Plasma for cancer treatment: How can RONS penetrate through the cell membrane? Answers from computer modeling

Abstract

Plasma is gaining increasing interest for cancer treatment, but the underlying mechanisms are not yet fully understood. Using computer simulations at the molecular level, we try to gain better insight in how plasma-generated reactive oxygen and nitrogen species (RONS) can penetrate through the cell membrane. Specifically, we compare the permeability of various (hydrophilic and hydrophobic) RONS across both oxidized and non-oxidized cell membranes. We also study pore formation, and how it is hampered by higher concentrations of cholesterol in the cell membrane, and we illustrate the much higher permeability of H₂O₂ through aquaporin channels. Both mechanisms may explain the selective cytotoxic effect of plasma towards cancer cells. Finally, we also discuss the synergistic effect of plasma-induced oxidation and electric fields towards pore formation.

Key words： plasma medicine; cancer treatment; computer modelling; cell membrane; reactive oxygen and nitrogen species

Acknowledgements

We acknowledge financial support from the Research Foundation−Flanders (FWO; Grant Nos. 1200216N and 11U5416N). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. We are also very thankful to R. Cordeiro for the very interesting discussions.

References

1 Keidar M, Walk R, Shashurin A, Srinivasan P, Sandler A, Dasgupta S, Ravi R, Guerrero-Preston R, Trink B. Cold plasma selectivity and the possibility of a paradigm shift in cancer therapy. British Journal of Cancer, 2011, 105(9): 1295–1301

2 Graves D B. Reactive species from cold atmospheric plasma: Implications for cancer therapy. Plasma Processes and Polymers, 2014, 11(12): 1120–1127

3 Lu X, Naidis G V, Laroussi M, Reuter S, Graves D B, Ostrikov K. Reactive species in non-equilibrium atmospheric-pressure plasmas: Generation, transport, and biological effects. Physics Reports, 2016, 630: 1–84

4 Hole P S, Zabkiewicz J, Munje C, Newton Z, Pearn L, White P, Marquez N, Hills R K, Burnett A K, Tonks A, Darley R L. Overproduction of NOX-derived ROS in AML promotes proliferation and is associated with defective oxidative stress signaling. Blood, 2013, 122(19): 3322–3330

5 Papadopoulos M C, Saadoun S. Key roles of aquaporins in tumor biology. Biochimica et Biophysica Acta (BBA) - Biomembranes, 2015, 1848(10): 2576–2583

6 Cordeiro R M. Molecular dynamics simulations of the transport of reactive oxygen species by mammalian and plant aquaporins. Biochimica et Biophysica Acta (BBA) - General Subjects, 2015, 1850(9): 1786–1794

7 Yan D, Talbot A, Nourmohammadi N, Sherman J H, Cheng X, Keidar M. Toward understanding the selective anticancer capacity of cold atmospheric plasma—a model based on aquaporins. Biointerphases, 2015, 10(4): 040801

8 Wong-Ekkabut J, Xu Z, Triampo W, Tang I M, Tieleman D P, Monticelli L. Effect of lipid peroxidation on the properties of lipid bilayers: A molecular dynamics study. Biophysical Journal, 2007, 93(12): 4225–4236

9 Beranova L, Cwiklik L, Jurkiewicz P, Hof M, Jungwirth P. Oxidation changes physical properties of phospholipid bilayers: Fluorescence spectroscopy and molecular simulations. Langmuir, 2010, 26(9): 6140–6144

10 Cwiklik L, Jungwirth P. Massive oxidation of phospholipid membranes leads to pore creation and bilayer disintegration. Chemical Physics Letters, 2010, 486(4-6): 99–103

11 Van der Paal J, Neyts E C, Verlackt C C W, Bogaerts A. Effect of lipid peroxidation on membrane permeability of cancer and normal cells subjected to oxidative stress. Chemical Science (Cambridge), 2016, 7(1): 489–498

12 Van der Paal J, Verheyen C, Neyts E C, Bogaerts A. Hampering effect of cholesterol on the permeation of reactive oxygen species through phospholipids bilayer: Possible explanation for plasma cancer selectivity. Scientific Reports, 2017, 7(1): 39526

13 Svarnas P, Matrali S H, Gazeli K, Antimisiaris S G. Assessment of atmospheric-pressure guided streamer (plasma bullet) influence on liposomes with different composition and physicochemical properties. Plasma Processes and Polymers, 2015, 12(7): 655–665

14 Hirst A M, Frame F M, Arya M, Maitland N J, O’Connell D. Low temperature plasmas as emerging cancer therapeutics: The state of play and thoughts for the future. Tumour Biology, 2016, 37(6): 7021–7031

15 Robert E, Darny T, Dozias S, Iseni S, Pouvesle J M. New insights on the propagation of pulsed atmospheric plasma streams: From single jet to multi jet arrays. Physics of Plasmas, 2015, 22(12): 122007

