Thermodynamics and Intermolecular Interactions during the Insertion of Anionic Naproxen into Model Cell Membranes

dc.contributor.affiliationRojas-Valencia, N., Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia, Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, Medellín, 050026, Colombia, Escuela de Ciencias y Humanidades, Departamento de Ciencias Básicas, Universidad Eafit, Medellín, AA 3300, Colombia
dc.contributor.affiliationGómez, S., Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, Pisa, 56126, Italy
dc.contributor.affiliationNúñez-Zarur, F., Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, Medellín, 050026, Colombia
dc.contributor.affiliationCappelli, C., Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, Pisa, 56126, Italy
dc.contributor.affiliationHadad, C., Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia
dc.contributor.affiliationRestrepo, A., Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia
dc.contributor.authorRojas-Valencia N
dc.contributor.authorGómez S
dc.contributor.authorNúñez-Zarur F
dc.contributor.authorCappelli C
dc.contributor.authorHadad C
dc.contributor.authorRestrepo A.
dc.date.accessioned2022-09-14T14:34:17Z
dc.date.available2022-09-14T14:34:17Z
dc.date.issued2021
dc.descriptionThe insertion process of Naproxen into model dimyristoylphosphatidylcholine (DMPC) membranes is studied by resorting to state-of-the-art classical and quantum mechanical atomistic computational approaches. Molecular dynamics simulations indicate that anionic Naproxen finds an equilibrium position right at the polar/nonpolar interphase when the process takes place in aqueous environments. With respect to the reference aqueous phase, the insertion process faces a small energy barrier of ≈5 kJ mol-1and yields a net stabilization of also ≈5 kJ mol-1. Entropy changes along the insertion path, mainly due to a growing number of realizable microstates because of structural reorganization, are the main factors driving the insertion. An attractive fluxional wall of noncovalent interactions is characterized by all-quantum descriptors of chemical bonding (natural bond orbitals, quantum theory of atoms in molecules, noncovalent interaction, density differences, and natural charges). This attractive wall originates in the accumulation of tiny transfers of electron densities to the interstitial region between the fragments from a multitude of individual intermolecular contacts stabilizing the tertiary drug/water/membrane system. © 2021 American Chemical Societyeng
dc.identifier.doi10.1021/acs.jpcb.1c06766
dc.identifier.instnameinstname:Universidad de Medellínspa
dc.identifier.issn15206106
dc.identifier.reponamereponame:Repositorio Institucional Universidad de Medellínspa
dc.identifier.repourlrepourl:https://repository.udem.edu.co/
dc.identifier.urihttp://hdl.handle.net/11407/7605
dc.language.isoeng
dc.publisherAmerican Chemical Societyspa
dc.publisher.facultyFacultad de Ciencias Básicasspa
dc.publisher.programCiencias Básicasspa
dc.relation.citationendpage10391
dc.relation.citationissue36
dc.relation.citationstartpage10383
dc.relation.citationvolume125
dc.relation.isversionofhttps://www.scopus.com/inward/record.uri?eid=2-s2.0-85115955204&doi=10.1021%2facs.jpcb.1c06766&partnerID=40&md5=aaf3be1a83deb4d0ffd7ca6981ea003a
dc.relation.referencesWongrakpanich, S., Wongrakpanich, A., Melhado, K., Rangaswami, J., A Comprehensive Review of Non-Steroidal Anti-Inflammatory Drug Use in the Elderly (2018) Aging Dis., 9, p. 143
dc.relation.referencesVane, J.R., Botting, R.M., Anti-inflammatory drugs and their mechanism of action (1998) J. Inflamm. Res., 47, pp. 78-87
