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Volumn 10, Issue 4, 2013, Pages 1216-1223

The contribution of atom accessibility to site of metabolism models for cytochromes P450

Author keywords

circular fingerprints; cytochromes P450; site of metabolism; solvent accessible surface area

Indexed keywords

CYTOCHROME P450; CYTOCHROME P450 1A2; CYTOCHROME P450 2A6; CYTOCHROME P450 2B6; CYTOCHROME P450 2C19; CYTOCHROME P450 2C8; CYTOCHROME P450 2C9; CYTOCHROME P450 2D6; CYTOCHROME P450 2E1; CYTOCHROME P450 3A4; ISOPROTEIN; SOLVENT;

EID: 84875797401     PISSN: 15438384     EISSN: 15438392     Source Type: Journal    
DOI: 10.1021/mp3005116     Document Type: Article
Times cited : (36)

References (52)
  • 1
    • 33645050104 scopus 로고    scopus 로고
    • Cytochrome P450s and other enzymes in drug metabolism and toxicity
    • Guengerich, F. P. Cytochrome P450s and other enzymes in drug metabolism and toxicity AAPS J. 2006, 8, E101-E111
    • (2006) AAPS J. , vol.8
    • Guengerich, F.P.1
  • 3
    • 80052949153 scopus 로고    scopus 로고
    • Potentially increasing the metabolic stability of drug candidates via computational site of metabolism prediction by CYP2C9: The utility of incorporating protein flexibility via an ensemble of structures
    • Danielson, M. L.; Desai, P. V; Mohutsky, M. A.; Wrighton, S. A.; Lill, M. A. Potentially increasing the metabolic stability of drug candidates via computational site of metabolism prediction by CYP2C9: The utility of incorporating protein flexibility via an ensemble of structures Eur. J. Med. Chem. 2011, 46, 3953-3963
    • (2011) Eur. J. Med. Chem. , vol.46 , pp. 3953-3963
    • Danielson, M.L.1    Desai, P.V.2    Mohutsky, M.A.3    Wrighton, S.A.4    Lill, M.A.5
  • 5
  • 6
    • 84855867453 scopus 로고    scopus 로고
    • Ligand-Based Site of Metabolism Prediction for Cytochrome P450 2D6
    • Rydberg, P.; Olsen, L. Ligand-Based Site of Metabolism Prediction for Cytochrome P450 2D6 ACS Med. Chem. Lett. 2012, 3, 69-73
    • (2012) ACS Med. Chem. Lett. , vol.3 , pp. 69-73
    • Rydberg, P.1    Olsen, L.2
  • 7
    • 79960704005 scopus 로고    scopus 로고
    • RS-Predictor: A New Tool for Predicting Sites of Cytochrome P450-Mediated Metabolism Applied to CYP 3A4
    • Zaretzki, J.; Bergeron, C.; Rydberg, P.; Huang, T.; wei; Bennett, K. P.; Breneman, C. M. RS-Predictor: A New Tool for Predicting Sites of Cytochrome P450-Mediated Metabolism Applied to CYP 3A4 J. Chem. Inf. Model. 2011, 51, 1667-1689
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 1667-1689
    • Zaretzki, J.1    Bergeron, C.2    Rydberg, P.3    Huang, T.4    Wei5    Bennett, K.P.6    Breneman, C.M.7
  • 8
    • 84862845373 scopus 로고    scopus 로고
    • RS-Predictor Models Augmented with SMARTCyp Reactivities: Robust Metabolic Regioselectivity Predictions for Nine CYP Isozymes
    • Zaretzki, J.; Rydberg, P.; Bergeron, C.; Bennett, K. P.; Olsen, L.; Breneman, C. M. RS-Predictor Models Augmented with SMARTCyp Reactivities: Robust Metabolic Regioselectivity Predictions for Nine CYP Isozymes J. Chem. Inf. Model. 2012, 52, 1637-1659
