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van der Westhuizen CJ, Stander A, Riley DL, Panayides JL. Discovery of Novel Acetylcholinesterase Inhibitors by Virtual Screening, In Vitro Screening, and Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:1550-1572. [PMID: 35139637 DOI: 10.1021/acs.jcim.1c01443] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Alzheimer's disease is the most common neurodegenerative disease and currently poses a significant socioeconomic problem. This study describes the uses of computer-aided drug discovery techniques to identify novel inhibitors of acetylcholinesterase, a target for Alzheimer's disease. High-throughput virtual screening was employed to predict potential inhibitors of acetylcholinesterase. Validation of enrichment was performed with the DUD-E data set, showing that an ensemble of binding pocket conformations is critical when a diverse set of ligands are being screened. A total of 720 compounds were submitted for in vitro screening, which led to 25 hits being identified with IC50 values of less than 50 μM. The majority of these hits belonged to two scaffolds: 1-ethyl-3-methoxy-3-methylpyrrolidine and 1H-pyrrolo[3,2-c]pyridin-6-amine both of which are noted to be promising compounds for further optimization. As various possible binding poses were suggested from molecular docking, molecular dynamics simulations were employed to validate the poses. In the case of the most active compounds identified, a critical, stable water bridge formed deep within the binding pocket was identified potentially explaining in part the lack of activity for subsets of compounds that are not able to form this water bridge.
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Affiliation(s)
- C Johan van der Westhuizen
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Pretoria 0028, South Africa.,Pharmaceutical Technologies, CSIR Future Production: Chemicals, Meiring Naudé Road, Pretoria 0184, South Africa
| | - André Stander
- Department of Physiology, Faculty of Health Science, University of Pretoria, Lynnwood Road, Pretoria 0031, South Africa
| | - Darren L Riley
- Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Pretoria 0028, South Africa
| | - Jenny-Lee Panayides
- Pharmaceutical Technologies, CSIR Future Production: Chemicals, Meiring Naudé Road, Pretoria 0184, South Africa
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Kong XP, Liu EY, Chen ZC, Xu ML, Yu AX, Wu QY, Xia YJ, Duan R, Dong TT, Tsim KW. Synergistic Inhibition of Acetylcholinesterase by Alkaloids Derived from Stephaniae Tetrandrae Radix, Coptidis Rhizoma and Phellodendri Chinensis Cortex. Molecules 2019; 24:molecules24244567. [PMID: 31847089 PMCID: PMC6943709 DOI: 10.3390/molecules24244567] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 11/30/2019] [Accepted: 12/10/2019] [Indexed: 12/28/2022] Open
Abstract
Alkaloids having acetylcholinesterase (AChE) inhibitory activity are commonly found in traditional Chinese medicine (TCM); for example, berberine from Coptis chinensis, galantamine from Lycoris radiata, and huperzine A from Huperzia serrata. In practice of TCM, Stephaniae Tetrandrae Radix (STR) is often combined with Coptidis Rhizoma (CR) or Phellodendri Chinensis Cortex (PCC) as paired herbs during clinical application. Fangchinoline from STR and coptisine and/or berberine from CR and/or PCC are active alkaloids in inhibiting AChE. The traditional usage of paired herbs suggests the synergistic effect of fangchinoline–coptisine or fangchinoline–berberine pairing in AChE inhibition. HPLC was applied to identify the main components in herbal extracts of STR, CR, and PCC, and the AChE inhibition of their main components was determined by Ellman assay. The synergism of herb combination and active component combination was calculated by median-effect principle. Molecular docking was applied to investigate the underlying binding mechanisms of the active components with the AChE protein. It was found that fangchinoline showed AChE inhibitory potency; furthermore, fangchinoline–coptisine/berberine pairs (at ratios of 1:5, 1:2, 1:1, and 2:1) synergistically inhibited AChE; the combination index (CI) at different ratios was less than one when Fa = 0.5, suggesting synergistic inhibition of AChE. Furthermore, the molecular docking simulation supported this enzymatic inhibition. Therefore, fangchinoline–coptisine/berberine pairs, or their parental herbal mixtures, may potentially be developed as a possible therapeutic strategy for Alzheimer’s patients.
