Cell-based permeability

Low permeability can itself be the cause of apparent discrepancies between biochemical and cell-based assays and may or may not have physiological relevance. Independent of the solubility limitation mentioned above, the selection of an appropriate loading concentration in cell-based permeability assays impacts on the assay outcome and depends on what information one wants to extract from the measurement loading at high concentration (i.e., 100 pM) will essentially cancel the effect of active transports unless passive diffusion is low. When high loading concentrations are used, poor recovery and bioanalytics are usually not an issue. 

Figure 10.4 Measured LogD versus cell-based permeability Logpapp for cyclic hexapeptides from ref. 49. ( Measured shake-flask Log D. Papp (RRCK) = cell based permeability in Ralph Russ canine kidney cell line in cm sec . Compound numbers refer to those in ref. 49.)...

A dual isotope labeling technique [85] has been used to measure membrane permeability in plant cells, based on the selective permeabiHty of the membranes of living cells to tritiated water and carbon-14 labeled mannitol. Kieran [29] showed that the results of the dual isotope labeling and Evan s Blue staining methods correlated well as indicators of cell viability however, the latter was preferable in terms of reagent cost and ease of analysis. 

PAMPA is typically used to make a prediction of the passive, transcellular absorption of a compound. Compounds which may be absorbed by a paracellular mechanism or may be substrates for active transport (uptake or efflux) are usually better assessed in a cell based system. A combination of assays can be applied to gain a greater understanding of the permeability and transport properties of a compound. 

Lee JW, Jung M, Rosania GR, Chang YT (2003) Development of novel cell-permeable DNA sensitive dyes using combinatorial synthesis and cell-based screening. Chem Commun 1852-1853... 

There are several approaches to estimating absorption using in vitro methods, notably Caco-2 and MDCK cell-based methods or using methods that assess passive permeability, for example the parallel artificial membrane permeation assay (PAMPA) method. These are reviewed elsewhere in this book. The assays are very useful, and usually have an important role in the screening cascades for drug discovery projects. However, as discussed below, the cell-based assays are not without their drawbacks, and it is often appropriate to use ex vivo and/or in vivo absorption assays. 

Other potent peptide mimetic NS3 protease inhibitors have been reported that incorporate a serine trap on the C-terminal end of the peptide. Thus, the inhibitory activity of telaprevir (VX-950, 59), (7nM vs. NS3, 300 nM vs. the la replicon) is based on truncation of the polypeptide substrate, maximizing binding by alteration of amino acids at the scissile site, and capping both N- and C-terminal ends, the latter with a known dicarbonyl serine trap. This compound has exhibited impressive antiviral activity in animals, and showed a 4.4 log drop in viral load in genotype 1-infected patients in a Phase lb clinical trial [110]. Telaprevir is expected to enter Phase 3 clinical trials in 2007. Additional bicyclo-proline-based P2 tetrapeptides, represented by analog 60 (Kj = 22 nM), have been explored. Although the compounds are selective inhibitors of NS3, little or no cell-based replicon activity was reported, presumably due to poor cellular permeability [111-114], A diastereomer of telaprevir, has been reported to inhibit the replicon with an EC50 of 0.55 pM [115]. 

Secondary assays depend on the project. Where the primary screen was a cell-based assay, the secondary assay may be a radioligand competition binding assay. In other cases, such as where the primary screen was a biochemical assay, the secondary assay may be a cellular assay, and may be functional or mechanistic. One of the issues that may arise at this stage is that compounds with reasonable activity in the primary assay may not show activity in the secondary assay. There can be a number of reasons for this, including insufficient potency, inability of the compound to get into cells, or a higher intracellular concentration of the natural ligand (e.g., ATP) if the inhibitor is a competitive inhibitor. It is often necessary at this stage to prepare additional compounds in the series to get compounds of sufficient potency and/or permeability so that cellular activity can be demonstrated. 

Kinetic solubility This pragmatic approach starts with a concentrated compound solution in pure DM SO further diluted in a buffer medium. The amount of compound in solution is measured after a few minutes incubation either by recording its UV absorbance (with or without a chromatographic step) or precipitate formation using an optical method (turbidimetry, nephelometry or flow cytometry). This approach mimics the typical path of the compound in biochemical, cellular assays or in vivo animal models. Kinetic solubility usually serves as a quality filter prior to cell based assays (see paragraphs on solubility, permeability and cellular assays). 

Significant interlaboratory differences in permeability measurements are observed with cell-based assays. It is important to standardize culture conditions and characterize a cell line within one s own laboratory. Permeability differences can be attributed to a number of factors, for example, heterogenecity of cell line, passage number, culture conditions, characteristics of the filter membrane, age of mono-layers and level of differentiation and experimental methodology used. Active... 

Volpe Donna, A. (2008) Variability in Caco-2 and MDCK cell-based intestinal permeability assays. Journal of Pharmaceutical Sciences, 97, 712-725. 

We are interested in the application of polymers as adsorbents, ion exchangers, fuel cells, and permeable materials. In this regard, the first resins with some of these properties were obtained by D Aleleio in 1944 based on the copolymerization of styrene and divinylbenzene. Unfunctionalized polystyrene resins cross-linked with divinylbenzene (Amberlite) are widely applied as adsorbents [191,192], In addition, the polystyrene-divinylbenzene resins functionalized with sulfuric acid (sulfonation) to create negatively charged sulfonic sites are applied as cation exchangers, and treated by chloromethylation followed by animation produce anionic resins [193,194],... 

We routinely use these substrates for kinetic characterizations of new aldolase catalysts. However, they are not suitable for cell-based screenings because both substrate and product are readily cell permeable. The solution to this problem came when we discovered that our aldolase antibodies catalyze the -elimination (or r ro-Michael reactions) of (3-hetero substituted ketones 37 [Scheme 8 (1)]. 

In contrast to enzyme assays, cell-based assays present the target in a more physiological milieu. With enzyme assays, it may be difficult to purify and express active kinases and phosphatases in their full-length forms and they may require the use of fusion proteins with kinase activity domains. Cell-based technologies, on the other hand, present the opportunity to express the targets with regulatory domains included. Furthermore, cell-based assays usually detect only cell-permeable inhibitors and have the potential to identify more unusual mechanisms, as described earlier. 

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