Cellular and Molecular Life Sciences

, Volume 67, Issue 17, pp 3005–3015 | Cite as

Enrichment of ligands with molecular dockings and subsequent characterization for human alcohol dehydrogenase 3

  • Mikko Hellgren
  • Jonas Carlsson
  • Linus J. Östberg
  • Claudia A. Staab
  • Bengt Persson
  • Jan-Olov Höög
Research Article

Abstract

Alcohol dehydrogenase 3 (ADH3) has been assigned a role in nitric oxide homeostasis due to its function as an S-nitrosoglutathione reductase. As altered S-nitrosoglutathione levels are often associated with disease, compounds that modulate ADH3 activity might be of therapeutic interest. We performed a virtual screening with molecular dockings of more than 40,000 compounds into the active site of human ADH3. A novel knowledge-based scoring method was used to rank compounds, and several compounds that were not known to interact with ADH3 were tested in vitro. Two of these showed substrate activity (9-decen-1-ol and dodecyltetraglycol), where calculated binding scoring energies correlated well with the logarithm of the k cat/K m values for the substrates. Two compounds showed inhibition capacity (deoxycholic acid and doxorubicin), and with these data three different lines for specific inhibitors for ADH3 are suggested: fatty acids, glutathione analogs, and cholic acids.

Keywords

Alcohol dehydrogenase Enzyme kinetics Inhibitors Molecular docking S-Nitrosoglutathione Virtual screening 

Abbreviations

ADH

Alcohol dehydrogenase

GSNO

S-Nitrosoglutathione

HMGSH

S-Hydroxymethylglutathione

MC

Monte Carlo

NO

Nitric oxide

VS

Virtual screening

12-HDA

12-Hydroxydodecanoic acid

Notes

Acknowledgments

This work was supported by grants from Karolinska Institutet and Linköping University.

