Skip to main content

From Structure to Recognition Principles: Mining in Crystal Data as a Prerequisite for Drug Design

  • Conference paper
Small Molecule — Protein Interactions

Part of the book series: Ernst Schering Research Foundation Workshop ((SCHERING FOUND,volume 42))

  • 145 Accesses

Abstract

The discovery of novel leads and their subsequent optimization into development compounds is the key element in any drug discovery process. During the last several years, substantial efforts have been dedicated to the establishment of high-throughput screening technologies (HTS) (Houston and Banks 1997). Computer tools have been developed to drive robotic systems to fully automate and speed up the experimental testing along with a sophisticated selection of compounds used in the various screening assays. Testing entire libraries within weeks or even days is now feasible. However, initial euphoria that was pronouncing the end of any rational or knowledge-based approach to lead discovery has been superseded by a more realistic view, mainly as a result of the considerable costs involved and disappointingly low hit rates (Lahana 1999).

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

Access this chapter

Chapter
USD 29.95
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 EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 209.00
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

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Abbate F, Supuran CT, Scozzafava A, Orioli P, Stubbs MT, Klebe G (2002) The sulfonamide group is an ideal anchor for potent human carbonic anhydrase inhibitors: evidence from a comparative crystallographic study. J Med Chem 45: 3583–3587

    Article  PubMed  CAS  Google Scholar 

  • Allen FH, Davies JE, Galloy JJ, Johnson O, Kennard O, Macrae CF, Mitchell EM, Mitchell GF, Smith JM, Watson DG (1991) The development of verion-3 and version-4 of the Cambridge Structural Database system. J Chem Info Comput Sci 31: 187–204

    Article  CAS  Google Scholar 

  • Anderson AC, O’Neil RH, Surti TS, Stroud RM (2001) Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking. Chem Biol 8: 445–457

    Article  PubMed  CAS  Google Scholar 

  • Bergner A, Gunther J, Hendlich M, Klebe G, Verdorsk M (2002) Use of Relibase for retrieving complex 3D interaction patterns including crystallographic packing effects. Nucl Acid Sci 61: 99–110

    CAS  Google Scholar 

  • Block P (2002) Diploma thesis, Univ. Marburg

    Google Scholar 

  • Blundell T, Jhoti H, Abell C (2002) High-throughput crystallography for lead discovery in drug design. Nat Rev Drug Discov 1: 45–54

    Article  PubMed  CAS  Google Scholar 

  • Bode W, Chen Z, Bartels K, Kutzbach C, Schmidt-Kastner G, Bartunik H (1983) Refined 2 Angstroms X-Ray crystal structure of porcine pancreatic kallikrein A, a specific trypsin-like serine proteinase. Crystallization, structure determination, crystallographic refinement, Structure and its comparison with bovine trypsin. J Mol Biol 164: 237–282

    Google Scholar 

  • Böhm HJ, Klebe G (1996) What can we learn from molecular recognition in protein—ligand complexes for the design of new drugs? Angew Chem Int Ed Engl 35: 2588–2614

    Article  Google Scholar 

  • Bossemeyer D, Engh RA, Kinzel V, Ponstingl H, Huber R (1993) Phosphotransferase and substrate binding mechanism of the cAMP- dependent protein kinase catalytic subunit from porcine heart as deduced from the 2.0 A structure of the complex with Mn2+ adenylyl imidodiphosphate and inhibitor peptide PKI(5–24) EMBO J 12: 849–859

    CAS  Google Scholar 

  • Broder S, Venter JC (2000) Sequencing the entire genomes of free-living organisms: the foundation of pharmacology in the new millennium. Annu Rev Pharmacol Toxicol 40: 97–132

    Article  PubMed  CAS  Google Scholar 

  • Burley SK, Almo SC, Bonanno JB, Capel M, Chance MR, Gaasterland T, Lin D, Sali A, Studier FW, Swaminathan S (1999) Structural genomics: beyond the Human Genome Project. Nat Genet 23: 151–157

    Article  PubMed  CAS  Google Scholar 

  • Chegwidden WR, Edwards Y, Carter N (2000) The Carbonic anhydrases — new horizons. Birkhäuser Verlag, Basel

    Google Scholar 

  • Claussen H, Buning C, Rarey M, Lengauer T (2001) FlexE: efficient molecular docking considering protein structure variations. J Mol Biol 308: 377–395

    Article  PubMed  CAS  Google Scholar 

  • Coll M, Guasch A, Aviles FX, Huber R (1991) Three-dimensional structure of porcine procarboxypeptidase B: a structural basis of its inactivity. EMBO J 10: 1–9

    CAS  Google Scholar 

  • Divne C, Stahlberg J, Reinikainen T, Ruohonen L, Pettersson G, Knowles JK, Teen TT, Jones TA (1994) The three-dimensional crystal structure of the catalytic core of cellobiohydrolase I from Trichoderma reesei. Science 265: 524–528

