Cationic biocides tend to embed into the inner layer of the model outer membrane vesicles of gram-negative bacteria: Computational insights

E. G. Kholina ; I. B. Kovalenko ; M. G. Strakhovskaya

Matematičeskaâ biologiâ i bioinformatika, Tome 19 (2024) no. 2, pp. 261-275

Résumé

The outer membrane vesicles (OMVs), produced by many pathogenic bacteria, play a significant role in bacterial pathogenesis. They promote bacterial resistance to antibiotics and act as natural protective barriers. The study of OMVs is essential both for understanding the general mechanisms of bacterial pathogenicity and for the development of the antibacterial drugs. In this paper, we created model vesicle that imitate the OMVs of Gram-negative bacteria using molecular modeling techniques. To investigate the interaction of the cationic antimicrobial compounds with the outer lipopolysaccharide (LPS) monolayer and the inner phospholipid monolayer of the OMV membrane, we performed molecular dynamics simulations by placing molecules of the cationic antiseptic octenidine on the outside or inside of model vesicles. The interaction of octenidine with the outer and inner monolayer was significantly different: octenidine interacted weakly with the outer LPS surface of the model OMV, but exhibited high affinity for the phospholipids of the inner monolayer. To study the translocation of cationic antimicrobial molecules within model OMV, we performed steered molecular dynamics simulations. For all three cationic biocide molecules, antiseptic octenidine, photosensitizer octakis(cholinyl)zinc phthalocyanine, and dye methylene blue, it turned out that, along with the LPS of the outer membrane of the OMV, the phosphates of lipid A molecules represent the final barrier to their penetration into the model OMV.

Bibliographie

[1] K. W.K. Tang, B. C. Millar, J. E. Moore, “Antimicrobial Resistance (AMR)”, Br. J. Biomed. Sci, 80 (2023), 11387 | DOI | DOI

[2] G. Cox, G. D. Wright, “Intrinsic Antibiotic Resistance: Mechanisms, Origins, Challenges and Solutions”, Int. J. Med. Microbiol, 303 (2013), 287–292 | DOI | DOI

[3] C. R. Lee, J. H. Lee, M. Park, K. S. Park, I. K. Bae, Y. B. Kim, C. J. Cha, B. C. Jeong, S. H. Lee, “Biology of Acinetobacter Baumannii: Pathogenesis, Antibiotic Resistance Mechanisms, and Prospective Treatment Options”, Front. Cell. Infect. Microbiol, 7 (2017), 55 | DOI | DOI

[4] A. O. Olaitan, S. Morand, J. M. Rolain, “Mechanisms of Polymyxin Resistance: Acquired and Intrinsic Resistance in Bacteria”, Front. Microbiol, 5 (2014), 643 | DOI | DOI

[5] Langsrud S., Sundheim G., Borgmann-Strahsen R., “Intrinsic and Acquired Resistance to Quaternary Ammonium Compounds in Food-Related Pseudomonas Spp”, J. Appl. Microbiol., 95 (2003), 874–882 | DOI | DOI

[6] H. Nikaido, “Molecular Basis of Bacterial Outer Membrane Permeability Revisited”, Microbiol. Mol. Biol. Rev, 67 (2003), 593–656 | DOI | DOI

[7] S. Khalid, C. Schroeder, P. J. Bond, A. L. Duncan, What Have Molecular Simulations Contributed to Understanding of Gram-Negative Bacterial Cell Envelopes?, Microbiology, 168 (2022) | DOI | DOI

[8] A. Kulp, M. J. Kuehn, “Biological Functions and Biogenesis of Secreted Bacterial Outer Membrane Vesicles”, Annu. Rev. Microbiol, 64 (2010), 163–184 | DOI | DOI

[9] M. J. Kuehn, N. C. Kesty, “Bacterial Outer Membrane Vesicles and the Host-Pathogen Interaction”, Genes Dev, 19 (2005), 2645–2655 | DOI | DOI

[10] C. Schwechheimer, M. J. Kuehn, “Outer-Membrane Vesicles from Gram-Negative Bacteria: Biogenesis and Functions”, Nat. Rev. Microbiol, 13 (2015), 605–619 | DOI | DOI

[11] N.; Wu M.; Wang L.; Tang M.; Xin H.; Deng K. Li, “Efficient Isolation of Outer Membrane Vesicles (OMVs) Secreted by Gram-Negative Bacteria via a Novel Gradient Filtration Method”, Membranes, 14 (2024), 135 | DOI | DOI

