora
- Univ. Grenoble Alpes, CEA, CNRS, Institute of Structural Biology, F-38044 Grenoble, France
| | - Benny Danilo Belviso
- Institute of Crystallography, National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | | | - Andrea Pinto
- Department of Food, Environmental and Nutritional Sciences (DeFENS), University of Milan, Via Celoria 2, 20133 Milano, Italy
| | - Annalisa De Palma
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Nunzio Denora
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Rocco Caliandro
- Institute of Crystallography, National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | | | - Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Orazio Nicolotti
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
| | - Cosimo Damiano Altomare
- Department of Pharmacy-Drug Sciences, University of Bari Aldo Moro, Via E. Orabona 4, 70125 Bari, Italy
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13
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D'Avila da Silva F, Nogara PA, Ochoa-Rodríguez E, Nuñez-Figueredo Y, Wong-Guerra M, Rosemberg DB, Rocha JBTD. Molecular docking and in vitro evaluation of a new hybrid molecule (JM-20) on cholinesterase activity from different sources. Biochimie 2019; 168:297-306. [PMID: 31770565 DOI: 10.1016/j.biochi.2019.11.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/20/2019] [Indexed: 10/25/2022]
Abstract
The main function of AChE is the hydrolysis of the neurotransmitter acetylcholine (ACh) at the neuromuscular and in cholinergic brain synapses. In some pathologies, loss of cholinergic neurons may be associated with a deficiency of ACh in specific brain areas. Consequently, the study of new safe drugs that inhibit AChE is important, because they can increase ACh levels in the synaptic cleft without adverse effects. Here, we evaluated the effects of JM-20 (a benzodiazepine-dihydropyridine hybrid molecule) on cholinesterase (ChE) activities from distinct sources (AChE from Electrophorus electricus (EeAChE), human erythrocyte membranes (HsAChE (ghost)), total erythrocyte (HsAChE (erythrocyte)) and BChE from plasma (HsBChE) and purified enzyme from the horse (EcBChE)). Kinetic parameters were determined in the presence of 0.05-1.6 mM of substrate concentration. The interactions ChEs with JM-20 were performed using molecular docking simulations. JM-20 inhibited all tested AChE but not BChE. The IC50 values were 123 nM ± 0.2 (EeAChE), 158 nM ± 0.1 (ghost HsAChE), and 172 nM ± 0.2 (erythrocytic HsAChE). JM-20 caused a mixed type of inhibition (it altered Km and Vmax of AChE). The molecular docking indicated the binding poses and the most plausible active isomer of JM-20. Besides giving important data for future drug design, our results help us understand the mode of action of JM-20 as a specific inhibitor of AChE enzymes.
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Affiliation(s)
- Fernanda D'Avila da Silva
- Programa de Pós-graduação Em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria, 97105-900, Santa Maria, RS, Brazil
| | - Pablo Andrei Nogara
- Programa de Pós-graduação Em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria, 97105-900, Santa Maria, RS, Brazil
| | - Estael Ochoa-Rodríguez
- Centro de Investigación y Desarrollo de Medicamentos, Ave 26, Nº 1605 Boyeros y Puentes Grandes, CP10600, La Habana, Cuba
| | - Yanier Nuñez-Figueredo
- Centro de Investigación y Desarrollo de Medicamentos, Ave 26, Nº 1605 Boyeros y Puentes Grandes, CP10600, La Habana, Cuba
| | - Maylin Wong-Guerra
- Centro de Investigación y Desarrollo de Medicamentos, Ave 26, Nº 1605 Boyeros y Puentes Grandes, CP10600, La Habana, Cuba
| | - Denis Broock Rosemberg
- Programa de Pós-graduação Em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria, 97105-900, Santa Maria, RS, Brazil
| | - João Batista Teixeira da Rocha
- Programa de Pós-graduação Em Ciências Biológicas: Bioquímica Toxicológica, Universidade Federal de Santa Maria, 97105-900, Santa Maria, RS, Brazil.
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14
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Park MS, Araya-Secchi R, Brackbill JA, Phan HD, Kehling AC, Abd El-Wahab EW, Dayeh DM, Sotomayor M, Nakanishi K. Multidomain Convergence of Argonaute during RISC Assembly Correlates with the Formation of Internal Water Clusters. Mol Cell 2019; 75:725-740.e6. [PMID: 31324450 DOI: 10.1016/j.molcel.2019.06.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 04/30/2019] [Accepted: 06/07/2019] [Indexed: 11/17/2022]
Abstract
Despite the relevance of Argonaute proteins in RNA silencing, little is known about the structural steps of small RNA loading to form RNA-induced silencing complexes (RISCs). We report the 1.9 Å crystal structure of human Argonaute4 with guide RNA. Comparison with the previously determined apo structure of Neurospora crassa QDE2 revealed that the PIWI domain has two subdomains. Binding of guide RNA fastens the subdomains, thereby rearranging the active-site residues and increasing the affinity for TNRC6 proteins. We also identified two water pockets beneath the nucleic acid-binding channel that appeared to stabilize the mature RISC. Indeed, mutating the water-pocket residues of Argonaute2 and Argonaute4 compromised RISC assembly. Simulations predict that internal water molecules are exchangeable with the bulk solvent but always occupy specific positions at the domain interfaces. These results suggest that after guide RNA-driven conformational changes, water-mediated hydrogen-bonding networks tie together the converged domains to complete the functional RISC structure.
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Affiliation(s)
- Mi Seul Park
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Raul Araya-Secchi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - James A Brackbill
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Hong-Duc Phan
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Audrey C Kehling
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Ekram W Abd El-Wahab
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel M Dayeh
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - Marcos Sotomayor
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA; Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA; Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA; Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.
