High-resolution crystallography and drug design

Journal of Molecular Recognition

Volumn 18, Issue 3, 2005, Pages 196-202

  Cachau, R E ^a   Podjarny, A D ^b  

^a NATIONAL CANCER INSTITUTE   (United States)

^b INSTITUT DE GÉNÉTIQUE ET DE BIOLOGIE MOLÉCULAIRE ET CELLULAIRE   (France)

Author keywords

Drug design; Macromolecular crystallography; Ultra high resolution

Indexed keywords

ANIMAL; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; HUMAN; MACROMOLECULE; PROTEIN CONFORMATION; REVIEW; X RAY CRYSTALLOGRAPHY;

ANIMALS; CRYSTALLOGRAPHY, X-RAY; DRUG DESIGN; HUMANS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; PROTEIN CONFORMATION;

EID: 18944379249     PISSN: 09523499     EISSN: None     Source Type: Journal    
DOI: 10.1002/jmr.738     Document Type: Review

References (42)

1. Afonine PV, Lunin VY, Muzet N, Urzhumtsev A. 2004. On the possibility of the observation of valence electron density for individual bonds in proteins in conventional difference maps. Acta Crystallogr. Sect. D Biol. Crystallogr. 60: 260.
2. Barrientos LG, O'Keefe BR, Bray M, Anthony S, Gronenborn AM, Boyd MR. 2003. Cyanovirin-N binds to the viral surface glycoprotein, GP(1,2) and inhibits infectivity of Ebola virus. Antiviral Res. 58(1): 47.
3. Bethanis K, Tzamalis P, Hountas A, Tsoucaris G. 2002. Ab initio determination of a crystal structure by means of the Schrodinger equation. Acta Crystallogr. Sect. A 58: 265.
4. Brenk R, Meyer EA, Reuter K, Stubbs MT, Garcia GA, Diederich F, Klebe G. 2004. Crystallographic study of in transglycosylase suggests pharmacophore for virtual hibitors of tRNA-guanine a new structure-based screening. J. Mol. Biol. 338(1): 55.
5. Brown ID. 2002. The Chemical Bond in Inorganic Chemistry: The Bond Valence Model. Oxford University Press: New York.
6. Cachau RE, Munshi S, Canady M, Johnson J. 1999. A self consistent time-averaged dynamic phase refinement protocol. Application to the refinement of Nudaurelia Omega Capensis virus. In XVIIIth International Union of Crystallography Congress and General Assembly, Glasgow.
7. Chernov AA, DeLucas LJ. 2002. View on biocrystallization from Jena. 2002. Acta Crystallogr. Sect. D Biol. Crystallogr. 58: 1511.
8. Cliff MJ, Ladbury JE. 2003. A survey of the year 2002 literature on applications of isothermal titration calorimetry. J. Mol. Recognit. 16(6): 383.
9. Darmanin C, Chevreux G, Potier N, Van Dorsselaer A, Hazemann I, Podjarny A, El-Kabbani O. 2004. Probing the ultra-high resolution structure of aldose reductase with molecular modelling and noncovalent mass spectrometry. Bioorg. Med. Chem. 12(14): 3797.
10. DePristo MA, de Bakker PIW, Blundell TL. 2004. Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. Structure 12(5): 831.
11. Fukui K. 1991. The role of frontier orbitals in chemical reactions. In Nobel Lectures, Chemistry 7987-7990, Bo G (ed.). World Scientific: Singapore.
12. Gloster TM, Williams SJ, Roberts S, Tarling CA, Wicki J, Withers SG, Davies GJ. 2004. Atomic resolution analyses of the binding of xylobiose-derived deoxynojirimycin and isofagomine to xylanase Xyn10A. Chem. Commun. 16: 1794.
13. Gros P, Vangunsteren WF, Hol WGJ. 1990. Inclusion of thermal motion in crystallographic structures by restrained molecular-dynamics. Science 249(4973): 1149.
14. Hehre WJ, Radom L, Pople JA. 1972. Molecular orbital theory of the electronic structure of organic compounds. XII. Conformations, stabilities, and charge distributions in monosubstituted benzenes. J. Am. Chem. Soc. 94(5): 1496-1504.
15. Hendlich M, Bergner A, Gunther J, Klebe G. 2003. Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. J. Mol. Biol. 326(2): 607.
16. Heyman K. 2004. Better structures through synergy. The Scientist 18(17): 17-21.
17. Howard EI, Lamour V, Mitschler A, Barth P, Moras D, Podjarny A. 1999. Resolution improvement to 0.9A in crystals of human aldose reductase. In XVIIIth International Union of Crystallography Congress and General Assembly, Glasgow.
18. Howard EI, Sanishvili R, Cachau RE, Mitschler A, Chevrier B, Barth P, Lamour V, Van Zandt M, Sibley E, Bon C, Moras D, Schneider TR, Joachimiak A, Podjarny A. 2004. Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 angstrom. Proteins Struct. Funct. Bioinform. 55(4): 792.
19. Jahnke W. 2003. NMR in drug discovery. Chimia 57(1-2): 59.
20. Jahnke W, Florsheimer A, Blommers MJJ, Paris CG, Heim J, Nalin CM, Perez LB. 2003. Second-site NMR screening and linker design. Curr. Top. Med. Chem. 3(1): 69.
