Skip to main content

Advertisement

SpringerLink
Log in

Investigation of the effect of external force and initial pressure on the stability of cancer cells using molecular dynamics simulation

  • Regular Article
  • Published:
The European Physical Journal Plus Aims and scope Submit manuscript

Abstract

Investigation of the behavior of cancer cells and their mechanical and physical characteristics can play an important role in the early diagnosis and treatment of cancer. In this paper, the molecular dynamics method (MDM) investigates cancer cells' atomic behavior and stability under different external forces and initial pressures. To investigate the atomic behavior of the simulated structures, the parameters of gyration radius, interaction energy, and interaction force were studied. The results show that by increasing the external force to 0.05 kcal/mol Å, the radius of gyration increases to 0.49 Å. Also, with the application of external force, interaction energy and force increase to − 533.44 kcal/mol and − 190.06 kcal/mol Å. In addition, increasing the initial pressure up to 5 bar changes the mentioned quantities of the radius of gyration, interaction energy, and interaction force to 68.46 Å, − 535.55 kcal/mol, − 195.44 kcal/mol Å, respectively. Since structures' atomic behavior and stability are important factors in diagnosing any disease, we expect that the MDM performed in this paper will be useful in treating and preventing diseases, including cancer.

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
Fig. 10
Fig. 11

Similar content being viewed by others

References

  1. Y. Feng, F. Li, J. Yan, X. Guo, F. Wang, H. Shi et al., Pan-cancer analysis and experiments with cell lines reveal that the slightly elevated expression of DLGAP5 is involved in clear cell renal cell carcinoma progression. Life Sci. (1973) 287, 120056 (2021). https://doi.org/10.1016/j.lfs.2021.120056

    Article  Google Scholar 

  2. Q. Jiang, Q. Jiang, S. Jin, S. Jin, Y. Jiang, Y. Jiang et al., Alzheimer’s disease variants with the genome-wide significance are significantly enriched in immune pathways and active in immune cells. Mol. Neurobiol. 54(1), 594–600 (2017). https://doi.org/10.1007/s12035-015-9670-8

    Article  Google Scholar 

  3. V.N. Tsarev, R.V. Ushakov, E.V. Ippolitov, M.S. Sarkisyan, T.V. Tsareva, T.P. Gerasimova, A.R. Ushakov, E.N. Nikolaeva, Significance of the interrelations of cardiovascular diseases with anaerobic bacteria of subgingival biofilm. J. Pharm. Negat. Results 12(1), 33–37 (2021). https://doi.org/10.47750/pnr.2021.12.01.006

    Article  Google Scholar 

  4. S. Srivatchava, S. Anitha Roy, S. Rajesh Kumar, S. Raghunandhakumar, L. Thangavelu, Biosynthesis of selenium nanoparticles using cassia oleoresin and its anticancer activity against liver cancer cell lines. J. Complem. Med. Res. 12(4), 48–54 (2021). https://doi.org/10.5455/jcmr.2021.12.04.07

    Article  Google Scholar 

  5. M.B. Patil, T. Lavanya, C.M. Kumari, S.R. Shetty, K. Gufran, V. Viswanath, C. Swarnalatha, J.S. Babu, A.S. Nayyar, Serum ceruloplasmin as cancer marker in oral pre-cancers and cancers. J. Carcinog. 20, 15 (2021)

    Article  Google Scholar 

  6. R.A. Siddeek, A. Gupta, S. Gupta, B. Goyal, A.K. Gupta, S. Agrawal, R. Roshan, U. Kumar, N. Kumar, M. Gupta, S. Kishore, R. Kant, Evaluation of platelet distribution width as novel biomarker in gall bladder cancer. J Carcinog 19, 5 (2020)

    Article  Google Scholar 

  7. N.O. Mousa, M. Gado, A. Osman, Multimodality of human epidermal growth factor receptor-2 antagonism restores the apoptotic capacity of liver cancer cells. J. Nat. Sci. Biol. Med. 17(4), 5213–5221 (2020)

