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Tunçer E, Bayramoğlu B. Molecular dynamics simulations of duodenal self assembly in the presence of different fatty acids. Colloids Surf A Physicochem Eng Asp 2022. [DOI: 10.1016/j.colsurfa.2022.128866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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2
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Nakmode D, Bhavana V, Thakor P, Madan J, Singh PK, Singh SB, Rosenholm JM, Bansal KK, Mehra NK. Fundamental Aspects of Lipid-Based Excipients in Lipid-Based Product Development. Pharmaceutics 2022; 14:pharmaceutics14040831. [PMID: 35456665 PMCID: PMC9025782 DOI: 10.3390/pharmaceutics14040831] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/31/2022] [Accepted: 04/06/2022] [Indexed: 12/15/2022] Open
Abstract
Poor aqueous solubility of drugs is still a foremost challenge in pharmaceutical product development. The use of lipids in designing formulations provides an opportunity to enhance the aqueous solubility and consequently bioavailability of drugs. Pre-dissolution of drugs in lipids, surfactants, or mixtures of lipid excipients and surfactants eliminate the dissolution/dissolving step, which is likely to be the rate-limiting factor for oral absorption of poorly water-soluble drugs. In this review, we exhaustively summarize the lipids excipients in relation to their classification, absorption mechanisms, and lipid-based product development. Methodologies utilized for the preparation of solid and semi-solid lipid formulations, applications, phase behaviour, and regulatory perspective of lipid excipients are discussed.
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Affiliation(s)
- Deepa Nakmode
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad 500037, India; (D.N.); (V.B.); (P.T.); (J.M.); (P.K.S.)
| | - Valamla Bhavana
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad 500037, India; (D.N.); (V.B.); (P.T.); (J.M.); (P.K.S.)
| | - Pradip Thakor
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad 500037, India; (D.N.); (V.B.); (P.T.); (J.M.); (P.K.S.)
| | - Jitender Madan
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad 500037, India; (D.N.); (V.B.); (P.T.); (J.M.); (P.K.S.)
| | - Pankaj Kumar Singh
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad 500037, India; (D.N.); (V.B.); (P.T.); (J.M.); (P.K.S.)
| | - Shashi Bala Singh
- Department of Pharmacology, National Institute of Pharmaceutical Education and Research, Hyderabad 500037, India;
| | - Jessica M. Rosenholm
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
| | - Kuldeep K. Bansal
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland;
- Correspondence: (K.K.B.); (N.K.M.)
| | - Neelesh Kumar Mehra
- Pharmaceutical Nanotechnology Research Laboratory, Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research, Hyderabad 500037, India; (D.N.); (V.B.); (P.T.); (J.M.); (P.K.S.)
- Correspondence: (K.K.B.); (N.K.M.)
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3
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Tuncer E, Bayramoglu B. Characterization of the self-assembly and size dependent structural properties of dietary mixed micelles by molecular dynamics simulations. Biophys Chem 2019; 248:16-27. [PMID: 30850307 DOI: 10.1016/j.bpc.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/27/2019] [Accepted: 02/01/2019] [Indexed: 01/05/2023]
Abstract
The bile salts and phospholipids are secreted by the gallbladder to form dietary mixed micelles in which the solvation of poorly absorbed lipophilic drugs and nutraceuticals take place. A comprehensive understanding of the micellization and structure of the mixed micelles are crucial to design effective delivery systems for such substances. In this study, the evolution of the dietary mixed micelle formation under physiologically relevant concentrations and the dependence of structural properties on micelle size were investigated through coarse-grained molecular dynamics simulations. The MARTINI force field was used to model cholate and POPC as the representative bile salt and phospholipid, respectively. The micellization behavior was similar under both fasted and fed state concentrations. Total lipids concentration and the micelle size did not affect the internal structure of the micelles. All the micelles were slightly ellipsoidal in shape independent of their size. The extent of deviation from spherical geometry was found to depend on the micellar POPC/cholate ratio. We also found that the surface and core packing density of the micelles increased with micelle size. The former resulted in more perpendicular alignments of cholates with respect to the surface, while the latter resulted in an improved alignment of POPC tails with the radial direction and more uniform core density.
