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At least three xenon binding sites in the glycine binding domain of the N-methyl D-aspartate receptor. Arch Biochem Biophys 2022; 724:109265. [DOI: 10.1016/j.abb.2022.109265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 11/21/2022]
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2
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Continuous molecular fields and the concept of molecular co-fields in structure-activity studies. Future Med Chem 2019; 11:2701-2713. [PMID: 31596146 DOI: 10.4155/fmc-2018-0360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The analysis of information on the spatial structure of molecules and the physical fields of their interactions with biological targets is extremely important for solving various problems in drug discovery. This mini-review article surveys the main features of the continuous molecular fields approach and its use for analyzing structure-activity relationships in 3D space, building 3D quantitative structure-activity models and conducting similarity based virtual screening. Particular attention is paid to the consideration of the concept of molecular co-fields and their use for the interpretation of 3D structure-activity models. The principles of molecular design based on the overlapping and the similarity of molecular fields with corresponding co-fields are formulated.
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Fu H, Chen Z, Josephson L, Li Z, Liang SH. Positron Emission Tomography (PET) Ligand Development for Ionotropic Glutamate Receptors: Challenges and Opportunities for Radiotracer Targeting N-Methyl-d-aspartate (NMDA), α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA), and Kainate Receptors. J Med Chem 2019; 62:403-419. [PMID: 30110164 PMCID: PMC6393217 DOI: 10.1021/acs.jmedchem.8b00714] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ionotropic glutamate receptors (iGluRs) mediate excitatory neurotransmission within the mammalian central nervous system. iGluRs exist as three main groups: N-methyl-d-aspartate receptors (NMDARs), α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors (AMPARs), and kainate receptors. The past decades have witnessed a remarkable development of PET tracers targeting different iGluRs including NMDARs and AMPARs, and several of the tracers have advanced to clinical imaging studies. Here, we assess the recent development of iGluR PET probes, focusing on tracer design, brain kinetics, and performance in PET imaging studies. Furthermore, this review will not only present challenges in the tracer development but also provide novel approaches in conjunction with most recent drug discovery efforts on these iGluRs, including subtype-selective NMDAR and transmembrane AMPAR regulatory protein modulators and positive allosteric modulators (PAMs) of AMPARs. These approaches, if successful as PET tracers, may provide fundamental knowledge to understand the roles of iGluR receptors under physiological and pathological conditions.
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Affiliation(s)
- Hualong Fu
- Division of Nuclear Medicine and Molecular Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St., Boston, MA 02114 USA
| | - Zhen Chen
- Division of Nuclear Medicine and Molecular Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St., Boston, MA 02114 USA
| | - Lee Josephson
- Division of Nuclear Medicine and Molecular Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St., Boston, MA 02114 USA
| | - Zijing Li
- State Key Laboratory of Molecular Vaccinology, Molecular Diagnosis & Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, P. R. China
| | - Steven H. Liang
- Division of Nuclear Medicine and Molecular Imaging, Department of Radiology, Massachusetts General Hospital and Harvard Medical School, 55 Fruit St., Boston, MA 02114 USA
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Exploration of structural and physicochemical properties of small molecules to inhibit NMDA functionality. Struct Chem 2018. [DOI: 10.1007/s11224-018-1103-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Prediction of N-Methyl-D-Aspartate Receptor GluN1-Ligand Binding Affinity by a Novel SVM-Pose/SVM-Score Combinatorial Ensemble Docking Scheme. Sci Rep 2017; 7:40053. [PMID: 28059133 PMCID: PMC5216401 DOI: 10.1038/srep40053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/30/2016] [Indexed: 01/24/2023] Open
Abstract
The glycine-binding site of the N-methyl-D-aspartate receptor (NMDAR) subunit GluN1 is a potential pharmacological target for neurodegenerative disorders. A novel combinatorial ensemble docking scheme using ligand and protein conformation ensembles and customized support vector machine (SVM)-based models to select the docked pose and to predict the docking score was generated for predicting the NMDAR GluN1-ligand binding affinity. The predicted root mean square deviation (RMSD) values in pose by SVM-Pose models were found to be in good agreement with the observed values (n = 30, r2 = 0.928–0.988, = 0.894–0.954, RMSE = 0.002–0.412, s = 0.001–0.214), and the predicted pKi values by SVM-Score were found to be in good agreement with the observed values for the training samples (n = 24, r2 = 0.967, = 0.899, RMSE = 0.295, s = 0.170) and test samples (n = 13, q2 = 0.894, RMSE = 0.437, s = 0.202). When subjected to various statistical validations, the developed SVM-Pose and SVM-Score models consistently met the most stringent criteria. A mock test asserted the predictivity of this novel docking scheme. Collectively, this accurate novel combinatorial ensemble docking scheme can be used to predict the NMDAR GluN1-ligand binding affinity for facilitating drug discovery.