16 Begum A, Laroussi M, Pervez M R. Atmospheric pressure He-air plasma jet: Breakdown process and propagation phenomenon. AIP Advances, 2013, 3(6): 062117

17 Weaver J C, Smith K C, Esser A T, Son R S, Gowrishankar T. A brief overview of electroporation pulse strength-duration space: A region where additional intracellular effects are expected. Bioelectrochemistry (Amsterdam, Netherlands), 2012, 87: 236–243

18 Vernier P T, Ziegler M J. Nanosecond field alignment of head group and water dipoles in electroporating phospholipid bilayers. Journal of Physical Chemistry B, 2007, 111(45): 12993–12996

19 Casciola M, Tarek M. A molecular insight into the electro-transfer of small molecules through electropores driven by electric fields. Biochimica et Biophysica Acta (BBA) - Biomembranes, 2016, 1858(10): 2278–2289

20 Marrink S J, de Vries A H, Tieleman D P. Lipids on the move: simulations of membrane pores, domains, stalks and curves. Biochimica et Biophysica Acta (BBA) - Biomembranes, 2009, 1788(1): 149–168

21 Tai W Y, Yang Y C, Lin H J, Huang C P, Cheng Y L, Chan M F, Yen H L, Liau I. Interplay between structure and fluidity of model lipid membranes under oxidative attack. Journal of Physical Chemistry B, 2010, 114(47): 15642–15649

22 Grzelinska E, Bartosz G, Gwozdzinski K, Leyko W. A spin-label study of the effect of gamma radiation on erythrocyte membrane. Influence of lipid peroxidation on membrane structure. International Journal of Radiation Biology, 1979, 36: 325–334

23 Wratten M L, Van Ginkel G, Van’t Veld A A, Bekker A, Van Faassen E E, Sevanian A. Structural and dynamic effects of oxidatively modified phospholipids in unsaturated lipid membranes. Biochemistry, 1992, 31(44): 10901–10907

24 Chen J J, Yu B P. Alterations in mitochondrial membrane fluidity by lipid peroxidation products. Free Radical Biology & Medicine, 1994, 17(5): 411–418

25 Richter C. Biophysical consequences of lipid peroxidation in membranes. Chemistry and Physics of Lipids, 1987, 44(2-4): 175–189

26 Mason R P, Walter M F, Mason P E. Effect of oxidative stress on membrane structure: Small-angle X-ray diffraction analysis. Free Radical Biology & Medicine, 1997, 23(3): 419–425

27 Szili E J, Hong S H, Short R D. On the effect of serum on the transport of reactive oxygen species across phospholipid membranes. Biointerphases, 2015, 10(2): 029511

28 Lee E H, Hsin J, Sotomayor M, Comellas G, Schulten K. Discovery through the computational microscope. Structure (London, England), 2009, 17(10): 1295–1306

29 Cordeiro R M. Reactive oxygen species at phospholipid bilayers: Distribution, mobility and permeation. Biochimica et Biophysica Acta (BBA) - Biomembranes, 2014, 1838(1): 438–444

30 Miotto R, Costa E B, Trellese E B, Neto A J P, Baptista M S, Ferraz A C, Cordeiro R M. Biomembranes under oxidative stress, Insights from molecular dynamics simulations. In: Tran Q N, Arabnia H R, eds. Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology: Systems and Applications. Amsterdam: Elsevier, 2016, 197–211

31 Yusupov M, Van der Paal J, Neyts E C, Bogaerts A. Synergistic effect of electric field and lipid oxidation on the permeability of cell membranes. Biochimica et Biophysica Acta (BBA) - General, 2017, 1861: 839–847

32 Yusupov M, Wende K, Kupsch S, Neyts E C, Reuter S, Bogaerts A. Effect of head group and lipid tail oxidation in the cell membrane revealed through integrated simulations and experiments. Scientific Reports, 2017, 7(1): 5761

33 Yusupov M, Yan D, Cordeiro R M, Bogaerts A. Atomic scale simulation of H₂O₂ permeation through aquaporin: Toward the understanding of plasma-cancer treatment. Journal of Physics. D, Applied Physics, 2018, 51(12): 125401

34 Razzokov J, Yusupov M, Cordeiro R M, Bogaerts A. Atomic scale understanding of the permeation of plasma species across native and oxidized membranes. Journal of Physics. D, Applied Physics, 2018, 51(36): 365203

35 Bogaerts A, Khosravian N, Van der Paal J, Verlackt C C W, Yusupov M, Kamaraj B, Neyts E C. Multi-level molecular modeling for plasma medicine. Journal of Physics. D, Applied Physics, 2016, 49(5): 054002

36 Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim Th, Suhai S, Seifert G. Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties. Physical Review. B, 1998, 58(11): 7260–7268

