1
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Kongkaew N, Hengphasatporn K, Shigeta Y, Rungrotmongkol T, Harada R. Preferential Door for Ligand Binding and Unbinding Pathways in Inhibited Human Acetylcholinesterase. J Phys Chem Lett 2024; 15:5696-5704. [PMID: 38768263 DOI: 10.1021/acs.jpclett.4c00514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Rising global population and increased food demands have resulted in the increased use of organophosphate pesticides (OPs), leading to toxin accumulation and transmission to humans. Pralidoxime (2-PAM), an FDA-approved drug, serves as an antidote for OP therapy. However, the atomic-level detoxification mechanisms regarding the design of novel antidotes remain unclear. This is the first study to examine the binding and unbinding pathways of 2-PAM to human acetylcholinesterase (HuAChE) through three identified doors using an enhanced sampling method called ligand-binding parallel cascade selection molecular dynamics (LB-PaCS-MD). Remarkably, LB-PaCS-MD could identify a predominant in-line binding mechanism through the acyl door at 63.79% ± 6.83%, also implicating it in a potential unbinding route (90.14% ± 4.22%). Interestingly, crucial conformational shifts in key residues, W86, Y341, and Y449, and the Ω loop significantly affect door dynamics and ligand binding modes. The LB-PaCS-MD technique can study ligand-binding pathways, thereby contributing to the design of antidotes and covalent drugs.
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Affiliation(s)
- Nalinee Kongkaew
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kowit Hengphasatporn
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ryuhei Harada
- Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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2
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Radić Z. Connectivity between surface and interior in catalytic subunits of acetylcholinesterases inferred from their X-ray structures. J Neurochem 2024; 168:386-396. [PMID: 36892323 PMCID: PMC10491739 DOI: 10.1111/jnc.15802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/10/2023]
Abstract
Catalytic activity and function of acetylcholinesterase (AChE; EC 3.1.1.7) have been recognized and studied for over a century and its quaternary and primary structures for about half a century, and its tertiary structure has been known for about 33 years. Clear understanding of relationships between the structure and the function is still pending for this enzyme. Hundreds of crystallographic, static snapshots of AChEs from different sources reveal largely one general backbone conformation with narrow entry into the active center gorge, tightly fit to accept one acetylcholine (ACh) molecule, in contrast to its high catalytic turnover. This short review of available X-ray structures of AChEs from electric ray Torpedo californica, mouse and human, finds some limited, yet consistent deviations in conformations of selected secondary structure elements of AChE relevant for its function. The observed conformational diversity of the acyl pocket loop of AChE, unlike the large Ω-loop, appears consistent with structurally dynamic INS data and solution-based SAXS experiments to explain its dominant role in controlling the size of the active center gorge opening, as well as connectivity between the immediate surroundings of the buried active Ser, and catalytically relevant sites on the AChE surface.
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Affiliation(s)
- Zoran Radić
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, California, USA
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3
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Jiang S, Gu Q, Yu X. Detection of insecticides by Tetronarce californica acetylcholinesterase via expression and in silico analysis. Appl Microbiol Biotechnol 2023; 107:7657-7671. [PMID: 37831186 DOI: 10.1007/s00253-023-12780-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/16/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023]
Abstract
The acetylcholinesterase (AChE) is involved in termination of synaptic transmission at cholinergic synapses and plays a vital role in the insecticide detection and inhibitor screening. Here, we report the heterologous expression of an AChE from Tetronarce californica (TcA) in Escherichia coli (E. coli) as a soluble active protein. TcA was immobilized in calcium alginate beads; the morphology, biochemical properties, and insecticide detection performance of free and immobilized TcA were characterized. Moreover, we used sequence, structure-based approaches, and molecular docking to investigate structural and functional characterization of TcA. The results showed that TcA exhibited a specific activity of 102 U/mg, with optimal activity at pH 8.0 and 30 °C. Immobilized TcA demonstrated superior thermal stability, pH stability, and storage stability compared to the free enzyme. The highest sensitivity of free TcA was observed with trichlorfon, whereas immobilized TcA showed reduced IC50 values towards tested insecticides by 3 to 180-fold. Molecular docking analysis revealed the interaction of trichlorfon, acephate, isoprocarb, λ-cyhalothrin, and fenpropathrin in the active site gorge of TcA, particularly mediated through the formation of hydrogen bonds and π-π stacking. Therefore, TcA expressed heterologously in E. coli is a promising candidate for applications in food safety and environmental analysis. KEY POINTS: • T. californica AChE was expressed solubly in prokaryotic system. • The biochemical properties of free/immobilized enzyme were characterized. • The sensitivity of enzyme to insecticides was evaluated in vitro and in silico.
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Affiliation(s)
- Shuoqi Jiang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Li-Hu Road, Bin-Hu District, Wuxi, Jiangsu, China
| | - Qiuya Gu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Li-Hu Road, Bin-Hu District, Wuxi, Jiangsu, China
| | - Xiaobin Yu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Li-Hu Road, Bin-Hu District, Wuxi, Jiangsu, China.
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4
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Mu X, Yuan S, Zhang D, Lai R, Liao C, Li G. Selective modulation of alkali metal ions on acetylcholinesterase. Phys Chem Chem Phys 2023; 25:30308-30318. [PMID: 37934509 DOI: 10.1039/d3cp02887a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Acetylcholinesterase (AChE) is an important hydrolase in cholinergic synapses and a candidate target in the treatment of Alzheimer's disease. The lithium treatment widely used in neurological disorders can alter the AChE activity, yet the underlying mechanism of how the ion species regulate the enzymatic activity remains unclear. In this work, we performed combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations and well-tempered metadynamics to understand the modulation of human AChE (hAChE) activity using three alkali metal ions (Li+, Na+, and K+) in different concentrations. Our simulations show that the binding affinity and catalytic activity are affected by different ion species through allosteric ion coordination geometries on the hAChE complex and distant electrostatic screening effect. A Li+ cluster involving D330, E393, and D397 residues and three Li+ ions was found to be highly conserved and can be critical to the enzyme activity. Binding energy calculations indicate that the electrostatic screening from allosterically bound cations can affect the key residues at the catalytic site and active-site gorge, including E199. Furthermore, an increase in ion concentration can lead to lower reactivity, especially for Li+ ions, which exhibit more cation-hAChE contacts than Na+ and K+. The selective ion binding and their preferred modulation on hAChE are highly related to ion species. This work provides a molecular perspective on selective modulation by different ion species of the enzyme catalytic processes.
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Affiliation(s)
- Xia Mu
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Shengwei Yuan
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
- University of Chinese Academy of Sciences, Beijing, China
| | - Dinglin Zhang
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Rui Lai
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Chenyi Liao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
| | - Guohui Li
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
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5
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Ramírez-Ruiz AM, Ávila-Cossío ME, Estolano-Cobián A, Cornejo-Bravo JM, Martinez AL, Córdova-Guerrero I, Cota-Ramírez BR, Carranza-Ambriz KP, Rivero IA, Serrano-Medina A. Inhibitory Activity of 4-Benzylidene Oxazolones Derivatives of Cinnamic Acid on Human Acetylcholinesterase and Cognitive Improvements in a Mouse Model. Molecules 2023; 28:7392. [PMID: 37959813 PMCID: PMC10649417 DOI: 10.3390/molecules28217392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/15/2023] Open
Abstract
We synthesized seven (Z)-benzylidene-2-(E)-styryloxazol-5(4H)-ones derivatives of cinnamic acid and evaluated the ability of these compounds to inhibit human acetylcholinesterase (hAChE). The most potent compound was evaluated for cognitive improvement in short-term memory. The seven compounds reversibly inhibited the hAChE between 51 and 75% at 300 μM, showed an affinity (Ki) from 2 to 198 μM, and an IC50 from 9 to 246 μM. Molecular docking studies revealed that all binding moieties are involved in the non-covalent interactions with hAChE for all compounds. In addition, in silico pharmacokinetic analysis was carried out to predict the compounds' blood-brain barrier (BBB) permeability. The most potent inhibitor of hAChE significantly improved cognitive impairment in a modified Y-maze test (5 μmol/kg) and an Object Recognition Test (10 μmol/kg). Our results can help the rational design of hAChE inhibitors to work as potential candidates for treating cognitive disorders.
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Affiliation(s)
- Alma Marisol Ramírez-Ruiz
- Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico (A.L.M.); (K.P.C.-A.)
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico; (A.E.-C.); (J.M.C.-B.); (I.C.-G.); (B.R.C.-R.)
| | - Martha Elena Ávila-Cossío
- Centro de Graduados e Investigación en Química, Tecnológico Nacional de Mexico/Instituto Tecnológico de Tijuana, Tijuana 22510, BC, Mexico;
| | - Arturo Estolano-Cobián
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico; (A.E.-C.); (J.M.C.-B.); (I.C.-G.); (B.R.C.-R.)
| | - José Manuel Cornejo-Bravo
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico; (A.E.-C.); (J.M.C.-B.); (I.C.-G.); (B.R.C.-R.)
| | - Ana Laura Martinez
- Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico (A.L.M.); (K.P.C.-A.)
| | - Iván Córdova-Guerrero
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico; (A.E.-C.); (J.M.C.-B.); (I.C.-G.); (B.R.C.-R.)
| | - Bibiana Roselly Cota-Ramírez
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico; (A.E.-C.); (J.M.C.-B.); (I.C.-G.); (B.R.C.-R.)
| | - Krysta Paola Carranza-Ambriz
- Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico (A.L.M.); (K.P.C.-A.)
| | - Ignacio A. Rivero
- Centro de Graduados e Investigación en Química, Tecnológico Nacional de Mexico/Instituto Tecnológico de Tijuana, Tijuana 22510, BC, Mexico;
| | - Aracely Serrano-Medina
- Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico (A.L.M.); (K.P.C.-A.)
