{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T19:39:06Z","timestamp":1776281946203,"version":"3.50.1"},"reference-count":87,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T00:00:00Z","timestamp":1740096000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","award":["UIDB\/00313\/2020"],"award-info":[{"award-number":["UIDB\/00313\/2020"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","award":["UIDP\/00313\/2020"],"award-info":[{"award-number":["UIDP\/00313\/2020"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","award":["SFRH\/BD\/120934\/2016"],"award-info":[{"award-number":["SFRH\/BD\/120934\/2016"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","award":["2022.11593.BD"],"award-info":[{"award-number":["2022.11593.BD"]}]},{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","award":["CENTRO-04-3559-FSE-000162"],"award-info":[{"award-number":["CENTRO-04-3559-FSE-000162"]}]},{"DOI":"10.13039\/501100001871","name":"FCT","doi-asserted-by":"publisher","award":["UIDB\/00313\/2020"],"award-info":[{"award-number":["UIDB\/00313\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"FCT","doi-asserted-by":"publisher","award":["UIDP\/00313\/2020"],"award-info":[{"award-number":["UIDP\/00313\/2020"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"FCT","doi-asserted-by":"publisher","award":["SFRH\/BD\/120934\/2016"],"award-info":[{"award-number":["SFRH\/BD\/120934\/2016"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"FCT","doi-asserted-by":"publisher","award":["2022.11593.BD"],"award-info":[{"award-number":["2022.11593.BD"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"FCT","doi-asserted-by":"publisher","award":["CENTRO-04-3559-FSE-000162"],"award-info":[{"award-number":["CENTRO-04-3559-FSE-000162"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014717","name":"Programa Operacional Regional do Centro","doi-asserted-by":"publisher","award":["UIDB\/00313\/2020"],"award-info":[{"award-number":["UIDB\/00313\/2020"]}],"id":[{"id":"10.13039\/501100014717","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014717","name":"Programa Operacional Regional do Centro","doi-asserted-by":"publisher","award":["UIDP\/00313\/2020"],"award-info":[{"award-number":["UIDP\/00313\/2020"]}],"id":[{"id":"10.13039\/501100014717","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014717","name":"Programa Operacional Regional do Centro","doi-asserted-by":"publisher","award":["SFRH\/BD\/120934\/2016"],"award-info":[{"award-number":["SFRH\/BD\/120934\/2016"]}],"id":[{"id":"10.13039\/501100014717","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014717","name":"Programa Operacional Regional do Centro","doi-asserted-by":"publisher","award":["2022.11593.BD"],"award-info":[{"award-number":["2022.11593.BD"]}],"id":[{"id":"10.13039\/501100014717","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100014717","name":"Programa Operacional Regional do Centro","doi-asserted-by":"publisher","award":["CENTRO-04-3559-FSE-000162"],"award-info":[{"award-number":["CENTRO-04-3559-FSE-000162"]}],"id":[{"id":"10.13039\/501100014717","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biomolecules"],"abstract":"<jats:p>Rifampicin is a broad-spectrum antibiotic, active against several bacterial infections such as tuberculosis. It is a relatively large and structurally complex molecule, including numerous polar groups. Although violating several of Lipinski\u2019s rules for efficient intestinal absorption, rifampicin shows good oral bioavailability, permeating through cell membranes in the absorption pathway and those of the target organisms. Some hypotheses have been proposed for its efficient membrane permeation, but the details are mostly unknown. In this work, the interaction of rifampicin with POPC lipid bilayers is studied using experimental biophysics methodologies and atomistic molecular dynamics simulations considering the two most prevalent ionic species at physiological pH, the anionic and the zwitterionic forms. The results show that both ionization forms of rifampicin establish favorable interactions with the membrane lipids, in agreement with the relatively high partition coefficient obtained experimentally. The results from MD simulations and isothermal titration calorimetry using different pH buffers show that the piperazine group inserts deeply in the membrane and is accompanied by a stabilization of its neutral form. The bulky nature of rifampicin and its deep insertion in the membrane lead to a strong perturbation in the lipids local order, decreasing the membrane barrier properties as evaluated from the rate of carboxyfluorescein leaching. Altogether, the comparison between the experimental and MD simulations results provides important insight regarding the rifampicin molecular features responsible for its relatively fast membrane permeation. The lipid POPC used in this study was selected as a simple membrane with relevance for different organisms across all kingdoms. Further studies using more complex lipid compositions will provide details on eventual specificities for rifampicin interaction with the membranes of distinct organisms.