Fragment-based prediction of skin sensitization using recursive partitioning

Journal of Computer-Aided Molecular Design

Volumn 25, Issue 9, 2011, Pages 885-893

  Lu, Jing ^a   Zheng, Mingyue ^a   Wang, Yong ^a   Shen, Qiancheng ^a   Luo, Xiaomin ^a   Jiang, Hualiang ^a,b   Chen, Kaixian ^a  

^a SHANGHAI INSTITUTE OF MATERIA MEDICA   (China)

^b EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

Fragment; LLNA; Recursive partitioning tree; SAR; Skin sensitization; Substructure mining algorithm

Indexed keywords

CHEMICAL DETECTION; CLASSIFICATION (OF INFORMATION); DATA MINING; FORESTRY; REGRESSION ANALYSIS; TREES (MATHEMATICS);

DESCRIPTORS; FRAGMENT; LLNA; MINING ALGORITHMS; RECURSIVE PARTITIONING; RECURSIVE PARTITIONING TREE; SKIN SENSITIZATION; SUBSTRUCTURE MINING ALGORITHM; TEST SETS; TRAINING SETS;

RISK ASSESSMENT;

ACCURACY; ARTICLE; CLASSIFICATION ALGORITHM; CONTROLLED STUDY; INTERMETHOD COMPARISON; LOCAL LYMPH NODE ASSAY; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYSICAL CHEMISTRY; PREDICTION; PRIORITY JOURNAL; PROCESS DEVELOPMENT; RECURSIVE PARTITIONING MODEL; RELIABILITY; SKIN SENSITIZATION; STATISTICAL MODEL; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS;

EID: 80054890103     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-011-9472-7     Document Type: Article

References (52)

