Molecular dynamics simulation of interaction of the anti-cancer drug paclitaxel with the cell membrane: investigation of changes in van der Waals energy and center of mass

Document Type : Chemistry Article

Authors

1 MSc student/University of Tehran

2 Assistant Professor/University of Tehran

3 Assistant professor/University of Tehran

Abstract

Due to increasing of cancers and production of new anti-cancer drugs for its treatment, in this study, the interaction of new hydrophobic anti-cancer drug paclitaxel with the cell membrane has been discussed using computational tools. We have done molecular dynamics simulation using NAMD and also the initial structures that were achieved from the protein data bank have been modified using VMD package. Langevin algorithm was used for temperature control in 310 K, the human body temperature and the Brandson algorithm was utilized for pressure control in 1 bar. The simulation has been done during 10 ns. The simulation equations were based on Newton’s Motion Law and a Lenard−Jones potential. The anti-cancer drug paclitaxel interaction with the cell membrane has been investigated from the van der Waals energy and center of mass (COM) perspectives that show less stability and low absorption of the drug to the cell membrane. Computational results of this study confirm the validity of previously published computational and laboratory studies. According to the drug hydrophobicity, less stability, low absorption and also low efficacy has been shown in interaction with the cell membrane. As a result, administration of the anti-cancer drug can be very effective and efficient by using new drug delivery methods.