[12] D. Anand, A. Chaudhuri, “Bacterial Outer Membrane Vesicles: New Insights and Applications”, Mol. Membr. Biol, 33 (2016), 125–137 | DOI | MR | DOI | MR

[13] G. Magana, C. Harvey, C. C. Taggart, A. M. Rodgers, “Bacterial Outer Membrane Vesicles: Role in Pathogenesis and Host-Cell Interactions”, Antibiotics, 13 (2023), 32 | DOI | DOI

[14] J. Y. Kim, J. W. Suh, J. S. Kang, S. B. Kim, Y. K. Yoon, J. W. Sohn, “Gram-Negative Bacteria's Outer Membrane Vesicles”, Infect. Chemother, 55 (2023), 1 | DOI | DOI

[15] A. T. Jan, “Outer Membrane Vesicles (OMVs) of Gram-Negative Bacteria: A Perspective Update”, Front. Microbiol, 8 (2017), 1053 | DOI | Zbl | DOI | Zbl

[16] L. M. Munoz-Echeverri, S. Benavides-Lopez, O. Geiger, M. A. Trujillo-Roldan, N. A. Valdez Cruz, “Bacterial Extracellular Vesicles: Biotechnological Perspective for Enhanced Productivity”, World J. Microbiol. Biotechnol, 40 (2024), 174 | DOI | DOI

[17] S. Combo, S. Mendes, K. M. Nielsen, G. J. Da Silva, S. Domingues, “The Discovery of the Role of Outer Membrane Vesicles against Bacteria”, Biomedicines, 10 (2022), 2399 | DOI | DOI

[18] S. N. Wai, A. Takade, K. Amako, “The Release of Outer Membrane Vesicles from the Strains of Enterotoxigenic Escherichia coli”, Microbiol. Immunol, 39 (1995), 451–456 | DOI | DOI

[19] G. L. Matthews K. R. Kolling, “Export of Virulence Genes and Shiga Toxin by Membrane Vesicles of Escherichia coli O157:H7”, Appl. Environ. Microbiol, 65 (1999), 1843–1848 | DOI | DOI

[20] D. Chatterjee, K. Chaudhuri, “Association of Cholera Toxin with Vibrio Cholerae Outer Membrane Vesicles Which Are Internalized by Human Intestinal Epithelial Cells”, FEBS Lett, 585 (2011), 1357–1362 | DOI | DOI

[21] A. Perez, M. Merino, S. Rumbo-Feal, L. Alvarez-Fraga, J. A. Vallejo, A. Beceiro, E. J. Ohneck, J. Mateos, P. Fernandez-Puente, L. A. Actis et al, “The FhaB/FhaC Two Partner Secretion System Is Involved in Adhesion of Acinetobacter Baumannii AbH12O-A2 Strain”, Virulence, 271:8 (2017), 959–974 | DOI | DOI

[22] S. J. Bauman, M. J. Kuehn, “Pseudomonas aeruginosa Vesicles Associate with and Are Internalized by Human Lung Epithelial Cells”, BMC Microbiol, 9 (2009), 26 | DOI | DOI

[23] T. N. Ellis, M. J. Kuehn, “Virulence and Immunomodulatory Roles of Bacterial Outer Membrane Vesicles”, Microbiol. Mol. Biol. Rev, 74 (2010), 81–94 | DOI | DOI

[24] A. Toledo, J. L. Coleman, C. J. Kuhlow, J. T. Crowley, J. L. Benach, “The Enolase of Borrelia Burgdorferi Is a Plasminogen Receptor Released in Outer Membrane Vesicles”, Infect. Immun., 80 (2012), 359–368 | DOI | DOI

[25] M. Lappann, A. Otto, D. Becher, U. Vogel, “Comparative Proteome Analysis of Spontaneous Outer Membrane Vesicles and Purified Outer Membranes of Neisseria meningitidis”, J. Bacteriol, 195 (2013), 4425–4435 | DOI | DOI

[26] T. Nagakubo, N. Nomura, M. Toyofuku, “Cracking Open Bacterial Membrane Vesicles”, Front. Microbiol, 10 (2020), 3026 | DOI | DOI

[27] H. Yonezawa, T. Osaki, S. Kurata, M. Fukuda, H. Kawakami, K. Ochiai, T. Hanawa, S. Kamiya, “Outer Membrane Vesicles of Helicobacter pylori TK1402 Are Involved in Biofilm Formation”, BMC Microbiol, 9 (2009), 197 | DOI | DOI

