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Tomašević N, Vujović M, Kostić E, Ragavendran V, Arsić B, Matić SL, Božović M, Fioravanti R, Proia E, Ragno R, Mladenović M. Molecular Docking Assessment of Cathinones as 5-HT 2AR Ligands: Developing of Predictive Structure-Based Bioactive Conformations and Three-Dimensional Structure-Activity Relationships Models for Future Recognition of Abuse Drugs. Molecules 2023; 28:6236. [PMID: 37687065 PMCID: PMC10488745 DOI: 10.3390/molecules28176236] [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: 08/03/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
Commercially available cathinones are drugs of long-term abuse drugs whose pharmacology is fairly well understood. While their psychedelic effects are associated with 5-HT2AR, the enclosed study summarizes efforts to shed light on the pharmacodynamic profiles, not yet known at the receptor level, using molecular docking and three-dimensional quantitative structure-activity relationship (3-D QSAR) studies. The bioactive conformations of cathinones were modeled by AutoDock Vina and were used to build structure-based (SB) 3-D QSAR models using the Open3DQSAR engine. Graphical inspection of the results led to the depiction of a 3-D structure analysis-activity relationship (SAR) scheme that could be used as a guideline for molecular determinants by which any untested cathinone molecule can be predicted as a potential 5-HT2AR binder prior to experimental evaluation. The obtained models, which showed a good agreement with the chemical properties of co-crystallized 5-HT2AR ligands, proved to be valuable for future virtual screening campaigns to recognize unused cathinones and similar compounds, such as 5-HT2AR ligands, minimizing both time and financial resources for the characterization of their psychedelic effects.
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Affiliation(s)
- Nevena Tomašević
- Kragujevac Center for Computational Biochemistry, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, P.O. Box 60, 34000 Kragujevac, Serbia
| | - Maja Vujović
- Department of Pharmacy, Faculty of Medicine, University of Niš, Bulevar Dr. Zorana Đinđića 81, 18000 Niš, Serbia; (M.V.); (E.K.)
| | - Emilija Kostić
- Department of Pharmacy, Faculty of Medicine, University of Niš, Bulevar Dr. Zorana Đinđića 81, 18000 Niš, Serbia; (M.V.); (E.K.)
| | - Venkatesan Ragavendran
- Department of Physics, Sri Chandrasekharendra Saraswathi Viswa Mahavidyalaya, Kanchipuram 631561, Tamil Nadu, India;
| | - Biljana Arsić
- Faculty of Sciences and Mathematics, University of Niš, Višegradska 33, 18000 Niš, Serbia;
| | - Sanja Lj. Matić
- Department of Science, Institute for Informational Technologies, University of Kragujevac, Jovana Cvijića bb, 34000 Kragujevac, Serbia;
| | - Mijat Božović
- Faculty of Science and Mathematics, University of Montenegro, Džordža Vašingtona bb, 81000 Podgorica, Montenegro;
| | - Rossella Fioravanti
- Department of Drug Chemistry and Technology, Faculty of Pharmacy and Medicine, Rome Sapienza University, P.le A. Moro 5, 00185 Rome, Italy;
| | - Eleonora Proia
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Faculty of Pharmacy and Medicine, Rome Sapienza University, P.le A. Moro 5, 00185 Rome, Italy; (E.P.); (R.R.)
| | - Rino Ragno
- Rome Center for Molecular Design, Department of Drug Chemistry and Technology, Faculty of Pharmacy and Medicine, Rome Sapienza University, P.le A. Moro 5, 00185 Rome, Italy; (E.P.); (R.R.)
| | - Milan Mladenović
- Kragujevac Center for Computational Biochemistry, Department of Chemistry, Faculty of Science, University of Kragujevac, Radoja Domanovića 12, P.O. Box 60, 34000 Kragujevac, Serbia
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Zhang X, Li X, Sivaguru P, Wu J, Zanoni G, Song JN, Ning Y. Difluorodiazoethane as a masked acetylene equivalent in formal [3 + 2] cycloadditions with ketones to access 2,3-functionalized furans. Org Chem Front 2022. [DOI: 10.1039/d2qo01045c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A transition-metal-free [3+2] cycloaddition of CF2HCHN2 with β-ketones is reported, which enables the synthesis of 2,3-functionalized furans. Sequential defluorination, nucleophilic addition, and cyclization are key elemental steps of the reaction.
