Investigation of metallacages for cisplatin encapsulation using Density Functional Theory (DFT)

Authors

  • Sadettin Y Ugurlu University of Birmingham
  • R. Enisoglu School of Science and Technology, City St George's, University of London

Abstract

Cancer is highly complex, including cross-talks between signalling pathways and multiple genes. Fortunately, successful anti-cancer drugs, such as cisplatin, are promising to treat cancer. Despite its clinical success, cisplatin presents several issues, including neurotoxicity, ototoxicity, nephrotoxicity and drug resistance. These limitations of the successful anti-cancer cisplatin can be overcome with the help of novel supramolecular drug delivery systems. This research aims to optimise novel supramolecular drug delivery systems – metallacage (M2L4 (M = metal, L = ligand) – that can be used to encapsulate cisplatin to protect it from metabolism. Specifically, we investigated the shape and stability of ten metallacages using different metals: Pt2+, Pd2+, Ni2+, Cu2+ and Au3+ using Density Functional Theory (DFT) methods to encapsulate one or two cisplatin molecules. Thus, we applied WebMo running PBE0 and Hartree Fock as theories, with LanL2DZ as a basis set. The results demonstrate that PBE0/LanL2DZ is the best method to describe the cages. The results show that Endo-N Ni2L4 and Endo-N Cu2L4 cages are the best option to encapsulate one and two cisplatin, while the least suitable system is Endo-C Pt2L4 and Endo-C Au2L4 for cisplatin encapsulation. Furthermore, endo-C cages are farther from ground state energy because of their higher energy than endo-N cages. Therefore, endo-N cages are superior to endo-C cages for the encapsulation of cisplatin.

Author Biography

R. Enisoglu, School of Science and Technology, City St George's, University of London

Northampton Square, London, EC1V 0HB

References

James C Dabrowiak. Metals in medicine. Inorganica Chimica Acta, 393:1–2, 2012.

Barnett Rosenberg, Loretta Vancamp, James E Trosko, and Virginia H Mansour. Platinum compounds: a new class of potent antitumour agents. nature, 222(5191):385–386, 1969.

Timothy C Johnstone, Kogularamanan Suntharalingam, and Stephen J Lippard. The next generation of platinum drugs: targeted pt (ii) agents, nanoparticle delivery, and pt (iv) pro-drugs. Chemical reviews, 116(5):3436–3486, 2016.

Dong Wang and Stephen J Lippard. Cellular processing of platinum anti-cancer drugs. Nature reviews Drug discovery, 4(4):307–320, 2005.

Zahid H Siddik. Cisplatin: mode of cytotoxic action and molecular basis of resistance. Onco-gene, 22(47):7265–7279, 2003.

Sumit Ghosh. Cisplatin: The first metal based anti-cancer drug. Bioorganic chemistry, 88:102925, 2019.

Takatoshi Karasawa and Peter S Steyger. An integrated view of cisplatin-induced nephrotox-icity and ototoxicity. Toxicology letters, 237(3):219–227, 2015.

GP Stathopoulos and T Boulikas. Lipoplatin formulation review article. Journal of drug delivery, 2012(1):581363, 2012.

Hardeep S Oberoi, Natalia V Nukolova, Alexander V Kabanov, and Tatiana K Bronich. Nanocarriers for delivery of platinum anti-cancer drugs. Advanced drug delivery reviews, 65(13-14):1667–1685, 2013.

Ana-Maria Florea and Dietrich B¨usselberg. Cisplatin as an anti-tumor drug: cellular mecha-nisms of activity, drug resistance and induced side effects. Cancers, 3(1):1351–1371, 2011.

Michail Nikolaou, Athanasia Pavlopoulou, Alexandros G Georgakilas, and Efthymios Kyrodi-mos. The challenge of drug resistance in cancer treatment: a current overview. Clinical & Experimental Metastasis, 35:309–318, 2018.

Xuan Wang, Haiyun Zhang, and Xiaozhuo Chen. Drug resistance and combating drug resis-tance in cancer. Cancer drug resistance, 2(2):141, 2019.