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15
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Mollazadeh M, Mohammadi-Khanaposhtani M, Zonouzi A, Nadri H, Najafi Z, Larijani B, Mahdavi M. New benzyl pyridinium derivatives bearing 2,4-dioxochroman moiety as potent agents for treatment of Alzheimer’s disease: Design, synthesis, biological evaluation, and docking study. Bioorg Chem 2019; 87:506-515. [DOI: 10.1016/j.bioorg.2019.03.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/22/2022]
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16
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Santoni G, de Sousa J, de la Mora E, Dias J, Jean L, Sussman JL, Silman I, Renard PY, Brown RCD, Weik M, Baati R, Nachon F. Structure-Based Optimization of Nonquaternary Reactivators of Acetylcholinesterase Inhibited by Organophosphorus Nerve Agents. J Med Chem 2018; 61:7630-7639. [DOI: 10.1021/acs.jmedchem.8b00592] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gianluca Santoni
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France
| | - Julien de Sousa
- Université de Strasbourg, ICPEES, UMR CNRS 7515, 67087 Strasbourg, France
- Department of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
| | | | - José Dias
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France
| | - Ludovic Jean
- Université de Normandie, COBRA, UMR 6014, FR 3038, Université de Rouen, INSA de Rouen, CNRS, 76821 Mont-Saint-Aignan, France
| | - Joel L. Sussman
- Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Pierre-Yves Renard
- Université de Normandie, COBRA, UMR 6014, FR 3038, Université de Rouen, INSA de Rouen, CNRS, 76821 Mont-Saint-Aignan, France
| | - Richard C. D. Brown
- Department of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
| | - Martin Weik
- Université Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France
| | - Rachid Baati
- Université de Strasbourg, ICPEES, UMR CNRS 7515, 67087 Strasbourg, France
| | - Florian Nachon
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France
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17
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Zueva IV, Lushchekina SV, Masson P. Water structure changes in oxime-mediated reactivation process of phosphorylated human acetylcholinesterase. Biosci Rep 2018; 38:BSR20180609. [PMID: 29773682 PMCID: PMC6048214 DOI: 10.1042/bsr20180609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/15/2018] [Accepted: 05/15/2018] [Indexed: 11/17/2022] Open
Abstract
The role of water in oxime-mediated reactivation of phosphylated cholinesterases (ChEs) has been asked with recurrence. To investigate oximate water structure changes in this reaction, reactivation of paraoxon-inhibited human acetylcholinesterase (AChE) was performed by the oxime asoxime (HI-6) at different pH in the presence and absence of lyotropic salts: a neutral salt (NaCl), a strong chaotropic salt (LiSCN) and strong kosmotropic salts (ammonium sulphate and phosphate HPO42-). At the same time, molecular dynamic (MD) simulations of enzyme reactivation under the same conditions were performed over 100 ns. Reactivation kinetics showed that the low concentration of chaotropic salt up to 75 mM increased the percentage of reactivation of diethylphosphorylated AChE whereas kosmotropic salts lead only to a small decrease in reactivation. This indicates that water-breaker salt induces destructuration of water molecules that are electrostricted around oximate ions. Desolvation of oximate favors nucleophilic attack on the phosphorus atom. Effects observed at high salt concentrations (>100 mM) result either from salting-out of the enzyme by kosmotropic salts (phosphate and ammonium sulphate) or denaturing action of chaotropic LiSCN. MDs simulations of diethylphosphorylated hAChE complex with HI-6 over 100 ns were performed in the presence of 100 mM (NH4)2SO4 and 50 mM LiSCN. In the presence of LiSCN, it was found that protein and water have a higher mobility, i.e. water is less organized, compared with the ammonium sulphate system. LiSCN favors protein solvation (hydrophobic hydration) and breakage of elelectrostricted water molecules around of oximate ion. As a result, more free water molecules participated to reaction steps accompanying oxime-mediated dephosphorylation.
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Affiliation(s)
- Irina V Zueva
- A.E. Arbuzov Institute of Organic and Physical Chemistry of Russian Academy of Sciences, Arbuzov str. 8, Kazan 420088, Russia
| | - Sofya V Lushchekina
- N.M. Emanuel Institute of Biochemical Physics of Russian Academy of Sciences, Kosygina str. 4, Moscow 119334, Russia
| | - Patrick Masson
- Kazan Federal University, Pharmacology Laboratory, Kremlevskaya str, 18, Kazan 420008, Russia
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18
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Caliandro R, Pesaresi A, Cariati L, Procopio A, Oliverio M, Lamba D. Kinetic and structural studies on the interactions of Torpedo californica acetylcholinesterase with two donepezil-like rigid analogues. J Enzyme Inhib Med Chem 2018; 33:794-803. [PMID: 29651884 PMCID: PMC6009889 DOI: 10.1080/14756366.2018.1458030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Acetylcholinesterase inhibitors were introduced for the symptomatic treatment of Alzheimer’s disease (AD). Among the currently approved inhibitors, donepezil (DNP) is one of the most preferred choices in AD therapy. The X-ray crystal structures of Torpedo californica AChE in complex with two novel rigid DNP-like analogs, compounds 1 and 2, have been determined. Kinetic studies indicated that compounds 1 and 2 show a mixed-type inhibition against TcAChE, with Ki values of 11.12 ± 2.88 and 29.86 ± 1.12 nM, respectively. The DNP rigidification results in a likely entropy-enthalpy compensation with solvation effects contributing primarily to AChE binding affinity. Molecular docking evidenced the molecular basis for the binding of compounds 1 and 2 to the active site of β-secretase-1. Overall, these simplified DNP derivatives may represent new structural templates for the design of lead compounds for a more effective therapeutic strategy against AD by foreseeing a dual AChE and BACE-1 inhibitory activity.
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Affiliation(s)
- Rosanna Caliandro
- a Istituto di Cristallografia, Consiglio Nazionale delle Ricerche , Trieste , Italy
| | - Alessandro Pesaresi
- a Istituto di Cristallografia, Consiglio Nazionale delle Ricerche , Trieste , Italy
| | - Luca Cariati
- b Dipartimento di Scienze della Salute , Università degli Studi "Magna Graecia" , Catanzaro , Italy
| | - Antonio Procopio
- b Dipartimento di Scienze della Salute , Università degli Studi "Magna Graecia" , Catanzaro , Italy
| | - Manuela Oliverio
- b Dipartimento di Scienze della Salute , Università degli Studi "Magna Graecia" , Catanzaro , Italy
| | - Doriano Lamba
- a Istituto di Cristallografia, Consiglio Nazionale delle Ricerche , Trieste , Italy
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19
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Nascimento ÉCM, Oliva M, Andrés J. Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase. J Comput Aided Mol Des 2018; 32:607-622. [DOI: 10.1007/s10822-018-0114-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 03/20/2018] [Indexed: 11/27/2022]
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20
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Comparison of the Binding of Reversible Inhibitors to Human Butyrylcholinesterase and Acetylcholinesterase: A Crystallographic, Kinetic and Calorimetric Study. Molecules 2017; 22:molecules22122098. [PMID: 29186056 PMCID: PMC6149722 DOI: 10.3390/molecules22122098] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 12/17/2022] Open
Abstract
Acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) hydrolyze the neurotransmitter acetylcholine and, thereby, function as coregulators of cholinergic neurotransmission. Although closely related, these enzymes display very different substrate specificities that only partially overlap. This disparity is largely due to differences in the number of aromatic residues lining the active site gorge, which leads to large differences in the shape of the gorge and potentially to distinct interactions with an individual ligand. Considerable structural information is available for the binding of a wide diversity of ligands to AChE. In contrast, structural data on the binding of reversible ligands to BChE are lacking. In a recent effort, an inhibitor competition approach was used to probe the overlap of ligand binding sites in BChE. Here, we extend this study by solving the crystal structures of human BChE in complex with five reversible ligands, namely, decamethonium, thioflavin T, propidium, huprine, and ethopropazine. We compare these structures to equivalent AChE complexes when available in the protein data bank and supplement this comparison with kinetic data and observations from isothermal titration calorimetry. This new information now allows us to define the binding mode of various ligand families and will be of importance in designing specific reversible ligands of BChE that behave as inhibitors or reactivators.