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Affiliation(s)
- Xiaolong Zhang
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Department of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Xin Li
- School of Life Science, Jilin University, Changchun 130012, China
| | - Paramasivam Sivaguru
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Department of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Jiayi Wu
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Department of Chemistry, Northeast Normal University, Changchun 130024, China
| | - Giuseppe Zanoni
- Department of Chemistry, University of Pavia, Viale Taramelli 12, Pavia 27100, Italy
| | - Jin-Na Song
- School of Life Science, Jilin University, Changchun 130012, China
| | - Yongquan Ning
- Jilin Province Key Laboratory of Organic Functional Molecular Design & Synthesis, Department of Chemistry, Northeast Normal University, Changchun 130024, China
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Dallemagne P, Zipfel P, Lalut J, Sopková-de Oliveira Santos J, Rochais C. Aminothiaindanone as an Accessible Scaffold for a Three-Point Chemical Diversity. SYNTHESIS-STUTTGART 2021. [DOI: 10.1055/a-1523-1409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractAminothiaindanone heterocycle appears to be a scaffold of interest in medicinal chemistry. To increase the chemical diversity in this series, the introduction of three-point chemical diversity on the cyclopenta[b]thiophen-4-one scaffold was explored. About thirty newly functionalized thiophene-containing bicycles were obtained using various chemical reactions, paving the way for novel possibilities in medicinal chemistry projects.
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Zanatta G, Della Flora Nunes G, Bezerra EM, da Costa RF, Martins A, Caetano EWS, Freire VN, Gottfried C. Two Binding Geometries for Risperidone in Dopamine D3 Receptors: Insights on the Fast-Off Mechanism through Docking, Quantum Biochemistry, and Molecular Dynamics Simulations. ACS Chem Neurosci 2016; 7:1331-1347. [PMID: 27434874 DOI: 10.1021/acschemneuro.6b00074] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Risperidone is an atypical antipsychotic used in the treatment of schizophrenia and of symptoms of irritability associated with autism spectrum disorder (ASD). Its main action mechanism is the blockade of D2-like receptors acting over positive and negative symptoms of schizophrenia with small risk of extrapyramidal symptoms (EPS) at doses corresponding to low/moderate D2 occupancy. Such a decrease in the side effect incidence can be associated with its fast unbinding from D2 receptors in the nigrostriatal region allowing the recovery of dopamine signaling pathways. We performed docking essays using risperidone and the D3 receptor crystallographic data and results suggested two possible distinct orientations for risperidone at the binding pocket. Orientation 1 is more close to the opening of the binding site and has the 6-fluoro-1,2 benzoxazole fragment toward the bottom of the D3 receptor cleft, while orientation 2 is deeper inside the binding pocket with the same fragment toward to the receptor surface. In order to unveil the implications of these two binding orientations, classical molecular dynamics and quantum biochemistry computations within the density functional theory formalism and the molecular fractionation with conjugate caps framework were performed. Quantum mechanics/molecular mechanics suggests that orientation 2 (considering the contribution of Glu90) is slightly more energetically stable than orientation 1 with the main contribution coming from residue Asp110. The residue Glu90, positioned at the opening of the binding site, is closer to orientation 1 than 2, suggesting that it may have a key role in stability through attractive interaction with risperidone. Therefore, although orientations 1 and 2 are both likely to occur, we suggest that the occurrence of the first may contribute to the reduction of side effects in patients taking risperidone due to the reduction of dopamine receptor occupancy in the nigrostriatal region through a mechanism of fast dissociation. The atypical effect may be obtained simply by either delaying D3R full blockage by spatial hindrance of orientation 1 at the binding site or through an effective blockade followed by orientation 1 fast dissociation. While the molecular interpretation suggested in this work shed some light on the potential molecular mechanisms accounting for the reduced extrapyramidal symptoms observed during risperidone treatment, further studies are necessary in order to evaluate the implications of both orientations during the receptor activation/inhibition. Altogether these data highlight important hot spots in the dopamine receptor binding site bringing relevant information for the development of novel/derivative agents with atypical profile.