Andrea Schmidt. Supramolecular metallocages as potential delivery systems for anti-cancer drugs. PhD thesis, Technische Universit¨at M¨unchen, 2016.

Matthew D Hall, Mitsunori Okabe, Ding-Wu Shen, Xing-Jie Liang, and Michael M Gottesman. The role of cellular accumulation in determining sensitivity to platinum-based chemotherapy. Annu. Rev. Pharmacol. Toxicol., 48(1):495–535, 2008.

Guocan Yu, Timothy R Cook, Yang Li, Xuzhou Yan, Dan Wu, Li Shao, Jie Shen, Guping Tang, Feihe Huang, Xiaoyuan Chen, et al. Tetraphenylethene-based highly emissive metal-lacage as a component of theranostic supramolecular nanoparticles. Proceedings of the National Academy of Sciences, 113(48):13720–13725, 2016.

Pieter CA Bruijnincx and Peter J Sadler. New trends for metal complexes with anti-cancer activity. Current opinion in chemical biology, 12(2):197–206, 2008.

Timothy R Cook and Peter J Stang. Recent developments in the preparation and chemistry of metallacycles and metallacages via coordination. Chemical reviews, 115(15):7001–7045, 2015.

Alexander P¨othig and Angela Casini. Recent developments of supramolecular metal-based structures for applications in cancer therapy and imaging. Theranostics, 9(11):3150, 2019.

Guocan Yu, Meijuan Jiang, Feihe Huang, and Xiaoyuan Chen. Supramolecular coordination complexes as diagnostic and therapeutic agents. Current opinion in chemical biology, 61:19–31, 2021.

Feng Chen, Yang Li, Xiongjie Lin, Huayu Qiu, and Shouchun Yin. Polymeric systems con-taining supramolecular coordination complexes for drug delivery. Polymers, 13(3):370, 2021.

Angela Casini, Benjamin Woods, and Margot Wenzel. The promise of self-assembled 3d supramolecular coordination complexes for biomedical applications, 2017.

Yang Bai, Chunli Liu, Yuying Shan, Tingting Chen, Yan Zhao, Chao Yu, and Huan Pang. Metal-organic frameworks nanocomposites with different dimensionalities for energy conver-sion and storage. Advanced Energy Materials, 12(4):2100346, 2022.

Changfeng Yin, Jiaxing Du, Bogdan Olenyuk, Peter J Stang, and Yan Sun. The applications of metallacycles and metallacages. Inorganics, 11(2):54, 2023.

Yiliang Wang, Taotao Liu, Yang-Yang Zhang, Bin Li, Liting Tan, Chunju Li, Xing-Can Shen, and Jun Li. Cross-catenation between position-isomeric metallacages. Nature Communica-tions, 15(1):1363, 2024.

Yang Li, Jinjin Zhang, Hui Li, Yiqi Fan, Tian He, Huayu Qiu, and Shouchun Yin. Metallacycle/metallacage-cored fluorescent supramolecular assemblies with aggregation-induced emission properties. Advanced Optical Materials, 8(14):1902190, 2020.

Hajar Sepehrpour, Wenxin Fu, Yan Sun, and Peter J Stang. Biomedically relevant self-assembled metallacycles and metallacages. Journal of the American Chemical Society, 141(36):14005–14020, 2019.

Yida Pang, Chonglu Li, Hongping Deng, and Yao Sun. Recent advances in luminescent metallacycles/metallacages for biomedical imaging and cancer therapy. Dalton Transactions, 51(43):16428–16438, 2022.

Jens Bunzen, Junji Iwasa, Pia Bonakdarzadeh, Eri Numata, Kari Rissanen, Sota Sato, and Makoto Fujita. Self-assembly of m 24 l 48 polyhedra based on empirical prediction. Angewandte Chemie International Edition, 13(51):3161–3163, 2012.

Casey Sandra Christie. New homoleptic and heteroleptic [Pd2L4] helicates. PhD thesis, Uni-versity of Otago, 2021.

Puhong Liao, Brian W Langloss, Amber M Johnson, Eric R Knudsen, Fook S Tham, Ryan R Julian, and Richard J Hooley. Two-component control of guest binding in a self-assembled cage molecule. Chemical communications, 46(27):4932–4934, 2010.

