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Wang Y, Chen X. QSPR model for Caco-2 cell permeability prediction using a combination of HQPSO and dual-RBF neural network. RSC Adv 2020; 10:42938-42952. [PMID: 35514900 PMCID: PMC9058322 DOI: 10.1039/d0ra08209k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/06/2020] [Indexed: 12/23/2022] Open
Abstract
The aim of this study is to establish a promising QSPR model for the Caco-2 permeability prediction.
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Affiliation(s)
- Yukun Wang
- School of Chemical Engineering
- University of Science and Technology Liaoning
- Anshan 114051
- China
- School of Electronic and Information Engineering
| | - Xuebo Chen
- School of Electronic and Information Engineering
- University of Science and Technology Liaoning
- Anshan 114051
- China
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2
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Pradhan J, Goyal A. Synthesis, anticonvulsant activity and QSAR studies of some new pyrazolyl pyridines. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1597-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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3
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Ul-Haq Z, Mahmood U, Reza S, Uddin R, Aleem M. Ligand-based 3D-QSAR studies of diaryl acyl-sulfonamide analogues as human umbilical vein endothelial cells inhibitors stimulated by VEGF. Chem Biol Drug Des 2011; 77:288-94. [PMID: 21251234 DOI: 10.1111/j.1747-0285.2011.01084.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diaryl acylsulfonamide derivatives were reported as Human Umbilical Vein Endothelial cell (HUVEC) inhibitors, stimulated by Vascular Endothelial Growth Factor (VEGF). VEGF has angiogenic property to cause colorectal cancer. A ligand-based 3D-QSAR technique was carried out on diaryl acylsulfonamide derivatives by using Comparative Molecular Field Analysis (CoMFA) studies to find relations between biological activities of inhibitors and their structures. In absence of binding mechanism for the ligand with VEGF receptor, current study hopes to shed some light on the inhibition mechanism of the ligands with HUVEC. 3D-QSAR technique was applied to a set of fifty ligands in order to facilitate the design of more potent inhibitors. However, the maximum cross-validated correlation coefficient value was found to be 0.417. The value is relatively low when compared to the usual acceptable cross-validated correlation coefficient, but no further improvements were observed by applying different available options. Therefore, the final model was used for further analysis. Additionally, the resulted CoMFA model was validated by an external set of 10 compounds yielding surprisingly, a satisfactory correlation coefficient value (r(2) (pred) ) 0.80. Moreover, the analysis of the individual generated 3D contours helped in understanding the possible structural modifications of molecules to improve the inhibitory potency.
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Affiliation(s)
- Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, Pakistan.
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4
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Ambaye ND, Gunzburg MJ, Lim RCC, Price JT, Wilce MCJ, Wilce JA. Benzopyrazine derivatives: A novel class of growth factor receptor bound protein 7 antagonists. Bioorg Med Chem 2010; 19:693-701. [PMID: 21134757 DOI: 10.1016/j.bmc.2010.10.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Revised: 10/08/2010] [Accepted: 10/12/2010] [Indexed: 11/15/2022]
Abstract
Growth factor receptor bound protein 7 (Grb7) is an adapter protein that functions as a downstream effector of growth factor mediated signal transduction. Over-expression of Grb7 has been implicated in a variety of cancers such as breast, blood, pancreatic, esophageal, and gastric carcinomas. Inhibition of Grb7 has been shown to reduce the migratory and proliferative potential of these cancers, making it an attractive therapeutic target. Starting with a known peptide antagonist, the present work reports the application of a succession of computational ligand design tools comprising a ligand shape based similarity search, molecular docking and a 2D-similarity search to identify small molecular antagonists of the Grb7-SH2 domain from the NCI chemical database. Binding to the Grb7-SH2 domain was then experimentally tested using melting point shift assays and isothermal titration calorimetry. Overall, a total of 11 benzopyrazine based small molecular antagonists were identified with affinity for the Grb7-SH2 domain. Representative compounds tested using ITC were revealed to possess moderate binding affinity in the low micromolar range. Finally, the lead compound (NSC642056) was found to reduce the growth of a Grb7-expressing breast cancer cell line with an IC(50) of 86μM. It is expected that the identified antagonists will be useful additions to further explore the function of Grb7 and for the development of inhibitors with therapeutic potential.
