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Molecular dynamics simulations of a central nervous system-penetrant drug AZD3759 with lipid bilayer. J Mol Model 2022; 28:261. [DOI: 10.1007/s00894-022-05266-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/11/2022] [Indexed: 10/15/2022]
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2
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Frigini EN, Porasso RD. Effect of Ionic Strength on Ibuprofenate Adsorption on a Lipid Bilayer of Dipalmitoylphosphatidylcholine from Molecular Dynamics Simulations. J Phys Chem B 2022; 126:1941-1950. [PMID: 35226503 DOI: 10.1021/acs.jpcb.1c09301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this work, the free energy change in the process of transferring ibuprofenate from the bulk solution to the center of a model of the dipalmitoylphosphatidylcholine bilayer at different NaCl concentrations was calculated. Two minima were found in the free energy profile: a local minimum, located in the vicinity of the membrane, and the global free energy minimum, found near the headgroup region. The downward shift of free energy minima with increasing NaCl concentration is consistent with the results of previous works. Conversely, the upward shift of the free energy maximum with increasing ionic strength is due to the competition of sodium ions and lipids molecules to coordinate with ibuprofenate and neutralize its charge. In addition, normal molecular dynamics simulations were performed to study the effects of the ibuprofenate on the lipid bilayer and in the presence of a high ibuprofenate concentration. The effect of ionic strength on the properties of the lipid bilayer and on lipid-drug interactions was analyzed. The area per lipid shrinking with increasing ionic strength, volume of lipids, and thickness of the bilayer is consistent with the experimental results. At a very high ibuprofenate concentration, the lipid bilayer dehydrates, and it consequently transforms into the gel phase, thus blocking the permeation.
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Affiliation(s)
- Ezequiel N Frigini
- Instituto de Matemáticas Aplicada San Luis, CONICET, Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Avenida Ejército de los Andes 950, 5700 San Luis, Argentina
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis, CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Avenida Ejército de los Andes 950, 5700 San Luis, Argentina
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3
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Gómez S, Rojas-Valencia N, Giovannini T, Restrepo A, Cappelli C. Ring Vibrations to Sense Anionic Ibuprofen in Aqueous Solution as Revealed by Resonance Raman. Molecules 2022; 27:molecules27020442. [PMID: 35056755 PMCID: PMC8780161 DOI: 10.3390/molecules27020442] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/31/2021] [Accepted: 01/04/2022] [Indexed: 12/07/2022] Open
Abstract
We unravel the potentialities of resonance Raman spectroscopy to detect ibuprofen in diluted aqueous solutions. In particular, we exploit a fully polarizable quantum mechanics/molecular mechanics (QM/MM) methodology based on fluctuating charges coupled to molecular dynamics (MD) in order to take into account the dynamical aspects of the solvation phenomenon. Our findings, which are discussed in light of a natural bond orbital (NBO) analysis, reveal that a selective enhancement of the Raman signal due to the normal mode associated with the C-C stretching in the ring, νC=C, can be achieved by properly tuning the incident wavelength, thus facilitating the recognition of ibuprofen in water samples.
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Affiliation(s)
- Sara Gómez
- Classe di Scienze, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy;
- Correspondence: (S.G.); (C.C.)
| | - Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellin 050010, Colombia; (N.R.-V.); (A.R.)
| | - Tommaso Giovannini
- Classe di Scienze, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy;
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellin 050010, Colombia; (N.R.-V.); (A.R.)
| | - Chiara Cappelli
- Classe di Scienze, Scuola Normale Superiore, Piazza dei Cavalieri 7, 56126 Pisa, Italy;
- Correspondence: (S.G.); (C.C.)
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Rojas-Valencia N, Gómez S, Núñez-Zarur F, Cappelli C, Hadad C, Restrepo A. Thermodynamics and Intermolecular Interactions during the Insertion of Anionic Naproxen into Model Cell Membranes. J Phys Chem B 2021; 125:10383-10391. [PMID: 34492187 DOI: 10.1021/acs.jpcb.1c06766] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
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-1 and 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.
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Affiliation(s)
- Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 050010Medellín, Colombia.,Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia.,Escuela de Ciencias y Humanidades, Departamento de Ciencias Básicas, Universidad Eafit, AA 3300 Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Francisco Núñez-Zarur
- Facultad de Ciencias Básicas, Universidad de Medellín, Carrera 87 No. 30-65, 050026 Medellín, Colombia
| | - Chiara Cappelli
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Cacier Hadad
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 050010Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, 050010Medellín, Colombia
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5
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Jaber N, Al-Akayleh F, Abdel-Rahem RA, Al-Remawi M. Characterization ex vivo skin permeation and pharmacological studies of ibuprofen lysinate-chitosan-gold nanoparticles. J Drug Deliv Sci Technol 2021. [DOI: 10.1016/j.jddst.2021.102399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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6
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Wadhwa R, Yadav NS, Katiyar SP, Yaguchi T, Lee C, Ahn H, Yun CO, Kaul SC, Sundar D. Molecular dynamics simulations and experimental studies reveal differential permeability of withaferin-A and withanone across the model cell membrane. Sci Rep 2021; 11:2352. [PMID: 33504873 PMCID: PMC7840742 DOI: 10.1038/s41598-021-81729-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/30/2020] [Indexed: 12/23/2022] Open
Abstract
Poor bioavailability due to the inability to cross the cell membrane is one of the major reasons for the failure of a drug in clinical trials. We have used molecular dynamics simulations to predict the membrane permeability of natural drugs-withanolides (withaferin-A and withanone) that have similar structures but remarkably differ in their cytotoxicity. We found that whereas withaferin-A, could proficiently transverse through the model membrane, withanone showed weak permeability. The free energy profiles for the interaction of withanolides with the model bilayer membrane revealed that whereas the polar head group of the membrane caused high resistance for the passage of withanone, the interior of the membrane behaves similarly for both withanolides. The solvation analysis further revealed that the high solvation of terminal O5 oxygen of withaferin-A was the major driving force for its high permeability; it interacted with the phosphate group of the membrane that led to its smooth passage across the bilayer. The computational predictions were tested by raising and recruiting unique antibodies that react to withaferin-A and withanone. The time-lapsed analyses of control and treated cells demonstrated higher permeation of withaferin-A as compared to withanone. The concurrence between the computation and experimental results thus re-emphasised the use of computational methods for predicting permeability and hence bioavailability of natural drug compounds in the drug development process.