Andrea Schmidt, Viviana Molano, Manuela Hollering, Alexander P¨othig, Angela Casini, and Fritz E K¨uhn. Evaluation of new palladium cages as potential delivery systems for the anti-cancer drug cisplatin. Chemistry–A European Journal, 22(7):2253–2256, 2016.

J Han, A Schmidt, T Zhang, H Permentier, GMM Groothuis, R Bischoff, FE K¨uhn, P Horvatovich, and A Casini. Bioconjugation strategies to couple supramolecular exo-functionalized palladium cages to peptides for biomedical applications. Chemical Commu-nications, 53(8):1405–1408, 2017.

William F Polik and JR Schmidt. Webmo: Web-based computational chemistry calculations in education and research. Wiley Interdisciplinary Reviews: Computational Molecular Science, 12(1):e1554, 2022.

Jorge Kohanoff. Electronic structure calculations for solids and molecules: theory and compu-tational methods. Cambridge university press, 2006.

Jake Graser, Steven K Kauwe, and Taylor D Sparks. Machine learning and energy minimiza-tion approaches for crystal structure predictions: a review and new horizons. Chemistry of Materials, 30(11):3601–3612, 2018.

CRA Catlow, ZX Guo, M Miskufova, SA Shevlin, AGH Smith, AA Sokol, Aron Walsh, DJ Wil-son, and SM Woodley. Advances in computational studies of energy materials. Philosoph-ical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 368(1923):3379–3456, 2010.

Jun-Ichi Iwata, Daisuke Takahashi, Atsushi Oshiyama, Taisuke Boku, Kenji Shiraishi, Susumu Okada, and Kazuhiro Yabana. A massively-parallel electronic-structure calculations based on real-space density functional theory. Journal of Computational Physics, 229(6):2339–2363, 2010.

J Ulises Reveles and Andreas M K¨oster. Geometry optimisation in density functional methods. Journal of computational chemistry, 25(9):1109–1116, 2004.

Zoe L Seeger and Ekaterina I Izgorodina. etry optimisations of ionic liquid clusters. 16(10):6735–6753, 2020. A systematic study of dft performance for geom-Journal of Chemical Theory and Computation,

Xiaobin Liao, Ruihu Lu, Lixue Xia, Qian Liu, Huan Wang, Kristin Zhao, Zhaoyang Wang, and Yan Zhao. Density functional theory for electrocatalysis. Energy & Environmental Materials, 5(1):157–185, 2022.

Udo Schnupf and Frank A Momany. Dft energy optimisation of a large carbohydrate: cyclo-maltohexaicosaose (ca-26). The Journal of Physical Chemistry B, 116(23):6618–6627, 2012.

Robert Palmer, Steve Barrus, Yu Yang, Ganesh Gopalakrishnan, and Robert M Kirby. Gauss: A framework for verifying scientific computing software. Electronic Notes in Theoretical Com-puter Science, 144(3):95–106, 2006.

Ian D Chivers and Jane Sleightholme. Introduction to programming with Fortran, volume 2. Springer, 2018.

John A Trangenstein. Scientific Computing. Springer, 2017.

Trygve Helgaker, POUL JØRGENSEN, Jeppe Olsen, and Wim Klopper. Wave function based quantum chemistry. Computational Medicinal Chemistry for Drug Discovery. New York–Basel: Marcel Dekker, pages 57–87, 2004.

Peter MW Gill and Paul von Rague Schleyer. Density functional theory (dft), hartree-fock (hf), and the self-consistent field. J. Chem. Phys, 100:5066–5075, 1994.

M Ya Amusia, AZ Msezane, and VR Shaginyan. Density functional theory versus the hartree– fock method: Comparative assessment. Physica Scripta, 68(6):C133, 2003.

Matthias Ernzerhof and Gustavo E Scuseria. Assessment of the perdew–burke–ernzerhof exchange-correlation functional. The Journal of chemical physics, 110(11):5029–5036, 1999.

