Sequential Application of Ligand and Structure Based Modeling Approaches to Index Chemicals for Their hH(4)R Antagonism (394 views)
Plosone (ISSN: 1932-6203, 1932-6203electronic, 1932-6203linking), 2014 Oct 16; 9(10): e109340-e109340.
Export to BibTeX Export to EndNote
Paper type: Abstract, Conference, Research Support, Non-U. S. Gov'T,
Impact factor: 3.234, 5-year impact factor: 3.702
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84908052935&partnerID=40&md5=93af7e22738d296615a56cd9de6cf2e3
Keywords: 1 (5 Chloro 2 Indolylcarbonyl) 4 Methylpiperazine, Histamine H4 Receptor, Histamine H4 Receptor Antagonist, Article, Chemoinformatics, Computer Prediction, Crystal Structure, Drug Database, High Throughput Screening, Information Science, Intelligent Learning Engine, Iterative Stochastic Elimination, Molecular Docking, Molecular Dynamics, Molecular Model,
Affiliations:
*** IBB - CNR ***
Department of Chemical Sciences, University of Catania, Catania, Italy.
Drug Discovery Informatics Lab, QRC-Qasemi Research Center, Al-Qasemi Academic College, Baka El-Garbiah, Israel.
Etnalead s.r.l., Scuola Superiore di Catania, University of Catania, Catania, Italy.
National Research Council, Institute of Biostructures and Bioimaging, Catania, Italy.
Department of Pharmaceutical Sciences, University of Catania, Catania, Italy.
Etnalead s. r. l., Scuola Superiore di Catania, University of CataniaCatania, Italy
References:
Gether, U., Uncovering molecular mechanisms involved in activation of G protein-coupled receptors (2000) Endocr Rev, 21, pp. 90-11
Calebiro, D., Nikolaev, V.O., Persani, L., Lohse, M.J., Signaling by internalized G-protein-coupled receptors (2010) Trends Pharmacol Sci
Foord, S.M., Bonner, T.I., Neubig, R.R., Rosser, E.M., Pin, J.P., International Union of Pharmacology. XLVI. G protein-coupled receptor list (2005) Pharmacol Rev, 57, pp. 279-288
Hough, L.B., Genomics meets histamine receptors: New subtypes, new receptors (2001) Mol Pharmacol, 59, pp. 415-419
Nguyen, T., Shapiro, D.A., George, S.R., Setola, V., Lee, D.K., Discovery of a novel member of the histamine receptor family (2001) Mol Pharmacol, 59, pp. 427-433
Oda, T., Morikawa, N., Saito, Y., Masuho, Y., Matsumoto, S., Molecular cloning and characterization of a novel type of histamine receptor preferentially expressed in leukocytes (2000) J Biol Chem, 275, pp. 36781-36786
Liu, C., Ma, X., Jiang, X., Wilson, S.J., Hofstra, C.L., Cloning and pharmacological characterization of a fourth histamine receptor (H(4)) expressed in bone marrow (2001) Mol Pharmacol, 59, pp. 420-426
Morse, K.L., Behan, J., Laz, T.M., West, R.E., Jr., Greenfeder, S.A., Cloning and characterization of a novel human histamine receptor (2001) J Pharmacol Exp Ther, 296, pp. 1058-1066
Zhu, Y., Michalovich, D., Wu, H., Tan, K.B., Dytko, G.M., Cloning, expression, and pharmacological characterization of a novel human histamine receptor (2001) Mol Pharmacol, 59, pp. 434-441
Dunford, P.J., O'Donnell, N., Riley, J.P., Williams, K.N., Karlsson, L., The histamine H4 receptor mediates allergic airway inflammation by regulating the activation of CD4+ T cells (2006) Journal of Immunology, 176, pp. 7062-7070