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21
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Xu Y, Cheng S, Sussman JL, Silman I, Jiang H. Computational Studies on Acetylcholinesterases. Molecules 2017; 22:molecules22081324. [PMID: 28796192 PMCID: PMC6152020 DOI: 10.3390/molecules22081324] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/07/2017] [Accepted: 08/07/2017] [Indexed: 01/18/2023] Open
Abstract
Functions of biomolecules, in particular enzymes, are usually modulated by structural fluctuations. This is especially the case in a gated diffusion-controlled reaction catalyzed by an enzyme such as acetylcholinesterase. The catalytic triad of acetylcholinesterase is located at the bottom of a long and narrow gorge, but it catalyzes the extremely rapid hydrolysis of the neurotransmitter, acetylcholine, with a reaction rate close to the diffusion-controlled limit. Computational modeling and simulation have produced considerable advances in exploring the dynamical and conformational properties of biomolecules, not only aiding in interpreting the experimental data, but also providing insights into the internal motions of the biomolecule at the atomic level. Given the remarkably high catalytic efficiency and the importance of acetylcholinesterase in drug development, great efforts have been made to understand the dynamics associated with its functions by use of various computational methods. Here, we present a comprehensive overview of recent computational studies on acetylcholinesterase, expanding our views of the enzyme from a microstate of a single structure to conformational ensembles, strengthening our understanding of the integration of structure, dynamics and function associated with the enzyme, and promoting the structure-based and/or mechanism-based design of new inhibitors for it.
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Affiliation(s)
- Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China.
| | - Shanmei Cheng
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China.
| | - Joel L Sussman
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot 76100, Israel.
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Hualiang Jiang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai 201203, China.
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22
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Assessing the binding of cholinesterase inhibitors by docking and molecular dynamics studies. J Mol Graph Model 2017; 76:36-42. [PMID: 28711758 DOI: 10.1016/j.jmgm.2017.06.027] [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: 11/15/2016] [Revised: 06/24/2017] [Accepted: 06/26/2017] [Indexed: 11/20/2022]
Abstract
In this report we assessed by docking and molecular dynamics the binding mechanisms of three FDA-approved Alzheimer drugs, inhibitors of the enzyme acetylcholinesterase (AChE): donepezil, galantamine and rivastigmine. Dockings by the softwares Autodock-Vina, PatchDock and Plant reproduced the docked conformations of the inhibitor-enzyme complexes within 2Å of RMSD of the X-ray structure. Free-energy scores show strong affinity of the inhibitors for the enzyme binding pocket. Three independent Molecular Dynamics simulation runs indicated general stability of donepezil, galantamine and rivastigmine in their respective enzyme binding pocket (also referred to as gorge) as well as the tendency to form hydrogen bonds with the water molecules. The binding of rivastigmine in the Torpedo California AChE binding pocket is interesting as it eventually undergoes carbamylation and breaks apart according to the X-ray structure of the complex. Similarity search in the ZINC database and targeted docking on the gorge region of the AChE enzyme gave new putative inhibitor molecules with high predicted binding affinity, suitable for potential biophysical and biological assessments.
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23
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Silman I, Sussman JL. Recent developments in structural studies on acetylcholinesterase. J Neurochem 2017; 142 Suppl 2:19-25. [PMID: 28503857 DOI: 10.1111/jnc.13992] [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] [Indexed: 11/29/2022]
Abstract
This review focuses on several recent developments concerning structure-function relationships in vertebrate acetylcholinesterase. These include studies on high-resolution structures of human acetylcholinesterase and its complexes; the first crystal structure of a snake venom acetylcholinesterase, in which open and closed states of the 'back door' are visualized; a powerful algorithm for redesigning proteins for enhanced expression in prokaryotic systems, as applied to human acetylcholinesterase, which has hitherto been an intractable target; in situ implementation of 'click chemistry' in crystalline acetylcholinesterase, which yields novel insights into the steric and dynamic changes involved in the reaction within the active-site gorge; and a study that demonstrates the effect of crystallization conditions on ligand alignment within a protein complex, in this case the methylene blue-Torpedo californica acetylcholinesterase complex, which highlights the relevance of the precipitant employed to structure-based drug design. This is an article for the special issue XVth International Symposium on Cholinergic Mechanisms.
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Affiliation(s)
- Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Joel L Sussman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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24
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Castillo-Ordóñez WO, Tamarozzi ER, da Silva GM, Aristizabal-Pachón AF, Sakamoto-Hojo ET, Takahashi CS, Giuliatti S. Exploration of the Acetylcholinesterase Inhibitory Activity of Some Alkaloids from Amaryllidaceae Family by Molecular Docking In Silico. Neurochem Res 2017; 42:2826-2830. [DOI: 10.1007/s11064-017-2295-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 04/27/2017] [Accepted: 05/06/2017] [Indexed: 01/24/2023]
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25
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Nascimento ÉCM, Oliva M, Świderek K, Martins JBL, Andrés J. Binding Analysis of Some Classical Acetylcholinesterase Inhibitors: Insights for a Rational Design Using Free Energy Perturbation Method Calculations with QM/MM MD Simulations. J Chem Inf Model 2017; 57:958-976. [DOI: 10.1021/acs.jcim.7b00037] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Érica C. M. Nascimento
- Department
of Analytical and Physical Chemistry, Jaume I University, 12071 Castellón, Spain
- Institute
of Chemistry, University of Brasília, 70910-000, Brasília-DF, Brazil
| | - Mónica Oliva
- Department
of Analytical and Physical Chemistry, Jaume I University, 12071 Castellón, Spain
| | - Katarzyna Świderek
- Department
of Analytical and Physical Chemistry, Jaume I University, 12071 Castellón, Spain
- Institute
of Applied Radiation Chemistry, Lodz University of Technology, 90-924 Lodz, Poland
| | - João B. L. Martins
- Institute
of Chemistry, University of Brasília, 70910-000, Brasília-DF, Brazil
| | - Juan Andrés
- Department
of Analytical and Physical Chemistry, Jaume I University, 12071 Castellón, Spain
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26
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Driant T, Nachon F, Ollivier C, Renard PY, Derat E. On the Influence of the Protonation States of Active Site Residues on AChE Reactivation: A QM/MM Approach. Chembiochem 2017; 18:666-675. [PMID: 28106328 DOI: 10.1002/cbic.201600646] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Indexed: 11/10/2022]
Abstract
Acetylcholinesterase (AChE), an enzyme of the serine hydrolase superfamily, is a mediator of signal transmission at cholinergic synapses by catalyzing acetylcholine cleavage into acetate and choline. This enzyme is vulnerable to covalent inhibition by organophosphate compounds (like VX). Covalent inhibition of AChE does not revert spontaneously. Known reactivator compounds have limited action in restoring catalytic activity. QM/MM simulations of VX-inhibited AChE reactivation by pralidoxime (2-PAM), a classical reactivator, were performed. These afforded a broad view of the effect of protonation states of active-site residues, and provide evidence for the role of Glu202, which needs to be protonated for reactivation to occur. In situ deprotonation of 2-PAM for both protonation states of Glu202 showed that His447 is able to deprotonate 2-PAM with the assistance of Glu202. Because the active site of serine hydrolases is highly conserved, this work provides new insights on the interplay between the catalytic triad residues and this glutamate, newly identified as protonatable.