Joachim Paier, Robin Hirschl, Martijn Marsman, and Georg Kresse. The perdew–burke– ernzerhof exchange-correlation functional applied to the g2-1 test set using a plane-wave basis set. The Journal of chemical physics, 122(23), 2005.

Oleg A Vydrov and Gustavo E Scuseria. Assessment of a long-range corrected hybrid func-tional. The Journal of chemical physics, 125(23), 2006.

T Gavin Williams and Angela K Wilson. Importance of the quality of metal and ligand basis sets in transition metal species. The Journal of chemical physics, 129(5), 2008.

S Chiodo, Nino Russo, and Emilia Sicilia. Lanl2dz basis sets recontracted in the framework of density functional theory. The Journal of chemical physics, 125(10), 2006.

Victor Christianto. A review of schr¨odinger equation and classical wave equation. Prespacetime Journal, 5(5), 2014.

Robert Withnall, Babur Z Chowdhry, Stephen Bell, and Trevor J Dines. Computational chem-istry using modern electronic structure methods. Journal of chemical education, 84(8):1364, 2007.

Steven M Bachrach. Computational organic chemistry. John Wiley & Sons, 2014.

Christopher M Baker and Guy H Grant. Modeling aromatic liquids: toluene, phenol, and pyridine. Journal of Chemical Theory and Computation, 3(2):530–548, 2007.

Christopher J Cramer. Essentials of computational chemistry: theories and models. John Wiley & Sons, 2013.

Michael E Foster and Karl Sohlberg. Empirically corrected dft and semi-empirical methods for non-bonding interactions. Physical chemistry chemical physics, 12(2):307–322, 2010.

Georg Schreckenbach, P Jeffrey Hay, and Richard L Martin. Density functional calculations on actinide compounds: Survey of recent progress and application to [uo2x4] 2-(x= f, cl, oh) and anf6 (an= u, np, pu). Journal of computational chemistry, 20(1):70–90, 1999.

David A Dixon, Thom H Dunning, Michel Dupuis, David Feller, Deborah Gracio, Robert J Harrison, Donald R Jones, Ricky A Kendall, Jefferey A Nichols, Karen Schuchardt, et al. Com-putational chemistry in the environmental molecular sciences laboratory. In High-Performance Computing, pages 215–228. Springer, 1999.

Trygve Helgaker, Sonia Coriani, Poul Jørgensen, Kasper Kristensen, Jeppe Olsen, and Ken-neth Ruud. Recent advances in wave function-based methods of molecular-property calcula-tions. Chemical reviews, 112(1):543–631, 2012.

Jonathan Thirman and Martin Head-Gordon. tron correlation in intermolecular interactions. 5(8):1380–1385, 2014. Electrostatic domination of the effect of elec-The Journal of Physical Chemistry Letters,

Biswajit Santra. Density-functional theory exchange-correlation functionals for hydrogen bonds in water. PhD thesis, Technische Universit¨at Berlin Berlin, 2010.

Mar´?a Luisa Senent and S Wilson. Intramolecular basis set superposition errors. International journal of quantum chemistry, 82(6):282–292, 2001.

Yue Yang, Michael N Weaver, and Kenneth M Merz Jr. Assessment of the “6-31+ g**+ lanl2dz” mixed basis set coupled with density functional theory methods and the effective core potential: prediction of heats of formation and ionisation potentials for first-row-transition-metal complexes. The Journal of Physical Chemistry A, 113(36):9843–9851, 2009.

Xin Xu and William A Goddard III. The extended perdew-burke-ernzerhof functional with improved accuracy for thermodynamic and electronic properties of molecular systems. The Journal of chemical physics, 121(9):4068–4082, 2004.

Reinhart Ahlrichs, Filipp Furche, and Stefan Grimme. Comment on “assessment of exchange correlation functionals”[aj cohen, nc handy, chem. phys. lett. 316 (2000) 160–166]. Chemical Physics Letters, 325(1-3):317–321, 2000.

Markus Bursch, Jan-Michael Mewes, Andreas Hansen, and Stefan Grimme. Best-practice dft protocols for basic molecular computational chemistry. Angewandte Chemie International Edition, 61(42):e202205735, 2022.

