Towards predictive resistance models for agrochemicals by combining chemical and protein similarity via proteochemometric modelling

Journal of Chemical Biology

Volumn 7, Issue 4, 2014, Pages 119-123

  van Westen, Gerard J P ^a   Bender, Andreas ^b   Overington, John P ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Cheminformatics; Machine learning; Polypharmacology; Resistance

Indexed keywords

AGRICULTURAL CHEMICAL; PESTICIDE;

ARTICLE; BIOLOGICAL ACTIVITY; CHEMICAL STRUCTURE; CHEMOMETRICS; MEDICINAL CHEMISTRY; POINT MUTATION; PREDICTIVE VALUE; PROTEIN TARGETING; PROTEOCHEMOMETRIC MODELLING; PROTEOMICS;

EID: 84919876073     PISSN: 18646158     EISSN: 18646166     Source Type: Journal    
DOI: 10.1007/s12154-014-0112-2     Document Type: Article

References (26)

1. Auer C, Frederick R (2009) Crop improvement using small RNAs: applications and predictive ecological risk assessments. Trends Biotechnol 27(11):644–51
2. Bloomquist JR (1996) Ion channels as targets for insecticides. Annu Rev Entomol 41(1):163–90
3. Buckingham SD, Biggin PC, Sattelle BM, Brown LA, Sattelle DB (2005) Insect GABA receptors: splicing, editing, and targeting by antiparasitics and insecticides. Mol Pharmacol 68(4):942–51
4. Caboni P, Sammelson RE, Casida JE (2003) Phenylpyrazole insecticide photochemistry, metabolism, and GABAergic action: ethiprole compared with fipronil. J Agric Food Chem 51(24):7055–61. doi:10.1021/jf030439l
5. Cherkasov A, Muratov EN, Fourches D, Varnek A, Baskin II, Cronin M, Dearden J, Gramatica P, Martin YC, Todeschini R, Consonni V, Kuz’min VE, Cramer R, Benigni R, Yang C, Rathman J, Terfloth L, Gasteiger J, Richard A, Tropsha A (2013) QSAR modeling: where have you been? Where are you going to? J Med Chem. doi:10.1021/jm4004285
6. Devine MD, Shukla A (2000) Altered target sites as a mechanism of herbicide resistance. Crop Prot 19(8):881–9
7. Erickson JM, Rahire M, Rochaix J-D, Mets L (1985) Herbicide resistance and cross-resistance: changes at three distinct sites in the herbicide-binding protein. Science 228(4696):204–7
8. Ffrench-Constant RH, Rocheleau TA, Steichen JC, Chalmers AE (1993) A point mutation in a Drosophila GABA receptor confers insecticide resistance. Nature 363(6428):449–51
9. Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 40(D1):D1100–7. doi:10.1093/nar/gkr777
10. Hosie AM, Baylis HA, Buckingham SD, Sattelle DB (1995) Actions of the insecticide fipronil, on dieldrin-sensitive and- resistant GABA receptors of Drosophila melanogaster. Br J Pharmacol 115(6):909–12. doi:10.1111/j.1476-5381.1995.tb15896.x
11. Hummel H, Boück A (1987) 23S ribosomal RNA mutations in halobacteria conferring resistance to the anti-80S ribosome targeted antibiotic anisomycin. Nucleic Acids Res 15(6):2431–43
12. Johnson VA, Calvez V, Paredes R, Pillay D, Shafer RW, Wensing AM, Richman DD (2013) Update of the drug resistance mutations in HIV-1: March 2013. Top Antivir Med 21:6–14
13. Kim JM, Kim JS, Kim N, Kim Y-J, Kim IY, Chee YJ, Lee C-H, Jung HC (2008) Gene mutations of 23S rRNA associated with clarithromycin resistance in Helicobacter pylori strains isolated from Korean patients. J Microbiol Biotechnol 18(9):1584–9
14. Lapins M, Eklund M, Spjuth O, Prusis P, Wikberg JES (2008) Proteochemometric modeling of HIV protease susceptibility. BMC Bioinforma 9:181. doi:10.1186/1471-2105-9-181
15. Lapinsh M, Prusis P, Gutcaits a, Lundstedt T, Wikberg JE (2001) Development of proteo-chemometrics: a novel technology for the analysis of drug-receptor interactions. Biochim Biophys Acta 1525:180–90
16. Ma Z, Michailides TJ (2005) Advances in understanding molecular mechanisms of fungicide resistance and molecular detection of resistant genotypes in phytopathogenic fungi. Crop Prot 24(10):853–63
17. Oakeshott JG, Devonshire AL, Claudianos C, Sutherland TD, Horne I, Campbell PM, Ollis DL, Russell RJ (2005) Comparing the organophosphorus and carbamate insecticide resistance mutations in cholin- and carboxyl-esterases. Chem Biol Interact 157:269–75
18. Poehlsgaard J, Douthwaite S (2005) The bacterial ribosome as a target for antibiotics. Nat Rev Microbiol 3(11):870–81
19. Prusis P, Lapins M, Yahorava S, Petrovska R, Niyomrattanakit P, Katzenmeier G, Wikberg JES (2008) Proteochemometrics analysis of substrate interactions with dengue virus NS3 proteases. Bioorg Med Chem 16:9369–77. doi:10.1016/j.bmc.2008.08.081
20. Van Westen GJP, Hendriks A, Wegner JK, IJzerman AP, Van Vlijmen HWT, Bender A (2013) Significantly improved HIV inhibitor efficacy prediction employing proteochemometric models generated from antivirogram data. PLoS Comput Biol 9(2):e1002899
21. Van Westen GJP, Van den Hoven OO, Van der Pijl R, Mulder-Krieger T, de Vries H, Wegner JK, IJzerman AP, Van Vlijmen HWT, Bender A (2012) Identifying novel adenosine receptor ligands by simultaneous proteochemometric modeling of rat and human bioactivity data. J Med Chem 55(16):7010–20. doi:10.1021/jm3003069
22. Van Westen GJP, Wegner JK, Geluykens P, Kwanten L, Vereycken I, Peeters A, IJzerman AP, Van Vlijmen HWT, Bender A (2011) Which compound to select in lead optimization? Prospectively validated proteochemometric models guide preclinical development. PLoS ONE 6:e27518. doi:10.1371/journal.pone.0027518
23. Van Westen GJP, Wegner JK, IJzerman AP, Van Vlijmen HWT, Bender A (2011) Proteochemometric modeling as a tool for designing selective compounds and extrapolating to novel targets. Med Chem Commun 2:16–30
24. Walsh C (2003) Antibiotics: actions, origins, resistance. Am Soc Microbiol (ASM)
25. Warwick SI (1991) Herbicide resistance in weedy plants: physiology and population biology. Annu Rev Ecol Evol Syst 22:95–114
26. Whyard S, Singh AD, Wong S (2009) Ingested double-stranded RNAs can act as species-specific insecticides. Insect Biochem Mol Biol 39(11):824–32