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 1637-1659
    • Zaretzki, J.1    Rydberg, P.2    Bergeron, C.3    Bennett, K.P.4    Olsen, L.5    Breneman, C.M.6
  • 9
    • 77956314063 scopus 로고    scopus 로고
    • Conformational Plasticity and Structure/Function Relationships in Cytochromes P450
    • Pochapsky, T. C.; Kazanis, S.; Dang, M. Conformational Plasticity and Structure/Function Relationships in Cytochromes P450 Antioxid. Redox Signaling 2010, 13, 1273-1296
    • (2010) Antioxid. Redox Signaling , vol.13 , pp. 1273-1296
    • Pochapsky, T.C.1    Kazanis, S.2    Dang, M.3
  • 10
    • 77953932263 scopus 로고    scopus 로고
    • SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism
    • Rydberg, P.; Gloriam, D. E.; Zaretzki, J.; Breneman, C.; Olsen, L. SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism ACS Med. Chem. Lett. 2010, 1, 96-100
    • (2010) ACS Med. Chem. Lett. , vol.1 , pp. 96-100
    • Rydberg, P.1    Gloriam, D.E.2    Zaretzki, J.3    Breneman, C.4    Olsen, L.5
  • 11
    • 78449309981 scopus 로고    scopus 로고
    • The SMARTCyp cytochrome P450 metabolism prediction server
    • Rydberg, P.; Gloriam, D. E.; Olsen, L. The SMARTCyp cytochrome P450 metabolism prediction server Bioinformatics 2010, 26, 2988-2989
    • (2010) Bioinformatics , vol.26 , pp. 2988-2989
    • Rydberg, P.1    Gloriam, D.E.2    Olsen, L.3
  • 13
    • 84862888243 scopus 로고    scopus 로고
    • Predicting Drug Metabolism by Cytochrome P450 2C9: Comparison with the 2D6 and 3A4 Isoforms
    • Rydberg, P.; Olsen, L. Predicting Drug Metabolism by Cytochrome P450 2C9: Comparison with the 2D6 and 3A4 Isoforms ChemMedChem 2012, 7, 1202-1209
    • (2012) ChemMedChem , vol.7 , pp. 1202-1209
    • Rydberg, P.1    Olsen, L.2
  • 14
    • 34447515639 scopus 로고    scopus 로고
    • Empirical regioselectivity models for human cytochromes p450 3A4, 2D6, and 2C9
    • Sheridan, R. P.; Korzekwa, K. R.; Torres, R. A.; Walker, M. J. Empirical regioselectivity models for human cytochromes p450 3A4, 2D6, and 2C9 J. Med. Chem. 2007, 50, 3173-3184
    • (2007) J. Med. Chem. , vol.50 , pp. 3173-3184
    • Sheridan, R.P.1    Korzekwa, K.R.2    Torres, R.A.3    Walker, M.J.4
  • 15
    • 65549171233 scopus 로고    scopus 로고
    • CypScore: Quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory
    • Hennemann, M.; Friedl, A.; Lobell, M.; Keldenich, J.; Hillisch, A.; Clark, T.; Göller, A. H. CypScore: Quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory ChemMedChem 2009, 4, 657-669
    • (2009) ChemMedChem , vol.4 , pp. 657-669
    • Hennemann, M.1    Friedl, A.2    Lobell, M.3    Keldenich, J.4    Hillisch, A.5    Clark, T.6    Göller, A.H.7
  • 16
    • 0015222647 scopus 로고
    • Interpretation of Protein Structures - Estimation of Static Accessibility
    • Lee, B.; Richards, F. M. Interpretation of Protein Structures-Estimation of Static Accessibility J. Mol. Biol. 1971, 55, 379-400
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 17
    • 0015866154 scopus 로고
    • Environment and Exposure to Solvent of Protein Atoms - Lysozyme and Insulin
