Skip to main content

X-Ray Crystallography in Drug Discovery

  • Protocol
  • First Online:
Book cover Ligand-Macromolecular Interactions in Drug Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 572))

Summary

Macromolecular X-ray crystallography is an important and powerful technique in drug discovery, used by pharmaceutical companies in the discovery process of new medicines. The detailed analysis of crystal structures of protein–ligand complexes allows the study of the specific interactions of a particular drug with its protein target at the atomic level. It is used to design and improve drugs. The starting point of these studies is the preparation of suitable crystals of complexes with potential ligands, which can be achieved by using different strategies described in this chapter. In addition, an introduction to X-ray crystallography is given, highlighting the fundamental steps necessary to determine the three-dimensional structure of protein–ligand complexes, as well as some of the tools and criteria to validate crystal structures available in databases.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Dror, O., Lasker, K., Nussinov, R., and Wolfson, H. (2007). EMatch: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies. Acta Crystallogr. D Biol. Crystallogr. 63, 42–49

    Article  PubMed  CAS  Google Scholar 

  2. Sigworth, F. J. (2007). From cryo-EM, multiple protein structures in one shot. Nat. Methods 4, 20–21

    Article  PubMed  CAS  Google Scholar 

  3. Hassell, A. M., An, G., Bledsoe, R. K., Bynum, J. M., Carter, H. L., III, Deng, S. J., Gampe, R. T., Grisard, T. E., Madauss, K. P., Nolte, R. T., Rocque, W. J., Wang, L., Weaver, K. L., Williams, S. P., Wisely, G. B., Xu, R., and Shewchuk, L. M. (2007). Crystallization of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 63, 72–79

    Article  PubMed  CAS  Google Scholar 

  4. Chung, C. W. (2007). The use of biophysical methods increases success in obtaining liganded crystal structures. Acta Crystallogr. D Biol. Crystallogr. 63, 62–71

    Article  PubMed  CAS  Google Scholar 

  5. Niesen, F. H., Berglund, H., and Vedadi, M. (2007). The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat. Protoc. 2, 2212–2221

    Article  PubMed  CAS  Google Scholar 

  6. Senisterra, G.A. (2006). Screening for ligands using a generic and high-throughput light-scattering assay. J. Biomol. Screen. 11, 940–948

    Article  PubMed  CAS  Google Scholar 

  7. Vedadi, M., Niesen, F. H., Allali-Hassani, A., Fedorov, O. Y., Finerty, P. J., Wasney, G. A., Yeung, R., Arrowsmith, C., Ball, L. J., Berglund, H., Hui, R., Marsden, B. D., Nordlund, P., Sundstrom, M., Weigelt, J., and Edwards, A. M. (2006). Chemical screening methods to identify ligands that promote protein stability, protein crystallization, and structure determination. Proc. Natl. Acad. Sci. U.S.A. 103, 15835–15840

    Article  PubMed  CAS  Google Scholar 

  8. Brown, W., Ed. (1993). Dynamic Light Scattering: The Method and Some Applications, Vol. 49. Monographs on the Physics and Chemistry of Materials. Oxford University Press, USA

    Google Scholar 

  9. Schmitz, K. S. (1990). An Introduction to Dynamic Light Scattering by Macromolecules. Academic Press, Boston

    Google Scholar 

  10. Feng, B. Y., Shelat, A., Doman, T. N., Guy, R. K., and Shoichet, B. K. (2005). High-throughput assays for promiscuous inhibitors. Nat. Chem. Biol. 1, 146–148

    Article  PubMed  CAS  Google Scholar 

  11. McNae, I. W., Kan, D., Kontopidis, G., Patterson, A., Taylor, P., Worrall, L., and Walkinshaw, M. D. (2005). Studying protein-ligand interactions using protein crystallography. Crystallogr. Rev. 11, 61–71

    Article  CAS  Google Scholar 

  12. Matthews, B. W. (1968). Solvent content of protein crystals. J. Mol. Biol. 33, 491–497

    Article  PubMed  CAS  Google Scholar 

  13. Vilenchik, L. Z., Griffith, J. P., St Clair, N., Navia, M. A., and Margolin, A. L. (1998). Protein crystals as novel microporous materials. J. Am. Chem. Soc. 120, 4290–4294