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Affiliation(s)
- Nigus D Ambaye
- Department of Biochemistry and Molecular Biology, Monash University, Wellington Road, Victoria 3800, Australia
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5
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Classification and Regression Tree Analysis for Molecular Descriptor Selection and Binding Affinities Prediction of Imidazobenzodiazepines in Quantitative Structure-Activity Relationship Studies. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.11.2717] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Berezhnoy D, Gibbs TT, Farb DH. Docking of 1,4-benzodiazepines in the alpha1/gamma2 GABA(A) receptor modulator site. Mol Pharmacol 2009; 76:440-50. [PMID: 19483108 DOI: 10.1124/mol.109.054650] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Positive allosteric modulation of the GABA(A) receptor (GABA(A)R) via the benzodiazepine recognition site is the mechanism whereby diverse chemical classes of therapeutic agents act to reduce anxiety, induce and maintain sleep, reduce seizures, and induce conscious sedation. The binding of such therapeutic agents to this allosteric modulatory site increases the affinity of GABA for the agonist recognition site. A major unanswered question, however, relates to how positive allosteric modulators dock in the 1,4-benzodiazepine (BZD) recognition site. In the present study, the X-ray structure of an acetylcholine binding protein from the snail Lymnea stagnalis and the results from site-directed affinity-labeling studies were used as the basis for modeling of the BZD binding pocket at the alpha(1)/gamma(2) subunit interface. A tethered BZD was introduced into the binding pocket, and molecular simulations were carried out to yield a set of candidate orientations of the BZD ligand in the binding pocket. Candidate orientations were refined based on known structure-activity and stereospecificity characteristics of BZDs and the impact of the alpha(1)H101R mutation. Results favor a model in which the BZD molecule is oriented such that the C5-phenyl substituent extends approximately parallel to the plane of the membrane rather than parallel to the ion channel. Application of this computational modeling strategy, which integrates site-directed affinity labeling with structure-activity knowledge to create a molecular model of the docking of active ligands in the binding pocket, may provide a basis for the design of more selective GABA(A)R modulators with enhanced therapeutic potential.
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Affiliation(s)
- D Berezhnoy
- Laboratory of Molecular Neurobiology, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA 02118, USA
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7
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Kortagere S, Krasowski MD, Ekins S. The importance of discerning shape in molecular pharmacology. Trends Pharmacol Sci 2009; 30:138-47. [PMID: 19187977 PMCID: PMC2854656 DOI: 10.1016/j.tips.2008.12.001] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Revised: 11/27/2008] [Accepted: 12/02/2008] [Indexed: 11/24/2022]
Abstract
Shape is a fundamentally important molecular feature that often determines the fate of a compound in terms of molecular interactions with preferred and non-preferred biological targets. Complementarity of binding in small-molecule-protein, peptide-receptor, antigen-antibody and protein-protein interactions is the key to life and survival and also to targeting molecules with bioactivity. We review the application of shape in various biological systems such as substrate recognition, ligand specificity or selectivity and antibody recognition in the context of computational methods such as docking, quantitative structure-activity relationships, classification models and similarity-search algorithms. These in silico pharmacology methods have recently demonstrated the importance and applicability of determining molecular shape in drug discovery, virtual screening and predictive toxicology. The results from recently published studies show that shape and shape-based descriptors are at least as useful as other traditional molecular descriptors.
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Affiliation(s)
- Sandhya Kortagere
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA 19129, USA
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8
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Quantitative structure–activity relationship studies of a series of non-benzodiazepine structural ligands binding to benzodiazepine receptor. Eur J Med Chem 2008; 43:1489-98. [DOI: 10.1016/j.ejmech.2007.09.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2007] [Revised: 07/30/2007] [Accepted: 09/06/2007] [Indexed: 11/18/2022]
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9
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Mukherjee S, Nagar S, Mullick S, Mukherjee A, Saha A. Pharmacophore mapping of arylbenzothiophene derivatives for MCF cell inhibition using classical and 3D space modeling approaches. J Mol Graph Model 2008; 26:884-92. [PMID: 17643328 DOI: 10.1016/j.jmgm.2007.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Revised: 06/11/2007] [Accepted: 06/11/2007] [Indexed: 11/19/2022]
Abstract
Considering the worth of developing non-steroidal estrogen analogs, the present study explores the pharmacophore features of arylbenzothiophene derivatives for inhibitory activity to MCF-7 cells using classical QSAR and 3D space modeling approaches. The analysis shows that presence of phenolic hydroxyl group and ketonic linkage in the basic side chain of 2-arylbenzothiophene core of raloxifene derivatives are crucial. Additionally piperidine ring connected through ether linkage is favorable for inhibition of breast cancer cell line. These features for inhibitory activity are also highlighted through 3D space modeling approach that explored importance of critical inter features distance among HB-acceptor lipid, hydrophobic and HB-donor features in the arylbenzothiophene scaffold for activity.