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Elenich OV, Lytvyn RZ, Skripskaya OV, Lyavinets OS, Pitkovych KE, Yagodinets PI, Obushak MD. Synthesis of nitrogen-containing heterocycles on the basis of 3-(4-acetylphenyl)-1-methylquinolin-2(1H)-one. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1070428016030131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Discovery of potent anticonvulsant ligands as dual NMDA and AMPA receptors antagonists by molecular modelling studies. Med Chem Res 2011. [DOI: 10.1007/s00044-011-9889-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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9
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Dual Allosteric Effect in Glycine/NMDA Receptor Antagonism: A Comparative QSAR Approach. Pharmaceuticals (Basel) 2010. [PMCID: PMC4034086 DOI: 10.3390/ph3103167] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A comparative Hansch type QSAR study was conducted using multiple regression analysis on various sets of quinoxalines, quinoxalin-4-ones, quinazoline-2-carboxylates, 4-hydroxyquinolin-2(1H)-ones, 2-carboxytetrahydroquinolines, phenyl-hydroxy-quinolones, nitroquinolones and 4-substituted-3-phenylquinolin-2(1H)-ones as selective glycine/NMDA site antagonists. Ten statistically validated equations were developed, which indicated the importance of CMR, Verloop’s sterimol L1 and ClogP parameters in contributing towards biological activity. Interestingly, normal and inverse parabolic relationships were found with CMR in different series, indicating a dual allosteric binding mode in glycine/NMDA antagonism. Equations reveal an optimum CMR of 10 ± 10% is required for good potency of antagonists. Other equations indicate the presence of anionic functionality at 4-position of quinoline/quinolone ring system is not absolutely required for effective binding. The observations are laterally validated and in accordance with previous studies.
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Jayashree BS, Thomas S, Nayak Y. Design and synthesis of 2-quinolones as antioxidants and antimicrobials: a rational approach. Med Chem Res 2009. [DOI: 10.1007/s00044-009-9184-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Ivanov AA, Wang B, Klutz AM, Chen VL, Gao ZG, Jacobson KA. Probing distal regions of the A2B adenosine receptor by quantitative structure-activity relationship modeling of known and novel agonists. J Med Chem 2008; 51:2088-99. [PMID: 18321038 PMCID: PMC6540094 DOI: 10.1021/jm701442d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The binding modes at the A 2B adenosine receptor (AR) of 72 derivatives of adenosine and its 5'- N-methyluronamide with diverse substitutions at the 2 and N (6) positions were studied using a molecular modeling approach. The compounds in their receptor-docked conformations were used to build CoMFA and CoMSIA quantitative structure-activity relationship models. Various parameters, including different types of atomic charges, were examined. The best statistical parameters were obtained with a joint CoMFA and CoMSIA model: R (2) = 0.960, Q (2) = 0.676, SEE = 0.175, F = 158, and R (2) test = 0.782 for an independent test set containing 18 compounds. On the basis of the modeling results, four novel adenosine analogues, having elongated or bulky substitutions at N (6) position and/or 2 position, were synthesized and evaluated biologically. All of the proposed compounds were potent, full agonists at the A 2B AR in adenylate cyclase studies. Thus, in support of the modeling, bulky substitutions at both positions did not prevent A 2B AR activation, which predicts separate regions for docking of these moieties.
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Affiliation(s)
- Andrei A. Ivanov
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Ben Wang
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Athena M. Klutz
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Vincent L. Chen
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Zhan-Guo Gao
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
| | - Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and DigestiVe and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892
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Kadieva MG, Oganesyan ÉT, Zefirova OH. Antagonists of AMPA/KA and NMDA (glycine site) glutamate receptors. Pharm Chem J 2008. [DOI: 10.1007/s11094-008-0063-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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14
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Salo OMH, Savinainen JR, Parkkari T, Nevalainen T, Lahtela-Kakkonen M, Gynther J, Laitinen JT, Järvinen T, Poso A. 3D-QSAR Studies on Cannabinoid CB1 Receptor Agonists: G-Protein Activation as Biological Data. J Med Chem 2005; 49:554-66. [PMID: 16420041 DOI: 10.1021/jm0505157] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
G-protein activation via the CB1 receptor was determined for a group of various CB1 ligands and utilized as biological activity data in subsequent CoMFA and CoMSIA studies. Both manual techniques and automated docking at CB1 receptor models were used to obtain a common alignment of endocannabinoid and classical cannabinoid derivatives. In the final alignment models, the endocannabinoid headgroup occupies a unique region distinct from the classical cannabinoid structures, supporting the hypothesis that these structurally diverse molecules overlap only partially within the receptor binding site. Both CoMFA and CoMSIA produce statistically significant models based on the manual alignment and a docking alignment at one receptor conformer. Leave-half-out cross-validation and progressive scrambling were successfully used in assessing the predictivity of the QSAR models.