1. S Golla S Madihally RL Robinson Jr KA Gasem 2009 Quantitative structure-property relationship modeling of skin sensitization: a quantitative prediction Toxicol In Vitro 23 454 465 10.1016/j.tiv.2008.12.025 1:CAS:528:DC%2BD1MXisFKlurk%3D
2. MA Warne JK Nicholson JC Lindon PD Guiney KP Gartland 2009 A QSAR investigation of dermal and respiratory chemical sensitizers based on computational chemistry properties SAR QSAR Environ Res 20 429 451 10.1080/10629360903278768 1:CAS:528:DC%2BD1MXhsVCqsrfF
3. EU, Directive 2003/15/EC of the European Parliament and the Council of 27 February 2003 Amending Council Directive 76/768/EEC on the Approximations of Laws of the Member States Relating to Cosmetic Products. Official Journal of the European Union, L: Legislation 66:26-35. http://www.eur-lex.europa.eu/ LexUriServ/LexUriServ.do?uri=OJ:L:2003:066:0026:0035:en:PDF
4. Commission of the European Communities, White Paper on the Strategy for a Future Chemicals Policy. COM 88 (2001) Brussels, Belgium. http://www.europa.eu. int/comm/environment/chemicals/whitepaper.htm
5. Commission of the European Communities, Proposal for a Regulation of the European Parliament and of the Council Concerning the Registration, Evaluation, Authorisation and Restriction of Chemicals(REACH), Establishing a European Chemicals Agency and Amending Directive 1999/45/EC and Regulation (EC) on Persistent Organic Pollutants (2003). http://www.europa.eu.int/comm/enterprise/ chemicals/chempol/whitepaper/reach.htm
6. Commission of the European Communities, Regulation (EC) No 1907/2006 of the European Parliament and of the Council of 18 December 2006 concerning the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH), establishing a European Chemicals Agency, Amending Directive 1999/45/EC and Repealing Council Regulation (EEC) No 793/93 and Commission Regulation (EC) No 1488/94 as well as Council Directive 76/769/EEC and Commission Directives 91/155/EEC, 93/67/EEC, 93/105/EC and 2000/21/EC. Official Journal of the European Union, L: Legislation 396,49:1-849 (pp 14, 374, 37s5). http://www.europa.eu.int/comm/enterprise/reach/index-en.htm
7. G Patlewicz AO Aptula DW Roberts E Uriarte 2008 A minireview of available skin sensitization (Q)SARs/Expert systems QSAR Comb Sci 27 60 76 10.1002/qsar.200710067 1:CAS:528:DC%2BD1cXlt1Wgtrw%3D (Pubitemid 351204935)
8. T Netzeva M Pavan AP Worth 2008 Review of (quantitative) structure-activity relationships for acute aquatic toxicity QSAR Comb Sci 27 77 90 10.1002/qsar.200710099 1:CAS:528:DC%2BD1cXlt1Wgtr0%3D (Pubitemid 351204936)
9. The CAESAR model for skin sensitization. http://www.caesar-project.eu/ workshop/info.htm, December 5, 2010
10. H Yuan J Huang C Cao 2009 Prediction of skin sensitization with a particle swarm optimized support vector machine Int J Mol Sci 10 3237 3254 10.3390/ijms10073237
11. A Rusinko 3rd MW Farmen CG Lambert PL Brown SS Young 1999 Analysis of a large structure/biological activity data set using recursive partitioning J Chem Inf Comput Sci 39 6 1017 1026 10.1021/ci9903049 1:CAS:528:DyaK1MXmvFWlu7o%3D (Pubitemid 129579834)
12. DW Roberts G Patlewicz PS Kern F Gerberick I Kimber RJ Dearman CA Ryan DA Basketter AO Aptula 2007 Mechanistic applicability domain classification of a local lymph node assay dataset for skin sensitization Chem Res Toxicol 20 1019 1030 10.1021/tx700024w 1:CAS:528:DC%2BD2sXmtFOmu70%3D (Pubitemid 47204815)
13. GF Gerberick JD Vassallo LM Foertsch BB Price JG Chaney JP Lepoittevin 2007 Quantification of chemical peptide reactivity for screening contact allergens: a classification tree model approach Toxicol Sci 97 417 427 10.1093/toxsci/kfm064 1:CAS:528:DC%2BD2sXmsV2isr8%3D (Pubitemid 47073857)
14. S Li A Fedorowicz ME Andrew 2007 A new descriptor selection scheme for SVM in unbalanced class problem: a case study using skin sensitisation dataset SAR QSAR Environ Res 18 423 441 10.1080/10629360701428474 (Pubitemid 47182743)