<\/jats:p>","DOI":"10.3390\/biom15030320","type":"journal-article","created":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T06:39:07Z","timestamp":1740119947000},"page":"320","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Interaction of the Antibiotic Rifampicin with Lipid Membranes"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0957-1665","authenticated-orcid":false,"given":"Rui M. S.","family":"Santos","sequence":"first","affiliation":[{"name":"Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal"},{"name":"Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal"}]},{"given":"Jaime","family":"Samelo","sequence":"additional","affiliation":[{"name":"Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal"},{"name":"Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7920-7773","authenticated-orcid":false,"given":"Alexandre C.","family":"Oliveira","sequence":"additional","affiliation":[{"name":"Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal"},{"name":"Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9404-831X","authenticated-orcid":false,"given":"Margarida M.","family":"Cordeiro","sequence":"additional","affiliation":[{"name":"Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal"},{"name":"Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0137-7910","authenticated-orcid":false,"given":"Maria Julia","family":"Mora","sequence":"additional","affiliation":[{"name":"Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal"},{"name":"Unidad de Investigaci\u00f3n y Desarrollo en Tecnolog\u00eda Farmac\u00e9utica (UNITEFA, CONICET) and Departamento de Ciencias Farmac\u00e9uticas, Facultad de Ciencias Qu\u00edmicas, Universidad Nacional de C\u00f3rdoba, Ciudad Universitaria, C\u00f3rdoba 5000, Argentina"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2142-1675","authenticated-orcid":false,"given":"Gladys E.","family":"Granero","sequence":"additional","affiliation":[{"name":"Unidad de Investigaci\u00f3n y Desarrollo en Tecnolog\u00eda Farmac\u00e9utica (UNITEFA, CONICET) and Departamento de Ciencias Farmac\u00e9uticas, Facultad de Ciencias Qu\u00edmicas, Universidad Nacional de C\u00f3rdoba, Ciudad Universitaria, C\u00f3rdoba 5000, Argentina"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6935-4307","authenticated-orcid":false,"given":"Hugo A. L.","family":"Filipe","sequence":"additional","affiliation":[{"name":"Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal"},{"name":"BRIDGES-Biotechnology Research, Innovation, and Design of Health Products, Polytechnic of Guarda, Av. Dr. Francisco S\u00e1 Carneiro, 50, 6300-559 Guarda, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1051-2312","authenticated-orcid":false,"given":"Lu\u00eds M. S.","family":"Loura","sequence":"additional","affiliation":[{"name":"Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal"},{"name":"CNC\u2014Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal"},{"name":"Faculty of Pharmacy, University of Coimbra, 3000-548 Coimbra, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3076-9905","authenticated-orcid":false,"given":"Maria Jo\u00e3o","family":"Moreno","sequence":"additional","affiliation":[{"name":"Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal"},{"name":"Department of Chemistry, Faculty of Sciences and Technology, University of Coimbra, 3004-535 Coimbra, Portugal"},{"name":"CNC\u2014Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal"}]}],"member":"1968","published-online":{"date-parts":[[2025,2,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.1021\/mp400713v","article-title":"Passive Lipoidal Diffusion and Carrier-Mediated Cell Uptake Are Both Important Mechanisms of Membrane Permeation in Drug Disposition","volume":"11","author":"Smith","year":"2014","journal-title":"Mol. Pharm."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.addr.2016.03.013","article-title":"Cell permeability beyond the rule of 5","volume":"101","author":"Matsson","year":"2016","journal-title":"Adv. Drug Deliv. Rev."