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Madaj R, Gostyński B, Chworos A, Cypryk M. Novichok Nerve Agents as Inhibitors of Acetylcholinesterase-In Silico Study of Their Non-Covalent Binding Affinity. Molecules 2024; 29:338. [PMID: 38257251 PMCID: PMC10819560 DOI: 10.3390/molecules29020338] [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: 12/01/2023] [Revised: 12/27/2023] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
In silico studies were performed to assess the binding affinity of selected organophosphorus compounds toward the acetylcholinesterase enzyme (AChE). Quantum mechanical calculations, molecular docking, and molecular dynamics (MD) with molecular mechanics Generalized-Born surface area (MM/GBSA) were applied to assess quantitatively differences between the binding energies of acetylcholine (ACh; the natural agonist of AChE) and neurotoxic, synthetic correlatives (so-called "Novichoks", and selected compounds from the G- and V-series). Several additional quantitative descriptors like root-mean-square fluctuation (RMSF) and the solvent accessible surface area (SASA) were briefly discussed to give-to the best of our knowledge-the first quantitative in silico description of AChE-Novichok non-covalent binding process and thus facilitate the search for an efficient and effective treatment for Novichok intoxication and in a broader sense-intoxication with other warfare nerve agents as well.
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Affiliation(s)
- Rafal Madaj
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (R.M.); (A.C.)
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Bartłomiej Gostyński
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (R.M.); (A.C.)
| | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (R.M.); (A.C.)
| | - Marek Cypryk
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland; (R.M.); (A.C.)
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2
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Shtaiwi M, Aljaar N, Al-Najjar L, Malakar CC, Shtaiwi A, Abu-Sini M, Al-Refai M. Design, Synthesis, Biological Activity, and Molecular Modeling of Novel Spiroquinazoline Derivatives as Acetylcholinesterase Inhibitors for Alzheimer Disease. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2022.2144911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Majed Shtaiwi
- Department of Chemistry, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Nayyef Aljaar
- Department of Chemistry, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Lana Al-Najjar
- Department of Chemistry, Faculty of Science, The Hashemite University, Zarqa, Jordan
| | - Chandi C. Malakar
- Department of Chemistry, National Institute of Technology Manipur, Imphal, India
| | - Amneh Shtaiwi
- Faculty of Pharmacy, Middle East University, Amman, Jordan
| | - Mohammad Abu-Sini
- Faculty of Pharmacy, Al-Zaytoonah University of Jordan, Amman, Jordan
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3
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Chalcone Scaffolds Exhibiting Acetylcholinesterase Enzyme Inhibition: Mechanistic and Computational Investigations. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103181. [PMID: 35630658 PMCID: PMC9145706 DOI: 10.3390/molecules27103181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 11/23/2022]
Abstract
This study was aimed to perform the mechanistic investigations of chalcone scaffold as inhibitors of acetylcholinesterase (AChE) enzyme using molecular docking and molecular dynamics simulation tools. Basic chalcones (C1–C5) were synthesized and their in vitro AChE inhibition was tested. Binding interactions were studied using AutoDock and Surflex-Dock programs, whereas the molecular dynamics simulation studies were performed to check the stability of the ligand–protein complex. Good AChE inhibition (IC50 = 22 ± 2.8 to 37.6 ± 0.75 μM) in correlation with the in silico results (binding energies = −8.55 to −8.14 Kcal/mol) were obtained. The mechanistic studies showed that all of the functionalities present in the chalcone scaffold were involved in binding with the amino acid residues at the binding site through hydrogen bonding, π–π, π–cation, π–sigma, and hydrophobic interactions. Molecular dynamics simulation studies showed the formation of stable complex between the AChE enzyme and C4 ligand.
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4
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Moghadam B, Ashouri M, Roohi H, Karimi-Jafari MH. Computational evidence of new putative allosteric sites in the acetylcholinesterase receptor. J Mol Graph Model 2021; 107:107981. [PMID: 34246109 DOI: 10.1016/j.jmgm.2021.107981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 06/27/2021] [Accepted: 06/29/2021] [Indexed: 10/21/2022]
Abstract
Acetylcholinesterase (AChE), with a rigid structure and buried active site at the end of a deep narrow gorge, is interesting enough to solve the paradox between high catalytic activity and unavailability of the active site in treatment of Alzheimer's disease (AD). In this way, the blind docking process is performed on an ensemble of AChE structures created with molecular dynamics (MD) simulations to survey the whole space of AChE to find multiple access pathways to the active site and ranking them based on their affinity scores. Our results show that there are other allosteric binding sites in the protein structure whose inhibition, can affect protein function by disrupting the release of the Acetylcholine (AC) degradation products. In this study, inhibitory activities of Hybride14 and two natural compounds (Papaverine and Palmatine) were evaluated for all possible allosteric sites via docking method. The results confirmed the non-competitive inhibition mechanism. The best binding mode for these inhibitors and efficacy of hydrogen bonds and hydrophobic interactions on inhibitory activities of ligands were also disclosed. Furthermore, our studies provide significant molecular insight for AChE inhibition that could aid in the development of new drugs for AD's treatment.
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Affiliation(s)
- Behnaz Moghadam
- Department of Chemistry, Faculty of Science, University of Guilan, Iran
| | - Mitra Ashouri
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran, Iran.
| | - Hossein Roohi
- Department of Chemistry, Faculty of Science, University of Guilan, Iran.
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Mahomoodally F, Abdallah HH, Suroowan S, Jugreet S, Zhang Y, Hu X. In silico Exploration of Bioactive Phytochemicals Against Neurodegenerative Diseases Via Inhibition of Cholinesterases. Curr Pharm Des 2021; 26:4151-4162. [PMID: 32178608 DOI: 10.2174/1381612826666200316125517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/09/2020] [Indexed: 02/07/2023]
Abstract
Neurodegenerative disorders are estimated to become the second leading cause of death worldwide by 2040. Despite the widespread use of diverse allopathic drugs, these brain-associated disorders can only be partially addressed and long term treatment is often linked with dependency and other unwanted side effects. Nature, believed to be an arsenal of remedies for any illness, presents an interesting avenue for the development of novel neuroprotective agents. Interestingly, inhibition of cholinesterases, involved in the breakdown of acetylcholine in the synaptic cleft, has been proposed to be neuroprotective. This review therefore aims to provide additional insight via docking studies of previously studied compounds that have shown potent activity against acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) in vitro. Indeed, the determination of potent plant-based ligands for this purpose through in silico methods enables the elimination of lengthy and costly traditional methods of drug discovery. Herein, a literature search was conducted to identify active phytochemicals which are cholinesterase inhibitors. Following which in silico docking methods were applied to obtain docking scores. Compound structures were extracted from online ZINC database and optimized using AM1 implemented in gaussian09 software. Noteworthy ligands against AChE highlighted in this study include: 19,20-dihydroervahanine A and 19, 20-dihydrotabernamine. Regarding BChE inhibition, the best ligands were found to be 8-Clavandurylkaempferol, Na-methylepipachysamine D; ebeiedinone; and dictyophlebine. Thus, ligand optimization between such phytochemicals and cholinesterases coupled with in vitro, in vivo studies and randomized clinical trials can lead to the development of novel drugs against neurodegenerative disorders.