    Article  PubMed  CAS  Google Scholar 

  • Dramburg I (2003) PhD thesis Univ. Marburg

    Google Scholar 

  • Drews J (2000) Drug discovery: a historical perspective. Science 287: 1960–1964

    Article  PubMed  CAS  Google Scholar 

  • Gerber PR, Müller K (1995) MAB, a generally applicable molecular force field for structure modelling in medicinal chemistry. J Comput Aided Mol Des 9: 251–268

    Article  PubMed  CAS  Google Scholar 

  • Grüneberg S, Wendt B, Klebe G (2001) Subnanomolar inhibitors from computer screening: A model study using human carbonic anhydrase II. Angew Chem Int Ed 40: 389–393

    Google Scholar 

  • Grüneberg S, Stubbs MT, Klebe G (2002) Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation. J Med Chem 45: 3588–3602

    Article  PubMed  Google Scholar 

  • Gulick AM, Song H, Endow SA, Rayment I (1998) X-ray crystal structure of the yeast Kar3 motor domain complexed with Mg.ADP to 2.3 A resolution. Biochemistry 37: 1769–1776

    Article  PubMed  CAS  Google Scholar 

  • Günther J, Bergner A, Hendlich M, Verdonk M, Klebe G (2003) Utilizing structural knowledge in drug design strategies — applications using Relibase. J Mol Biol (in press)

    Google Scholar 

  • Hakansson K, Carlsson M, Svensson AL, Liljas A (1992) Structure of native and apo carbonic anhydrase II and structure of some of its anion-ligand complexes. J Mol Biol 227: 1192–1204

    Article  PubMed  CAS  Google Scholar 

  • Hemm K, Aberer K, Hendlich M (1995) Constituting a receptor-ligand information base from quality-enriched data ISMB 3: 170–178

    CAS  Google Scholar 

  • Hendlich M (1998) Databases for protein—ligand complexes. Acta Crystallogr D Biol Crystallogr 54: 1178–1182

    Article  PubMed  CAS  Google Scholar 

  • Hendlich M, Günther J, Bergner A, Verdonk M, Klebe G (2003) Relibase — design and development of a database for comprehensive analysis of protein—ligand interactions. J Mol Biol (in press)

    Google Scholar 

  • Hol W, Wierenga RK (1984) The a-helix dipole and the binding of phosphate groups of coenzymes and substrates by proteins. In: Horn AS, De Ranter CJ (eds) X-ray crystallography and drug design. Clarendon Press, Oxford, pp 151–168

    Google Scholar 

  • Houston JG, Banks M (1997) The chemical-biological interface: developments in automated and miniaturised screening technology. Curr Opin Biotechnol 8: 734–740

    Article  PubMed  CAS  Google Scholar 

  • Kador PF, Kinoshita JH, Sharpless NE (1985) Aldose reductase inhibitors: a potential new class of agents for the pharmacological control of certain diabetic complications. J Med Chem 28: 841–849

    Article  PubMed  CAS  Google Scholar 

  • Kim C-Y, Chandra PP, Jain A, Christianson DW (2001) Fluoroaromaticfluoroarmatic interactions between inhibitors bound in the crystal lattice of human carbonic anhydrase II. J Am Chem Soc 123: 9620–9627

    Article  PubMed  CAS  Google Scholar 

  • Klaholz BP, Mitschler A, Belema M, Zusi C, Moras D (2000) Enantiomer Discrimination Illustrated by high Resolution Structures of the Human Nuclear Receptor hRAR. Proc Nat Acad Sci 97: 6322–6327

    Article  PubMed  CAS  Google Scholar 

  • Lahana R (1999) How many leads from HTS? Drug Discov Today 4: 447–448

    Article  PubMed  Google Scholar 

  • Lam PY, Jadhav PK, Eyermann CJ, Hodge CN, Ru Y, Bacheler LT, Meek JL, Otto MJ, Rayner MM, WongYN, et al (1994) Rational design of potent, bioavailable, nonpeptide cyclic ureas as HIV protease inhibitors. Science 263: 380–384

    Article  PubMed  CAS  Google Scholar 

  • Lander ES, Linton LM, Binen B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, et al (2001) Initial sequencing and analysis of the human genome. Nature 409: 860–921

    Article  PubMed  CAS  Google Scholar 

  • Martin JL, Begun J, Schindeler A, Wickramasinghe WA, Alewood D, Alewood PF, Bergman DA, Brinkworth RI, Abbenante G, March DR, Reid RC, Fair-lie DP (1999) Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease. Biochemistry 38: 7978–7988

    Article  PubMed  CAS  Google Scholar 

  • Mikol V, Papageorgiou C, Borer X (1995) The role of water molecules in the structure-based design of (5-hydroxynorvaline)-2-cyclosporin: synthesis, biological activity, and crystallographic analysis with cyclophilin A. J Med Chem 38: 3361–3367