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Affiliation(s)
- Outi M H Salo
- Department of Pharmaceutical Chemistry, University of Kuopio, FIN-70211 Kuopio, Finland.
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Abstract
The recent decline in drug approvals and the increase in late-stage failures indicate that the ability to generate and screen large numbers of molecules has not improved the drug pipeline. Perhaps the pharmaceutical industry should follow the example of the automotive industry and agree upon a shared modeling language with vendors and academics to enable integration of predictive computational tools across the industry. This will then enable the virtual 'crash-testing' of drugs before synthesis, biological testing and, most importantly, clinical trials. This represents an ambitiously progressive approach using the models for simulating every stage of the drug discovery and development process. Combining the relevant computational algorithms into a grand unified model would enable prioritization of the best ideas before pursuing a discovery program, selecting a target or synthesizing a molecule. The successful application of these virtual crash-testing principles by any of its current proponents could revitalize the pharmaceutical industry so that failure is avoided.
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Affiliation(s)
- Peter W Swaan
- Department of Pharmaceutical Sciences, University of Maryland, 20 Penn Street, Baltimore, MD 21201, USA.
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Varano F, Catarzi D, Colotta V, Calabri FR, Lenzi O, Filacchioni G, Galli A, Costagli C, Deflorian F, Moro S. 1-Substituted pyrazolo[1,5-c]quinazolines as novel Gly/NMDA receptor antagonists: Synthesis, biological evaluation, and molecular modeling study. Bioorg Med Chem 2005; 13:5536-49. [PMID: 16087341 DOI: 10.1016/j.bmc.2005.07.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2005] [Revised: 06/29/2005] [Accepted: 07/01/2005] [Indexed: 11/28/2022]
Abstract
A new set of 5,6-dihydro-pyrazolo[1,5-c]quinazoline-2-carboxylates (2-18), bearing different substituents (COOEt, Cl, Br, CH(3), and COOH) at position-1, were synthesized in order to investigate the influence of various groups at this specific position on Gly/NMDA receptor affinity and/or selectivity. All the herein reported compounds were evaluated for their binding at the Gly/NMDA, AMPA, and KA receptors. Some selected compounds were also tested for their functional antagonistic activity at both the AMPA and NMDA receptor-ion channels. The results obtained in this study have highlighted that a C-1 lipophilic substituent on the pyrazolo[1,5-c]quinazoline-2-carboxylate core shifts selectivity toward the Gly/NMDA receptor, while a C-1 anionic carboxylate residue is able to increase affinity toward this receptor subtype. In particular, the 2-carboxylic acids 15 and 16, bearing a chlorine atom at position-1, are not only potent (K(i)=0.18 and 0.16muM, respectively), but also highly Gly/NMDA versus AMPA selective (selectivity ratio>500). Furthermore, the 1,2-dicarboxylic acids 13 and 14 are endowed with the highest Gly/NMDA receptor binding activity (K(i)=0.09 and 0.059muM, respectively), among the pyrazoloquinazoline series of derivatives. A molecular modeling study has been carried out to better understand receptor affinity and selectivity of these new pyrazoloquinazoline derivatives.
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Affiliation(s)
- Flavia Varano
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Firenze, Polo Scientifico, via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy.