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Affiliation(s)
- Fawzi Mahomoodally
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Vietnam
| | - Hassan H Abdallah
- Chemistry Department, College of Education, Salahaddin University, 44002 Erbil, Iraq
| | - Shanoo Suroowan
- Department of Health Sciences, Faculty of Science, University of Mauritius, Mauritius
| | - Sharmeen Jugreet
- Department of Health Sciences, Faculty of Science, University of Mauritius, Mauritius
| | - Yansheng Zhang
- Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai, 200444, China
| | - Xuebo Hu
- College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, China
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6
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Lushchekina SV, Inidjel G, Martinez N, Masson P, Trovaslet-Leroy M, Nachon F, Koza MM, Seydel T, Peters J. Impact of Sucrose as Osmolyte on Molecular Dynamics of Mouse Acetylcholinesterase. Biomolecules 2020; 10:biom10121664. [PMID: 33322722 PMCID: PMC7763276 DOI: 10.3390/biom10121664] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/01/2020] [Accepted: 12/11/2020] [Indexed: 01/28/2023] Open
Abstract
The enzyme model, mouse acetylcholinesterase, which exhibits its active site at the bottom of a narrow gorge, was investigated in the presence of different concentrations of sucrose to shed light on the protein and water dynamics in cholinesterases. The study was conducted by incoherent neutron scattering, giving access to molecular dynamics within the time scale of sub-nano to nanoseconds, in comparison with molecular dynamics simulations. With increasing sucrose concentration, we found non-linear effects, e.g., first a decrease in the dynamics at 5 wt% followed by a gain at 10 wt% sucrose. Direct comparisons with simulations permitted us to understand the following findings: at 5 wt%, sugar molecules interact with the protein surface through water molecules and damp the motions to reduce the overall protein mobility, although the motions inside the gorge are enhanced due to water depletion. When going to 10 wt% of sucrose, some water molecules at the protein surface are replaced by sugar molecules. By penetrating the protein surface, they disrupt some of the intra-protein contacts, and induce new ones, creating new pathways for correlated motions, and therefore, increasing the dynamics. This exhaustive study allowed for an explanation of the detail interactions leading to the observed non-linear behavior.
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Affiliation(s)
- Sofya V. Lushchekina
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Gaetan Inidjel
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
- Université Grenoble Alpes, UFR PhITEM, LiPhy, CNRS, 38000 Grenoble, France
| | - Nicolas Martinez
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
- Université Grenoble Alpes, UFR PhITEM, LiPhy, CNRS, 38000 Grenoble, France
| | - Patrick Masson
- Neuropharmacology Laboratory, Kazan Federal University, Kremlevskaya str 18, 480002 Kazan, Russia;
| | - Marie Trovaslet-Leroy
- Institut de Recherche Biomédicale des Armées, 91223 Brétigny sur Orge, France; (M.T.-L.); (F.N.)
| | - Florian Nachon
- Institut de Recherche Biomédicale des Armées, 91223 Brétigny sur Orge, France; (M.T.-L.); (F.N.)
| | - Michael Marek Koza
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
| | - Tilo Seydel
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
| | - Judith Peters
- Institut Laue Langevin, 38000 Grenoble, France; (G.I.); (N.M.); (M.M.K.); (T.S.)
- Université Grenoble Alpes, UFR PhITEM, LiPhy, CNRS, 38000 Grenoble, France
- Correspondence: ; Tel.: +33-4-7620-7560
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Spontaneous Hinge-Bending Motions of Angiotensin I Converting Enzyme: Role in Activation and Inhibition. Molecules 2020; 25:molecules25061288. [PMID: 32178362 PMCID: PMC7146279 DOI: 10.3390/molecules25061288] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 11/28/2022] Open
Abstract
The inhibition of human angiotensin I converting enzyme (ACE) has been regarded as a promising approach for the treatment of hypertension. Despite research attempts over many years, our understanding the mechanisms of activation and inhibition of ACE is still far from complete. Here, we present results of all atom molecular dynamics simulations of ACE with and without ligands. Two types of inhibitors, competitive and mixed non-competitive, were used to model the ligand bound forms. In the absence of a ligand the simulation showed spontaneous large hinge-bending motions of multiple conversions between the closed and open states of ACE, while the ligand bound forms were stable in the closed state. Our simulation results imply that the equilibrium between pre-existing backbone conformations shifts in the presence of a ligand. The hinge-bending motion of ACE is considered as an essential to the enzyme function. A mechanistic model of activation and the inhibition may provide valuable information for novel inhibitors of ACE.
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Alawi MS, Awad TA, Mohamed MA, Khalid A, Ismail EMO, Alfatih F, Naz S, UL-Haq Z. Insights into the molecular basis of acetylcholinesterase inhibition by xanthones: an integrative in silico and in vitro approach. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2019.1691203] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mohammed Saeed Alawi
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
| | - Talal Ahmed Awad
- Department of Biochemistry, Medicinal and Aromatic Plants Traditional Medicine and Research Institute, National Center for Research, Khartoum, Sudan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Science and Technology, Khartoum, Sudan
| | - Magdi Awadalla Mohamed
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Khartoum, Khartoum, Sudan
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Asaad Khalid
- Department of Biochemistry, Medicinal and Aromatic Plants Traditional Medicine and Research Institute, National Center for Research, Khartoum, Sudan
- Substance Abuse and Toxicology Research Center, Jazan University, Jazan, Saudi Arabia
| | - Esraa M. O. Ismail
- Department of Biochemistry, Medicinal and Aromatic Plants Traditional Medicine and Research Institute, National Center for Research, Khartoum, Sudan
| | - Fatima Alfatih
- Department of Biochemistry, Medicinal and Aromatic Plants Traditional Medicine and Research Institute, National Center for Research, Khartoum, Sudan
| | - Sehrish Naz
- Dr. Pajwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan
| | - Zaheer UL-Haq
- Dr. Pajwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan
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9
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Li D, Ji B. Protein conformational transitions coupling with ligand interactions: Simulations from molecules to medicine. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2019. [DOI: 10.1016/j.medntd.2019.100026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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10
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Gorge Motions of Acetylcholinesterase Revealed by Microsecond Molecular Dynamics Simulations. Sci Rep 2017; 7:3219. [PMID: 28607438 PMCID: PMC5468367 DOI: 10.1038/s41598-017-03088-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 04/11/2017] [Indexed: 11/27/2022] Open
Abstract
Acetylcholinesterase, with a deep, narrow active-site gorge, attracts enormous interest due to its particularly high catalytic efficiency and its inhibitors used for treatment of Alzheimer’s disease. To facilitate the massive pass-through of the substrate and inhibitors, “breathing” motions to modulate the size of the gorge are an important prerequisite. However, the molecular mechanism that governs such motions is not well explored. Here, to systematically investigate intrinsic motions of the enzyme, we performed microsecond molecular dynamics simulations on the monomer and dimer of Torpedo californica acetylcholinesterase (TcAChE) as well as the complex of TcAChE bound with the drug E2020. It has been revealed that protein-ligand interactions and dimerization both keep the gorge in bulk, and opening events of the gorge increase dramatically compared to the monomer. Dynamics of three subdomains, S3, S4 and the Ω-loop, are tightly associated with variations of the gorge size while the dynamics can be changed by ligand binding or protein dimerization. Moreover, high correlations among these subdomains provide a basis for remote residues allosterically modulating the gorge motions. These observations are propitious to expand our understanding of protein structure and function as well as providing clues for performing structure-based drug design.
