Screening and in situ synthesis using crystals of a NAD kinase lead to a potent antistaphylococcal compound

Structure

Volumn 20, Issue 6, 2012, Pages 1107-1117

  Gelin, Muriel ^a   Poncet Montange, Guillaume ^a   Assairi, Liliane ^b,c   Morellato, Laurence ^d,e   Huteau, Valérie ^d,e   Dugué, Laurence ^d,e   Dussurget, Olivier ^d,f,g,h   Pochet, Sylvie ^d,e   Labesse, Gilles ^a  

^a CENTRE DE BIOCHIMIE STRUCTURALE   (France)

^b INSTITUT CURIE   (France)

^c Centre Universitaire   (France)

^d INSTITUT PASTEUR   (France)

^e CNRS   (France)

^f INSERM   (France)

^g INRAUSC2020   (France)

^h UNIVERSITÉ PARIS DESCARTES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

5' AMINO 5' DEOXYADENOSINE; ADENOSINE; ANTIINFECTIVE AGENT; CARBOXYLIC ACID; NICOTINAMIDE ADENINE DINUCLEOTIDE KINASE;

AMIDATION; ARTICLE; BACTERICIDAL ACTIVITY; CATALYSIS; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; HUMAN; HUMAN CELL; LISTERIA MONOCYTOGENES; NONHUMAN; PRIORITY JOURNAL; STAPHYLOCOCCUS; STAPHYLOCOCCUS AUREUS; SYNTHESIS; X RAY CRYSTALLOGRAPHY;

ADENOSINE; AMINO ACID MOTIFS; ANTI-BACTERIAL AGENTS; BIOCATALYSIS; CATALYTIC DOMAIN; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LISTERIA MONOCYTOGENES; MODELS, MOLECULAR; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); PROTEIN BINDING; STAPHYLOCOCCUS AUREUS;

LISTERIA MONOCYTOGENES; STAPHYLOCOCCUS AUREUS;

EID: 84861993424     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2012.03.024     Document Type: Article

References (25)

1. Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., et al. (2010). PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213-221.
2. Chessari, G., and Woodhead, A.J. (2009). From fragment to clinical candidate-a historical perspective. Drug Discov. Today 14, 668-675.
3. Collaborative Computational Project, Number 4. (1994). The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763.
4. Congreve, M.S., Davis, D.J., Devine, L., Granata, C., O'Reilly, M., Wyatt, P.G., and Jhoti, H. (2003). Detection of ligands from a dynamic combinatorial library by X-ray crystallography. Angew. Chem. Int. Ed. Engl. 42, 4479-4482.
5. Emsley, P., Lohkamp, B., Scott, W.G., and Cowtan, K. (2010). Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486-501.
6. Evans, P. (2006). Scaling and assessment of data quality. Acta Crystallogr. D Biol. Crystallogr. 62, 72-82.
7. Fischbach, M.A., and Walsh, C.T. (2009). Antibiotics for emerging pathogens. Science 325, 1089-1093.
8. Funabashi, M., Yang, Z., Nonaka, K., Hosobuchi, M., Fujita, Y., Shibata, T., Chi, X., and Van Lanen, S.G. (2010). An ATP-independent strategy for amide bond formation in antibiotic biosynthesis. Nat. Chem. Biol. 6, 581-586.
9. Gill, A.L., Frederickson, M., Cleasby, A., Woodhead, S.J., Carr, M.G., Woodhead, A.J., Walker, M.T., Congreve, M.S., Devine, L.A., Tisi, D., et al. (2005). Identification of novel p38alpha MAP kinase inhibitors using fragment-based lead generation. J. Med. Chem. 48, 414-426.
10. Hajduk, P.J., and Greer, J. (2007). A decade of fragment-based drug design: strategic advances and lessons learned. Nat. Rev. Drug Discov. 6, 211-219.
11. Katz, B.A., Finer-Moore, J., Mortezaei, R., Rich, D.H., and Stroud, R.M. (1995). Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface. Biochemistry 34, 8264-8280.
12. Kawai, S., Mori, S., Mukai, T., Suzuki, S., Yamada, T., Hashimoto, W., and Murata, K. (2000). Inorganic Polyphosphate/ATP-NAD kinase of Micrococcus flavus and Mycobacterium tuberculosis H37Rv. Biochem. Biophys. Res. Commun. 276, 57-63.
13. Labesse, G., Douguet, D., Assairi, L., and Gilles, A.-M. (2002). Diacylglyceride kinases, sphingosine kinases and NAD kinases: distant relatives of 6-phosphofructokinases. Trends Biochem. Sci. 27, 273-275.
14. Leslie, A.G. (2006). The integration of macromolecular diffraction data. Acta Crystallogr. D Biol. Crystallogr. 62, 48-57.
15. Murshudov, G.N., Skubák, P., Lebedev, A.A., Pannu, N.S., Steiner, R.A., Nicholls, R.A., Winn, M.D., Long, F., and Vagin, A.A. (2011). REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355-367.
16. Petrelli, R., Sham, Y.Y., Chen, L., Felczak, K., Bennett, E., Wilson, D., Aldrich, C., Yu, J.S., Cappellacci, L., Franchetti, P., et al. (2009). Selective inhibition of nicotinamide adenine dinucleotide kinases by dinucleoside disulfide mimics of nicotinamide adenine dinucleotide analogues. Bioorg. Med. Chem. 17, 5656-5664.
17. Poncet-Montange, G., Assairi, L., Arold, S., Pochet, S., and Labesse, G. (2007). NAD kinases use substrate-assisted catalysis for specific recognition of NAD. J. Biol. Chem. 282, 33925-33934.
18. Rouse, M.S., Steckelberg, J.M., and Patel, R. (2007). In vitro activity of ceftobiprole, daptomycin, linezolid, and vancomycin against methicillin-resistant staphylococci associated with endocarditis and bone and joint infection. Diagn. Microbiol. Infect. Dis. 58, 363-365.
19. Schindler, T., Bornmann, W., Pellicena, P., Miller, W.T., Clarkson, B., and Kuriyan, J. (2000). Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. Science 289, 1938-1942.
20. Schmidt, M.F., and Rademann, J. (2009). Dynamic template-assisted strategies in fragment-based drug discovery. Trends Biotechnol. 27, 512-521.
21. Schulz, M.N., and Hubbard, R.E. (2009). Recent progress in fragment-based lead discovery. Curr. Opin. Pharmacol. 9, 615-621.
22. Scott, D.E., Dawes, G.J., Ando, M., Abell, C., and Ciulli, A. (2009). A fragment-based approach to probing adenosine recognition sites by using dynamic combinatorial chemistry. ChemBioChem 10, 2772-2779.
23. Simmons, K.J., Chopra, I., and Fishwick, C.W. (2010). Structure-based discovery of antibacterial drugs. Nat. Rev. Microbiol. 8, 501-510.
24. Villoutreix, B.O., Eudes, R., and Miteva, M.A. (2009). Structure-based virtual ligand screening: recent success stories. Comb. Chem. High Throughput Screen. 12, 1000-1016.
25. Zappelli, P., Rossodivita, A., Prosperi, G., Pappa, R., and Re, L. (1976). New coenzymically-active soluble and insoluble macromolecular NAD+ derivatives. Eur. J. Biochem. 62, 211-215.