Compound toxicity screening and structure-activity relationship modeling in Escherichia coli

Biotechnology and Bioengineering

Volumn 109, Issue 3, 2012, Pages 846-850

  Planson, Anne Gaëlle ^a   Carbonell, Pablo ^a   Paillard, Elodie ^a   Pollet, Nicolas ^a   Faulon, Jean Loup ^a  

^a UNIVERSITÉ D EVRY VAL D ESSONNE   (France)

Author keywords

Metabolic engineering; QSAR; Toxicity

Indexed keywords

ANTIBACTERIAL AGENT; BIOSYNTHETIC PATHWAY; CHEMICAL DIVERSITY; CHEMICAL LIBRARIES; DATA SETS; E. COLI; HETEROLOGOUS EXPRESSION; METABOLIC ENGINEERING; METABOLIC PATHWAYS; METABOLOMES; NEW STRATEGY; PRODUCTION CELLS; PRODUCTION RATES; QSAR; QSAR MODEL; STRUCTURE ACTIVITY RELATIONSHIPS; SYNTHETIC BIOLOGY; TOXIC INTERMEDIATES; TOXICITY PREDICTIONS; WEB SERVERS;

BYPRODUCTS; CHEMICAL COMPOUNDS; CLUSTERING ALGORITHMS; COMPUTATIONAL CHEMISTRY; ESCHERICHIA COLI; METABOLISM; MOLECULAR GRAPHICS; PROFESSIONAL ASPECTS;

TOXICITY;

ALGORITHM; ESCHERICHIA COLI; EUKARYOTE; IC 50; LETTER; METABOLIC ENGINEERING; METABOLISM; METABOLITE; METABOLOME; NONHUMAN; PREDICTOR VARIABLE; QUANTITATIVE STRUCTURE ACTIVITY RELATION; REFERENCE DATABASE; TOXICITY;

BIOTECHNOLOGY; DRUG EVALUATION, PRECLINICAL; DRUG TOXICITY; ESCHERICHIA COLI; INTERNET; METABOLIC ENGINEERING; PHARMACEUTICAL PREPARATIONS; STRUCTURE-ACTIVITY RELATIONSHIP;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; EUKARYOTA;

EID: 84855946759     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.24356     Document Type: Letter

References (18)

1. Ajikumar PK, Xiao WH, Tyo KE, Wang Y, Simeon F, Leonard E, Mucha O, Phon TH, Pfeifer B, Stephanopoulos G. 2010. Isoprenoid pathway optimization for Taxol precursor overproduction in Escherichia coli. Science 330(6000): 70-74.
2. Alper H, Fischer C, Nevoigt E, Stephanopoulos G. 2005. Tuning genetic control through promoter engineering. Proc Natl Acad Sci USA 102(36): 12678-12683.
3. Anthony JR, Anthony LC, Nowroozi F, Kwon G, Newman JD, Keasling JD. 2009. Optimization of the mevalonate-based isoprenoid biosynthetic pathway in Escherichia coli for production of the anti-malarial drug precursor amorpha-4, 11-diene. Metab Eng 11(1): 13-19.
4. Carbonell P, Planson AG, Fichera D, Faulon JL. 2011. A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Syst Biol 5: 122.
5. De La Fuente R, Sonawane ND, Arumainayagam D, Verkman AS. 2006. Small molecules with antimicrobial activity against E. coli and P. aeruginosa identified by high-throughput screening. Br J Pharmacol 149(5): 551-559.
6. Dunlop MJ, Dossani ZY, Szmidt HL, Chu HC, Lee TS, Keasling JD, Hadi MZ, Mukhopadhyay A. 2011. Engineering microbial biofuel tolerance and export using efflux pumps. Mol Syst Biol 7: 487.
7. Edwards JS, Palsson BO. 2000. The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97(10): 5528-5533.
8. Faulon J-LL, Collins MJ, Carr RD. 2004. The signature molecular descriptor. 4. Canonizing molecules using extended valence sequences. J Chem Inf Comput Sci 44(2): 427-436.
9. Hansch C, Leo A, Hoekman D. 1996. Exploring QSAR: American Chemical Society.
10. Harder A, Escher BI, Schwarzenbach ReP. 2003. Applicability and limitation of QSARs for the toxicity of electrophilic chemicals. Environ Sci Technol 37(21): 4955-4961.
11. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Res 36 (Database issue): D480-D484.
12. Ma SM, Garcia DE, Redding-Johanson AM, Friedland GD, Chan R, Batth TS, Haliburton JR, Chivian D, Keasling JD, Petzold CJ, Soon Lee T, Chhabra SR. 2011. Optimization of a heterologous mevalonate pathway through the use of variant HMG-CoA reductases. Metab Eng 13(5): 588-597.
13. Mevik B-H, Wehrens R. 2007. The pls package: Principal component and partial least squares regression in R. J Stat Software 18(2): 1-24.
14. Pitera DJ, Paddon CJ, Newman JD, Keasling JD. 2007. Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli. Metab Eng 9(2): 193-207.
15. Rogers D, Hahn M. 2010. Extended-connectivity fingerprints. J Chem Inf Model 50(5): 742-754.
16. Tropsha A, Golbraikh A. 2010. Predictive quantitative structure-activity relationship modeling. Development and validation of QSAR models. Handbook of chemoinformatics algorithms. Boca Raton, FL, USA: Chapman and Hall/CRC. p 211-232.
17. Worth AP, Bassan A, De Bruijn J, Gallegos Saliner A, Netzeva T, Patlewicz G, Pavan M, Tsakovska I, Eisenreich S. 2007. The role of the European Chemicals Bureau in promoting the regulatory use of (Q)SAR methods. SAR QSAR Environ Res 18(1-2): 111-125.
18. Zaldivar J, Ingram LO. 1999. Effect of organic acids on the growth and fermentation of ethanologenic Escherichia coli LY01. Biotechnol Bioeng 66(4): 203-210.