[28] T. Henriquez, C. Falciani, “Extracellular Vesicles of Pseudomonas: Friends and Foes”, Antibiotics, 12 (2023), 703 | DOI | DOI

[29] B. Jiang, Y. Lai, W. Xiao, T. Zhong, F. Liu, J. Gong, J. Huang, “Microbial Extracellular Vesicles Contribute to Antimicrobial Resistance”, PLOS Pathog., 20 (2024), e1012143 | DOI | DOI

[30] E. S. Medvedeva, N. B. Baranova, A. A. Mouzykantov, T. Yu. Grigorieva, M. N. Davydova, M. V. Trushin, O. A. Chernova, V. M. Chernov, “Adaptation of Mycoplasmas to Antimicrobial Agents: Acholeplasma laidlawii Extracellular Vesicles Mediate the Export of Ciprofloxacin and a Mutant Gene Related to the Antibiotic Target”, Sci. World J., 2014 (2014), 1–7 | DOI | DOI

[31] J. L. Kadurugamuwa, T. J. Beveridge, “Bacteriolytic Effect of Membrane Vesicles from Pseudomonas aeruginosa on Other Bacteria Including Pathogens: Conceptually New Antibiotics”, J. Bacteriol, 178 (1996), 2767–2774 | DOI | DOI

[32] A. J. Manning, M. J. Kuehn, “Contribution of Bacterial Outer Membrane Vesicles to Innate Bacterial Defense”, BMC Microbiol, 11 (2011), 258 | DOI | DOI

[33] M. D. Balhuizen, A. Van Dijk, J. W.A. Jansen, C. H.A. Van De Lest, E. J.A. Veldhuizen, H. P. Haagsman, “Outer Membrane Vesicles Protect Gram-Negative Bacteria against Host Defense Peptides”, mSphere, 6 (2021), e00523-21 | DOI | DOI

[34] J. Park, M. Kim, B. Shin, M. Kang, J. Yang, T. K. Lee, W. Park, “A Novel Decoy Strategy for Polymyxin Resistance in Acinetobacter baumannii”, eLife, 10 (2021), e66988 | DOI | DOI

[35] D. Grenier, J. Bertrand, D. Mayrand, “Porphyromonas gingivalis Outer Membrane Vesicles Promote Bacterial Resistance to Chlorhexidine”, Oral Microbiol. Immunol, 10 (1995), 319–320 | DOI | DOI

[36] S. W. Kim, S. B. Park, S. P. Im, J. S. Lee, J. W. Jung, T. W. Gong, J. M.S. Lazarte, J. Kim, J. S. Seo, J. H. Kim et al, “Outer Membrane Vesicles from $\beta$-Lactam-Resistant Escherichia coli Enable the Survival of $\beta$-Lactam-Susceptible E coli in the Presence of $\beta$-Lactam Antibiotics”, Sci. Rep, 8 (2018), 5402 | DOI | DOI

[37] R. Stentz, N. Horn, K. Cross, L. Salt, C. Brearley, D. M. Livermore, S. R. Carding, “Cephalosporinases Associated with Outer Membrane Vesicles Released by Bacteroides Spp. Protect Gut Pathogens and Commensals against $\beta$-Lactam Antibiotics”, J. Antimicrob. Chemother, 70 (2015), 701–709 | DOI | DOI

[38] S. J. Marrink, H. J. Risselada, S. Yefimov, D. P. Tieleman, A. H. De Vries, “The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations”, J. Phys. Chem. B, 111 (2007), 7812–7824 | DOI | DOI

[39] P. Hsu, B. M.H. Bruininks, D. Jefferies, P. Cesar Telles De Souza, J. Lee, D.S. Patel, S.J. Marrink, Y. Qi, S. Khalid, W. Im, “CHARMM-GUI Martini Maker for Modeling and Simulation of Complex Bacterial Membranes with Lipopolysaccharides”, J. Comput. Chem, 38 (2017), 2354–2363 | DOI | DOI

[40] D. Jefferies, J. Shearer, S. Khalid, “Role of O-Antigen in Response to Mechanical Stress of the E coli Outer Membrane: Insights from Coarse-Grained MD Simulations”, J. Phys. Chem. B, 123 (2019), 3567–3575 | DOI | DOI