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Affiliation(s)
- Geancarlo Zanatta
- Department of Biochemistry, Federal University of Rio Grande do Sul, 90035-003 Porto
Alegre, RS Brazil
| | - Gustavo Della Flora Nunes
- Department of Biochemistry, Federal University of Rio Grande do Sul, 90035-003 Porto
Alegre, RS Brazil
| | - Eveline M. Bezerra
- Post-graduate Program in Pharmaceutical Sciences, Pharmacy Faculty, Federal University of Ceará, 60430-372 Fortaleza, CE Brazil
| | - Roner F. da Costa
- Department of Physics, Universidade Federal Rural do Semi-Árido, 59780-000 Caraúbas, RN Brazil
| | - Alice Martins
- Post-graduate Program in Pharmaceutical Sciences, Pharmacy Faculty, Federal University of Ceará, 60430-372 Fortaleza, CE Brazil
| | - Ewerton W. S. Caetano
- Federal Institute of Education, Science and Technology, 60040-531 Fortaleza, CE Brazil
| | - Valder N. Freire
- Department of Physics, Federal University of Ceará, 60455-760 Fortaleza, CE Brazil
| | - Carmem Gottfried
- Department of Biochemistry, Federal University of Rio Grande do Sul, 90035-003 Porto
Alegre, RS Brazil
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Bali A, Sen U, Peshin T. Synthesis, docking and pharmacological evaluation of novel indole based potential atypical antipsychotics. Eur J Med Chem 2014; 74:477-90. [DOI: 10.1016/j.ejmech.2013.09.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 10/26/2022]
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Ermondi G, Caron G, Pintos IG, Gerbaldo M, Pérez M, Pérez DI, Gándara Z, Martínez A, Gómez G, Fall Y. An application of two MIFs-based tools (Volsurf+ and Pentacle) to binary QSAR: the case of a palinurin-related data set of non-ATP competitive glycogen synthase kinase 3β (GSK-3β) inhibitors. Eur J Med Chem 2011; 46:860-9. [PMID: 21281991 DOI: 10.1016/j.ejmech.2010.12.024] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 11/18/2010] [Accepted: 12/21/2010] [Indexed: 11/26/2022]
Abstract
VolSurf+ and GRIND descriptors extract the information present in MIFs calculated by GRID: the first are simpler to interpret and generally applied to ADME-Tox topics, whereas the latter are more sophisticated and thus more suited for pharmacodynamics events. Here we present a study which compares binary QSAR models obtained with VolSurf+ descriptors and GRIND for a data set of non-ATP competitive GSK-3β inhibitors chemically related to palinurin for which the biological activity is expressed in binary format. Results suggest not only that the simpler Volsurf+ descriptors are good enough to predict and chemically interpret the investigated phenomenon but also a bioactive conformation of palinurin which may guide future design of ATP non-competitive GSK-3 inhibitors.
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Affiliation(s)
- Giuseppe Ermondi
- CASSMedChem Laboratory, DSTF at the Centre for Innovation, Università di Torino, Via Quarello 11, 10135 Torino, Italy
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Barceló M, Raviña E, Varela MJ, Brea J, Loza MI, Masaguer CF. Potential atypical antipsychotics: synthesis, binding affinity and SAR of new heterocyclic bioisosteric butyrophenone analogues as multitarget ligands. MEDCHEMCOMM 2011. [DOI: 10.1039/c1md00202c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kramer V, Herth MM, Santini MA, Palner M, Knudsen GM, Rösch F. Research Letter: Structural Combination of Established 5-HT2A Receptor Ligands: New Aspects of the Binding Mode. Chem Biol Drug Des 2010; 76:361-6. [DOI: 10.1111/j.1747-0285.2010.01011.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pecic S, Makkar P, Chaudhary S, Reddy BV, Navarro HA, Harding WW. Affinity of aporphines for the human 5-HT2A receptor: insights from homology modeling and molecular docking studies. Bioorg Med Chem 2010; 18:5562-75. [PMID: 20621490 DOI: 10.1016/j.bmc.2010.06.043] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 06/08/2010] [Accepted: 06/14/2010] [Indexed: 11/29/2022]
Abstract
Analogs of nantenine were docked into a modeled structure of the human 5-HT(2A) receptor using ICM Pro, GLIDE, and GOLD docking methods. The resultant docking scores were used to correlate with observed in vitro apparent affinity (K(e)) data. The GOLD docking algorithm when used with a homology model of 5-HT(2A), based on a bovine rhodopsin template and built by the program MODELLER, gives results which are most in agreement with the in vitro results. Further analysis of the docking poses among members of a C1 alkyl series of nantenine analogs, indicate that they bind to the receptor in a similar orientation, but differently than nantenine. Besides an important interaction between the protonated nitrogen of the C1 alkyl analogs and residue Asp155, we identified Ser242, Phe234, and Gly238 as key residues responsible for the affinity of these compounds for the 5-HT(2A) receptor. Specifically, the ability of some of these analogs to establish a H-bond with Ser242 and hydrophobic interactions with Phe234 and Gly238 appears to explain their enhanced affinity as compared to nantenine.
