Computers in Biology and Medicine
Volume 42, Issue 2 , Pages 156-163 , February 2012

Explication of interactions between HMGCR isoform 2 and various statins through In silico modeling and docking

  • M.V.K. Karthik

      Affiliations

    • Enzyme Technology Laboratory, Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
    • ,
  • M.V.K.N. Satya Deepak

      Affiliations

    • Department of Pharmacy, SASTRA University, Thanjavur, Tamilnadu
    • ,
  • Pratyoosh Shukla

      Affiliations

    • Enzyme Technology Laboratory, Department of Biotechnology, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India
    • Corresponding Author InformationCorresponding author. Tel.: +91 9431171157; fax: +91 651 2275401.

Received 29 April 2011 ,Accepted 7 November 2011.

References 

  1. M.D. Bethesda, Third Report of the National Cholesterol Education Program (NCEP) Expert Panel on Detection, Evaluation, and Treatment of High Blood Cholesterol in Adults (Adult Treatment Panel III): Executive Summary: National Institutes of Health. National Heart, Lung, and Blood Institute, National Cholesterol Education Program, NIH Publication no. 01-3670, 2001, pp. 40.
  2. National Collaborating Centre for Primary Care . NICE Clinical Guideline 67: Lipid Modification. London: National Institute for Health and Clinical Excellence; 2010;pp. 38
  3. Farnier M, Davignon J. Current and future treatment of hyperlipidemia: the role of statins. Am. J. Cardiol. 1998;82:3J–10J
  4. Maron DJ, Fazio S, Linton MF. Current perspectives on statins. Circulation. 2000;101:207–213
  5. Bochar DA, Stauffacher CV, Rodwell VW. Sequence comparisons reveal two classes of 3-hydroxy-3-methylglutaryl coenzyme A reductase. Mol. Genet. Metab. 1999;66:122–127
  6. Koning AJ, Roberts CJ, Wright RL. Different sub-cellular localization of Saccharomyces cerevisiae HMG-CoA reductase isozymes at elevated levels corresponds to distinct endoplasmic reticulum membrane proliferations. Mol. Biol. Cell. 1996;7:769–789
  7. Keller GA, Barton MC, Shapiro DJ, Singer SJ. 3-Hydroxy-3-methylglutaryl coenzyme A reductase is present in peroxisomes in normal rat liver cells. Proc. Natl. Acad. Sci. USA. 1985;82:770–774
  8. Keller GA, Pazirandeh M, Krisans S. 3-Hydroxy-3-methylglutaryl coenzyme A reductase localization in rat liver peroxisome and microsomes of control and cholestyramine-treated animals quantitative biochemical and immunoelectron microscopical analyses. J. Cell Biol. 1986;103:875–886
  9. Appelkvist EL, Kalen A. Biosynthesis of dolichol by rat liver peroxisomes. Eur. J. Biochem. 1989;185:503–509
  10. Hashimoto F, Hamada S, Hayashi H. Effect of gemfibrozil on centrifugal behavior of rat peroxisomes and activities of peroxisomal enzymes involved in lipid metabolism. Biol. Pharm. Bull. 1989;20:315–321
  11. Engfelt WH, Masuda KR, Paton VG, Krisans SK. Splice donor site mutations in the 3-hydroxy-3-methylglutaryl co-enzyme A reductase gene cause a deficiency of the endoplasmic reticulum 3-hydroxy-3-methylglutaryl coenzyme A reductase protein in UT2 cells. J. Lipid Res. 1998;39:2182–2191
  12. Rusnak N, Krisans SK. Diurnal variation of HMG-CoA reductase activity in rat liver peroxisomes. Biochem. Biophys. Res. Commun. 1987;148:890–895
  13. Aboushadi N, Shackelford JE, Jessani N, Gentile A, Krisans SK. Characterization of peroxisomal 3-hydroxy-3-methylglutaryl coenzyme A reductase in UT2 cells: sterol biosynthesis phosphorylation, degradation, and statin inhibition. Biochemistry. 2000;39:237–247
