Prospective virtual screening with ultrafast shape recognition: The identification of novel inhibitors of arylamine N-acetyltransferases

Journal of the Royal Society Interface

Volumn 7, Issue 43, 2010, Pages 335-342

  Ballester, Pedro J ^a,b   Westwood, Isaac ^a,c   Laurieri, Nicola ^a   Sim, Edith ^a   Richards, W Graham ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

Drug lead identification; Ligand receptor shape complementarity; Molecular shape similarity; Prospective virtual screening

Indexed keywords

PROBES;

DRUG LEADS; LIGAND-RECEPTOR; MOLECULAR SHAPES; SHAPE COMPLEMENTARITY; VIRTUAL SCREENING;

LIGANDS;

ARYLAMINE ACETYLTRANSFERASE; LIGAND;

ARTICLE; CHEMICAL REACTION; CHEMICAL STRUCTURE; SCREENING; VIRTUAL REALITY;

EID: 74049126603     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2009.0170     Document Type: Article

References (45)

1. Ballester, P. J. 2007 Shape recognition methods and systems for searching molecular databases. US Patent No. 12/127559.
2. Ballester, P. J. & Richards, W. G. 2007a Ultrafast shape recognition for similarity search in molecular databases. Proc. R. Soc. A 463, 1307-1321. (doi:10.1098/rspa.2007.1823)
3. Ballester, P. J. & Richards, W. G. 2007b Ultrafast shape recognition to search compound databases for similar molecular shapes. J. Comput. Chem. 28, 1711-1723. (doi:10.1002/jcc.20681)
4. Ballester, P. J., Finn, P. W. & Richards, W. G. 2009 Ultrafast shape recognition: evaluating a new ligand-based virtual screening technology. J. Mol. Graph. Model. 27, 836-845. (doi:10.1016/j.jmgm.2009.01.001)
5. Boukouvala, S., Price, N. & Sim, E. 2002 Identification and functional characterization of novel polymorphisms associated with the genes for arylamine N-acetyltransferases in mice. Pharmacogenetics 12, 385-394. (doi:10.1097/00008571-200207000-00006)
6. Brooke, E. W., Davies, S. G., Mulvaney, A. W., Pompeo, F., Sim, E. & Vickers, R. J. 2003a An approach to identifying novel substrates of bacterial arylamine N-acetyltransferases. Bioorg. Med. Chem. 11, 1227-1234. (doi:10.1016/S0968-0896(02)00642-9)
7. Brooke, E. W., Davies, S. G., Mulvaney, A. W., Okada, M., Pompeo, F., Sim, E., Vickers, R. J. & Westwood, I. M. 2003b Synthesis and in vitro evaluation of novel small molecule inhibitors of bacterial arylamine N-acetyltransferases (NATs). Bioorg. Med. Chem. Lett. 13, 2527-2530. (doi:10.1016/S0960-894X(03)00484-0)
8. Cannon, E. O., Nigsch, F. & Mitchell, J. B. O. 2008 A novel hybrid ultrafast shape descriptor method for use in virtual screening. Chem. Cent. J. 2, 3. (doi:10.1186/1752-153X-2-3)
9. Chung, J. G., Levy, G. N. & Weber, W. W. 1993 Distribution of 2-aminofluorene and p-aminobenzoic acid N-acetyltransferase activity in tissues of C57BL/6J rapid and B6.A-NatS slow acetylator congenic mice. Drug Metab. Dispos. 21, 1057-1063.
10. Cribb, A. E., Grant, D. M., Miller, M. A. & Spielberg, S. P. 1991 Expression of monomorphic arylamine N-acetyltransferase (NAT1) in human leukocytes. J. Pharmacol. Exp. Ther. 259, 1241-1246.
11. Dobson, C. M. 2004 Chemical space and biology. Nature 432, 824-828. (doi:10.1038/nature03192)
12. Hawkins, P. C. D., Skillman, A. G. & Nicholls, A. 2007 Comparison of shape-matching and docking as virtual screening tools. J. Med. Chem. 50, 74-82. (doi:10.1021/jm0603365)
13. Hein, D. W., Doll, M. A., Nerland, D. E. & Fretland, A. J. 2006. Tissue distribution of N-acetyltransferase 1 and 2 catalyzing the N-acetylation of 4-aminobiphenyl and Oacetylation of N-hydroxy-4- aminobiphenyl in the congenic rapid and slow acetylator Syrian hamster. Mol. Carcinog. 45, 230-238. (doi:10.1002/mc.20164)