- Facultad de Ciencias Químicas e Ingeniería, Universidad Autónoma de Baja California, Calzada Universidad 14418, Parque Industrial Internacional, Tijuana 22424, BC, Mexico; (A.E.-C.); (J.M.C.-B.); (I.C.-G.); (B.R.C.-R.)
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6
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Richmond V, Falcone BN, Maier MS, Arroyo Máñez P. Putting the Puzzle Together To Get the Whole Picture: Molecular Basis of the Affinity of Two Steroid Derivatives to Acetylcholinesterase. ACS OMEGA 2023; 8:25610-25622. [PMID: 37483177 PMCID: PMC10357547 DOI: 10.1021/acsomega.3c03749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 06/14/2023] [Indexed: 07/25/2023]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that has no cure because its etiology is still unknown, and its main treatment is the administration of acetylcholinesterase (AChE) inhibitors. The study of the mechanism of action of this family of compounds is critical for the design of new more potent and specific inhibitors. In this work, we study the molecular basis of an uncompetitive inhibitor (compound 1, 2β, 3α-dihydroxy-5α-cholestan-6-one disulfate), which we have proved to be a peripheral anionic site (PAS)-binding AChE inhibitor. The pipeline designed in this work is key to the development of other PAS inhibitors that not only inhibit the esterase action of the enzyme but could also modulate the non-cholinergic functions of AChE linked to the process of amylogenesis. Our studies showed that 1 inhibits the enzyme not simply by blocking the main gate but by an allosteric mechanism. A detailed and careful analysis of the ligand binding position and the protein dynamics, particularly regarding their secondary gates and active site, was necessary to conclude this. The same analysis was executed with an inactive analogue (compound 2, 2β, 3α-dihydroxy-5α-cholestan-6-one). Our first computational results showed no differences in affinity to AChE between both steroids, making further analysis necessary. This work highlights the variables to be considered and develops a refined methodology, for the successful design of new potent dual-action drugs for AD, particularly PAS inhibitors, an attractive strategy to combat AD.
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Affiliation(s)
- Victoria Richmond
- Facultad
de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad
de Microanálisis y Métodos Físicos aplicados
a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Pabellón 2 de Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Bruno N. Falcone
- Facultad
de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad
de Microanálisis y Métodos Físicos aplicados
a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Pabellón 2 de Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Marta S. Maier
- Facultad
de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires C1428EGA, Argentina
- Unidad
de Microanálisis y Métodos Físicos aplicados
a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Pabellón 2 de Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
| | - Pau Arroyo Máñez
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Doctor Moliner 50, Burjassot, Valencia 46100, Spain
- Departamento
de Química Orgánica, Universitat
de València, Doctor Moliner 50, Burjassot, Valencia 46100, Spain
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7
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Dolezal R. Accuracy and precision of binding free energy prediction for a tacrine related lead inhibitor of acetylcholinesterase with an arsenal of supercomputerized molecular modelling methods: a comparative study. J Biomol Struct Dyn 2022; 40:11291-11319. [PMID: 34323654 DOI: 10.1080/07391102.2021.1957716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Nowadays, advanced computational chemistry methods offer various strategies for revealing prospective hit structures in drug development essentially through accurate binding free energy predictions. After the era of molecular docking and quantitative structure-activity relationships, much interest has been lately oriented to perturbed molecular dynamic approaches like replica exchange with solute tempering and free energy perturbation (REST/FEP) and the potential of the mean force with adaptive biasing and accelerated weight histograms (PMF/AWH). Both of these receptor-based techniques can exploit exascale CPU&GPU supercomputers to achieve high throughput performance. In this fundamental study, we have compared the predictive power of a panel of supercomputerized molecular modelling methods to distinguish the major binding modes and the corresponding binding free energies of a promising tacrine related potential antialzheimerics in human acetylcholinesterase. The binding free energies were estimated using flexible molecular docking, molecular mechanics/generalized Born surface area/Poisson-Boltzmann surface area (MM/GBSA/PBSA), transmutation REST/FEP with 12 x 5 ns/λ windows, annihilation FEP with 20 x 5 ns/λ steps, PMF with weight histogram analysis method (WHAM) and 40 x 5 ns samples, and PMF/AWH with 10 x 100 ns replicas. Confrontation of the classical approaches such as canonical molecular dynamics and molecular docking with alchemical calculations and steered molecular dynamics enabled us to show how large errors in ΔG predictions can be expected if these in silico methods are employed in the elucidation of a common case of enzyme inhibition.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rafael Dolezal
- Department of Chemistry, Faculty of Science, University of Hradec Kralove, Hradec Kralove, Czech Republic.,Biomedical Research Center, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
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8
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Inhibitory Action of Omega-3 and Omega-6 Fatty Acids Alpha-Linolenic, Arachidonic and Linoleic acid on Human Erythrocyte Acetylcholinesterase. Protein J 2022; 42:96-103. [PMID: 36538202 DOI: 10.1007/s10930-022-10088-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Acetylcholinesterase (AChE, E.C. 3.1.1.7) termed as the true cholinesterase functions to end cholinergic transmission at synapses. Due to its diverse expression in non-neural tissues such as erythrocytes and bones along with its various molecular forms, researchers seek a non-classical role for this protein. Here, the inhibitory action of unsaturated 18 carbon fatty acids linoleic acid and alpha-linolenic acid and 20 carbon fatty acid arachidonic acid on AChE were investigated. Enzyme activity was measured in kinetic assay method according to Ellman assay utilizing acetylthiocholine. Analysis of the activity data revealed that among the fatty acids examined the IC50 values differed according to the length of the fatty acid and the number of the double bonds. Arachidonic acid, a 20-carbon fatty acid with 4 unsaturated bonds (20:4 n-6, cis 5,8,11,14) displayed an IC50 value of 2.78 µM and Ki value of 396.35 µM. Linoleic acid, an essential 18-carbon fatty acid (18:2 n-6, cis 9,12) had an IC50 value of 7.95 µM and Ki value of 8027.55 µM. The IC50 value of alpha-linolenic acid, 18-carbon fatty acid (18:3 n-3, cis-9,12,15) was found as 179.11 µM. Analysis of the data fit the inhibition mechanism for linoleic, alpha-linolenic and arachidonic acid as mixed-type; non-competitive. Molecular docking complied with these results yielding the best score for arachidonic acid. The alkenyl chain of the fatty acids predictably reached to the catalytic site while the carboxylate strongly interacted with the peripheric anionic site.
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Hormozi Jangi SR, Akhond M. Introducing a covalent thiol-based protected immobilized acetylcholinesterase with enhanced enzymatic performances for biosynthesis of esters. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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10
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Nguyen HL, Thai NQ, Li MS. Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution. J Chem Theory Comput 2022; 18:3860-3872. [PMID: 35512104 PMCID: PMC9202309 DOI: 10.1021/acs.jctc.1c01158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
Steered molecular
dynamics (SMD) simulation is a powerful method
in computer-aided drug design as it can be used to access the relative
binding affinity with high precision but with low computational cost.
The success of SMD depends on the choice of the direction along which
the ligand is pulled from the receptor-binding site. In most simulations,
the unidirectional pathway was used, but in some cases, this choice
resulted in the ligand colliding with the complex surface of the exit
tunnel. To overcome this difficulty, several variants of SMD with
multidirectional pulling have been proposed, but they are not completely
devoid of disadvantages. Here, we have proposed to determine the direction
of pulling with a simple scoring function that minimizes the receptor–ligand
interaction, and an optimization algorithm called differential evolution
is used for energy minimization. The effectiveness of our protocol
was demonstrated by finding expulsion pathways of Huperzine A and
camphor from the binding site of Torpedo California acetylcholinesterase
and P450cam proteins, respectively, and comparing them with the previous
results obtained using memetic sampling and random acceleration molecular
dynamics. In addition, by applying this protocol to a set of ligands
bound with LSD1 (lysine specific demethylase 1), we obtained a much
higher correlation between the work of pulling force and experimental
data on the inhibition constant IC50 compared to that obtained using
the unidirectional approach based on minimal steric hindrance.