  14. Engfelt WH, Shackelford JE, Aboushadi N, Jessani N, Masuda K, Paton VG, et al. Characterization of UT2 cells. The induction of peroxisomal 3-hydroxy-3-methylglutaryl-coenzyme a reductase. J. Biol. Chem. 1997;272:24579–24587
  15. Biardi L, Krisans SK. Compartmentalization of cholesterol biosynthesis. Conversion of mevalonate to farnesyl diphosphate occurs in the peroxisomes. J. Biol. Chem. 1996;271:1784–1788
  16. Larkin MA, Blackshields G, Brown NP. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23:2947–2948
  17. Page RDM. TreeView: an application to display phylogenetic trees on personal computers. Comput. Appl. Biosci. 1996;12:357–358
  18. Arnold K, Bordoli L, Kopp J, Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modeling. Bioinformatics. 2006;22:195–201
  19. Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 1997;18:2714–2723
  20. Kopp J, Schwede T. The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res. 2004;32:D230–D234
  21. Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T. The SWISS-MODEL Repository and associated resources. Nucleic Acids Res. 2009;37:D387–92
  22. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 2003;31:3381–3385
  23. Laskoswki RA, MacArthur MW, Moss DS, Thorton JM. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993;26:283–291
  24. Pontius J, Richelle J, Wodak SJ. Deviations from standard atomic volumes as a quality measure for protein crystal structure. J. Mol. Biol. 1996;264:121–136
  25. Heinig M, Frishman D. STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins. Nucl. Acids Res. 2004;32:W500–2
  26. Macindoe G, Mavridis L, Venkatraman V, Devignes MD, Ritchie DW. HexServer: an FFT-based protein docking server powered by graphics processors. Nucl. Acids Res. 2010;38:W445–W449
  27. Peitsch MC. ProMod and Swiss-Model: internet-based tools for automated comparative protein modeling. Biochem. Soc. Trans. 1996;24:274–279
  28. Christen M, Hünenberger PH, Bakowies D, Baron R, Bürgi R, Geerke DP, et al. The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem. 2005;26:1719–1751
  29. Hooft RWW, Sander C, Vriend G. Verification of protein structures: side-chain planarity. J. Appl. Crystallogr. 1996;29:714–716
  30. Wiederstein Sippl. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucl. Acids Res. 2007;35:W407–W410
  31. Melo F, Devos D, Depiereux E, Feytmans E. ANOLEA: a www server to assess protein structures. Intell. Syst. Mol. Biol. 1997;97:110–113
  32. Luthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992;356:83–85
  33. L. Feng, L. Zhou, S. Yao, J. Gui, P. Wu, J. Wan, Y. Ren, S. Qiu, X. Wei, Specific inhibitions of annonaceous acetogenins on class II 3-hydroxy-3-methylglutaryl coenzyme A reductase from Streptococcus pneumoniae, Bioorg, Med. Chem., [in press: doi:10.1016/j.bmc.2011.04.019].
  34. Pfefferkorn JA, Litchfield J, Hutchings R, Cheng XM, Larsen SD, et al. Discovery of novel hepatoselective HMG-CoA reductase inhibitors for treating hypercholesterolemia: a bench-to-bedside case study on tissue selective drug distribution. Bioorg. Med. Chem. Lett. 2011;21:2725–2731
  35. Argüelles N, et al. Design, synthesis, and docking of highly hypolipidemic agents: Schizosaccharomyces pombe as a new model for evaluating a-asarone-based HMG-CoA reductase inhibitors. Bioorg. Med. Chem. 2010;18:4238–4248

PII: S0010-4825(11)00222-8

doi: 10.1016/j.compbiomed.2011.11.003

Computers in Biology and Medicine
Volume 42, Issue 2 , Pages 156-163 , February 2012

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