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11
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Friedrich SM, Liu KJ, Wang TH. Single Molecule Hydrodynamic Separation Allows Sensitive and Quantitative Analysis of DNA Conformation and Binding Interactions in Free Solution. J Am Chem Soc 2016; 138:319-27. [PMID: 26684193 PMCID: PMC4812671 DOI: 10.1021/jacs.5b10983] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Limited tools exist that are capable of monitoring nucleic acid conformations, fluctuations, and distributions in free solution environments. Single molecule free solution hydrodynamic separation enables the unique ability to quantitatively analyze nucleic acid biophysics in free solution. Single molecule fluorescent burst data and separation chromatograms can give layered insight into global DNA conformation, binding interactions, and molecular distributions. First, we show that global conformation of individual DNA molecules can be directly visualized by examining single molecule fluorescent burst shapes and that DNA exists in a dynamic equilibrium of fluctuating conformations as it is driven by Poiseuille flow through micron-sized channels. We then show that this dynamic equilibrium of DNA conformations is reflected as shifts in hydrodynamic mobility that can be perturbed using salt and ionic strength to affect packing density. Next, we demonstrate that these shifts in hydrodynamic mobility can be used to investigate hybridization thermodynamics and binding interactions. We distinguish and classify multiple interactions within a single sample, and demonstrate quantification amidst large concentration differences for the detection of rare species. Finally, we demonstrate that these differences can resolve perfect complement, 2 bp mismatched, and 3 bp mismatched sequences. Such a system can be used to garner diverse information about DNA conformation and structure, and potentially be extended to other molecules and mixed-species interactions, such as between nucleic acids and proteins or synthetic polymers.
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Affiliation(s)
- Sarah M. Friedrich
- Biomedical Engineering Department, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Kelvin J. Liu
- Biomedical Engineering Department, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
- Mechanical Engineering Department, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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12
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Abdelhameed R, Elgawish MS, Mira A, Ibrahim AK, Ahmed SA, Shimizu K, Yamada K. Anti-choline esterase activity of ceramides from the Red Sea marine sponge Mycale euplectellioides. RSC Adv 2016. [DOI: 10.1039/c5ra26424c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
New ceramides were isolated, and structurally elucidated, from the marine sponge Mycale euplectellioides. The isolated compounds showed moderate anti-choline esterase activity in vitro and tight binding to AChE as confirmed through a docking study.
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Affiliation(s)
- Reda Abdelhameed
- Graduate School of Biomedical Sciences
- Nagasaki University
- Nagasaki 852-8521
- Japan
- Pharmacognosy Department
| | - Mohamed Saleh Elgawish
- Medicinal Chemistry Department
- Faculty of Pharmacy
- Suez Canal University
- Ismailia 41522
- Egypt
| | - Amira Mira
- Pharmacognosy Department
- Faculty of Pharmacy
- Mansoura University
- Mansoura 35516
- Egypt
| | - Amany K. Ibrahim
- Pharmacognosy Department
- Faculty of Pharmacy
- Suez Canal University
- Ismailia 41522
- Egypt
| | - Safwat A. Ahmed
- Pharmacognosy Department
- Faculty of Pharmacy
- Suez Canal University
- Ismailia 41522
- Egypt
| | - Kuniyoshi Shimizu
- Division of Systematic Forest and Forest Products Sciences
- Department of Agroenvironmental Sciences
- Faculty of Agriculture
- Graduate School of Kyushu University
- Fukouka 812-8581
| | - Koji Yamada
- Graduate School of Biomedical Sciences
- Nagasaki University
- Nagasaki 852-8521
- Japan
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13
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Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis. Future Med Chem 2015; 7:2317-31. [DOI: 10.4155/fmc.15.150] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aim: Molecular dynamics simulations and normal mode analysis are well-established approaches to generate receptor conformational ensembles (RCEs) for ligand docking and virtual screening. Here, we report new fast molecular dynamics-based and normal mode analysis-based protocols combined with conformational pocket classifications to efficiently generate RCEs. Materials & Methods: We assessed our protocols on two well-characterized protein targets showing local active site flexibility, dihydrofolate reductase and large collective movements, CDK2. The performance of the RCEs was validated by distinguishing known ligands of dihydrofolate reductase and CDK2 among a dataset of diverse chemical decoys. Results & discussion: Our results show that different simulation protocols can be efficient for generation of RCEs depending on different kind of protein flexibility.[Formula: see text]
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14
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Mottin M, Souza PCT, Skaf MS. Molecular Recognition of PPARγ by Kinase Cdk5/p25: Insights from a Combination of Protein–Protein Docking and Adaptive Biasing Force Simulations. J Phys Chem B 2015; 119:8330-9. [DOI: 10.1021/acs.jpcb.5b04269] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Melina Mottin
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, Campinas, São Paulo 13082-864, Brazil
| | - Paulo C. T. Souza
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, Campinas, São Paulo 13082-864, Brazil
| | - Munir S. Skaf
- Institute of Chemistry, University of Campinas-UNICAMP, P.O. Box 6154, Campinas, São Paulo 13082-864, Brazil
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15
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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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16
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Trapp M, Tehei M, Trovaslet M, Nachon F, Martinez N, Koza MM, Weik M, Masson P, Peters J. Correlation of the dynamics of native human acetylcholinesterase and its inhibited huperzine A counterpart from sub-picoseconds to nanoseconds. J R Soc Interface 2015; 11:20140372. [PMID: 24872501 DOI: 10.1098/rsif.2014.0372] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It is a long debated question whether catalytic activities of enzymes, which lie on the millisecond timescale, are possibly already reflected in variations in atomic thermal fluctuations on the pico- to nanosecond timescale. To shed light on this puzzle, the enzyme human acetylcholinesterase in its wild-type form and complexed with the inhibitor huperzine A were investigated by various neutron scattering techniques and molecular dynamics simulations. Previous results on elastic neutron scattering at various timescales and simulations suggest that dynamical processes are not affected on average by the presence of the ligand within the considered time ranges between 10 ps and 1 ns. In the work presented here, the focus was laid on quasi-elastic (QENS) and inelastic neutron scattering (INS). These techniques give access to different kinds of individual diffusive motions and to the density of states of collective motions at the sub-picoseconds timescale. Hence, they permit going beyond the first approach of looking at mean square displacements. For both samples, the autocorrelation function was well described by a stretched-exponential function indicating a linkage between the timescales of fast and slow functional relaxation dynamics. The findings of the QENS and INS investigation are discussed in relation to the results of our earlier elastic incoherent neutron scattering and molecular dynamics simulations.
