Skip to main content
SpringerLink
Log in

A Molecular Dynamics Study Proposing the Existence of Structural Interaction Between Cancer Cell Receptor and RNA Aptamer

  • Published:
Journal of Inorganic and Organometallic Polymers and Materials Aims and scope Submit manuscript

Abstract

The (1 1 0) facet of TiO2 nanosheet was used as drug carrier to deliver the RNA aptamer using molecular dynamics simulation. The molecular simulations had been performed using NAMD. We have measured energetic and structural parameters. The centre of mass of receptor and aptamer, the RMSF, RMSD and DSSP of protein and the attractive forces were computed. We had considered the water molecules effect along the adsorption. Results show that aptamer can interact with receptor in the absence and also presence of TiO2 nanosheet. Besides, the superior interaction between receptor and aptamer was observed when aptamer detached from nanosheet.

Graphic Abstract

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

Similar content being viewed by others

References

  1. J. Stamos, M.X. Sliwkowski, C. Eigenbrot, Structure of the epidermal growth factor receptor kinase domain alone and in complex with a 4-anilinoquinazoline inhibitor. J. Biol. Chem. 277, 46265–46272 (2002)

    CAS  PubMed  Google Scholar 

  2. M.A. Lemmon, J. Schlessinger, Cell signaling by receptor tyrosine kinases. Cell 141, 1117–1134 (2010)

    CAS  PubMed  PubMed Central  Google Scholar 

  3. S.R. Hubbard, Juxtamembrane autoinhibition in Receptor Tyrosine Kinases. Nat. Rev. Mol. Cell. Biol. 5, 464–470 (2004)

    CAS  PubMed  Google Scholar 

  4. S.R. Hubbard, Structural analysis of receptor tyrosine kinases. Prog. Biophys. Mol. Biol. 71, 343–358 (1999)

    CAS  PubMed  Google Scholar 

  5. Z. Zhao, W.H. Leister, R.G. Robinson, S.F. Barnett, D.D. Jones, R.E. Jones, G.D. Hartman, J.R. Huff, H.E. Huber, M.E. Duggan, C.W. Lindsley, Discovery of 2,3,5-trisubstituted pyridine derivatives as potent Akt1 and Akt2 dual inhibitors. Med. Chem. Lett. 15, 905–909 (2005)

    CAS  Google Scholar 

  6. S.R. Hubbard, J.H. Till, Protein tyrosine kinase structure and function. Annu. Rev. Biochem. 69, 373–398 (2000)

    CAS  PubMed  Google Scholar 

  7. I.D. Campbell, P. Bork, Epidermal growth factor-like modules. Curr. Opin. Struct. Biol. 3, 385–392 (1993)

    CAS  Google Scholar 

  8. B.W. Jester, K.J. Cox, A. Gaj, C.D. Shomin, J.R. Porter, I. Ghosh, A coiled-coil enabled split-luciferase three-hybrid system: applied towards profiling inhibitors of protein kinases. J. Am. Chem. Soc. 132, 11727–11735 (2010)

    CAS  PubMed  PubMed Central  Google Scholar 

  9. W.J. Gullick, The type 1 growth factor receptors and their ligands considered as a complex system. Endocr. Relat. Cancer 8, 75–82 (2001)

    CAS  PubMed  Google Scholar 

  10. J. Schlessinger, Cell signaling by receptor tyrosine kinases. Cell 103, 211–225 (2000)

    CAS  PubMed  Google Scholar 

  11. M. McTigue, B.M. Murray, J.H. Chen, Y.L. Deng, J. Solowiej, R.S. Kania, Molecular conformations, interactions, and properties associated with drug efficiency and clinical performance among VEGFR TK inhibitors. Proc. Natl. Acad. Sci. 109, 18281–18289 (2012)

    CAS  PubMed  Google Scholar 

  12. E. Arighi, M.G. Borrello, H. Sariola, RET tyrosine kinase signaling in development and cancer. Cytokine Growth Factor Rev. 16, 441–467 (2005)

    CAS  PubMed  Google Scholar 

  13. F. Caiazza, E.J. Ryan, G. Doherty, D.C. Winter, K. Sheahan, Estrogen receptors and their implications in colorectal carcinogenesis. J. Front. Oncol. 2, 5–19 (2015)

    Google Scholar 

  14. A. Ostman, F.D. Bohmer, Regulation of receptor tyrosine kinase signaling by protein tyrosine phosphatases. Trends. Cell. Biol. 11, 258–266 (2001)

    CAS  PubMed  Google Scholar 

  15. R. Mansouri, A. Azadbakht, Correction to: aptamer-based approach as potential tools for construction the electrochemical aptasensor. J. Inorg. Organomet. Polym. 29, 643 (2019)