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Affiliation(s)
- Thomas Driant
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Florian Nachon
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, 1 Place Général Valérie André, 91223, Brétigny-sur-Orge Cédex, France
| | - Cyril Ollivier
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
| | - Pierre-Yves Renard
- Normandie Université, COBRA, UMR 6014 and FR 3038, Université Rouen-Normandie, INSA Rouen, CNRS, 1 rue Tesnière, 76821, Mont-Saint-Aignan Cedex, France
| | - Etienne Derat
- Sorbonne Universités, UPMC UNIV Paris 06, Institut Parisien de Chimie Moléculaire, UMR CNRS 8232, Case 229, 4 Place Jussieu, 75252, Paris Cedex 05, France
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27
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Ochoa R, Rodriguez CA, Zuluaga AF. Perspectives for the structure-based design of acetylcholinesterase reactivators. J Mol Graph Model 2016; 68:176-183. [PMID: 27450771 DOI: 10.1016/j.jmgm.2016.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/31/2016] [Accepted: 07/17/2016] [Indexed: 02/03/2023]
Abstract
Rational design of active molecules through structure-based methods has been gaining adepts during the last decades due to the wider availability of protein structures, most of them conjugated with relevant ligands. Acetylcholinesterase (AChE) is a molecular target with a considerable amount of data related to its sequence and 3-dimensional structure. In addition, there are structural insights about the mechanism of action of the natural substrate and drugs used in Alzheimer's disease, organophosphorus compounds, among others. We looked for AChE structural data useful for in silico design of potential interacting molecules. In particular, we focused on information regarding the design of ligands aimed to reactivate AChE catalytic activity. The structures of 178 AChE were annotated and categorized on different subsets according to the nature of the ligand, source organisms and experimental details. We compared sequence homology among the active site from Torpedo californica, Mus musculus and Homo sapiens with the latter two species having the closest relationship (88.9% identity). In addition, the mechanism of organophosphorus binding and the design of effective reactivators are reviewed. A curated data collection obtained with information from several sources was included for researchers working on the field. Finally, a molecular dynamics simulation with human AChE indicated that the catalytic pocket volume stabilizes around 600 Å(3), providing additional clues for drug design.
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Affiliation(s)
- Rodrigo Ochoa
- CIEMTO: Centro de Información y Estudio de Medicamentos y Tóxicos, Departamento de Farmacología y Toxicología, Facultad de Medicina, Universidad de Antioquia, Carrera 51D No. 62-42 Medellín, Colombia.
| | - Carlos A Rodriguez
- CIEMTO: Centro de Información y Estudio de Medicamentos y Tóxicos, Departamento de Farmacología y Toxicología, Facultad de Medicina, Universidad de Antioquia, Carrera 51D No. 62-42 Medellín, Colombia; GRIPE: Grupo Investigador de Problemas en Enfermedades Infecciosas, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
| | - Andres F Zuluaga
- CIEMTO: Centro de Información y Estudio de Medicamentos y Tóxicos, Departamento de Farmacología y Toxicología, Facultad de Medicina, Universidad de Antioquia, Carrera 51D No. 62-42 Medellín, Colombia; GRIPE: Grupo Investigador de Problemas en Enfermedades Infecciosas, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.
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28
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Goldenzweig A, Goldsmith M, Hill SE, Gertman O, Laurino P, Ashani Y, Dym O, Unger T, Albeck S, Prilusky J, Lieberman RL, Aharoni A, Silman I, Sussman JL, Tawfik DS, Fleishman SJ. Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability. Mol Cell 2016; 63:337-346. [PMID: 27425410 PMCID: PMC4961223 DOI: 10.1016/j.molcel.2016.06.012] [Citation(s) in RCA: 287] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/18/2016] [Accepted: 06/07/2016] [Indexed: 12/28/2022]
Abstract
Upon heterologous overexpression, many proteins misfold or aggregate, thus resulting in low functional yields. Human acetylcholinesterase (hAChE), an enzyme mediating synaptic transmission, is a typical case of a human protein that necessitates mammalian systems to obtain functional expression. We developed a computational strategy and designed an AChE variant bearing 51 mutations that improved core packing, surface polarity, and backbone rigidity. This variant expressed at ∼2,000-fold higher levels in E. coli compared to wild-type hAChE and exhibited 20°C higher thermostability with no change in enzymatic properties or in the active-site configuration as determined by crystallography. To demonstrate broad utility, we similarly designed four other human and bacterial proteins. Testing at most three designs per protein, we obtained enhanced stability and/or higher yields of soluble and active protein in E. coli. Our algorithm requires only a 3D structure and several dozen sequences of naturally occurring homologs, and is available at http://pross.weizmann.ac.il. A new computational method is used to stabilize five recalcitrant proteins Designed variants show higher expression and stability with unmodified function A designed human acetylcholinesterase variant expresses solubly in bacteria The method is fully automated and implemented on a webserver
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Affiliation(s)
- Adi Goldenzweig
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Moshe Goldsmith
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shannon E Hill
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Or Gertman
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 8410501, Israel
| | - Paola Laurino
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yacov Ashani
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel; Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Orly Dym
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Unger
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shira Albeck
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jaime Prilusky
- Bioinformatics & Biological Computing Unit, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
| | - Amir Aharoni
- Department of Life Sciences, Ben-Gurion University of the Negev, P.O.B. 653, Beer-Sheva 8410501, Israel
| | - Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Joel L Sussman
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel.