    • Shrake, A.; Rupley, J. A. Environment and Exposure to Solvent of Protein Atoms-Lysozyme and Insulin J. Mol. Biol. 1973, 79, 351-371
    • (1973) J. Mol. Biol. , vol.79 , pp. 351-371
    • Shrake, A.1    Rupley, J.A.2
  • 18
    • 0000408363 scopus 로고    scopus 로고
    • Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
    • Weiser, J.; Shenkin, P. S.; Still, W. C. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO) J. Comput. Chem. 1999, 20, 217-230
    • (1999) J. Comput. Chem. , vol.20 , pp. 217-230
    • Weiser, J.1    Shenkin, P.S.2    Still, W.C.3
  • 19
    • 40549111613 scopus 로고    scopus 로고
    • FACTS: Fast analytical continuum treatment of solvation
    • Haberthur, U.; Caflisch, A. FACTS: Fast analytical continuum treatment of solvation J. Comput. Chem. 2008, 29, 701-715
    • (2008) J. Comput. Chem. , vol.29 , pp. 701-715
    • Haberthur, U.1    Caflisch, A.2
  • 20
    • 0038792211 scopus 로고    scopus 로고
    • New analytic approximation to the standard molecular volume definition and its application to generalized born calculations
    • Lee, M. S.; Feig, M.; Salsbury, F. R.; Brooks, C. L. New analytic approximation to the standard molecular volume definition and its application to generalized born calculations J. Comput. Chem. 2003, 24, 1348-1356
    • (2003) J. Comput. Chem. , vol.24 , pp. 1348-1356
    • Lee, M.S.1    Feig, M.2    Salsbury, F.R.3    Brooks, C.L.4
  • 21
    • 0042121261 scopus 로고    scopus 로고
    • POPS: A fast algorithm for solvent accessible surface areas at atomic and residue level
    • Cavallo, L.; Kleinjung, J.; Fraternali, F. POPS: a fast algorithm for solvent accessible surface areas at atomic and residue level Nucleic Acids Res. 2003, 31, 3364-3366
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3364-3366
    • Cavallo, L.1    Kleinjung, J.2    Fraternali, F.3
  • 22
    • 0001308921 scopus 로고
    • A rapid approximation to the solvent accessible surface areas of atoms
    • Hasel, W.; Hendrickson, T. F.; Still, W. C. A rapid approximation to the solvent accessible surface areas of atoms Tetrahedron Comput. Methodol. 1988, 1, 103-116
    • (1988) Tetrahedron Comput. Methodol. , vol.1 , pp. 103-116
    • Hasel, W.1    Hendrickson, T.F.2    Still, W.C.3
  • 23
    • 34249085274 scopus 로고    scopus 로고
    • How can structural similarity analysis help in category formation?
    • Jaworska, J.; Nikolova-Jeliazkova, N. How can structural similarity analysis help in category formation? SAR QSAR Environ. Res. 2007, 18, 195-207
    • (2007) SAR QSAR Environ. Res. , vol.18 , pp. 195-207
    • Jaworska, J.1    Nikolova-Jeliazkova, N.2
  • 24
    • 84897497330 scopus 로고    scopus 로고
    • Open Source Tools for Read-Across and Category Formation
    • In; Cronin, M. Madden, J. RSC Publishing: Cambridge, U.K.
    • Jeliazkova, N.; Jaworska, J.; Worth, A. Open Source Tools for Read-Across and Category Formation. In In Silico Toxicology: Principles and Applications; Cronin, M.; Madden, J., Eds.; RSC Publishing: Cambridge, U.K., 2010; pp 408-445.
