Identification of the binding modes of N-phenylphthalimides inhibiting bacterial thymidylate synthase through X-ray crystallography screening

Journal of Medicinal Chemistry

Volumn 54, Issue 15, 2011, Pages 5454-5467

  Mangani, Stefano ^b   Cancian, Laura ^a   Leone, Rosalida ^b,c   Pozzi, Cecilia ^b   Lazzari, Sandra ^a   Luciani, Rosaria ^a   Ferrari, Stefania ^a   Costi, M Paola ^a  

^a UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

^b UNIVERSITY OF SIENA   (Italy)

^c Roche Pharma Schweiz AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; N PHENYLPHTHALIMIDE DERIVATIVE; PHENOLPHTHALEIN; THYMIDYLATE SYNTHASE; THYMIDYLATE SYNTHASE INHIBITOR; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; COMPARATIVE STUDY; DRUG BINDING; DRUG DESIGN; DRUG IDENTIFICATION; DRUG SCREENING; DRUG STRUCTURE; ENZYME INHIBITION; LACTOBACILLUS CASEI; NONHUMAN; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; ENTEROCOCCUS FAECALIS; ENZYME INHIBITORS; ESCHERICHIA COLI; HUMANS; LACTOBACILLUS CASEI; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHENOLPHTHALEIN; PHTHALIMIDES; PROTEIN BINDING; SEQUENCE ALIGNMENT; STRUCTURE-ACTIVITY RELATIONSHIP; THYMIDYLATE SYNTHASE;

EID: 79961245361     PISSN: 00222623     EISSN: 15204804     Source Type: Journal    
DOI: 10.1021/jm2005018     Document Type: Article

References (34)