15. MD Miller DM Yourtee AG Glaros CC Chappelow JD Eick AJ Holder 2005 Quantum mechanical structure-activity relationship analyses for skin sensitization J Chem Inf Model 45 924 929 10.1021/ci050018z 1:CAS:528: DC%2BD2MXjvFKgt7s%3D (Pubitemid 41156691)
16. A Natsch R Emter G Ellis 2009 Filling the concept with data: integrating data from different in vitro and in silico assays on skin sensitizers to explore the battery approach for animal-free skin sensitization testing Toxicol Sci 107 106 121 10.1093/toxsci/kfn204 1:CAS:528:DC%2BD1cXhsV2ku7nJ
17. G Patlewicz SD Dimitrov LK Low PS Kern GD Dimitrova MI Comber AO Aptula RD Phillips J Niemela C Madsen EB Wedebye DW Roberts PT Bailey OG Mekenyan 2007 TIMES-SS-a promising tool for the assessment of skin sensitization hazard. A characterization with respect to the OECD validation principles for (Q)SARs and an external evaluation for predictivity Regul Toxicol Pharmacol 48 225 239 10.1016/j.yrtph.2007.03.003 1:CAS:528:DC%2BD2sXmtVKjsLs%3D (Pubitemid 46830834)
18. http://www.toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?HSDB, May 23, 2011
19. http://www.inchem.org/pages/sids.html, May 24, 2011
20. R Kreiling HM Hollnagel L Hareng D Eigler MS Lee P Griem B Dreessen M Kleber A Albrecht C Garcia A Wendel 2008 Comparison of the skin sensitizing potential of unsaturated compounds as assessed by the murine local lymph node assay (LLNA) and the guinea pig maximization test (GPMT) Food Chem Toxicol 46 6 1896 1904 10.1016/j.fct.2008.01.019 1:CAS:528:DC%2BD1cXlvVSiu7s%3D
21. MA Bergstrom SI Andersson K Broo K Luthman AT Karlberg 2008 Oximes: metabolic activation and structure-allergenic activity relationships J Med Chem 51 8 2541 2550 10.1021/jm701092n (Pubitemid 351628516)
22. A Fedorowicz H Singh E Demchuk 2004 QSAR study of skin sensitization using local lymph node assay data Int J Mol Sci 5 56 66 10.3390/i5020056 1:CAS:528:DC%2BD2cXjs12gu7g%3D (Pubitemid 38760916)
23. Sybyl, Tripos Inc.: St. Louis, MO 63144-2913
24. AMPAC, Semichem, Inc.: Shawnee, KS 66216
25. A Fedorowicz H Singh S Soderholm E Demchuk 2005 Structure-activity models for contact sensitization Chem Res Toxicol 18 954 969 10.1021/tx0497806 1:CAS:528:DC%2BD2MXjvFKjtbs%3D (Pubitemid 40880884)
26. Comprehensive Descriptors for Structural and Statistical Analysis (CODESSA), Semichem, Inc.: Shawnee, KS 66216
27. Accelrys Discovery Studio, Accelrys Software Inc.: San Diego, CA
28. PK Chattaraj U Sarkar DR Roy 2006 Electrophilicity index Chem Rev 106 2065 2091 10.1021/cr040109f 1:CAS:528:DC%2BD28XkvVGgtrc%3D
29. Nijssen S, Kok J (2004) A quickstart in frequent structure mining can make a difference. In: 10th ACM SIGKDD international conference on knowledge discovery and data mining (KDD), pp 647-652 (Pubitemid 40114985)
30. J Kazius S Nijssen J Kok T Back AP Ijzerman 2006 Substructure mining using elaborate chemical representation J Chem Inf Model 46 597 605 10.1021/ci0503715 1:CAS:528:DC%2BD28XkvFKisA%3D%3D
31. Pipeline Pilot, Accelrys Software Inc.: San Diego, CA
32. S Li A Fedorowicz H Singh SC Soderholm 2005 Application of the random forest method in studies of local lymph node assay based skin sensitization data J Chem Inf Model 45 952 964 10.1021/ci050049u 1:CAS:528:DC%2BD2MXjtl2jtrs%3D (Pubitemid 41156694)
33. M Zheng X Luo Q Shen Y Wang Y Du W Zhu H Jiang 2009 Site of metabolism prediction for six biotransformations mediated by cytochromes P450 Bioinformatics 25 1251 1258 10.1093/bioinformatics/btp140 1:CAS:528: DC%2BD1MXlslGgtL0%3D
34. WJ Youden 1950 Index for rating diagnostic tests Cancer 3 1 32 35 10.1002/1097-0142(1950)3:1<32::AID-CNCR2820030106>3.0.CO;2-3 1:STN:280:DyaG3c%2FhsFeisw%3D%3D
35. DW Roberts AO Aptula G Patlewicz C Pease 2008 Chemical reactivity indices and mechanism-based read-across for non-animal based assessment of skin sensitisation potential J Appl Toxicol 28 443 454 10.1002/jat.1293 1:CAS:528:DC%2BD1cXmsVOksrg%3D (Pubitemid 351727978)
36. K Langton GY Patlewicz A Long CA Marchant DA Basketter 2006 Structure-activity relationships for skin sensitization: recent improvements to Derek for Windows Contact Derm 55 342 347 10.1111/j.1600-0536.2006.00969.x 1:CAS:528:DC%2BD2sXmtl2isQ%3D%3D (Pubitemid 44730152)