Fung-Leung, W.P., Thurmond, R.L., Ling, P., Karlsson, L., Histamine H4 receptor antagonists: The new antihistamines? (2004) Curr Opin Investig Drugs, 5, pp. 1174-1183
Gutzmer, R., Diestel, C., Mommert, S., Kother, B., Stark, H., Histamine H4 receptor stimulation suppresses IL-12p70 production and mediates chemotaxis in human monocyte-derived dendritic cells (2005) Journal of Immunology, 174, pp. 5224-5232
Zhang, M., Thurmond, R.L., Dunford, P.J., The histamine H(4) receptor: A novel modulator of inflammatory and immune disorders (2007) Pharmacol Ther, 113, pp. 594-606
Thurmond, R.L., Desai, P.J., Dunford, P.J., Fung-Leung, W.P., Hofstra, C.L., A potent and selective histamine H4 receptor antagonist with anti-inflammatory properties (2004) J Pharmacol Exp Ther, 309, pp. 404-413
Jablonowski, J.A., Grice, C.A., Chai, W., Dvorak, C.A., Venable, J.D., The first potent and selective non-imidazole human histamine H4 receptor antagonists (2003) J Med Chem, 46, pp. 3957-3960
Lim, H.D., Smits, R.A., Bakker, R.A., Van Dam, C.M., De Esch, I.J., Discovery of S-(2-guanidylethyl)-isothiourea (VUF 8430) as a potent nonimidazole histamine H4 receptor agonist (2006) J Med Chem, 49, pp. 6650-6651
Smits, R.A., Leurs, R., De Esch, I.J., Major advances in the development of histamine H4 receptor ligands (2009) Drug Discov Today, 14, pp. 745-753
Rayan, A., Siew, N., Cherno-Schwartz, S., Matzner, Y., Bautsch, W., A novel computational method for predicting the transmembrane structure of G-protein coupled receptors: Application to human C5aR and C3aR (2000) Receptors Channels, 7, pp. 121-137
Srinivasan, R., Rose, G.D., Ab initio prediction of protein structure using LINUS (2002) Proteins, 47, pp. 489-495
Sirci, F., Istyastono, E.P., Vischer, H.F., Kooistra, A.J., Nijmeijer, S., Virtual fragment screening: Discovery of histamine H3 receptor ligands using ligand-based and protein-based molecular fingerprints (2012) J Chem Inf Model, 52, pp. 3308-3324
Kooistra, A.J., Roumen, L., Leurs, R., De Esch, I.J., De Graaf, C., From heptahelical bundle to hits from the Haystack: Structure-based virtual screening for GPCR ligands (2013) Methods Enzymol, 522, pp. 279-336
Engelhardt, H., Schultes, S., De Graaf, C., Nijmeijer, S., Vischer, H.F., Bispyrimidines as potent histamine H(4) receptor ligands: Delineation of structure-activity relationships and detailed H(4) receptor binding mode (2013) J Med Chem, 56, pp. 4264-4276
Paoletta, S., Steventon, G.B., Wildeboer, D., Ehrman, T.M., Hylands, P.J., Screening of herbal constituents for aromatase inhibitory activity (2008) Bioorg Med Chem, 16, pp. 8466-8470
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Foord, S. M., Bonner, T. I., Neubig, R. R., Rosser, E. M., Pin, J. P., International Union of Pharmacology. XLVI. G protein-coupled receptor list (2005) Pharmacol Rev, 57, pp. 279-288
Hough, L. B., Genomics meets histamine receptors: New subtypes, new receptors (2001) Mol Pharmacol, 59, pp. 415-419
Morse, K. L., Behan, J., Laz, T. M., West, R. E., Jr., Greenfeder, S. A., Cloning and characterization of a novel human histamine receptor (2001) J Pharmacol Exp Ther, 296, pp. 1058-1066
Dunford, P. J., O'Donnell, N., Riley, J. P., Williams, K. N., Karlsson, L., The histamine H4 receptor mediates allergic airway inflammation by regulating the activation of CD4+ T cells (2006) Journal of Immunology, 176, pp. 7062-7070