[41] W. Im, S. Khalid, “Molecular Simulations of Gram-Negative Bacterial Membranes Come of Age”, Annu. Rev. Phys. Chem, 71 (2020), 171–188 | DOI | DOI

[42] A. J. Rzepiela, D. Sengupta, N. Goga, S. J. Marrink, “Membrane Poration by Antimicrobial Peptides Combining Atomistic and Coarse-Grained Descriptions”, Faraday Discuss, 144 (2010), 431–443 | DOI | DOI

[43] G. Balatti, E. Ambroggio, G. Fidelio, M. Martini, M. Pickholz, “Differential Interaction of Antimicrobial Peptides with Lipid Structures Studied by Coarse-Grained Molecular Dynamics Simulations”, Molecules, 22 (2017), 1775 | DOI | MR | DOI | MR

[44] R. Talandashti, F. Mehrnejad, K. Rostamipour, F. Doustdar, A. Lavasanifar, “Molecular Insights into Pore Formation Mechanism, Membrane Perturbation, and Water Permeation by the Antimicrobial Peptide Pleurocidin: A Combined All-Atom and Coarse-Grained Molecular Dynamics Simulation Study”, J. Phys. Chem. B, 125 (2021), 7163–7176 | DOI | DOI

[45] H. Lee, “Heterodimer and Pore Formation of Magainin 2 and PGLa: The Anchoring and Tilting of Peptides in Lipid Bilayers”, Biochim. Biophys. Acta BBA Biomembr, 1862 (2020), 183305 | DOI | DOI

[46] G. E. Balatti, M. F. Martini, M. Pickholz, “A Coarse-Grained Approach to Studying the Interactions of the Antimicrobial Peptides Aurein 1.2 and Maculatin 1.1 with POPG/POPE Lipid Mixtures”, J. Mol. Model, 24 (2018), 208 | DOI | DOI

[47] A. Catte, M. R. Wilson, M. Walker, V. S. Oganesyan, “Antimicrobial Action of the Cationic Peptide, Chrysophsin-3: A Coarse-Grained Molecular Dynamics Study”, Soft Matter, 14 (2018), 2796–2807 | DOI | DOI

[48] Q. Li, X. Zhong, L. Sun, L. Dai, Enhancement of Cell Membrane Poration by the Antimicrobial Peptide Melp5, 2024, arXiv: 2310.11156 [physics.bio-ph] | DOI | DOI

[49] A. Melcrova, S. Maity, J. Melcr, N. A.W. De Kok, M. Gabler, J. Van Der Eyden, W. Stensen, J. S.M. Svendsen, A. J.M. Driessen, S. J. Marrink et al, “Lateral Membrane Organization as Target of an Antimicrobial Peptidomimetic Compound”, Nat. Commun, 14 (2023), 4038 | DOI | DOI

[50] P. C. Hsu, D. Jefferies, S. Khalid, “Molecular Dynamics Simulations Predict the Pathways via Which Pristine Fullerenes Penetrate Bacterial Membranes”, J. Phys. Chem. B, 120 (2016), 11170–11179 | DOI | DOI

[51] E. T. Rietschel, T. Kirikae, F. U. Schade, U. Mamat, G. Schmidt, H. Loppnow, A. J. Ulmer, U. Zahringer, U. Seydel, F. Di Padova et al, “Bacterial Endotoxin: Molecular Relationships of Structure to Activity and Function”, FASEB J., 8 (1994), 217–225 | DOI | DOI

[52] B. Van Oosten, D. Marquardt, T. A. Harroun, “Testing High Concentrations of Membrane Active Antibiotic Chlorhexidine Via Computational Titration and Calorimetry”, J. Phys. Chem. B, 121 (2017), 4657–4668 | DOI | DOI

[53] S. O. Yesylevskyy, L. V. Schafer, D. Sengupta, S. J. Marrink, “Polarizable Water Model for the Coarse-Grained MARTINI Force Field”, PLoS Comput. Biol., 6 (2010), e1000810 | DOI | DOI

[54] M. J. Abraham, T. Murtola, R. Schulz, S. Pall, J. C. Smith, B. Hess, E. Lindahl, “GROMACS: High Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers”, SoftwareX, 1:2 (2015), 19–25 | DOI | DOI