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Affiliation(s)
- Subhendu Mukherjee
- Department of Chemical Technology, University of Calcutta, 92, A.P.C. Road, Kolkata 700009, India
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10
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Librowski T, Kubacka M, Meusel M, Scolari S, Müller CE, Gütschow M. Evaluation of anticonvulsant and analgesic effects of benzyl- and benzhydryl ureides. Eur J Pharmacol 2006; 559:138-49. [PMID: 17250826 DOI: 10.1016/j.ejphar.2006.12.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 11/30/2006] [Accepted: 12/06/2006] [Indexed: 10/23/2022]
Abstract
The anticonvulsant effects of benzyl- and benzhydryl ureides in mice models of seizures (maximal electroshock seizure test, pentylenetetrazol test, picrotoxin-induced seizure test) and the influence on spontaneous locomotor activity has been assessed. Furthermore, the analgesic effect of ureide derivatives was studied in the hot-plate test in mice. Selected compounds were investigated for their in vitro interaction with adenosine receptors as well as the benzodiazepine binding site of GABA(A) receptors. This study demonstrated the strong anticonvulsant activity of several ureides in electrically or chemically induced seizure models, and structure-activity relationships were discussed. 1-Benzyl-3-butyrylurea (9) was found to be equipotent to ethosuximide in the pentylenetetrazol test with regard to the number of attacks as well as the time of the onset of seizures. The ureide 9 also revealed the highest protective activity against seizures in the other models, maximal electroshock seizure and picrotoxin test. Moreover, 1-benzyl-3-butyrylurea was not neurotoxic at doses up to 200 mg/kg. Benzylureides 8-10 showed affinity to the adenosine A1 receptors at low micromolar concentrations. However, the apparent anticonvulsant activity in different seizure models does not appear to result from direct activation of adenosine A1 receptors or GABA(A) receptors, respectively. In the hot-plate test, the majority of investigated compounds exhibited analgesic activity. Again, compound 9 was superior to the other substances investigated, suggesting a potential therapeutic value of that ureide derivative.
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Affiliation(s)
- Tadeusz Librowski
- Department of Pharmacodynamics, Medical College, Jagiellonian University, Medyczna 9, 30-688 Kraków, Poland.
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11
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Urbano Cuadrado M, Luque Ruiz I, Gómez-Nieto MA. Refinement and Use of the Approximate Similarity in QSAR Models for Benzodiazepine Receptor Ligands. J Chem Inf Model 2006; 46:2022-9. [PMID: 16995733 DOI: 10.1021/ci600216h] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several considerations for refining the approximate similarity measurements have been introduced in this paper: the use of topological invariants for the calculation of similarity indexes and the development of new similarity correction processes. The quality of the new similarity measurements obtained with the proposed methods has permitted the development of fast, cheap, and simple quantitative structure-activity relationship models for the prediction of biological activities of nonbenzodiazepine gamma-aminobutyric acid(A)/benzodiazepine receptor ligands (58 compounds). Internal and external validations were carried out for the approximate similarity matrices computed using different approaches. Satisfactory results which compare reasonably well with a 3D approach were obtained: Q2= 0.65 and standard error in cross validation SECV= 0.83 for the training stage; r = 0.79 and error in external prediction = 0.82 for the test step. In addition, the method proposed was compared with other topological approaches based on constitutional similarity and on fingerprints. Satisfactory results were obtained.
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Affiliation(s)
- Manuel Urbano Cuadrado
- Institute of Chemical Research of Catalonia ICIQ, Avinguda Països Catalans 16, E-43007 Tarragona, Spain.