    Google Scholar 

  8. P. Singh, D. Augustine, R.S. Rao, S. Patil, K.H. Awan, S.V. Sowmya, V.C. Haragannavar, K. Prasad, Role of cancer stem cells in head-and-neck squamous cell carcinoma—a systematic review. J. Carcinog. 20, 12 (2021)

    Article  Google Scholar 

  9. S.S. Shetty, M. Sharma, S.P. Kabekkodu, N.V. Anil Kumar, K. Satyamoorthy, R. Radhakrishnan, Understanding the molecular mechanism associated with reversal of oral submucous fibrosis targeting hydroxylysine aldehyde-derived collagen cross-links. J Carcinog 20, 9 (2021)

    Article  Google Scholar 

  10. Q. Zou, P. Xing, L. Wei, B. Liu, Gene2vec: gene subsequence embedding for prediction of mammalian N 6 -methyladenosine sites from mRNA. RNA (Cambridge) 25(2), 205–218 (2019). https://doi.org/10.1261/rna.069112.118

    Article  Google Scholar 

  11. L. Chen, Y. Huang, X. Yu, J. Lu, W. Jia, J. Song, M. Li, Corynoxine protects dopaminergic neurons through inducing autophagy and diminishing neuroinflammation in rotenone-induced animal models of Parkinson’s disease. Front. Pharmacol. 12, 642900 (2021). https://doi.org/10.3389/fphar.2021.642900

    Article  Google Scholar 

  12. J. Yan, Y. Yao, S. Yan, R. Gao, W. Lu, Chiral protein supraparticles for tumor suppression and synergistic immunotherapy: an enabling strategy for bioactive supramolecular chirality construction. Nano Lett. 20(8), 5844–5852 (2020). https://doi.org/10.1021/acs.nanolett.0c01757

    Article  ADS  Google Scholar 

  13. S. Ebrahimi, M. Tahmasebipour, Numerical study of a centrifugal platform for the inertial separation of circulating tumor cells using contraction-expansion array microchannels. Arch. Razi Inst. 77(2), 647–660 (2022). https://doi.org/10.22092/ari.2022.357477.2046

    Article  Google Scholar 

  14. I. Ellinger, A. Ellinger, Smallest unit of life cell biology, Comparative medicine (Springer, Berlin, 2014), pp.19–33

    Google Scholar 

  15. T. Kamperman, M. Karperien, S. Le Gac, J. Leijten, Single-cell microgels: technology, challenges, and applications. Trends Biotechnol. 36(8), 850–865 (2018)

    Article  Google Scholar 

  16. P.L. Yeagle, Cholesterol and the cell membrane. Biochim. Biophy. Acta Rev. Biomemb. 822(3–4), 267–287 (1985)

    Article  Google Scholar 

  17. C.L. Chaffer, R.A. Weinberg, A perspective on cancer cell metastasis. Science 331(6024), 1559–1564 (2011)

    Article  ADS  Google Scholar 

  18. M. Lekka, K. Pogoda, J. Gostek, O. Klymenko, S. Prauzner-Bechcicki, J. Wiltowska-Zuber, J. Jaczewska, J. Lekki, Z. Stachura, Cancer cell recognition–mechanical phenotype. Micron 43(12), 1259–1266 (2012)

    Article  Google Scholar 

  19. S. Suresh, Biomechanics and biophysics of cancer cells. Acta Mater. 55(12), 3989–4014 (2007)

    Article  ADS  Google Scholar 

  20. M.F. Leber, T. Efferth, Molecular principles of cancer invasion and metastasis. Int. J. Oncol. 34(4), 881–895 (2009)

    Google Scholar 

  21. J.R. Heath, M.E. Davis, Nanotechnology and cancer. Annu. Rev. Med. 59, 251–265 (2008)

    Article  Google Scholar 

  22. F. Alexis, J.-W. Rhee, J.P. Richie, A.F. Radovic-Moreno, R. Langer, O.C. Farokhzad, New frontiers in nanotechnology for cancer treatment. Urol. Oncol. Semin. Orig. Investig. 26, 74–85 (2008)