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29
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Ibrahim SS, Ndula M, Riveron JM, Irving H, Wondji CS. The P450 CYP6Z1 confers carbamate/pyrethroid cross-resistance in a major African malaria vector beside a novel carbamate-insensitive N485I acetylcholinesterase-1 mutation. Mol Ecol 2016; 25:3436-52. [PMID: 27135886 PMCID: PMC4950264 DOI: 10.1111/mec.13673] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 03/30/2016] [Accepted: 04/14/2016] [Indexed: 01/14/2023]
Abstract
Carbamates are increasingly used for vector control notably in areas with pyrethroid resistance. However, a cross‐resistance between these insecticides in major malaria vectors such as Anopheles funestus could severely limit available resistance management options. Unfortunately, the molecular basis of such cross‐resistance remains uncharacterized in An. funestus, preventing effective resistance management. Here, using a genomewide transcription profiling, we revealed that metabolic resistance through upregulation of cytochrome P450 genes is driving carbamate resistance. The P450s CYP6P9a,CYP6P9b and CYP6Z1 were the most upregulated detoxification genes in the multiple resistant mosquitoes. However, in silico docking simulations predicted CYP6Z1 to metabolize both pyrethroids and carbamates, whereas CYP6P9a and CYP6P9b were predicted to metabolize only the pyrethroids. Using recombinant enzyme metabolism and inhibition assays, we demonstrated that CYP6Z1 metabolizes bendiocarb and pyrethroids, whereas CYP6P9a and CYP6P9b metabolize only the pyrethroids. Other upregulated gene families in resistant mosquitoes included several cuticular protein genes suggesting a possible reduced penetration resistance mechanism. Investigation of the target‐site resistance in acetylcholinesterase 1 (ace‐1) gene detected and established the association between the new N485I mutation and bendiocarb resistance (odds ratio 7.3; P < 0.0001). The detection of multiple haplotypes in single mosquitoes after cloning suggested the duplication of ace‐1. A TaqMan genotyping of the N485I in nine countries revealed that the mutation is located only in southern Africa with frequency of 10–15% suggesting its recent occurrence. These findings will help in monitoring the spread and evolution of carbamate resistance and improve the design of effective resistance management strategies to control this malaria vector.
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Affiliation(s)
- Sulaiman S Ibrahim
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Miranda Ndula
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Jacob M Riveron
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Helen Irving
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
| | - Charles S Wondji
- Vector Biology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK
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30
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Allgardsson A, Berg L, Akfur C, Hörnberg A, Worek F, Linusson A, Ekström FJ. Structure of a prereaction complex between the nerve agent sarin, its biological target acetylcholinesterase, and the antidote HI-6. Proc Natl Acad Sci U S A 2016; 113:5514-9. [PMID: 27140636 PMCID: PMC4878515 DOI: 10.1073/pnas.1523362113] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Organophosphorus nerve agents interfere with cholinergic signaling by covalently binding to the active site of the enzyme acetylcholinesterase (AChE). This inhibition causes an accumulation of the neurotransmitter acetylcholine, potentially leading to overstimulation of the nervous system and death. Current treatments include the use of antidotes that promote the release of functional AChE by an unknown reactivation mechanism. We have used diffusion trap cryocrystallography and density functional theory (DFT) calculations to determine and analyze prereaction conformers of the nerve agent antidote HI-6 in complex with Mus musculus AChE covalently inhibited by the nerve agent sarin. These analyses reveal previously unknown conformations of the system and suggest that the cleavage of the covalent enzyme-sarin bond is preceded by a conformational change in the sarin adduct itself. Together with data from the reactivation kinetics, this alternate conformation suggests a key interaction between Glu202 and the O-isopropyl moiety of sarin. Moreover, solvent kinetic isotope effect experiments using deuterium oxide reveal that the reactivation mechanism features an isotope-sensitive step. These findings provide insights into the reactivation mechanism and provide a starting point for the development of improved antidotes. The work also illustrates how DFT calculations can guide the interpretation, analysis, and validation of crystallographic data for challenging reactive systems with complex conformational dynamics.
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Affiliation(s)
- Anders Allgardsson
- Department of CBRN Defence and Security, Swedish Defence Research Agency, SE-90182 Umea, Sweden
| | - Lotta Berg
- Department of Chemistry, Umeå University, SE-90187 Umea, Sweden
| | - Christine Akfur
- Department of CBRN Defence and Security, Swedish Defence Research Agency, SE-90182 Umea, Sweden
| | | | - Franz Worek
- Department of Toxicological Enzymology, Bundeswehr Institute of Pharmacology and Toxicology, 80937 Munich, Germany
| | - Anna Linusson
- Department of Chemistry, Umeå University, SE-90187 Umea, Sweden;
| | - Fredrik J Ekström
- Department of CBRN Defence and Security, Swedish Defence Research Agency, SE-90182 Umea, Sweden;
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31
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Dym O, Song W, Felder C, Roth E, Shnyrov V, Ashani Y, Xu Y, Joosten RP, Weiner L, Sussman JL, Silman I. The impact of crystallization conditions on structure-based drug design: A case study on the methylene blue/acetylcholinesterase complex. Protein Sci 2016; 25:1096-114. [PMID: 26990888 DOI: 10.1002/pro.2923] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/07/2016] [Indexed: 11/05/2022]
Abstract
Structure-based drug design utilizes apoprotein or complex structures retrieved from the PDB. >57% of crystallographic PDB entries were obtained with polyethylene glycols (PEGs) as precipitant and/or as cryoprotectant, but <6% of these report presence of individual ethyleneglycol oligomers. We report a case in which ethyleneglycol oligomers' presence in a crystal structure markedly affected the bound ligand's position. Specifically, we compared the positions of methylene blue and decamethonium in acetylcholinesterase complexes obtained using isomorphous crystals precipitated with PEG200 or ammonium sulfate. The ligands' positions within the active-site gorge in complexes obtained using PEG200 are influenced by presence of ethyleneglycol oligomers in both cases bound to W84 at the gorge's bottom, preventing interaction of the ligand's proximal quaternary group with its indole. Consequently, both ligands are ∼3.0Å further up the gorge than in complexes obtained using crystals precipitated with ammonium sulfate, in which the quaternary groups make direct π-cation interactions with the indole. These findings have implications for structure-based drug design, since data for ligand-protein complexes with polyethylene glycol as precipitant may not reflect the ligand's position in its absence, and could result in selecting incorrect drug discovery leads. Docking methylene blue into the structure obtained with PEG200, but omitting the ethyleneglycols, yields results agreeing poorly with the crystal structure; excellent agreement is obtained if they are included. Many proteins display features in which precipitants might lodge. It will be important to investigate presence of precipitants in published crystal structures, and whether it has resulted in misinterpreting electron density maps, adversely affecting drug design.