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Affiliation(s)
- Esra Tuncer
- İzmir Institute of Technology, Food Engineering Department, Gulbahce Campus,Urla, Izmir 35430, Turkey.
| | - Beste Bayramoglu
- İzmir Institute of Technology, Food Engineering Department, Gulbahce Campus,Urla, Izmir 35430, Turkey.
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4
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Location of Solvated Probe Molecules Within Nonionic Surfactant Micelles Using Molecular Dynamics. J Pharm Sci 2019; 108:205-213. [DOI: 10.1016/j.xphs.2018.10.055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/11/2018] [Accepted: 10/12/2018] [Indexed: 12/18/2022]
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5
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Warren DB, McPhee E, Birru WA, Benameur H, Chalmers DK, Pouton CW. Improvement in the Predicted Partitioning of Alcohol and Polyethylene Oxide Groups Between Water and Octanol (logP) in Molecular Dynamics Simulations. J Pharm Sci 2019; 108:214-222. [DOI: 10.1016/j.xphs.2018.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 11/09/2018] [Accepted: 11/09/2018] [Indexed: 11/30/2022]
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6
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Suys EJA, Warren DB, Porter CJH, Benameur H, Pouton CW, Chalmers DK. Computational Models of the Intestinal Environment. 3. The Impact of Cholesterol Content and pH on Mixed Micelle Colloids. Mol Pharm 2017; 14:3684-3697. [DOI: 10.1021/acs.molpharmaceut.7b00446] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
| | | | | | - Hassan Benameur
- Capsugel Research & Development, Parc d’Innovation, Strasbourg, France
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7
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Birru WA, Warren DB, Headey SJ, Benameur H, Porter CJH, Pouton CW, Chalmers DK. Computational Models of the Gastrointestinal Environment. 1. The Effect of Digestion on the Phase Behavior of Intestinal Fluids. Mol Pharm 2017; 14:566-579. [PMID: 28099023 DOI: 10.1021/acs.molpharmaceut.6b00888] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Improved models of the gastrointestinal environment have great potential to assist the complex process of drug formulation. Molecular dynamics (MD) is a powerful method for investigating phase behavior at a molecular level. In this study we use multiple MD simulations to calculate phase diagrams for bile before and after digestion. In these computational models, undigested bile is represented by mixtures of palmitoyl-oleoylphosphatidylcholine (POPC), sodium glycodeoxycholate (GDX), and water. Digested bile is modeled using a 1:1 mixture of oleic acid and palmitoylphosphatidylcholine (lysophosphatidylcholine, LPC), GDX, and water. The computational phase diagrams of undigested and digested bile are compared, and we describe the typical intermolecular interactions that occur between phospholipids and bile salts. The diffusion coefficients measured from MD simulation are compared to experimental diffusion data measured by DOSY-NMR, where we observe good qualitative agreement. In an additional set of simulations, the effect of different ionization states of oleic acid on micelle formation is investigated.