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12
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Romeiro NC, Albuquerque MG, de Alencastro RB, Ravi M, Hopfinger AJ. Free-energy force-field three-dimensional quantitative structure–activity relationship analysis of a set of p38-mitogen activated protein kinase inhibitors. J Mol Model 2006; 12:855-68. [PMID: 16541250 DOI: 10.1007/s00894-006-0106-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2005] [Accepted: 01/23/2006] [Indexed: 11/28/2022]
Abstract
The p38-mitogen-activated protein kinases (p38-MAPKs) belong to a family of serine-threonine kinases activated by pro-inflammatory or stressful stimuli that are known to be involved in several diseases. Their biological importance, related to the release of inflammatory pro-cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1 (IL-1), has generated many studies aiming at the development of selective inhibitors for the treatment of inflammatory diseases. In this work, we developed receptor-based three dimensional (3D) quantitative structure-activity relationship (QSAR) models for a series of 33 pyridinyl imidazole compounds [Liverton et al. (1999) 42:2180], using a methodology named free-energy force-field (FEFF) [Tokarski and Hopfinger (1997) 37:792], in which scaled intra- and intermolecular energy terms of the Assisted Model Building Energy Refinement (AMBER) force field combined with a hydration-shell solvation model are the independent variables used in the QSAR studies. Multiple temperature molecular-dynamics simulations (MDS) of ligand-protein complexes and genetic-function approximation (GFA) were employed using partial least squares (PLS) as the fitting functions to develop FEFF-3D-QSAR models for the binding process. The best model obtained in the FEFF-3D-QSAR receptor-dependent (RD) method shows the importance of the van der Waals energy change upon binding and the electrostatic energy in the interaction of ligands with the receptor. The QSAR equations described here show good predictability and may be regarded as representatives of the binding process of ligands to p38-MAPK. Additionally, we have compared the top FEFF-3D-QSAR model with receptor independent (RI) 4D-QSAR models developed in a recent study [Romeiro et al. (2005) 19:385].
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Affiliation(s)
- Nelilma Correia Romeiro
- Laboratório de Modelagem Molecular, Departamento de Química Orgânica, Instituto de Química, CCMN, Universidade Federal do Rio de Janeiro, CT, Bloco A, Sala 609, Ilha do Fundão, Rio de Janeiro, 21949-900, Brazil.
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13
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Menegatti R, Silva GMS, Zapata-Sudo G, Raimundo JM, Sudo RT, Barreiro EJ, Fraga CAM. Design, synthesis, and pharmacological evaluation of new neuroactive pyrazolo[3,4-b]pyrrolo[3,4-d]pyridine derivatives with in vivo hypnotic and analgesic profile. Bioorg Med Chem 2005; 14:632-40. [PMID: 16198114 DOI: 10.1016/j.bmc.2005.08.042] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 08/20/2005] [Accepted: 08/22/2005] [Indexed: 10/25/2022]
Abstract
The present study describes the synthesis and pharmacological profiles of four novel pyrazolo[3,4-b]pyrrolo[3,4-d]pyridine derivatives 2-5, which were structurally designed by using the sedative and analgesic drug zolpidem 1 as lead compound. The heterotricyclic system present in the target compounds 2-5 was constructed in good yields, exploiting a regioselective hetero Diels-Alder reaction of the key azabutadiene derivative 7 and functionalized N-phenylmaleimides 9-12. Additionally, we identified that 1-methyl-7-(4-nitrophenyl)-3-phenyl-3,6,7,8-tetrahydropyrazolo[3,4-b]pyrrolo[3,4-d]pyridine-6,8-dione derivative (LASSBio-873, 5) presented not only the most potent ability to promote sedation, which was similar to that induced by the standard benzodiazepine drug midazolam, but also potent central antinociceptive effect.
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Affiliation(s)
- Ricardo Menegatti
- Laboratory of Evaluation and Synthesis of Bioactive Substances (LASSBio), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, PO Box 68023, Rio de Janeiro 21944-971, RJ, Brazil
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14
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de Mattos Duarte C, Verli H, de Araújo-Júnior JX, de Medeiros IA, Barreiro EJ, Fraga CAM. New optimized piperamide analogues with potent in vivo hypotensive properties. Eur J Pharm Sci 2004; 23:363-9. [PMID: 15567289 DOI: 10.1016/j.ejps.2004.08.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2004] [Revised: 07/22/2004] [Accepted: 08/31/2004] [Indexed: 11/24/2022]
Abstract
We describe herein the structural optimization of new piperamide analogues, designed from two natural prototypes, piperine 1 and piperdardine 2, obtained from Piper tuberculatum Jacq. (Piperaceae). Molecular modeling studies using semiempirical AM1 method were made in order to establish rational modifications to optimize them by molecular simplification. The targeted compounds (10) and (11) were respectively obtained using benzaldehyde (12) and para-anisaldehyde (13) as starting materials. 1H NMR spectra showed that the target compounds were diastereoselectively obtained as the (E)-isomer, the same geometry of the natural prototypes. These new synthetic amides presented significant hypotensive effects in cardiovascular essays using in vivo methodologies. Compound 11 (N-[5-(4'-methoxyphenyl)-2(E)-pentenoyl]thiomorpholine) showed a potency 10,000 times greater than its prototype 5, evidencing an optimization of the molecular architecture for this class of hypotensive drug candidates.