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1016\/j.chembiol.2014.08.013","article-title":"Oral Druggable Space beyond the Rule of 5: Insights from Drugs and Clinical Candidates","volume":"21","author":"Doak","year":"2014","journal-title":"Chem. Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/S0169-409X(96)00423-1","article-title":"Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings","volume":"23","author":"Lipinski","year":"1997","journal-title":"Adv. Drug Deliv. Rev."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1016\/j.addr.2016.04.029","article-title":"Rule of five in 2015 and beyond: Target and ligand structural limitations, ligand chemistry structure and drug discovery project decisions","volume":"101","author":"Lipinski","year":"2016","journal-title":"Adv. Drug Deliv. Rev."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"e202202798","DOI":"10.1002\/chem.202202798","article-title":"Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds","volume":"29","author":"Wieske","year":"2022","journal-title":"Chem. A Eur. J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"105802","DOI":"10.1016\/j.ejps.2021.105802","article-title":"Rifampicin as an example of beyond-rule-of-5 compound: Ionization beyond water and lipophilicity beyond octanol\/water","volume":"161","author":"Ermondi","year":"2021","journal-title":"Eur. J. Pharm. Sci."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1016\/j.addr.2016.02.001","article-title":"When barriers ignore the \u201crule-of-five\u201d","volume":"101","author":"Kramer","year":"2016","journal-title":"Adv. Drug Deliv. Rev."},{"key":"ref_9","unstructured":"ChemAxon (2025, January 16). Marvin Sketch, Version 22.9.0. Available online: http:\/\/www.chemaxon.com."},{"key":"ref_10","unstructured":"(2024, October 04). DrugBank Online, Rifampicin. Available online: https:\/\/go.drugbank.com\/drugs\/DB01045."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"3930","DOI":"10.1021\/acs.molpharmaceut.0c00689","article-title":"\u201cFlexible-Acceptor\u201d General Solubility Equation for beyond Rule of 5 Drugs","volume":"17","author":"Avdeef","year":"2020","journal-title":"Mol. Pharm."},{"key":"ref_12","first-page":"468","article-title":"Rifampin","volume":"5","author":"Gallo","year":"1976","journal-title":"Anal. Profiles Drug Subst."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.ejps.2017.03.040","article-title":"Kinetics of lipid bilayer permeation of a series of ionisable drugs and their correlation with human transporter-independent intestinal permeability","volume":"104","author":"Hermann","year":"2017","journal-title":"Eur. J. Pharm. Sci."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"636","DOI":"10.1016\/j.molcel.2016.04.002","article-title":"Lipidomics Analyses Reveal Temporal and Spatial Lipid Organization and Uncover Daily Oscillations in Intracellular Organelles","volume":"62","author":"Aviram","year":"2016","journal-title":"Mol. Cell"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1083\/jcb.201108175","article-title":"Quantitative analysis of the lipidomes of the influenza virus envelope and MDCK cell apical membrane","volume":"196","author":"Gerl","year":"2012","journal-title":"J. Cell Biol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Pradas, I., Huynh, K., Cabre, R., Ayala, V., Meikle, P.J., Jove, M., and Pamplona, R. (2018). Lipidomics Reveals a Tissue-Specific Fingerprint. Front. Physiol., 9.","DOI":"10.3389\/fphys.2018.01165"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Klose, C., Surma, M.A., Gerl, M.J., Meyenhofer, F., Shevchenko, A., and Simons, K. (2012). Flexibility of a Eukaryotic Lipidome\u2014Insights from Yeast Lipidomics. PLoS ONE, 7.","DOI":"10.1371\/journal.pone.0035063"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1016\/j.bbalip.2008.07.008","article-title":"Mass spectrometric analysis of lipid species of human circulating blood cells","volume":"1781","author":"Leidl","year":"2008","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Moreno, M.J., Martins, P.A.T., Bernardino, E.F., Abel, B., and Ambudkar, S.V. (2021). Characterization of the Lipidome and Biophysical Properties of Membranes from High Five Insect Cells Expressing Mouse P-Glycoprotein. Biomolecules, 11.","DOI":"10.20944\/preprints202102.0204.v1"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1016\/j.ceb.2013.03.005","article-title":"Organellar lipidomics\u2014Background and perspectives","volume":"25","author":"Klose","year":"2013","journal-title":"Curr. Opin. Cell Biol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"6863","DOI":"10.1021\/acsomega.7b01145","article-title":"Partition of Amphiphilic Molecules to Lipid Bilayers by ITC: Low-Affinity Solutes","volume":"2","author":"Samelo","year":"2017","journal-title":"ACS Omega"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1016\/S0006-3495(92)81849-0","article-title":"Structure of a Fluid Dioleoylphosphatidylcholine Bilayer Determined by Joint Refinement of X-ray and Neutron-Diffraction Data. 3. Complete Structure","volume":"61","author":"Wiener","year":"1992","journal-title":"Biophys. J."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"4184","DOI":"10.1021\/ja209917q","article-title":"Kinetics and Thermodynamics of Chlorpromazine Interaction with Lipid Bilayers: Effect of Charge and Cholesterol","volume":"134","author":"Martins","year":"2012","journal-title":"J. Am. Chem. Soc."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"8846","DOI":"10.1021\/bi0497087","article-title":"Kinetics of dye efflux and lipid flip-flop induced by delta-lysin in phosphatidylcholine vesicles and the mechanism of graded release by amphipathic, alpha-helical peptides","volume":"43","author":"Pokorny","year":"2004","journal-title":"Biochemistry"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1016\/0005-2736(84)90152-4","article-title":"Weak Acid-Induced Release of Liposome-Encapsulated Carboxyfluorescein","volume":"772","author":"Barbet","year":"1984","journal-title":"Biochim. Biophys. Acta (BBA)-Biomembr."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"2897","DOI":"10.1093\/bioinformatics\/btv292","article-title":"MemGen: A general web server for the setup of lipid membrane simulation systems","volume":"31","author":"Knight","year":"2015","journal-title":"Bioinformatics"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1007\/s00249-011-0700-9","article-title":"Definition and testing of the GROMOS force-field versions 54A7 and 54B7","volume":"40","author":"Schmid","year":"2011","journal-title":"Eur. Biophys. J. Biophys. Lett."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1002\/jcc.21396","article-title":"A New Force Field for Simulating Phosphatidylcholine Bilayers","volume":"31","author":"Poger","year":"2010","journal-title":"J. Comput. Chem."},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Pullman, B. (1981). Interaction Models for Water in Relation to Protein Hydration. Intermolecular Forces, Springer.","DOI":"10.1007\/978-94-015-7658-1"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"4026","DOI":"10.1021\/ct200196m","article-title":"An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0","volume":"7","author":"Malde","year":"2011","journal-title":"J. Chem. Theory Comput."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"5834","DOI":"10.1021\/acs.jctc.8b00768","article-title":"Automated Topology Builder Version 3.0: Prediction of Solvation Free Enthalpies in Water and Hexane","volume":"14","author":"Stroet","year":"2018","journal-title":"J. Chem. Theory Comput."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"154102","DOI":"10.1063\/5.0005188","article-title":"Recent developments in the general atomic and molecular electronic structure system","volume":"152","author":"Barca","year":"2020","journal-title":"J. Chem. Phys."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"8822","DOI":"10.1103\/PhysRevB.33.8822","article-title":"Density-Functional Approximation for the Correlation-Energy of the Inhomogeneous Electron-Gas","volume":"33","author":"Perdew","year":"1986","journal-title":"Phys. Rev. B"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"5648","DOI":"10.1063\/1.464913","article-title":"Density-functional thermochemistry. III. The role of exact exchange","volume":"98","author":"Becke","year":"1993","journal-title":"J. Chem. Phys."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1002\/jcc.540050204","article-title":"An Approach to Computing Electrostatic Charges for Molecules","volume":"5","author":"Singh","year":"1984","journal-title":"J. Comput. Chem."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1002\/jcc.540110404","article-title":"Atomic Charges Derived from Semiempirical Methods","volume":"11","author":"Besler","year":"1990","journal-title":"J. Comput. Chem."},{"key":"ref_37","unstructured":"Lindahl, E., Abraham, M.J., Hess, B., and Van der Spoel, D. (2025, January 16). GROMACS 2019.4 Source Code. Available online: https:\/\/zenodo.org\/records\/3460414."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers","volume":"1","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1093\/bioinformatics\/btt055","article-title":"GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit","volume":"29","author":"Pronk","year":"2013","journal-title":"Bioinformatics"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1021\/ct700301q","article-title":"GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation","volume":"4","author":"Hess","year":"2008","journal-title":"J. Chem. Theory Comput."