    • (2010) Silico Toxicology: Principles and Applications , pp. 408-445
    • Jeliazkova, N.1    Jaworska, J.2    Worth, A.3
  • 25
    • 0036628547 scopus 로고    scopus 로고
    • Novel methods for the prediction of logP, pK(a), and logD
    • Xing, L.; Glen, R. C. Novel methods for the prediction of logP, pK(a), and logD J. Chem. Inf. Comput. Sci. 2002, 42, 796-805
    • (2002) J. Chem. Inf. Comput. Sci. , vol.42 , pp. 796-805
    • Xing, L.1    Glen, R.C.2
  • 27
    • 77954048869 scopus 로고    scopus 로고
    • Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse
    • Carlsson, L.; Spjuth, O.; Adams, S.; Glen, R. C.; Boyer, S. Use of historic metabolic biotransformation data as a means of anticipating metabolic sites using MetaPrint2D and Bioclipse BMC Bioinf. 2010, 11, 362
    • (2010) BMC Bioinf. , vol.11 , pp. 362
    • Carlsson, L.1    Spjuth, O.2    Adams, S.3    Glen, R.C.4    Boyer, S.5
  • 28
    • 84855757480 scopus 로고    scopus 로고
    • 2011.10; Chemical Computing Group Inc. 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7.
    • Molecular Operating Environment (MOE), 2011.10; Chemical Computing Group Inc., 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2011.
    • (2011) Molecular Operating Environment (MOE)
  • 29
    • 13844312649 scopus 로고    scopus 로고
    • ZINC - A free database of commercially available compounds for virtual screening
    • Irwin, J. J.; Shoichet, B. K. ZINC-A free database of commercially available compounds for virtual screening J. Chem. Inf. Model. 2005, 45, 177-182
    • (2005) J. Chem. Inf. Model. , vol.45 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 30
    • 84875795561 scopus 로고    scopus 로고
    • version 1.2; Schrödinger L.L.C. New York, NY.
    • Canvas, version 1.2; Schrödinger L.L.C.: New York, NY, 2009.
    • (2009) Canvas
  • 31
    • 0001074005 scopus 로고
    • Mathematical analysis of documentation systems
    • Soergel, D. Mathematical analysis of documentation systems Inf. Storage Retr. 1967, 3, 129-173
    • (1967) Inf. Storage Retr. , vol.3 , pp. 129-173
    • Soergel, D.1
  • 33
    • 84875761837 scopus 로고    scopus 로고
    • version 2.0; Schrödinger L.L.C. New York, NY.
    • Epik, version 2.0; Schrödinger L.L.C.: New York, NY, 2009.
    • (2009) Epik
  • 35
    • 84875801120 scopus 로고    scopus 로고
    • version 2.1; Schrödinger L.L.C. New York, NY.
    • Confgen, version 2.1; Schrödinger L.L.C.: New York, NY, 2009.
    • (2009) Confgen
  • 36
    • 0346735076 scopus 로고
    • A Theory of Water and Ionic Solution, with Particular Reference to Hydrogen and Hydroxyl Ions
    • Bernal, J. D.; Fowler, R. H. A Theory of Water and Ionic Solution, with Particular Reference to Hydrogen and Hydroxyl Ions J. Chem. Phys. 1933, 1, 515
    • (1933) J. Chem. Phys. , vol.1 , pp. 515
    • Bernal, J.D.1    Fowler, R.H.2
  • 38
    • 20544433165 scopus 로고
    • Van der Waals Volumes + Radii
    • Bondi, A. Van der Waals Volumes + Radii J. Phys. Chem. 1964, 68, 441-451
    • (1964) J. Phys. Chem. , vol.68 , pp. 441-451
    • Bondi, A.1
  • 39
    • 33947338532 scopus 로고
    • Van der Waals Volumes and Radii of Metals in Covalent Compounds
    • Bondi, A. Van der Waals Volumes and Radii of Metals in Covalent Compounds J. Phys. Chem. 1966, 70, 3006-3007
    • (1966) J. Phys. Chem. , vol.70 , pp. 3006-3007
    • Bondi, A.1
  • 40
    • 0003012394 scopus 로고    scopus 로고
    • On highly discriminating molecular topological index
    • Hu, C. Y.; Xu, L. On highly discriminating molecular topological index J. Chem. Inf. Comput. Sci. 1996, 36, 82-90
    • (1996) J. Chem. Inf. Comput. Sci. , vol.36 , pp. 82-90
    • Hu, C.Y.1    Xu, L.2
  • 41
  • 43
    • 33745135773 scopus 로고    scopus 로고
    • Recent developments of the Chemistry Development Kit (CDK) - An open-source Java library for chemo- and bioinformatics
    • Steinbeck, C.; Hoppe, C.; Kuhn, S.; Floris, M.; Guha, R.; Willighagen, E. L. Recent developments of the Chemistry Development Kit (CDK)-An open-source Java library for chemo- and bioinformatics Curr. Pharm. Des. 2006, 12, 2111-2120
    • (2006) Curr. Pharm. Des. , vol.12 , pp. 2111-2120
    • Steinbeck, C.1    Hoppe, C.2    Kuhn, S.3    Floris, M.4    Guha, R.5    Willighagen, E.L.6
  • 44
    • 84875762070 scopus 로고    scopus 로고
    • version 11; Umetrics AB: UmeaÌŠ Sweden.