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Bergström CAS, Charman WN, Porter CJH. Computational prediction of formulation strategies for beyond-rule-of-5 compounds. Adv Drug Deliv Rev 2016; 101:6-21. [PMID: 26928657 DOI: 10.1016/j.addr.2016.02.005] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 02/11/2016] [Accepted: 02/17/2016] [Indexed: 12/12/2022]
Abstract
The physicochemical properties of some contemporary drug candidates are moving towards higher molecular weight, and coincidentally also higher lipophilicity in the quest for biological selectivity and specificity. These physicochemical properties move the compounds towards beyond rule-of-5 (B-r-o-5) chemical space and often result in lower water solubility. For such B-r-o-5 compounds non-traditional delivery strategies (i.e. those other than conventional tablet and capsule formulations) typically are required to achieve adequate exposure after oral administration. In this review, we present the current status of computational tools for prediction of intestinal drug absorption, models for prediction of the most suitable formulation strategies for B-r-o-5 compounds and models to obtain an enhanced understanding of the interplay between drug, formulation and physiological environment. In silico models are able to identify the likely molecular basis for low solubility in physiologically relevant fluids such as gastric and intestinal fluids. With this baseline information, a formulation scientist can, at an early stage, evaluate different orally administered, enabling formulation strategies. Recent computational models have emerged that predict glass-forming ability and crystallisation tendency and therefore the potential utility of amorphous solid dispersion formulations. Further, computational models of loading capacity in lipids, and therefore the potential for formulation as a lipid-based formulation, are now available. Whilst such tools are useful for rapid identification of suitable formulation strategies, they do not reveal drug localisation and molecular interaction patterns between drug and excipients. For the latter, Molecular Dynamics simulations provide an insight into the interplay between drug, formulation and intestinal fluid. These different computational approaches are reviewed. Additionally, we analyse the molecular requirements of different targets, since these can provide an early signal that enabling formulation strategies will be required. Based on the analysis we conclude that computational biopharmaceutical profiling can be used to identify where non-conventional gateways, such as prediction of 'formulate-ability' during lead optimisation and early development stages, are important and may ultimately increase the number of orally tractable contemporary targets.
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Affiliation(s)
- Christel A S Bergström
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia; Department of Pharmacy, Uppsala University, Uppsala Biomedical Center, P.O. Box 580, SE-751 23 Uppsala, Sweden.
| | - William N Charman
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
| | - Christopher J H Porter
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia; ARC Centre of Excellence in Convergent Nano-Bio Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria 3052, Australia
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9
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Jiang J, Li J, Zhang Z, Sun E, Feng L, Jia X. Mechanism of enhanced antiosteoporosis effect of circinal-icaritin by self-assembled nanomicelles in vivo with suet oil and sodium deoxycholate. Int J Nanomedicine 2015; 10:2377-89. [PMID: 25848257 PMCID: PMC4381633 DOI: 10.2147/ijn.s76191] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Circinal-icaritin (CIT), one new active aglycone of Epimedium, can exert a beneficial effect on osteoporotic bone. However, its low bioavailability limits its clinical efficacy for the treatment of osteoporosis. MATERIALS AND METHODS In this paper, suet oil (SO) was used to improve the oral bioavailability of CIT and enhance its antiosteoporosis effect and absorption. After oral administration of CIT together with SO, the CIT and SO self-assembled into nanomicelles under the action of sodium deoxycholate (DOC) by bile secretion. The antiosteoporosis effects of the CIT-SO-DOC nanomicelles were evaluated in osteoporotic rats by bone mineral density, serum biochemical markers, bone microarchitecture, bone biomechanical properties, and related protein and gene expressions. We examined the bioavailability of CIT and its nanomicelles in vivo, and subsequently the nanomicelles were verified using transmission electron microscopy. Finally, we evaluated absorption across a rat intestinal perfusion model. RESULTS Compared with CIT, in the CIT-SO groups, protein and messenger ribonucleic acid expressions of osteoprotegerin were increased, while expressions of receptor activator of nuclear factor-κB ligand in bone tissue were decreased; bone-turnover markers in serum of hydroxyproline, alkaline phosphatase, tartrate-resistant acid phosphatase 5b, and receptor activator of nuclear factor-κB ligand levels were decreased, while osteoprotegerin and osteocalcin levels were increased; and trabecular bone mass, microarchitecture, and bone biomechanical strength were enhanced. The relative bioavailabilities of CIT-SO high dosage, CIT-SO medium dosage, and CIT-SO low dosage (area under concentration-time curve [AUC]0-∞) compared with that of raw CIT high dosage, CIT medium dosage, and CIT low dosage (AUC0-∞) were 127%, 121%, and 134%, respectively. The average particle size of CIT-DOC was significantly decreased after adding SO (P<0.01), and the intestinal permeability coefficients of CIT-SO-DOC nanomicelles in the duodenum, jejunum, ileum, and colon were all significantly improved (P<0.01). CONCLUSION The increased antiosteoporosis effects and bioavailability of CIT-SO-DOC self-assembled nanomicelles were due to an increase in absorption of CIT by reducing the particle sizes of CIT. SO may be a practical oral carrier for antiosteoporosis drugs with low bioavailability.