References

  1. 1.
    Höög J-O, Hedberg JJ, Strömberg P, Svensson S (2001) Mammalian alcohol dehydrogenase—functional and structural implications. J Biomed Sci 8:71–76CrossRefPubMedGoogle Scholar
  2. 2.
    Danielsson O, Jörnvall H (1992) “Enzymogenesis”: classical liver alcohol dehydrogenase origin from the glutathione-dependent formaldehyde dehydrogenase line. Proc Natl Acad Sci USA 89:9247–9251CrossRefPubMedGoogle Scholar
  3. 3.
    Koivusalo M, Baumann M, Uotila L (1989) Evidence for the identity of glutathione-dependent formaldehyde dehydrogenase and class III alcohol dehydrogenase. FEBS Lett 257:105–109CrossRefPubMedGoogle Scholar
  4. 4.
    Jensen DE, Belka GK, Du Bois GC (1998) S-Nitrosoglutathione is a substrate for rat alcohol dehydrogenase class III isoenzyme. Biochem J 331:659–668PubMedGoogle Scholar
  5. 5.
    Staab CA, Hellgren M, Höög J-O (2008) Medium- and short-chain dehydrogenase/reductase gene and protein families: dual functions of alcohol dehydrogenase 3: implications with focus on formaldehyde dehydrogenase and S-nitrosoglutathione reductase activities. Cell Mol Life Sci 65:3950–3960CrossRefPubMedGoogle Scholar
  6. 6.
    Jörnvall H, Höög J-O, Persson B (1999) SDR and MDR: completed genome sequences show these protein families to be large, of old origin, and of complex nature. FEBS Lett 445:261–264CrossRefPubMedGoogle Scholar
  7. 7.
    Lee SL, Wang MF, Lee AI, Yin SJ (2003) The metabolic role of human ADH3 functioning as ethanol dehydrogenase. FEBS Lett 544:143–147CrossRefPubMedGoogle Scholar
  8. 8.
    Hedberg JJ, Höög J-O, Nilsson JA, Xi Z, Elfwing Å, Grafström RC (2000) Expression of alcohol dehydrogenase 3 in tissue and cultured cells from human oral mucosa. Am J Pathol 157:1745–1755PubMedGoogle Scholar
  9. 9.
    Liu L, Yan Y, Zeng M, Zhang J, Hanes MA, Ahearn G, McMahon TJ, Dickfeld T, Marshall HE, Que LG, Stamler JS (2004) Essential roles of S-nitrosothiols in vascular homeostasis and endotoxic shock. Cell 116:617–627CrossRefPubMedGoogle Scholar
  10. 10.
    Molotkov A, Fan X, Deltour L, Foglio MH, Martras S, Farrés J, Parés X, Duester G (2002) Stimulation of retinoic acid production and growth by ubiquitously expressed alcohol dehydrogenase Adh3. Proc Natl Acad Sci USA 99:5337–5342CrossRefPubMedGoogle Scholar
  11. 11.
    Haqqani AS, Do SK, Birnboim HC (2003) The role of a formaldehyde dehydrogenase-glutathione pathway in protein S-nitrosation in mammalian cells. Nitric Oxide 9:172–181CrossRefPubMedGoogle Scholar
  12. 12.
    Staab CA, Ålander J, Brandt M, Lengqvist J, Morgenstern R, Grafström RC, Höög J-O (2008) Reduction of S-nitrosoglutathione by alcohol dehydrogenase 3 is facilitated by substrate alcohols via direct cofactor recycling and leads to GSH-controlled formation of glutathione transferase inhibitors. Biochem J 413:493–504CrossRefPubMedGoogle Scholar
  13. 13.
    Que LG, Yang Z, Stamler JS, Lugogo NL, Kraft M (2009) S-nitrosoglutathione reductase: an important regulator in human asthma. Am J Respir Crit Care Med 180:226–231CrossRefPubMedGoogle Scholar
  14. 14.
    Iborra FJ, Renau-Piqueras J, Portoles M, Boleda MD, Guerri C, Parés X (1992) Immunocytochemical and biochemical demonstration of formaldehyde dehydrogenase (class III alcohol dehydrogenase) in the nucleus. J Histochem Cytochem 40:1865–1878PubMedGoogle Scholar
  15. 15.
    Staab CA, Hellgren M, Grafström RC, Höög J-O (2009) Medium-chain fatty acids and glutathione derivatives as inhibitors of S-nitrosoglutathione reduction mediated by alcohol dehydrogenase 3. Chem Biol Interact 180:113–118CrossRefPubMedGoogle Scholar
  16. 16.
    Sanghani PC, Davis WI, Fears SL, Green SL, Zhai L, Tang Y, Martin E, Bryan NS, Sanghani SP (2009) Kinetic and cellular characterization of novel inhibitors of S-nitrosoglutathione reductase. J Biol Chem 284:24354–24362CrossRefPubMedGoogle Scholar
  17. 17.
    Totrov M, Abagyan R (2001) High-throughput docking for lead generation. Curr Opin Chem Biol 5:375–382CrossRefPubMedGoogle Scholar
  18. 18.
    Carlsson J, Boukharta L, Åqvist J (2008) Combining docking, molecular dynamics and the linear interaction energy method to predict binding modes and affinities for non-nucleoside inhibitors to HIV-1 reverse transcriptase. J Med Chem 51:2648–2656CrossRefPubMedGoogle Scholar
  19. 19.
    Deng Y, Roux B (2009) Computations of standard binding free energies with molecular dynamics simulations. J Phys Chem B 113:2234–2246CrossRefPubMedGoogle Scholar
  20. 20.
    Abagyan R, Totrov M (1994) Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 235:983–1002CrossRefPubMedGoogle Scholar
  21. 21.
    Bursulaya BD, Totrov M, Abagyan R, Brooks CL (2003) 3rd Comparative study of several algorithms for flexible compound docking. J Comput Aided Mol Des 17:755–763CrossRefPubMedGoogle Scholar