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Affiliation(s)
- M Trapp
- Helmholtz-Zentrum Berlin für Materialien und Energie, Lise-Meitner Campus, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - M Tehei
- School of Chemistry, University of Wollongong, New South Wales 2522, Australia Centre for Medical Bioscience, Australian Institute of Nuclear Science and Engineering (AINSE), Menai, New South Wales, Australia
| | - M Trovaslet
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075, CNRS-CEA-UJF, 38042 Grenoble Cédex 9, France Institut de Recherche Biomédicale des Armées, 91223 Brétigny sur Orge, France
| | - F Nachon
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075, CNRS-CEA-UJF, 38042 Grenoble Cédex 9, France Institut de Recherche Biomédicale des Armées, 91223 Brétigny sur Orge, France
| | - N Martinez
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075, CNRS-CEA-UJF, 38042 Grenoble Cédex 9, France Institut Laue Langevin, 38042 Grenoble Cédex 9, France Université Joseph Fourier, UFR PhITEM, 38041 Grenoble Cédex 9, France
| | - M M Koza
- Institut Laue Langevin, 38042 Grenoble Cédex 9, France
| | - M Weik
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075, CNRS-CEA-UJF, 38042 Grenoble Cédex 9, France
| | - P Masson
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075, CNRS-CEA-UJF, 38042 Grenoble Cédex 9, France
| | - J Peters
- Institut de Biologie Structurale J.-P. Ebel, UMR 5075, CNRS-CEA-UJF, 38042 Grenoble Cédex 9, France Institut Laue Langevin, 38042 Grenoble Cédex 9, France Université Joseph Fourier, UFR PhITEM, 38041 Grenoble Cédex 9, France
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17
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Tanoli NU, Tanoli SAK, Ferreira AG, Gul S, Ul-Haq Z. Evaluation of binding competition and group epitopes of acetylcholinesterase inhibitors by STD NMR, Tr-NOESY, DOSY and molecular docking: an old approach but new findings. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00231a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We suggest that the small inhibitors of AChE like coumarin and gallic acid's structure-based scaffolds may help in controlling Alzheimer's disease.
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Affiliation(s)
- Nazish U. Tanoli
- Laboratory of Nuclear Magnetic Resonance Federal University of Sao Carlos
- Rodovia Washington Luiz
- Brazil
| | - Sheraz A. K. Tanoli
- Laboratory of Nuclear Magnetic Resonance Federal University of Sao Carlos
- Rodovia Washington Luiz
- Brazil
| | - Antonio G. Ferreira
- Laboratory of Nuclear Magnetic Resonance Federal University of Sao Carlos
- Rodovia Washington Luiz
- Brazil
| | - Sana Gul
- Dr. Panjwani Center for Molecular Medicine and Drug Research
- International Center for Chemicals and Biological Sciences
- University of Karachi
- Karachi-75210
- Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research
- International Center for Chemicals and Biological Sciences
- University of Karachi
- Karachi-75210
- Pakistan
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18
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Seniya C, Khan GJ, Uchadia K. Identification of potential herbal inhibitor of acetylcholinesterase associated Alzheimer's disorders using molecular docking and molecular dynamics simulation. Biochem Res Int 2014; 2014:705451. [PMID: 25054066 PMCID: PMC4099354 DOI: 10.1155/2014/705451] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 03/31/2014] [Indexed: 11/17/2022] Open
Abstract
Cholinesterase inhibitors (ChE-Is) are the standard for the therapy of AD associated disorders and are the only class of approved drugs by the Food and Drug Administration (FDA). Additionally, acetylcholinesterase (AChE) is the target for many Alzheimer's dementia drugs which block the function of AChE but have some side effects. Therefore, in this paper, an attempt was made to elucidate cholinesterase inhibition potential of secondary metabolite from Cannabis plant which has negligible or no side effect. Molecular docking of 500 herbal compounds, against AChE, was performed using Autodock 4.2 as per the standard protocols. Molecular dynamics simulations have also been carried out to check stability of binding complex in water for 1000 ps. Our molecular docking and simulation have predicted high binding affinity of secondary metabolite (C28H34N2O6) to AChE. Further, molecular dynamics simulations for 1000 ps suggest that ligand interaction with the residues Asp72, Tyr70-121-334, and Phe288 of AChE, all of which fall under active site/subsite or binding pocket, might be critical for the inhibitory activity of AChE. This approach might be helpful to understand the selectivity of the given drug molecule in the treatment of Alzheimer's disease. The study provides evidence for consideration of C28H34N2O6 as a valuable small ligand molecule in treatment and prevention of AD associated disorders and further in vitro and in vivo investigations may prove its therapeutic potential.
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Affiliation(s)
- Chandrabhan Seniya
- Department of Biotechnology, Madhav Institute of Technology and Science, Race Course Road, Gola Ka Mandir, Gwalior 474005, India
- School of Engineering, The University of Warwick, Coventry CV4 7AL, UK
| | - Ghulam Jilani Khan
- Profarm Seed India Pvt. Ltd, 9 Anthem, Gundala Pochampally Village, Secunderabad, Andhra Pradesh 500014, India
| | - Kuldeep Uchadia
- Department of Biotechnology, Madhav Institute of Technology and Science, Race Course Road, Gola Ka Mandir, Gwalior 474005, India
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19
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Molecular dynamics simulations indicate an induced-fit mechanism for LSD1/CoREST-H3-histone molecular recognition. BMC BIOPHYSICS 2013; 6:15. [PMID: 24274367 PMCID: PMC4175114 DOI: 10.1186/2046-1682-6-15] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 10/30/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND Lysine Specific Demethylase (LSD1 or KDM1A) in complex with its co-repressor protein CoREST catalyzes the demethylation of the H3 histone N-terminal tail and is currently one of the most promising epigenetic targets for drug discovery against cancer and neurodegenerative diseases. Models of non-covalent binding, such as lock and key, induced-fit, and conformational selection could help explaining the molecular mechanism of LSD1/CoREST-H3-histone association, thus guiding drug discovery and design efforts. Here, we quantify the extent to which LSD1/CoREST substrate binding is consistent with these hypothetical models using LSD1/CoREST conformational ensembles obtained through extensive explicit solvent molecular dynamics (MD) simulations. RESULTS We find that an induced-fit model is the most representative of LSD1/CoREST-H3-histone non-covalent binding and accounts for the local conformational changes occurring in the H3-histone binding site. We also show that conformational selection - despite in principle not ruled out by this finding - is minimal, and only relevant when global properties are considered, e.g. the nanoscale motion of the LSD1/CoREST clamp. CONCLUSION The induced-fit mechanism revealed by our MD simulation study will aid the inclusion of protein dynamics for the discovery and design of LSD1 inhibitors targeting the H3-histone binding region. On a general basis, our study indicates the importance of using multiple metrics or selection schemes when testing alternative hypothetical mechanistic models of non-covalent binding.