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Affiliation(s)
- Xiang-Peng Kong
- Shenzhen Key Laboratory of Edible and Medicinal Bioresources, HKUST Shenzhen Research Institute, Hi-Tech Park, Shenzhen 518057, China; (X.-P.K.); (Z.-C.C.); (M.L.X.); (Q.-Y.W.); (Y.-J.X.); (R.D.)
- Institute of Pharmaceutical & Food Engineering, Shanxi University of Chinese Medicine, 121 Daxue Road, Yuci District, Jinzhong 030619, China
| | - Etta Y.L. Liu
- Shenzhen Key Laboratory of Edible and Medicinal Bioresources, HKUST Shenzhen Research Institute, Hi-Tech Park, Shenzhen 518057, China; (X.-P.K.); (Z.-C.C.); (M.L.X.); (Q.-Y.W.); (Y.-J.X.); (R.D.)
- Division of Life Science and Center for Chinese Medicine, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Zhi-Cong Chen
- Shenzhen Key Laboratory of Edible and Medicinal Bioresources, HKUST Shenzhen Research Institute, Hi-Tech Park, Shenzhen 518057, China; (X.-P.K.); (Z.-C.C.); (M.L.X.); (Q.-Y.W.); (Y.-J.X.); (R.D.)
- Division of Life Science and Center for Chinese Medicine, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Miranda Li Xu
- Shenzhen Key Laboratory of Edible and Medicinal Bioresources, HKUST Shenzhen Research Institute, Hi-Tech Park, Shenzhen 518057, China; (X.-P.K.); (Z.-C.C.); (M.L.X.); (Q.-Y.W.); (Y.-J.X.); (R.D.)
- Division of Life Science and Center for Chinese Medicine, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Anna X.D. Yu
- Shenzhen Key Laboratory of Edible and Medicinal Bioresources, HKUST Shenzhen Research Institute, Hi-Tech Park, Shenzhen 518057, China; (X.-P.K.); (Z.-C.C.); (M.L.X.); (Q.-Y.W.); (Y.-J.X.); (R.D.)
- Division of Life Science and Center for Chinese Medicine, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Qi-Yun Wu
- Shenzhen Key Laboratory of Edible and Medicinal Bioresources, HKUST Shenzhen Research Institute, Hi-Tech Park, Shenzhen 518057, China; (X.-P.K.); (Z.-C.C.); (M.L.X.); (Q.-Y.W.); (Y.-J.X.); (R.D.)
- Division of Life Science and Center for Chinese Medicine, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Ying-Jie Xia
- Shenzhen Key Laboratory of Edible and Medicinal Bioresources, HKUST Shenzhen Research Institute, Hi-Tech Park, Shenzhen 518057, China; (X.-P.K.); (Z.-C.C.); (M.L.X.); (Q.-Y.W.); (Y.-J.X.); (R.D.)
- Division of Life Science and Center for Chinese Medicine, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Ran Duan
- Shenzhen Key Laboratory of Edible and Medicinal Bioresources, HKUST Shenzhen Research Institute, Hi-Tech Park, Shenzhen 518057, China; (X.-P.K.); (Z.-C.C.); (M.L.X.); (Q.-Y.W.); (Y.-J.X.); (R.D.)
- Division of Life Science and Center for Chinese Medicine, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
| | - Tina T.X. Dong
- Shenzhen Key Laboratory of Edible and Medicinal Bioresources, HKUST Shenzhen Research Institute, Hi-Tech Park, Shenzhen 518057, China; (X.-P.K.); (Z.-C.C.); (M.L.X.); (Q.-Y.W.); (Y.-J.X.); (R.D.)
- Division of Life Science and Center for Chinese Medicine, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Correspondence: (T.T.X.D.); (K.W.K.T.); Tel.: +86-755-8671-5683 (T.T.X.D.); +852-2358-7332 (K.W.K.T.)
| | - Karl W.K. Tsim
- Shenzhen Key Laboratory of Edible and Medicinal Bioresources, HKUST Shenzhen Research Institute, Hi-Tech Park, Shenzhen 518057, China; (X.-P.K.); (Z.-C.C.); (M.L.X.); (Q.-Y.W.); (Y.-J.X.); (R.D.)
