QSAR study on permeability of hydrophobic compounds with artificial membranes
Graphical abstract
To investigate PAMPA permeability of hydrophobic compounds, we experimentally measured the Papp-pampa of compounds with high hydrophobicity, including several pesticides, and compared the measured Papp-pampa values with those calculated from the QSAR equation derived in our previous study. The new bilinear QSAR model explained the PAMPA permeability of the whole dataset of compounds, whether they were hydrophilic or hydrophobic, with the same parameters as the equation in the previous study. In addition, the PAMPA permeability coefficients correlated well with Caco-2 cell permeability coefficients.
Introduction
In recent years, in vitro methods for predicting oral drug absorption have progressed. In vitro models of intestinal absorption generally focus on determining membrane permeability using Caco-2 cells, MDCK cells, artificial membranes, and immobilized artificial membrane (IAM) columns.1 The parallel artificial membrane permeation assay (PAMPA), proposed by Kansy et al. in 1998,2 is a high throughput in vitro assay system that evaluates transcellular permeation. In PAMPA, a 96-well microtiter plate completely filled with aqueous buffer solutions is covered with a hydrophobic filter coated with lipids in an organic solvent solution in a sandwich construction.2 The PAMPA permeability of several drugs has been evaluated using various lipids dissolved in organic solvents, such as an egg lecithin in n-dodecane2, 3 or 1,9-decadiene,4, 5, 6 the composition of the lipid membrane that mimics the intestinal brush border membrane in 1,7-octadiene (Bio-mimetic PAMPA),7, 8, 9 the porcine polar brain lipid in dodecane,10 100% n-hexadecane (HDM-PAMPA),11 diolphosphatidylcholine in dodecane (DOPC-PAMPA)12, and a phospholipid mixture in dodecane (Double-Sink PAMPA).12 The PAMPA is used to screen for human intestinal absorption in pharmaceutical research because several papers indicated that PAMPA permeability is correlated with both Caco-2 cell permeability and human intestinal absorption.2, 3, 5, 6, 7, 9, 13, 14, 15, 16 PAMPA is also applicable for predicting passive blood–brain penetration10 and human skin permeability.17
In our previous study,6 we reported a classical QSAR equation for PAMPA permeability coefficients (Papp-pampa) of structurally diverse compounds with simple physicochemical parameters, log Poct, where Poct is the partition coefficient in the 1-octanol/water system, the absolute value of the difference between the pKa value of the compound and the experimental pH 7.3, |pKa − pH|, the surface area occupied by the hydrogen-bond acceptor and donor atoms of each modeled conformer, SAHA, and SAHD; however, desipramine, imipramine, and testosterone, having high log Poct, were excluded from the QSAR equation because their measured Papp-pampa values were lower than calculated. Although we attempted the bilinear analysis of PAMPA permeability coefficients including these three compounds, it was difficult to obtain a statistically significant equation because there were few hydrophobic compounds in the dataset. Since many chemicals and agrochemicals used widely are hydrophobic, it is inevitable that humans are exposed to these hydrophobic chemicals as residues in food and water, or in occupational use;18 therefore, it is desirable to predict exposure using in vitro or in silico methods such as PAMPA.
In the present study, we experimentally measured the Papp-pampa of more compounds which have particularly high apparent hydrophobicity at the experimental pH, including several pesticides. Then, the Papp-pampa of the compounds, including the hydrophobic compounds, was analyzed using the QSAR approach to investigate whether other physiochemical parameters were significant in determining PAMPA permeability of the hydrophobic compounds. We also examined the effect of the unstirred water layer (UWL) and membrane retention on PAMPA permeability. Furthermore, PAMPA permeability of the hydrophobic compounds was compared with their Caco-2 cell permeability to investigate whether PAMPA is applicable for high-throughput evaluation to predict the exposure of humans to hydrophobic chemicals and agrochemicals, as well as drugs.
Section snippets
Permeability with artificial membranes
Table 1 shows the permeability coefficient through an artificial membrane, Papp-pampa values of added 22 chemicals and 15 agrochemicals with the data reported previously.6 We used Tris–HCl buffer (pH 7.3) containing 5–30% DMSO for the measurement of PAMPA permeability (5% DMSO: imidacloprid and 21 chemicals except pyrene; 20% DMSO: 13 agrochemicals except biphenyl and imidacloprid; 30% DMSO: biphenyl and pyrene). The log Papp-pampa values of added compounds were in the range of −5.95 (biphenyl)
Permeability with artificial membranes of hydrophobic compounds
It is important to predict the oral absorption of hydrophobic compounds from the perspective of not only effective screening for drug candidates in the early drug discovery stage but also risk assessment for agrochemicals and endocrine-disrupting chemicals in the environment. In the present study, we measured the PAMPA permeability coefficients of hydrophobic compounds which are useful for the prediction of human intestinal absorption.
The measured log Papp-pampa values of added hydrophobic
Conclusions
In this study, we clarified the barrier by the UWL on membrane surfaces and the membrane retention influencing PAMPA permeability of hydrophobic compounds. The bilinear QSAR model explained the PAMPA permeability of diverse compounds, whether hydrophilic or hydrophobic, with the same physicochemical parameters as those in the previous study. It was shown the PAMPA permeability is able to predict Caco-2 cell permeability, including hydrophobic compounds, which is used for the evaluation of human
Materials
Thirty-eight commercial drugs, 28 chemicals, and 11 agrochemicals were purchased from Nacalai Tesque (Kyoto, Japan), Kokusan Chemical Co. Ltd (Tokyo, Japan), Wako Pure Chemical Industries (Osaka, Japan), Bachem AG (Bubendorf, Switzerland), Kanto Chemical (Tokyo, Japan), Sigma–Aldrich Japan (Tokyo, Japan), Tocris Cookson Ltd (Bristol, UK) or BIOMOL Research Laboratories Inc. (PA, USA). Lecithin from egg yolk was purchased from Sigma (MO, USA). Hydrophobic filter plates (MultiScreen-IP, Clear
Acknowledgments
We are grateful to Nippon Kayaku Co., Ltd and Sankyo Agro Co., Ltd for providing a test compound, chromafenozide, and Dr. Yoshiaki Nakagawa (Kyoto University) for providing compounds, tebufenozide, methoxifenozide, and halofenozide. We also thank Emeritus Professor Toshio Fujita (Kyoto University) and Dr. Kiyohiko Sugano (Pfizer Japan Inc.) for helpful advice and comments on QSAR, and advice on the permeability experiment, respectively. The Caco-2 cell permeability coefficients of
References and notes (38)
- et al.
Eur. J. Med. Chem.
(2002) - et al.
Bioorg. Med. Chem.
(2004) - et al.
Bioorg. Med. Chem.
(2004) - et al.
Bioorg. Med. Chem.
(2005) - et al.
J. Biomol. Screen
(2001) - et al.
Int. J. Phram.
(2002) - et al.
Int. J. Pharm.
(2003) - et al.
Eur. J. Med. Chem.
(2003) - et al.
Eur. J. Pharm. Sci.
(2004) - et al.
Eur. J. Pharm. Sci.
(2005)
J. Pharm. Sci.
Eur. J. Pharm. Sci.
Eur. J. Pharm. Sci.
J. Med. Chem.
Occup. Environ. Med.
Curr. Topics Med. Chem.
J. Med. Chem.
J. Med. Chem.
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