Identification of Inhibitor Binding Site in Human Sirtuin 2 Using Molecular Docking and Dynamics Simulations

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Sakkiah, Sugunadevi ^a,b   Arooj, Mahreen ^c   Kumar, Manian Rajesh ^b   Eom, Soo Hyun ^a   Lee, Keun Woo ^c  

^a Gwangju Institute of Science and Technology (GIST)   (South Korea)

^b Chonnam National University   (South Korea)

^c Gyeongsang National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN INHIBITOR; SIRTUIN 2;

ARTICLE; BINDING AFFINITY; BINDING SITE; HYDROGEN BOND; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; QUANTUM CHEMISTRY;

BINDING SITES; CATALYTIC DOMAIN; DRUG DISCOVERY; HISTONE DEACETYLASE INHIBITORS; HUMANS; HYDROGEN BONDING; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; SIRTUIN 2; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 84873860094     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0051429     Document Type: Article

References (41)

1. Haigis MC, Guarente LP, (2006) Mammalian sirtuins-emerging roles in physiology, aging, and calorie restriction. Genes Dev 20: 2913-2921.
2. Frye RA, (2000) Phylogenetic classification of prokaryotic and eukaryotic Sir2-like proteins. Biochem Biophys Res Commun 273: 793-798.
3. Du J, Jiang H, Lin H, (2009) Investigating the ADP-ribosyltransferase activity of sirtuins with NAD analogues and 32P-NAD. Biochemistry 48: 2878-2890.
4. Schwer B, Verdin E, (2008) Conserved metabolic regulatory functions of sirtuins. Cell Metab 7: 104-112.
5. Bao J, Sack MN, (2010) Protein deacetylation by sirtuins: delineating a posttranslational regulatory program responsive to nutrient and redox stressors Cell. Mol Life Sci 67: 3073-3087.
6. Finnin MS, Donigian JR, Pavletich NP, (2001) Structure of the histone deacetylase SIRT2. Nat Struct Biol 2001; 8: 621-625.
7. Tissenbaum HA, Guarente L, (2001) Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans. Nature 410: 227-230.
8. Kaeberlein M, Andalis AA, Fink GR, Guarente L, (2002) High osmolarity extends life span in Saccharomyces cerevisiae by a mechanism related to calorie restriction. Mol Cell Biol 22: 8056-66.
9. Kaeberlein M, McVey M, Guarente L, (1999) The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. Genes Dev 13: 2570-2580.
10. Howitz KT, Bitterman KJ, Cohen HY, Lamming DW, Lavu S, et al. (2003) Small molecule sirtuin activators that extend S. cerevisiae lifespan. Nature 425: 191-196.
11. Cohen HY, Miller C, Bitterman KJ, Wall NR, Hekking B, et al. (2004) Calorie restriction promotes mammalian cell survival by inducing the SIRT1 deacetylase. Science 305: 390-92.
12. Picard F, Kurtev M, Chung N, Topark-Ngarm A, Senawong T, et al. (2004) Sirt1 promotes fat mobilization in white adipocytes by repressing PPAR-gamma. Nature 429: 771-76.
13. Moynihan KA, Grimm AA, Plueger MM, Bernal-Mizrachi E, Ford E, et al. (2005) Increased dosage of mammalian Sir2 in pancreatic beta cells enhances glucose-stimulated insulin secretion in mice. Cel Metab 2: 105-117.
14. Anderson RM, Bitterman KJ, Wood JG, Medvedik O, Sinclair DA, (2003) Nicotinamide and Pnc1 govern lifespan extension by calorie restriction in S, cerevisiae. Nature 423: 181-185.
15. Brunet A, Sweeney LB, Sturgill JF, Chua KF, Greer PL, et al. (2004) Stress-dependent regulation of FOXO transcription factors by the SIRT1 deacetylase. Science 303: 2011-2015.
16. Araki T, Sasaki Y, Milbrandt J, (2004) Increased nuclear NAD biosynthesis and SIRT1 activation prevent axonal degeneration. Science 305: 1010-1013.
17. Muth V, Nadaud S, Grummt I, Voit R, (2001) Epidermal growth factor receptor (EGFR) inhibitors in cancer therapy. EMBO J 20: 1353-6132.
18. Starai VJ, Celic I, Cole RN, Boeke JD, Escalante-Semerena JC, (2002) Sir2-dependent activation of acetyl-CoA synthetase by deacetylation of active lysine. Science 298: 2390-2392.