Fung-Leung, W. P., Thurmond, R. L., Ling, P., Karlsson, L., Histamine H4 receptor antagonists: The new antihistamines? (2004) Curr Opin Investig Drugs, 5, pp. 1174-1183
Thurmond, R. L., Desai, P. J., Dunford, P. J., Fung-Leung, W. P., Hofstra, C. L., A potent and selective histamine H4 receptor antagonist with anti-inflammatory properties (2004) J Pharmacol Exp Ther, 309, pp. 404-413
Jablonowski, J. A., Grice, C. A., Chai, W., Dvorak, C. A., Venable, J. D., The first potent and selective non-imidazole human histamine H4 receptor antagonists (2003) J Med Chem, 46, pp. 3957-3960
Lim, H. D., Smits, R. A., Bakker, R. A., Van Dam, C. M., De Esch, I. J., Discovery of S- (2-guanidylethyl) -isothiourea (VUF 8430) as a potent nonimidazole histamine H4 receptor agonist (2006) J Med Chem, 49, pp. 6650-6651
Smits, R. A., Leurs, R., De Esch, I. J., Major advances in the development of histamine H4 receptor ligands (2009) Drug Discov Today, 14, pp. 745-753
Kooistra, A. J., Roumen, L., Leurs, R., De Esch, I. J., De Graaf, C., From heptahelical bundle to hits from the Haystack: Structure-based virtual screening for GPCR ligands (2013) Methods Enzymol, 522, pp. 279-336
Li, H., Yap, C. W., Ung, C. Y., Xue, Y., Li, Z. R., Machine learning approaches for predicting compounds that interact with therapeutic and ADMET related proteins (2007) J Pharm Sci, 96, pp. 2838-2860
Efremov, R. G., Chugunov, A. O., Pyrkov, T. V., Priestle, J. P., Arseniev, A. S., Molecular lipophilicity in protein modeling and drug design (2007) Curr Med Chem, 14, pp. 393-415
Mussa, H. Y., Hawizy, L., Nigsch, F., Glen, R. C., Classifying large chemical data sets: Using a regularized potential function method (2011) J Chem Inf Model, 51, pp. 4-14
Simmons, K. J., Chopra, I., Fishwick, C. W., Structure-based discovery of antibacterial drugs (2010) Nat Rev Microbiol, 8, pp. 501-510
Altenbach, R. J., Adair, R. M., Bettencourt, B. M., Black, L. A., Fix-Stenzel, S. R., Structure-activity studies on a series of a 2-aminopyrimidine-containing histamine H4 receptor ligands (2008) J Med Chem, 51, pp. 6571-6580
Smits, R. A., Lim, H. D., Stegink, B., Bakker, R. A., De Esch, I. J., Characterization of the histamine H4 receptor binding site. Part 1. Synthesis and pharmacological evaluation of dibenzodiazepine derivatives (2006) J Med Chem, 49, pp. 4512-4516
Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Scalable molecular dynamics with NAMD (2005) Journal of Computational Chemistry, 26, pp. 1781-1802
Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Comparison of simple potential functions for simulating liquid water (1983) Journal of Chemical Physics, 79, pp. 926-935
Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility (2009) J Comput Chem, 30, pp. 2785-2791
Jain, A. K., Data clustering: 50 Years beyond K-means (2010) Pattern Recognition Letters, 31, pp. 651-666
Lim, H. D., De Graaf, C., Jiang, W., Sadek, P., McGovern, P. M., Molecular determinants of ligand binding to H4R species variants (2010) Mol Pharmacol, 77, pp. 734-743
Plosone (ISSN: 1932-6203, 1932-6203electronic, 1932-6203linking), 2014 Oct 16; 9(10): e109340-e109340.