dc.relation.referencesLichtenberger, L.M., Zhou, Y., Jayaraman, V., Doyen, J.R., O’Neil, R.G., Dial, E.J., Volk, D.E., Krishnamoorti, R., Insight into NSAID-induced membrane alterations, pathogenesis and therapeutics: Characterization of interaction of NSAIDs with phosphatidylcholine (2012) Biochim. Biophys. Acta, Mol. Cell Biol. Lipids, 1821, pp. 994-1002
dc.relation.referencesManrique-Moreno, M., Villena, F., Sotomayor, C.P., Edwards, A.M., Muñoz, M.A., Garidel, P., Suwalsky, M., Human cells and cell membrane molecular models are affected in vitro by the nonsteroidal anti-inflammatory drug ibuprofen (2011) Biochim. Biophys. Acta, 1808, pp. 2656-2664
dc.relation.referencesManrique-Moreno, M., Howe, J., Suwalsky, M., Garidel, P., Brandenburg, K., Physicochemical Interaction Study of Non-Steroidal Anti-Inflammatory Drugs with Dimyristoylphosphatidylethanolamine Liposomes (2010) Lett. Drug Des. Discov., 7, pp. 50-56
dc.relation.referencesManrique-Moreno, M., Suwalsky, M., Villena, F., Garidel, P., Effects of the nonsteroidal anti-inflammatory drug naproxen on human erythrocytes and on cell membrane molecular models (2010) Biophys. Chem., 147, pp. 53-58
dc.relation.referencesYousefpour, A., Amjad Iranagh, S., Nademi, Y., Modarress, H., Molecular dynamics simulation of nonsteroidal antiinflammatory drugs, naproxen and relafen, in a lipid bilayer membrane (2013) Int. J. Quantum Chem., 113, pp. 1919-1930
dc.relation.referencesBoggara, M.B., Mihailescu, M., Krishnamoorti, R., Structural Association of Nonsteroidal Anti-Inflammatory Drugs with Lipid Membranes (2012) J. Am. Chem. Soc., 134, pp. 19669-19676. , PMID: 23134450
dc.relation.referencesRojas-Valencia, N., Lans, I., Manrique-Moreno, M., Hadad, C.Z., Restrepo, A., Entropy drives the insertion of ibuprofen into model membranes (2018) Phys. Chem. Chem. Phys., 20, pp. 24869-24876
dc.relation.referencesRojas-Valencia, N., Gómez, S., Montillo, S., Manrique-Moreno, M., Cappelli, C., Hadad, C., Restrepo, A., Evolution of Bonding during the Insertion of Anionic Ibuprofen into Model Cell Membranes (2020) J. Phys. Chem. B, 124, pp. 79-90. , PMID: 31790579
dc.relation.referencesKlauda, J.B., Venable, R.M., Freites, J.A., O’Connor, J.W., Tobias, D.J., Mondragon-Ramirez, C., Vorobyov, I., Pastor, R.W., Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types (2010) J. Phys. Chem. B, 114, pp. 7830-7843. , PMID: 20496934
dc.relation.referencesVanommeslaeghe, K., MacKerell, A.D., Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing (2012) J. Chem. Inf. Model., 52, pp. 3144-3154. , PMID: 23146088
dc.relation.referencesVanommeslaeghe, K., Raman, E.P., MacKerell, A.D., Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges (2012) J. Chem. Inf. Model., 52, pp. 3155-3168. , PMID: 23145473
dc.relation.referencesJorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L., Comparison of simple potential functions for simulating liquid water (1983) J. Chem. Phys., 79, pp. 926-935
dc.relation.referencesReed, A.E., Curtiss, L.A., Weinhold, F., Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint (1988) Chem. Rev., 88, pp. 899-926
dc.relation.referencesWeinhold, F., Landis, C.R., Glendening, E.D., What is NBO analysis and how is it useful? (2016) Int. Rev. Phys. Chem., 35, pp. 399-440
dc.relation.referencesWeinhold, F., Landis, C.R., (2012) Discovering Chemistry with Natural Bond Orbitals, p. 319. , Wiley-VCH : Hoboken NJ p
dc.relation.referencesBader, R., (1990) Atoms in Molecules: A Quantum Theory, , Oxford University Press : Oxford
dc.relation.referencesPopelier, P.L., (2000) Atoms in Molecules: An Introduction, , Prentice Hall : London
dc.relation.referencesGrabowski, S.J., What Is the Covalency of Hydrogen Bonding? (2011) Chem. Rev., 111, pp. 2597-2625
dc.relation.referencesJohnson, E.R., Keinan, S., Mori-Sánchez, P., Contreras-García, J., Cohen, A.J., Yang, W., Revealing Noncovalent Interactions (2010) J. Am. Chem. Soc., 132, pp. 6498-6506
