Springer Nature is making Coronavirus research free. View research | View latest news | Sign up for updates

Location, Orientation and Aggregation of Bardoxolone-ME, CDDO-ME, in a Complex Phospholipid Bilayer Membrane

  • 40 Accesses


Bardoxolone methyl (CDDO-Me), a synthetic derivative of the naturally occurring triterpenoid oleanolic acid, displays strong antioxidant, anticancer and anti-inflammatory activities, according to different bibliographical sources. However, the understanding of its molecular mechanism is missing. Furthermore, CDDO-Me has displayed a significant cytotoxicity against various types of cancer cells. CDDO-Me has a noticeable hydrophobic character and several of its effects could be attributed to its ability to be incorporated inside the biological membrane and therefore modify its structure and specifically interact with its components. In this study, we have used full-atom molecular dynamics to determine the location, orientation and interactions of CDDO-Me in phospholipid model membranes. Our results support the location of CDDO-Me in the middle of the membrane, it specifically orients so that the cyano group lean towards the phospholipid interface and it specifically interacts with particular phospholipids. Significantly, in the membrane the CDDO-Me molecules specifically interact with POPE and POPS. Moreover, CDDO-Me does not aggregates in the membrane but it forms a complex conglomerate in solution. The formation of a complex aggregate in solution might hamper its biological activity and therefore it should be taken into account when intended to be used in clinical assays. This work should aid in the development of these molecules opening new avenues for future therapeutic developments.

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

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6


  1. Anézo C, de Vries AH, Höltje H-D, Tieleman DP, Marrink S-J (2003) Methodological issues in lipid bilayers simulations. J. Phys. Chem. B 107:9424–9433

  2. Baylon JL, Tajkhorshid E (2015) Capturing spontaneous membrane insertion of the influenza virus hemagglutinin fusion Peptide. J Phys Chem B 119:7882–7893

  3. Bera I, Klauda JB (2017) Molecular simulations of mixed lipid bilayers with sphingomyelin, glycerophospholipids, and cholesterol. J Phys Chem B 121:5197–5208

  4. Best RB, Zhu X, Shim J, Lopes PE, Mittal J, Feig M, Mackerell AD Jr (2012) Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone phi, psi and side-chain chi(1) and chi(2) dihedral angles. J Chem Theory Comput 8:3257–3273

  5. Bockmann RA, Hac A, Heimburg T, Grubmuller H (2003) Effect of sodium chloride on a lipid bilayer. Biophys J 85:1647–1655

  6. Camer D, Yu Y, Szabo A, Wang H, Dinh CH, Huang XF (2016) Bardoxolone methyl prevents obesity and hypothalamic dysfunction. Chem Biol Interact 256:178–187

  7. Chin MP, Reisman SA, Bakris GL, O'Grady M, Linde PG, McCullough PA, Packham D, Vaziri ND, Ward KW, Warnock DG, Meyer CJ (2014) Mechanisms contributing to adverse cardiovascular events in patients with type 2 diabetes mellitus and stage 4 chronic kidney disease treated with bardoxolone methyl. Am J Nephrol 39:499–508

  8. de Zeeuw D, Akizawa T, Audhya P, Bakris GL, Chin M, Christ-Schmidt H, Goldsberry A, Houser M, Krauth M, Lambers Heerspink HJ, McMurray JJ, Meyer CJ, Parving HH, Remuzzi G, Toto RD, Vaziri ND, Wanner C, Wittes J, Wrolstad D, Chertow GM, Investigators BT (2013) Bardoxolone methyl in type 2 diabetes and stage 4 chronic kidney disease. N Engl J Med 369:2492–2503

  9. Deeb D, Gao X, Jiang H, Dulchavsky SA, Gautam SC (2009) Oleanane triterpenoid CDDO-Me inhibits growth and induces apoptosis in prostate cancer cells by independently targeting pro-survival Akt and mTOR. Prostate 69:851–860

  10. Dzubak P, Hajduch M, Vydra D, Hustova A, Kvasnica M, Biedermann D, Markova L, Urban M, Sarek J (2006) Pharmacological activities of natural triterpenoids and their therapeutic implications. Nat Prod Rep 23:394–411

  11. Galiano V, Villalain J (2015) Oleuropein aglycone in lipid bilayer membranes. A molecular dynamics study. Biochim Biophys Acta 1848:2849–2858

  12. Galiano V, Villalain J (2016) The location of the protonated and unprotonated forms of arbidol in the membrane: a molecular dynamics study. J Membr Biol 249(3):381–391

  13. Gao X, Deeb D, Liu Y, Liu P, Zhang Y, Shaw J, Gautam SC (2015) CDDO-Me inhibits tumor growth and prevents recurrence of pancreatic ductal adenocarcinoma. Int J Oncol 47:2100–2106