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Affiliation(s)
- Hoang Linh Nguyen
- Life Science Lab, Institute for Computational Science and Technology, QuangTrung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 729110, Vietnam.,Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 740500, Vietnam.,Vietnam National University, Ho Chi Minh City 71300, Vietnam
| | - Nguyen Quoc Thai
- Life Science Lab, Institute for Computational Science and Technology, QuangTrung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 729110, Vietnam.,Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap 81100, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, Warsaw 02-668, Poland
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Kim S, Yoon KA, Cho S, Lee SH. Molecular and kinetic characterization of two acetylcholinesterases with particular focus on the roles of two amino acid substitutions (Y390N and F392W) in Bemisia tabaci. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 182:105039. [PMID: 35249657 DOI: 10.1016/j.pestbp.2022.105039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Two acetylcholinesterases (AChEs) are present in Bemisia tabaci (BtAChE1 and BtAChE2). A conserved AChE mutation conferring organophosphate (OP) resistance (F392W in BtAChE1) is saturated in field populations despite its potential fitness cost, and a highly conserved amino acid residue forming the backdoor of AChE is substituted with a unique amino acid (Y390N in BtAChE1) in B. tabaci. Thus, the roles and relationships of the two amino acid substitutions in the evolutionary adaptation of B. tabaci remain to be elucidated, and little information is available on the catalytic and molecular properties of BtAChE1 and BtAChE2. To determine which AChE is a more relevant target of OPs and carbamates, the molecular and kinetic properties of BtAChE1 and BtAChE2 were investigated. Both BtAChE1 and BtAChE2 were exclusively expressed in head and thorax but not in abdomen, bound to the membrane via GPI anchoring, and present as dimeric forms. Soluble monomeric form was detected only in BtAChE2. The catalytic activity of baculovirus-expressed BtAChE1 was 19.5-fold higher than that of BtAChE2. The inhibition assay revealed that the F392W mutation in BtAChE1 enhanced resistance to OPs. The artificial substitution of N390 (wild form) to Y (putative ancient form) led to reduced catalytic efficiency and increased inhibition by glycoalkaloids, suggesting that the Y390N substitution in BtAChE1 may have been required for Solanaceae host adaptation. BtAChE1 was proven to function as a main catalytic enzyme for ACh hydrolysis, thus being the main target of OPs and carbamates.
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Affiliation(s)
- Sanghyeon Kim
- Research Institute of Agriculture and Life Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Kyungjae Andrew Yoon
- Research Institute of Agriculture and Life Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - SuSie Cho
- Entomology Program, Department of Agricultural Biotechnology, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Si Hyeock Lee
- Entomology Program, Department of Agricultural Biotechnology, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea.
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12
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Walczak-Nowicka ŁJ, Herbet M. Acetylcholinesterase Inhibitors in the Treatment of Neurodegenerative Diseases and the Role of Acetylcholinesterase in their Pathogenesis. Int J Mol Sci 2021; 22:9290. [PMID: 34502198 PMCID: PMC8430571 DOI: 10.3390/ijms22179290] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 12/21/2022] Open
Abstract
Acetylcholinesterase (AChE) plays an important role in the pathogenesis of neurodegenerative diseases by influencing the inflammatory response, apoptosis, oxidative stress and aggregation of pathological proteins. There is a search for new compounds that can prevent the occurrence of neurodegenerative diseases and slow down their course. The aim of this review is to present the role of AChE in the pathomechanism of neurodegenerative diseases. In addition, this review aims to reveal the benefits of using AChE inhibitors to treat these diseases. The selected new AChE inhibitors were also assessed in terms of their potential use in the described disease entities. Designing and searching for new drugs targeting AChE may in the future allow the discovery of therapies that will be effective in the treatment of neurodegenerative diseases.
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Affiliation(s)
| | - Mariola Herbet
- Chair and Department of Toxicology, Faculty of Pharmacy, Medical University of Lublin, Jaczewskiego 8bStreet, 20-090 Lublin, Poland;
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13
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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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14
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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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15
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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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16
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Hrvat NM, Kovarik Z. Counteracting poisoning with chemical warfare nerve agents. Arh Hig Rada Toksikol 2020; 71:266-284. [PMID: 33410774 PMCID: PMC7968514 DOI: 10.2478/aiht-2020-71-3459] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/01/2020] [Accepted: 11/01/2020] [Indexed: 12/14/2022] Open
Abstract
Phosphylation of the pivotal enzyme acetylcholinesterase (AChE) by nerve agents (NAs) leads to irreversible inhibition of the enzyme and accumulation of neurotransmitter acetylcholine, which induces cholinergic crisis, that is, overstimulation of muscarinic and nicotinic membrane receptors in the central and peripheral nervous system. In severe cases, subsequent desensitisation of the receptors results in hypoxia, vasodepression, and respiratory arrest, followed by death. Prompt action is therefore critical to improve the chances of victim's survival and recovery. Standard therapy of NA poisoning generally involves administration of anticholinergic atropine and an oxime reactivator of phosphylated AChE. Anticholinesterase compounds or NA bioscavengers can also be applied to preserve native AChE from inhibition. With this review of 70 years of research we aim to present current and potential approaches to counteracting NA poisoning.
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Affiliation(s)
| | - Zrinka Kovarik
- Institute for Medical Research and Occupational Health, Zagreb, Croatia
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17
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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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18
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Bouknight KD, Jurkouich KM, Compton JR, Khavrutskii IV, Guelta MA, Harvey SP, Legler PM. Structural and kinetic evidence of aging after organophosphate inhibition of human Cathepsin A. Biochem Pharmacol 2020; 177:113980. [PMID: 32305437 DOI: 10.1016/j.bcp.2020.113980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/14/2020] [Indexed: 11/30/2022]
Abstract
Human Cathepsin A (CatA) is a lysosomal serine carboxypeptidase of the renin-angiotensin system (RAS) and is structurally similar to acetylcholinesterase (AChE). CatA can remove the C-terminal amino acids of endothelin I, angiotensin I, Substance P, oxytocin, and bradykinin, and can deamidate neurokinin A. Proteomic studies identified CatA and its homologue, SCPEP1, as potential targets of organophosphates (OP). CatA could be stably inhibited by low µM to high nM concentrations of racemic sarin (GB), soman (GD), cyclosarin (GF), VX, and VR within minutes to hours at pH 7. Cyclosarin was the most potent with a kinetically measured dissociation constant (KI) of 2 µM followed by VR (KI = 2.8 µM). Bimolecular rate constants for inhibition by cyclosarin and VR were 1.3 × 103 M-1sec-1 and 1.2 × 103 M-1sec-1, respectively, and were approximately 3-orders of magnitude lower than those of human AChE indicating slower reactivity. Notably, both AChE and CatA bound diisopropylfluorophosphate (DFP) comparably and had KIDFP = 13 µM and 11 µM, respectively. At low pH, greater than 85% of the enzyme spontaneously reactivated after OP inhibition, conditions under which OP-adducts of cholinesterases irreversibly age. At pH 6.5 CatA remained stably inhibited by GB and GF and <10% of the enzyme spontaneously reactivated after 200 h. A crystal structure of DFP-inhibited CatA was determined and contained an aged adduct. Similar to AChE, CatA appears to have a "backdoor" for product release. CatA has not been shown previously to age. These results may have implications for: OP-associated inflammation; cardiovascular effects; and the dysregulation of RAS enzymes by OP.
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Affiliation(s)
- Kayla D Bouknight
- Hampton University, 100 E Queen St, Hampton, VA 23668, United States
| | - Kayla M Jurkouich
- Case Western Reserve University, Dept. of Biomedical Engineering, Cleveland, 10900 Euclid Avenue, OH 44106, United States
| | - Jaimee R Compton
- U.S. Naval Research Laboratory, 4555 Overlook Ave., Washington, DC 20375, United States
| | - Ilja V Khavrutskii
- Uniformed Services University, Armed Forces Radiobiology Research Institute, 4301 Jones Bridge Rd., Bethesda, MD 20889-5648, United States
| | - Mark A Guelta
- U.S. Army Combat Capabilities and Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, MD 21010, United States
| | - Steven P Harvey
- U.S. Army Combat Capabilities and Development Command Chemical Biological Center, 5183 Blackhawk Road, Aberdeen Proving Ground, MD 21010, United States
| | - Patricia M Legler
- U.S. Naval Research Laboratory, 4555 Overlook Ave., Washington, DC 20375, United States.