dc.relation.referencesDiLabio, G.A., Otero-De-la-Roza, A., Noncovalent Interactions in Density Functional Theory (2016) Reviews in Computational Chemistry, pp. 1-97. , John Wiley & Sons Ltd Chapter 1
dc.relation.referencesGiovannini, T., Egidi, F., Cappelli, C., Molecular spectroscopy of aqueous solutions: a theoretical perspective (2020) Chem. Soc. Rev., 49, pp. 5664-5677
dc.relation.referencesCappelli, C., Integrated QM/polarizable MM/continuum approaches to model chiroptical properties of strongly interacting solute-solvent systems (2016) Int. J. Quant. Chem., 116, pp. 1532-1542
dc.relation.referencesEtienne, T., Very, T., Perpète, E.A., Monari, A., Assfeld, X., A QM/MM Study of the Absorption Spectrum of Harmane in Water Solution and Interacting with DNA: The Crucial Role of Dynamic Effects (2013) J. Phys. Chem. B, 117, pp. 4973-4980
dc.relation.referencesEgidi, F., Lo Gerfo, G., Macchiagodena, M., Cappelli, C., On the nature of charge-transfer excitations for molecules in aqueous solution: a polarizable QM/MM study (2018) Theor. Chem. Acc., 137, p. 82
dc.relation.referencesGiovannini, T., Del Frate, G., Lafiosca, P., Cappelli, C., Effective computational route towards vibrational optical activity spectra of chiral molecules in aqueous solution (2018) Phys. Chem. Chem. Phys., 20, pp. 9181-9197
dc.relation.referencesGiovannini, T., Macchiagodena, M., Ambrosetti, M., Puglisi, A., Lafiosca, P., Lo Gerfo, G., Egidi, F., Cappelli, C., Simulating vertical excitation energies of solvated dyes: From continuum to polarizable discrete modeling (2019) Int. J. Quant. Chem., 119, p. e25684
dc.relation.referencesPuglisi, A., Giovannini, T., Antonov, L., Cappelli, C., Interplay between conformational and solvent effects in UV-visible absorption spectra: curcumin tautomers as a case study (2019) Phys. Chem. Chem. Phys., 21, pp. 15504-15514
dc.relation.referencesCwiklik, L., Aquino, A.J.A., Vazdar, M., Jurkiewicz, P., Pittner, J., Hof, M., Lischka, H., Absorption and Fluorescence of PRODAN in Phospholipid Bilayers: A Combined Quantum Mechanics and Classical Molecular Dynamics Study (2011) J. Phys. Chem. A, 115, pp. 11428-11437
dc.relation.referencesGómez, S., Giovannini, T., Cappelli, C., Absorption spectra of xanthines in aqueous solution: a computational study (2020) Phys. Chem. Chem. Phys., 22, pp. 5929-5941
dc.relation.referencesAbraham, M.J., Murtola, T., Schulz, R., Páll, S., Smith, J.C., Hess, B., Lindahl, E., GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers (2015) SoftwareX, pp. 19-25
dc.relation.referencesGlendening, E.D., Badenhoop, J.K., Reed, A.E., Carpenter, J.E., Bohmann, J.A., Morales, C.M., Landis, C.R., Weinhold, F., (2013) NBO 6.0, , Theoretical Chemistry Institute University of Wisconsin : Madison
dc.relation.referencesFrisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Petersson, G.A., (2009) Gaussian 09, , Revision E.01Gaussian Inc: Wallingford CT
dc.relation.referencesKeith, T., (2019) AIMALL, , aim.tkgristmill.com, (version 19.10.12)TK Gristmill Software : Overland Park KS USA
dc.relation.referencesContreras-García, J., Johnson, E.R., Keinan, S., Chaudret, R., Piquemal, J.-P., Beratan, D.N., Yang, W., NCIPLOT: A Program for Plotting Noncovalent Interaction Regions (2011) J. Chem. Theory Comput., 7, pp. 625-632
dc.relation.referencesMoreno, M.M., Garidel, P., Suwalsky, M., Howe, J., Brandenburg, K., The membrane-activity of Ibuprofen, Diclofenac, and Naproxen: A physico-chemical study with lecithin phospholipids (2009) Biochim. Biophys. Acta, 1788, pp. 1296-1303
dc.relation.referencesPereira-Leite, C., Figueiredo, M., Burdach, K., Nunes, C., Reis, S., Unraveling the Role of Drug-Lipid Interactions in NSAIDs-Induced Cardiotoxicity (2021) Membranes, 11, p. 24