    Article  CAS  Google Scholar 

  14. Lusty, C. J. (1999). A gentle vapor-diffusion technique for cross-linking of protein crystals for cryocrystallography. J. Appl. Crystallogr. 32, 106–112

    Article  CAS  Google Scholar 

  15. Danley, D. E. (2006). Crystallization to obtain protein-ligand complexes for structure-aided drug design. Acta Crystallogr. D Biol. Crystallogr. 62, 569–575

    Article  PubMed  Google Scholar 

  16. Skarzynski, T. and Thorpe, J. (2006). Industrial perspective on X-ray data collection and analysis. Acta Crystallogr. D Biol. Crystallogr. 62, 102–107

    Article  PubMed  Google Scholar 

  17. Hiller, N., Fritz-Wolf, K., Deponte, M., Wende, W., Zimmermann, H., and Becker, K. (2006). Plasmodium falciparum glutathione S-transferase – structural and mechanistic studies on ligand binding and enzyme inhibition. Protein Sci. 15, 281–289

    Article  PubMed  CAS  Google Scholar 

  18. Williams, S. P. and Sigler, P. B. (1998). Atomic structure of progesterone complexed with its receptor. Nature 393, 392–396

    Article  PubMed  CAS  Google Scholar 

  19. Matias, P. M., Donner, P., Coelho, R., Thomaz, M., Peixoto, C., Macedo, S., Otto, N., Joschko, S., Scholz, P., Wegg, A., Basler, S., Schafer, M., Egner, U., and Carrondo, M. A. (2000). Structural evidence for ligand specificity in the binding domain of the human androgen receptor. Implications for pathogenic gene mutations. J. Biol. Chem. 275, 26164–26171

    Article  PubMed  CAS  Google Scholar 

  20. Hope, H. (1988). Cryocrystallography of biological macromolecules: a generally applicable method. Acta Crystallogr B 44 (Pt 1), 22–26

    Article  PubMed  Google Scholar 

  21. Garman, E. F. and Schneider, T. R. (1997). Macromolecular cryocrystallography. J. Appl. Crystallogr. 30, 211–237

    Article  Google Scholar 

  22. Read, R. J. (1999). Detecting outliers in non-redundant diffraction data. Acta Crystallogr. D Biol. Crystallogr. 55, 1759–1764

    Article  PubMed  CAS  Google Scholar 

  23. Otwinowsky, Z. (1991). CCP4 Daresbury Study Weekend Proceedings

    Google Scholar 

  24. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998). Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905–921

    Article  PubMed  CAS  Google Scholar 

  25. delaFortelle, E. and Bricogne, G. (1997). Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Meth. Enzymol. 276, 472–494

    Article  CAS  Google Scholar 

  26. Terwilliger, T. C. and Berendzen, J. (1999). Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr. 55, 849–861

    Article  PubMed  CAS  Google Scholar 

  27. Tong, L. and Rossmann, M. G. (1990). The locked rotation function. Acta Crystallogr. A 46, 783–792

    Article  PubMed  Google Scholar 

  28. Navaza, J. (1994). Amore – an automated package for molecular replacement. Acta Crystallogr. A 50, 157–163

    Article  Google Scholar 

  29. Kissinger, C. R., Gehlhaar, D. K., and Fogel, D. B. (1999). Rapid automated molecular replacement by evolutionary search. Acta Crystallogr. D Biol. Crystallogr. 55, 484–491

    Article  PubMed  CAS  Google Scholar 

  30. Read, R. J. (2001). Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr. D Biol. Crystallogr. 57, 1373–1382

    Article  PubMed  CAS  Google Scholar 

  31. Long, F., Vagin, A. A., Young, P., and Murshudov, G. N. (2007). BALBES: a molecular-replacement pipeline. Acta Crystallogr. D Biol. Crystallogr. 64, 125–132

    Article  PubMed  Google Scholar 

  32. Engh, R. A. and Huber, R. (1991). Accurate bond and angle parameters for X-ray protein-structure refinement. Acta Crystallogr. A 47, 392–400

    Article  Google Scholar 

  33. Engh, R. A. and Huber, R. (2001). Structure quality and target parameters. In: Rossmann, M. G., and Arnold, E. (eds.) International Tables for Crystallography, Vol. F. Kluwer, Dordrecht, The Netherlands, pp. 382–392

    Chapter  Google Scholar 

  34. Hendrickson, W. A. (1985). Stereochemically restrained refinement of macromolecular structures. Methods Enzymol. 115, 252–270

    Article  PubMed  CAS  Google Scholar 

  35. Parkinson, G., Vojtechovsky, J., Clowney, L., Brunger, A. T., and Berman, H. M. (1996). New parameters for the refinement of nucleic acid-containing structures. Acta Crystallogr. D Biol. Crystallogr. 52, 57–64

    Article  PubMed  CAS  Google Scholar 

  36. Priestle, J. P. (2003). Improved dihedral-angle restraints for protein structure refinement. J. Appl. Crystallogr. 36, 34–42

    Article  CAS  Google Scholar 

  37. Brunger, A. T. (1992). X-Plor Version 3.1: A System for X-ray Crystallography and NMR, Yale University Press, New Haven

    Google Scholar 

  38. Emsley, P., and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132

    Article  PubMed  Google Scholar 

  39. Kleywegt, G. J. (2000). Validation of protein crystal structures. Acta Crystallogr. D Biol. Crystallogr. 56, 249–265

    Article  PubMed  CAS  Google Scholar 

  40. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000). The Protein Data Bank. Nucleic Acids Res. 28, 235–242

    Article  PubMed  CAS  Google Scholar 

  41. Terwilliger, T. C., Klei, H., Adams, P. D., Moriarty, N. W., and Cohn, J. D. (2006). Automated ligand fitting by core-fragment fitting and extension into density. Acta Crystallogr. D Biol. Crystallogr. 62, 915–922

    Article  PubMed  Google Scholar 

  42. Adams, P. D., Grosse-Kunstleve, R. W., Hung, L. W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., and Terwilliger, T. C. (2002). PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr. 58, 1948–1954

    Article  PubMed  Google Scholar 

  43. Murshudov, G. N., Vagin, A. A., and Dodson, E. J. (1997). Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255

    Article  PubMed  CAS  Google Scholar 

  44. Blanc, E., Roversi, P., Vonrhein, C., Flensburg, C., Lea, S. M., and Bricogne, G. (2004). Refinement of severely incomplete structures with maximum likelihood in BUSTER-TNT. Acta Crystallogr. D Biol. Crystallogr. 60, 2210–2221

    Article  PubMed  CAS  Google Scholar 

  45. Roversi, P., Blanc, E., Vonrhein, C., Evans, G., and Bricogne, G. (2000). Modelling prior distributions of atoms for macromolecular refinement and completion. Acta Crystallogr. D Biol. Crystallogr. 56, 1316–1323

    Article  PubMed  CAS  Google Scholar 

  46. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991). Improved methods for building protein models in electron-density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119

    Article  PubMed  Google Scholar 

  47. Evans, P. R. (2007). An introduction to stereochemical restraints. Acta Crystallogr. D Biol. Crystallogr. 63, 58–61

    Article  PubMed  CAS  Google Scholar 

  48. Kleywegt, G. J., Henrick, K., Dodson, E. J., and van Aalten, D. M. F. (2003). Pound-wise but penny-foolish: how well do micromolecules fare in macromolecular refinement? Structure 11, 1051–1059

    Article  PubMed  CAS  Google Scholar 

  49. Kleywegt, G. J. (2007). Crystallographic refinement of ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 63, 94–100

    Article  PubMed  CAS  Google Scholar 

  50. Feng, Z. K., Chen, L., Maddula, H., Akcan, O., Oughtred, R., Berman, H. M., and Westbrook, J. (2004). Ligand Depot: a data warehouse for ligands bound to macromolecules. Bioinformatics 20, 2153–2155

    Article  PubMed  CAS  Google Scholar 

  51. Schuttelkopf, A. W. and van Aalten, D. M. F. (2004). PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. D Biol. Crystallogr. 60, 1355–1363

    Article  PubMed  Google Scholar 

  52. vanAalten, D. M. F., Bywater, R., Findlay, J. B. C., Hendlich, M., Hooft, R. W. W., and Vriend, G. (1996). PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J. Comput. Aided Mol. Des. 10, 255–262