37 Khosravian N, Kamaraj B, Neyts E C, Bogaerts A. Structural modification of P-glycoprotein induced by OH radicals: Insights from atomistic simulations. Scientific Reports, 2016, 6(1): 19466

38 Verlackt C C W, Van Boxem W, Dewaele D, Lemière F, Sobott F, Benedikt J, Neyts E C, Bogaerts A. Mechanisms of peptide oxidation by hydroxyl radicals: Insight at the molecular scale. Journal of Physical Chemistry C, 2017, 121(10): 5787–5799

39 Verlackt C C W, Neyts E C, Bogaerts A. Atomic scale behavior of oxygen-based radicals in water. Journal of Physics. D, Applied Physics, 2017, 50(11): 11LT01

40 Brenner D W. Empirical potential for hydrocarbons for use in simulating the chemical vapor deposition of diamond films. Physical Review. B, 1990, 42(15): 9458–9471

41 van Duin A C T, Dasgupta S, Lorant F, Goddard W A, Reax F F. A reactive force field for hydrocarbons. Journal of Physical Chemistry A, 2001, 105(41): 9396–9409

42 Yusupov M, Neyts E C, Khalilov U, Snoeckx R, van Duin A C T, Bogaerts A. Atomic scale simulations of plasma species interacting with bacterial cell walls. New Journal of Physics, 2012, 14(9): 093043

43 Yusupov M, Bogaerts A, Huygh S, Snoeckx S, van Duin A C T, Neyts E C. Plasma-induced destruction of bacterial cell wall components: A reactive molecular dynamics simulation. Journal of Physical Chemistry C, 2013, 117(11): 5993–5998

44 Yusupov M, Neyts E C, Verlackt C C, Khalilov U, van Duin A C T, Bogaerts A. Inactivation of the endotoxic biomolecule lipid A by oxygen plasma species: A reactive molecular dynamics study. Plasma Processes and Polymers, 2015, 12(2): 162–171

45 Babaeva N Y, Ning N, Graves D B, Kushner M J. Ion activation energy delivered to wounds by atmospheric pressure dielectric-barrier discharges: Sputtering of lipid-like surfaces. Journal of Physics. D, Applied Physics, 2012, 45(11): 115203

46 Van der Paal J, Aernouts S, van Duin A C T, Neyts E C, Bogaerts A. Interaction of O and OH radicals with a simple model system for lipids in the skin barrier: A reactive molecular dynamics simulation for plasma medicine. Journal of Physics. D, Applied Physics, 2013, 46(39): 395201

47 Van der Paal J, Verlackt C C, Yusupov M, Neyts E C, Bogaerts A. Structural modification of the skin barrier by OH radicals: A reactive molecular dynamics study for plasma medicine. Journal of Physics. D, Applied Physics, 2015, 48(15): 155202

48 Abolfath R M, Biswas P K, Rajnarayanam R, Brabec T, Kodym R, Papiez L. Multiscale QM/MM molecular dynamics study on the first steps of guanine damage by free hydroxyl radicals in solution. Journal of Physical Chemistry A, 2012, 116(15): 3940–3945

49 Verlackt C C M, Neyts E C, Jacob T, Fantauzzi D, Golkaram M, Shin Y K, van Duin A C T, Bogaerts A. Atomic-scale insight in the interactions between hydroxyl radicals and DNA in solution using the ReaxFF reactive force field. New Journal of Physics, 2015, 17(10): 103005

50 Yusupov M, Neyts E C, Simon P, Bergiyorov G, Snoeckx R, van Duin A C T, Bogaerts A. Reactive molecular dynamics simulations of oxygen species in a liquid water layer of interest for plasma medicine. Journal of Physics. D, Applied Physics, 2014, 47(2): 025205

51 Khosravian N, Bogaerts A, Huygh S, Yusupov M, Neyts E C. How do plasma-generated OH radicals react with biofilm components? Insights from atomic scale simulations. Biointerphases, 2015, 10(2): 029501

52 Berger O, Edholm O, Jähnig F. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. Biophysical Journal, 1997, 72(5): 2002–2013

53 Cornell W D, Cieplak P, Bayly C I, Gould I R, Merz K M Jr, Ferguson D M, Spellmeyer D C, Fox T, Caldwell J W, Kollman P A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. Journal of the American Chemical Society, 1995, 117(19): 5179–5197

54 Yu W, He X, Vanommeslaeghe K, MacKerell A D Jr. Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations. Journal of Computational Chemistry, 2012, 33(31): 2451–2468

55 van Gunsteren W F, Berendsen H J C. Groningen Molecular Simulation (GROMOS) Library Manual. Groningen, The Netherlands: Biomos, 1987, 1–221