14. Hickman, D., Pope, J., Patil, S. D., Fakis, G., Smelt, V., Stanley, L. A., Payton, M., Unadkat, J. D. & Sim, E. 1998 Expression of arylamine N-acetyltransferase in human intestine. Gut 42, 402-409. (doi:10.1136/gut.42.3.402)
15. Irwin, J. J. & Shoichet, B. K. 2005. ZINC - a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 45, 177-182. (doi:10.1021/ci049714+)
16. Kaiser, J. 2008 Industrial-style screening meets academic biology. Science 321, 764-766. (doi:10.1126/science.321.5890.764)
17. Kawamura, A., Graham, J., Mushtaq, A., Tsiftsoglou, S. A., Vath, G. M., Hanna, P. E., Wagner, C. R. & Sim, E. 2005 Eukaryotic arylamine N-acetyltransferase: investigation of substrate specificity by high-throughput screening. Biochem. Pharmacol. 69, 347-359. (doi:10.1016/j.bcp.2004.09.014)
18. Kawamura, A., Westwood, I., Wakefield, L., Long, H., Zang, N., Walters, K., Redfield, C. & Sim, E. 2008 Mouse N-acetyltransferase type 2, the homologue of human N-acetyltransferase type 1. Biochem. Pharmacol. 75, 1550-1560. (doi:10.1016/j.bcp.2007.12.012)
19. Kirchmair, J., Distinto, S., Markt, P., Schuster, D., Spitzer, G. M., Liedl, K. R. & Wolber, G. 2009 How to optimize shape-based virtual screening: choosing the right query and including chemical information. J. Chem. Inf. Model. 49, 678-692. (doi:10.1021/ci8004226)
20. Kortagere, S., Krasowski, M. D. & Ekins, S. 2009 The importance of discerning shape in molecular pharmacology. Trends Pharmacol. Sci. 30, 138-147. (doi:10.1016/j.tips.2008.12.001)
21. Lee, J. H., Chung, J. G., Lai, J. M., Levy, G. N. & Weber, W. W. 1997 Kinetics of arylamine N-acetyltransferase in tissues from human breast cancer. Cancer Lett. 111, 39-50. (doi:10.1016/S0304-3835(96)04491- 6)
22. Lee, J. H., Lu, H. F., Wang, D. Y., Chen, D. R., Su, C. C., Chen, Y. S., Yang, J. H. & Chung, J. G. 2004 Effects of tamoxifen on DNA adduct formation and arylamines N-acetyltransferase activity in human breast cancer cells. Res. Commun. Mol. Pathol. Pharmacol. 115-116, 217-233.
23. Loehle, J. A., Cornish, V., Wakefield, L., Doll, M. A., Neale, J. R., Zang, Y., Sim, E. & Hein, D. W. 2006 N-acetyltransferase (Nat) 1 and 2 expression in Nat2 knockout mice. J. Pharmacol. Exp. Ther. 319, 724-728. (doi:10.1124/jpet.106.108662)
24. Lu, K. H., Lin, K. L., Hsia, T. C., Hung, C. F., Chou, M. C., Hsiao, Y. M. & Chung, J. G. 2001 Tamoxifen inhibits arylamine N- acetyltransferase activity and DNA-2-aminofluorene adduct in human leukemia HL-60 cells. Res. Commun. Mol. Pathol. Pharmacol. 109, 319-331.
25. Minchin, R. F. 1995 Acetylation of p-aminobenzoylglutamate, a folic acid catabolite, by recombinant human arylamine N-acetyltransferase and U937 cells. Biochem. J. 307, 1-3.
26. 2O)nn≤8. J. Phys. Chem. A 112, 6257-6261. (doi:10.1021/jp802118j)
27. Ohsako, S. & Deguchi, T. 1990 Cloning and expression of cDNAs for polymorphic and monomorphic arylamine N-acetyltransferases from human liver. J. Biol. Chem. 265, 4630-4634.
28. Peakman, T., Franks, S., White, C. & Beggs, M. 2003 Delivering the power of discovery in large pharmaceutical organizations. Drug Discov. Today 8, 203-211. (doi:10.1016/S1359-6446(03)02612-6)
29. Richards, V. E., Chau, B., White, M. R. & McQueen, C. A. 2004 Hepatic gene expression and lipid homeostasis in C57BL/6 mice exposed to hydrazine or acetylhydrazine. Toxicol. Sci. 82, 318-332. (doi:10.1093/toxsci/ kfh232)