- Division of Life Science and Center for Chinese Medicine, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
- Correspondence: (T.T.X.D.); (K.W.K.T.); Tel.: +86-755-8671-5683 (T.T.X.D.); +852-2358-7332 (K.W.K.T.)
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Liu JX, Zhu MY, Feng CY, Ding HB, Zhan Y, Zhao Z, Ding YM. Bamboo leaf extract improves spatial learning ability in a rat model with senile dementia. J Zhejiang Univ Sci B 2016; 16:593-601. [PMID: 26160717 DOI: 10.1631/jzus.b1400249] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Senile dementia (SD) is a syndrome characterized by progressive neurological deterioration. Treatment for the disease is still under investigation. Bamboo leaf extract (B-extract) has been known for its biological efficacy in anti-oxidant and anti-cancer activities. However, study on B-extract for its protection against dementia is very limited. The effect of B-extract on a rat model with SD was examined. B-extract improved spatial learning ability of the dementia rats. The hippocampus of dementia model rats showed reduced levels of acetylcholine (ACh), epinephrine (E), norepinephrine (NE), and dopamine (DA), and increased activities of acetylcholine esterase (AChE) and monoamine oxidase (MAO). Treatment with B-extract 20 mg/(kg·d) for 7 weeks significantly inhibited the enzyme activity compared with untreated dementia rats, and raised the levels of ACh, E, and DA in the hippocampus. In addition, treatment with B-extract elevated the level of γ-aminobutyric acid (GABA), but reduced the level of glutamate (Glu) in the brain. These data suggest that B-extract might be a potential drug in treating impairment of spatial memory in dementia rats by regulating the central neurotransmitter function.
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Affiliation(s)
- Jian-xiang Liu
- Department of Clinical Medicine, School of Medicine, Zhejiang University City College, Hangzhou 310015, China
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Berg L, Mishra BK, Andersson CD, Ekström F, Linusson A. The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes. Chemistry 2016; 22:2672-81. [DOI: 10.1002/chem.201503973] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Lotta Berg
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
| | | | | | - Fredrik Ekström
- CBRN Defense and Security; Swedish Defense Research Agency; 906 21 Umeå Sweden
| | - Anna Linusson
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
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Kim WJ, Son WS, Ryu KS, Lee SK, Choi KH, Lee JS, Lee BJ. Bacterial peptide deformylase inhibitor PMT analogs inhibit cancer cell growth by interacting with human peptide deformylase. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11434-014-0498-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Determination of Bis(9)-(-)-Meptazinol, a bis-ligand for Alzheimer's disease, in rat plasma by liquid chromatography-tandem mass spectrometry: application to pharmacokinetics study. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 881-882:126-30. [PMID: 22204875 DOI: 10.1016/j.jchromb.2011.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 12/03/2011] [Accepted: 12/03/2011] [Indexed: 11/21/2022]
Abstract
A rapid, simple and sensitive LC-MS/MS method was developed and validated for the determination of Bis(9)-(-)-Meptazinol (B9M) in rat plasma. Protein precipitation method was used for sample preparation, using five volumes of methanol as the precipitation agent. The analytes were separated by a Zorbax Extend-C18 column with the mobile phase of methanol-water (containing 5mM ammonium formate, pH 9.8) (95:5, v/v), and monitored by positive electrospray ionization in multiple reaction monitoring (MRM) mode. Retention time of IS (Bis(5)-(-)-Meptazinol) and B9M were 1.9 min and 3.3 min, respectively. The limit of detection was 0.1 ng/ml and the linear range was 1-500 ng/ml. The relative standard deviation (RSD) of intra-day and inter-day variation was 4.4-6.2% and 6.2-8.9%, respectively. The extraction recoveries of B9M in plasma were over 95%. The method proved to be applicable to the pharmacokinetic study of B9M in rat after intravenous and subcutaneous administration.