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"7182","DOI":"10.1063\/1.328693","article-title":"Polymorphic Transitions in Single-Crystals\u2014A New Molecular-Dynamics Method","volume":"52","author":"Parrinello","year":"1981","journal-title":"J. Appl. Phys."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1063\/1.447334","article-title":"A Unified Formulation of the Constant Temperature Molecular-Dynamics Methods","volume":"81","author":"Nose","year":"1984","journal-title":"J. Chem. Phys."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1695","DOI":"10.1103\/PhysRevA.31.1695","article-title":"Canonical Dynamics\u2014Equilibrium Phase-Space Distributions","volume":"31","author":"Hoover","year":"1985","journal-title":"Phys. Rev. A"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"952","DOI":"10.1002\/jcc.540130805","article-title":"SETTLE\u2014An Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models","volume":"13","author":"Miyamoto","year":"1992","journal-title":"J. Comput. Chem."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: A linear constraint solver for molecular simulations","volume":"18","author":"Hess","year":"1997","journal-title":"J. Comput. Chem."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A Smooth Particle Mesh Ewald Method","volume":"103","author":"Essmann","year":"1995","journal-title":"J. Chem. Phys."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/0021-9991(77)90121-8","article-title":"Non-Physical Sampling Distributions in Monte-Carlo Free-Energy Estimation\u2014Umbrella Sampling","volume":"23","author":"Torrie","year":"1977","journal-title":"J. Comput. Phys."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"3713","DOI":"10.1021\/ct100494z","article-title":"g_wham-A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates","volume":"6","author":"Hub","year":"2010","journal-title":"J. Chem. Theory Comput."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1002\/jcc.540130812","article-title":"The Weighted Histogram Analysis Method for Free-Energy Calculations on Biomolecules. 1. The Method","volume":"13","author":"Kumar","year":"1992","journal-title":"J. Comput. Chem."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"9097","DOI":"10.1021\/acs.langmuir.5b01810","article-title":"Interaction of Bile Salts with Model Membranes Mimicking the Gastrointestinal Epithelium: A Study by Isothermal Titration Calorimetry","volume":"31","author":"Martins","year":"2015","journal-title":"Langmuir"},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1063\/1.1416902","article-title":"Thermodynamic Quantities for the Ionization Reactions of Buffers","volume":"31","author":"Goldberg","year":"2002","journal-title":"J. Phys. Chem. Ref. Data"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1002\/(SICI)1097-0134(19981101)33:2<159::AID-PROT2>3.0.CO;2-E","article-title":"Enthalpy and heat capacity changes for the proton dissociation of various buffer components in 0.1 M potassium chloride","volume":"33","author":"Fukada","year":"1998","journal-title":"Protein. Struct. Funct. Genet."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1016\/j.ab.2009.11.015","article-title":"Partition of amphiphilic molecules to lipid bilayers by isothermal titration calorimetry","volume":"399","author":"Moreno","year":"2010","journal-title":"Anal. Biochem."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/S0070-2161(08)60677-2","article-title":"Electrostatic Potentials at Membrane-Solution Interfaces","volume":"Volume 9","author":"Bronner","year":"1977","journal-title":"Current Topics in Membranes and Transport"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1021\/la034780b","article-title":"Zeta-Potential Measurements as a Tool to Quantify the Effect of Charged Drugs on the Surface Potential of Egg Phosphatidylcholine Liposomes","volume":"20","author":"Matos","year":"2004","journal-title":"Langmuir"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1021\/bi00401a058","article-title":"Fluorescent-Probes of Electrostatic Potential 1-Nm from the Membrane-Surface","volume":"27","author":"Winiski","year":"1988","journal-title":"Biochemistry"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"5213","DOI":"10.1021\/bi00590a028","article-title":"Adsorption of Mono-Valent Cations to Bilayer Membranes Containing Negative Phospholipids","volume":"18","author":"Eisenberg","year":"1979","journal-title":"Biochemistry"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1021\/jp307874v","article-title":"Synthesis and Characterization of a Lipidic Alpha Amino Acid: Solubility and Interaction with Serum Albumin and Lipid Bilayers","volume":"117","author":"Filipe","year":"2013","journal-title":"J. Phys. Chem. B"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1016\/0005-2736(83)90060-3","article-title":"Binding of Hydrophobic Drugs to Lipid Bilayers and to the (CA2++MG2+)-ATPase","volume":"732","author":"Rooney","year":"1983","journal-title":"Biochim. Biophys. Acta (BBA)-Biomembr."