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Affiliation(s)
- Stevan Pecic
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, New York, NY 10065, USA
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The development and validation of a novel virtual screening cascade protocol to identify potential serotonin 5-HT(7)R antagonists. Bioorg Med Chem Lett 2010; 20:2465-8. [PMID: 20346662 DOI: 10.1016/j.bmcl.2010.03.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Revised: 03/01/2010] [Accepted: 03/02/2010] [Indexed: 01/16/2023]
Abstract
In an attempt to identify new ligands for the 5-HT(7) receptor (5-HT(7)R), we developed and tested a hierarchical multi-step strategy of virtual screening (VS) based on two-dimensional (2D) pharmacophore similarity, physicochemical scalar descriptors, an ADME/Tox filter, three-dimensional (3D) pharmacophore searches and a docking protocol. Six chemical classes of 5-HT(7)R antagonists were used as query structures in a double-path virtual screening scheme. The Enamine screening database, consisting of approximately 730,000 commercially available drug-like compounds, was adopted and used as a source of structures. A biological evaluation of 26 finally selected virtual hits resulted in finding two benzodioxane derivatives with significant affinity (K(i)=197 and 265 nM). The approach described in this case study can be easily used as a general rational drug design tool for other biological targets.
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Varin T, Gutiérrez-de-Terán H, Castro M, Brea J, Fabis F, Dauphin F, Åqvist J, Lepailleur A, Perez P, Burgueño J, Vela JM, Loza MI, Rodrigo J. Phe369(7.38) at human 5-HT(7) receptors confers interspecies selectivity to antagonists and partial agonists. Br J Pharmacol 2010; 159:1069-81. [PMID: 19922537 PMCID: PMC2839265 DOI: 10.1111/j.1476-5381.2009.00481.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2009] [Revised: 07/22/2009] [Accepted: 07/31/2009] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND AND PURPOSE Human and rat 5-HT(7) receptors were studied with a particular emphasis on the molecular interactions involved in ligand binding, searching for an explanation to the interspecies selectivity observed for a set of compounds. We performed affinity studies, molecular modelling and site-directed mutagenesis, with special focus on residue Phe(7.38) of the human 5-HT(7) receptor [Cys(7.38) in rat]. EXPERIMENTAL APPROACH Competition binding studies were performed for seven 5-HT(7) receptor ligands at three different 5-HT(7) receptors. The functional behaviour was evaluated by measuring 5-carboxytryptamine-stimulated cAMP production. Computational simulations were carried out to explore the structural bases in ligand binding observed for these compounds. KEY RESULTS Competition experiments showed a remarkable selectivity for the human receptor when compared with the rat receptor. These results indicate that mutating Cys to Phe at position 7.38 profoundly affects the binding affinities at the 5-HT(7) receptor. Computational simulations provide a structural interpretation for this key finding. Pharmacological characterization of compounds mr25020, mr25040 and mr25053 revealed a competitive antagonistic behaviour. Compounds mr22423, mr22433, mr23284 and mr25052 behaved as partial agonists. CONCLUSIONS AND IMPLICATIONS We propose that the interspecies difference in binding affinities observed for the compounds at human and rat 5-HT(7) receptors is due to the nature of the residue at position 7.38. Our molecular modelling simulations suggest that Phe(7.38) in the human receptor is integrated in the hydrophobic pocket in the central part of the binding site [Phe(6.51)-Phe(6.52)] and allows a tighter binding of the ligands when compared with the rat receptor.