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19
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Nachon F, Rosenberry TL, Silman I, Sussman JL. A Second Look at the Crystal Structures of Drosophila melanogaster Acetylcholinesterase in Complex with Tacrine Derivatives Provides Insights Concerning Catalytic Intermediates and the Design of Specific Insecticides. Molecules 2020; 25:molecules25051198. [PMID: 32155891 PMCID: PMC7179448 DOI: 10.3390/molecules25051198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/03/2020] [Accepted: 03/04/2020] [Indexed: 11/16/2022] Open
Abstract
Over recent decades, crystallographic software for data processing and structure refinement has improved dramatically, resulting in more accurate and detailed crystal structures. It is, therefore, sometimes valuable to have a second look at "old" diffraction data, especially when earlier interpretation of the electron density maps was rather difficult. Here, we present updated crystal structures of Drosophila melanogaster acetylcholinesterase (DmAChE) originally published in [Harel et al., Prot Sci (2000) 9:1063-1072], which reveal features previously unnoticed. Thus, previously unmodeled density in the native active site can be interpreted as stable acetylation of the catalytic serine. Similarly, a strong density in the DmAChE/ZA complex originally attributed to a sulfate ion is better interpreted as a small molecule that is covalently bound. This small molecule can be modeled as either a propionate or a glycinate. The complex is reminiscent of the carboxylate butyrylcholinesterase complexes observed in crystal structures of human butyrylcholinesterases from various sources, and demonstrates the remarkable ability of cholinesterases to stabilize covalent complexes with carboxylates. A very strong peak of density (10 σ) at covalent distance from the Cβ of the catalytic serine is present in the DmAChE/ZAI complex. This can be undoubtedly attributed to an iodine atom, suggesting an unanticipated iodo/hydroxyl exchange between Ser238 and the inhibitor, possibly driven by the intense X-ray irradiation. Finally, the binding of tacrine-derived inhibitors, such as ZA (1DX4) or the iodinated analog, ZAI (1QON) results in the appearance of an open channel that connects the base of the active-site gorge to the solvent. This channel, which arises due to the absence of the conserved tyrosine present in vertebrate cholinesterases, could be exploited to design inhibitors specific to insect cholinesterases. The present study demonstrates that updated processing of older diffraction images, and the re-refinement of older diffraction data, can produce valuable information that could not be detected in the original analysis, and strongly supports the preservation of the diffraction images in public data banks.
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Affiliation(s)
- Florian Nachon
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France
- Correspondence: ; Tel.: +33-178-65-1877
| | - Terrone L. Rosenberry
- Departments of Neuroscience and Pharmacology, Mayo Clinic College of Medicine, Jacksonville, FL 32224, USA;
| | - Israel Silman
- Department of Neurobiology, Weizmann Institute of Science, 7610001 Rehovot, Israel;
| | - Joel L. Sussman
- Department of Structural Biology, Weizmann Institute of Science, 7610001 Rehovot, Israel;
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20
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Pinto GP, Vavra O, Filipovic J, Stourac J, Bednar D, Damborsky J. Fast Screening of Inhibitor Binding/Unbinding Using Novel Software Tool CaverDock. Front Chem 2019; 7:709. [PMID: 31737596 PMCID: PMC6828983 DOI: 10.3389/fchem.2019.00709] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 10/09/2019] [Indexed: 11/20/2022] Open
Abstract
Protein tunnels and channels are attractive targets for drug design. Drug molecules that block the access of substrates or release of products can be efficient modulators of biological activity. Here, we demonstrate the applicability of a newly developed software tool CaverDock for screening databases of drugs against pharmacologically relevant targets. First, we evaluated the effect of rigid and flexible side chains on sets of substrates and inhibitors of seven different proteins. In order to assess the accuracy of our software, we compared the results obtained from CaverDock calculation with experimental data previously collected with heat shock protein 90α. Finally, we tested the virtual screening capabilities of CaverDock with a set of oncological and anti-inflammatory FDA-approved drugs with two molecular targets—cytochrome P450 17A1 and leukotriene A4 hydrolase/aminopeptidase. Calculation of rigid trajectories using four processors took on average 53 min per molecule with 90% successfully calculated cases. The screening identified functional tunnels based on the profile of potential energies of binding and unbinding trajectories. We concluded that CaverDock is a sufficiently fast, robust, and accurate tool for screening binding/unbinding processes of pharmacologically important targets with buried functional sites. The standalone version of CaverDock is available freely at https://loschmidt.chemi.muni.cz/caverdock/ and the web version at https://loschmidt.chemi.muni.cz/caverweb/.
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Affiliation(s)
- Gaspar P Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czechia
| | - Ondrej Vavra
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czechia
| | - Jiri Filipovic
- Institute of Computer Science, Masaryk University, Brno, Czechia
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czechia
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czechia
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czechia
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21
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Sánchez-Aparicio JE, Sciortino G, Herrmannsdoerfer DV, Chueca PO, Pedregal JRG, Maréchal JD. GPathFinder: Identification of Ligand-Binding Pathways by a Multi-Objective Genetic Algorithm. Int J Mol Sci 2019; 20:E3155. [PMID: 31261636 PMCID: PMC6651367 DOI: 10.3390/ijms20133155] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 12/21/2022] Open
Abstract
Protein-ligand docking is a widely used method to generate solutions for the binding of a small molecule with its target in a short amount of time. However, these methods provide identification of physically sound protein-ligand complexes without a complete view of the binding process dynamics, which has been recognized to be a major discriminant in binding affinity and ligand selectivity. In this paper, a novel piece of open-source software to approach this problem is presented, called GPathFinder. It is built as an extension of the modular GaudiMM platform and is able to simulate ligand diffusion pathways at atomistic level. The method has been benchmarked on a set of 20 systems whose ligand-binding routes were studied by other computational tools or suggested from experimental "snapshots". In all of this set, GPathFinder identifies those channels that were already reported in the literature. Interestingly, the low-energy pathways in some cases indicate novel possible binding routes. To show the usefulness of GPathFinder, the analysis of three case systems is reported. We believe that GPathFinder is a software solution with a good balance between accuracy and computational cost, and represents a step forward in extending protein-ligand docking capacities, with implications in several fields such as drug or enzyme design.
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Affiliation(s)
| | - Giuseppe Sciortino
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | | | - Pablo Orenes Chueca
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | | | - Jean-Didier Maréchal
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain.
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22
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Roca C, Requena C, Sebastián-Pérez V, Malhotra S, Radoux C, Pérez C, Martinez A, Antonio Páez J, Blundell TL, Campillo NE. Identification of new allosteric sites and modulators of AChE through computational and experimental tools. J Enzyme Inhib Med Chem 2018; 33:1034-1047. [PMID: 29873262 PMCID: PMC6010107 DOI: 10.1080/14756366.2018.1476502] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/09/2018] [Accepted: 05/09/2018] [Indexed: 11/15/2022] Open
Abstract
Allosteric sites on proteins are targeted for designing more selective inhibitors of enzyme activity and to discover new functions. Acetylcholinesterase (AChE), which is most widely known for the hydrolysis of the neurotransmitter acetylcholine, has a peripheral allosteric subsite responsible for amyloidosis in Alzheimer's disease through interaction with amyloid β-peptide. However, AChE plays other non-hydrolytic functions. Here, we identify and characterise using computational tools two new allosteric sites in AChE, which have allowed us to identify allosteric inhibitors by virtual screening guided by structure-based and fragment hotspot strategies. The identified compounds were also screened for in vitro inhibition of AChE and three were observed to be active. Further experimental (kinetic) and computational (molecular dynamics) studies have been performed to verify the allosteric activity. These new compounds may be valuable pharmacological tools in the study of non-cholinergic functions of AChE.
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Affiliation(s)
- Carlos Roca
- a Centro de Investigaciones Biológicas (CIB-CSIC), C/Ramiro de Maeztu , Madrid , Spain
| | - Carlos Requena
- a Centro de Investigaciones Biológicas (CIB-CSIC), C/Ramiro de Maeztu , Madrid , Spain
| | | | - Sony Malhotra
- b Department of Biochemistry , University of Cambridge , Cambridge , UK
| | - Chris Radoux
- b Department of Biochemistry , University of Cambridge , Cambridge , UK
- c Cambridge Crystallographic Data Centre , Cambridge , UK
| | - Concepción Pérez
- d Instituto de Química Médica (IQM-CSIC) , C/Juan de la Cierva , Madrid , Spain
| | - Ana Martinez
- a Centro de Investigaciones Biológicas (CIB-CSIC), C/Ramiro de Maeztu , Madrid , Spain
| | - Juan Antonio Páez
- d Instituto de Química Médica (IQM-CSIC) , C/Juan de la Cierva , Madrid , Spain
| | - Tom L Blundell
- b Department of Biochemistry , University of Cambridge , Cambridge , UK
| | - Nuria E Campillo
- a Centro de Investigaciones Biológicas (CIB-CSIC), C/Ramiro de Maeztu , Madrid , Spain
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23
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de Almeida JSFD, Cavalcante SFA, Dolezal R, Kuca K, Musilek K, Jun D, França TCC. Molecular modeling studies on the interactions of aflatoxin B1 and its metabolites with the peripheral anionic site of human acetylcholinesterase. J Biomol Struct Dyn 2018; 37:2041-2048. [DOI: 10.1080/07391102.2018.1475259] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Joyce S. F. D. de Almeida
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMDQB), Military Institute of Engineering, Praça General Tibúrcio, Rio de Janeiro, Brazil
| | - Samir F. A. Cavalcante
- Brazilian Army CBRN Defense Institute - IDQBRN, Avenida das Américas, Rio de Janeiro, Brazil
- Natural Products Research Institute - IPPN, Federal University of Rio de Janeiro - UFRJ, Bl. H, Ilha do Fundão, Rio de Janeiro, Brazil
| | - Rafael Dolezal
- Department of Chemistry, University of Hradec Králové, Rokitanskeho, Hradec Kralove, Czech Republic
- Faculty of Informatics and Management, Center for Basic and Applied Research, University of Hradec Králové, Rokitanskeho, 62, Hradec Králove, Czech Republic
| | - Kamil Kuca
- Department of Chemistry, University of Hradec Králové, Rokitanskeho, Hradec Kralove, Czech Republic
| | - Kamil Musilek
- Department of Chemistry, University of Hradec Králové, Rokitanskeho, Hradec Kralove, Czech Republic
| | - Daniel Jun
- Department of Toxicology, University of Defense, Trebesska, Hradec Kralové, Czech Republic
| | - Tanos C. C. França
- Laboratory of Molecular Modeling Applied to Chemical and Biological Defense (LMDQB), Military Institute of Engineering, Praça General Tibúrcio, Rio de Janeiro, Brazil
- Faculty of Informatics and Management, Center for Basic and Applied Research, University of Hradec Králové, Rokitanskeho, 62, Hradec Králove, Czech Republic
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24
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Design, synthesis, cholinesterase inhibition and molecular modelling study of novel tacrine hybrids with carbohydrate derivatives. Bioorg Med Chem 2018; 26:5566-5577. [DOI: 10.1016/j.bmc.2018.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/05/2018] [Accepted: 10/07/2018] [Indexed: 02/03/2023]
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25
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Molecular Modeling Studies on the Interactions of Aflatoxin B1 and Its Metabolites with Human Acetylcholinesterase. Part II: Interactions with the Catalytic Anionic Site (CAS). Toxins (Basel) 2018; 10:toxins10100389. [PMID: 30257474 PMCID: PMC6215247 DOI: 10.3390/toxins10100389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Revised: 09/13/2018] [Accepted: 09/20/2018] [Indexed: 11/16/2022] Open
Abstract
The most common type of aflatoxin (AFT) found in nature is aflatoxin B1 (AFB1). This micotoxin is extremely hepatotoxic and carcinogenic to mammals, with acute and chronic effects. It is believed that this could be related to the capacity of AFB1 and its metabolites in inhibiting the enzyme acetylcholinesterase (AChE). In a previous work, we performed an inedited theoretical investigation on the binding modes of these molecules on the peripheral anionic site (PAS) of human AChE (HssAChE), revealing that the metabolites can also bind in the PAS in the same way as AFB1. Here, we investigated the binding modes of these compounds on the catalytic anionic site (CAS) of HssAChE to compare the affinity of the metabolites for both binding sites as well as verify which is the preferential one. Our results corroborated with experimental studies pointing to AFB1 and its metabolites as mixed-type inhibitors, and pointed to the residues relevant for the stabilization of these compounds on the CAS of HssAChE.