30. Riddles, P. W., Blakeley, R. L. & Zerner, B. 1983 Reassessment of Ellman's reagent. Methods Enzymol. 91, 49-60. (doi:10.1016/S0076- 6879(83)91010-8)
31. Risch, A., Smelt, V., Lane, D., Stanley, L., van der Slot, W., Ward, A. & Sim, E. 1996 Arylamine N-acetyltransferase in erythrocytes of cystic fibrosis patients. Pharmacol. Toxicol. 8, 235-240. (doi:10.1111/j.1600-0773.1996.tb00211.x)
32. Rush III, T. S., Grant, J. A., Mosyak, L. & Nicholls, A. 2005 A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. J. Med. Chem. 48, 1489-1495. (doi:10.1021/jm040163o)
33. Russell, A. J. et al. 2009 Selective small molecule inhibitors of the potential breast cancer marker, human arylamine N-acetyltransferase 1, and its murine homologue, mouse arylamine N-acetyltransferase 2. Bioorg. Med. Chem. 17, 905-918. (doi:10.1016/j.bmc.2008.11.032)
34. Schreyer, A. & Blundell, T. L. 2009 CREDO: a proteinligand interaction database for drug discovery. Chem. Biol. Drug Des. 73, 157-167. (doi:10.1111/j.1747-0285.2008.00762.x)
35. Shoichet, B. K. 2004 Virtual screening of chemical libraries. Nature 432, 862-865. (doi:10.1038/nature03197)
36. Sim, E., Walters, K. & Boukouvala, S. 2008 Arylamine N-acetyltransferases: from structure to function. Drug Metab. Rev. 40, 479-510. (doi:10.1080/03602530802186603)
37. Smit, B. & Maesen, T. L. M. 2008 Towards a molecular understanding of shape selectivity. Nature 451, 671-678. (doi:10.1038/nature06552)
38. Sommer, I., Müller, O., Domingues, F. S., Sander, O.,Weickert, J. & Lengauer, T. 2007 Moment invariants as shape recognition technique for comparing protein binding sites. Bioinformatics 23, 3139-3146. (doi:10.1093/bioinformatics/btm503)
39. Stanley, L. A., Coroneos, E., Cuff, R., Hickman, D.,Ward, A. & Sim, E. 1996 Immunochemical detection of arylamine N-acetyltransferase in normal and neoplastic bladder. J. Histochem. Cytochem. 44, 1059-1067.
40. Tozlu, S., Girault, I., Vacher, S., Vendrell, J., Andrieu, C., Spyratos, F., Cohen, P., Lidereau, R. & Bieche, I. 2006 Identification of novel genes that co-cluster with estrogen receptor alpha in breast tumor biopsy specimens, using a large-scale real-time reverse transcription-PCR approach. Endocr. Relat. Cancer 13, 1109-1120. (doi:10.1677/erc.1.01120)
41. Wakefield, L., Cornish, V., Long, H., Griffiths, W. J. & Sim, E. 2007 Deletion of a xenobiotic-metabolizing gene in mice affects folate metabolism. Biochem. Biophys. Res. Commun. 364, 556-560. (doi:10.1016/j.bbrc. 2007.10.026)
42. Wakefield, L., Robinson, J., Long, H., Ibbitt, J. C., Cooke, S., Hurst, H. C. & Sim, E. 2008 Arylamine N-acetyltransferase 1 expression in breast cancer cell lines: a potential marker in estrogen receptor-positive tumors. 2Genes Chromosomes Cancer 47, 118-126. (doi:10.1002/gcc.20512)
43. Walraven, J. M., Barker, D. F., Doll, M. A. & Hein, D. W. 2007 Tissue expression and genomic sequences of rat N-acetyltransferases rNat1, rNat2, rNat3, and functional characterization of a novel rNat3*2 genetic variant. Toxicol. Sci. 99, 413-421. (doi:10.1093/toxsci/kfm159)
44. Wu, H., Dombrovsky, L., Tempel, W., Martin, F., Loppnau, P., Goodfellow, G. H., Grant, D. M. & Plotnikov, A. N. 2007 Structural basis of substrate-binding specificity of human arylamine N-acetyltransferases. J. Biol. Chem. 282, 30 189-30 197. (doi:10.1074/jbc.M704138200)
45. Zauhar, R. J., Moyna, G., Tian, L., Li, Z. &Welsh,W. J. 2003 Shape signatures, a new approach to computer-aided ligand- and receptor-based drug design. J. Med. Chem. 46, 5674-5690. (doi:10.1021/jm030242k)