# Patent

## Title
Processes and kits for determining multi-drug resistance of cells

## Abstract

This invention relates to multi-drug resistance (MDR) in cells, and the use of certain xanthene compounds for determining drug resistance in cells and the effect of test compounds on cell membrane transport by the membrane transporters MDR1, MRP and BCRP. Processes and kits for making these determinations and measuring these effects are described and provided.

## Background
FIELD OF THE INVENTION
This invention relates to the field of multi-drug resistance (MDR) in cells, and in tissues, organs and organisms containing such cells. This invention also relates to the use of certain xanthene compounds in MDR directed to, among other applications: determining drug resistance of cells, detecting and profiling multidrug resistant phenotypes in cells of interest, determining activity levels of membrane transporters involved in drug resistance, and determining the effect of test compounds on membrane transport by such membrane transporters.
All patents, patent applications, patent publications, scientific articles and the like, cited or identified in this application are hereby incorporated by reference in their entirety in order to describe more fully the state of the art to which the present invention pertains.
BACKGROUND OF THE INVENTION
Multidrug resistance relates to resistance of tumor cells to a whole range of chemotherapy drugs with different structures and cellular targets [Leonard et al., The Oncologist 8:411-424 (2003)]. The phenomenon of multi drug resistance (MDR) is a well known problem in oncology and thus warrants profound consideration in considering various cancer treatments. One of the underlying molecular rationales for MDR is the up-regulation of a family of MDR transporter proteins that cause chemotherapy resistance in cancer by actively extruding a large variety of therapeutic compounds from the malignant cells. MDR transporters belong to the evolutionarily conserved family of the ATP binding cassette (ABC) proteins, and are presented in practically all living organisms from prokaryotes to mammals [Gottesman et al., Nat Rev Cancer 2:48-58 (2002)]. ABC transporters play an important protective function against toxic compounds in a variety of cells and tissues, especially in secretory organs, at the sites of absorption, and at blood-tissue barriers. The three major multidrug resistance ABC proteins are MDR1 (including P-glycoprotein, ABCB1), multidrug resistance associated protein 1 (including MRP1, ABCC1) and ABCG2 (including placenta-specific ABC transporter, ABCP/breast cancer resistance protein, BCRP/mitoxantrone resistance protein and MXR). MDR1 and MRP1 can transport a large variety of hydrophobic drugs, and MRP1 can also extrude anionic drugs or drug conjugates. Other members of the MRP/ABCC family have also been indicated to be involved in cancer multidrug resistance (for details, see [Haimeur et al., Curr Drug Metab 5:21-53 (2004)]). The transport properties of ABCG2 are overlapping with those of both MDR1 and the MRP type proteins; thus these three proteins form a special network in chemo-defense mechanisms.
Because of a significant role that ABC transporters play in cancer multidrug resistance and the body's protection against xenobiotics, sensitive and specific quantitative assays are required for the detection of the activity of these proteins. High throughput assay systems are also required to screen for potential transporter-interacting partners. The estimation of the activity of ABC transporter is not easily achieved by the routinely available classical non-functional methods, such as Northern blotting, RNase protection, RNA in situ hybridization, RT PCR or immunostaining. MDR-ABC protein expression is often not correlated with mRNA levels or is often below the detection threshold, as relatively few active transporter molecules may cause major alterations in drug transport. Additionally, functional activity of ABC transporters may not correlate with their expression levels determined by the foregoing methods.
The ability of ABC transporters to actively transport compounds against the concentration gradient across the cell membrane has allowed the development of a number of functional assays to measure the level and function of transporter protein. Lipophilic dyes are capable of diffusing across cell membranes. Upon the loading of the cells with the dye(s), the resulting fluorescence intensity will depend on the activity of ABC transporters; the cells with highly active transporters will demonstrate lower fluorescence because of the increased efflux of the dye/substrate. The functions of MDR-ABC transporters have been characterized by measuring the cellular uptake, efflux, or steady-state distribution of a number of fluorescent substrates (summarized in Table 1, FIG. 1) using flow cytometry, fluorescent microscopy or fluorimetry. Substrate specificities of Pgp, MRP and BCRP are distinct, but also overlapping [Litman et al., Cell Mol Life Sci. 58:931-959 (2001)], as shown in Table 1, FIG. 1.