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Rydzewski J, Jakubowski R, Nowak W, Grubmüller H. Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways. J Chem Theory Comput 2018; 14:2843-2851. [PMID: 29715428 DOI: 10.1021/acs.jctc.8b00173] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The dissociation of huperzine A (hupA) from Torpedo californica acetylcholinesterase ( TcAChE) was investigated by 4 μs unbiased and biased all-atom molecular dynamics (MD) simulations in explicit solvent. We performed our study using memetic sampling (MS) for the determination of reaction pathways (RPs), metadynamics to calculate free energy, and maximum-likelihood estimation (MLE) to recover kinetic rates from unbiased MD simulations. Our simulations suggest that the dissociation of hupA occurs mainly via two RPs: a front door along the axis of the active-site gorge (pwf) and through a new transient side door (pws), i.e., formed by the Ω-loop (residues 67-94 of TcAChE). An analysis of the inhibitor unbinding along the RPs suggests that pws is opened transiently after hupA and the Ω-loop reach a low free-energy transition state characterized by the orientation of the pyridone group of the inhibitor directed toward the Ω-loop plane. Unlike pws, pwf does not require large structural changes in TcAChE to be accessible. The estimated free energies and rates agree well with available experimental data. The dissociation rates along the unbinding pathways are similar, suggesting that the dissociation of hupA along pws is likely to be relevant. This indicates that perturbations to hupA- TcAChE interactions could potentially induce pathway hopping. In summary, our results characterize the slow-onset inhibition of TcAChE by hupA, which may provide the structural and energetic bases for the rational design of the next-generation slow-onset inhibitors with optimized pharmacokinetic properties for the treatment of Alzheimer's disease.
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Affiliation(s)
- J Rydzewski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University , Grudziadzka 5 , 87-100 Toruń , Poland
| | - R Jakubowski
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University , Grudziadzka 5 , 87-100 Toruń , Poland.,Centre of New Technologies, University of Warsaw , Banacha 2c , 02-097 Warsaw , Poland
| | - W Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University , Grudziadzka 5 , 87-100 Toruń , Poland
| | - H Grubmüller
- Max Planck Institute for Biophysical Chemistry , Am Faßberg 11 , 37077 Göttingen , Germany
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Costanzi S, Machado JH, Mitchell M. Nerve Agents: What They Are, How They Work, How to Counter Them. ACS Chem Neurosci 2018; 9:873-885. [PMID: 29664277 DOI: 10.1021/acschemneuro.8b00148] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nerve agents are organophosphorus chemical warfare agents that exert their action through the irreversible inhibition of acetylcholinesterase, with a consequent overstimulation of cholinergic transmission followed by its shutdown. Beyond warfare, they have notoriously been employed in acts of terrorism as well as high profile assassinations. After a brief historical introduction on the development and deployment of nerve agents, this review provides a survey of their chemistry, the way they affect cholinergic transmission, the available treatment options, and the current directions for their improvement. As the review illustrates, despite their merits, the currently available treatment options present several shortcomings. Current research directions involve the search for improved antidotes, antagonists of the nicotinic receptors, small-molecule pretreatment options, as well as bioscavengers as macromolecular pretreatment options. These efforts are making good progress in many different directions and, hopefully, will lead to a lower target susceptibility, thus reducing the appeal of nerve agents as chemical weapons.
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Affiliation(s)
| | - John-Hanson Machado
- Department of Chemistry, The George Washington University, 800 22nd Street NW, Washington, DC 20052, United States
- Computational Biology Institute, The George Washington University, 45085 University Drive Suite 305, Ashburn, Virginia 20147, United States
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28
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Stefanachi A, Leonetti F, Pisani L, Catto M, Carotti A. Coumarin: A Natural, Privileged and Versatile Scaffold for Bioactive Compounds. Molecules 2018; 23:E250. [PMID: 29382051 PMCID: PMC6017103 DOI: 10.3390/molecules23020250] [Citation(s) in RCA: 290] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 01/22/2018] [Accepted: 01/25/2018] [Indexed: 12/22/2022] Open
Abstract
Many naturally occurring substances, traditionally used in popular medicines around the world, contain the coumarin moiety. Coumarin represents a privileged scaffold for medicinal chemists, because of its peculiar physicochemical features, and the versatile and easy synthetic transformation into a large variety of functionalized coumarins. As a consequence, a huge number of coumarin derivatives have been designed, synthesized, and tested to address many pharmacological targets in a selective way, e.g., selective enzyme inhibitors, and more recently, a number of selected targets (multitarget ligands) involved in multifactorial diseases, such as Alzheimer's and Parkinson's diseases. In this review an overview of the most recent synthetic pathways leading to mono- and polyfunctionalized coumarins will be presented, along with the main biological pathways of their biosynthesis and metabolic transformations. The many existing and recent reviews in the field prompted us to make some drastic selections, and therefore, the review is focused on monoamine oxidase, cholinesterase, and aromatase inhibitors, and on multitarget coumarins acting on selected targets of neurodegenerative diseases.
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Affiliation(s)
- Angela Stefanachi
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, I-70125 Bari, Italy.
| | - Francesco Leonetti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, I-70125 Bari, Italy.
| | - Leonardo Pisani
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, I-70125 Bari, Italy.
| | - Marco Catto
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, I-70125 Bari, Italy.
| | - Angelo Carotti
- Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", via E. Orabona 4, I-70125 Bari, Italy.
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29
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Liu WQ, Amara P, Mouesca JM, Ji X, Renoux O, Martin L, Zhang C, Zhang Q, Nicolet Y. 1,2-Diol Dehydration by the Radical SAM Enzyme AprD4: A Matter of Proton Circulation and Substrate Flexibility. J Am Chem Soc 2018; 140:1365-1371. [DOI: 10.1021/jacs.7b10501] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Wan-Qiu Liu
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | | | | | - Xinjian Ji
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | | | | | - Chen Zhang
- Department
of Chemistry, Fudan University, Shanghai 200433, China
| | - Qi Zhang
- Department
of Chemistry, Fudan University, Shanghai 200433, China
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30
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Ranjan A, Chauhan A, Jindal T. In-silico and in-vitro evaluation of human acetylcholinesterase inhibition by organophosphates. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2018; 57:131-140. [PMID: 29272792 DOI: 10.1016/j.etap.2017.12.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/25/2017] [Accepted: 12/16/2017] [Indexed: 06/07/2023]
Abstract
Organophosphates (OP) inhibit the acetylcholinesterase (AChE) activity and devastate the nervous system of pest however its mode of action is ubiquitous and acts similarly on human AChE (hAChE). Screening of OP was carried out by molecular docking with hAChE using Glide docking module of Schrodinger suite as the structural information of hAChE and OP together as co-crystal structure is rarely available. The docking was done at three different precision levels, high throughput virtual screening (HTVS), standard precision and extra precision. The ranking was done using over all binding energy i.e. dock score and molecular modelling generalized born surface area (MM-GBSA). Investigation reported Tryptophan (Trp86) residue involved in most interactions by forming a π-cation interaction apart from Ser203 on anionic subsite of hAChE. The top rank ligand was Phoxim ethyl phosphonate (PEP) interacting with Trp86, Gly121 and Ser203. However contact with Gly121 was lost during simulation and Asp74 appeared and sustained. Molecular dynamic simulation (GROMACS 4.5.5) of hAChE-PEP complex for 4 × 104 pico-second with SPC16 water system at 310 K temperature explained the evident role of Trp86 in stabilizing the ligand at P-site of the enzyme. Asp74 and Tyr124 were noticed in conveying H-bonds. Trp86 has shown consistent and better stability of bond based on distance between residues and ligand. The top ranked OP i.e. PEP was used to establish a dose response relationship between OP and hAChE. PEP inhibits half of the enzyme activity at concertation of 29.99 μM (calculated by sigmoid plot) at R2 = 0.996 and P < 0.0001.