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20
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Masson P. Time-dependent kinetic complexities in cholinesterase-catalyzed reactions. BIOCHEMISTRY (MOSCOW) 2013; 77:1147-61. [PMID: 23157295 DOI: 10.1134/s0006297912100070] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Cholinesterases (ChEs) display a hysteretic behavior with certain substrates and inhibitors. Kinetic cooperativity in hysteresis of ChE-catalyzed reactions is characterized by a lag or burst phase in the approach to steady state. With some substrates damped oscillations are shown to superimpose on hysteretic lags. These time dependent peculiarities are observed for both butyrylcholinesterase and acetylcholinesterase from different sources. Hysteresis in ChE-catalyzed reactions can be interpreted in terms of slow transitions between two enzyme conformers E and E'. Substrate can bind to E and/or E', both Michaelian complexes ES and Ε'S can be catalytically competent, or only one of them can make products. The formal reaction pathway depends on both the chemical structure of the substrate and the type of enzyme. In particular, damped oscillations develop when substrate exists in different, slowly interconvertible, conformational, and/or micellar forms, of which only the minor form is capable of binding and reacting with the enzyme. Biphasic pseudo-first-order progressive inhibition of ChEs by certain carbamates and organophosphates also fits with a slow equilibrium between two reactive enzyme forms. Hysteresis can be modulated by medium parameters (pH, chaotropic and kosmotropic salts, organic solvents, temperature, osmotic pressure, and hydrostatic pressure). These studies showed that water structure plays a role in hysteretic behavior of ChEs. Attempts to provide a molecular mechanism for ChE hysteresis from mutagenesis studies or crystallographic studies failed so far. In fact, several lines of evidence suggest that hysteresis is controlled by the conformation of His438, a key residue in the catalytic triad of cholinesterases. Induction time may depend on the probability of His438 to adopt the operative conformation in the catalytic triad. The functional significance of ChE hysteresis is puzzling. However, the accepted view that proteins are in equilibrium between preexisting functional and non-functional conformers, and that binding of a ligand to the functional form shifts equilibrium towards the functional conformation, suggests that slow equilibrium between two conformational states of these enzymes may have a regulatory function in damping out the response to certain ligands and irreversible inhibitors. This is particularly true for immobilized (membrane bound) enzymes where the local substrate and/or inhibitor concentrations depend on influx in crowded organellar systems, e.g. cholinergic synaptic clefts. Therefore, physiological or toxicological relevance of the hysteretic behavior and damped oscillations in ChE-catalyzed reactions and inhibition cannot be ruled out.
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Affiliation(s)
- P Masson
- Institut de Recherches Biomédicales des Armées-CRSSA, La Tronche, Cedex 38702, France.
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21
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Carletti E, Colletier JP, Schopfer LM, Santoni G, Masson P, Lockridge O, Nachon F, Weik M. Inhibition Pathways of the Potent Organophosphate CBDP with Cholinesterases Revealed by X-ray Crystallographic Snapshots and Mass Spectrometry. Chem Res Toxicol 2013; 26:280-9. [DOI: 10.1021/tx3004505] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eugénie Carletti
- Institut de Biologie Structurale
J.P. Ebel, Commissariat à l’Energie Atomique, 41, rue Jules Horowitz, F-38027 Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, F-38000 Grenoble, France
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, 24 avenue des Marquis du Grésivaudan, 38702 La Tronche,
France
| | - Jacques-Philippe Colletier
- Institut de Biologie Structurale
J.P. Ebel, Commissariat à l’Energie Atomique, 41, rue Jules Horowitz, F-38027 Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, F-38000 Grenoble, France
| | - Lawrence M. Schopfer
- Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska
68198-5950, United States
| | - Gianluca Santoni
- Institut de Biologie Structurale
J.P. Ebel, Commissariat à l’Energie Atomique, 41, rue Jules Horowitz, F-38027 Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, F-38000 Grenoble, France
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, 24 avenue des Marquis du Grésivaudan, 38702 La Tronche,
France
| | - Patrick Masson
- Institut de Biologie Structurale
J.P. Ebel, Commissariat à l’Energie Atomique, 41, rue Jules Horowitz, F-38027 Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, F-38000 Grenoble, France
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, 24 avenue des Marquis du Grésivaudan, 38702 La Tronche,
France
- Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska
68198-5950, United States
| | - Oksana Lockridge
- Eppley Institute, University of Nebraska Medical Center, Omaha, Nebraska
68198-5950, United States
| | - Florian Nachon
- Département de Toxicologie, Institut de Recherche Biomédicale des Armées, 24 avenue des Marquis du Grésivaudan, 38702 La Tronche,
France
| | - Martin Weik
- Institut de Biologie Structurale
J.P. Ebel, Commissariat à l’Energie Atomique, 41, rue Jules Horowitz, F-38027 Grenoble, France
- CNRS, UMR5075, F-38027 Grenoble,
France
- Université Joseph Fourier, F-38000 Grenoble, France
- ESRF, 6
rue Jules Horowitz, BP 220, 38043 Grenoble Cedex, France
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22
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Minh DDL. Implicit ligand theory: rigorous binding free energies and thermodynamic expectations from molecular docking. J Chem Phys 2012; 137:104106. [PMID: 22979849 PMCID: PMC3460968 DOI: 10.1063/1.4751284] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 08/23/2012] [Indexed: 01/24/2023] Open
Abstract
A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor configurations only need to be sampled once, facilitating the use of binding free energy calculations in virtual screening. Demonstrative calculations on a host-guest system yield good agreement with previous free energy calculations and isothermal titration calorimetry measurements. Implicit ligand theory provides guidance on how to improve existing molecular docking algorithms and insight into the concepts of induced fit and conformational selection in noncovalent macromolecular recognition.
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Affiliation(s)
- David D L Minh
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA.