    CAS  Google Scholar 

  16. R. Mansouri, A. Azadbakht, Aptamer-based approach as potential tools for construction the electrochemical aptasensor. J. Inorg. Organomet. Polym. 29, 517–527 (2019)

    CAS  Google Scholar 

  17. K. Germer, M. Leonard, X. Zhang, RNA aptamer and their therapeutic and diagnostic application. Int. J. Biochem. Mol. Biol. 4, 27–40 (2013)

    CAS  PubMed  PubMed Central  Google Scholar 

  18. A.D. Ellington, J.W. Szostak, In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818–822 (1990)

    CAS  PubMed  Google Scholar 

  19. A. Rudolph, C. Toth, M. Hoffmeister, W. Roth, E. Herpel, L. Jansen et al., Expression of oestrogen receptor β and prognosis of colorectal cancer. Br. J. Cancer 107, 831–839 (2012)

    CAS  PubMed  PubMed Central  Google Scholar 

  20. M. Habibzadeh Mashatooki, J. Jahanbin Sardroodi, A. Rastkar Ebrahimzadeh, The boron nitride nanotube, an ideal host structure for efficient immobilization and delivery of RNA aptamer: classical molecular dynamics simulation. J. Inorg. Organomet. Polym. 30, 789–800 (2020)

    CAS  Google Scholar 

  21. B.M. Warfield, P.C. Anderson, Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state. PLoS ONE 12, 0176229 (2017)

    Google Scholar 

  22. W.C. Winkler, R.R. Breaker, Regulation of bacterial gene expression by riboswitches. Annu. Rev. Microbiol. 59, 487–517 (2005)

    CAS  PubMed  Google Scholar 

  23. R.R. White, B.A. Sullenger, C.P. Rusconi, Developing aptamers into therapeutics. J. Clin. Invest. 106, 929–934 (2000)

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Y. Morita, M. Leslie, H. Kameyama, D. Volk, T. Tanaka, Aptamer therapeutics in cancer: current and future. Cancers 10, 80 (2018)

    PubMed Central  Google Scholar 

  25. M. Ilgu, J. Ray, L. Bendickson, T. Wang, I.M. Geraskin, G.A. Kraus, M. Nilsen-Hamilton, Light-up and FRET aptamer reporters; evaluating their applications for imaging transcription in eukaryotic cells. Methods 98, 26–33 (2016)

    CAS  PubMed  Google Scholar 

  26. M. Habibzadeh Mashatooki, J. Jahanbin Sardroodi, A. Rastkar Ebrahimzadeh, Molecular dynamics investigation of the interactions between RNA aptamer and graphene-monoxide/boron-nitride surfaces: applications to novel drug delivery systems. J. Inorg. Organomet. Polym. 29, 1252–1264 (2019)

    CAS  Google Scholar 

  27. A. Autour, E. Westhof, M. Ryckelynck, iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications. Nucleic Acids Res. 44, 2491–2500 (2016)

    PubMed  PubMed Central  Google Scholar 

  28. L. Cerchia, Aptamers: promising tools for cancer diagnosis and therapy. Cancers 10, 132 (2018)

    PubMed Central  Google Scholar 

  29. N. Li, H.H. Nguyen, M. Byrom, A.D. Ellington, Inhibition of cell proliferation by an anti- EGFR aptamer. PLoS ONE 6, 20299 (2011)

    Google Scholar 

  30. J. Bala, S. Chinnapaiyan, R.K. Dutta, H. Unwalla, Aptamers in HIV research diagnosis and therapy. RNA Biol. 15, 327–337 (2018)

    PubMed  PubMed Central  Google Scholar 

  31. X. Yu, S. Ghamande, H. Liu, L. Xue, S. Zhao, W. Tan, L. Zhao, S.C. Tang, D. Wu, H. Korkaya, N.J. Maihle, H.Y. Liu, Targeting EGFR/HER2/HER3 with a three-in-one aptamer-siRNA chimera confers superior activity against HER2 + breast cancer. Mol. Ther. Nucleic Acids 10, 317–330 (2018)

    CAS  PubMed  Google Scholar 

  32. V. Romanucci, A. Zarrelli, S. Liekens, S. Noppen, C. Pannecouque, G. Di Fabio, New findings on the d(TGGGAG) sequence: surprising anti-HIV-1 activity. Eur. J. Med. Chem. 145, 425–430 (2018)

    CAS  PubMed  Google Scholar 

  33. J.L. Henri, J. Macdonald, M. Strom, W. Duan, S. Shigdar, Aptamers as potential therapeutic agents for ovarian cancer. Biochimie 145, 34–44 (2018)