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Affiliation(s)
- Anuj Ranjan
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida, Uttar Pradesh, India.
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida, Uttar Pradesh, India
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida, Uttar Pradesh, India
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Bourne Y, Marchot P. Hot Spots for Protein Partnerships at the Surface of Cholinesterases and Related α/β Hydrolase Fold Proteins or Domains-A Structural Perspective. Molecules 2017; 23:molecules23010035. [PMID: 29295471 PMCID: PMC5943944 DOI: 10.3390/molecules23010035] [Citation(s) in RCA: 5] [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: 12/05/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 12/12/2022] Open
Abstract
The hydrolytic enzymes acetyl- and butyryl-cholinesterase, the cell adhesion molecules neuroligins, and the hormonogenic macromolecule thyroglobulin are a few of the many members of the α/β hydrolase fold superfamily of proteins. Despite their distinctive functions, their canonical subunits, with a molecular surface area of ~20,000 Å2, they share binding patches and determinants for forming homodimers and for accommodating structural subunits or protein partners. Several of these surface regions of high functional relevance have been mapped through structural or mutational studies, while others have been proposed based on biochemical data or molecular docking studies. Here, we review these binding interfaces and emphasize their specificity versus potentially multifunctional character.
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Affiliation(s)
- Yves Bourne
- Centre National de la Recherche Scientifique, Aix-Marseille Université, "Architecture et Fonction des Macromolécules Biologiques" Laboratory, 13288 Marseille, France.
| | - Pascale Marchot
- Centre National de la Recherche Scientifique, Aix-Marseille Université, "Architecture et Fonction des Macromolécules Biologiques" Laboratory, 13288 Marseille, France.
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32
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Cheung J, Mahmood A, Kalathur R, Liu L, Carlier PR. Structure of the G119S Mutant Acetylcholinesterase of the Malaria Vector Anopheles gambiae Reveals Basis of Insecticide Resistance. Structure 2017; 26:130-136.e2. [PMID: 29276037 DOI: 10.1016/j.str.2017.11.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/01/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
Malaria is a devastating disease in sub-Saharan Africa and is transmitted by the mosquito Anopheles gambiae. While indoor residual spraying of anticholinesterase insecticides has been useful in controlling the spread of malaria, widespread application of these compounds has led to the rise of an insecticide-resistant mosquito strain that harbors a G119S mutation in the nervous system target enzyme acetylcholinesterase. We demonstrate the atomic basis of insecticide resistance through structure determination of the G119S mutant acetylcholinesterase of An. gambiae in the ligand-free state and bound to a potent difluoromethyl ketone inhibitor. These structures reveal specific features within the active-site gorge distinct from human acetylcholinesterase, including an open channel at the base of the gorge, and provide a means for improving species selectivity in the rational design of improved insecticides for malaria vector control.
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Affiliation(s)
- Jonah Cheung
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA.
| | - Arshad Mahmood
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - Ravi Kalathur
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - Lixuan Liu
- Department of Chemistry, Virginia Tech, Blacksburg, VA 24061, USA
| | - Paul R Carlier
- Department of Chemistry, Virginia Tech, Blacksburg, VA 24061, USA
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33
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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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34
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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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35
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Ismaili L, Refouvelet B, Benchekroun M, Brogi S, Brindisi M, Gemma S, Campiani G, Filipic S, Agbaba D, Esteban G, Unzeta M, Nikolic K, Butini S, Marco-Contelles J. Multitarget compounds bearing tacrine- and donepezil-like structural and functional motifs for the potential treatment of Alzheimer's disease. Prog Neurobiol 2017; 151:4-34. [DOI: 10.1016/j.pneurobio.2015.12.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 11/11/2015] [Accepted: 12/11/2015] [Indexed: 01/16/2023]
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36
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Marques SM, Daniel L, Buryska T, Prokop Z, Brezovsky J, Damborsky J. Enzyme Tunnels and Gates As Relevant Targets in Drug Design. Med Res Rev 2016; 37:1095-1139. [PMID: 27957758 DOI: 10.1002/med.21430] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 10/11/2016] [Accepted: 11/07/2016] [Indexed: 12/28/2022]
Abstract
Many enzymes contain tunnels and gates that are essential to their function. Gates reversibly switch between open and closed conformations and thereby control the traffic of small molecules-substrates, products, ions, and solvent molecules-into and out of the enzyme's structure via molecular tunnels. Many transient tunnels and gates undoubtedly remain to be identified, and their functional roles and utility as potential drug targets have received comparatively little attention. Here, we describe a set of general concepts relating to the structural properties, function, and classification of these interesting structural features. In addition, we highlight the potential of enzyme tunnels and gates as targets for the binding of small molecules. The different types of binding that are possible and the potential pharmacological benefits of such targeting are discussed. Twelve examples of ligands bound to the tunnels and/or gates of clinically relevant enzymes are used to illustrate the different binding modes and to explain some new strategies for drug design. Such strategies could potentially help to overcome some of the problems facing medicinal chemists and lead to the discovery of more effective drugs.
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Affiliation(s)
- Sergio M Marques
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lukas Daniel
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Tomas Buryska
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Faculty of Science, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment, RECETOX, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
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37
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Arduini F, Neagu D, Pagliarini V, Scognamiglio V, Leonardis M, Gatto E, Amine A, Palleschi G, Moscone D. Rapid and label-free detection of ochratoxin A and aflatoxin B1 using an optical portable instrument. Talanta 2016; 150:440-8. [DOI: 10.1016/j.talanta.2015.12.048] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/09/2015] [Accepted: 12/14/2015] [Indexed: 11/17/2022]
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38
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PrinCCes: Continuity-based geometric decomposition and systematic visualization of the void repertoire of proteins. J Mol Graph Model 2015; 62:118-127. [PMID: 26409191 DOI: 10.1016/j.jmgm.2015.09.013] [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: 05/03/2015] [Revised: 07/20/2015] [Accepted: 09/14/2015] [Indexed: 11/20/2022]
Abstract
Grooves and pockets on the surface, channels through the protein, the chambers or cavities, and the tunnels connecting the internal points to each other or to the external fluid environment are fundamental determinants of a wide range of biological functions. PrinCCes (Protein internal Channel & Cavity estimation) is a computer program supporting the visualization of voids. It includes a novel algorithm for the decomposition of the entire void volume of the protein or protein complex to individual entities. The decomposition is based on continuity. An individual void is defined by uninterrupted extension in space: a spherical probe can freely move between any two internal locations of a continuous void. Continuous voids are detected irrespective of their topological complexity, they may contain any number of holes and bifurcations. The voids of a protein can be visualized one by one or in combinations as triangulated surfaces. The output is automatically exported to free VMD (Visual Molecular Dynamics) or Chimera software, allowing the 3D rotation of the surfaces and the production of publication quality images. PrinCCes with graphic user interface and command line versions are available for MS Windows and Linux. The source code and executable can be downloaded at any of the following links: http://scholar.semmelweis.hu/czirjakgabor/s/princces/#t1 https://github.com/CzirjakGabor/PrinCCes http://1drv.ms/1bP9iJ3.
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39
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Legler PM, Soojhawon I, Millard CB. A conformational change in the peripheral anionic site of Torpedo californica acetylcholinesterase induced by a bis-imidazolium oxime. ACTA ACUST UNITED AC 2015; 71:1788-98. [PMID: 26327369 DOI: 10.1107/s1399004715011281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/09/2015] [Indexed: 08/30/2023]
Abstract
As part of ongoing efforts to design improved nerve agent antidotes, two X-ray crystal structures of Torpedo californica acetylcholinesterase (TcAChE) bound to the bis-pyridinium oxime, Ortho-7, or its experimental bis-imidazolium analogue, 2BIM-7, were determined. Bis-oximes contain two oxime groups connected by a hydrophobic linker. One oxime group of Ortho-7 binds at the entrance to the active-site gorge near Trp279, and the second binds at the bottom near Trp84 and Phe330. In the Ortho-7-TcAChE complex the oxime at the bottom of the gorge was directed towards the nucleophilic Ser200. In contrast, the oxime group of 2BIM-7 was rotated away from Ser200 and the oxime at the entrance induced a significant conformational change in the peripheral anionic site (PAS) residue Trp279. The conformational change alters the surface of the PAS and positions the imidazolium oxime of 2BIM-7 further from Ser200. The relatively weaker binding and poorer reactivation of VX-inhibited, tabun-inhibited or sarin-inhibited human acetylcholinesterase by 2BIM-7 compared with Ortho-7 may in part be owing to the unproductively bound states caught in crystallo. Overall, the reactivation efficiency of 2BIM-7 was comparable to that of 2-pyridine aldoxime methyl chloride (2-PAM), but unlike 2-PAM the bis-imidazolium oxime lacks a fixed charge, which may affect its membrane permeability.