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17
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Abele E, Abele R, Rubina K, Lukevics E. Quinoline Oximes: Synthesis, Reactions, and Biological Activity. (Review). Chem Heterocycl Compd (N Y) 2005. [DOI: 10.1007/s10593-005-0119-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Boeckler F, Lanig H, Gmeiner P. Modeling the Similarity and Divergence of Dopamine D2-like Receptors and Identification of Validated Ligand−Receptor Complexes. J Med Chem 2005; 48:694-709. [PMID: 15689154 DOI: 10.1021/jm049612a] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Focusing on the similarity and divergence of GPCR subtypes and their ligand interactions, we generated dopamine D2, D3, and D4 receptor models based on the rhodopsin crystal structure and refined these with an extensive MM/MD protocol. After validation by diagnostic experimental data, subtype-specific relative positions of TM1, 2, 6, and 7 and bending angles of TM7 were found. To sample the conformational space of the complex, we performed simulated-annealing runs of the receptor protein with the sub-nanomolar antagonist spiperone. Docking a representative set of ligands, we were able to identify one superior model for each subtype when excellent correlations between predicted energies of binding and experimental affinities (r2 = 0.72 for D2, 0.91 for D3 and 0.77 for D4) could be observed. Further analysis revealed general ligand interactions with ASP3.32 and aromatic residues in TM6/7 and individual key interactions with TM1 and TM2 residues of the D3 and D4 receptor models, respectively.
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Affiliation(s)
- Frank Boeckler
- Department of Medicinal Chemistry, Emil Fischer Center, Friedrich-Alexander University, Schuhstrasse 19, D-91052 Erlangen, Germany
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Blaise MC, Sowdhamini R, Rao MRP, Pradhan N. Evolutionary trace analysis of ionotropic glutamate receptor sequences and modeling the interactions of agonists with different NMDA receptor subunits. J Mol Model 2004; 10:305-16. [PMID: 15597199 DOI: 10.1007/s00894-004-0196-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2004] [Accepted: 06/03/2004] [Indexed: 11/26/2022]
Abstract
The ionotropic N-methyl- d-aspartate (NMDA) receptor is of importance in neuronal development, functioning, and degeneration in the mammalian central nervous system. The functional NMDA receptor is a heterotetramer comprising two NR1 and two NR2 or NR3 subunits. We have carried out evolutionary trace (ET) analysis of forty ionotropic glutamate receptor (IGRs) sequences to identify and characterize the residues forming the binding socket. We have also modeled the ligand binding core (S1S2) of NMDA receptor subunits using the recently available crystal structure of NR1 subunit ligand binding core which shares approximately 40% homology with other NMDA receptor subunits. A short molecular dynamics simulation of the glycine-bound form of wild-type and double-mutated (D481N; K483Q) NR1 subunit structure shows considerable RMSD at the hinge region of S1S2 segment, where pore forming transmembrane helices are located in the native receptor. It is suggested that the disruption of domain closure could affect ion-channel activation and thereby lead to perturbations in normal animal behavior. In conclusion, we identified the amino acids that form the ligand-binding pocket in many ionotropic glutamate receptors and studied their hydrogen bonded and nonbonded interaction patterns. Finally, the disruption in the S1S2 domain conformation (of NR1 subunit- crystal structure) has been studied with a short molecular dynamics simulation and correlated with some experimental observations. [figure: see text]. The figure shows the binding mechanism of glutamate with NR2B subunit of the NMDA receptor. Glutamate is shown in cpk, hydrogen bonds in dotted lines and amino acids in blue. The amino acids shown here are within a 4-A radius of the ligand (glutamate).
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Affiliation(s)
- Mathias-Costa Blaise
- Department of Psychopharmacology, National Institute of Mental Health and Neuro Sciences (NIMHANS), 560029, Bangalore, India
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Baskin II, Tikhonova IG, Palyulin VA, Zefirov NS. Selectivity fields: comparative molecular field analysis (CoMFA) of the glycine/NMDA and AMPA receptors. J Med Chem 2003; 46:4063-9. [PMID: 12954059 DOI: 10.1021/jm030833a] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An approach for evaluation of binding selectivity was suggested and exemplified using glycine/NMDA and AMPA receptors. For analyzing the pairwise selectivity, we propose to use the difference between biological activities (expressed as -log Ki) of ligands with respect to different receptor subtypes as a dependent variable for building comparative molecular field analysis (CoMFA) models. The resulting fields (which will be referred to as the "selectivity fields") indicate the ways of increasing selectivity of binding, inhibition, etc. As an example, CoMFA of a set of pyrazolo[1,5-c]quinazolines and triazolo[1,5-c]quinazolines was used for considering the binding selectivity with respect to glycine/NMDA and AMPA receptors. In addition, the mapping of these fields onto the molecular models of the corresponding receptors makes it possible to reveal the reasons for experimentally observed selectivity as well as to suggest additional ways of increasing selectivity.
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Affiliation(s)
- Igor I Baskin
- Department of Chemistry, Moscow State University, Moscow 119992, Russia
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