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Berg L, Andersson CD, Artursson E, Hörnberg A, Tunemalm AK, Linusson A, Ekström F. Targeting acetylcholinesterase: identification of chemical leads by high throughput screening, structure determination and molecular modeling. PLoS One 2011; 6:e26039. [PMID: 22140425 PMCID: PMC3227566 DOI: 10.1371/journal.pone.0026039] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 09/16/2011] [Indexed: 11/19/2022] Open
Abstract
Acetylcholinesterase (AChE) is an essential enzyme that terminates cholinergic transmission by rapid hydrolysis of the neurotransmitter acetylcholine. Compounds inhibiting this enzyme can be used (inter alia) to treat cholinergic deficiencies (e.g. in Alzheimer's disease), but may also act as dangerous toxins (e.g. nerve agents such as sarin). Treatment of nerve agent poisoning involves use of antidotes, small molecules capable of reactivating AChE. We have screened a collection of organic molecules to assess their ability to inhibit the enzymatic activity of AChE, aiming to find lead compounds for further optimization leading to drugs with increased efficacy and/or decreased side effects. 124 inhibitors were discovered, with considerable chemical diversity regarding size, polarity, flexibility and charge distribution. An extensive structure determination campaign resulted in a set of crystal structures of protein-ligand complexes. Overall, the ligands have substantial interactions with the peripheral anionic site of AChE, and the majority form additional interactions with the catalytic site (CAS). Reproduction of the bioactive conformation of six of the ligands using molecular docking simulations required modification of the default parameter settings of the docking software. The results show that docking-assisted structure-based design of AChE inhibitors is challenging and requires crystallographic support to obtain reliable results, at least with currently available software. The complex formed between C5685 and Mus musculus AChE (C5685•mAChE) is a representative structure for the general binding mode of the determined structures. The CAS binding part of C5685 could not be structurally determined due to a disordered electron density map and the developed docking protocol was used to predict the binding modes of this part of the molecule. We believe that chemical modifications of our discovered inhibitors, biochemical and biophysical characterization, crystallography and computational chemistry provide a route to novel AChE inhibitors and reactivators.
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Affiliation(s)
- Lotta Berg
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Elisabet Artursson
- Swedish Defence Research Agency, CBRN Defence and Security, Umeå, Sweden
| | - Andreas Hörnberg
- Swedish Defence Research Agency, CBRN Defence and Security, Umeå, Sweden
| | | | - Anna Linusson
- Department of Chemistry, Umeå University, Umeå, Sweden
- * E-mail: (FE); (AL)
| | - Fredrik Ekström
- Swedish Defence Research Agency, CBRN Defence and Security, Umeå, Sweden
- * E-mail: (FE); (AL)
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Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco/endoplasmic reticulum calcium ATPase. Biophys Chem 2010. [DOI: 10.1016/j.bpc.2010.01.011 pmid: 20167416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Zaheer-ul-Haq, Halim SA, Uddin R, Madura JD. Benchmarking docking and scoring protocol for the identification of potential acetylcholinesterase inhibitors. J Mol Graph Model 2010; 28:870-82. [DOI: 10.1016/j.jmgm.2010.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2010] [Revised: 03/14/2010] [Accepted: 03/16/2010] [Indexed: 11/25/2022]
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Lape M, Elam C, Paula S. Comparison of current docking tools for the simulation of inhibitor binding by the transmembrane domain of the sarco/endoplasmic reticulum calcium ATPase. Biophys Chem 2010; 150:88-97. [PMID: 20167416 DOI: 10.1016/j.bpc.2010.01.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 01/27/2010] [Accepted: 01/28/2010] [Indexed: 01/04/2023]
Abstract
Inhibitors of the transmembrane protein sarco/endoplasmic reticulum calcium ATPase (SERCA) are invaluable tools for the study of the enzyme's physiological functions and they have been recognized as a promising new class of anticancer agents. For the discovery of novel enzyme inhibitors, small molecule docking for virtual screens of large compound libraries has become increasingly important. Since the performance of various docking routines varies considerably, depending on the target and the chemical nature of the ligand, we critically evaluated the performance of four frequently used programs - GOLD, AutoDock, Surflex-Dock, and FRED - for the docking of SERCA inhibitors based on the structures of thapsigargin, di-tert-butylhydroquinone, and cyclopiazonic acid. Evaluation criteria were docking accuracy using crystal structures as references, docking reproducibility, and correlation between docking scores and known bioactivities. The best overall results were obtained by GOLD and FRED. Docking runs with conformationally flexible binding sites produced no significant improvement of the results.
