Skip to main content
SpringerLink
Log in

The mechanism of the effect of U18666a on blocking the activity of 3β-hydroxysterol Δ-24-reductase (DHCR24): molecular dynamics simulation study and free energy analysis

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

DHCR24 encodes 3β-hydroxysterol-Δ24-reductase (DHCR24) catalyzing the cholesterol synthesis from desmosterol using the flavin adenine dinucleotide (FAD) as a co-factor. It is generally accepted that U18666a inhibits the reductase activity of DHCR24, but the detailed mechanism remains elusive. To explore the mechanism of the inhibitory effect of U18666a on DHCR24, we performed molecular dynamics (MD) simulations of two complexes including complexes of DHCR24-FAD-desmosterol enzymatic reactive components with and without the inhibitor U18666a. We found that the U18666a bound into the hydrophobic package near the FAD package of DHCR24. Furthermore, binding free energy of DHCR24 and desmosterol without U18666a is −54.86 kcal/mol, while the system with U18666a is −62.23 kcal/mol, suggesting that the affinity of the substrate desmosterol to DHCR24 was increased in response to the U18666a. In addition, U18666a interacts with FAD by newly forming three hydrogen bonds with Lys292, Lys367, and Gly438 of DHCR24. Finally, secondary structural analysis data obtained from the surrounding hot spots showed that U18666a induced dramatic secondary structural changes around the key residues in the interaction of DHCR24, FAD, and desmosterol. Taken together, these results for the first time demonstrate at the molecular structure level that U18666a blocks DHCR24 activity through an allosteric inhibiting mechanism, which may provide new insight into the development of a new type of cholesterol-lowering drug targeting to block the activity of DHCR24.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

References

  1. Greeve I, Hermans-Borgmeyer I, Brellinger C, Kasper D, Gomez-Isla T, Behl C, Levkau B, Nitsch RM (2000) The human DIMINUTO/DWARF1 homolog seladin-1 confers resistance to Alzheimer’s disease-associated neurodegeneration and oxidative stress. J Neurosci 20(19):7345–7352

    CAS  Google Scholar 

  2. Iivonen S, Hiltunen M, Alafuzoff I, Mannermaa A, Kerokoski P, Puolivali J, Salminen A, Helisalmi S, Soininen H (2002) Seladin-1 transcription is linked to neuronal degeneration in Alzheimer’s disease. Neuroscience 113(2):301–310

    Article  CAS  Google Scholar 

  3. Mushegian AR, Koonin EV (1995) A putative FAD-binding domain in a distinct group of oxidases including a protein involved in plant development. Protein Sci 4(6):1243–1244. doi:10.1002/pro.5560040623

    Article  CAS  Google Scholar 

  4. Pedretti A, Bocci E, Maggi R, Vistoli G (2008) Homology modelling of human DHCR24 (seladin-1) and analysis of its binding properties through molecular docking and dynamics simulations. Steroids 73(7):708–719. doi:10.1016/j.steroids.2008.02.007

    Article  CAS  Google Scholar 

  5. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucleic Acids Res 38(Database issue):D211–222. doi:10.1093/nar/gkp985

    Article  CAS  Google Scholar 

  6. Klahre U, Noguchi T, Fujioka S, Takatsuto S, Yokota T, Nomura T, Yoshida S, Chua NH (1998) The Arabidopsis DIMINUTO/DWARF1 gene encodes a protein involved in steroid synthesis. Plant Cell 10(10):1677–1690

    Article  CAS  Google Scholar 

  7. Waterham HR, Koster J, Romeijn GJ, Hennekam RC, Vreken P, Andersson HC, FitzPatrick DR, Kelley RI, Wanders RJ (2001) Mutations in the 3beta-hydroxysterol Delta24-reductase gene cause desmosterolosis, an autosomal recessive disorder of cholesterol biosynthesis. Am J Hum Genet 69(4):685–694. doi:10.1086/323473

    Article  CAS  Google Scholar 

  8. Andersson HC, Kratz L, Kelley R (2002) Desmosterolosis presenting with multiple congenital anomalies and profound developmental delay. Am J Med Genet 113(4):315–319. doi:10.1002/ajmg.b.10873

    Article  Google Scholar 

  9. Wu C, Miloslavskaya I, Demontis S, Maestro R, Galaktionov K (2004) Regulation of cellular response to oncogenic and oxidative stress by seladin-1. Nature 432(7017):640–645. doi:10.1038/nature03173