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Affiliation(s)
- Thibault Varin
- Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), UFR des Sciences Pharmaceutiques, Université de Caen Basse-NormandieCaen, France
| | - Hugo Gutiérrez-de-Terán
- Fundación Pública Galega de Medicina Xenómica, Hospital Clínico Universitario de SantiagoSantiago de Compostela, Spain
| | - Marián Castro
- BioFarma Research Group, Departamento de Farmacoloxia, Facultade de Farmacia, Instituto de Farmacia Industrial, Universidade de Santiago de CompostelaSantiago de Compostela, Spain
| | - José Brea
- BioFarma Research Group, Departamento de Farmacoloxia, Facultade de Farmacia, Instituto de Farmacia Industrial, Universidade de Santiago de CompostelaSantiago de Compostela, Spain
| | - Frederic Fabis
- Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), UFR des Sciences Pharmaceutiques, Université de Caen Basse-NormandieCaen, France
| | - François Dauphin
- Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), UFR des Sciences Pharmaceutiques, Université de Caen Basse-NormandieCaen, France
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala UniversityUppsala, Sweden
| | - Alban Lepailleur
- Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), UFR des Sciences Pharmaceutiques, Université de Caen Basse-NormandieCaen, France
| | - Pilar Perez
- Department of Pharmacology, Laboratorios EsteveBarcelona, Spain
| | - Javier Burgueño
- Department of Pharmacology, Laboratorios EsteveBarcelona, Spain
| | | | - Maria Isabel Loza
- BioFarma Research Group, Departamento de Farmacoloxia, Facultade de Farmacia, Instituto de Farmacia Industrial, Universidade de Santiago de CompostelaSantiago de Compostela, Spain
| | - Jordi Rodrigo
- Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), UFR des Sciences Pharmaceutiques, Université de Caen Basse-NormandieCaen, France
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Sippl W. 3D-QSAR – Applications, Recent Advances, and Limitations. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-1-4020-9783-6_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Carro L, Raviña E, Domínguez E, Brea J, Loza MI, Masaguer CF. Synthesis and binding affinity of potential atypical antipsychotics with the tetrahydroquinazolinone motif. Bioorg Med Chem Lett 2009; 19:6059-62. [DOI: 10.1016/j.bmcl.2009.09.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Revised: 09/11/2009] [Accepted: 09/11/2009] [Indexed: 10/20/2022]
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14
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Liu X, Bai F, Ouyang S, Wang X, Li H, Jiang H. Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation. BMC Bioinformatics 2009; 10:101. [PMID: 19335906 PMCID: PMC2678094 DOI: 10.1186/1471-2105-10-101] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2008] [Accepted: 03/31/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm. RESULTS The conformational perturbation is subjected to evolutionary operation on the genome encoded with dihedral torsions. Various objectives are designated to render the generated Pareto optimal conformers to be energy-favoured as well as evenly scattered across the conformational space. An optional objective concerning the degree of molecular extension is added to achieve geometrically extended or compact conformations which have been observed to impact the molecular bioactivity (J Comput -Aided Mol Des 2002, 16: 105-112). Testing the performance of Cyndi against a test set consisting of 329 small molecules reveals an average minimum RMSD of 0.864 A to corresponding bioactive conformations, indicating Cyndi is highly competitive against other conformation generation methods. Meanwhile, the high-speed performance (0.49 +/- 0.18 seconds per molecule) renders Cyndi to be a practical toolkit for conformational database preparation and facilitates subsequent pharmacophore mapping or rigid docking. The copy of precompiled executable of Cyndi and the test set molecules in mol2 format are accessible in Additional file 1. CONCLUSION On the basis of MOEA algorithm, we present a new, highly efficient conformation generation method, Cyndi, and report the results of validation and performance studies comparing with other four methods. The results reveal that Cyndi is capable of generating geometrically diverse conformers and outperforms other four multiple conformer generators in the case of reproducing the bioactive conformations against 329 structures. The speed advantage indicates Cyndi is a powerful alternative method for extensive conformational sampling and large-scale conformer database preparation.
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Affiliation(s)
- Xiaofeng Liu
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, PR China.
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Selent J, López L, Sanz F, Pastor M. Multi-receptor binding profile of clozapine and olanzapine: a structural study based on the new beta2 adrenergic receptor template. ChemMedChem 2008; 3:1194-8. [PMID: 18465762 DOI: 10.1002/cmdc.200800074] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Jana Selent
- Research Unit on Biomedical Informatics (GRIB), IMIM/Universitat Pompeu Fabra, Avinguda Dr. Aiguader 88, 08003 Barcelona, Spain
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Runyon SP, Mosier PD, Roth BL, Glennon RA, Westkaemper RB. Potential modes of interaction of 9-aminomethyl-9,10-dihydroanthracene (AMDA) derivatives with the 5-HT2A receptor: a ligand structure-affinity relationship, receptor mutagenesis and receptor modeling investigation. J Med Chem 2008; 51:6808-28. [PMID: 18847250 DOI: 10.1021/jm800771x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effects of 3-position substitution of 9-aminomethyl-9,10-dihydroanthracene (AMDA) on 5-HT 2A receptor affinity were determined and compared to a parallel series of DOB-like 1-(2,5-dimethoxyphenyl)-2-aminopropanes substituted at the 4-position. The results were interpreted within the context of 5-HT 2A receptor models that suggest that members of the DOB-like series can bind to the receptor in two distinct modes that correlate with the compounds' functional activity. Automated ligand docking and molecular dynamics suggest that all of the AMDA derivatives, the parent of which is a 5-HT 2A antagonist, bind in a fashion analogous to that for the sterically demanding antagonist DOB-like compounds. The failure of the F340 (6.52)L mutation to adversely affect the affinity of AMDA and the 3-bromo derivative is consistent with the proposed modes of orientation. Evaluation of ligand-receptor complex models suggest that a valine/threonine exchange between the 5-HT 2A and D 2 receptors may be the origin of selectivity for AMDA and two substituted derivatives.