Keywords

Main Subjects

References

[1] I. Ali, Rahis-Uddin, K. Salim, M.A. Rather, W.A. Wani, A. Haque, "Advances in nano drugs for cancer chemotherapy", Curr. Cancer Drug Targets, Vol. 11, 2011, pp. 135-146.
[2] D. J. Tobias, K. Tu, M. L. Klein, "Atomic-scale molecular dynamics simulations of lipid membranes", Curr. Opin. Colloid Interface Sci., Vol. 2, 1997, pp. 15-26.
[3] S. E. Feller, "Molecular dynamics simulations of lipid bilayers", Curr. Opin. Colloid Interface Sci., Vol. 5, 2000, pp. 217-223.
[4] F. Keshavarz, M.M. Alavianmehr, R. Yousefi, "Molecular dynamics simulation and docking studies on the binding properties of several anticancer drugs to human serum albumin", Mol. Biol. Res. Commun., Vol. 1, 2012, pp. 65-73.
[5] J. D. Durrant, J. A. McCammon, "Molecular dynamics simulations and drug discovery", BMC biology, Vol. 9, No. 71, 2011, pp. 1-9.
[6] C. Peetla, A. Stine, and V. Labhasetwar, "Biophysical interactions with model lipid membranes: applications in drug discovery and drug delivery," Molecular pharmaceutics, vol. 6, pp. 1264-1276, 2009.
Cachau, et al., "Study. N. Avila-Salas, C. Sandoal, J. Caballero, S. Guinez-Molinos, L. S. Santos, R. l. E. [7] F
of interaction energies between the PAMAM dendrimer and nonsteroidal anti-inflammatory drug using a distributed computational strategy and experimental analysis by ESI-MS/MS", The Journal of Physical Chemistry B, vol. 116, 2012, pp. 2031-2039.
[8] J. P. Jämbeck, E. S. Eriksson, A. Laaksonen, A. P. Lyubartsev, L.A. Eriksson, "Molecular Dynamics Studies of Liposomes as Carriers for Photosensitizing Drugs: Development, Validation, and Simulations with a Coarse-Grained Model", J. Chem. Theory Comput., Vol. 10, 2014, pp. 5-13.
[9] M. Kang, S. M., Loverde, "Molecular Simulation of the Concentration-Dependent Interaction of Hydrophobic Drugs with Model Cellular Membranes", J. Phys. Chem. B, Vol. 118, 2014, pp. 11965-11972.
[10] Y. Cheng, Q. X. Pei, H. Gao, "Molecular-dynamics studies of competitive replacement in peptide–nanotube assembly for control of drug release", Nanotechnology, vol. 20, 2009, p. 145101.
[11] H. Maeda, J. Wu, T. Sawa, Y. Matsumura, K. Hori, "Tumor vascular permeability and the EPR effect in macromolecular therapeutics: a review", Journal of controlled release, vol. 65, 2000, pp. 271-284.
[12] H. Maeda, T. Sawa, and T. Konno, "Mechanism of tumor-targeted delivery of macromolecular drugs, including the EPR effect in solid tumor and clinical overview of the prototype polymeric drug SMANCS", Journal of controlled release, vol. 74, 2001, pp. 47-61.
[13] K. Yagi, N. Ohishi, A. Hamada, M. Shamoto, M. Ohbayashi, N. Ishida, et al., "Basic study on gene therapy of human malignant glioma by use of the cationic multilamellar liposome-entrapped human interferon beta gene", Human gene therapy, vol. 10, 1999, pp. 1975-1982.
[14] Z. Hasanzade, H. Raissi, "Investigation of graphene-based nanomaterial as nanocarrier for adsorption of paclitaxel anticancer drug: a molecular dynamics simulation study", J Mol Model, Vol. 23, No. 36, 2017, pp. 1-8.
[15] R. Bernardi, D. Gomes, P. Pascutti, A. Ito, C. Taft, and A. Ota, "Water solvent and local anesthetics: A computational study", Int. J. Quantum Chem., Vol. 107, 2007, pp. 1642-1649.
[16] Z. Bonyadi and A. Razavi Zadeh, "Molecular dynamic simulation of releasing process of anticancer drug paclitaxel into carbonic nanotube capsulated by bio membrane dipalmitoylphosphatidylcholine", Ind. J. Fund. Appl Life Sci., 2016, Vol. 6, pp. 216-227.
]17[ غلامعلی شفابخش، حسین نادرپور و مانا معتمدی. "مدل‌سازی پاسخ بهینه روسازی آسفالتی به کمک روش اجزای محدود"، نشریه مدل‌سازی در مهندسی، دوره 14، شماره 47، زمستان 1395، صفحه 33-40.
]18[ سعید روحی، یونس علیزاده و رضا انصاری. "بررسی خواص مکانیکی پلی وینیل پیرولیدون تقویت شده با نانولوله­های کربنی تک جداره با استفاده از روش شبیه­سازی دینامیک مولکولی و مدلسازی المان محدود"، نشریه مدل‌سازی در مهندسی، دوره 16، شماره 52، بهار 1397، صفحه 30-40.
]19[ امین یاسینی و محمود شریعتی. "مدل سازی و شبیه سازی رفتار کمانشی نانو سیم های سیلیسیم و با استفاده از روش مکانیک ساختاری"، نشریه مدل‌سازی در مهندسی، دوره 15، شماره 50، پاییز 1396، صفحه 85-93.
[20] J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, K. Schulten, "Scalable Molecular Dynamics with NAMD", J. Comput. Chem., Vol. 26, 2005, pp. 1781-1802.
[21] W. Humphrey, A. Dalke, K. Schulten, "VMD: Visual Molecular Dynamics", J. Mol. Graph., Vol. 14, 1996, pp. 33-38.
[22] B. R. Brooks, C.L. 3rd. Brooks, A.D. Jr. Mackerell, L. Nilsson, R.J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, "CHARMM: The Biomolecular Simulation Program", J. Comput. Chem., Vol. 30, 2009, pp. 1545-1614.
[23] B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, M. Karplus, "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations", J. Comput. Chem., Vol. 4, 1983, pp. 187-217.
[24] T. Panczyk, T. Da Ros, G. Pastorin, A. Jagusiak, J. Narkiewicz-Michalek, "Role of Intermolecular Interactions in Assemblies of Nanocontainers Composed of Carbon Nanotubes and Magnetic Nanoparticles: A Molecular Dynamics Study", J. Phys. Chem. C., Vol. 118, 2014, pp. 1353-1363.
[25] Y. F. Xing, C. L. Yang, Y. F. Mo, M. S. Wang, X. G. Ma, "Dynamic Mechanism of Single-Stranded DNA Encapsulated into Single-Wall Carbon Nanotubes: A Molecular Dynamics Simulation Study", J. Phys. Soc. Jpn., Vol. 83, 2014, pp. 024801:1-7.
[26] W. Schreiner, R. Karch, B. Knapp, N. Ilieva, "Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations", Computational and mathematical methods in medicine, vol. 2012, pp. 1-9.
[27] U. Schieborr, S. Sreeramulu, B. Elshorst, M. Maurer, K. Saxena, T. Stehle, et al., "MOTOR: Model assisted software for NMR structure determination," Proteins: Structure, Function, and Bioinformatics, vol. 81, 2013, pp. 2007-2022.
[28] M. R. Wenk, A. Fahr, R. Reszka, J. Seelig, "Paclitaxel partitioning into lipid bilayers", J. Pharm. Sci., Vol. 85, 1996, pp. 228-231.
 
 
Journal of Modeling in Engineering
Volume 17, Issue 57
July 2019
Pages 15-25

Files

History

  • Receive Date: 01 May 2018
  • Revise Date: 26 November 2018
  • Accept Date: 05 December 2018

Share

How to cite

Statistics