A protein recycling system for nuclear magnetic resonance-based screening of drug candidates

Analytical Biochemistry

Volumn 353, Issue 1, 2006, Pages 99-107

  Hirayama, Aya ^a   Shirota, Osamu ^a   Nomura, Mitsuru ^b   Nagadoi, Aritaka ^b   Nishimura, Yoshifumi ^b  

^a SHISEIDO RESEARCH CENTER   (Japan)

^b YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

15N labeled protein; Drug screening; Mixed function phase; Protein recycling system; SAR by NMR

Indexed keywords

DATA ACQUISITION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; PROTEINS; RECYCLING; SCREENING;

DRUG SCREENING; LABELED PROTEINS; MIXED-FUNCTION PHASE; NMR MEASUREMENTS; NUCLEAR MAGNETIC RESONANCE(NMR); RECYCLING SYSTEMS; REPRESENTATIVE COMPOUND; TEST OPERATIONS;

NUCLEAR MAGNETIC RESONANCE;

ACETAMIDE DERIVATIVE; ACETAMIDOPHENOL; DIHYDROFOLATE REDUCTASE; METHOTREXATE; UNCLASSIFIED DRUG; DRUG; HYDROGEN; MYOGLOBIN; NITROGEN; PROTEIN; RADIOISOTOPE;

ARTICLE; DRUG SCREENING; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; INFORMATION PROCESSING; NITROGEN NUCLEAR MAGNETIC RESONANCE; NONHUMAN; PRIORITY JOURNAL; CELL FREE SYSTEM; CHEMISTRY; DRUG DESIGN; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROTEIN BINDING;

CELL-FREE SYSTEM; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; DRUG DESIGN; HYDROGEN; MAGNETIC RESONANCE SPECTROSCOPY; MYOGLOBIN; NITROGEN RADIOISOTOPES; PHARMACEUTICAL PREPARATIONS; PROTEIN BINDING; PROTEINS; RADIOISOTOPES; RESEARCH DESIGN; TETRAHYDROFOLATE DEHYDROGENASE;

EID: 33746500967     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2006.03.024     Document Type: Article

References (33)