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Affiliation(s)
- Scott P Runyon
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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17
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Aranda R, Villalba K, Raviña E, Masaguer CF, Brea J, Areias F, Domínguez E, Selent J, López L, Sanz F, Pastor M, Loza MI. Synthesis, Binding Affinity, and Molecular Docking Analysis of New Benzofuranone Derivatives as Potential Antipsychotics. J Med Chem 2008; 51:6085-94. [DOI: 10.1021/jm800602w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Reyes Aranda
- Departamento de Química Orgánica, Laboratorio de Química Farmacéutica, and Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, and Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Karen Villalba
- Departamento de Química Orgánica, Laboratorio de Química Farmacéutica, and Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, and Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Enrique Raviña
- Departamento de Química Orgánica, Laboratorio de Química Farmacéutica, and Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, and Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Christian F. Masaguer
- Departamento de Química Orgánica, Laboratorio de Química Farmacéutica, and Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, and Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - José Brea
- Departamento de Química Orgánica, Laboratorio de Química Farmacéutica, and Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, and Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Filipe Areias
- Departamento de Química Orgánica, Laboratorio de Química Farmacéutica, and Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, and Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Eduardo Domínguez
- Departamento de Química Orgánica, Laboratorio de Química Farmacéutica, and Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, and Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Jana Selent
- Departamento de Química Orgánica, Laboratorio de Química Farmacéutica, and Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, and Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Laura López
- Departamento de Química Orgánica, Laboratorio de Química Farmacéutica, and Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, and Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Ferran Sanz
- Departamento de Química Orgánica, Laboratorio de Química Farmacéutica, and Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, and Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - Manuel Pastor
- Departamento de Química Orgánica, Laboratorio de Química Farmacéutica, and Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, and Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
| | - María I. Loza
- Departamento de Química Orgánica, Laboratorio de Química Farmacéutica, and Departamento de Farmacología, Facultad de Farmacia, Universidad de Santiago de Compostela, E-15782 Santiago de Compostela, Spain, and Research Unit on Biomedical Informatics (GRIB), IMIM, Universitat Pompeu Fabra, Dr. Aiguader 88, E-08003 Barcelona, Spain
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Dewkar GK, Peddi S, Mosier PD, Roth BL, Westkaemper RB. Methoxy-substituted 9-aminomethyl-9,10-dihydroanthracene (AMDA) derivatives exhibit differential binding affinities at the 5-HT(2A) receptor. Bioorg Med Chem Lett 2008; 18:5268-71. [PMID: 18774714 DOI: 10.1016/j.bmcl.2008.08.059] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 08/15/2008] [Accepted: 08/18/2008] [Indexed: 10/21/2022]
Abstract
The effects of methoxy-substitution at the 1-, 2-, 3-, and 4-positions of 9-aminomethyl-9,10-dihydroanthracene (AMDA) on h5-HT(2A) receptor affinity were determined. Racemic mixtures of these compounds were found to show the following affinity trend: 3-MeO > 4-MeO > 1-MeO approximately 2-MeO. Comparison of the effects of these substitutions, with the aid of computational molecular modeling techniques, suggest that the various positional and stereochemical isomers of the methoxy-substituted AMDA compounds interact differently with the h5-HT(2A) receptor. It is predicted that for the compounds with higher affinities, the methoxy oxygen atom is able to interact with hydrogen bond-donating sidechains within alternative h5-HT(2A) receptor binding sites, whereas the lower-affinity isomers lack this ability.
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Affiliation(s)
- Gajanan K Dewkar
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, 410 N. 12th Street, PO Box 980540, Richmond, VA 23298-0540, USA
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19
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Straßer A, Striegl B, Wittmann HJ, Seifert R. Pharmacological Profile of Histaprodifens at Four Recombinant Histamine H1Receptor Species Isoforms. J Pharmacol Exp Ther 2007; 324:60-71. [DOI: 10.1124/jpet.107.129601] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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