56 Marrink S J, Risselada H J, Yefimov S, Tieleman D P, De Vries A H. The MARTINI force field: Coarse grained model for biomolecular simulations. Journal of Physical Chemistry B, 2007, 111(27): 7812–7824

57 Åqvist J, Warshel A. Simulation of enzyme reactions using valence bond force fields and other hybrid quantum/classical approaches. Chemical Reviews, 1993, 93(7): 2523–2544

58 Neyts E C, Yusupov M, Verlackt C C, Bogaerts A. Computer simulations of plasma-biomolecule and plasma-tissue interactions for a better insight in plasma medicine. Journal of Physics. D, Applied Physics, 2014, 47(29): 293001

59 Möller M N, Li Q, Lancaster J R Jr, Denicola A. Acceleration of nitric oxide autoxidation and nitrosation by membranes. IUBMB Life, 2007, 59(4): 243–248

60 Subczynski W K, Lomnicka M, Hyde J S. Permeability of nitric oxide through lipid bilayer membranes. Free Radical Research, 1996, 24(5): 343–349

61 Shinitzky M. Membrane fluidity in malignancy adversative and recuperative. Biochimica et Biophysica Acta (BBA) - Revue Canadienne, 1984, 738: 251–261

62 Reis A, Domingues M R M, Amado F M L, Ferrer-Correia A J V, Domingues P. Separation of peroxidation products of diacyl-phosphatidylcholines by reversed-phase liquid chromatography-mass spectrometry. Biomedical Chromatography, 2005, 19(2): 129–137

63 Haluska C K, Baptista M S, Fernades A U, Schroder A P, Marques C M, Itri R. Photo-activated phase separation in giant vesicles made from different lipid mixture. Biochimica et Biophysica Acta (BBA) - Biomembranes, 2012, 1818: 666–672

64 Lackmann J W, Schneider S, Edengeiser E, Jarzina F, Brinckmann S, Steinborn E, Havenith M, Benedikt J, Bandow J E. Photons and particles emitted from cold atmospheric-pressure plasma inactivate bacteria and biomolecules independently and synergistically. Journal of the Royal Society, Interface, 2013, 10(89): 20130591

65 Chung T Y, Ning N, Chu J W, Graves D B, Bartis E, Seog J, Oehrlein G S. Plasma deactivation of endotoxic biomolecules: Vacuum ultraviolet photon and radical beam effects on Lipid A. Plasma Processes and Polymers, 2013, 10(2): 167–180

66 Bartis E A J, Graves D B, Seog J, Oehrlein G S. Atmospheric pressure plasma treatment of lipopolysaccharide in a controlled environment. Journal of Physics. D, Applied Physics, 2013, 46(31): 312002 doi:10.1088/0022-3727/46/31/312002

67 Bartis E A J, Barrett C, Chung T Y, Ning N, Chu J W, Graves D B, Seog J, Oehrlein G S. Deactivation of lipopolysaccharide by Ar and H₂ inductively coupled low-pressure plasma. Journal of Physics. D, Applied Physics, 2014, 47(4): 045202

68 Park J H, Kumar N, Park D H, Yusupov M, Neyts E C, Verlackt C C W, Bogaerts A, Kang M H, Uhm H S, Choi E H, A comparative study for the inactivation of multidrug resistance bacteria using dielectric barrier discharge and nano-second pulsed plasma. Scientific Reports, 2015, 5(1): 13849

69 Marschewski M, Hirschberg J, Omairi T, Hofft O, Viol W, Emmert S, Maus-Friedrichs W. Electron spectroscopic analysis of the human lipid skin barrier: Cold atmospheric plasma-induced changes in lipid composition. Experimental Dermatology, 2012, 21(12): 921–925

70 Takai E, Kitamura T, Kuwabara J, Ikawa S, Yoshizawa S, Shiraki K, Kawasaki H, Arakawa R, Kitano K. Chemical modification of amino acids by atmospheric-pressure cold plasma in aqueous solution. Journal of Physics. D, Applied Physics, 2014, 47(28): 285403

71 Madugundu G S, Cadet J, Wagner J R. Hydroxyl-radical-induced oxidation of 5-methylcytosine in isolated and cellular DNA. Nucleic Acids Research, 2014, 42(11): 7450–7460

72 Hong S H, Szili E J, Jenkins A T A, Short R D. Ionized gas (plasma) delivery of reactive oxygen species (ROS) into artificial cells. Journal of Physics. D, Applied Physics, 2014, 47(36): 362001

73 Szili E J, Bradley J W, Short R D. A ‘tissue model’ to study the plasma delivery of reactive oxygen species. Journal of Physics. D, Applied Physics, 2014, 47(15): 152002

74 Hammer M U, Forbrig E, Kupsch S, Weltmann K D, Reuter S. Influence of plasma treatment on the structure and function of lipids. Plasma Medicine, 2013, 3(1-2): 97–114