    Google Scholar 

  23. R. Misra, S. Acharya, S.K. Sahoo, Cancer nanotechnology: application of nanotechnology in cancer therapy. Drug Discov. Today 15(19–20), 842–850 (2010)

    Article  Google Scholar 

  24. X. Wang, L. Yang, Z. Chen, D.M. Shin, Application of nanotechnology in cancer therapy and imaging. CA Cancer J. Clin. 58(2), 97–110 (2008)

    Article  Google Scholar 

  25. N. Dehneshin, H. Raissi, Z. Hasanzade, F. Farzad, Using molecular dynamics simulation to explore the binding of the three potent anticancer drugs sorafenib, streptozotocin, and sunitinib to functionalized carbon nanotubes. J. Mol. Model. 25(6), 1–15 (2019)

    Article  Google Scholar 

  26. X. Liu, W. Tian, J. Cheng, D. Li, T. Liu, L. Zhang, Microsecond molecular dynamics simulations reveal the allosteric regulatory mechanism of p53 R249S mutation in p53-associated liver cancer. Comput. Biol. Chem. 84, 107194 (2020)

    Article  Google Scholar 

  27. S. Srivastava, A. Pandey, Computational screening of anticancer drugs targeting miRNA155 synthesis in breast cancer. Ind. J. Biochem. Biophys. 57, 389–394 (2020)

    Google Scholar 

  28. G. Zaccai, Molecular dynamics in cells: a neutron view. Biochim. Biophys. Acta (BBA) General Sub. 1864(3), 129475 (2020)

    Article  Google Scholar 

  29. L. Liang, J.-W. Shen, Q. Wang, Molecular dynamics study on DNA nanotubes as drug delivery vehicle for anticancer drugs. Coll. Surf. B 153, 168–173 (2017)

    Article  Google Scholar 

  30. D.K. Yadav, S. Kumar, E.-H. Choi, P. Sharma, S. Misra, M.-H. Kim, Insight into the molecular dynamic simulation studies of reactive oxygen species in native skin membrane. Front. Pharmacol. 9, 644 (2018)

    Article  Google Scholar 

  31. H. Shaki, H. Raissi, F. Mollania, H. Hashemzadeh, Modeling the interaction between anti-cancer drug penicillamine and pristine and functionalized carbon nanotubes for medical applications: density functional theory investigation and a molecular dynamics simulation. J. Biomol. Struct. Dyn. 38, 1322–1334 (2019)

    Article  Google Scholar 

  32. N.A. Alsaif, T.A. Wani, A.H. Bakheit, S. Zargar, Multi-spectroscopic investigation, molecular docking and molecular dynamic simulation of competitive interactions between flavonoids (quercetin and rutin) and sorafenib for binding to human serum albumin. Int. J. Biol. Macromol. 165, 2451–2461 (2020)

    Article  Google Scholar 

  33. Z. Hasanzade, H. Raissi, Density functional theory calculations and molecular dynamics simulations of the adsorption of ellipticine anticancer drug on graphene oxide surface in aqueous medium as well as under controlled pH conditions. J. Mol. Liq. 255, 269–278 (2018)

    Article  Google Scholar 

  34. M. Shahabi, H. Raissi, Payload delivery of anticancer drug Tegafur with the assistance of graphene oxide nanosheet during biomembrane penetration: Molecular dynamics simulation survey. Appl. Surf. Sci. 517, 146186 (2020)

    Article  Google Scholar 

  35. S. Karimzadeh, B. Safaei, T.-C. Jen, Investigate the importance of mechanical properties of SWCNT on doxorubicin anti-cancer drug adsorption for medical application: a molecular dynamic study. J Mol Graph Model 101(2020), 107745 (2020)

    Article  Google Scholar 

  36. N. Semenova, V.V. Tuchin, 3D models of the dynamics of cancer cells under external pressure. Chaos Interdiscip. J. Nonlinear Sci. 31(8), 083122 (2021)