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23
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Ode H, Nakashima M, Kitamura S, Sugiura W, Sato H. Molecular dynamics simulation in virus research. Front Microbiol 2012; 3:258. [PMID: 22833741 PMCID: PMC3400276 DOI: 10.3389/fmicb.2012.00258] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 07/02/2012] [Indexed: 01/24/2023] Open
Abstract
Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the structures and dynamics of the proteins. Molecular dynamics (MD) simulation is a powerful computational method for delineating motions of proteins at an atomic-scale via theoretical and empirical principles in physical chemistry. Recent advances in the hardware and software for biomolecular simulation have rapidly improved the precision and performance of this technique. Consequently, MD simulation is quickly extending the range of applications in biology, helping to reveal unique features of protein structures that would be hard to obtain by experimental methods alone. In this review, we summarize the recent advances in MD simulations in the study of virus–host interactions and evolution, and present future perspectives on this technique.
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Affiliation(s)
- Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center Nagoya, Aichi, Japan
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24
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Kondo HX, Okimoto N, Morimoto G, Taiji M. Free-Energy Landscapes of Protein Domain Movements upon Ligand Binding. J Phys Chem B 2011; 115:7629-36. [DOI: 10.1021/jp111902t] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hiroko X. Kondo
- High-Performance Molecular Simulation Team, Computational Systems Biology Research Group, RIKEN Advanced Science Institute, 61-1 Ono-cho, Tsurumi, Yokohama, Japan 230-0046
- Department of Computational Biology, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Japan 277-8561
| | - Noriaki Okimoto
- High-Performance Molecular Simulation Team, Computational Systems Biology Research Group, RIKEN Advanced Science Institute, 61-1 Ono-cho, Tsurumi, Yokohama, Japan 230-0046
| | - Gentaro Morimoto
- High-Performance Molecular Simulation Team, Computational Systems Biology Research Group, RIKEN Advanced Science Institute, 61-1 Ono-cho, Tsurumi, Yokohama, Japan 230-0046
| | - Makoto Taiji
- High-Performance Molecular Simulation Team, Computational Systems Biology Research Group, RIKEN Advanced Science Institute, 61-1 Ono-cho, Tsurumi, Yokohama, Japan 230-0046
- Department of Computational Biology, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Japan 277-8561
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25
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Lu SH, Wu JW, Liu HL, Zhao JH, Liu KT, Chuang CK, Lin HY, Tsai WB, Ho Y. The discovery of potential acetylcholinesterase inhibitors: a combination of pharmacophore modeling, virtual screening, and molecular docking studies. J Biomed Sci 2011; 18:8. [PMID: 21251245 PMCID: PMC3036604 DOI: 10.1186/1423-0127-18-8] [Citation(s) in RCA: 115] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Accepted: 01/21/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common cause of dementia characterized by progressive cognitive impairment in the elderly people. The most dramatic abnormalities are those of the cholinergic system. Acetylcholinesterase (AChE) plays a key role in the regulation of the cholinergic system, and hence, inhibition of AChE has emerged as one of the most promising strategies for the treatment of AD. METHODS In this study, we suggest a workflow for the identification and prioritization of potential compounds targeted against AChE. In order to elucidate the essential structural features for AChE, three-dimensional pharmacophore models were constructed using Discovery Studio 2.5.5 (DS 2.5.5) program based on a set of known AChE inhibitors. RESULTS The best five-features pharmacophore model, which includes one hydrogen bond donor and four hydrophobic features, was generated from a training set of 62 compounds that yielded a correlation coefficient of R = 0.851 and a high prediction of fit values for a set of 26 test molecules with a correlation of R² = 0.830. Our pharmacophore model also has a high Güner-Henry score and enrichment factor. Virtual screening performed on the NCI database obtained new inhibitors which have the potential to inhibit AChE and to protect neurons from Aβ toxicity. The hit compounds were subsequently subjected to molecular docking and evaluated by consensus scoring function, which resulted in 9 compounds with high pharmacophore fit values and predicted biological activity scores. These compounds showed interactions with important residues at the active site. CONCLUSIONS The information gained from this study may assist in the discovery of potential AChE inhibitors that are highly selective for its dual binding sites.
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Affiliation(s)
- Shin-Hua Lu
- Graduate Institute of Biotechnology, National Taipei University of Technology, 1 Sec. 3 ZhongXiao E, Rd., Taipei, 10608, Taiwan
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27
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Mining electron density for functionally relevant protein polysterism in crystal structures. Cell Mol Life Sci 2010; 68:1829-41. [PMID: 21190057 PMCID: PMC3092063 DOI: 10.1007/s00018-010-0611-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 11/18/2010] [Accepted: 12/09/2010] [Indexed: 11/26/2022]
Abstract
This review focuses on conceptual and methodological advances in our understanding and characterization of the conformational heterogeneity of proteins. Focusing on X-ray crystallography, we describe how polysterism, the interconversion of pre-existing conformational substates, has traditionally been analyzed by comparing independent crystal structures or multiple chains within a single crystal asymmetric unit. In contrast, recent studies have focused on mining electron density maps to reveal previously ‘hidden’ minor conformational substates. Functional tests of the importance of minor states suggest that evolutionary selection shapes the entire conformational landscape, including uniquely configured conformational substates, the relative distribution of these substates, and the speed at which the protein can interconvert between them. An increased focus on polysterism may shape the way protein structure and function is studied in the coming years.
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29
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Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework. Q Rev Biophys 2010; 43:295-332. [DOI: 10.1017/s0033583510000119] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AbstractEnergy landscape theories have provided a common ground for understanding the protein folding problem, which once seemed to be overwhelmingly complicated. At the same time, the native state was found to be an ensemble of interconverting states with frustration playing a more important role compared to the folding problem. The landscape of the folded protein – the native landscape – is glassier than the folding landscape; hence, a general description analogous to the folding theories is difficult to achieve. On the other hand, the native basin phase volume is much smaller, allowing a protein to fully sample its native energy landscape on the biological timescales. Current computational resources may also be used to perform this sampling for smaller proteins, to build a ‘topographical map’ of the native landscape that can be used for subsequent analysis. Several major approaches to representing this topographical map are highlighted in this review, including the construction of kinetic networks, hierarchical trees and free energy surfaces with subsequent structural and kinetic analyses. In this review, we extensively discuss the important question of choosing proper collective coordinates characterizing functional motions. In many cases, the substates on the native energy landscape, which represent different functional states, can be used to obtain variables that are well suited for building free energy surfaces and analyzing the protein's functional dynamics. Normal mode analysis can provide such variables in cases where functional motions are dictated by the molecule's architecture. Principal component analysis is a more expensive way of inferring the essential variables from the protein's motions, one that requires a long molecular dynamics simulation. Finally, the two popular models for the allosteric switching mechanism, ‘preexisting equilibrium’ and ‘induced fit’, are interpreted within the energy landscape paradigm as extreme points of a continuum of transition mechanisms. Some experimental evidence illustrating each of these two models, as well as intermediate mechanisms, is presented and discussed.
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30
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Bahar I, Lezon TR, Yang LW, Eyal E. Global dynamics of proteins: bridging between structure and function. Annu Rev Biophys 2010; 39:23-42. [PMID: 20192781 DOI: 10.1146/annurev.biophys.093008.131258] [Citation(s) in RCA: 446] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for elucidating the collective dynamics intrinsically accessible under native state conditions, including in particular the global modes of motions that are robustly defined by the overall architecture. With increasing availability of structural data for well-studied proteins in different forms (liganded, complexed, or free), there is increasing evidence in support of the correspondence between functional changes in structures observed in experiments and the global motions predicted by these coarse-grained analyses. These observed correlations suggest that computational methods may be advantageously employed for assessing functional changes in structure and allosteric mechanisms intrinsically favored by the native fold.
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Affiliation(s)
- Ivet Bahar
- Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
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31
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Dvir H, Silman I, Harel M, Rosenberry TL, Sussman JL. Acetylcholinesterase: from 3D structure to function. Chem Biol Interact 2010; 187:10-22. [PMID: 20138030 DOI: 10.1016/j.cbi.2010.01.042] [Citation(s) in RCA: 456] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Revised: 01/26/2010] [Accepted: 01/28/2010] [Indexed: 11/28/2022]
Abstract
By rapid hydrolysis of the neurotransmitter, acetylcholine, acetylcholinesterase terminates neurotransmission at cholinergic synapses. Acetylcholinesterase is a very fast enzyme, functioning at a rate approaching that of a diffusion-controlled reaction. The powerful toxicity of organophosphate poisons is attributed primarily to their potent inhibition of acetylcholinesterase. Acetylcholinesterase inhibitors are utilized in the treatment of various neurological disorders, and are the principal drugs approved thus far by the FDA for management of Alzheimer's disease. Many organophosphates and carbamates serve as potent insecticides, by selectively inhibiting insect acetylcholinesterase. The determination of the crystal structure of Torpedo californica acetylcholinesterase permitted visualization, for the first time, at atomic resolution, of a binding pocket for acetylcholine. It also allowed identification of the active site of acetylcholinesterase, which, unexpectedly, is located at the bottom of a deep gorge lined largely by aromatic residues. The crystal structure of recombinant human acetylcholinesterase in its apo-state is similar in its overall features to that of the Torpedo enzyme; however, the unique crystal packing reveals a novel peptide sequence which blocks access to the active-site gorge.
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Affiliation(s)
- Hay Dvir
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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32
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Sanson B, Nachon F, Colletier JP, Froment MT, Toker L, Greenblatt HM, Sussman JL, Ashani Y, Masson P, Silman I, Weik M. Crystallographic snapshots of nonaged and aged conjugates of soman with acetylcholinesterase, and of a ternary complex of the aged conjugate with pralidoxime. J Med Chem 2009; 52:7593-603. [PMID: 19642642 DOI: 10.1021/jm900433t] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Organophosphate compounds (OP) are potent inhibitors of acetylcholinesterases (AChEs) and can cause lethal poisoning in humans. Inhibition of AChEs by the OP soman involves phosphonylation of the catalytic serine, and subsequent dealkylation produces a form known as the "aged" enzyme. The nonaged form can be reactivated to a certain extent by nucleophiles, such as pralidoxime (2-PAM), whereas aged forms of OP-inhibited AChEs are totally resistant to reactivation. Here, we solved the X-ray crystal structures of AChE from Torpedo californica (TcAChE) conjugated with soman before and after aging. The absolute configuration of the soman stereoisomer adduct in the nonaged conjugate is P(S)C(R). A structural reorientation of the catalytic His440 side chain was observed during the aging process. Furthermore, the crystal structure of the ternary complex of the aged conjugate with 2-PAM revealed that the orientation of the oxime function does not permit nucleophilic attack on the phosphorus atom, thus providing a plausible explanation for its failure to reactivate the aged soman/AChE conjugate. Together, these three crystal structures provide an experimental basis for the design of new reactivators.
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Affiliation(s)
- Benoît Sanson
- Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale Jean-Pierre Ebel, Commissariat à l'Energie Atomique, Centre National de la Recherche Scientifique, Université Joseph Fourier, 41 Rue Jules Horowitz, 38027 Grenoble, France
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33
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Fernandes CL, Sachett LG, Pol-Fachin L, Verli H. GROMOS96 43a1 performance in predicting oligosaccharide conformational ensembles within glycoproteins. Carbohydr Res 2009; 345:663-71. [PMID: 20106471 DOI: 10.1016/j.carres.2009.12.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 12/14/2009] [Accepted: 12/18/2009] [Indexed: 11/29/2022]
Abstract
In previous work [Pol-Fachin, L.; Fernandes, C. L.; Verli, H.; Carbohydr. Res.2009, 344, 491-500], we had demonstrated that GROMOS96 43a1 force field and Löwdin HF/6-31G * *-derived atomic charges, adequately represent a glycoprotein's conformational ensemble in aqueous solutions, taking as the starting geometries NMR-determined structures. Based on such data, the present work intends to evaluate the use of the main solution conformations of isolated disaccharides, to build the carbohydrate moiety of glycoproteins, for which no previous experimental information is available. The observed results suggested that the entire glycoprotein scaffold appears unable to promote major modifications in the conformational behavior of glycosidic linkages. Additionally, when compared to energy contour plots, the results support the use of solution ensembles, to refine vacuum conformations of carbohydrate databases in the assembling of glycoproteins 3D structures. Finally, such approach is applied to build a full glycosylated model for COX-1 and COX-2 enzymes.
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Affiliation(s)
- C L Fernandes
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Av Bento Gonçalves 9500, CP 15005, Porto Alegre 91500-970, RS, Brazil
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Bartolucci C, Haller LA, Jordis U, Fels G, Lamba D. Probing Torpedo californica Acetylcholinesterase Catalytic Gorge with Two Novel Bis-functional Galanthamine Derivatives. J Med Chem 2009; 53:745-51. [DOI: 10.1021/jm901296p] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cecilia Bartolucci
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Area della Ricerca di Roma, P.O. Box 10, I-00016 Monterotondo Stazione(Roma), Italy
| | - Lars A. Haller
- Department of Chemistry, University of Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany
| | - Ulrich Jordis
- Vienna University of Technology, Institute for Organic Chemistry, Getreidemarkt 9, A-1060 Wien, Austria
| | - Gregor Fels
- Department of Chemistry, University of Paderborn, Warburger Strasse 100, D-33098 Paderborn, Germany
| | - Doriano Lamba
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, UOS di Trieste, Area Science Park, Basovizza S.S 14 Km 163.5, I-34149 Trieste, Italy
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35
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Glazer DS, Radmer RJ, Altman RB. Improving structure-based function prediction using molecular dynamics. Structure 2009; 17:919-29. [PMID: 19604472 DOI: 10.1016/j.str.2009.05.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 05/06/2009] [Accepted: 05/06/2009] [Indexed: 10/20/2022]
Abstract
The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca(2+) binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods.
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Affiliation(s)
- Dariya S Glazer
- Department of Genetics, Stanford University, Clark Center, Stanford, CA 94305, USA
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36
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Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin. Proc Natl Acad Sci U S A 2009; 106:19346-51. [PMID: 19887638 DOI: 10.1073/pnas.0906966106] [Citation(s) in RCA: 156] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Noncovalent binding interactions between proteins are the central physicochemical phenomenon underlying biological signaling and functional control on the molecular level. Here, we perform an extensive structural analysis of a large set of bound and unbound ubiquitin conformers and study the level of residual induced fit after conformational selection in the binding process. We show that the region surrounding the binding site in ubiquitin undergoes conformational changes that are significantly more pronounced compared with the whole molecule on average. We demonstrate that these induced-fit structural adjustments are comparable in magnitude to conformational selection. Our final model of ubiquitin binding blends conformational selection with the subsequent induced fit and provides a quantitative measure of their respective contributions.
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37
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Rashin AA, Rashin AHL, Jernigan RL. Protein flexibility: coordinate uncertainties and interpretation of structural differences. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009; 65:1140-61. [PMID: 19923711 PMCID: PMC2777169 DOI: 10.1107/s090744490903145x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2009] [Accepted: 08/10/2009] [Indexed: 11/10/2022]
Abstract
Valid interpretations of conformational movements in protein structures determined by X-ray crystallography require that the movement magnitudes exceed their uncertainty threshold. Here, it is shown that such thresholds can be obtained from the distance difference matrices (DDMs) of 1014 pairs of independently determined structures of bovine ribonuclease A and sperm whale myoglobin, with no explanations provided for reportedly minor coordinate differences. The smallest magnitudes of reportedly functional motions are just above these thresholds. Uncertainty thresholds can provide objective criteria that distinguish between true conformational changes and apparent 'noise', showing that some previous interpretations of protein coordinate changes attributed to external conditions or mutations may be doubtful or erroneous. The use of uncertainty thresholds, DDMs, the newly introduced CDDMs (contact distance difference matrices) and a novel simple rotation algorithm allows a more meaningful classification and description of protein motions, distinguishing between various rigid-fragment motions and nonrigid conformational deformations. It is also shown that half of 75 pairs of identical molecules, each from the same asymmetric crystallographic cell, exhibit coordinate differences that range from just outside the coordinate uncertainty threshold to the full magnitude of large functional movements. Thus, crystallization might often induce protein conformational changes that are comparable to those related to or induced by the protein function.
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Rueda M, Bottegoni G, Abagyan R. Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. J Chem Inf Model 2009; 49:716-25. [PMID: 19434904 DOI: 10.1021/ci8003732] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The representation of protein flexibility is still a challenge for the state-of-the-art flexible ligand docking protocols. In this article, we use a large and diverse benchmark to prove that is possible to improve consistently the cross-docking performance against a single receptor conformation, using an equilibrium ensemble of binding site conformers. The benchmark contained 28 proteins, and our method predicted the top-ranked near native ligand poses 20% more efficiently than using a single receptor. The multiple conformations were derived from the collective variable space defined by all heavy-atom elastic network normal modes, including backbone and side chains. We have found that the binding site displacements for best positioning of the ligand seem rather independent from the global collective motions of the protein. We also found that the number of binding site conformations needed to represent nonredundant flexibility was < 100. The ensemble of receptor conformations can be generated at our Web site at http://abagyan.scripps.edu/MRC.
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Affiliation(s)
- Manuel Rueda
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, Mail TPC-28, La Jolla, California 92037, USA
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39
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Managing protein flexibility in docking and its applications. Drug Discov Today 2009; 14:394-400. [DOI: 10.1016/j.drudis.2009.01.003] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 12/18/2008] [Accepted: 01/06/2009] [Indexed: 11/21/2022]
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40
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Antoniou C, Lam VQ, Fung LWM. Conformational changes at the tetramerization site of erythroid alpha-spectrin upon binding beta-spectrin: a spin label EPR study. Biochemistry 2008; 47:10765-72. [PMID: 18783249 DOI: 10.1021/bi800840p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We used cysteine scanning, isothermal titration calorimetry (ITC) and spin label EPR methods to study the two regions that flank the partial domain Helix C' of the N-terminal end of alpha-spectrin (residues 14-20 and residues 44-54) in the absence and presence of a model protein of the beta-spectrin C-terminal end. In the absence of beta-spectrin, residues 14-20 and 46-52 were known to be unstructured. The EPR spectral values of the inverse line width (Delta H (-1)) and of the width between the low field peak and the central peak ( aZ) of residues in part of the first unstructured region (residues 17-20) and of most residues in the second unstructured junction region (residues 46-52) changed dramatically upon association with beta-spectrin, suggesting that the two regions undergo a conformational change, becoming more rigid and likely becoming helical. ITC results showed that three of the seven residues in the junction region (residues 46-52) were very important in its association with beta-spectrin, in the following order: L49 > G46 > K48. In general, our results suggest that any mutations that affect the propensity of helical formation in the region spanning residues 17-52 in alpha-spectrin, or that affect hydrophobic clustering and/or salt-bridge stabilization of the bundled helices, would affect spectrin tetramer formation, and may lead to blood disorders.
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Affiliation(s)
- Chloe Antoniou
- Department of Chemistry, University of Illinois at Chicago, 845 West Taylor Street, MC 111, Chicago, Illinois 60607, USA
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Flexibility of aromatic residues in the active-site gorge of acetylcholinesterase: X-ray versus molecular dynamics. Biophys J 2008; 95:2500-11. [PMID: 18502801 DOI: 10.1529/biophysj.108.129601] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The high aromatic content of the deep and narrow active-site gorge of acetylcholinesterase (AChE) is a remarkable feature of this enzyme. Here, we analyze conformational flexibility of the side chains of the 14 conserved aromatic residues in the active-site gorge of Torpedo californica AChE based on the 47 three-dimensional crystal structures available for the native enzyme, and for its complexes and conjugates, and on a 20-ns molecular dynamics (MD) trajectory of the native enzyme. The degree of flexibility of these 14 aromatic side chains is diverse. Although the side-chain conformations of F330 and W279 are both very flexible, the side-chain conformations of F120, W233, W432, Y70, Y121, F288, F290 and F331 appear to be fixed. Residues located on, or adjacent to, the Omega-loop (C67-C94), namely W84, Y130, Y442, and Y334, display different flexibilities in the MD simulations and in the crystal structures. An important outcome of our study is that the majority of the side-chain conformations observed in the 47 Torpedo californica AChE crystal structures are faithfully reproduced by the MD simulation on the native enzyme. Thus, the protein can assume these conformations even in the absence of the ligand that permitted their experimental detection. These observations are pertinent to structure-based drug design.
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