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Affiliation(s)
- Michael Lape
- Department of Chemistry, Northern Kentucky University, Highland Heights, KY 41099-1905, USA
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Fernández-Bachiller MI, Pérez C, Campillo NE, Páez JA, González-Muñoz GC, Usán P, García-Palomero E, López M, Villarroya M, García A, Martínez A, Rodríguez-Franco MI. Tacrine-Melatonin Hybrids as Multifunctional Agents for Alzheimer's Disease, with Cholinergic, Antioxidant, and Neuroprotective Properties. ChemMedChem 2009; 4:828-41. [DOI: 10.1002/cmdc.200800414] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Khan MTH. Molecular interactions of cholinesterases inhibitors using in silico methods: current status and future prospects. N Biotechnol 2009; 25:331-46. [PMID: 19491049 DOI: 10.1016/j.nbt.2009.03.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by a low amount of acetylcholine (ACh) in hippocampus and cortex. Acetylcholinesterase (AChE) is one of the most important enzymes in many living organisms including human being and other vertebrates, insects like mosquitoes, among others. Several reports have been published where it has been clearly shown that the genesis of amyloid protein plaques associated with AD is connected to modifications of both AChE and butyrylcholinesterase (BChE), since the plaque is significantly decreased in AD patients using cholinesterase inhibitors (ChEIs). This review gives some examples of these inhibitors discovered during past couple of years that have shown very prominent interactions at the active site triad of the proteins as well as different other parts of the active site like, peripheral anionic site (PAS), oxyanionic hole, anionic subsite or acyl binding pocket (ABP). Most of the inhibition and their interactions have been visualized by X-ray crystallography, but some of the other inhibitors have been studied either by molecular docking or molecular dynamic (MD) simulations or by both the in silico methods. Some of these prominent studies have been crucially observed and reported here.
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Affiliation(s)
- Mahmud Tareq Hassan Khan
- Department of Pharmacology, Institute of Medical Biology, University of Tromsø, 9037 Tromsø, Norway(1)
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Paz A, Xie Q, Greenblatt HM, Fu W, Tang Y, Silman I, Qiu Z, Sussman JL. The Crystal Structure of a Complex of Acetylcholinesterase with a Bis-(−)-nor-meptazinol Derivative Reveals Disruption of the Catalytic Triad. J Med Chem 2009; 52:2543-9. [DOI: 10.1021/jm801657v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aviv Paz
- Departments of Structural Biology and Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 200032, P.R. China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237 P.R. China
| | - Qiong Xie
- Departments of Structural Biology and Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 200032, P.R. China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237 P.R. China
| | - Harry M. Greenblatt
- Departments of Structural Biology and Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 200032, P.R. China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237 P.R. China
| | - Wei Fu
- Departments of Structural Biology and Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 200032, P.R. China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237 P.R. China
| | - Yun Tang
- Departments of Structural Biology and Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 200032, P.R. China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237 P.R. China
| | - Israel Silman
- Departments of Structural Biology and Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 200032, P.R. China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237 P.R. China
| | - Zhuibai Qiu
- Departments of Structural Biology and Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 200032, P.R. China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237 P.R. China
| | - Joel L. Sussman
- Departments of Structural Biology and Neurobiology, Weizmann Institute of Science, Rehovot 76100, Israel, Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 200032, P.R. China, School of Pharmacy, East China University of Science and Technology, Shanghai 200237 P.R. China
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Srivani P, Sastry GN. Potential choline kinase inhibitors: a molecular modeling study of bis-quinolinium compounds. J Mol Graph Model 2008; 27:676-88. [PMID: 19147382 DOI: 10.1016/j.jmgm.2008.10.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 10/10/2008] [Accepted: 10/27/2008] [Indexed: 11/19/2022]
Abstract