    Article  PubMed  CAS  Google Scholar 

  • Muller-Dieckmann HJ, Schulz GE (1995) Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase. J Mol Biol 246: 522–530

    Article  PubMed  CAS  Google Scholar 

  • Poornima CS, Dean PM (1995) Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein—ligand interactions. J Comput Aided Mol Des 9: 500–512

    Google Scholar 

  • Rost B (1998) Marrying structure and genomics. Structure 6: 259–263

    Article  PubMed  CAS  Google Scholar 

  • Rubin GM, Yandell MD, Wortman JR, Miklos GLG, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O’Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Zhong F, Zhong W, Gibbs R, Venter JC, Adams MD, Lewis S (2000) Comparative genomics of the eukaryotes. Science 287: 2204–2215

    Article  PubMed  CAS  Google Scholar 

  • Schmitt S, Hendlich M, Klebe G (2001) From structure to function: a new approach to detect functional similarity among proteins independent from sequence and fold homology. Angew Chem Int Ed 40: 3141–3144

    Article  CAS  Google Scholar 

  • Schmitt S, Kuhn D, Klebe G (2002) A new method to detect related function among proteins independent of sequence and fold homology. J Mol Biol 323: 387–406

    Article  PubMed  CAS  Google Scholar 

  • Schnecke V, Swanson CA, Getzoff ED, Tainer JA, Kuhn LA (1998) Screening a peptidyl database for potential ligands to proteins with side-chain flexibility. Proteins 33: 74–87

    Article  PubMed  CAS  Google Scholar 

  • Smith GM, Alexander RS, Christianson DW, McKeever BM, Ponticello GS, Springer JP, Randall WC, Baldwin JJ, Habecker CN (1994) Positions of His-64 and a bound water in human carbonic anhydrase II upon binding three structurally related inhibitors. Protein Sci 3: 118–125

    Article  PubMed  CAS  Google Scholar 

  • Stahlberg J, Divne C, Koivula A, Piens K, Claeyssens M, Teeri TT, Jones TA (1996) Activity studies and crystal structures of catalytically deficient mutants of cellobiohydrolase I from Trichoderma reesei. J Mol Biol 264: 337–349

    Article  PubMed  CAS  Google Scholar 

  • Supuran CT, Scozzafava A (2000) Carbonic anhydrase inhibitors and their therapeutic potential. Exp Opin Ther Patents 10: 575–601

    Article  CAS  Google Scholar 

  • Supuran CT, Scozzafava A (2001) Carbonic anhydrase inhibitors. Curr Med Chem Imm Endoc Metab Agents 1: 61–97

    Article  CAS  Google Scholar 

  • Surgrue MF (2000) Pharmacological and ocular hypotensive properties of topical carbonic anhydrase inhibitors. Progr Ret Eye Res 19: 87–112

    Article  Google Scholar 

  • Tranter R, Read JA, Jones R, Brady RL (2000) Effector sites in the three dimensional structure of mammalian sperm beta-acrosin structure. Struct Fold Des 8: 1179–1188

    Article  CAS  Google Scholar 

  • Urzhumtsev A, Tete-Favier F, Mitschler A, Barbanton J, Barth P, Urzhumtseva L, Biellmann JF, Podjarny A, Moras D (1997) A `specificity’ pocket inferred from the crystal structures of the complexes of aldose reductase with the pharmaceutically important inhibitors tolrestat and sorbinil. Structure 5: 601–612

    Article  PubMed  CAS  Google Scholar 

  • Wang H, Ben-Naim A (1996) A possible involvement of solvent-induced interactions in drug design. J Med Chem 39: 1531–1539

    Article  PubMed  CAS  Google Scholar 

  • Xue Y, Liljas A, Jonsson BH, Lindskog S (1993) Structural analysis of the zinc hydroxide — Thr 199 — Glu 106 hydrogen-bond network in human carbonic anhydrase II. Proteins: Struct Funct Genet 10: 93–106

    Google Scholar 

  • Zhang Y, Bond CS, Bailey S, Cunningham ML, Fairlamb AH, Hunter WN (1996) The crystal structure of trypanothione reductase from the human pathogen Trypanosoma cruzi at 2.3 A resolution. Protein Sci 5: 52–61

    Article  PubMed  Google Scholar 

Download references

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Klebe, G. (2003). From Structure to Recognition Principles: Mining in Crystal Data as a Prerequisite for Drug Design. In: Waldmann, H., Koppitz, M. (eds) Small Molecule — Protein Interactions. Ernst Schering Research Foundation Workshop, vol 42. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-05314-0_8

Download citation

  • DOI: https://doi.org/10.1007/978-3-662-05314-0_8

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-662-05316-4

  • Online ISBN: 978-3-662-05314-0

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics