Journal of Computer-Aided Molecular Design

, Volume 26, Issue 7, pp 865–881 | Cite as

Understanding the molecular interactions of different radical scavengers with ribonucleotide reductase M2 (hRRM2) domain: opening the gates and gaining access

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Abstract

We employed a combination of molecular docking and dynamics to understand the interaction of three different radical scavengers (SB-HSC21, ABNM13 and trimidox) with ribonucleotide reductase M2 (hRRM2) domain. On the basis of the observed results, we can propose how these ligands interact with the enzyme, and cease the radical transfer step from the di-iron center to TYR176. All the ligands alter the electron density over TYR176, –OH group by forming an extremely stable H-bond with either –NHOH group, or with phenolic hydroxyl group of the ligands. This change in electronic density disrupts the water bridge between TYR176, –OH and the di-iron center, which stops the single electron transfer process from TYR176, –OH to iron. As a consequence the enzyme is inhibited. Another interesting observation that we are reporting is the two stage gate keeping mechanism of the RR active site tunnel. We describe these as the outer Gate-1 controlled by ARG330, and the inner Gate-2 controlled by SER263, PHE240, and PHE236. We also observed a dynamic conformational shift in these residues, the incoming ligands can go through, and interact with the underlying TYR176, –OH group. From the study we found the active—site of hRRM2 is extremely flexible and shows a significant induced fit.

Keywords

Molecular dynamics Ribonucleotide reductase (RR) Gate keeper residues Molecular docking 
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Notes

Acknowledgments

We thank University Grants Commission for providing necessary financial support for the current work. We also thank Mrs. Nibha Mishra and Dr. Venkatesan J for proofreading our manuscript.

Supplementary material

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Supplementary material 1 (DOC 534 kb)
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Supplementary material 2 (DOC 534 kb)
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Supplementary material 3 (DOC 534 kb)
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Supplementary material 4 (DOC 535 kb)

