dc.contributor.author | Rojas-Valencia N | |
dc.contributor.author | Gómez S | |
dc.contributor.author | Núñez-Zarur F | |
dc.contributor.author | Cappelli C | |
dc.contributor.author | Hadad C | |
dc.contributor.author | Restrepo A. | |
dc.date.accessioned | 2022-09-14T14:34:17Z | |
dc.date.available | 2022-09-14T14:34:17Z | |
dc.date.created | 2021 | |
dc.identifier.issn | 15206106 | |
dc.identifier.uri | http://hdl.handle.net/11407/7605 | |
dc.description | The 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 Society | eng |
dc.language.iso | eng | |
dc.publisher | American Chemical Society | |
dc.relation.isversionof | https://www.scopus.com/inward/record.uri?eid=2-s2.0-85115955204&doi=10.1021%2facs.jpcb.1c06766&partnerID=40&md5=aaf3be1a83deb4d0ffd7ca6981ea003a | |
dc.source | Journal of Physical Chemistry B | |
dc.title | Thermodynamics and Intermolecular Interactions during the Insertion of Anionic Naproxen into Model Cell Membranes | |
dc.type | Article | |
dc.rights.accessrights | info:eu-repo/semantics/restrictedAccess | |
dc.publisher.program | Ciencias Básicas | |
dc.type.spa | Artículo | |
dc.identifier.doi | 10.1021/acs.jpcb.1c06766 | |
dc.subject.keyword | Computation theory | eng |
dc.subject.keyword | Cytology | eng |
dc.subject.keyword | Ions | eng |
dc.subject.keyword | Molecular dynamics | eng |
dc.subject.keyword | Quantum theory | eng |
dc.subject.keyword | Thermodynamics | eng |
dc.subject.keyword | Atomistics | eng |
dc.subject.keyword | Computational approach | eng |
dc.subject.keyword | Dimyristoylphosphatidylcholine | eng |
dc.subject.keyword | Insertion process | eng |
dc.subject.keyword | Intermolecular interactions | eng |
dc.subject.keyword | Naproxens | eng |
dc.subject.keyword | Non-covalent interaction | eng |
dc.subject.keyword | Quantum mechanical | eng |
dc.subject.keyword | State of the art | eng |
dc.subject.keyword | Thermodynamic interactions | eng |
dc.subject.keyword | Chemical bonds | eng |
dc.relation.citationvolume | 125 | |
dc.relation.citationissue | 36 | |
dc.relation.citationstartpage | 10383 | |
dc.relation.citationendpage | 10391 | |
dc.publisher.faculty | Facultad de Ciencias Básicas | |
dc.affiliation | Rojas-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.affiliation | Gómez, S., Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, Pisa, 56126, Italy | |
dc.affiliation | Núñez-Zarur, F., Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, Medellín, 050026, Colombia | |
dc.affiliation | Cappelli, C., Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, Pisa, 56126, Italy | |
dc.affiliation | Hadad, C., Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia | |
dc.affiliation | Restrepo, A., Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, 050010, Colombia | |
dc.relation.references | Wongrakpanich, 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.references | Vane, J.R., Botting, R.M., Anti-inflammatory drugs and their mechanism of action (1998) J. Inflamm. Res., 47, pp. 78-87 | |
dc.relation.references | Lichtenberger, 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.references | Manrique-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.references | Manrique-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.references | Manrique-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.references | Yousefpour, 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.references | Boggara, 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.references | Rojas-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.references | Rojas-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.references | Klauda, 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.references | Vanommeslaeghe, 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.references | Vanommeslaeghe, 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.references | Jorgensen, 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.references | Reed, 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.references | Weinhold, 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.references | Weinhold, F., Landis, C.R., (2012) Discovering Chemistry with Natural Bond Orbitals, p. 319. , Wiley-VCH : Hoboken NJ p | |
dc.relation.references | Bader, R., (1990) Atoms in Molecules: A Quantum Theory, , Oxford University Press : Oxford | |
dc.relation.references | Popelier, P.L., (2000) Atoms in Molecules: An Introduction, , Prentice Hall : London | |
dc.relation.references | Grabowski, S.J., What Is the Covalency of Hydrogen Bonding? (2011) Chem. Rev., 111, pp. 2597-2625 | |
dc.relation.references | Johnson, 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.references | DiLabio, 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.references | Giovannini, T., Egidi, F., Cappelli, C., Molecular spectroscopy of aqueous solutions: a theoretical perspective (2020) Chem. Soc. Rev., 49, pp. 5664-5677 | |
dc.relation.references | Cappelli, 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.references | Etienne, 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.references | Egidi, 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.references | Giovannini, 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.references | Giovannini, 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.references | Puglisi, 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.references | Cwiklik, 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.references | Gómez, 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.references | Abraham, 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.references | Glendening, 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.references | Frisch, 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.references | Keith, T., (2019) AIMALL, , aim.tkgristmill.com, (version 19.10.12)TK Gristmill Software : Overland Park KS USA | |
dc.relation.references | Contreras-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.references | Moreno, 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.references | Pereira-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.references | Sodeifian, 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.references | Liu, 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.references | Wanat, 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.references | MacCallum, 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.references | Micieli, 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.references | Salazar-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.references | Gómez, 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.references | Gómez, 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.references | Hadad, 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.references | Flórez, E., Acelas, N., Ramírez, F., Hadad, C., Restrepo, A., Microsolvation of F- (2018) Phys. Chem. Chem. Phys., 20, pp. 8909-8916 | |
dc.relation.references | Flórez, 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.references | Rojas-Valencia, N., Ibargüen, C., Restrepo, A., Molecular interactions in the microsolvation of dimethylphosphate (2015) Chem. Phys. Lett., 635, pp. 301-305 | |
dc.relation.references | Zapata-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.references | Romero, 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.references | Gonzalez, 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.references | Acelas, 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.references | Ramírez-Rodríguez, F., Restrepo, A., Structures, energies, and bonding in the microsolvation of Na+ (2021) Chem. Phys., 544, p. 111106 | |
dc.relation.references | Chamorro, Y., Flórez, E., Maldonado, A., Aucar, G., Restrepo, A., Microsolvation of heavy halides (2021) Int. J. Quantum Chem., 121, p. e26571 | |
dc.relation.references | Velásquez, 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.references | Uribe, 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.references | Ben-Amotz, D., Water-Mediated Hydrophobic Interactions (2016) Annu. Rev. Phys. Chem., 67, pp. 617-638. , PMID: 27215821 | |
dc.relation.references | Tomar, 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.references | Espinosa, 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.references | Cremer, 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.references | Weinhold, 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.references | Ramírez, 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.references | Farfán, 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.references | Alkorta, 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.references | Knop, 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.references | Knop, 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 | |
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