Friedhelm Bechstedt. Non-local exchange and correlation. In Many-Body Approach to Elec-tronic Excitations: Concepts and Applications, pages 163–195. Springer, 2014.

Jochen Heyd, Gustavo E Scuseria, and Matthias Ernzerhof. Hybrid functionals based on a screened coulomb potential. The Journal of chemical physics, 118(18):8207–8215, 2003.

Jochen Heyd, Juan E Peralta, Gustavo E Scuseria, and Richard L Martin. Energy band gaps and lattice parameters evaluated with the heyd-scuseria-ernzerhof screened hybrid functional. The Journal of chemical physics, 123(17), 2005.

Emmanuel Mitry, Pascal Hammel, Ga¨el Deplanque, Fran¸coise Mornex, Philippe Levy, Jean-Fran¸cois Seitz, Alain Moussy, Jean-Pierre Kinet, Olivier Hermine, Philippe Rougier, et al. Safety and activity of masitinib in combination with gemcitabine in patients with advanced pancreatic cancer. Cancer chemotherapy and pharmacology, 66:395–403, 2010.

Carl H Schiesser, Michelle L Styles, and Lisa M Wild. Ab initio study of some free-radical homolytic substitution reactions at silicon, germanium and tin. Journal of the Chemical Society, Perkin Transactions 2, (11):2257–2262, 1996.

Xuefei Xu and Donald G Truhlar. Accuracy of effective core potentials and basis sets for density functional calculations, including relativistic effects, as illustrated by calculations on arsenic compounds. Journal of chemical theory and computation, 7(9):2766–2779, 2011.

Tom´a?s Kuba?r and Marcus Elstner. A hybrid approach to simulation of electron transfer in complex molecular systems. Journal of The Royal Society Interface, 10(87):20130415, 2013.

Richard A Friesner. Ab initio quantum chemistry: Methodology and applications. Proceedings of the National Academy of Sciences, 102(19):6648–6653, 2005.

Igor Lyskov, Martin Kleinschmidt, and Christel M Marian. Redesign of the dft/mrci hamil-tonian. The Journal of chemical physics, 144(3), 2016.

Jos´e Canosa and Roberto Gomes De Oliveira. A new method for the solution of the schr¨odinger equation. Journal of computational physics, 5(2):188–207, 1970.

Brett Barwick, Glen Gronniger, Lu Yuan, Sy-Hwang Liou, and Herman Batelaan. A measure-ment of electron-wall interactions using transmission diffraction from nanofabricated gratings. Journal of Applied Physics, 100(7), 2006.

Roger Bach, Damian Pope, Sy-Hwang Liou, and Herman Batelaan. Controlled double-slit electron diffraction. New Journal of Physics, 15(3):033018, 2013.

Nika N Danial and Stanley J Korsmeyer. Cell death: critical control points. Cell, 116(2):205– 219, 2004.

GA Arteca, FM Fern´andez, EA Castro, GA Arteca, FM Fern´andez, and EA Castro. Rayleigh-schrodinger perturbation theory (rspt). Large Order Perturbation Theory and Summation Methods in Quantum Mechanics, pages 45–71, 1990.

Chr Møller and Milton S Plesset. Note on an approximation treatment for many-electron systems. Physical review, 46(7):618, 1934.

Christopher W Murray, Gregory J Laming, Nicholas C Handy, and Roger D Amos. Kohn—sham bond lengths and frequencies calculated with accurate quadrature and large basis sets. Chemical physics letters, 199(6):551–556, 1992.

Daniel Finkelstein-Shapiro, Stephen K Davidowski, Paul B Lee, Chengchen Guo, Gregory P Holland, Tijana Rajh, Kimberly A Gray, Jeffery L Yarger, and Monica Calatayud. Direct evidence of chelated geometry of catechol on tio2 by a combined solid-state nmr and dft study. The Journal of Physical Chemistry C, 120(41):23625–23630, 2016.