References

  1. 1.
    Shao J, Zhou B, Chu B, Yen Y (2006) Ribonucleotide reductase inhibitors and future drug design. Curr Cancer Drug Targets 6:409CrossRefGoogle Scholar
  2. 2.
    Cerqueira NM, Pereira S, Fernandes PA, Ramos MJ (2005) Overview of ribonucleotide reductase inhibitors: an appealing target in anti-tumour therapy. Curr Med Chem 12:1283CrossRefGoogle Scholar
  3. 3.
    Stubbe JA, Nocera DG, Yee CS, Chang MCY (2003) Radical initiation in the class I ribonucleotide reductase: long-range proton-coupled electron transfer? Chem Rev 103:2167CrossRefGoogle Scholar
  4. 4.
    Stubbe JA, van der Donk WA (1998) Protein radicals in enzyme catalysis. Chem Rev 98:705CrossRefGoogle Scholar
  5. 5.
    Jordan A, Reichard P (1998) Ribonucleotide reductases. Annu Rev Biochem 67:71CrossRefGoogle Scholar
  6. 6.
    Reichard P (1993) From RNA to DNA, why so many ribonucleotide reductases? Science 260:1773CrossRefGoogle Scholar
  7. 7.
    Reichard P, Ehrenberg A (1983) Ribonucleotide reductase—a radical enzyme. Science 221:514CrossRefGoogle Scholar
  8. 8.
    Jordan A, Pontis E, Atta M, Krook M, Gibert I, Barbe J, Reichard P (1994) A second class I ribonucleotide reductase in enterobacteriaceae: characterization of the Salmonella typhimurium enzyme. Proc Natl Acad Sci USA 91:12892CrossRefGoogle Scholar
  9. 9.
    Högbom M, Stenmark P, Voevodskaya N, McClarty G, Gräslund A, Nordlund P (2004) The radical site in chlamydial ribonucleotide reductase defines a new R2 subclass. Science 305:245CrossRefGoogle Scholar
  10. 10.
    Smith BD, Karp JE (2003) Ribonucleotide reductase: an old target with new potential. Leuk Res 27:1075CrossRefGoogle Scholar
  11. 11.
    Nocentini G (1996) Ribonucleotide reductase inhibitors: new strategies for cancer chemotherapy. Crit Rev Oncol Hematol 22:89CrossRefGoogle Scholar
  12. 12.
    Holland KP, Elford HL, Bracchi V, Annis CG, Schuster SM, Chakrabarti D (1998) Antimalarial activities of polyhydroxyphenyl and hydroxamic acid derivatives. Antimicrob Agents Chemother 42:2456Google Scholar
  13. 13.
    Yun D, Saleh L, García-Serres R, Chicalese BM, An YH, Huynh BH, Bollinger JM Jr (2007) Addition of oxygen to the diiron (II/II) cluster is the slowest step in formation of the tyrosyl radical in the W103Y variant of ribonucleotide reductase protein R2 from mouse. Biochemistry 46:13067CrossRefGoogle Scholar
  14. 14.
    Smith P, Zhou B, Ho N, Yuan YC, Su L, Tsai SC, Yen Y (2009) 2.6 Å X-ray crystal structure of human p53R2, a p53-inducible ribonucleotide reductase. Biochemistry 48:11134CrossRefGoogle Scholar
  15. 15.
    Strand KR, Karlsen S, Kolberg M, Røhr ÅK, Görbitz CH, Andersson KK (2004) Crystal structural studies of changes in the native dinuclear iron center of ribonucleotide reductase protein R2 from mouse. J Biol Chem 279:46794CrossRefGoogle Scholar
  16. 16.
    Logan DT, Su XD, Åberg A, Regnström K, Hajdu J, Eklund H, Nordlund P (1996) Crystal structure of reduced protein R2 of ribonucleotide reductase: the structural basis for oxygen activation at a dinuclear iron site. Structure 4:1053CrossRefGoogle Scholar
  17. 17.
    Nordlund P, Sjöberg BM, Eklund H (1990) Three-dimensional structure of the free radical protein of ribonucleotide reductase. Nature 345:593Google Scholar
  18. 18.
    Nordlund P, Eklund H (1993) Structure and function of the Escherichia coli ribonucleotide reductase protein R2. J Mol Biol 232:123CrossRefGoogle Scholar
  19. 19.
    Končić MZ, Barbarić M, Perković I, Zorc B (2011) Antiradical, chelating and antioxidant activities of hydroxamic acids and hydroxyureas. Molecules 16:6232CrossRefGoogle Scholar
  20. 20.
    Fritzer-Szekeres M, Grusch M, Luxbacher C, Horvath S, Krupitza G, Elford HL, Szekeres T (2000) Trimidox, an inhibitor of ribonucleotide reductase, induces apoptosis and activates caspases in HL-60 promyelocytic leukemia cells. Exp Hematol 28:924CrossRefGoogle Scholar
  21. 21.
    Ren S, Wang R, Komatsu K, Bonaz-Krause P, Zyrianov Y, McKenna CE, Csipke C, Tokes ZA, Lien EJ (2002) Synthesis, biological evaluation, and quantitative structure-activity relationship analysis of new Schiff bases of hydroxysemicarbazide as potential antitumor agents. J Med Chem 45:410CrossRefGoogle Scholar
  22. 22.
    Shao J, Zhou B, Zhu L, Bilio AJ, Su L, Yuan YC, Ren S, Lien EJ, Shih J, Yen Y (2005) Determination of the potency and subunit-selectivity of ribonucleotide reductase inhibitors with a recombinant-holoenzyme-based in vitro assay. Biochem Pharmacol 69:627CrossRefGoogle Scholar
  23. 23.
    Elford HL (1994) assignee. Method of treating hemoglobinopathies. US Patent 5,366,996Google Scholar
  24. 24.
    Basu A, Sinha BN, Saiko P, Graser G, Szekeres T (2011) N-hydroxy-N′-aminoguanidines as anti-cancer lead molecule: QSAR, synthesis and biological evaluation. Bioorg Med Chem Lett 21:3324Google Scholar
  25. 25.
    Saiko P, Graser G, Giessrigl B, Lackner A, Grusch M, Krupitza G, Basu A, Sinha B, Jayaprakash V, Jaeger W (2011) A novel N-hydroxy-N′-aminoguanidine derivative inhibits ribonucleotide reductase activity: effects in human HL-60 promyelocytic leukemia cells and synergism with arabinofuranosylcytosine (Ara-C). Biochem Pharmacol 81:50CrossRefGoogle Scholar
  26. 26.
    Krishnan K, Prathiba K, Jayaprakash V, Basu A, Mishra N, Zhou B, Hu S, Yen Y (2008) Synthesis and ribonucleotide reductase inhibitory activity of thiosemicarbazones. Bioorg Med Chem Lett 18:6248CrossRefGoogle Scholar
  27. 27.
    Himo F, Siegbahn PEM (2003) Quantum chemical studies of radical-containing enzymes. Chem Rev 103:2421CrossRefGoogle Scholar
  28. 28.
    Torrent M, Musaev DG, Basch H, Morokuma K (2002) Computational studies of reaction mechanisms of methane monooxygenase and ribonucleotide reductase. J Comput Chem 23:59CrossRefGoogle Scholar
  29. 29.
    Lynch J, Juarez-Garcia C, Münck E, Que L Jr (1989) Mössbauer and EPR studies of the binuclear iron center in ribonucleotide reductase from Escherichia coli. a new iron-to-protein stoichiometry. J Biol Chem 264:8091Google Scholar
  30. 30.
    Elgren TE, Hendrich MP, Que L Jr (1993) Azide binding to the diferrous clusters of the R2 protein of ribonucleotide reductase from Escherichia coli. J Am Chem Soc 115:9291CrossRefGoogle Scholar
  31. 31.
    Bell CL, Nambury C, Bauer L (1964) The structure of amidoximes. J Org Chem 29:2873CrossRefGoogle Scholar
  32. 32.
    Kjøller Larsen I, Sjöoberg BM, Thelander L (1982) Characterization of the active site of ribonucleotide reductase of Escherichia coli, bacteriophage T4 and mammalian cells by inhibition studies with hydroxyurea analogues. Eur J Biochem 125:75CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  1. 1.Department of Pharmaceutical SciencesBirla Institute of TechnologyRanchiIndia

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