    CAS  PubMed  Google Scholar 

  34. M. Salazar-Villanueva, A.B. Hernandez, J.J.Q. Briones, E.C. Anota, F.S. Carrillo, Influence of doping on chain-like TiO2 clusters: a DFT study. Curr. Appl. Phys. 16, 197–206 (2016)

    Google Scholar 

  35. S. Haq, W. Rehman, M. Waseem, Adsorption efficiency of anatase TiO2 nanoparticles against cadmium ions. J. Inorg. Organomet. Polym. 29, 651–658 (2019)

    CAS  Google Scholar 

  36. Z. Fei Yin, L. Wu, H. Gui Yang, Y. Hua Su, Recent progress in biomedical applications of titanium dioxide. Phys. Chem. Chem. Phys. 15, 4844 (2013)

    Google Scholar 

  37. T. Zhang, Z. Dai, B. Liang, Y. Mu, Facile synthesis of SnO2/SiC nanosheets for photocatalytic degradation of MO. J. Inorg. Organomet. Polym. (2020). https://doi.org/10.1007/s10904-020-01702-7

    Article  Google Scholar 

  38. J.I. Jung, S.R. Han, S.W. Lee, Development of RNA aptamer that inhibits methyltransferase activity of dengue virus. Biotechnol. Lett. 40, 315–324 (2018)

    CAS  PubMed  Google Scholar 

  39. Z. Liang, D. Huang, L. Zhao, Y. Nie, Z. Zhou, T. Hao, S. Li, Self-healing polyurethane elastomer based on molecular design: combination of reversible hydrogen bonds and high segment mobility. J. Inorg. Organomet. Polym. (2020). https://doi.org/10.1007/s10904-020-01697-1

    Article  Google Scholar 

  40. M. Setvin, X. Hao, B. Daniel, J. Pavelec, U. Diebold, Charge trapping at the step edges of TiO2 anatase (101). Angew. Chem. Int. Ed. 53, 4714–4716 (2014)

    CAS  Google Scholar 

  41. X. Chen, S.S. Mao, Titanium dioxide nanomaterials: synthesis, properties, modifications, and applications. Chem. Rev. 107, 2891–2959 (2007)

    CAS  PubMed  Google Scholar 

  42. M.R. Ranade, A. Navrotsky, H.Z. Zhang, J.F. Banfield, S.H. Elder, A. Zaban, P.H. Borse, S.K. Kulkarni, G.S. Doran, H.J. Whitfield, Energetics of nanocrystalline TiO2. Proc. Natl. Acad. Sci. 99, 6476–6481 (2002)

    CAS  PubMed  Google Scholar 

  43. H. Zhang, J.F. Banfield, Structural characteristics and mechanical and thermodynamic properties of nanocrystalline TiO2. Chem. Rev. 114, 9613–9644 (2014)

    CAS  PubMed  Google Scholar 

  44. U. Diebold, The surface science of titanium dioxide. Surf. Sci. Rep. 48, 53–229 (2003)

    CAS  Google Scholar 

  45. R.S. Kavathekar, P. Dev, N.J. English, J.M.D. MacElroy, Molecular dynamics study of water in contact with TiO2 rutile-110, 100, 101, 001 and anatase-101, 001 surface. Mol. Phys. 109, 1649–1656 (2011)

    CAS  Google Scholar 

  46. K.H. Choi, Intracellular expression of the T-cell factor-1 RNA aptamer as an intramer. Mol. Cancer Ther. 5, 2428–2434 (2006)

    CAS  PubMed  Google Scholar 

  47. J. Mi, Y. Liu, Z.N. Rabbani, Z. Yang, J.H. Urban, B.A. Sullenger, B.M. Clary, In vivo selection of tumor-targeting RNA motifs. Nat. Chem. Biol. 6, 22–24 (2010)

    CAS  PubMed  Google Scholar 

  48. M. Habibzadeh Mashatooki, A. Rastkar Ebrahimzadeh, J. Jahanbin Sardroodi, A. Abbasi, Investigation of TiO2 anatase (1 0 1), (1 0 0) and (1 1 0) facets as immobilizer for a potential anticancer RNA aptamer: a classical molecular dynamics simulation. Mol. Simul. 45, 849–858 (2019)

    CAS  Google Scholar 

  49. M. Habibzadeh Mashatooki, A. Abbasi, J. Jahanbin Sardroodi, In silico studies of the interaction between colon cancer receptor and RNA aptamer in complex with (1 0 1) facet of TiO2 nanosheet: a molecular dynamics study. Adsorption 26, 941–954 (2020)