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Affiliation(s)
- Jun Jiang
- Key Laboratory of New Drug Delivery System of Chinese Materia Medica, Jiangsu Provincial Academy of Chinese Medicine, Nanjing, People’s Republic of China
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Jie Li
- Key Laboratory of New Drug Delivery System of Chinese Materia Medica, Jiangsu Provincial Academy of Chinese Medicine, Nanjing, People’s Republic of China
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Zhenhai Zhang
- Key Laboratory of New Drug Delivery System of Chinese Materia Medica, Jiangsu Provincial Academy of Chinese Medicine, Nanjing, People’s Republic of China
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - E Sun
- Key Laboratory of New Drug Delivery System of Chinese Materia Medica, Jiangsu Provincial Academy of Chinese Medicine, Nanjing, People’s Republic of China
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Liang Feng
- Key Laboratory of New Drug Delivery System of Chinese Materia Medica, Jiangsu Provincial Academy of Chinese Medicine, Nanjing, People’s Republic of China
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
| | - Xiaobin Jia
- Key Laboratory of New Drug Delivery System of Chinese Materia Medica, Jiangsu Provincial Academy of Chinese Medicine, Nanjing, People’s Republic of China
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, People’s Republic of China
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10
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Glyceride Lipid Formulations: Molecular Dynamics Modeling of Phase Behavior During Dispersion and Molecular Interactions Between Drugs and Excipients. Pharm Res 2013; 30:3238-53. [DOI: 10.1007/s11095-013-1206-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Accepted: 09/12/2013] [Indexed: 10/26/2022]
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11
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Bennett WD, Chen AW, Donnini S, Groenhof G, Tieleman DP. Constant pH simulations with the coarse-grained MARTINI model — Application to oleic acid aggregates. CAN J CHEM 2013. [DOI: 10.1139/cjc-2013-0010] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Long chain fatty acids are biologically important molecules with complex and pH sensitive aggregation behavior. The carboxylic head group of oleic acid is ionizable, with the pKa shifting to larger values, even above a value of 7, in certain aggregate states. While experiments have determined the macroscopic phase behavior, we have yet to understand the molecular level details for this complex behavior. This level of detail is likely required to fully appreciate the role of fatty acids in biology and for nanoscale biotechnological and industrial applications. Here, we introduce the use of constant pH molecular dynamics (MD) simulations with the coarse-grained MARTINI model and apply the method to oleic acid aggregates and a model lipid bilayer. By running simulations at different constant pH values, we determined titration curves and the resulting pKa for oleic acid in different environments. The coarse-grained model predicts positive pKa shifts, with a shift from 4.8 in water to 6.5 in a small micelle, and 6.6 in a dioleoylphosphatidylcholine (DOPC) bilayer, similar to experimental estimates. The size of the micelles increased as the pH increased, and correlated with the fraction of deprotonated oleic acid. We show this combination of constant pH MD and the coarse-grained MARTINI model can be used to model pH-dependent surfactant phase behavior. This suggests a large number of potential new applications of large-scale MARTINI simulations in other biological systems with ionizable molecules.