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/0005-2736(83)90467-4","article-title":"Interaction of Fatty-Acids with Lipid Bilayers","volume":"728","author":"Rooney","year":"1983","journal-title":"Biochim. Biophys. Acta (BBA)-Biomembr."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"2761","DOI":"10.1016\/j.bbamem.2011.07.022","article-title":"Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature","volume":"1808","author":"Kucerka","year":"2011","journal-title":"Biochim. Biophys. Acta (BBA)-Biomembr."},{"key":"ref_62","doi-asserted-by":"crossref","unstructured":"Figueira, T.N., Freire, J.M., Cunha-Santos, C., Heras, M., Gon\u00e7alves, J., Moscona, A., Porotto, M., Veiga, A.S., and Castanho, M. (2017). Quantitative analysis of molecular partition towards lipid membranes using surface plasmon resonance. Sci. Rep., 7.","DOI":"10.1038\/srep45647"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"108165","DOI":"10.1016\/j.celrep.2020.108165","article-title":"Principles of Membrane Adaptation Revealed through Environmentally Induced Bacterial Lipidome Remodeling","volume":"32","author":"Chwastek","year":"2020","journal-title":"Cell Rep."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1002\/rcm.3013","article-title":"Lipid composition of membranes of Escherichia coli by liquid chromatography\/tandem mass spectrometry using negative electrospray ionization","volume":"21","author":"Oursel","year":"2007","journal-title":"Rapid Commun. Mass Spectrom."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1146\/annurev.micro.57.030502.090851","article-title":"Bacterial membrane lipids: Where do we stand?","volume":"57","author":"Cronan","year":"2003","journal-title":"Annu. Rev. Microbiol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1038\/nrm2330","article-title":"Membrane lipids: Where they are and how they behave","volume":"9","author":"Voelker","year":"2008","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1016\/S0092-8674(01)00286-0","article-title":"Structural Mechanism for Rifampicin Inhibition of Bacterial RNA Polymerase","volume":"104","author":"Campbell","year":"2001","journal-title":"Cell"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"1405","DOI":"10.1002\/cphc.200900270","article-title":"110 Years of the Meyer-Overton Rule: Predicting Membrane Permeability of Gases and Other Small Compounds","volume":"10","author":"Missner","year":"2009","journal-title":"Chemphyschem"},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Chattopadhyay, A. (2017). Interaction of Amphiphilic Molecules with Lipid Bilayers: Kinetics of Insertion, Desorption and Translocation. Membrane Organization and Dynamics, Springer International Publishing.","DOI":"10.1007\/978-3-319-66601-3"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/S0009-3084(98)00088-7","article-title":"Effects of PEG-lipids on permeability of phosphatidylcholine\/cholesterol liposomes in buffer and in human serum","volume":"97","author":"Silvander","year":"1998","journal-title":"Chem. Phys. Lipids"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2244","DOI":"10.1021\/ar4002729","article-title":"The Importance of Membrane Defects-Lessons from Simulations","volume":"47","author":"Bennett","year":"2014","journal-title":"Acc. Chem. Res."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.ijpharm.2020.119198","article-title":"Liposomal membrane permeability assessment by fluorescence techniques: Main permeabilizing agents, applications and challenges","volume":"580","author":"Nasr","year":"2020","journal-title":"Int. J. Pharmaceut."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"14000","DOI":"10.1074\/jbc.M112.407635","article-title":"Induction of Highly Curved Structures in Relation to Membrane Permeabilization and Budding by the Triterpenoid Saponins, \u03b1- and \u03b4-Hederin","volume":"288","author":"Lorent","year":"2013","journal-title":"J. Biol. Chem."