Export to BibTeX Export to EndNote
Paper type: Abstract, Conference, Research Support, Non-U. S. Gov'T,
Impact factor: 3.234, 5-year impact factor: 3.702
Url: http://www.scopus.com/inward/record.url?eid=2-s2.0-84908052935&partnerID=40&md5=93af7e22738d296615a56cd9de6cf2e3
Keywords: 1 (5 Chloro 2 Indolylcarbonyl) 4 Methylpiperazine, Histamine H4 Receptor, Histamine H4 Receptor Antagonist, Article, Chemoinformatics, Computer Prediction, Crystal Structure, Drug Database, High Throughput Screening, Information Science, Intelligent Learning Engine, Iterative Stochastic Elimination, Molecular Docking, Molecular Dynamics, Molecular Model,
Affiliations:
*** IBB - CNR ***
Department of Chemical Sciences, University of Catania, Catania, Italy.
Drug Discovery Informatics Lab, QRC-Qasemi Research Center, Al-Qasemi Academic College, Baka El-Garbiah, Israel.
Etnalead s.r.l., Scuola Superiore di Catania, University of Catania, Catania, Italy.
National Research Council, Institute of Biostructures and Bioimaging, Catania, Italy.
Department of Pharmaceutical Sciences, University of Catania, Catania, Italy.
Etnalead s. r. l., Scuola Superiore di Catania, University of CataniaCatania, Italy
References:
Gether, U., Uncovering molecular mechanisms involved in activation of G protein-coupled receptors (2000) Endocr Rev, 21, pp. 90-11
Calebiro, D., Nikolaev, V.O., Persani, L., Lohse, M.J., Signaling by internalized G-protein-coupled receptors (2010) Trends Pharmacol Sci
Foord, S.M., Bonner, T.I., Neubig, R.R., Rosser, E.M., Pin, J.P., International Union of Pharmacology. XLVI. G protein-coupled receptor list (2005) Pharmacol Rev, 57, pp. 279-288
Hough, L.B., Genomics meets histamine receptors: New subtypes, new receptors (2001) Mol Pharmacol, 59, pp. 415-419
Nguyen, T., Shapiro, D.A., George, S.R., Setola, V., Lee, D.K., Discovery of a novel member of the histamine receptor family (2001) Mol Pharmacol, 59, pp. 427-433
Oda, T., Morikawa, N., Saito, Y., Masuho, Y., Matsumoto, S., Molecular cloning and characterization of a novel type of histamine receptor preferentially expressed in leukocytes (2000) J Biol Chem, 275, pp. 36781-36786
Liu, C., Ma, X., Jiang, X., Wilson, S.J., Hofstra, C.L., Cloning and pharmacological characterization of a fourth histamine receptor (H(4)) expressed in bone marrow (2001) Mol Pharmacol, 59, pp. 420-426
Morse, K.L., Behan, J., Laz, T.M., West, R.E., Jr., Greenfeder, S.A., Cloning and characterization of a novel human histamine receptor (2001) J Pharmacol Exp Ther, 296, pp. 1058-1066
Zhu, Y., Michalovich, D., Wu, H., Tan, K.B., Dytko, G.M., Cloning, expression, and pharmacological characterization of a novel human histamine receptor (2001) Mol Pharmacol, 59, pp. 434-441
Dunford, P.J., O'Donnell, N., Riley, J.P., Williams, K.N., Karlsson, L., The histamine H4 receptor mediates allergic airway inflammation by regulating the activation of CD4+ T cells (2006) Journal of Immunology, 176, pp. 7062-7070
Fung-Leung, W.P., Thurmond, R.L., Ling, P., Karlsson, L., Histamine H4 receptor antagonists: The new antihistamines? (2004) Curr Opin Investig Drugs, 5, pp. 1174-1183
Gutzmer, R., Diestel, C., Mommert, S., Kother, B., Stark, H., Histamine H4 receptor stimulation suppresses IL-12p70 production and mediates chemotaxis in human monocyte-derived dendritic cells (2005) Journal of Immunology, 174, pp. 5224-5232
Zhang, M., Thurmond, R.L., Dunford, P.J., The histamine H(4) receptor: A novel modulator of inflammatory and immune disorders (2007) Pharmacol Ther, 113, pp. 594-606
Thurmond, R.L., Desai, P.J., Dunford, P.J., Fung-Leung, W.P., Hofstra, C.L., A potent and selective histamine H4 receptor antagonist with anti-inflammatory properties (2004) J Pharmacol Exp Ther, 309, pp. 404-413