  14. Gielen E, Smisdom N, van de Ven M, De Clercq B, Gratton E, Digman M, Rigo JM, Hofkens J, Engelborghs Y, Ameloot M (2009) Measuring diffusion of lipid-like probes in artificial and natural membranes by raster image correlation spectroscopy (RICS): use of a commercial laser-scanning microscope with analog detection. Langmuir 25:5209–5218

  15. Guixa-Gonzalez R, Rodriguez-Espigares I, Ramirez-Anguita JM, Carrio-Gaspar P, Martinez-Seara H, Giorgino T, Selent J (2014) MEMBPLUGIN: studying membrane complexity in VMD. Bioinformatics 30:1478–1480

  16. Hong DS, Kurzrock R, Supko JG, He X, Naing A, Wheler J, Lawrence D, Eder JP, Meyer CJ, Ferguson DA, Mier J, Konopleva M, Konoplev S, Andreeff M, Kufe D, Lazarus H, Shapiro GI, Dezube BJ (2012) A phase I first-in-human trial of bardoxolone methyl in patients with advanced solid tumors and lymphomas. Clin Cancer Res 18:3396–3406

  17. Huang Z, Mou Y, Xu X, Zhao D, Lai Y, Xu Y, Chen C, Li P, Peng S, Tian J, Zhang Y (2017) Novel derivative of bardoxolone methyl improves safety for the treatment of diabetic nephropathy. J Med Chem 60:8847–8857

  18. Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph 14(33–8):27–28

  19. Itokawa H, Morris-Natschke SL, Akiyama T, Lee KH (2008) Plant-derived natural product research aimed at new drug discovery. J Nat Med 62:263–280

  20. Jin UH, Cheng Y, Zhou B, Safe S (2017) Bardoxolone methyl and a related triterpenoid downregulate cMyc expression in leukemia cells. Mol Pharmacol 91:438–450

  21. Jorgensen WLC, Madura J, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926–935

  22. Kandt C, Ash WL, Tieleman DP (2007) Setting up and running molecular dynamics simulations of membrane proteins. Methods 41:475–488

  23. Kim S, Lee J, Jo S, Brooks CL 3rd, Lee HS, Im W (2017) CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. J Comput Chem 38:1879–1886

  24. Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, Mondragon-Ramirez C, Vorobyov I, MacKerell AD Jr, Pastor RW (2010) Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. J Phys Chem B 114:7830–7843

  25. Kopec W, Telenius J, Khandelia H (2013) Molecular dynamics simulations of the interactions of medicinal plant extracts and drugs with lipid bilayer membranes. FEBS J 280:2785–2805

  26. Kosinova P, Berka K, Wykes M, Otyepka M, Trouillas P (2012) Positioning of antioxidant quercetin and its metabolites in lipid bilayer membranes: implication for their lipid-peroxidation inhibition. J Phys Chem B 116:1309–1318

  27. Leth-Larsen R, Lund RR, Ditzel HJ (2010) Plasma membrane proteomics and its application in clinical cancer biomarker discovery. Mol Cell Proteom 9:1369–1382

  28. Liby KT, Sporn MB (2012) Synthetic oleanane triterpenoids: multifunctional drugs with a broad range of applications for prevention and treatment of chronic disease. Pharmacol Rev 64:972–1003

  29. Margina D, Ilie M, Manda G, Neagoe I, Mocanu M, Ionescu D, Gradinaru D, Ganea C (2012) Quercetin and epigallocatechin gallate effects on the cell membranes biophysical properties correlate with their antioxidant potential. Gen Physiol Biophys 31:47–55

  30. Mathis BJ, Cui T (2016) CDDO and its role in chronic diseases. Adv Exp Med Biol 929:291–314

  31. Mukhopadhyay P, Monticelli L, Tieleman DP (2004) Molecular dynamics simulation of a palmitoyl-oleoyl phosphatidylserine bilayer with Na+ counterions and NaCl. Biophys J 86:1601–1609

  32. Murzyn K, Rog T, Jezierski G, Takaoka Y, Pasenkiewicz-Gierula M (2001) Effects of phospholipid unsaturation on the membrane/water interface: a molecular simulation study. Biophys J 81:170–183

  33. Peron G, Marzaro G, Dall Acqua S (2018) Known triterpenes and their derivatives as scaffolds for the development of new therapeutic agents for cancer. Curr Med Chem 25:1259–1269

  34. Refaat A, Pararasa C, Arif M, Brown JE, Carmichael A, Ali SS, Sakurai H, Griffiths HR (2017) Bardoxolone-methyl inhibits migration and metabolism in MCF7 cells. Free Radic Res 51:211–221

  35. Samudio I, Konopleva M, Pelicano H, Huang P, Frolova O, Bornmann W, Ying Y, Evans R, Contractor R, Andreeff M (2006) A novel mechanism of action of methyl-2-cyano-3,12 dioxoolean-1,9 diene-28-oate: direct permeabilization of the inner mitochondrial membrane to inhibit electron transport and induce apoptosis. Mol Pharmacol 69:1182–1193