dc.relation.referencesSodeifian, G., Razmimanesh, F., Diffusional interaction behavior of NSAIDs in lipid bilayer membrane using molecular dynamics (MD) simulation: Aspirin and Ibuprofen (2019) J. Biomol. Struct. Dyn., 37, pp. 1666-1684. , PMID: 29695194
dc.relation.referencesLiu, W., Zhang, S., Meng, F., Tang, L., Molecular simulation of ibuprofen passing across POPC membrane (2014) J. Theor. Comput. Chem., 13, p. 1450033
dc.relation.referencesWanat, K., Biological barriers, and the influence of protein binding on the passage of drugs across them (2020) Mol. Biol. Rep., 47, pp. 3221-3231
dc.relation.referencesMacCallum, J.L., Tieleman, D.P., Computer Simulation of the Distribution of Hexane in a Lipid Bilayer: Spatially Resolved Free Energy, Entropy, and Enthalpy Profiles (2006) J. Am. Chem. Soc., 128, pp. 125-130. , PMID: 16390139
dc.relation.referencesMicieli, D., Giuffrida, M.C., Pignatello, R., Castelli, F., Sarpietro, M.G., Interaction of naproxen amphiphilic derivatives with biomembrane models evaluated by differential scanning calorimetry and Langmuir-Blodgett studies (2011) J. Colloid Interface Sci., 360, pp. 359-369
dc.relation.referencesSalazar-Cano, J.-R., Guevara-García, A., Vargas, R., Restrepo, A., Garza, J., Hydrogen bonds in methane-water clusters (2016) Phys. Chem. Chem. Phys., 18, pp. 23508-23515
dc.relation.referencesGómez, S.A., Rojas-Valencia, N., Gómez, S., Egidi, F., Cappelli, C., Restrepo, A., Binding of SARS-CoV-2 to Cell Receptors: A Tale of Molecular Evolution (2021) ChemBioChem, 22, pp. 724-732
dc.relation.referencesGómez, S., Rojas-Valencia, N., Gómez, S.A., Cappelli, C., Merino, G., Restrepo, A., A molecular twist on hydrophobicity (2021) Chem. Sci., 12, pp. 9233-9245
dc.relation.referencesHadad, C., Florez, E., Acelas, N., Merino, G., Restrepo, A., Microsolvation of small cations and anions (2019) Int. J. Quant. Chem., 119, p. e25766
dc.relation.referencesFlórez, E., Acelas, N., Ramírez, F., Hadad, C., Restrepo, A., Microsolvation of F- (2018) Phys. Chem. Chem. Phys., 20, pp. 8909-8916
dc.relation.referencesFlórez, E., Acelas, N., Ibargüen, C., Mondal, S., Cabellos, J.L., Merino, G., Restrepo, A., Microsolvation of NO3-: structural exploration and bonding analysis (2016) RSC Adv., 6, pp. 71913-71923
dc.relation.referencesRojas-Valencia, N., Ibargüen, C., Restrepo, A., Molecular interactions in the microsolvation of dimethylphosphate (2015) Chem. Phys. Lett., 635, pp. 301-305
dc.relation.referencesZapata-Escobar, A., Manrique-Moreno, M., Guerra, D., Hadad, C.Z., Restrepo, A., A combined experimental and computational study of the molecular interactions between anionic ibuprofen and water (2014) J. Chem. Phys., 140, p. 184312
dc.relation.referencesRomero, J., Reyes, A., David, J., Restrepo, A., Understanding microsolvation of Li+: structural and energetical analyses (2011) Phys. Chem. Chem. Phys., 13, pp. 15264-15271
dc.relation.referencesGonzalez, J.D., Florez, E., Romero, J., Reyes, A., Restrepo, A., Microsolvation of Mg2+, Ca2+: strong influence of formal charges in hydrogen bond networks (2013) J. Mol. Model., 19, pp. 1763-1777
dc.relation.referencesAcelas, N., Flórez, E., Hadad, C., Merino, G., Restrepo, A., A Comprehensive Picture of the Structures, Energies, and Bonding in [SO4(H2O)n]2-, n = 1-6 (2019) J. Phys. Chem. A, 123, pp. 8650-8656
dc.relation.referencesRamírez-Rodríguez, F., Restrepo, A., Structures, energies, and bonding in the microsolvation of Na+ (2021) Chem. Phys., 544, p. 111106
dc.relation.referencesChamorro, Y., Flórez, E., Maldonado, A., Aucar, G., Restrepo, A., Microsolvation of heavy halides (2021) Int. J. Quantum Chem., 121, p. e26571