Jablonowski, J.A., Grice, C.A., Chai, W., Dvorak, C.A., Venable, J.D., The first potent and selective non-imidazole human histamine H4 receptor antagonists (2003) J Med Chem, 46, pp. 3957-3960
Lim, H.D., Smits, R.A., Bakker, R.A., Van Dam, C.M., De Esch, I.J., Discovery of S-(2-guanidylethyl)-isothiourea (VUF 8430) as a potent nonimidazole histamine H4 receptor agonist (2006) J Med Chem, 49, pp. 6650-6651
Smits, R.A., Leurs, R., De Esch, I.J., Major advances in the development of histamine H4 receptor ligands (2009) Drug Discov Today, 14, pp. 745-753
Rayan, A., Siew, N., Cherno-Schwartz, S., Matzner, Y., Bautsch, W., A novel computational method for predicting the transmembrane structure of G-protein coupled receptors: Application to human C5aR and C3aR (2000) Receptors Channels, 7, pp. 121-137
Srinivasan, R., Rose, G.D., Ab initio prediction of protein structure using LINUS (2002) Proteins, 47, pp. 489-495
Sirci, F., Istyastono, E.P., Vischer, H.F., Kooistra, A.J., Nijmeijer, S., Virtual fragment screening: Discovery of histamine H3 receptor ligands using ligand-based and protein-based molecular fingerprints (2012) J Chem Inf Model, 52, pp. 3308-3324
Kooistra, A.J., Roumen, L., Leurs, R., De Esch, I.J., De Graaf, C., From heptahelical bundle to hits from the Haystack: Structure-based virtual screening for GPCR ligands (2013) Methods Enzymol, 522, pp. 279-336
Engelhardt, H., Schultes, S., De Graaf, C., Nijmeijer, S., Vischer, H.F., Bispyrimidines as potent histamine H(4) receptor ligands: Delineation of structure-activity relationships and detailed H(4) receptor binding mode (2013) J Med Chem, 56, pp. 4264-4276
Paoletta, S., Steventon, G.B., Wildeboer, D., Ehrman, T.M., Hylands, P.J., Screening of herbal constituents for aromatase inhibitory activity (2008) Bioorg Med Chem, 16, pp. 8466-8470
Jiang, X., Kumar, K., Hu, X., Wallqvist, A., Reifman, J., DOVIS 2.0: An efficient and easy to use parallel virtual screening tool based on AutoDock 4.0 (2008) Chem Cent J, 2, p. 18
Luksch, T., Chan, N.S., Brass, S., Sotriffer, C.A., Klebe, G., Computeraided design and synthesis of nonpeptidic plasmepsin II and IV inhibitors (2008) ChemMedChem, 3, pp. 1323-1336
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Hao, M., Zhang, S., Qiu, J., Toward the Prediction of FBPase Inhibitory Activity Using Chemoinformatic Methods (2012) Int J Mol Sci, 13, pp. 7015-7037
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Altenbach, R. J., Adair, R. M., Bettencourt, B. M., Black, L. A., Fix-Stenzel, S. R., Structure-activity studies on a series of a 2-aminopyrimidine-containing histamine H4 receptor ligands (2008) J Med Chem, 51, pp. 6571-6580
Smits, R. A., Lim, H. D., Stegink, B., Bakker, R. A., De Esch, I. J., Characterization of the histamine H4 receptor binding site. Part 1. Synthesis and pharmacological evaluation of dibenzodiazepine derivatives (2006) J Med Chem, 49, pp. 4512-4516
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Lim, H. D., De Graaf, C., Jiang, W., Sadek, P., McGovern, P. M., Molecular determinants of ligand binding to H4R species variants (2010) Mol Pharmacol, 77, pp. 734-743
Sequential Application of Ligand and Structure Based Modeling Approaches to Index Chemicals for Their hH(4)R Antagonism