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Affiliation(s)
- Orly Dym
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, 76100, Israel.,Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Wanling Song
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai (22), China
| | - Clifford Felder
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Esther Roth
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Valery Shnyrov
- Department of Biochemistry and Molecular Biology, Universidad de Salamanca, Salamanca, 37007, Spain
| | - Yacov Ashani
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Yechun Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), Shanghai (22), China
| | - Robbie P Joosten
- Department of Biochemistry, Netherlands Cancer Institute, Amsterdam, CX, 1066, the Netherlands
| | - Lev Weiner
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Joel L Sussman
- Israel Structural Proteomics Center, Weizmann Institute of Science, Rehovot, 76100, Israel.,Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, 76100, Israel
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32
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Saeedi M, Golipoor M, Mahdavi M, Moradi A, Nadri H, Emami S, Foroumadi A, Shafiee A. Phthalimide-DerivedN-Benzylpyridinium Halides Targeting Cholinesterases: Synthesis and Bioactivity of New Potential Anti-Alzheimer's Disease Agents. Arch Pharm (Weinheim) 2016; 349:293-301. [DOI: 10.1002/ardp.201500425] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/28/2016] [Accepted: 02/01/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Mina Saeedi
- Medicinal Plants Research Center, Faculty of Pharmacy; Tehran University of Medical Sciences; Tehran Iran
- Persian Medicine and Pharmacy Research Center; Tehran University of Medical Sciences; Tehran Iran
| | - Maedeh Golipoor
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center; Tehran University of Medical Sciences; Tehran Iran
| | - Mohammad Mahdavi
- Drug Design and Development Research Center; Tehran University of Medical Sciences; Tehran Iran
| | - Alireza Moradi
- Faculty of Pharmacy, Department of Medicinal Chemistry; Shahid Sadoughi University of Medical Sciences; Yazd Iran
| | - Hamid Nadri
- Faculty of Pharmacy, Department of Medicinal Chemistry; Shahid Sadoughi University of Medical Sciences; Yazd Iran
| | - Saeed Emami
- Faculty of Pharmacy, Department of Medicinal Chemistry and Pharmaceutical Sciences Research Center; Mazandaran University of Medical Sciences; Sari Iran
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center; Tehran University of Medical Sciences; Tehran Iran
| | - Abbas Shafiee
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center; Tehran University of Medical Sciences; Tehran Iran
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33
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Synthesis and structure-activity relationship study of benzofuran-based chalconoids bearing benzylpyridinium moiety as potent acetylcholinesterase inhibitors. Eur J Med Chem 2015; 103:361-9. [PMID: 26363872 DOI: 10.1016/j.ejmech.2015.08.061] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/30/2015] [Accepted: 08/31/2015] [Indexed: 11/23/2022]
Abstract
A series of benzofuran-based chalconoids 6a-v were designed and synthesized as new potential AChE inhibitors. The in vitro assay of synthesized compounds 6a-v showed that most compounds had significant anti-AChE activity at micromolar or sub-micromolar levels. Among the tested compounds, 3-pyridinium derivative 6m bearing N-(2-bromobenzyl) moiety and 7-methoxy substituent on the benzofuran ring exhibited superior activity. This compound with IC₅₀ value of 0.027 μM was as potent as standard drug donepezil.
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34
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Statistical survey of the buried waters in the Protein Data Bank. Amino Acids 2015; 48:193-202. [PMID: 26315961 DOI: 10.1007/s00726-015-2064-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/29/2015] [Indexed: 12/18/2022]
Abstract
The structures of buried water molecules were studied in an ensemble of high-quality and non-redundant protein crystal structures. Buried water molecules were clustered and classified in lake-like clusters, which are completely isolated from the bulk solvent, and bay-like clusters, which are in contact with the bulk solvent through a surface water molecule. Buried water molecules are extremely common: lake-like clusters are found in 89 % of the protein crystal structures and bay-like clusters in 93 %. Clusters with only one water molecule are much more common than larger clusters. Both cluster types incline to be surrounded by loop residues, and to a minor extent by residues in extended secondary structure. Helical residues on the contrary do not tend to surround clusters of buried water molecules. One buried water molecule is found every 30-50 amino acid residues, depending on the secondary structures that are more abundant in the protein. Both main- and side-chain atoms are in contact with buried waters; they form four hydrogen bonds with the first water and 1-1.5 additional hydrogen bond for each additional water in the cluster. Consequently, buried water molecules appear to be firmly packed and rigid like the protein atoms. In this regard, it is remarkable to observe that prolines often surround water molecules buried in the protein interior. Interestingly, clusters of buried water molecules tend to be just beneath the protein surface. Moreover, water molecules tend to form a one-dimensional wire rather than more compact arrangements. This agrees with recent evidence of the mechanisms of solvent exchange between internal cavities and bulk solvent.
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35
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Arab S, Sadat-Ebrahimi SE, Mohammadi-Khanaposhtani M, Moradi A, Nadri H, Mahdavi M, Moghimi S, Asadi M, Firoozpour L, Pirali-Hamedani M, Shafiee A, Foroumadi A. Synthesis and Evaluation of Chroman-4-One Linked to N-Benzyl Pyridinium Derivatives as New Acetylcholinesterase Inhibitors. Arch Pharm (Weinheim) 2015; 348:643-9. [PMID: 26192069 DOI: 10.1002/ardp.201500149] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 06/17/2015] [Accepted: 06/23/2015] [Indexed: 01/20/2023]
Abstract
A novel series of chroman-4-one derivatives containing the N-benzyl pyridinium moiety were designed, synthesized, and evaluated for their acetylcholinesterase (AChE) inhibitory activities. Among the various synthesized compounds, (E)-1-(2,3-dibromobenzyl)-4-((7-ethoxy-4-oxochroman-3-ylidene)methyl)pyridinium bromide (8l) depicted the most potent anti-AChE activity (IC50 = 0.048 μM). In addition, the molecular modeling study allowed us to detect possible binding modes that are in full compliance with the observed results through in vitro experiments.
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Affiliation(s)
- Saman Arab
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed-Esmail Sadat-Ebrahimi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Mohammadi-Khanaposhtani
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Moradi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Hamid Nadri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Mahdavi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Setareh Moghimi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Asadi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Loghman Firoozpour
- Drug Design and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Morteza Pirali-Hamedani
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Shafiee
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, Iran.,Drug Design and Development Research Center, Tehran University of Medical Sciences, Tehran, Iran
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36
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Ivanir-Dabora H, Nimerovsky E, Madhu PK, Goldbourt A. Site-Resolved Backbone and Side-Chain Intermediate Dynamics in a Carbohydrate-Binding Module Protein Studied by Magic-Angle Spinning NMR Spectroscopy. Chemistry 2015; 21:10778-85. [DOI: 10.1002/chem.201500856] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 12/12/2022]
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37
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Chinnadurai RK, Saravanaraman P, Boopathy R. Understanding the molecular mechanism of aryl acylamidase activity of acetylcholinesterase - An in silico study. Arch Biochem Biophys 2015; 580:1-13. [PMID: 26072115 DOI: 10.1016/j.abb.2015.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 06/03/2015] [Accepted: 06/04/2015] [Indexed: 11/30/2022]
Abstract
Acetylcholinesterase (AChE) exhibits two different activities, namely esterase and aryl acylamidase (AAA). Unlike esterase, AAA activity of AChE is inhibited by the active site inhibitors while remaining unaffected by the peripheral anionic site inhibitors. This differential inhibitory pattern of active and peripheral anionic site inhibitors on the AAA activity remains unanswered. To answer this, we investigated the mechanism of binding and trafficking of AAA substrates using in silico tools. Molecular docking of serotonin and AAA substrates (o-nitroacetanilide, and o-nitrotrifluoroacetanilide,) onto AChE shows that these compounds bind at the side door of AChE. Thus, we conceived that the AAA substrates prefer the side door to reach the active site for their catalysis. Further, steered molecular dynamics simulations show that the force required for binding and trafficking of the AAA substrate through the side door is comparatively lesser than their dissociation (900kJ/mol/nm). Among the two substrates, o-nitrotrifluoroacetanilide required lesser force (380kJ/mol/nm) than o-nitroacetanilide the (550kJ/mol/nm) for its binding, thus validating o-nitrotrifluoroacetanilide as a better substrate. With these observations, we resolve that the AAA activity of AChE is mediated through its side door. Therefore, binding of PAS inhibitors at the main door of AChE remain ineffective against AAA activity.