    Article  CAS  Google Scholar 

  10. Sarkar D, Imai T, Kambe F, Shibata A, Ohmori S, Siddiq A, Hayasaka S, Funahashi H, Seo H (2001) The human homolog of diminuto/Dwarf1 gene (hDiminuto): a novel ACTH-responsive gene overexpressed in benign cortisol-producing adrenocortical adenomas. J Clin Endocrinol Metab 86(11):5130–5137. doi:10.1210/jcem.86.11.8032

    Article  CAS  Google Scholar 

  11. Lu X, Kambe F, Cao X, Kozaki Y, Kaji T, Ishii T, Seo H (2008) 3beta-hydroxysteroid-delta24 reductase is a hydrogen peroxide scavenger, protecting cells from oxidative stress-induced apoptosis. Endocrinology 149(7):3267–3273. doi:10.1210/en.2008-0024

    Article  CAS  Google Scholar 

  12. Cenedella RJ (2009) Cholesterol synthesis inhibitor U18666A and the role of sterol metabolism and trafficking in numerous pathophysiological processes. Lipids 44(6):477–487. doi:10.1007/s11745-009-3305-7

    Article  CAS  Google Scholar 

  13. Cheung NS, Koh CH, Bay BH, Qi RZ, Choy MS, Li QT, Wong KP, Whiteman M (2004) Chronic exposure to U18666A induces apoptosis in cultured murine cortical neurons. Biochem Biophys Res Commun 315(2):408–417. doi:10.1016/j.bbrc.2004.01.066

    Article  CAS  Google Scholar 

  14. Koh CH, Cheung NS (2006) Cellular mechanism of U18666A-mediated apoptosis in cultured murine cortical neurons: bridging Niemann–Pick disease type C and Alzheimer’s disease. Cell Signal 18(11):1844–1853. doi:10.1016/j.cellsig.2006.04.006

    Article  CAS  Google Scholar 

  15. Cenedella RJ, Sarkar CP, Towns L (1982) Studies on the mechanism of the epileptiform activity induced by U18666A. II. Concentration, half-life and distribution of radiolabeled U18666A in the brain. Epilepsia 23(3):257–268

    Article  CAS  Google Scholar 

  16. Liscum L, Faust JR (1989) The intracellular transport of low density lipoprotein-derived cholesterol is inhibited in Chinese hamster ovary cells cultured with 3-beta-[2-(diethylamino)ethoxy]androst-5-en-17-one. J Biol Chem 264(20):11796–11806

    CAS  Google Scholar 

  17. Liscum L (1990) Pharmacological inhibition of the intracellular transport of low-density lipoprotein-derived cholesterol in Chinese hamster ovary cells. Biochim Biophys Acta 1045(1):40–48

    Article  CAS  Google Scholar 

  18. Sexton RC, Panini SR, Azran F, Rudney H (1983) Effects of 3 beta-[2-(diethylamino)ethoxy]androst-5-en-17-one on the synthesis of cholesterol and ubiquinone in rat intestinal epithelial cell cultures. Biochemistry 22(25):5687–5692

    Article  CAS  Google Scholar 

  19. Bae SH, Paik YK (1997) Cholesterol biosynthesis from lanosterol: development of a novel assay method and characterization of rat liver microsomal lanosterol delta 24-reductase. Biochem J 326(Pt 2):609–616

    Article  CAS  Google Scholar 

  20. Xue W, Yang Y, Wang X, Liu H, Yao X (2014) Computational study on the inhibitor binding mode and allosteric regulation mechanism in hepatitis C virus NS3/4A protein. PLoS One 9(2):e87077. doi:10.1371/journal.pone.0087077

    Article  Google Scholar 

  21. UniProt C (2008) The universal protein resource (UniProt). Nucleic Acids Res 36 (Database issue):D190–195. doi:10.1093/nar/gkm895

    Google Scholar 

  22. Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinforma 9:40. doi:10.1186/1471-2105-9-40

    Article  Google Scholar 

  23. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kale L, Schulten K (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26(16):1781–1802. doi:10.1002/jcc.20289

    Article  CAS  Google Scholar 

  24. Abbate EA, Berger JM, Botchan MR (2004) The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2. Genes Dev 18(16):1981–1996. doi:10.1101/gad.1220104

    Article  CAS  Google Scholar 

  25. Luo J, Graslund A (2011) Ribonucleotide reductase inhibition by p-alkoxyphenols studied by molecular docking and molecular dynamics simulations. Arch Biochem Biophys 516(1):29–34. doi:10.1016/j.abb.2011.09.003