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Affiliation(s)
- Patricia M Legler
- CBMSE, U.S. Naval Research Laboratory, 4555 Overlook Avenue, Washington, DC 20375, USA
| | - Iswarduth Soojhawon
- Bacterial Diseases, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
| | - Charles B Millard
- Division of Biochemistry, Walter Reed Army Institute of Research, 503 Robert Grant Avenue, Silver Spring, MD 20910, USA
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40
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Bennion BJ, Essiz SG, Lau EY, Fattebert JL, Emigh A, Lightstone FC. A wrench in the works of human acetylcholinesterase: soman induced conformational changes revealed by molecular dynamics simulations. PLoS One 2015; 10:e0121092. [PMID: 25874456 PMCID: PMC4395452 DOI: 10.1371/journal.pone.0121092] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 01/27/2015] [Indexed: 01/06/2023] Open
Abstract
Irreversible inactivation of human acetylcholinesterase (hAChE) by organophosphorous pesticides (OPs) and chemical weapon agents (CWA) has severe morbidity and mortality consequences. We present data from quantum mechanics/molecular mechanics (QM/MM) and 80 classical molecular dynamics (MD) simulations of the apo and soman-adducted forms of hAChE to investigate the effects on the dynamics and protein structure when the catalytic Serine 203 is phosphonylated. We find that the soman phosphonylation of the active site Ser203 follows a water assisted addition-elimination mechanism with the elimination of the fluoride ion being the highest energy barrier at 6.5 kcal/mole. We observe soman-dependent changes in backbone and sidechain motions compared to the apo form of the protein. These alterations restrict the soman-adducted hAChE to a structural state that is primed for the soman adduct to be cleaved and removed from the active site. The altered motions and resulting structures provide alternative pathways into and out of the hAChE active site. In the soman-adducted protein both side and back door pathways are viable for soman adduct access. Correlation analysis of the apo and soman adducted MD trajectories shows that the correlation of gorge entrance and back door motion is disrupted when hAChE is adducted. This supports the hypothesis that substrate and product can use two different pathways as entry and exit sites in the apo form of the protein. These alternative pathways have important implications for the rational design of medical countermeasures.
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Affiliation(s)
- Brian J. Bennion
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore CA, United States of America
| | - Sebnem G. Essiz
- Bioinformatics and Genetics Department, Faculty of Engineering and Natural Sciences, Kadir Has University, 34083 Fatih, Istanbul, Turkey
| | - Edmond Y. Lau
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore CA, United States of America
| | - Jean-Luc Fattebert
- Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore CA, United States of America
| | - Aiyana Emigh
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore CA, United States of America
| | - Felice C. Lightstone
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore CA, United States of America
- * E-mail:
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41
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Cha DJ, Lee SH. Evolutionary origin and status of two insect acetylcholinesterases and their structural conservation and differentiation. Evol Dev 2015; 17:109-19. [DOI: 10.1111/ede.12111] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Deok Jea Cha
- Department of Agricultural Biotechnology; Seoul National University; Gwanakno; Gwanakgu Seoul 151-742 Republic of Korea
| | - Si Hyeock Lee
- Department of Agricultural Biotechnology; Seoul National University; Gwanakno; Gwanakgu Seoul 151-742 Republic of Korea
- Research Institute for Agriculture and Life Science; Seoul National University; Seoul 151-742 Republic of Korea
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42
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Nagy GN, Marton L, Contet A, Ozohanics O, Ardelean LM, Révész Á, Vékey K, Irimie FD, Vial H, Cerdan R, Vértessy BG. Composite Aromatic Boxes for Enzymatic Transformations of Quaternary Ammonium Substrates. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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43
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Bourne Y, Renault L, Marchot P. Crystal structure of snake venom acetylcholinesterase in complex with inhibitory antibody fragment Fab410 bound at the peripheral site: evidence for open and closed states of a back door channel. J Biol Chem 2014; 290:1522-35. [PMID: 25411244 DOI: 10.1074/jbc.m114.603902] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The acetylcholinesterase found in the venom of Bungarus fasciatus (BfAChE) is produced as a soluble, non-amphiphilic monomer with a canonical catalytic domain but a distinct C terminus compared with the other vertebrate enzymes. Moreover, the peripheral anionic site of BfAChE, a surface site located at the active site gorge entrance, bears two substitutions altering sensitivity to cationic inhibitors. Antibody Elec410, generated against Electrophorus electricus acetylcholinesterase (EeAChE), inhibits EeAChE and BfAChE by binding to their peripheral sites. However, both complexes retain significant residual catalytic activity, suggesting incomplete gorge occlusion by bound antibody and/or high frequency back door opening. To explore a novel acetylcholinesterase species, ascertain the molecular bases of inhibition by Elec410, and document the determinants and mechanisms for back door opening, we solved a 2.7-Å resolution crystal structure of natural BfAChE in complex with antibody fragment Fab410. Crystalline BfAChE forms the canonical dimer found in all acetylcholinesterase structures. Equally represented open and closed states of a back door channel, associated with alternate positions of a tyrosine phenol ring at the active site base, coexist in each subunit. At the BfAChE molecular surface, Fab410 is seated on the long Ω-loop between two N-glycan chains and partially occludes the gorge entrance, a position that fully reflects the available mutagenesis and biochemical data. Experimentally based flexible molecular docking supports a similar Fab410 binding mode onto the EeAChE antigen. These data document the molecular and dynamic peculiarities of BfAChE with high frequency back door opening, and the mode of action of Elec410 as one of the largest peptidic inhibitors targeting the acetylcholinesterase peripheral site.
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Affiliation(s)
- Yves Bourne
- From Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, campus Luminy, 13228 Marseille cedex 09, France, CNRS, Architecture et Fonction des Macromolécules Biologiques, campus Luminy, 13228 Marseille cedex 09, France, and
| | - Ludovic Renault
- CNRS/Aix-Marseille Université, Ingénierie des Protéines, Faculté de Médecine-Secteur Nord, 13344 Marseille cedex 15, France
| | - Pascale Marchot
- From Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, campus Luminy, 13228 Marseille cedex 09, France, CNRS, Architecture et Fonction des Macromolécules Biologiques, campus Luminy, 13228 Marseille cedex 09, France, and CNRS/Aix-Marseille Université, Ingénierie des Protéines, Faculté de Médecine-Secteur Nord, 13344 Marseille cedex 15, France
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44
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Nagy GN, Marton L, Contet A, Ozohanics O, Ardelean LM, Révész A, Vékey K, Irimie FD, Vial H, Cerdan R, Vértessy BG. Composite aromatic boxes for enzymatic transformations of quaternary ammonium substrates. Angew Chem Int Ed Engl 2014; 53:13471-6. [PMID: 25283789 DOI: 10.1002/anie.201408246] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Indexed: 11/07/2022]
Abstract
Cation-π interactions to cognate ligands in enzymes have key roles in ligand binding and enzymatic catalysis. We have deciphered the key functional role of both charged and aromatic residues within the choline binding subsite of CTP:phosphocholine cytidylyltransferase and choline kinase from Plasmodium falciparum. Comparison of quaternary ammonium binding site structures revealed a general composite aromatic box pattern of enzyme recognition sites, well distinguished from the aromatic box recognition site of receptors.
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Affiliation(s)
- Gergely N Nagy
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, 1111 Budapest (Hungary); Institute of Enzymology, Research Centre of National Sciences, HAS, 1117 Budapest (Hungary).
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45
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Cheung J, Gary EN, Shiomi K, Rosenberry TL. Structures of human acetylcholinesterase bound to dihydrotanshinone I and territrem B show peripheral site flexibility. ACS Med Chem Lett 2013; 4:1091-6. [PMID: 24900610 DOI: 10.1021/ml400304w] [Citation(s) in RCA: 186] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 09/23/2013] [Indexed: 11/30/2022] Open
Abstract
Acetylcholinesterase is a critical enzyme that regulates neurotransmission by degrading the neurotransmitter acetylcholine in synapses of the nervous system. It is an important target for both therapeutic drugs that treat Alzheimer's disease and chemical warfare agents that cripple the nervous system and cause death through paralysis. The enzyme has both catalytic and peripheral sites to which inhibitors may bind. Structures of recombinant human acetylcholinesterase in complex with the natural product inhibitors dihydrotanshinone I and territrem B reveal dihydrotanshinone I binding that is specific to only the peripheral site and territrem B binding that spans both sites and distorts the protein backbone in the peripheral site. These inhibitors may function as important molecular templates for therapeutics used for treatment of disease and protection against nerve agents.