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Affiliation(s)
- Raj Kumar Chinnadurai
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India
| | - Ponne Saravanaraman
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India
| | - Rathanam Boopathy
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India.
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Benzofuran-derived benzylpyridinium bromides as potent acetylcholinesterase inhibitors. Eur J Med Chem 2015; 93:196-201. [DOI: 10.1016/j.ejmech.2015.02.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/04/2015] [Accepted: 02/06/2015] [Indexed: 11/20/2022]
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Low molecular weight precursor applicable for Alzheimer disease drugs synthesis (AChE and BChE inhibition, BACE inhibition, antioxidant properties and in silico modulation). J Appl Biomed 2014. [DOI: 10.1016/j.jab.2014.01.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Ibrahim F, Andre C, Iutzeler A, Guillaume YC. Analysis of the activation of acetylcholinesterase by carbon nanoparticles using a monolithic immobilized enzyme microreactor: role of the water molecules in the active site gorge. J Enzyme Inhib Med Chem 2014; 28:1010-4. [PMID: 24020636 DOI: 10.3109/14756366.2012.705835] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A biochromatographic system was used to study the direct effect of carbon nanoparticles (CNPs) on the acetylcholinesterase (AChE) activity. The AChE enzyme was covalently immobilized on a monolithic CIM-disk via its NH2 residues. Our results showed an increase in the AChE activity in presence of CNPs. The catalytic constant (k(cat)) was increased while the Michaelis constant (K(m)) was slightly decreased. This indicated an increase in the enzyme efficiency with increase of the substrate affinity to the active site. The thermodynamic data of the activation mechanism of the enzyme, i.e. ΔH* and ΔS*, showed no change in the substrate interaction mechanism with the anionic binding site. The increase of the enthalpy (ΔH*) and the entropy (ΔS*) with decrease in the free energy of activation (Ea) was related to structural conformation change in the active site gorge. This affected the stability of water molecules in the active site gorge and facilitated water displacement by substrate for entering to the active site of the enzyme.
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Indolinone-based acetylcholinesterase inhibitors: synthesis, biological activity and molecular modeling. Eur J Med Chem 2014; 84:375-81. [PMID: 25036795 DOI: 10.1016/j.ejmech.2014.01.017] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 01/07/2014] [Accepted: 01/09/2014] [Indexed: 11/24/2022]
Abstract
A series of indolinone-based compounds bearing benzylpyridinium moiety was designed as dual-binding inhibitors of acetylcholinesterase (AChE). The target compounds 3a-u were synthesized by condensation of oxindole and pyridin-4-carbalehyde, and subsequent N-benzylation. The anti-cholinesterase activity evaluation of synthesized compounds revealed that most of them had very potent inhibitory activity against AChE, superior to standard drug donepezil. Particularly, 2-chlorobenzyl derivative 3c was the most potent compound against AChE with IC50 value of 0.44 nM, being 32-fold more potent than donepezil. Also, most of compounds were more potent than standard drug donepezil against butyrylcholinesterase (BuChE). Docking study revealed that the hydrophobic aromatic part (indoline) of representative compound 3c binds to the PAS and the N-benzylpyridinium residue binds to the CAS of AChE.
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Crystal structures of human cholinesterases in complex with huprine W and tacrine: elements of specificity for anti-Alzheimer's drugs targeting acetyl- and butyryl-cholinesterase. Biochem J 2013; 453:393-9. [PMID: 23679855 DOI: 10.1042/bj20130013] [Citation(s) in RCA: 294] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The multifunctional nature of Alzheimer's disease calls for MTDLs (multitarget-directed ligands) to act on different components of the pathology, like the cholinergic dysfunction and amyloid aggregation. Such MTDLs are usually on the basis of cholinesterase inhibitors (e.g. tacrine or huprine) coupled with another active molecule aimed at a different target. To aid in the design of these MTDLs, we report the crystal structures of hAChE (human acetylcholinesterase) in complex with FAS-2 (fasciculin 2) and a hydroxylated derivative of huprine (huprine W), and of hBChE (human butyrylcholinesterase) in complex with tacrine. Huprine W in hAChE and tacrine in hBChE reside in strikingly similar positions highlighting the conservation of key interactions, namely, π-π/cation-π interactions with Trp86 (Trp82), and hydrogen bonding with the main chain carbonyl of the catalytic histidine residue. Huprine W forms additional interactions with hAChE, which explains its superior affinity: the isoquinoline moiety is associated with a group of aromatic residues (Tyr337, Phe338 and Phe295 not present in hBChE) in addition to Trp86; the hydroxyl group is hydrogen bonded to both the catalytic serine residue and residues in the oxyanion hole; and the chlorine substituent is nested in a hydrophobic pocket interacting strongly with Trp439. There is no pocket in hBChE that is able to accommodate the chlorine substituent.