The human histamine H-4 receptor (hH (4) R), a member of the G-protein coupled receptors (GPCR) family, is an increasingly attractive drug target. It plays a key role in many cell pathways and many hH (4) R ligands are studied for the treatment of several inflammatory, allergic and autoimmune disorders, as well as for analgesic activity. Due to the challenging difficulties in the experimental elucidation of hH (4) R structure, virtual screening campaigns are normally run on homology based models. However, a wealth of information about the chemical properties of GPCR ligands has also accumulated over the last few years and an appropriate combination of these ligand-based knowledge with structure-based molecular modeling studies emerges as a promising strategy for computer-assisted drug design. Here, two chemoinformatics techniques, the Intelligent Learning Engine (ILE) and Iterative Stochastic Elimination (ISE) approach, were used to index chemicals for their hH (4) R bioactivity. An application of the prediction model on external test set composed of more than 160 hH (4) R antagonists picked from the chEMBL database gave enrichment factor of 16. 4. A virtual high throughput screening on ZINC database was carried out, picking similar to 4000 chemicals highly indexed as H4R antagonists' candidates. Next, a series of 3D models of hH (4) R were generated by molecular modeling and molecular dynamics simulations performed in fully atomistic lipid membranes. The efficacy of the hH (4) R 3D models in discrimination between actives and non-actives were checked and the 3D model with the best performance was chosen for further docking studies performed on the focused library. The output of these docking studies was a consensus library of 11 highly active scored drug candidates. Our findings suggest that a sequential combination of ligand-based chemoinformatics approaches with structure-based ones has the potential to improve the success rate in discovering new biologically active GPCR drugs and increase the enrichment factors in a synergistic manner
The human histamine H-4 receptor (hH (4) R), a member of the G-protein coupled receptors (GPCR) family, is an increasingly attractive drug target. It plays a key role in many cell pathways and many hH (4) R ligands are studied for the treatment of several inflammatory, allergic and autoimmune disorders, as well as for analgesic activity. Due to the challenging difficulties in the experimental elucidation of hH (4) R structure, virtual screening campaigns are normally run on homology based models. However, a wealth of information about the chemical properties of GPCR ligands has also accumulated over the last few years and an appropriate combination of these ligand-based knowledge with structure-based molecular modeling studies emerges as a promising strategy for computer-assisted drug design. Here, two chemoinformatics techniques, the Intelligent Learning Engine (ILE) and Iterative Stochastic Elimination (ISE) approach, were used to index chemicals for their hH (4) R bioactivity. An application of the prediction model on external test set composed of more than 160 hH (4) R antagonists picked from the chEMBL database gave enrichment factor of 16. 4. A virtual high throughput screening on ZINC database was carried out, picking similar to 4000 chemicals highly indexed as H4R antagonists' candidates. Next, a series of 3D models of hH (4) R were generated by molecular modeling and molecular dynamics simulations performed in fully atomistic lipid membranes. The efficacy of the hH (4) R 3D models in discrimination between actives and non-actives were checked and the 3D model with the best performance was chosen for further docking studies performed on the focused library. The output of these docking studies was a consensus library of 11 highly active scored drug candidates. Our findings suggest that a sequential combination of ligand-based chemoinformatics approaches with structure-based ones has the potential to improve the success rate in discovering new biologically active GPCR drugs and increase the enrichment factors in a synergistic manner
Sequential Application of Ligand and Structure Based Modeling Approaches to Index Chemicals for Their hH(4)R Antagonism
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