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Affiliation(s)
- W.F. Drew Bennett
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Alexander W. Chen
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
| | - Serena Donnini
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Gerrit Groenhof
- Department of Chemistry and Nanoscience Center, University of Jyväskylä, P.O. Box 35, FI-40014 Jyväskylä, Finland
| | - D. Peter Tieleman
- Department of Biological Sciences and Institute for Biocomplexity and Informatics, University of Calgary, 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada
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12
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Kindt JT. Accounting for Finite-Number Effects on Cluster Size Distributions in Simulations of Equilibrium Aggregation. J Chem Theory Comput 2012; 9:147-52. [DOI: 10.1021/ct300686u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- James T. Kindt
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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13
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Turner DC, Yin F, Kindt JT, Zhang H. Understanding pharmacokinetic food effects using molecular dynamics simulation coupled with physiologically based pharmacokinetic modeling. Biopharm Drug Dispos 2012; 33:510-21. [PMID: 23065939 DOI: 10.1002/bdd.1818] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 08/22/2012] [Accepted: 10/09/2012] [Indexed: 12/23/2022]
Abstract
In this study, a molecular dynamics (MD) method is assessed as a new front-end tool for deriving relevant drug-micelle partitioning rates for use in conjunction with a compartmental-style gastrointestinal absorption model. A refined mechanistic approach for handling micelle-associated vs unbound drug is presented and examined in terms of its utility for projecting human oral pharmacokinetic food/formulation effects. Similar to predecessor oral absorption models, the intestinal drug absorption rate is formulated as a function of the combined permeability through the unstirred water layer and the epithelial membrane, however, an additional diffusion coefficient adjustment is applied to account for the viscosity changes of the postprandial small intestine. Bulk passage of drug particles through the GI tract is simulated by compartmental transit through a network of nine compartments comprising the stomach, small intestine and colon. The tandem MD simulation/compartmental absorption algorithm is applied to identify factors influencing the fed vs fasted absorption ratios of a structurally diverse set of orally administered drugs. The data illustrate the interplay and apparent compromise between micelle solubilization and permeability.
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Affiliation(s)
- David C Turner
- Department of Pharmaceutical Sciences, Mercer University, Atlanta, GA 30341, USA
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14
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Abel S, Dupradeau FY, Marchi M. Molecular Dynamics Simulations of a Characteristic DPC Micelle in Water. J Chem Theory Comput 2012; 8:4610-23. [DOI: 10.1021/ct3003207] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Stéphane Abel
- Commissariat à l’Energie Atomique et aux Energies Alternatives, DSV/iBiTEC-S/SB2SM/LBMS, Saclay, France, CNRS UMR 8221, Saclay,
France
| | - François-Yves Dupradeau
- Laboratoire des glucides, UFR de Pharmacie & CNRS FRE 3517, Université de Picardie-Jules Verne, Amiens, France
| | - Massimo Marchi
- Commissariat à l’Energie Atomique et aux Energies Alternatives, DSV/iBiTEC-S/SB2SM/LBMS, Saclay, France, CNRS UMR 8221, Saclay,
France
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15
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Prakash P, Sayyed-Ahmad A, Zhou Y, Volk DE, Gorenstein DG, Dial E, Lichtenberger LM, Gorfe AA. Aggregation behavior of ibuprofen, cholic acid and dodecylphosphocholine micelles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:3040-7. [PMID: 22885171 DOI: 10.1016/j.bbamem.2012.07.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 07/20/2012] [Accepted: 07/30/2012] [Indexed: 12/21/2022]
Abstract
Non-steroidal anti-inflammatory drugs (NSAIDs) are frequently used to treat chronic pain and inflammation. However, prolonged use of NSAIDs has been known to result in Gastrointestinal (GI) ulceration/bleeding, with a bile-mediated mechanism underlying their toxicity to the lower gut. Bile acids (BAs) and phosphatidylcholines (PCs), the major components of bile, form mixed micelles to reduce the membrane disruptive actions of monomeric BAs and simple BA micelles. NSAIDs are suspected to alter the BA/PC balance in the bile, but the molecular interactions of NSAID-BA or NSAID-BA-PC remain undetermined. In this work, we used a series of all-atom molecular dynamics simulations of cholic acid (CA), ibuprofen (IBU) and dodecylphosphocholine (DPC) mixtures to study the spontaneous aggregation of CA and IBU as well as their adsorption on a DPC micelle. We found that the size of CA-IBU mixed micelles varies with their molar ratio in a non-linear manner, and that micelles of different sizes adopt similar shapes but differ in composition and internal interactions. These observations are supported by NMR chemical shift changes, NMR ROESY crosspeaks between IBU and CA, and dynamic light scattering experiments. Smaller CA-IBU aggregates were formed in the presence of a DPC micelle due to the segregation of CA and IBU away from each other by the DPC micelle. While the larger CA-IBU aggregates arising from higher IBU concentrations might be responsible for NSAID-induced intestinal toxicity, the absence of larger CA-IBU aggregates in the presence of DPC micelles may explain the observed attenuation of NSAID toxicity by PCs.