    Article  CAS  Google Scholar 

  53. Gasteiger, J., Rudolph, C., and Sadowski, J. (1992). Automatic Generation of 3D-Atomic Coordinates for Organic Molecules. Tetrahedron Comput. Method. 3, 537–547

    Article  Google Scholar 

  54. Peat, T. S., Christopher, J. A., and Newman, J. (2005). Tapping the protein data bank for crystallization information. Acta Crystallogr. D Biol. Crystallogr. 61, 1662–1669

    Article  PubMed  Google Scholar 

  55. Perrakis, A., Morris, R., and Lamzin, V. S. (1999). Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6, 458–463

    Article  PubMed  CAS  Google Scholar 

  56. Evrard, G. X., Langer, G. G., Perrakis, A., and Lamzin, V. S. (2007). Assessment of automatic ligand building in ARP/wARP. Acta Crystallogr. D Biol. Crystallogr. 63, 108–117

    Article  PubMed  CAS  Google Scholar 

  57. Levinson, N. M., Kuchment, O., Shen, K., Young, M. A., Koldobskiy, M., Karplus, M., Cole, P. A., and Kuriyan, J. (2006). A Src-like inactive conformation in the Abl tyrosine kinase domain. PLoS. Biol. 4, 753–767

    Article  CAS  Google Scholar 

  58. Kleywegt, G. J. and Jones, T. A. (1998). Databases in protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 54, 1119–1131

    Article  PubMed  CAS  Google Scholar 

  59. Bragg, W. H. and Bragg, W. L. (1913). The reflection of X-rays by crystals. Proc. R. soc. Lond. Ser. A-Contain. Pap. Math. Phys. Character 88, 428–428

    Article  CAS  Google Scholar 

  60. Sheldrick, G. M. (1995). Structure solution by iterative peaklist optimization and tangent expansion in-space group P1. Acta Crystallogr. B 51, 423–431

    Article  Google Scholar 

  61. Weeks, C. M. and Miller, R. (1999). Optimizing Shake-and-Bake for proteins. Acta Crystallogr. D Biol. Crystallogr. 55, 492–500

    Article  PubMed  CAS  Google Scholar 

  62. Ten Eyck, L. F. and Watenpaugh, K. D. (2006). Introduction to refinement. In: Rossmann, M. G., and Arnold, E. (eds.) Crystallography of Biological Macromolecules, Vol. F. Kluwer, Dordrecht, The Netherlands, pp. 369–374

    Chapter  Google Scholar 

  63. Wang, B. C. (1985). Resolution of phase ambiguity in macromolecular crystallography. Meth. Enzymol. 115, 90–112

    Article  PubMed  CAS  Google Scholar 

  64. Leslie, A. G. W. (1987). A reciprocal-space method for calculating a molecular envelope using the algorithm of Wang, B.C. Acta Crystallogr. A 43, 134–136

    Article  Google Scholar 

  65. Hodel, A., Kim, S. H., and Brunger, A. T. (1992). Model bias in macromolecular crystal-structures. Acta Crystallogr. A 48, 851–858

    Article  Google Scholar 

  66. Read, R. J. (1986). Improved Fourier coefficients for maps using phases from partial structures with error. Acta Crystallogr. A 42, 140–149

    Article  Google Scholar 

  67. Potterton, E., McNicholas, S., Krissinel, E., Cowtan, K., and Noble, M. (2002). The CCP4 molecular-graphics project. Acta Crystallogr. D Biol. Crystallogr. 58, 1955–1957

    Article  PubMed  Google Scholar 

Download references

Acknowledgments

The authors acknowledge Dr. Shabir Najmudin and Dr. Abhik Mukhopadhyay for critical reading of the manuscript.

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Humana Press

About this protocol

Cite this protocol

Carvalho, A.L., Trincão, J., Romão, M.J. (2010). X-Ray Crystallography in Drug Discovery. In: Roque, A. (eds) Ligand-Macromolecular Interactions in Drug Discovery. Methods in Molecular Biology, vol 572. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-244-5_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-60761-244-5_3

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-60761-243-8

  • Online ISBN: 978-1-60761-244-5

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics