شبیه سازی مکانیک کوانتومی داروی ضد سرطان شبه نوکلئوتیدی سیتارابین با نانو لوله های کربنی عامل دار شده (5، 5) و (8، 8) در یک سیستم دارورسانی هدفمند
محورهای موضوعی : تحقیقات در علوم مهندسی سطح و نانو مواد
فاطمه موسوی
1
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ندا حسن زاده
2
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حوریه یحیایی
3
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آیه رعیت زاده
4
1 - گروه شیمی، واحد اهواز، دانشگاه آزاد اسلامی، اهواز، ایران
2 - گروه شیمی، واحد اهواز، دانشگاه آزاد اسلامی، اهواز، ایران
3 - گروه شیمی، واحد زنجان، دانشگاه آزاد اسلامی،زنجان، ایران
4 - گروه شیمی، واحد اهواز، دانشگاه آزاد اسلامی، اهواز، ایران
کلید واژه: داروی ضد سرطان سیتارابین , نانو لوله های کربنی عامل دار شده , اوربیتال پیوندی طبیعی, مکانیک کوانتومی,
چکیده مقاله :
شبیه سازی مکانیک کوانتوم بر روی برهمکنش داروی ضد سرطان شبه نوکلئوتیدی سیتارابین و نانو لوله های کربنی عامل دار شده (5، 5) و (8، 8) با کربوکسیل توسط محاسبات مکانیک کوانتومی با استفاده از نظریۀ تابعیت چگالی و محاسبات NBO با سطح تئوری B3LYP/6-31+G* صورت گرفت. نتایج NBO برهمکنش های π-π نانولوله های کربنی عام لدار شده (5، 5) و (8، 8) و سیتارابین نشان میدهد که وجود برهمکنش های واندروالسی، یونی و هیدروژنی بــه دلیل حضور تعداد زیادی از گروه های عاملی اکسـیژن دار است که این امر تاثیر شگرفی در تثبیـت داروی ضد سرطان سیتارابین خواهد داشت. همچنین کاهش انرژی برهم کنش با افزایش قطر نانولوله از (5، 5) به (8، 8) نشان میدهد که انحنای نانولوله نقش مهمی در واکنش پذیری دارد و نانولوله با قطر باریکتر (5، 5) نسبت به نانولوله با قطر بزرگتر(8، 8) از لحاظ ترمودینامیکی مناسبتر است و این در حالی است که قدرت رهایش دارو با افزایش قطر نانولوله کربنی عاملدار شده رابطه مستقیم دارد.
The quantum mechanical (QM) simulation investigated the interaction between the pseudo nucleotide anticancer drug cytarabine, and carboxyl functionalized carbon nanotubes (5,5) and (8,8). This study utilized quantum mechanical calculations based on density functional theory and NBO (Natural Bond Orbital) analysis, employing the B3LYP/6-31+G* level of theory. The NBO results of π-π interactions of functionalized carbon nanotubes (5, 5) and (8, 8) and cytarabine show that the existence of van der Waals, ionic, and hydrogen interactions due to the presence of a large number of oxygen functional groups. It is believed that this will have a tremendous effect on the stabilization of the anti-cancer drug cytarabine. Also, the decrease in the interaction energy with the increase in the diameter of the nanotube from (5, 5) to (8, 8) shows that the curvature of the nanotube has an important role in the reactivity, and the nanotube with a narrower diameter (5, 5) than the nanotube with a larger diameter (8, 8) is more appropriate in terms of thermodynamics, while the power of drug release has a direct relationship with increasing the diameter of functionalized carbon nanotubes.
[1] A. Pigneux, V. Perreau, E. Jourdan, N. Vey, N. Dastugue, F. Huguet, J.-J. Sotto, L. R. Salmi, N. Ifrah, J. Reiffers, Adding lomustine to idarubicin and cytarabine for induction chemotherapy in older patients with acute myeloid leukemia: the BGMT 95 trial results." Haematologica , 10 (2007) 1327-1334.
[2] G. Vitale, S. Amadio, F. Liguori, C. Volonté, Empowering the NSC-34 cell line as a motor neuron model: cytosine arabinoside's action. Neural Regeneration Research, 10-4103.
[3] B. S. Chhikara K. Parang, "Development of cytarabine prodrugs and delivery systems for leukemia treatment." Expert opinion on drug delivery , 12 (2010) 1399-1414.
[4] M. L. Clarke, J. R. Mackey, S. A. Baldwin, J. D. Young, C. E. Cass, "The role of membrane transporters in cellular resistance to anticancer nucleoside drugs." Clinically Relevant Resistance in Cancer Chemotherapy (2002) 27-47.
[5] J. Fischer, C. R. Ganellin, "Analogue-based drug discovery." Chemistry International--Newsmagazine for IUPAC, 4 (2010) 12-15.
[6] J. Shelton, X. Lu, J. A. Hollenbaugh, J. H. Cho, F. Amblard, R. F. Schinazi, "Metabolism, biochemical actions, and chemical synthesis of anticancer nucleosides, nucleotides, and base analogs." Chemical reviews, 23 (2016) 14379-14455.
[7] J. A. Hollenbaugh, J. Shelton, S. Tao, S. Amiralaei, P. Liu, X. Lu, R. W. Goetze, L. Zhou, J. H. Nettles, R. F. Schinazi, "Substrates and Inhibitors of SAMHD1." PloS one , 1 (2017) e0169052.
[8] C. Schneider, T. Oellerich, H.-M. Baldauf, S.-M. Schwarz, D. Thomas, R. Flick, H. Bohnenberger, L. Kaderali, L. Stegmann, A. Cremer, "SAMHD1 is a biomarker for cytarabine response and a therapeutic target in acute myeloid leukemia." Nature medicine , 2 (2017) 250-255
[9] M. Korani, S. Korani, E. Zendehdel, A. R. Nikpoor, M. R. Jaafari, H. M. Orafai, T. P. Johnston, A. Sahebkar, "Enhancing the therapeutic efficacy of bortezomib in cancer therapy using polymeric nanostructures." Current pharmaceutical design ,46 (2019) 4883-4892.
[10] J. Faver, K. M. Merz Jr, "Utility of the hard/soft acid− base principle via the fukui function in biological systems." Journal of chemical theory and computation ,2 (2010) 548-559.
[11] S. Darwish, R. Elbayaa, H. Ashour, M. Khalil, E. Badawey, "Potential anticancer agents: Design, synthesis of new pyrido [1, 2-a] benzimidazoles and related derivatives linked to alkylating fragments." Medicinal Chemistry (Los Angeles) 8 (2018): 86-95.
[12] S. A. Siadati, E. Vessally, A. Hosseinian, L. Edjlali, "Possibility of sensing, adsorbing, and destructing the Tabun-2D-skeletal (Tabun nerve agent) by C20 fullerene and its boron and nitrogen doped derivatives." Synthetic Metals ,220 (2016) 606-611.
[13] J. Mercero, J. Matxain, X. Lopez, D. York, A. Largo, L. Eriksson, J. Ugalde, "Theoretical methods that help understanding the structure and reactivity of gas phase ions." International Journal of Mass Spectrometry , 1 (2005) 37-99.
[14] H. Kaur, R. Garg, S. Singh, A. Jana, C. Bathula, H.-S. Kim, S. G. Kumbar, M. Mittal, "Progress and challenges of graphene and its congeners for biomedical applications." Journal of molecular liquids ,368 (2022) 120703.
[15] S. M. Mousavi, S. A. Hashemi, M. Y. Kalashgrani, N. Omidifar, S. Bahrani, N. Vijayakameswara Rao, A. Babapoor, A. Gholami, W.-H. Chiang, "Bioactive graphene quantum dots based polymer composite for biomedical applications." Polymers , 3 (2022) 617.
[16] S. H. Chen, D. R. Bell, B. Luan, "Understanding interactions between biomolecules and two-dimensional nanomaterials using in silico microscopes." Advanced drug delivery reviews, 186 (2022) 114336.
[17] Y. Han, J. Zhao, X. Guo, T. Jiao, "Enhanced Methane Storage in Graphene Oxide Induced by an External Electric Field: A Study by MD Simulations and DFT Calculation." Langmuir , 22 (2023) 7648-7659.
[18] A. S. Palma, B. R. Casadei, M. C. "A short review on the applicability and use of cubosomes as nanocarriers." Biophysical Reviews ,4 (2023) 553-567.
[19] M. Matiyani, A. Rana, M. Pal, S. Dokwal, N. G. Sahoo, "Polyamidoamine dendrimer decorated graphene oxide as a pH-sensitive nanocarrier for the delivery of hydrophobic anticancer drug quercetin: a remedy for breast cancer." Journal of Pharmacy and Pharmacology , 6 (2023) 859-872
[20] M. Spivak, J. E. Stone, J. Ribeiro, J. Saam, P. L. Freddolino, R. C. Bernardi, E. Tajkhorshid, "VMD as a platform for interactive small molecule preparation and visualization in quantum and classical simulations." Journal of chemical information and modeling ,15 (2023) 4664-4678.
[21] P. U. Kulkarni, H. Shah, V. K. Vyas, "Hybrid quantum mechanics/molecular mechanics (QM/MM) simulation: a tool for structure-based drug design and discovery." Mini Reviews in Medicinal Chemistry , 8 (2022) 1096-1107A.
[22] Vidal-Limon, J. E. Aguilar-Toalá, A. M. Liceaga, "Integration of molecular docking analysis and molecular dynamics simulations for studying food proteins and bioactive peptides." Journal of Agricultural and Food Chemistry ,4 (2022) 934-943.
[23] Z. Shuli, L. Linlin, G. Li, Z. Yinghu, S. Nan, W. Haibin, X. Hongyu, "Bioinformatics and computer simulation approaches to the discovery and analysis of bioactive peptides." Current Pharmaceutical Biotechnology ,13 (2022) 1541-1555.
[24] Y. Vander Meersche, G. Cretin, A. Gheeraert, J.-C. Gelly, T. Galochkina, "ATLAS: protein flexibility description from atomistic molecular dynamics simulations." Nucleic acids research , D1 (2024): D384-D392.
[25] S. K. Kordylewski, R. Bugno, A. J. Bojarski, S. Podlewska, "Uncovering the unique characteristics of different groups of 5-HT5AR ligands with reference to their interaction with the target protein." Pharmacological Reports , 5 (2024) 1130-1146.
[26] R. Saker, O. Jójárt-Laczkovich, G. Regdon Jr, T. Takács, I. Szenti, N. Bózsity-Faragó, I. Zupkó, T. Sovány, "Surface Modification of Titanate Nanotubes with a Carboxylic Arm for Further Functionalization Intended to Pharmaceutical Applications." Pharmaceutics , 12 (2023): 2780.
[27] C. K. Thakur, C. Karthikeyan, C. R. Ashby Jr, R. Neupane, V. Singh, R. J. Babu, N. H. Narayana Moorthy, A. K. Tiwari, "Ligand-conjugated multiwalled carbon nanotubes for cancer targeted drug delivery." Frontiers in Pharmacology ,15 (2024): 1417399.
[28] B. Karunarathna, J. D. Wanniarachchi, M. Prashantha, K. Govender, "Enhancing styrene monomer recovery from polystyrene pyrolysis: insights from density functional theory." Journal of Molecular Modeling ,8 (2023) 255.
[29] G. Cárdenas, J. Lucia‐Tamudo, H. Mateo‐delaFuente, V. F. Palmisano, N. Anguita‐Ortiz, L. Ruano, Á. Pérez‐Barcia, S. Díaz‐Tendero, M. Mandado, J. J. Nogueira "MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations." Journal of Computational Chemistry , 4 (2023) 516-533.
[30] R. Morad, M. Akbari, M. Maaza, "Theoretical study of chemical reactivity descriptors of some repurposed drugs for COVID-19." Mrs Advances , 11 (2023) 656-660.
[31] S. CJ, A. MFB, "Vibrational, spectroscopic, chemical reactivity, molecular docking and in vitro anticancer activity studies against A549 lung cancer cell lines of 5-Bromo-indole-3-carboxaldehyde." Journal of Molecular Recognition: JMR , 3 (2020) e2873-e2873.
[32] Y. Wu, Y. Zhang, X. Wu, Q. Li, S. Ebrahimiasl, "Quantum chemical studies to functionalization of boron nitride nanotube (BNNT) as effective nanocarriers." Brazilian Journal of Chemical Engineering , 3 (2022) 835-842.
[33] A. Nandi, R. Conte, C. Qu, P. L. Houston, Q. Yu, J. M. Bowman, "Quantum calculations on a new CCSD (T) machine-learned potential energy surface reveal the leaky nature of gas-phase trans and gauche ethanol conformers." Journal of Chemical Theory and Computation , 9 (2022) 5527-5538.
[34] H. O. Edet, H. Louis, T. E. Gber, P. S. Idante, T. C. Egemonye, P. B. Ashishie, E. E. Oyo-Ita, I. Benjamin, A. S. Adeyinka, "Heteroatoms (B, N, S) doped quantum dots as potential drug delivery system for isoniazid: insight from DFT, NCI, and QTAIM." Heliyon ,1 (2023).
[35] T. Chutia, D. J. Kalita, "Theoretical investigation of fused N-methyl-dithieno-pyrrole derivatives in the context of acceptor–donor–acceptor approach." RSC advances , 23 (2022) 14422-14434.
[36] Z. Jiang, Q. Yu, Z. Zhao, X. Song, Y. Zhang, "Reason for the increased electroactivity of extracellular polymeric substances with electrical stimulation: Structural change of α-helix peptide of protein." Water Research, 238 (2023) 119995.
[37] G. Ejuh, J. Ndjaka, F. Tchangnwa Nya, P. Ndukum, C. Fonkem, Y. Tadjouteu Assatse, R. Yossa Kamsi, "Determination of the structural, electronic, optoelectronic and thermodynamic properties of the methylxanthine molecules theophylline and theobromine." Optical and quantum electronics 52 (2020) 1-22.