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Affiliation(s)
- Priyanka Prakash
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, 6431 Fannin St., Houston, TX 77030, USA
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16
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King DT, Warren DB, Pouton CW, Chalmers DK. Using molecular dynamics to study liquid phase behavior: simulations of the ternary sodium laurate/sodium oleate/water system. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:11381-11393. [PMID: 21838286 DOI: 10.1021/la2022903] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The prediction of surfactant phase behavior has applications in a wide range of areas. An accurate modeling of liquid phase behavior can aid our understanding of colloidal process or be used to design phases that respond in a defined way to their environment. In this work, we use molecular dynamics to model the phase behavior of the ternary sodium laurate/sodium oleate/water system and compare the simulation results to experimental data. Simulations were performed with the GROMOS 53A6 united-atom force field and cover the entire ternary phase diagram, producing micellar, hexagonal, and lamellar phases. The aggregate simulation time for the 33 simulations performed during this study is 4.4 μs. We find that the simulations were able to model the experimentally observed liquid phase behavior accurately, showing that the carboxylate and lipid parameters of the 53A6 force field give very good quality results for the in silico prediction of liquid system phase behavior.
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Affiliation(s)
- Dylan T King
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
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17
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Lemkul JA, Allen WJ, Bevan DR. Practical considerations for building GROMOS-compatible small-molecule topologies. J Chem Inf Model 2010; 50:2221-35. [PMID: 21117688 DOI: 10.1021/ci100335w] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Molecular dynamics simulations are being applied to increasingly complex systems, including those involving small endogenous compounds and drug molecules. In order to obtain meaningful and accurate data from these simulations, high-quality topologies for small molecules must be generated in a manner that is consistent with the derivation of the force field applied to the system. Often, force fields are designed for use with macromolecules such as proteins, making their transferability to other species challenging. Investigators are increasingly attracted to automated topology generation programs, although the quality of the resulting topologies remains unknown. Here we assess the applicability of the popular PRODRG server that generates small-molecule topologies for use with the GROMOS family of force fields. We find that PRODRG does not reproduce topologies for even the most well-characterized species in the force field due to inconsistent charges and charge groups. We assessed the effects of PRODRG-derived charges on several systems: pure liquids, amino acids at a hydrophobic-hydrophilic interface, and an enzyme-cofactor complex. We found that partial atomic charges generated by PRODRG are largely incompatible with GROMOS force fields, and the behavior of these systems deviates substantially from that of simulations using GROMOS parameters. We conclude by proposing several points as "best practices" for parametrization of small molecules under the GROMOS force fields.
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Affiliation(s)
- Justin A Lemkul
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
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18
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Kuriabova T, Betterton MD, Glaser MA. Linear aggregation and liquid-crystalline order: comparison of Monte Carlo simulation and analytic theory. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/c0jm02355h] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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