Choline kinase (ChoK) is reported to involve in cell signaling pathways and cell growth by regulating the intermediate, phosphocholine (PCho), which is the first step to biosynthesis a membrane phospholipid, phosphatidylcholine. The PCho levels are overexpressed due to elevated activation of the protein under carcinogenesis conditions. ChoK has thus evolved as a novel target for various cancers and a range of compounds has been reported in this course as potent ChoK inhibitors. However, not much information is known about the binding site of the inhibitors. Therefore, we ventured to unravel the possible binding site of 39 bis-quinolinium inhibitors from which the structural requirement for better protein-ligand complex was delved. Molecular docking and 3D-QSAR studies namely comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on the series. The knowledge of the active site was obtained from the site id search and molcad surface calculations of Sybyl, which was further considered for docking studies. In 3D-QSAR, the best predictions were obtained from the model where 29 compounds were considered in the training set and remaining 10 in the test set. The best CoMFA statistics were obtained with r(2) of 0.99 and q(2) of 0.81 while, CoMSIA was resulted with r(2) of 0.98 and q(2) of 0.77. A comparative analysis was done with the resulted 3D-QSAR maps and the docked poses by overlaying the maps on the active site residues. Since, there is no reported ligand co-crystallized structure of ChoK the present study provides valuable clues on the binding conformation of the ligand and its interactions with the active site.
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Affiliation(s)
- P Srivani
- Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500007, India
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Xie Q, Wang H, Xia Z, Lu M, Zhang W, Wang X, Fu W, Tang Y, Sheng W, Li W, Zhou W, Zhu X, Qiu Z, Chen H. Bis-(−)-nor-meptazinols as Novel Nanomolar Cholinesterase Inhibitors with High Inhibitory Potency on Amyloid-β Aggregation. J Med Chem 2008; 51:2027-36. [DOI: 10.1021/jm070154q] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Qiong Xie
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Hao Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Zheng Xia
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Meiyan Lu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Weiwei Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Xinghai Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Wei Fu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Yun Tang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Wei Sheng
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Wei Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Wei Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Xu Zhu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Zhuibai Qiu
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
| | - Hongzhuan Chen
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, 138 Yixueyuan Road, Shanghai 200032, P. R. China, Department of Pharmacology, Institute of Medical Sciences, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, P. R. China, and School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, P. R. China
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Shen LL, Liu GX, Tang Y. Molecular docking and 3D-QSAR studies of 2-substituted 1-indanone derivatives as acetylcholinesterase inhibitors. Acta Pharmacol Sin 2007; 28:2053-63. [PMID: 18031622 DOI: 10.1111/j.1745-7254.2007.00664.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
AIM To explore the binding mode of 2-substituted 1-indanone derivatives with acetylcholinesterase (AChE) and provide hints for the future design of new derivatives with higher potency and specificity. METHODS The GOLD-docking conformations of the compounds in the active site of the enzyme were used in subsequent studies. The highly reliable and predictive three-dimensional quantitative structure-activity relationship (3D-QSAR) models were achieved by comparative molecular field analysis (CoMFA) and comparative molecular similarity analysis (CoMSIA) methods. The predictive capabilities of the models were validated by an external test set. Moreover, the stabilities of the 3D-QSAR models were verified by the leave-4-out cross-validation method. RESULTS The CoMFA and CoMSIA models were constructed successfully with a good cross-validated coefficient (q(2)) and a non-cross-validated coefficient (r(2)). The q(2)and r(2)obtained from the leave-1-out cross validation method were 0.784 and 0.974 in the CoMFA model and 0.736 and 0.947 in the CoMSIA model, respectively. The coefficient isocontour maps obtained from these models were compatible with the geometrical and physicochemical properties of AChE. CONCLUSION The contour map demonstrated that the binding affinity could be enhanced when the small protonated nitrogen moiety was replaced by a more hydrophobic and bulky group with a highly partial positive charge. The present study provides a better understanding of the interaction between the inhibitors and AChE, which is helpful for the discovery of new compounds with more potency and selective activity.
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Affiliation(s)
- Liang-liang Shen
- Laboratory of Molecular Modeling and Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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