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Affiliation(s)
- Jonah Cheung
- New York Structural
Biology Center, New York, New
York 10027, United States
| | - Ebony N. Gary
- New York Structural
Biology Center, New York, New
York 10027, United States
| | - Kazuro Shiomi
- Kitasato
Institute for Life Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Terrone L. Rosenberry
- Departments
of Neuroscience and Pharmacology, Mayo Clinic Florida, Jacksonville, Florida 32224, United States
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46
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Bourne Y, Renault L, Essono S, Mondielli G, Lamourette P, Boquet D, Grassi J, Marchot P. Molecular characterization of monoclonal antibodies that inhibit acetylcholinesterase by targeting the peripheral site and backdoor region. PLoS One 2013; 8:e77226. [PMID: 24146971 PMCID: PMC3795623 DOI: 10.1371/journal.pone.0077226] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 09/02/2013] [Indexed: 11/19/2022] Open
Abstract
The inhibition properties and target sites of monoclonal antibodies (mAbs) Elec403, Elec408 and Elec410, generated against Electrophorus electricus acetylcholinesterase (AChE), have been defined previously using biochemical and mutagenesis approaches. Elec403 and Elec410, which bind competitively with each other and with the peptidic toxin inhibitor fasciculin, are directed toward distinctive albeit overlapping epitopes located at the AChE peripheral anionic site, which surrounds the entrance of the active site gorge. Elec408, which is not competitive with the other two mAbs nor fasciculin, targets a second epitope located in the backdoor region, distant from the gorge entrance. To characterize the molecular determinants dictating their binding site specificity, we cloned and sequenced the mAbs; generated antigen-binding fragments (Fab) retaining the parental inhibition properties; and explored their structure-function relationships using complementary x-ray crystallography, homology modeling and flexible docking approaches. Hypermutation of one Elec403 complementarity-determining region suggests occurrence of antigen-driven selection towards recognition of the AChE peripheral site. Comparative analysis of the 1.9Å-resolution structure of Fab408 and of theoretical models of its Fab403 and Fab410 congeners evidences distinctive surface topographies and anisotropic repartitions of charges, consistent with their respective target sites and inhibition properties. Finally, a validated, data-driven docking model of the Fab403-AChE complex suggests a mode of binding at the PAS that fully correlates with the functional data. This comprehensive study documents the molecular peculiarities of Fab403 and Fab410, as the largest peptidic inhibitors directed towards the peripheral site, and those of Fab408, as the first inhibitor directed toward the backdoor region of an AChE and a unique template for the design of new, specific modulators of AChE catalysis.
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Affiliation(s)
- Yves Bourne
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS/Aix-Marseille Université, Campus Luminy, Marseille, France
| | - Ludovic Renault
- Ingénierie des Protéines, CNRS/Aix-Marseille Université, Faculté de Médecine - Secteur Nord, Marseille, France
| | - Sosthène Essono
- CEA, iBiTecS, Service de Pharmacologie et Immunologie (SPI), Laboratoire d’Etude et de Recherche en Immunoanalyse (LERI), Gif-sur-Yvette, France
| | - Grégoire Mondielli
- Centre de Recherche en Neurobiologie-Neurophysiologie de Marseille (CRN2M), CNRS/Aix-Marseille Université, Faculté de Médecine - Secteur Nord, Marseille, France
| | - Patricia Lamourette
- CEA, iBiTecS, Service de Pharmacologie et Immunologie (SPI), Laboratoire d’Etude et de Recherche en Immunoanalyse (LERI), Gif-sur-Yvette, France
| | - Didier Boquet
- CEA, iBiTecS, Service de Pharmacologie et Immunologie (SPI), Laboratoire d’Ingénierie des Anticorps pour la Santé (LIAS), Gif-sur-Yvette, France
| | - Jacques Grassi
- CEA, iBiTecS, Service de Pharmacologie et Immunologie (SPI), Laboratoire d’Etude et de Recherche en Immunoanalyse (LERI), Gif-sur-Yvette, France
| | - Pascale Marchot
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS/Aix-Marseille Université, Campus Luminy, Marseille, France
- Ingénierie des Protéines, CNRS/Aix-Marseille Université, Faculté de Médecine - Secteur Nord, Marseille, France
- Centre de Recherche en Neurobiologie-Neurophysiologie de Marseille (CRN2M), CNRS/Aix-Marseille Université, Faculté de Médecine - Secteur Nord, Marseille, France
- * E-mail:
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47
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Beri V, Wildman SA, Shiomi K, Al-Rashid ZF, Cheung J, Rosenberry TL. The natural product dihydrotanshinone I provides a prototype for uncharged inhibitors that bind specifically to the acetylcholinesterase peripheral site with nanomolar affinity. Biochemistry 2013; 52:7486-99. [PMID: 24040835 DOI: 10.1021/bi401043w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cholinergic synaptic transmission often requires extremely rapid hydrolysis of acetylcholine by acetylcholinesterase (AChE). AChE is inactivated by organophosphates (OPs) in chemical warfare nerve agents. The resulting accumulation of acetylcholine disrupts cholinergic synaptic transmission and can lead to death. A potential long-term strategy for preventing AChE inactivation by OPs is based on evidence that OPs must pass through a peripheral site or P-site near the mouth of the AChE active site gorge before reacting with a catalytic serine in an acylation site or A-site at the base of the gorge. An ultimate goal of this strategy is to design compounds that bind tightly at or near the P-site and exclude OPs from the active site while interfering minimally with the passage of acetylcholine. However, to target the AChE P-site with ligands and potential drugs that selectively restrict access, much more information must be gathered about the structure-activity relationships of ligands that bind specifically to the P-site. We apply here an inhibitor competition assay that can correctly determine whether an AChE inhibitor binds to the P-site, the A-site, or both sites. We have used this assay to examine three uncharged, natural product inhibitors of AChE, including aflatoxin B1, dihydrotanshinone I, and territrem B. The first two of these inhibitors are predicted by the competition assay to bind selectively to the P-site, while territrem B is predicted to span both the P- and A-sites. These predictions have recently been confirmed by X-ray crystallography. Dihydrotanshinone I, with an observed binding constant (KI) of 750 nM, provides a good lead compound for the development of high-affinity, uncharged inhibitors with specificity for the P-site.
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Affiliation(s)
- Veena Beri
- Departments of Neuroscience and Pharmacology, Mayo Clinic College of Medicine , Jacksonville, Florida 32224, United States
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48
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Hou LN, Xu JR, Zhao QN, Gao XL, Cui YY, Xu J, Wang H, Chen HZ. A new motif in the N-terminal of acetylcholinesterase triggers amyloid-β aggregation and deposition. CNS Neurosci Ther 2013; 20:59-66. [PMID: 23981668 DOI: 10.1111/cns.12161] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/14/2013] [Accepted: 07/15/2013] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND AND PURPOSE As a molecular chaperone, acetylcholinesterase (AChE; EC 3.1.1.7) plays a critical role in the pathogenesis of Alzheimer's disease (AD). The peripheral anionic site (PAS) of AChE has been indicated as the amyloid-β (Aβ) binding domain. The goal of this study was to determine other motifs in AChE involved in Aβ aggregation and deposition. METHODS AND RESULTS The β-hairpin in monomeric Aβ is the key motif of nucleation-dependent Aβ self-aggregation. As AChE could induce Aβ aggregation and deposition, we searched AChE for β-hairpin structures. In A11-specific dot blot assay, AChE was detected by an oligomer-specific antibody A11, implying the existence of β-hairpin structures in AChE as β-hairpin was the core motif of oligomers. A molecular superimposing approach further revealed that the N-terminal region, from Glu7 to Ile20, in AChE (AChE 7-20) was similar to the β-hairpin domain in Aβ. The results of further dot blot assays, thioflavin T fluorescence assays, and electron microscopy imaging experiments, indicated that the N-terminal synthetic peptide AChE7-20 had nearly the same ability as AChE with regard to triggering Aβ aggregation and deposition. CONCLUSIONS AChE 7-20, a β-hairpin region in AChE, might be a new motif in AChE capable of triggering Aβ aggregation and deposition. This finding will be helpful to design new and more effective Aβ aggregation inhibitors for AD treatment.
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Affiliation(s)
- Li-Na Hou
- Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, Shanghai, China
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49
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Sehnal D, Svobodová Vařeková R, Berka K, Pravda L, Navrátilová V, Banáš P, Ionescu CM, Otyepka M, Koča J. MOLE 2.0: advanced approach for analysis of biomacromolecular channels. J Cheminform 2013; 5:39. [PMID: 23953065 PMCID: PMC3765717 DOI: 10.1186/1758-2946-5-39] [Citation(s) in RCA: 227] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 08/13/2013] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. RESULTS We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability. We also assessed the variability in physicochemical properties of eighty X-ray structures of two members of the cytochrome P450 superfamily. CONCLUSION Estimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels. Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at http://mole.chemi.muni.cz.
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Affiliation(s)
- David Sehnal
- National Centre for Biomolecular Research, Faculty of Science and CEITEC-Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic.
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50
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Affiliation(s)
- Artur Gora
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories,
Department
of Experimental Biology and Research Centre for Toxic Compounds in
the Environment, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic
- International Centre for Clinical
Research, St. Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
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