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"6300","DOI":"10.1021\/jf070094x","article-title":"Interaction of four monoterpenes contained in essential oils with model membranes: Implications for their antibacterial activity","volume":"55","author":"Cristani","year":"2007","journal-title":"J. Agric. Food Chem."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"2474","DOI":"10.1128\/AAC.49.6.2474-2478.2005","article-title":"Mechanisms of antibacterial action of three monoterpenes","volume":"49","author":"Trombetta","year":"2005","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1016\/S0301-4622(01)00139-9","article-title":"Tamoxifen perturbs lipid bilayer order and permeability: Comparison of DSC, fluorescence anisotropy, Laurdan generalized polarization and carboxyfluorescein leakage studies","volume":"90","author":"Engelke","year":"2001","journal-title":"Biophys. Chem."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1083\/jcb.56.2.519","article-title":"Structure of Membrane Holes in Osmotic and Saponin Hemolysis","volume":"56","author":"Seeman","year":"1973","journal-title":"J. Cell Biol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1126\/science.835007","article-title":"Liposome-Cell Interaction\u2014Transfer and Intracellular Release of a Trapped Fluorescent Marker","volume":"195","author":"Weinstein","year":"1977","journal-title":"Science"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/0003-2697(88)90412-5","article-title":"Mechanism of Fluorescence Concentration Quenching of Carboxyfluorescein in Liposomes\u2014Energy-Transfer to Nonfluorescent Dimers","volume":"172","author":"Chen","year":"1988","journal-title":"Anal. Biochem."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/S0006-3495(01)75690-1","article-title":"Membrane stress and permeabilization induced by asymmetric incorporation of compounds","volume":"81","author":"Heerklotz","year":"2001","journal-title":"Biophys. J."},{"key":"ref_81","first-page":"721","article-title":"Molecular properties, including chameleonicity, as essential tools for designing the next generation of oral beyond rule of five drugs","volume":"12","author":"Jimenez","year":"2024","journal-title":"ADMET DMPK"},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Neves, M.C., Filipe, H.A.L., Reis, R.L., Ramalho, J.P.P., Coreta-Gomes, F., Moreno, M.J., and Loura, L.M.S. (2019). Interaction of Bile Salts with Lipid Bilayers: An Atomistic Molecular Dynamics Study. Front. Physiol., 10.","DOI":"10.3389\/fphys.2019.00393"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"3572","DOI":"10.1021\/jp501622d","article-title":"How To Tackle the Issues in Free Energy Simulations of Long Amphiphiles Interacting with Lipid Membranes: Convergence and Local Membrane Deformations","volume":"118","author":"Filipe","year":"2014","journal-title":"J. Phys. Chem. B"},{"key":"ref_84","doi-asserted-by":"crossref","unstructured":"Magalhaes, N., Sim\u00f5es, G.M., Ramos, C., Samelo, J., Oliveira, A.C., Filipe, H.A.L., Ramalho, J.P.P., Moreno, M.J., and Loura, L.M.S. (2022). Interactions between Rhodamine Dyes and Model Membrane Systems\u2014Insights from Molecular Dynamics Simulations. Molecules, 27.","DOI":"10.3390\/molecules27041420"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"2673","DOI":"10.1021\/acs.molpharmaceut.3c00766","article-title":"Liposomal Copermeation Assay Reveals Unexpected Membrane Interactions of Commonly Prescribed Drugs","volume":"21","author":"Balouch","year":"2024","journal-title":"Mol. Pharm."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1007\/s10895-012-1120-7","article-title":"On the Photophysicochemical Properties of Selected Fluoroquinolones: Solvatochromic and Fluorescence Spectroscopy Study","volume":"23","author":"Hammad","year":"2013","journal-title":"J. Fluoresc."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"15252","DOI":"10.3390\/ijms131115252","article-title":"Simple Estimation of Forster Resonance Energy Transfer (FRET) Orientation Factor Distribution in Membranes","volume":"13","author":"Loura","year":"2012","journal-title":"Int. J. Mol. Sci."}],"container-title":["Biomolecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2218-273X\/15\/3\/320\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:39:45Z","timestamp":1760027985000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2218-273X\/15\/3\/320"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,21]]},"references-count":87,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2025,3]]}},"alternative-id":["biom15030320"],"URL":"https:\/\/doi.org\/10.3390\/biom15030320","relation":{},"ISSN":["2218-273X"],"issn-type":[{"value":"2218-273X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,21]]}}}