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Affiliation(s)
- Renu Wadhwa
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305 8565, Japan
| | - Neetu Singh Yadav
- DAILAB, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110 016, India
| | - Shashank P Katiyar
- DAILAB, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110 016, India
| | - Tomoko Yaguchi
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305 8565, Japan
| | - Chohee Lee
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305 8565, Japan.,Department of Bioengineering, College of Engineering, Hanyang University, 222 Wangsinmi-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Hyomin Ahn
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305 8565, Japan.,Department of Bioengineering, College of Engineering, Hanyang University, 222 Wangsinmi-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.,GeneMedicine Co., Ltd, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Chae-Ok Yun
- Department of Bioengineering, College of Engineering, Hanyang University, 222 Wangsinmi-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.,GeneMedicine Co., Ltd, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.,Institute of Nano Science and Technology (INST), 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Sunil C Kaul
- AIST-INDIA DAILAB, DBT-AIST International Center for Translational and Environmental Research (DAICENTER), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305 8565, Japan.
| | - Durai Sundar
- DAILAB, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Hauz Khas, New Delhi, 110 016, India.
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Rojas-Valencia N, Lans I, Manrique-Moreno M, Hadad CZ, Restrepo A. Entropy drives the insertion of ibuprofen into model membranes. Phys Chem Chem Phys 2018; 20:24869-24876. [DOI: 10.1039/c8cp04674c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Entropy drives the insertion of ibuprofen into cell membranes.
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Affiliation(s)
| | - Isaias Lans
- Grupo de Bioquímica Teórica, Universidad Industrial de Santander
- Bucaramanga
- Colombia
- Max Planck Tandem Group, Universidad de Antioquia UdeA
- Medellín
| | | | - C. Z. Hadad
- Instituto de Química, Universidad de Antioquia UdeA
- Medellín
- Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA
- Medellín
- Colombia
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Sezer D, Oruç T. Protonation Kinetics Compromise Liposomal Fluorescence Assay of Membrane Permeation. J Phys Chem B 2017; 121:5218-5227. [DOI: 10.1021/acs.jpcb.7b01881] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Deniz Sezer
- Faculty of Engineering and
Natural Sciences, Sabancı University, Orhanlı-Tuzla, 34956 Istanbul, Turkey
| | - Tuğçe Oruç
- Faculty of Engineering and
Natural Sciences, Sabancı University, Orhanlı-Tuzla, 34956 Istanbul, Turkey
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Lopes D, Jakobtorweihen S, Nunes C, Sarmento B, Reis S. Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations. Prog Lipid Res 2017; 65:24-44. [DOI: 10.1016/j.plipres.2016.12.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/30/2016] [Accepted: 12/03/2016] [Indexed: 12/20/2022]
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10
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Bunker A, Magarkar A, Viitala T. Rational design of liposomal drug delivery systems, a review: Combined experimental and computational studies of lipid membranes, liposomes and their PEGylation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2334-2352. [DOI: 10.1016/j.bbamem.2016.02.025] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/09/2016] [Accepted: 02/10/2016] [Indexed: 01/22/2023]
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11
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Wang H, Meng F. Concentration effect of cimetidine with POPC bilayer: a molecular dynamics simulation study. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2016.1185793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Huanjie Wang
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, P.R. China
| | - Fancui Meng
- Tianjin Key Laboratory of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, P.R. China
- State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin, P.R. China
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12
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Oruç T, Küçük SE, Sezer D. Lipid bilayer permeation of aliphatic amine and carboxylic acid drugs: rates of insertion, translocation and dissociation from MD simulations. Phys Chem Chem Phys 2016; 18:24511-25. [DOI: 10.1039/c6cp05278a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The overabundance of drugs containing aliphatic amine and carboxylic acid groups is rationalized in terms of their membrane permeability.
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Affiliation(s)
- Tuğçe Oruç
- Faculty of Engineering and Natural Sciences
- Sabanc University
- 34956 Istanbul
- Turkey
| | - Sami Emre Küçük
- Faculty of Engineering and Natural Sciences
- Sabanc University
- 34956 Istanbul
- Turkey
| | - Deniz Sezer
- Faculty of Engineering and Natural Sciences
- Sabanc University
- 34956 Istanbul
- Turkey
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13
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Wang H, Ren X, Meng F. Molecular dynamics simulation of six β-blocker drugs passing across POPC bilayer. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1008470] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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