  22. 22.
    Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C (2009) Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J Chem Inf Model 49:1455–1474CrossRefPubMedGoogle Scholar
  23. 23.
    Abagyan R, Totrov M, Kuznetsov DN (1994) ICM—a new method for protein modeling and design. Applications to docking and structure prediction from the distorted native conformation. J Comput Chem 15:488–506CrossRefGoogle Scholar
  24. 24.
    Nemethy G, Gibson KD, Palmer KA, Yoon CN, Paterlini G, Zagari A, Rumsey S, Scheraga HA (1992) Energy parameters in polypeptides. 10. Improved geometrical parameters and nonbonded interactions for use in the ECEPP/3 algorithm, with application to proline-containing peptides. J Phys Chem 96:6472–6484CrossRefGoogle Scholar
  25. 25.
    Schapira M, Raaka BM, Samuels HH, Abagyan R (2000) Rational discovery of novel nuclear hormone receptor antagonists. Proc Natl Acad Sci USA 97:1008–1013CrossRefPubMedGoogle Scholar
  26. 26.
    Han L, Wang Y, Bryant SH (2008) Developing and validating predictive decision tree models from mining chemical structural fingerprints and high-throughput screening data in PubChem. BMC Bioinform 9:401CrossRefGoogle Scholar
  27. 27.
    Ferrari AM, Wei BQ, Costantino L, Shoichet BK (2004) Soft Docking and multiple receptor conformation in virtual screening. J Med Chem 47:5076–5084CrossRefPubMedGoogle Scholar
  28. 28.
    Totrov M, Abagyan R (1997) Flexible protein-compound docking by global energy optimization in internal coordinates. Proteins (Suppl 1):215–220Google Scholar
  29. 29.
    Eklund H, Müller-Wille P, Horjales E, Futer O, Holmquist B, Vallee BL, Höög J-O, Kaiser R, Jörnvall H (1990) Comparison of three classes of human liver alcohol dehydrogenase. Emphasis on different substrate binding pockets. Eur J Biochem 193:303–310CrossRefPubMedGoogle Scholar
  30. 30.
    Totrov M, Abagyan R (2001) Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide. Biopolymers 60:124–133CrossRefPubMedGoogle Scholar
  31. 31.
    Höög J-O, Eklund H, Jörnvall H (1992) A single-residue exchange gives human recombinant ββ alcohol dehydrogenase γγ isozyme properties. Eur J Biochem 205:519–526CrossRefPubMedGoogle Scholar
  32. 32.
    Sanghani PC, Bosron WF, Hurley TD (2002) Human glutathione-dependent formaldehyde dehydrogenase. Structural changes associated with ternary complex formation. Biochemistry 41:15189–15194CrossRefPubMedGoogle Scholar
  33. 33.
    Estonius M, Höög J-O, Danielsson O, Jörnvall H (1994) Residues specific for class III alcohol dehydrogenase. Site-directed mutagenesis of the human enzyme. Biochemistry 33:15080–15085CrossRefPubMedGoogle Scholar
  34. 34.
    Engeland K, Höög J-O, Holmquist B, Estonius M, Jörnvall H, Vallee BL (1993) Mutation of Arg-115 of human class III alcohol dehydrogenase: a binding site required for formaldehyde dehydrogenase activity and fatty acid activation. Proc Natl Acad Sci USA 90:2491–2494CrossRefPubMedGoogle Scholar
  35. 35.
    Fornari FA, Randolph JK, Yalowich JC, Ritke MK, Gewirtz DA (1994) Interference by doxorubicin with DNA unwinding in MCF-7 breast tumor cells. Mol Pharmacol 45:649–656PubMedGoogle Scholar
  36. 36.
    Ohlson S (2008) Designing transient binding drugs: a new concept for drug discovery. Drug Discov Today 13:433–439CrossRefPubMedGoogle Scholar
  37. 37.
    Marschall H-U, Opperman UCT, Svensson S, Nordling E, Persson B, Höög J-O, Jörnvall H (2000) Human liver class I alcohol dehydrogenase γγ isozyme: the sole cytosolic 3β-hydroxysteroid dehydrogenase of iso-bile acids. Hepatology 31:990–996CrossRefPubMedGoogle Scholar
  38. 38.
    Hedberg JJ, Strömberg P, Höög J-O (1998) An attempt to transform class characteristics within the alcohol dehydrogenase family. FEBS Lett 436:67–70CrossRefPubMedGoogle Scholar
  39. 39.
    Hedberg JJ, Griffiths WJ, Nilsson SJ, Höög J-O (2003) Reduction of S-nitrosoglutathione by human alcohol dehydrogenase 3 is an irreversible reaction as analysed by electrospray mass spectrometry. Eur J Biochem 270:1249–1256CrossRefPubMedGoogle Scholar

Copyright information

© Springer Basel AG 2010

Authors and Affiliations

  • Mikko Hellgren
    • 1
  • Jonas Carlsson
    • 2
  • Linus J. Östberg
    • 1
  • Claudia A. Staab
    • 1
    • 4
  • Bengt Persson
    • 2
    • 3
  • Jan-Olov Höög
    • 1
  1. 1.Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
  2. 2.IFM BioinformaticsLinköping UniversityLinköpingSweden
  3. 3.Department of Cell and Molecular BiologyKarolinska InstitutetStockholmSweden
  4. 4.Institute of Toxicology and Pharmacology for Natural ScientistsUniversity Medical School Schleswig-HolsteinKielGermany

Personalised recommendations