21. Jayatilaka D, Grimwood DJ. 2001. Wavefunctions derived from experiment. I. Motivation and theory. Acta Crystallogr. Sect. A 57: 76.
22. Jelsch C, Teeter MM, Lamzin V, Pichon-Pesme V, Blessing RH, Lecomte C. 2000. Accurate protein crystallography at ultra-high resolution: valence electron distribution in crambin. Proc. Natl. Acad. Scie. USA 97(7): 3171.
23. Kadri A, Damak M, Jenner G, Lorber B, Giege R, 2003a. Investigating the nucleation of protein crystals with hydrostatic pressure. J. Phys. Condensed Matter 15(49): 8253.
24. Kadri A, Damak M, Lorber B, Giege R, Jenner G, 2003b. Pressure versus pH phase diagrams of two lysozymes crystallized in agarose gel. High Press. Res. 23(4): 485.
25. Klebe G, Kramer O, Sotriffer C. 2004. Strategies for the design of inhibitors of aldose reductase, an enzyme showing pronounced induced-fit adaptations. Cell. Mol. Life Sci. 61(7-8): 783.
26. Kuhn P, Knapp M, Soltis SM, Ganshaw G, Thoene M, Bott R. 1998. The 0.78 angstrom structure of a serine protease: Bacillus lentus subtilisin. Biochemistry 37(39): 13446.
27. Lecomte C, Guillot B, Muzet N, Pichon-Pesme V, Jelsch C. 2004. Ultra-high-resolution X-ray structure of proteins. Cell. Mol. Life Sci. 61(7-8): 774.
28. Lorber B, Theobald-Dietrich A, Charron C, Sauter C, Ng JD, Zhu DW, Giege R. 2002. From conventional crystallization to better crystals from space: a review on pilot crystallogenesis studies with aspartyl-tRNA synthetases. Acta Crystallogr. Sect. D Biol. Crystallogr. 58: 1674.
29. Mizwicki MT, Keidel D, Bula CM, Bishop JE, Zanello LP, Wurtz JM, Moras D, Norman AW. 2004. Identification of an alternative ligand-binding pocket in the nuclear vitamin D receptor and its functional importance in 1 alpha,25(OH)(2)-vitamin D-3 signaling. Proc. Natl. Acad. Sci. USA 101(35): 12876.
30. Morris RJ, Perrakis A, Lamzin VS. 2003. ARP/wARP and automatic interpretation of protein electron density maps. Methods Enzymol. 374: 229-244.
31. Morris RJ, Zwart PH, Cohen S, Fernandez FJ, Kakaris M, Kirillova O, Vonrhein C, Perrakis A, Lamzin VS. 2004. Breaking good resolutions with ARP/wARP. J. Synchrotron Radiat. 11: 56.
32. Parker CL, Ventura ON, Burt SK, Cachau RE. 2003. DYNGA: a general purpose QM-MM-MD program. I. Application to water. Mol. Phys. 101(17): 2659.
33. Pichon-Pesme V, Jelsch C, Guillot B, Lecomte C. 2004. A comparison between experimental and theoretical aspherical-atom scattering factors for charge-density refinement of large molecules. Acta Crystallogr. Sect. A 60: 204.
34. Podjarny A, Schneider TR, Cachau RE, Joachimiak A. 2003. Structural information content at high resolution: MAD versus native. Meth. Enzymol. 374: 321-341.
35. Rauh D, Gunther J, Stubbs MT, Klebe G. 2003. Protein flexibility: the ultimate limitation to structure-based drug design? Abstr. Papers Am. Chem. Soc. 225: U790.
36. Schiffer C, Hermans J. 2003. Promise of advances in simulation methods for protein crystallography: implicit solvent models, time-averaging refinement, and quantum mechanical modeling. Meth. Enzymol. 374: 412-461.
37. Schiltz M, Dumas P, Ennifar E, Flensburg C, Paciorek W, Vonrhein C, Bricogne G. 2004. Phasing in the presence of severe-site specific radiation damage through dose-dependent modelling of heavy atoms. Acta Crystallogr. Sect. D Biol. Crystallogr. 60: 1024.
38. Schneider TR, Sheldrick GM. 2002. Substructure solution with SHELXD. Acta Crystallogr. Sect. D Biol. Crystallogr. 58: 1772.
39. Streitwieser A Jr, Mowery PC, Jesaitis RG, Lewis A. 1970. Semiempirical SCF MO calculations on electrophilic aromatic substitution. J. Am. Chem. Soc. 92(22): 6529-6533.
40. Tie YF, Boross PI, Wang YF, Gaddis L, Hussain AK, Leshchenko S, Ghoshl AK, Louis JM, Harrison RW, Weber IT. 2004. High resolution crystal structures of HIV-1 protease with a potent non-peptide inhibitor (UIC-94017) active against multi-drug-resistant clinical strains. J. Mol. Biol. 338(2): 341.
41. Tocchini-Valentini G, Rochel N, Wurtz JM, Moras D. 2004. Crystal structures of the vitamin D nuclear receptor liganded with the vitamin D side chain analogues calcipotriol and seocalcitol, receptor agonists of clinical importance. Insights into a structural basis for the switching of calcipotriol to a receptor antagonist by further side chain modification. J. Med. Chem. 47(8): 1956.
42. Vicens Q, Westhof E. 2003. RNA as a drug target: the case of aminoglycosides. ChemBioChem 4: 1018-1023.