1. Erlanson D.A., McDowell R.S., and O'Brien T. Fragment-based drug discovery. J. Med. Chem. 47 (2004) 3463-3482
2. Diercks T., Coles M., and Kessler H. Applications of NMR in drug discovery. Curr. Opin. Chem. Biol. 5 (2001) 285-291
3. Chen A., and Shapiro M.J. NOE pumping: a novel NMR technique for identification of compounds with binding affinity to macromolecules. J. Am. Chem. Soc. 120 (1998) 10258-10259
4. Chen A., and Shapiro M.J. NOE pumping: II. A high-throughput method to determine compounds with binding affinity to macromolecules by NMR. J. Am. Chem. Soc. 122 (2000) 414-415
5. Casset F., Imberty A., Perez S., Etzler M.E., Paulsen H., and Peters T. Transferred nuclear Overhauser enhancement (NOE) and rotating-frame NOE experiments reflect the size of the bound segment of the Forssman pentasaccharide in the binding site of Dolichos biflorus lectin. Eur. J. Biochem. 244 (1997) 242-250
6. Eisenmesser E.Z., Zabell A.P.R., and Post C.B. Accuracy of bound peptide structures determined by exchange transferred nuclear Overhauser data: a simulation study. J. Biomol. NMR 17 (2000) 17-32
7. Miura T., Klaus W., Ross A., Sakata K., Masubuchi M., and Senn H. Protein-bound conformation of a specific inhibitor against Candida albicans myristoyl-CoA:protein N-myristoyltransferase in the ternary complex with CaNmt and myristoyl-CoA by transferred NOE measurements. Eur. J. Biochem. 268 (2001) 4833-4841
8. Fejzo J., Lepre A.L., Peng J.W., Bemis G.W., Ajay, Murcko M.A., and Moore J.M. The SHAPES strategy: an NMR-based approach for lead generation in drug discovery. Chem. Biol. 6 (1999) 755-769
9. Moore J.M. NMR techniques for characterization of ligand binding: utility for lead generation and optimization in drug discovery. Biopolymers 51 (1999) 221-243
10. Moore J.M. NMR screening in drug discovery. Curr. Opin. Biotechnol. 10 (1999) 54-58
11. Shuker S.B., Hajduk P.J., Meadows R.P., and Fesik S.W. Discovering high-affinity ligands for proteins: SAR by NMR. Science 274 (1996) 1531-1534
12. Hajduk P.J., Meadows R.P., and Fesik S.W. Discovering high-affinity ligands for proteins. Science 278 (1997) 497-499
13. Hajduk P.J., Sheppard G., Nettesheim D.G., Olejniczak E.T., Shuker S.B., Meadows R.P., Steinman D.H., Carrera Jr. G.M., Marcotte P.A., Severin J., Walter K., Smith H., Gubbins E., Simmer R., Holzman T.F., Morgan D.W., Davidsen S.K., Summers J.B., and Fesik S.W. Discovery of potent nonpeptide inhibitors of stromelysin using SAR by NMR. J. Am. Chem. Soc. 119 (1997) 5818-5827
14. Olejniczak E.T., Hajduk P.J., Marcotte P.A., Nettesheim D.G., Meadows R.P., Edalji R., Holzman T.F., and Fesik S.W. Stromelysin inhibitors designed from weakly bound fragments: effects of linking and cooperativity. J. Am. Chem. Soc. 119 (1997) 5828-5832
15. Hajduk P.J., Dinges J., Miknis G.F., Merlock M., Middleton T., Kempf D.J., Egan D.A., Walter K.A., Robins T.S., Shuker S.B., Holzman T.F., and Fesik S.W. NMR-based discovery of lead inhibitors that block DNA binding of the human papillomavirus E2 protein. J. Med. Chem. 40 (1997) 3144-3150
16. Hajduk P.J., Dinges J., Schkeryantz J.M., Janowick D., Kaminski M., Tufano M., Augeri D.J., Petros A., Nienaber V., Zhong P., Hammond R., Coen M., Beutel B., Katz L., and Fesik S.W. Novel inhibitors of Erm methyltransferases from NMR and parallel synthesis. J. Med. Chem. 42 (1999) 3852-3859
17. Hajduk P.J., Boyd S., Nettesheim D.G., Nienaber V., Severin J., Smith R., Davidson D., Rockway T., and Fesik S.W. Identification of novel inhibitors of urokinase via NMR-based screening. J. Med. Chem. 43 (2000) 3862-3866
18. Hajduk P.J., Gomtsyan A., Didomenico S., Cowart M., Bayburt E.K., Solomon L., Severin J., Smith R., Walter K., Holzman T.F., Stewart A., McGaraughty S., Jarvis M.F., Kowaluk E.A., and Fesik S.W. Design of adenosine kinase inhibitors from the NMR-based screening of fragments. J. Med. Chem. 43 (2000) 4781-4786
19. Hajduk P.J., Zhou M.M., and Fesik S.W. NMR-based discovery of phosphotyrosine mimetics that bind to the Lck SH2 domain. Bioorg. Med. Chem. Lett. 9 (1999) 2403-2406
20. Huth J.R., Yu L., Collins I., Mack J., Mendoza R., Isaac B., Braddock D.T., Muchmore S.W., Comess K.M., Fesik S.W., Clore G.M., Levens D., and Hajduk P.J. NMR-driven discovery of benzoylanthranilic acid inhibitors of far upstream element binding protein binding to the human oncogene c-myc promoter. J. Med. Chem. 47 (2004) 4851-4857
21. Zech S.G., Olejniczak E.T., Hajduk P.J., Mack J., and McDermott A.E. Characterization of protein-ligand interactions by high-resolution solid-state NMR spectroscopy. J. Am. Chem. Soc. 126 (2004) 13948-13953
22. Bertini I., Fragai M., Giachetti A., Luchinat C., Maletta M., Parigi G., and Yeo K.J. Combining in silico tools and NMR data to validate protein-ligand structural models: application to matrix metalloproteinases. J. Med. Chem. 48 (2005) 7544-7559
23. Ross A., Schlotterbeck G., Klaus W., and Senn H. Automation of NMR measurements and data evaluation for systematically screening interactions of small molecules with target proteins. J. Biomol. NMR 16 (2000) 139-146
24. Ross A., and Senn H. Automation of measurements and data evaluation in biomolecular NMR screening. Drug Discov. Today 6 (2001) 583-593
25. Yamazaki T., Otomo T., Oda N., Kyogoku Y., Uegaki K., Ito N., Ishino Y., and Nakamura H. Segmental isotope labeling for protein NMR using peptide splicing. J. Am. Chem. Soc. 120 (1998) 5591-5592
26. Hayano T., Takahashi N., Kato S., Maki N., and Suzuki M. Two distinct forms of peptidylprolyl-cis-trans-isomerase are expressed separately in periplasmic and cytoplasmic compartments of Escherichia coli cells. Biochemistry 30 (1991) 3041-3048
27. 15N resonance assignments of an 18-kDa protein, E. coli peptidyl-proryl cis-trans isomerase b (EPPIb). J. Biomol. NMR 18 (2000) 75-76
28. Kigawa T., Yabuki T., Matsuda N., Matsuda T., Nakajima R., Tanaka A., and Yokoyama S. Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J. Struct. Funct. Genom. 5 (2004) 63-68
29. Kay L.E., Keifer P., and Saarinien T. Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. J. Am. Chem. Soc. 114 (1992) 10663-10665
30. Hajduk P.J., Gerfin T., Boehlen J.M., Haberli M., Marek D., and Fesik S.W. High-throughput nuclear magnetic resonance-based screening. J. Med. Chem. 42 (1999) 2315-2317
31. Kanda T., Kutsuna H., Ohtsu Y., and Yamaguchi M. Synthesis of polymer-coated mixed-functional packing materials for direct analysis of drug-containing serum and plasma by high-performance liquid chromatography. J. Chromatogr. A 672 (1994) 51-57
32. Kanda T., Shirota O., Ohtsu Y., and Yamaguchi M. Synthesis and characterization of polymer-coated mixed-functional stationary phases with several different hydrophobic groups for direct analysis of biological samples by liquid chromatography. J. Chromatogr. A 722 (1996) 115-121
33. Chunduru S.K., Cody V., Luft J.R., Pangborn W., Appleman J.R., and Blakley R.L. Methotrexate-resistant variants of human dihydrofolate reductase. J. Biol. Chem. 269 (1994) 9547-9555