dc.relation.referencesVelásquez, A., Chamorro, Y., Maldonado, A., Aucar, G., Restrepo, A., Microsolvation of Sr2+, Ba2+: Structures, energies, bonding, and nuclear magnetic shieldings (2021) Int. J. Quantum Chem., 121, p. e26753
dc.relation.referencesUribe, L., Gómez, S., Giovannini, T., Egidi, F., Restrepo, A., An efficient and robust procedure to calculate absorption spectra of aqueous charged species applied to NO2- (2021) Phys. Chem. Chem. Phys., 23, pp. 14857-14872
dc.relation.referencesBen-Amotz, D., Water-Mediated Hydrophobic Interactions (2016) Annu. Rev. Phys. Chem., 67, pp. 617-638. , PMID: 27215821
dc.relation.referencesTomar, D.S., Paulaitis, M.E., Pratt, L.R., Asthagiri, D.N., Hydrophilic Interactions Dominate the Inverse Temperature Dependence of Polypeptide Hydration Free Energies Attributed to Hydrophobicity (2020) J. Phys. Chem. Lett., 11, pp. 9965-9970. , PMID: 33170720
dc.relation.referencesEspinosa, E., Alkorta, I., Elguero, J., Molins, E., From weak to strong interactions: A comprehensive analysis of the topological and energetic properties of the electron density distribution involving X-H···F-Y systems (2002) J. Chem. Phys., 117, pp. 5529-5542
dc.relation.referencesCremer, D., Kraka, E., A description of the chemical bond in terms of local properties of electron density and energy (1984) Croat. Chem. Acta, 57, pp. 1259-1281
dc.relation.referencesWeinhold, F., Natural bond critical point analysis: Quantitative relationships between natural bond orbital-based and QTAIM-based topological descriptors of chemical bonding (2012) J. Comput. Chem., 33, pp. 2440-2449
dc.relation.referencesRamírez, F., Hadad, C.Z., Guerra, D., David, J., Restrepo, A., Structural studies of the water pentamer (2011) Chem. Phys. Lett., 507, pp. 229-233
dc.relation.referencesFarfán, P., Echeverri, A., Diaz, E., Tapia, J.D., Gómez, S., Restrepo, A., Dimers of formic acid: Structures, stability, and double proton transfer (2017) J. Chem. Phys., 147, p. 044312
dc.relation.referencesAlkorta, I., Rozas, I., Elguero, J., Bond Length-Electron Density Relationships: From Covalent Bonds to Hydrogen Bond Interactions (1998) Struct. Chem., 9, pp. 243-247
dc.relation.referencesKnop, O., Rankin, K.N., Boyd, R.J., Coming to Grips with N-H···N Bonds. 1. Distance Relationships and Electron Density at the Bond Critical Point (2001) J. Phys. Chem. A, 105, pp. 6552-6566
dc.relation.referencesKnop, O., Rankin, K.N., Boyd, R.J., Coming to Grips with N-H···N Bonds. 2. Homocorrelations between Parameters Deriving from the Electron Density at the Bond Critical Point (2003) J. Phys. Chem. A, 107, pp. 272-284
dc.rights.accessrightsinfo:eu-repo/semantics/restrictedAccess
dc.sourceJournal of Physical Chemistry B
dc.subject.proposalComputation theoryeng
dc.subject.proposalCytologyeng
dc.subject.proposalIonseng
dc.subject.proposalMolecular dynamicseng
dc.subject.proposalQuantum theoryeng
dc.subject.proposalThermodynamicseng
dc.subject.proposalAtomisticseng
dc.subject.proposalComputational approacheng
dc.subject.proposalDimyristoylphosphatidylcholineeng
dc.subject.proposalInsertion processeng
dc.subject.proposalIntermolecular interactionseng
dc.subject.proposalNaproxenseng
dc.subject.proposalNon-covalent interactioneng
dc.subject.proposalQuantum mechanicaleng
dc.subject.proposalState of the arteng
dc.subject.proposalThermodynamic interactionseng
dc.subject.proposalChemical bondseng
dc.titleThermodynamics and Intermolecular Interactions during the Insertion of Anionic Naproxen into Model Cell Membranes
dc.typeArticle
dc.type.coarhttp://purl.org/coar/resource_type/c_6501
dc.type.driverinfo:eu-repo/semantics/article
dc.type.localArtículospa
dc.type.versioninfo:eu-repo/semantics/publishedVersion

Archivos

Colecciones