    CAS  Google Scholar 

  50. H.K. Lee, Y.S. Choi, Y.A. Park, S. Jeong, Modulation of oncogenic transcription and alternative splicing by -catenin and an RNA aptamer in colon cancer cells. Cancer Res. 66, 10560–10566 (2006)

    CAS  PubMed  Google Scholar 

  51. A. Xayaphoummine, T. Bucher, H. Isambert, Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucleic Acids Res. 33, 605–610 (2005)

    Google Scholar 

  52. M. Magnus, M.J. Boniecki, W. Dawson, J.M. Bujnicki, SimRNAweb: a web server for RNA 3D structure modeling with optional restraints. Nucleic Acids Res. 44, 315–319 (2016)

    Google Scholar 

  53. American mineralogist crystal structure database. (n.d.). https://rruff.geo.arizona.edu/AMS/amcsd.php. Accessed 8 June 2018

  54. S. Fleming, A. Rohl, GDIS: a visualization program for molecular and periodic systems. Z. Kristallogr. Cryst. Mater. 220, 580–584 (2005)

    CAS  Google Scholar 

  55. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kalé, K. Schulten, Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781–1802 (2005)

    CAS  PubMed  PubMed Central  Google Scholar 

  56. K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, A.D. Mackerell, 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 (2009)

    Google Scholar 

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

    CAS  PubMed  Google Scholar 

  58. R. Kubo, M. Toda, N. Hashitsume, Statistical physics II: nonequi- librium statistical mechanics, 2nd edn. (Springer, New York, 1991)

    Google Scholar 

  59. S.E. Feller, Y. Zhang, R.W. Pastor, B.R. Brooks, Constant pressure molecular dynamics simulation: the langevin piston method. J. Chem. Phys. 103, 4613 (1995)

    CAS  Google Scholar 

  60. T. Sakamoto, E. Ennifar, Y. Nakamura, Thermodynamic study of aptamers binding to their target proteins. Biochimie 145, 91–97 (2017)

    PubMed  Google Scholar 

  61. A.D. Gelinas, D.R. Davies, N. Janjic, Embracing proteins: structural themes in aptamer-protein complexes. Curr. Opin. Struct. Biol. 36, 122–132 (2016)

    CAS  PubMed  Google Scholar 

  62. N. Bjerregaard, P.A. Andreasen, D.M. Dupont, Expected and unexpected features of protein-binding RNA aptamers. WIREs RNA 7, 744–757 (2016)

    CAS  PubMed  Google Scholar 

  63. Y. Wang, Z. Li, T.J. Weber, D. Hu, C.T. Lin, J. Li, Y. Lin, In situ live cell sensing of multiple nucleotides exploiting DNA/RNA aptamers and graphene oxide Nanosheets. Anal. Chem. 85, 6775–6782 (2013)

    CAS  PubMed  Google Scholar 

  64. D.A. McQuarrie, Statistical thermodynamics (University Science Books, Mill Valley, 1984)

    Google Scholar 

  65. E. Heydari-Bafrooei, M. Amini, M. HatefiArdakani, An electrochemical aptasensor based on TiO2/MWCNT and a novel synthesized Schiff base nanocomposite for the ultrasensitive detection of thrombin. Biosens Bioelectron. 85, 828–836 (2016)

    CAS  PubMed  Google Scholar 

Download references

Funding

Present work was supported by Azarbaijan Shahid Madani University.

Author information

Authors and Affiliations

  1. Molecular Simulation Laboratory (MSL), Azarbaijan Shahid Madani University, Tabriz, Iran

    Mohaddeseh Habibzadeh Mashatooki & Jaber Jahanbin Sardroodi

  2. Computational Nanomaterials Research Group (CNRG), Azarbaijan Shahid Madani University, Tabriz, Iran

    Mohaddeseh Habibzadeh Mashatooki & Jaber Jahanbin Sardroodi

  3. Department of Chemistry, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran

    Mohaddeseh Habibzadeh Mashatooki & Jaber Jahanbin Sardroodi

Authors
  1. Mohaddeseh Habibzadeh Mashatooki
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jaber Jahanbin Sardroodi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Mohaddeseh Habibzadeh Mashatooki or Jaber Jahanbin Sardroodi.

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 (DOCX 24 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Habibzadeh Mashatooki, M., Jahanbin Sardroodi, J. A Molecular Dynamics Study Proposing the Existence of Structural Interaction Between Cancer Cell Receptor and RNA Aptamer. J Inorg Organomet Polym 30, 4520–4532 (2020). https://doi.org/10.1007/s10904-020-01740-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10904-020-01740-1

Keywords

Search

Navigation