    Article  CAS  Google Scholar 

  26. Lu SY, Jiang YJ, Lv J, Wu TX, Yu QS, Zhu WL (2010) Molecular docking and molecular dynamics simulation studies of GPR40 receptor-agonist interactions. J Mol Graph Model 28(8):766–774. doi:10.1016/j.jmgm.2010.02.001

    Article  CAS  Google Scholar 

  27. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(1):33–38, 27–38

    Article  CAS  Google Scholar 

  28. Zoete V, Meuwly M, Karplus M (2005) Study of the insulin dimerization: binding free energy calculations and per-residue free energy decomposition. Proteins 61(1):79–93. doi:10.1002/prot.20528

    Article  CAS  Google Scholar 

  29. Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8(10):785–786. doi:10.1038/nmeth.1701

    Article  CAS  Google Scholar 

  30. Viklund H, Elofsson A (2008) OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar. Bioinformatics 24(15):1662–1668. doi:10.1093/bioinformatics/btn221

    Article  CAS  Google Scholar 

  31. Bernsel A, Viklund H, Hennerdal A, Elofsson A (2009) TOPCONS: consensus prediction of membrane protein topology. Nucleic Acids Res 37(Web Server issue):W465–468. doi:10.1093/nar/gkp363

    Article  CAS  Google Scholar 

  32. FitzPatrick DR, Keeling JW, Evans MJ, Kan AE, Bell JE, Porteous ME, Mills K, Winter RM, Clayton PT (1998) Clinical phenotype of desmosterolosis. Am J Med Genet 75(2):145–152

    Article  CAS  Google Scholar 

  33. Schaaf CP, Koster J, Katsonis P, Kratz L, Shchelochkov OA, Scaglia F, Kelley RI, Lichtarge O, Waterham HR, Shinawi M (2011) Desmosterolosis-phenotypic and molecular characterization of a third case and review of the literature. Am J Med Genet A 155A(7):1597–1604. doi:10.1002/ajmg.a.34040

    Article  Google Scholar 

  34. Horvat S, McWhir J, Rozman D (2011) Defects in cholesterol synthesis genes in mouse and in humans: lessons for drug development and safer treatments. Drug Metab Rev 43(1):69–90. doi:10.3109/03602532.2010.540580

    Article  CAS  Google Scholar 

  35. Rozman D, Monostory K (2010) Perspectives of the non-statin hypolipidemic agents. Pharmacol Ther 127(1):19–40. doi:10.1016/j.pharmthera.2010.03.007

    Article  CAS  Google Scholar 

Download references

Acknowledgments

Our appreciation goes out to Maryam Faisal Abdelrahim and Sam-Ukoh Bryan for proofreading this manuscript. The study was supported by a grant of National Natural Science Foundation of China (No. 31271494 and No. 81570632) and Innovation Team Project from the Education Department of Liaoning Province (No: LT2015011).

Author information

Authors and Affiliations

  1. The School of Life Science, Liaoning University, Chongshanzhong-lu No. 66, Huanggu-qu, Shenyang, 110036, China

    Xiaoping Quan, Xiuqiang Chen, Deliang Sun, Bo Xu, Linlin Zhao, Xiaoqian Shi, Hongsheng Liu & Xiuli Lu

  2. Department of Cell Biology and Genetics, School of Basic Medical Science, Shenyang Medical College, Huang-he-bei-dajie, No. 146, Shenyang, 110034, China

    Bing Gao

  3. Research Center for Computer Simulating and Information Processing of Bio-macromolecules of Liaoning Province, Shenyang, China

    Xiuli Lu

Authors
  1. Xiaoping Quan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Xiuqiang Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Deliang Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Bo Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Linlin Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Xiaoqian Shi
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Hongsheng Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Bing Gao
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Xiuli Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Bing Gao or Xiuli Lu.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Figure 1

(GIF 1162 kb)

High resolution image (TIF 603 kb)

Supplementary Figure 2

(GIF 2190 kb)

High resolution image (TIF 3171 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Quan, X., Chen, X., Sun, D. et al. The mechanism of the effect of U18666a on blocking the activity of 3β-hydroxysterol Δ-24-reductase (DHCR24): molecular dynamics simulation study and free energy analysis. J Mol Model 22, 46 (2016). https://doi.org/10.1007/s00894-016-2907-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-016-2907-2

Keywords

Search

Navigation