A Molecular Dynamics Study of the Interaction Between Graphene as a Carrier and Gemcitabine as a Chemotherapy.

Farhad Z.Ahmed; Amir A.Ahmad; B.Kharazian

doi:10.21271/ZJPAS.35.1.3

Authors

Farhad Z.Ahmed Department of Physics, College of Science, Salahaddin University-Erbil, Kurdistan Region, Iraq
Amir A.Ahmad Department of Physics, College of Science, Salahaddin University-Erbil, Kurdistan Region, Iraq
B.Kharazian 1Department of Physical Chemistry, Tarbiat Modares University, Tehran, Iran / 2Department of Pharmaceutics, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran

DOI:

https://doi.org/10.21271/ZJPAS.35.1.3

Keywords:

Drug delivery system, MD simulation, Chemotherapy drug, Graphene nanoparticle, Gemcitabine.

Abstract

Drug delivery is the technique or method of administering a pharmaceutical compound to earn a more satisfactory therapeutic impact for human diseases. Based on the good characteristics (high surface area, high capacity for loading a drug and high biological compatibility and degradability) of the graphene nanoparticles, they are widely used in medicine, particularly drug delivery. Hence, in this research, a two-dimensional graphene sheet as a nanocarrier and Gemcitabine (GEM) as chemotherapy have been used to form a (graphene/GEM) system. Moreover, the interactions between the nanocarrier and GEM molecule were explored via Molecular Dynamics (MD) simulation. To investigate the interaction between GEM and graphene, the dynamics of GEM molecule, radial distribution function (RDF), root mean square deviation (RMSD), radius of gyration (Rg), and solvent-accessible surface area (SASA) parameters are analyzed. Results indicate that GEM on the graphene has a more stable structure in comparison with the free GEM molecule. Therefore, the graphene/GEM system can be considered a useful therapeutic system for cancer treatment with minimum side effects.

References

BAIG, M. H., SUDHAKAR, D. R., KALAIARASAN, P., SUBBARAO, N., WADHAWA, G., LOHANI, M., KHAN, M. K. A. & KHAN, A. U. 2014. Insight into the effect of inhibitor resistant S130G mutant on physico-chemical properties of SHV type beta-lactamase: a molecular dynamics study. PLoS One, 9, e112456.

DE, S., PATRA, K., GHOSH, D., DUTTA, K., DEY, A., SARKAR, G., MAITI, J., BASU, A., RANA, D. & CHATTOPADHYAY, D. 2018. Tailoring the efficacy of multifunctional biopolymeric graphene oxide quantum dot-based nanomaterial as nanocargo in cancer therapeutic application. ACS Biomaterials Science & Engineering, 4, 514-531.

EWALD, P. P. 1921. Ewald summation. Ann. Phys, 369, 1-2.2.

GONZÁLEZ, M. 2011. Force fields and molecular dynamics simulations. École thématique de la Société Française de la Neutronique, 12, 169-200.

HASANZADE, Z. & RAISSI, H. 2017. Investigation of graphene-based nanomaterial as nanocarrier for adsorption of paclitaxel anticancer drug: a molecular dynamics simulation study. Journal of molecular modeling, 23, 1-8.

HAUME, K. 2018. Computational Modelling of Radiosensitising Properties of Nanoparticles, Open University (United Kingdom).

HOSEINI-GHAHFAROKHI, M., MIRKIANI, S., MOZAFFARI, N., SADATLU, M. A. A., GHASEMI, A., ABBASPOUR, S., AKBARIAN, M., FARJADAIN, F. & KARIMI, M. 2020. Applications of Graphene and Graphene Oxide in Smart Drug/Gene Delivery: Is the World Still Flat? International Journal of Nanomedicine, 15, 9469.

HUMPHREY, W., DALKE, A. & SCHULTEN, K. 1996. VMD: visual molecular dynamics. Journal of molecular graphics, 14, 33-38.

JIANG, T., SUN, W., ZHU, Q., BURNS, N. A., KHAN, S. A., MO, R. & GU, Z. 2015. Furin‐mediated sequential delivery of anticancer cytokine and small‐molecule drug shuttled by graphene. Advanced materials, 27, 1021-1028.

KHARAZIAN, B., AHMAD, A. & MABUDI, A. 2021. A molecular dynamics study on the binding of gemcitabine to human serum albumin. Journal of Molecular Liquids, 337, 116496.