37. SJ Enoch DW Roberts MT Cronin 2009 Electrophilic reaction chemistry of low molecular weight respiratory sensitizers Chem Res Toxicol 22 1447 1453 10.1021/tx9001463 1:CAS:528:DC%2BD1MXos1Ogu70%3D
38. DW Roberts AO Aptula G Patlewicz 2007 Electrophilic chemistry related to skin sensitization. Reaction mechanistic applicability domain classification for a published data set of 106 chemicals tested in the mouse local lymph node assay Chem Res Toxicol 20 44 60 10.1021/tx060121y 1:CAS:528:DC%2BD28Xht12qt7%2FN (Pubitemid 46220154)
39. http://www.sdsc.edu/CCMS/Packages/cambridge/pluto/atom-types.html
40. GF Gerberick CA Ryan PS Kern H Schlatter RJ Dearman I Kimber GY Patlewicz DA Basketter 2005 Compilation of historical local lymph node data for evaluation of skin sensitization alternative methods Dermatitis 16 157 202 10.2310/6620.2005.05040 (Pubitemid 43053764)
41. GY Patlewicz ZM Wright DA Basketter CK Pease JP Lepoittevin EG Arnau 2002 Structure-activity relationships for selected fragrance allergens Contact Derm 47 219 226 10.1034/j.1600-0536.2002.470406.x 1:CAS:528:DC%2BD3sXot1Sjtw%3D%3D (Pubitemid 36132488)
42. J Burton E Danloy DP Vercauteren 2009 Fragment-based prediction of cytochromes P450 2D6 and 1A2 inhibition by recursive partitioning SAR QSAR Environ Res 20 185 205 10.1080/10629360902726650 1:CAS:528:DC%2BD1MXhtVWns7rI
43. N Gulyaeva A Zaslavsky A Chait B Zaslavsky 2001 Measurement of the relative hydrophobicity of organic compounds without organic solvent Effects of salt composition and pH on organic acids and nonionic compounds J Pharm Sci 90 9 1366 1374 10.1002/jps.1089 1:CAS:528:DC%2BD3MXmvFGjs7g%3D (Pubitemid 32867985)
44. DW Roberts AO Aptula G Patlewicz 2006 Mechanistic applicability domains for non-animal based prediction of toxicological endpoints. QSAR analysis of the schiff base applicability domain for skin sensitization Chem Res Toxicol 19 1228 1233 10.1021/tx060102o 1:CAS:528:DC%2BD28XosVSmtb4%3D (Pubitemid 44454040)
45. DW Roberts DA Basketter 2000 Quantitative structure-activity relationships: sulfonate esters in the local lymph node assay Contact Derm 42 154 161 10.1034/j.1600-0536.2000.042003154.x 1:CAS:528:DC%2BD3cXhs1yhtrY%3D (Pubitemid 30102928)
46. JG Lee HY Jeong H Lee 2003 An efficient method to compute partial atomic charges of large molecules using reassociation of fragments Bull Korean Chem Soc 24 369 376 10.5012/bkcs.2003.24.3.369 1:CAS:528:DC%2BD3sXivFCmsbs%3D
47. NS Zefirov MA Kirpichenok FF Ismailov MI Trofimov 1987 Calculation schemes for atomic electronegativities in molecular graphs within the framework of Sanderson principle Dokl Akad Nauk SSSR 296 883 887 1:CAS:528: DyaL1cXmt1ymsg%3D%3D
48. MA Kirpichenok NS Zefirov 1987 Electronegativity and molecular geometry. I. General principles of the method and analysis of the effect of short-range electrostatic interactions on bond lengths in organic molecules Zh Org Khim 23 673 691 1:CAS:528:DyaL1cXptlyhtg%3D%3D
49. D Basketter A Dooms-Goossens AT Karlberg JP Lepoittevin 1995 The chemistry of contact allergy: why is a molecule allergenic? Contact Derm 32 65 73 10.1111/j.1600-0536.1995.tb00748.x 1:CAS:528:DyaK2MXkslCksbk%3D
50. M Divkovic CK Pease GF Gerberick DA Basketter 2005 Hapten-protein binding: from theory to practical application in the in vitro prediction of skin sensitization Contact Derm 53 189 200 10.1111/j.0105-1873.2005.00683.x 1:CAS:528:DC%2BD2MXht1WktbbP (Pubitemid 41508973)
51. WJ Pichler 2001 Predictive drug allergy testing: an alternative viewpoint Toxicology 158 31 41 10.1016/S0300-483X(00)00399-1 1:CAS:528: DC%2BD3MXnsVShtw%3D%3D (Pubitemid 32119494)
52. DT Stanton PC Jurs 1990 Development and use of charged partial surface area structural descriptors in computer-assisted quantitative structure-property relationship studies Anal Chem 62 2323 2329 10.1021/ac00220a013 1:CAS:528:DyaK3cXlvFSlurs%3D