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Effects of viscosity and osmotic stress on the reaction of human butyrylcholinesterase with cresyl saligenin phosphate, a toxicant related to aerotoxic syndrome: kinetic and molecular dynamics studies. Biochem J 2013; 454:387-99. [DOI: 10.1042/bj20130389] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
CSP (cresyl saligenin phosphate) is an irreversible inhibitor of human BChE (butyrylcholinesterase) that has been involved in the aerotoxic syndrome. Inhibition under pseudo-first-order conditions is biphasic, reflecting a slow equilibrium between two enzyme states E and E′. The elementary constants for CSP inhibition of wild-type BChE and D70G mutant were determined by studying the dependence of inhibition kinetics on viscosity and osmotic pressure. Glycerol and sucrose were used as viscosogens. Phosphorylation by CSP is sensitive to viscosity and is thus strongly diffusion-controlled (kon≈108 M−1·min−1). Bimolecular rate constants (ki) are about equal to kon values, making CSP one of the fastest inhibitors of BChE. Sucrose caused osmotic stress because it is excluded from the active-site gorge. This depleted the active-site gorge of water. Osmotic activation volumes, determined from the dependence of ki on osmotic pressure, showed that water in the gorge of the D70G mutant is more easily depleted than that in wild-type BChE. This demonstrates the importance of the peripheral site residue Asp70 in controlling the active-site gorge hydration. MD simulations provided new evidence for differences in the motion of water within the gorge of wild-type and D70G enzymes. The effect of viscosogens/osmolytes provided information on the slow equilibrium E⇌E′, indicating that alteration in hydration of a key catalytic residue shifts the equilibrium towards E′. MD simulations showed that glycerol molecules that substitute for water molecules in the enzyme active-site gorge induce a conformational change in the catalytic triad residue His438, leading to the less reactive form E′.
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Structure-based search for new inhibitors of cholinesterases. Int J Mol Sci 2013; 14:5608-32. [PMID: 23478436 PMCID: PMC3634507 DOI: 10.3390/ijms14035608] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 01/31/2013] [Accepted: 02/28/2013] [Indexed: 01/14/2023] Open
Abstract
Cholinesterases are important biological targets responsible for regulation of cholinergic transmission, and their inhibitors are used for the treatment of Alzheimer’s disease. To design new cholinesterase inhibitors, of different structure-based design strategies was followed, including the modification of compounds from a previously developed library and a fragment-based design approach. This led to the selection of heterodimeric structures as potential inhibitors. Synthesis and biological evaluation of selected candidates confirmed that the designed compounds were acetylcholinesterase inhibitors with IC50 values in the mid-nanomolar to low micromolar range, and some of them were also butyrylcholinesterase inhibitors.
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de Aquino RAN, Modolo LV, Alves RB, de Fátima Â. Synthesis, kinetic studies and molecular modeling of novel tacrine dimers as cholinesterase inhibitors. Org Biomol Chem 2013; 11:8395-409. [DOI: 10.1039/c3ob41762j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Hu Y, Zhang J, Chandrashankra O, Ip FCF, Ip NY. Design, synthesis and evaluation of novel heterodimers of donepezil and huperzine fragments as acetylcholinesterase inhibitors. Bioorg Med Chem 2012; 21:676-83. [PMID: 23273608 DOI: 10.1016/j.bmc.2012.11.044] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 11/26/2012] [Accepted: 11/27/2012] [Indexed: 11/20/2022]
Abstract
Four series of novel heterodimers comprised of donepezil and huperzine A (HupA) fragments were designed, synthesized, and evaluated in search of potent acetylcholinesterase (AChE) inhibitors as potential therapeutic treatment for Alzheimer's disease. Heterodimers comprised of dimethoxyindanone (from donepezil), hupyridone (from HupA), and connected with a multimethylene linker, were identified as potent and selective inhibitors of AChE. Diastereomeric heterodimers (RS,S)-17b (with a tetramethylene linker) exhibited the highest potency of inhibition towards AChE with an IC(50) value of 9 nM and no detectable inhibitory effect on butyrylcholinesterase at 1mM.
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Affiliation(s)
- Yueqing Hu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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Haddad GL, Young SC, Heindel ND, Bornhop DJ, Flowers RA. Back-Scattering Interferometry: An Ultrasensitive Method for the Unperturbed Detection of Acetylcholinesterase-Inhibitor Interactions. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Haddad GL, Young SC, Heindel ND, Bornhop DJ, Flowers RA. Back-scattering interferometry: an ultrasensitive method for the unperturbed detection of acetylcholinesterase-inhibitor interactions. Angew Chem Int Ed Engl 2012; 51:11126-30. [PMID: 23037915 DOI: 10.1002/anie.201203640] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 08/24/2012] [Indexed: 11/12/2022]
Abstract
A series of inhibitors of acetylcholinesterase (AChE) have been screened by back-scattering interferometry (BSI). Enzyme levels as low as 100 pM (22,000 molecules of AChE) can be detected. This method can be used to screen for mixed AChE inhibitors, agents that have shown high efficacy against Alzheimer's disease, by detecting dual-binding interactions. E = enzyme, I = inhibitor, S = substrate.
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Galland N, Kone S, Le Questel JY. Mapping of the interaction sites of galanthamine: a quantitative analysis through pairwise potentials and quantum chemistry. J Comput Aided Mol Des 2012; 26:1111-26. [PMID: 22972560 DOI: 10.1007/s10822-012-9602-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 09/05/2012] [Indexed: 11/29/2022]
Abstract
A quantitative analysis of the interaction sites of the anti-Alzheimer drug galanthamine with molecular probes (water and benzene molecules) representative of its surroundings in the binding site of acetylcholinesterase (AChE) has been realized through pairwise potentials calculations and quantum chemistry. This strategy allows a full and accurate exploration of the galanthamine potential energy surface of interaction. Significantly different results are obtained according to the distances of approaches between the various molecular fragments and the conformation of the galanthamine N-methyl substituent. The geometry of the most relevant complexes has then been fully optimized through MPWB1K/6-31 + G(d,p) calculations, final energies being recomputed at the LMP2/aug-cc-pVTZ(-f) level of theory. Unexpectedly, galanthamine is found to interact mainly from its hydrogen-bond donor groups. Among those, CH groups in the vicinity of the ammonium group are prominent. The trends obtained provide rationales to the predilection of the equatorial orientation of the galanthamine N-methyl substituent for binding to AChE. The analysis of the interaction energies pointed out the independence between the various interaction sites and the rigid character of galanthamine. The comparison between the cluster calculations and the crystallographic observations in galanthamine-AChE co-crystals allows the validation of the theoretical methodology. In particular, the positions of several water molecules appearing as strongly conserved in galanthamine-AChE co-crystals are predicted by the calculations. Moreover, the experimental position and orientation of lateral chains of functionally important aminoacid residues are in close agreement with the ones predicted theoretically. Our study provides relevant information for a rational drug design of galanthamine based AChE inhibitors.
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Affiliation(s)
- Nicolas Galland
- UMR CNRS 6230, Chimie Et Interdisciplinarité: Synthèse, Analyse, Modélisation (CEISAM), UFR Sciences & Techniques, Université de Nantes, NANTES Cedex, France
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Brazzolotto X, Wandhammer M, Ronco C, Trovaslet M, Jean L, Lockridge O, Renard PY, Nachon F. Human butyrylcholinesterase produced in insect cells: huprine-based affinity purification and crystal structure. FEBS J 2012; 279:2905-16. [DOI: 10.1111/j.1742-4658.2012.08672.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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