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Affiliation(s)
- Carolina de Mattos Duarte
- LASSBio-Laboratório de Avaliação e Síntese de Substâncias Bioativas, Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, C.P. 68006, 21944-970, Rio de Janeiro, RJ, Brazil
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15
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Hemmateenejad B, Miri R, Tabarzad M, Jafarpour M, Zand F. Molecular modeling and QSAR analysis of the anticonvulsant activity of some N-phenyl-N′-(4-pyridinyl)-urea derivatives. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.theochem.2004.06.039] [Citation(s) in RCA: 8] [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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16
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Sperandio da Silva GM, Sant'Anna CMR, Barreiro EJ. A novel 3D-QSAR comparative molecular field analysis (CoMFA) model of imidazole and quinazolinone functionalized p38 MAP kinase inhibitors. Bioorg Med Chem 2004; 12:3159-66. [PMID: 15158784 DOI: 10.1016/j.bmc.2004.04.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2004] [Accepted: 04/06/2004] [Indexed: 11/23/2022]
Abstract
In this study we describe a new comparative molecular field analysis (CoMFA) model of dihydroquinazolinone and tetrasubstituted imidazole compounds with p38 MAPK inhibitory activity. A series of 51 (a training set of 40 and a test set of 11) dihydroquinazolinone [Bioorg. Med. Chem. Lett. 2003, 13, 277.] and tetrasubstituted imidazole [J. Med. Chem. 1999, 42, 2180.] derivatives known as p38 mitogen-activated protein kinase (p38 MAPK) selective inhibitors was studied by quantitative structure-activity relationship (3D-QSAR) analysis using comparative molecular field analysis. The 3D-QSAR models were generated and evaluated by a scheme that combines a genetic algorithm (GA) optimization with partial least squares (PLS) regression and by crossvalidation using the leave-one-out technique. The model was able to efficiently predict the activities of the compounds of the test set, suggesting that it can be used for the planning of new p38 MAPK inhibitor candidates useful to treat chronic inflammatory states.
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Affiliation(s)
- Gilberto M Sperandio da Silva
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro (UFRJ), P.O. Box 68006, ZIP 21944-910, Rio de Janeiro, RJ, Brazil
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17
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Azevedo Martins RC, Girão Albuquerque M, Bicca de Alencastro R. LIV-3D-QSAR models for PGI2 receptor ligands using multiple conformations. Eur J Med Chem 2004; 39:359-67. [PMID: 15072844 DOI: 10.1016/j.ejmech.2004.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2003] [Revised: 02/11/2004] [Accepted: 02/12/2004] [Indexed: 11/30/2022]
Abstract
A new 3D descriptor, the local intersection volume (LIV), was developed by our group and applied to the construction of 3D-QSAR models for ligands of the PGI(2) receptor (IP). The target compounds are a set of 42 aromatic heterocyclic derivatives [Meanwell et al., J. Med. Chem. 36 (1993), 3884], which show agonist activities in the IP receptor and are inhibitors of platelet aggregation. The LIV-3D-QSAR models were obtained through the analysis of 30% of the generated conformations for each compound, using a combined Genetic Algorithm (GA) and Partial Least Square (PLS) approach [Rogers and Hopfinger, J. Inf. Comput. Sci. 34 (1994) 854]. Statistically, Model 3 is the best as well as the most comprehensive in a mechanistic sense. Furthermore, it can be applied to design new IP ligands.
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Affiliation(s)
- Rita Cristina Azevedo Martins
- Laboratório de Modelagem Molecular (LabMMol), Departamento de Química Orgânica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, CT, Bloco A, Sala 609, Rio de Janeiro, RJ 21949-900, Brasil
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