1. Carreras, C. W.; Santi, D. V. The catalytic mechanism and structure of thymidylate synthase Annu. Rev. Biochem. 1995, 64, 721-762
2. Chu, E.; Callender, M. A.; Farrell, M. P.; Schmitz, J. C. Thymidylate synthase inhibitors as anticancer agents: from bench to bedside Cancer Chemother. Pharmacol. 2003, 52 (Suppl1) S80-S89
3. Shoichet, B. K; Stroud, R. M.; Santi, D. V.; Kuntz, I. D.; Perry, K. M. Structure-based discovery of inhibitors of thymidylate synthase Science 1993, 259, 1445-1450 (Pubitemid 23101379)
4. Finer-Moore, J. S.; Blaney, J.; Stroud, R. M., Computational and Structural Approaches to Drug Discovery; Stroud, R. M.; Finer-Moore, J. S., Eds; RSC: Cambridge, UK, 2008. p 9.
5. Stout, T. J.; Tondi, D.; Rinaldi, M.; Barlocco, D.; Pecorari, P.; Santi, D. V.; Kuntz, I. D.; Stroud, R. M.; Shoichet, B. K.; Costi, M. P. Structure-based design of inhibitors specific for bacterial thymidylate synthase Biochemistry 1999, 38, 1607-1617
6. Costi, M. P.; Rinaldi, M.; Tondi, D.; Pecorari, P.; Barlocco, D.; Ghelli, S.; Stroud, R. M.; Santi, D. V.; Stout, T. J.; Musiu, C.; Marangiu, E. M.; Pani, A.; Congiu, D.; Loi, G. A.; La Colla, P. Phthalein derivatives as a new tool for selectivity in thymidylate synthase inhibition J. Med. Chem. 1999, 42, 2112-2124 (Pubitemid 29284231)
7. Ghelli, S.; Rinaldi, M.; Barlocco, D.; Gelain, A.; Pecorari, P.; Tondi, D.; Rastelli, G.; Costi, M. P. ortho -Halogen naphthaleins as specific inhibitors of Lactobacillus casei thymidylate synthase. Conformational properties and biological activity Bioorg. Med. Chem. 2003, 11, 951-963 (Pubitemid 36287054)
8. Calò, S.; Tondi, D.; Venturelli, A.; Ferrari, S.; Pecorari, P.; Rinaldi, M.; Ghelli, S.; Costi, M. P. A step further in the discovery of phthalein derivatives as thymidylate synthase inhibitors ARKIVOC 2004, 382-396 (Pubitemid 38773764)
9. Finer-Moore, J. S.; Anderson, A. C.; O'Neil, R. H.; Costi, M. P.; Ferrari, S.; Krucinski, J.; Stroud, R. The structure of Cryptococcus neoformans thymidylate synthase suggests strategies for using target dynamics for species-specific inhibition Acta Crystallogr., Sect. D: Biol. Crystallogr. 2005, D61, 1320-1334 (Pubitemid 43943130)
10. Costi, M. P.; Gelain, A.; Barlocco, D.; Ghelli, S.; Soragni, F.; Raniero, F.; Rossi, T.; Ruberto, A.; Guillou, C.; Cavazzuti, A.; Casolari, C.; Ferrari, S. Anti-bacterial agent discovery using thymidylate synthase bio-library screening J. Med. Chem. 2006, 49, 5958-5968 (Pubitemid 44484942)
11. Babaoglu, K.; Shoichet, B. K. Deconstructing fragment-based inhibitor discovery Nature Chem. Biol. 2006, 2, 720-723 (Pubitemid 44764214)
12. ChemFinder Ultra Database 7.0; Cambridge Soft Corporation, htpp://www.cambridgesoft.com.
13. ACDlab 6.0 Software; Cambridge Soft Corporation, htpp://www. cambridgesoft.com.
14. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug Delivery Rev. 2001, 46, 3-26 (Pubitemid 33653411)
15. Hardy, L. W.; Finer-Moore, J. S.; Montfort, W. R.; Jones, M. O; Santi, D. V.; Stroud, R. M. Atomic structure of thymidylate synthase: target for rational drug design Science 1987, 235, 448-455 (Pubitemid 17009578)
16. Finer-Moore, J.; Fauman, E. B.; Foster, P. G.; Perry, K. M.; Santi, D. V.; Stroud, R. Refined structures of substrate-bound and phosphate-bound thymidylate synthase from Lactobacillus casei J. Mol. Biol. 1993, 232, 1101-1116 (Pubitemid 23276424)
17. Ferrari, S.; Losasso, V.; Costi, M. P. Sequence-Based identification of specific drug target regions in the thymidylate synthase enzyme family ChemMedChem 2008, 3, 392-401
18. Ferrari, S.; Costi, M. P.; Wade, R. Inhibitor specificity via protein dynamics: insights from the design of antibacterial agents targeted against thymidylate synthase Chem. Biol. 2003, 10, 1183-1193 (Pubitemid 38050972)
19. Kealey, J. T.; Santi, D. V. Purification methods for recombinant Lactobacillus casei thymidylate synthase and mutants: a general, automated procedure Protein Expression Purif. 1992, 4, 380-385
20. Maley, G. F.; Maley, F. Properties of a defined mutant of Escherichia coli thymidylate synthase J. Biol. Chem. 1988, 263, 7620-7627
21. Pedersen-Lane, J.; Maley, G. F.; Chu, E.; Maley, F. High-level expression of human thymidylate synthase Protein Expression Purif. 1997, 10, 256-262 (Pubitemid 27288790)
22. Pogolotti, A. L., Jr. ; Danenberg, P. V.; Santi, D. V. Kinetics and mechanism of interaction of 10-propargyl-5,8-dideazafolate with thymidylate synthase J. Med. Chem. 1986, 29, 478-482 (Pubitemid 16034764)
23. Segel, I. H. Enzyme Kinetics. Behaviour and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems; John Wiley and Sons: New York, 1975, p 105.
24. Cavazzuti, A; Paglietti, G; Hunter, W. N.; Gamarro, F; Piras, S; Loriga, M; Alleca, S; Corona, P; McLuskey, K; Tolloch, L.; Gibellini, F.; Ferrari, S.; Costi, M. P. Discovery of potent pteridine reductase inhibitors ot guide antiparasite drug development Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 1448-1453 (Pubitemid 351346534)
25. Jaspard, E. Role of protein-solvent interactions in refolding: effects of cosolvent additives on the renaturation of porcine pancreatic elastase at various pHs Arch. Biochem. Biophys. 2000, 15, 220-228 (Pubitemid 30158378)
26. Bhattacharjya, S.; Balaram, P. Effects of organic solvents on protein structures: observation of a structured helical core in hen egg-white lysozyme in aqueous dimethylsulfoxide Proteins 1997, 29, 492-507 (Pubitemid 27520202)
27. Leslie, A. G. W. Crystallographic Computing V; Moras, D.; Podjarny, A. D.; Thierry, J.-C., Eds.; Oxford University Press: Oxford, 1991; pp 50-61.
28. Collaborative Computational Project, No. 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr., Sect. D: Biol. Crystallogr. 1994, 50, 760-763.
29. Evans, P. R. SCALA, continuous scaling program. Joint CCP4 ESF-EACBM Newsletter 1997, 33, 22-24.
30. Vagin, A; Teplyakov, A. MOLREP: an automated program for molecular replacement J. Appl. Crystallogr. 1997, 30, 1022-1025 (Pubitemid 127485985)
31. Murshudov, G. N.; Vagin, A. A.; Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method Acta Crystallogr., Sect. D: Biol. Crystallogr. 1997, 53, 240-255 (Pubitemid 27235885)
32. Perrakis, A.; Morris, R. J. H.; Lamzin, V. S. Automated protein model building combined with iterative structure refinement Nature Struct. Biol. 1999, 6, 458-463 (Pubitemid 29218016)
33. McRee, D. E. XtalView/Xfit-a versatile program for manipulating atomic coordinates and electron density J. Struct. Biol. 1999, 125, 156-165 (Pubitemid 29402600)
34. UCSF Chimera, Production Version 1 Build 2038 2004/10/18, 2004.