[55] I. B. Kovalenko, O. S. Knyazeva, T. K. Antal, V. Y. Ponomarev, G. Y. Riznichenko, A. B. Rubin, “Multiparticle Brownian Dynamics Simulation of Experimental Kinetics of Cytochrome Bf Oxidation and Photosystem I Reduction by Plastocyanin”, Physiol. Plant, 161 (2017), 88–96 | DOI | DOI

[56] V. A. Fedorov, I. B. Kovalenko, S. S. Khruschev, D. M. Ustinin, T. K. Antal, G. Y. Riznichenko, A. B. Rubin, “Comparative Analysis of Plastocyanin-Cytochrome f Complex Formation in Higher Plants, Green Algae and Cyanobacteria”, Physiol. Plant, 166 (2019), 320–335 | DOI | DOI

[57] The PyMOL Molecular Graphics System, Version 2.4, Schrodinger, LLC

[58] P. S. Orekhov, E. G. Kholina, M. E. Bozdaganyan, A. M. Nesterenko, I. B. Kovalenko, M. G. Strakhovskaya, “Molecular Mechanism of Uptake of Cationic Photoantimicrobial Phthalocyanine across Bacterial Membranes Revealed by Molecular Dynamics Simulations”, J. Phys. Chem. B, 122 (2018), 3711–3722 | DOI | DOI

[59] E. G. Kholina, I. B. Kovalenko, M. E. Bozdaganyan, M. G. Strakhovskaya, P. S. Orekhov, “Cationic Antiseptics Facilitate Pore Formation in Model Bacterial Membranes”, J. Phys. Chem. B, 124 (2020), 8593–8600 | DOI | DOI

[60] G. A. Meerovich, E. V. Akhlyustina, I. D. Romanishkin, E. A. Makarova, I. G. Tiganova, V. G. Zhukhovitsky, E. G. Kholina, I. B. Kovalenko, Y. M. Romanova, V. B. Loschenov et al, “Photodynamic Inactivation of Bacteria: Why It Is Not Enough to Excite a Photosensitizer”, Photodiagnosis Photodyn. Ther., 44 (2023), 103853 | DOI | DOI

[61] H. I. Zgurskaya, V. V. Rybenkov, “Permeability Barriers of Gram-negative Pathogens”, Ann. N. Y. Acad. Sci, 1459 (2020), 5–18 | DOI | DOI

[62] C. Maher, K. A. Hassan, “The Gram-Negative Permeability Barrier: Tipping the Balance of the in and the Out”, mBio, 14 (2023), e01205-23 | DOI | DOI

[63] C. Gonzalez-Fernandez, E. Bringas, C. Oostenbrink, I. Ortiz, In silico Investigation and Surmounting of Lipopolysaccharide Barrier in Gram-Negative Bacteria: How Far Has Molecular Dynamics Come?, Comput. Struct. Biotechnol. J., 20 (2022), 5886–5901 | DOI | DOI

[64] G. Pier, “Pseudomonas aeruginosa Lipopolysaccharide: A Major Virulence Factor, Initiator of Inflammation and Target for Effective Immunity”, Int. J. Med. Microbiol, 297 (2007), 277–295 | DOI | DOI

[65] S. A. Makin, T. J. Beveridge, “Pseudomonas aeruginosa PAO1 Ceases to Express Serotype-Specific Lipopolysaccharide at 45 Degrees C”, J. Bacteriol, 178 (1996), 3350–3352 | DOI | DOI

[66] J. D. King, D. Kocincova, E. L. Westman, J. S. Lam, “Review: Lipopolysaccharide Biosynthesis in Pseudomonas aeruginosa”, Innate Immun, 15 (2009), 261–312 | DOI | DOI

[67] A. N. Vereshchagin, N. A. Frolov, K. S. Egorova, M. M. Seitkalieva, V. P. Ananikov, “Quaternary Ammonium Compounds (QACs) and Ionic Liquids (ILs) as Biocides: From Simple Antiseptics to Tunable Antimicrobials”, Int. J. Mol. Sci, 22 (2021), 6793 | DOI | DOI

[68] D. Vejzovic, A. Iftic, A. On, E. F. Semeraro, N. Malanovic, Octenidine's Efficacy: A Matter of Interpretation or the Influence of Experimental Setups?, Antibiotics, 11 (2022), 1665 | DOI | DOI

[69] S. Nasrollahian, J. P. Graham, M. Halaji, “A Review of the Mechanisms That Confer Antibiotic Resistance in Pathotypes of E coli”, Front. Cell. Infect. Microbiol, 14 (2024), 1387497 | DOI | DOI