  36. Samudio I, Kurinna S, Ruvolo P, Korchin B, Kantarjian H, Beran M, Dunner K Jr, Kondo S, Andreeff M, Konopleva M (2008) Inhibition of mitochondrial metabolism by methyl-2-cyano-3,12-dioxooleana-1,9-diene-28-oate induces apoptotic or autophagic cell death in chronic myeloid leukemia cells. Mol Cancer Ther 7:1130–1139

  37. Schutters K, Reutelingsperger C (2010) Phosphatidylserine targeting for diagnosis and treatment of human diseases. Apoptosis 15:1072–1082

  38. Shanmugam MK, Dai X, Kumar AP, Tan BK, Sethi G, Bishayee A (2014) Oleanolic acid and its synthetic derivatives for the prevention and therapy of cancer: preclinical and clinical evidence. Cancer Lett 346:206–216

  39. Sheng H, Sun H (2011) Synthesis, biology and clinical significance of pentacyclic triterpenes: a multi-target approach to prevention and treatment of metabolic and vascular diseases. Nat Prod Rep 28:543–593

  40. The Pymol Molecular Graphics System, version 1.7.4. Schrödinger, LLC

  41. Tieleman DP, Marrink SJ, Berendsen HJ (1997) A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. Biochim Biophys Acta 1331:235–270

  42. Tsai HH, Lee JB, Li HS, Hou TY, Chu WY, Shen PC, Chen YY, Tan CJ, Hu JC, Chiu CC (2015) Geometrical effects of phospholipid olefinic bonds on the structure and dynamics of membranes: A molecular dynamics study. Biochim Biophys Acta 1848:1234–1247

  43. Tsuchiya H (2015) Membrane interactions of phytochemicals as their molecular mechanism applicable to the discovery of drug leads from plants. Molecules 20:18923–18966

  44. Utsugi T, Schroit AJ, Connor J, Bucana CD, Fidler IJ (1991) Elevated expression of phosphatidylserine in the outer membrane leaflet of human tumor cells and recognition by activated human blood monocytes. Cancer Res 51:3062–3066

  45. van Meer G, Voelker DR, Feigenson GW (2008) Membrane lipids: where they are and how they behave. Nat Rev Mol Cell Biol 9:112–124

  46. Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD Jr (2010) CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem 31:671–690

  47. Villalain J (2019) Epigallocatechin-3-gallate location and interaction with late endosomal and plasma membrane model membranes by molecular dynamics. J Biomol Struct Dyn 37:3122–3134

  48. Wang Y, Markwick PR, de Oliveira CA, McCammon JA (2011) Enhanced lipid diffusion and mixing in accelerated molecular dynamics. J Chem Theory Comput 7:3199–3207

  49. Wang XY, Zhang XH, Peng L, Liu Z, Yang YX, He ZX, Dang HW, Zhou SF (2017) Bardoxolone methyl (CDDO-Me or RTA402) induces cell cycle arrest, apoptosis and autophagy via PI3K/Akt/mTOR and p38 MAPK/Erk1/2 signaling pathways in K562 cells. Am J Transl Res 9:4652–4672

  50. Wang YY, Zhe H, Zhao R (2014) Preclinical evidences toward the use of triterpenoid CDDO-Me for solid cancer prevention and treatment. Mol Cancer 13:30

  51. Wu EL, Cheng X, Jo S, Rui H, Song KC, Davila-Contreras EM, Qi Y, Lee J, Monje-Galvan V, Venable RM, Klauda JB, Im W (2014) CHARMM-GUI Membrane Builder toward realistic biological membrane simulations. J Comput Chem 35:1997–2004

  52. Yore MM, Kettenbach AN, Sporn MB, Gerber SA, Liby KT (2011) Proteomic analysis shows synthetic oleanane triterpenoid binds to mTOR. PLoS ONE 6:e22862

  53. Zalba S, Ten Hagen TL (2017) Cell membrane modulation as adjuvant in cancer therapy. Cancer Treat Rev 52:48–57

Download references


We would like to thank Prof. T. Giorgino for his invaluable help using the VMD Diffusion Coefficient plugin. NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champain. We are very grateful to SIATDI, Universidad Miguel Hernández (UMH) for the generous use of the UMH Computer Cluster. This work was not funded by any external or internal funding agencies.

Author information

Correspondence to José Villalaín.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary file1 (PDF 1194 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Galiano, V., Encinar, J.A. & Villalaín, J. Location, Orientation and Aggregation of Bardoxolone-ME, CDDO-ME, in a Complex Phospholipid Bilayer Membrane. J Membrane Biol (2020).

Download citation


  • Bardoxolone methyl
  • CDDO-me
  • Molecular dynamics
  • Membrane location