    Article  MathSciNet  Google Scholar 

  37. W. Yu, S. Sharma, E. Rao, A.C. Rowat, J.K. Gimzewski, D. Han, J. Rao, Cancer cell mechanobiology: a new frontier for cancer research. J. Natl. Cancer Center 2, 10–17 (2021)

    Article  Google Scholar 

  38. B.L. Ricca, G. Venugopalan, S. Furuta, K. Tanner, W.A. Orellana, C.D. Reber, D.G. Brownfield, M.J. Bissell, D.A. Fletcher, Transient external force induces phenotypic reversion of malignant epithelial structures via nitric oxide signaling. Elife 7, e26161 (2018)

    Article  Google Scholar 

  39. J.M. Haile, I. Johnston, A.J. Mallinckrodt, S. McKay, Molecular dynamics simulation: elementary methods. Comput. Phys. 7(6), 625–625 (1993)

    Article  ADS  Google Scholar 

  40. K. Binder, Monte Carlo and Molecular Dynamics Simulations in Polymer Science (Oxford University Press, Oxford, 1995)

    Google Scholar 

  41. M. Allen, D. Tildesley, Computer Simulation of Liquids (Clarendon Press, Oxford, 1987)

    MATH  Google Scholar 

  42. D. Frenkel, B. Smit, M.A. Ratner, Understanding Molecular Simulation: From Algorithms to Applications (Academic press, San Diego, 1996)

    MATH  Google Scholar 

  43. J.E. Lennard-Jones, On the determination of molecular fields. II. From the equation of state of gas. Proc. Roy. Soc. A 106, 463–477 (1924)

    ADS  Google Scholar 

  44. H. Berendsen, J. Grigera, T. Straatsma, The missing term in effective pair potentials. J. Phys. Chem. 91(24), 6269–6271 (1987)

    Article  Google Scholar 

  45. A.K. Rappé, C.J. Casewit, K. Colwell, W.A. Goddard III., W.M. Skiff, UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations. J. Am. Chem. Soc. 114(25), 10024–10035 (1992)

    Article  Google Scholar 

  46. M. Tohidi, D. Toghraie, The effect of geometrical parameters, roughness and the number of nanoparticles on the self-diffusion coefficient in Couette flow in a nanochannel by using of molecular dynamics simulation. Physica B 518, 20–32 (2017)

    Article  ADS  Google Scholar 

  47. H. Noorian et al., Molecular dynamics simulation of Poiseuille flow in a rough nano channel with checker surface roughnesses geometry. Heat Mass Transf. 50(1), 105–113 (2014)

    Article  ADS  Google Scholar 

  48. H. Noorian et al., The effects of surface roughness geometry of flow undergoing Poiseuille flow by molecular dynamics simulation. Heat Mass Transf. 50(1), 95–104 (2014)

    Article  ADS  Google Scholar 

Download references

Acknowledgements

Not applicable.

Funding

Not applicable.

Author information

Authors and Affiliations

  1. Department of Biomedical Engineering, Khomeinishahr Branch, Islamic Azad University, Khomeinishahr, Iran

    Ali Asghar Kamali Kashab, Alireza Seifzadeh & Seyed Iman Mousavian

  2. Department of Mechanical Engineering, Khomeinishahr Branch, Islamic Azad University, Khomeinishahr, Iran

    Davood Toghraie & Ali Mokhtarian

Authors
  1. Ali Asghar Kamali Kashab
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alireza Seifzadeh
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Davood Toghraie
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Ali Mokhtarian
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Seyed Iman Mousavian
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Not applicable.

Corresponding authors

Correspondence to Alireza Seifzadeh or Davood Toghraie.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest statement.

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Availability of data and materials

Not applicable.

Rights and permissions

Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kashab, A.A.K., Seifzadeh, A., Toghraie, D. et al. Investigation of the effect of external force and initial pressure on the stability of cancer cells using molecular dynamics simulation. Eur. Phys. J. Plus 137, 952 (2022). https://doi.org/10.1140/epjp/s13360-022-03192-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1140/epjp/s13360-022-03192-7

Search

Navigation