LAMICHHANE, T. R. & GHIMIRE, M. P. 2021. Evaluation of SARS-CoV-2 main protease and inhibitor interactions using dihedral angle distributions and radial distribution function. Heliyon, 7, e08220.

LAVAN, D. A., MCGUIRE, T. & LANGER, R. 2003. Small-scale systems for in vivo drug delivery. Nature biotechnology, 21, 1184-1191.

LIU, J., CUI, L. & LOSIC, D. 2013. Graphene and graphene oxide as new nanocarriers for drug delivery applications. Acta biomaterialia, 9, 9243-9257.

LIU, Z., ROBINSON, J. T., TABAKMAN, S. M., YANG, K. & DAI, H. 2011. Carbon materials for drug delivery & cancer therapy. Materials today, 14, 316-323.

MAINARDES, R. M. & SILVA, L. P. 2004. Drug delivery systems: past, present, and future. Current drug targets, 5, 449-455.

MANSOORI, G. A. 1993. Radial distribution functions and their role in modeling of mixtures behavior. Fluid phase equilibria, 87, 1-22.

PAN, Y., SAHOO, N. G. & LI, L. 2012. The application of graphene oxide in drug delivery. Expert opinion on drug delivery, 9, 1365-1376.

PARKS, M. L., LEHOUCQ, R. B., PLIMPTON, S. J. & SILLING, S. A. 2008. Implementing peridynamics within a molecular dynamics code. Computer Physics Communications, 179, 777-783.

PARVEEN, S., MISRA, R. & SAHOO, S. K. 2012. Nanoparticles: a boon to drug delivery, therapeutics, diagnostics and imaging. Nanomedicine: Nanotechnology, Biology and Medicine, 8, 147-166.

PLIMPTON, S. 1995. Fast parallel algorithms for short-range molecular dynamics. Journal of computational physics, 117, 1-19.

SHARMA, S., KUMAR, P., CHANDRA, R., SINGH, S., MANDAL, A. & DONDAPATI, R. 2019. Overview of BIOVIA materials studio, LAMMPS, and GROMACS. Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs, Amsterdam, Netherlands: Elsevier, 39-100.

SHRAKE, A. & RUPLEY, J. A. 1973. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. Journal of molecular biology, 79, 351-371.

SINGH, A., VANGA, S. K., ORSAT, V. & RAGHAVAN, V. 2018. Application of molecular dynamic simulation to study food proteins: A review. Critical reviews in food science and nutrition, 58, 2779-2789.

SUN, X., LIU, Z., WELSHER, K., ROBINSON, J. T., GOODWIN, A., ZARIC, S. & DAI, H. 2008. Nano-graphene oxide for cellular imaging and drug delivery. Nano research, 1, 203-212.

VINOTHINI, K., RAJENDRAN, N. K., RAJAN, M., RAMU, A., MARRAIKI, N. & ELGORBAN, A. M. 2020. A magnetic nanoparticle functionalized reduced graphene oxide-based drug carrier system for a chemo-photodynamic cancer therapy. New Journal of Chemistry, 44, 5265-5277.

VINOTHINI, K., RAJENDRAN, N. K., RAMU, A., ELUMALAI, N. & RAJAN, M. 2019. Folate receptor targeted delivery of paclitaxel to breast cancer cells via folic acid conjugated graphene oxide grafted methyl acrylate nanocarrier. Biomedicine & Pharmacotherapy, 110, 906-917.

WANG, C., LI, J., AMATORE, C., CHEN, Y., JIANG, H. & WANG, X. M. 2011. Gold nanoclusters and graphene nanocomposites for drug delivery and imaging of cancer cells. Angewandte Chemie, 123, 11848-11852.

YANG, X., WANG, Y., HUANG, X., MA, Y., HUANG, Y., YANG, R., DUAN, H. & CHEN, Y. 2011. Multi-functionalized graphene oxide based anticancer drug-carrier with dual-targeting function and pH-sensitivity. Journal of materials chemistry, 21, 3448-3454.

ZHANG, L., XIA, J., ZHAO, Q., LIU, L. & ZHANG, Z. 2010. Functional graphene oxide as a nanocarrier for controlled loading and targeted delivery of mixed anticancer drugs. small, 6, 537-544.