    • SIMCA-P, version 11; Umetrics AB: UmeaÌŠ, Sweden, 2005.
    • (2005) SIMCA-P
  • 45
    • 0001098205 scopus 로고
    • Estimation of principal components and related models by iterative least squares
    • In; Krishnaiaah, P. R. Academic Press: New York
    • Wold, H. Estimation of principal components and related models by iterative least squares. In Multivariate Analysis; Krishnaiaah, P. R., Ed.; Academic Press: New York, 1966; pp 391-420.
    • (1966) Multivariate Analysis , pp. 391-420
    • Wold, H.1
  • 47
    • 34249753618 scopus 로고
    • Support-vector networks
    • Cortes, C.; Vapnik, V. Support-vector networks Mach. Learn. 1995, 20, 273-297
    • (1995) Mach. Learn. , vol.20 , pp. 273-297
    • Cortes, C.1    Vapnik, V.2
  • 48
    • 84862894909 scopus 로고    scopus 로고
    • 2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes
    • Liu, R.; Liu, J.; Tawa, G.; Wallqvist, A. 2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes J. Chem. Inf. Model. 2012, 52, 1698-1712
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 1698-1712
    • Liu, R.1    Liu, J.2    Tawa, G.3    Wallqvist, A.4
  • 49
    • 26944462419 scopus 로고    scopus 로고
    • Structures of human microsomal cytochrome P450 2A6 complexed with coumarin and methoxsalen
    • Yano, J. K.; Hsu, M.-H.; Griffin, K. J.; Stout, C. D.; Johnson, E. F. Structures of human microsomal cytochrome P450 2A6 complexed with coumarin and methoxsalen Nat. Struct. Mol. Biol. 2005, 12, 822-823
    • (2005) Nat. Struct. Mol. Biol. , vol.12 , pp. 822-823
    • Yano, J.K.1    Hsu, M.-H.2    Griffin, K.J.3    Stout, C.D.4    Johnson, E.F.5
  • 50
    • 57749122048 scopus 로고    scopus 로고
    • Structures of human cytochrome P-450 2E1. Insights into the binding of inhibitors and both small molecular weight and fatty acid substrates
    • Porubsky, P. R.; Meneely, K. M.; Scott, E. E. Structures of human cytochrome P-450 2E1. Insights into the binding of inhibitors and both small molecular weight and fatty acid substrates J. Biol. Chem. 2008, 283, 33698-33707
    • (2008) J. Biol. Chem. , vol.283 , pp. 33698-33707
    • Porubsky, P.R.1    Meneely, K.M.2    Scott, E.E.3
  • 51
    • 84871813154 scopus 로고    scopus 로고
    • Structural characterization of human cytochrome P450 2C19: Active site differences between P450′s 2C8, 2C9 and 2C19
    • Reynald, R. L.; Sansen, S.; Stout, C. D.; Johnson, E. F. Structural characterization of human cytochrome P450 2C19: active site differences between P450′s 2C8, 2C9 and 2C19 J. Biol. Chem. 2012, 287, 44581-44591
    • (2012) J. Biol. Chem. , vol.287 , pp. 44581-44591
    • Reynald, R.L.1    Sansen, S.2    Stout, C.D.3    Johnson, E.F.4


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