19. McMurray MA, Gottschling DE, (2003) Aging and Genetic Instability in Yeast. Science 301: 1908-1911.
20. Gottlieb S, Esposito RE, (1989) A new role for a yeast transcriptional silencer gene, SIR2, in regulation of recombination in ribosomal DNA. Cell 56: 771-776.
21. Smith JS, Boeke JD, (1997) An unusual form of transcriptional silencing in yeast ribosomal DNA. Genes Dev 11: 241-254.
22. Perez-Martin J, Uria JA, Johnson AD, (1999) Phenotypic switching in Candida albicans is controlled by a SIR2 gene. EMBO J 18: 2580-2592.
23. Motta MC, Divecha N, Lemieux M, Kamel C, Chen D, et al. (2004) Mammalian SIRT1 represses forkhead transcription factors. Cell 116: 551-563.
24. Vaziri H, Dessain SK, Ng-Eaton E, Imai SI, Frye RA, et al. (2001) hSIR2(SIRT1) functions as an NAD-dependent p53 deacetylase. Cell 107: 149-159.
25. Sauve Anthony A, Wolberger Cynthia, Schramm Vern L, Boeke Jef D, (2006) The Biochemistry of Sirtuins. Annu Rev Biochem 75: 435-465.
26. Lara E, Mai A, Calvanese V, Altucci L, Lopez-Nieva P, et al. (2009) Salermide, a sirtuin inhibitor with a strong cancer-specific proapoptotic effect. Oncogene 28: 781-791.
27. Palazzo A, Ackerman B, Gundersen GG, (2003) Cell biology: Tubulin acetylation and cell motility. Nature 421: 230.
28. Pellegrini F, Budman DR, (2005) Review: Tubulin function, action of antitubulin drugs, and new drug development. Cancer Invest 23: 264-273.
29. Matsuyama A, Shimazu T, Sumida Y, Saito A, Yoshimatsu Y, et al. (2002) In vivo destabilization of dynamic microtubules by HDAC6-mediated deacetylation. EMBO J 21: 6820-6831.
30. Neugebauer RC, Uchiechowska U, Meier R, Hruby H, Valkov V, et al. (2008) Structure-activity studies on splitomicin derivatives as sirtuin inhibitors and computational prediction of binding mode. J Med Chem 51: 1203-1213.
31. Wang F, Nguyen M, Qin FX, Tong Q, (2007) SIRT2 deacetylates FOXO3a in response to oxidative stress and caloric restriction. Aging Cell 6: 505-514.
32. Hiratsuka T, Inoue T, Toda N, Kimura Y, Shirayoshi H, et al. (2003) Proteomics-based identification of differentially expressed genes in human gliomas: sown-regulation of SIRT2 gene. Biochemical and Biophysical Research Communications 309: 558-566.
33. Outerio TF, Kontopoulos E, Altmann SM, Kufareva I, Strathearn KE, et al. (2007) Sirtuin 2 Inhibitor Rescue a-Synuclein-Mediated Toxicity in Models of Parkinson's disease. Science 317: 516-519.
34. Sakkiah S, Chandrasekaran M, Lee Y, Kim S, Lee KW, (2012) Molecular Modeling Study for Conformational Changes of Sirtuin2 due to Substrate and Inhibitor Binding. Journal of Biomolecular Structure & Dynamics 30: 235-254.
35. Choi SH, Quinti L, Kazantsev AG, Silverman RB, (2012) 3-(N-arylsulfamoyl) benzamides, inhibitors of human Sirtuin type 2 (SIRT2). Bioorg Med Chem Lett 22: 2789-2793.
36. Gaussian (2004) Revision C.03; Gaussian, Inc.: Wallingford, CT, USA.
37. Maria Lara PMA, Jose do PHA, Nelson RS, Valdemar LJ, Jose MP et al, (2010) Electrochemical and theoretical evaluation of the interaction between dna and amodiaquine. Evidence of the guanine adduct formation. Quim Nova 33: 1291-1296.
38. Singh RK, Suresh KV, Prabhu DS, (2011) DFT based Study of interaction between Frontier Orbitals of Transition Metal Halides and Thioamides. Int J of ChemTech Res 3: 1571-1579.
39. Erol E, Hasan T, Semra G, Selami P, Oral O, (2007) A DFT-Based QSARs Study of Acetazolamide/Sulfanilamide Derivatives with Carbonic Anhydrase (CA-II) Isozyme Inhibitory Activity. Int J Mol Sci 8: 145-155.
40. Tervo AJ, Kyrylenko S, Niskanen P, Salminen A, Leppanen J, et al. (2004) An in silico approach to discovering novel inhibitors of human sirtuin type 2. J Med Chem 47: 6292-6298.
41. Sakkiah S, Thangapandian S, Park C, Son M, Lee KW, (2012) Molecular docking and dynamics simulation, receptor-based hypothesis: application to identify novel Sirtuin 2 inhibitors. Chem Biol Drug Des 80: 315-327.