Robert B Murphy, Michael D Beachy, Richard A Friesner, and Murco N Ringnalda. Pseu-dospectral localised mo/ller–plesset methods: Theory and calculation of conformational ener-gies. The Journal of chemical physics, 103(4):1481–1490, 1995.

Seiji Tsuzuki and Hans P L¨uthi. Interaction energies of van der waals and hydrogen bonded systems calculated using density functional theory: Assessing the pw91 model. The Journal of Chemical Physics, 114(9):3949–3957, 2001.

Seiji Tsuzuki, Tadafumi Uchimaru, and Kazutoshi Tanabe. Intermolecular interaction poten-tials of methane and ethylene dimers calculated with the møller–plesset, coupled cluster and density functional methods. Chemical physics letters, 287(1-2):202–208, 1998.

John P Perdew, Kieron Burke, and Matthias Ernzerhof. Generalised gradient approximation made simple. Physical review letters, 77(18):3865, 1996.

Javier Carmona-Esp´?ndola, Jos´e L G´azquez, Alberto Vela, and SB Trickey. Generalised gra-dient approximation exchange energy functional with correct asymptotic behavior of the cor-responding potential. The Journal of Chemical Physics, 142(5), 2015.

Benjamin G Janesko. Rung 3.5 density functionals: Another step on jacob’s ladder. Interna-tional Journal of Quantum Chemistry, 113(2):83–88, 2013.

Frank Jensen. Introduction to computational chemistry. John wiley & sons, 2017.

A Bende, A Vibok, GJ Halasz, and S Suhai. Bsse-free description of the formamide dimers. International Journal of Quantum Chemistry, 84(6):617–622, 2001.

D Moncrieff and S Wilson. A universal basis set for high-precision molecular electronic struc-ture studies: correlation effects in the ground states of, co, bf and. Journal of Physics B: Atomic, Molecular and Optical Physics, 31(17):3819, 1998.

Ugurlu, S.Y., McDonald, D., & He, S. (2024). MEF-AlloSite: An accurate and robust Multimodel Ensemble Feature selection for the Allosteric Site identification model. Journal of Cheminformatics, 16(1), 116.

Ugurlu, S.Y., et al. (2024). Cobdock: An accurate and practical machine learning-based consensus blind docking method. Journal of Cheminformatics, 16(1), 5.

Schmidt, A., Simonovic, S., Kalenius, E., Nissinen, M., & Rissanen, K. (2016). Supramolecular exo-functionalized palladium cages: fluorescent properties and biological activity. Dalton Transactions, 45(20), 8556–8565.

Duan, X., et al. "Nanoparticle formulations of cisplatin for cancer therapy." Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, 8(5):776-791, 2016.

Boulikas, T. "Molecular mechanisms of cisplatin and its liposomally encapsulated form, Lipoplatin™. Lipoplatin™ as a chemotherapy and antiangiogenesis drug." Cancer Therapy, 5:351-376, 2007.

Pourmadadi, M., et al. "Cisplatin-loaded nanoformulations for cancer therapy: A comprehensive review." Journal of Drug Delivery Science and Technology, 77:103928, 2022.

Li, X., et al. "Superior antitumor efficiency of cisplatin-loaded nanoparticles by intratumoral delivery with decreased tumor metabolism rate." European Journal of Pharmaceutics and Biopharmaceutics, 70(3):726-734, 2008.

Jang, B., et al. "Dual delivery of biological therapeutics for multimodal and synergistic cancer therapies." Advanced Drug Delivery Reviews, 98:113-133, 2016.

Dai, W., et al. "Combination antitumor therapy with targeted dual-nanomedicines." Advanced Drug Delivery Reviews, 115:23-45, 2017.

Gurunathan, S., et al. "Nanoparticle-mediated combination therapy: two-in-one approach for cancer." International Journal of Molecular Sciences, 19(10):3264, 2018.

Downloads

Published

2024-12-17

How to Cite

Ugurlu, S. Y., & Enisoglu, R. (2024). Investigation of metallacages for cisplatin encapsulation using Density Functional Theory (DFT). OAJ Materials and Devices, 8. Retrieved from http://caip.co-ac.com/index.php/materialsanddevices/article/view/177