Several drawbacks have been noted relating to the sensitivity of most fluorophores used in this application because of protein binding, sequestration, or changes in fluorescence due to the intracellular milieu such as pH or free calcium levels [Hollo et al., Biochem Piophys Acta 1191:384-388 (1994)]. To increase sensitivity of the method, hydrophobic ester derivatives, such as AM esters of the fluorescent dyes have been used. These cell permeable derivatives of fluorescent dyes are also actively exported from cells by MDR proteins. When these ester derivatives reach the cytosol, however, intracellular esterases cleave the ester groups so that the dyes are now impermeable and require active transport. The resulting free dye can now be actively exported by MDR proteins in the cells [Homolya et al., J Biol. Chem. 268:21493-21496 (1993); Liming a et al., Exp Cell Res. 212:291-296 (1994)]. Some of the dyes are only fluorescent after AM hydrolysis.
Clinicians are especially interested in identifying the drug resistance profile, and the substrate specificity and drug extrusion activity of the various multi-drug resistance proteins expressed in a given tumor sample. The demonstration of the transport activity of various multi-drug resistance proteins in the plasma membrane requires a sensitive and reproducible in vitro multi-drug resistance assay. To date, BCRP has gained prominence as one of the three major ATP-binding cassette (ABC) membrane efflux transporters alongside P-gp and MRP, conferring drug resistance in cancer and inflammation chemotherapies [Litman et al., J Cell Sci. 113:2011-2021 (2000); van der Heijden et al., Arthritis Rheum. 60:669-677 (2009); Koshiba et al., Xenobiotica 38:863-868 (2008)]. Besides being present in drug-resistant cancer and T-cells, BCRP is also endogenously expressed at a high level in human placenta and to a lesser extent in liver, small intestine and colon, ovary, veins, capillaries, kidney, adrenal, and lung, with little to no expression in brain, heart, stomach, prostate, spleen, and cervix [Doyle et al., Oncogene 22(47):7340-7358 (2003)]. It has been demonstrated that calcein AM is useful for the quantitative functional analysis of the presence of active ABCB and ABCC but not ABCG transporters in cells Litman et al., J Cell Sci. 113:2011-2021 (2000)]. Thus, it is important to have a simple, reproducible and sensitive method to determine activity of all three types of ABC transporters in live cells.
To detect functional activity of drug efflux pumps, two assays using fluorescent dyes are commonly employed: one measures cellular dye accumulation and the other measures dye retention. The accumulation assay measures dye uptake in the presence or absence of known pump modulators. In the retention assay, the cells are loaded with the substrate in the absence of any reversal agent, washed, and then further incubated without dye but in the presence of reversing agents to allow time for the substrate to be transported out of the cell by a drug efflux pump. The distinction between accumulation and retention is necessary when evaluating cells for MDR phenotypes, as substrates act differently under different experimental conditions. Accumulation/retention assays offer high throughput, generic readouts (increase in fluorescence intensity), and are readily automated. These assays are not designed, however, to distinguish Pgp substrates from inhibitors [Tiberqhien, F. and Loor, F., Anticancer Drugs 7:568-578 (1996)] and do not directly measure transport.
The cell-based bidirectional permeability assay (or monolayer efflux assay) is currently accepted as the “method of choice” for determining the P-gp inhibition potential of test compounds in drug discovery laboratories and across the industry [Horio et al., J Biol. Chem. 264:14880-14884 (1989); Horio et al., Proc Natl Acad Sci USA. 85:3580-3584 (1988); Polli et al., J Pharmacol Exp Ther. 299:620-628 (2001); Rautio et al., Drug Metab Dispos 34(5) 786-792 (2006)]. The FDA guidance document [Drug Guidance for Industry, www.fda.gov/cder/guidance/6695dft.pdf, (2006)] also recommends conducting bidirectional permeability studies using Caco-2 cells or other cell lines (e.g., MDCK, LLC-PK1 etc.), either wild-type or transfected (with P-gp or other MDR proteins), to determine the P-gp inhibition potential of test compounds [Zhang et al., Xenobiotica 38:709-724 (2008)]. The experimental protocol for this assay is well established and quite uniform across different laboratories. Typically, bidirectional permeability of a well accepted MDR substrate is assessed alone and in the presence of a single concentration of test compound to estimate the inhibition potential.
This type of the assay is generally conducted for studying in vitro drug interactions with membrane transporter proteins that belong to two major superfamilies—ABC transporters [rev. in Schinkel, A. H. and Jonker, J. W., Adv Drug Deli Rev. 55:3-29 (2003)] and solute carrier (SLC) transporters [rev. in Hediger et al., Pflugers Arch. 447:465-468 (2004)]. Many pharmaceutical agents and toxins are transported by multispecific SLC transporters for organic anions (e.g., OATP-SLCO/SLC21 and OAT-SLC22A1-3) and organic cations (OCT-SLC 22A4-5). These solute carriers, often called “uptake transporters,” include a large variety of related membrane proteins, and in many cases possess overlapping substrate profiles with the MDR-ABC proteins [Marzolini et al., Pharmacogenomics 5:273-282 (2004); Miyazaki et al., Trends Pharmacol Sci 25:654-662 (2004)]. Some of these transporters perform obligatory exchange of organic compounds (e.g., OAT3), while in others transport is modulated and/or driven by monovalent ions and the membrane potential (e.g., OCTN). Moreover, there is a coordinated expression pattern for various SLC and ABC transporters in the liver, kidney, and BBB, which may govern the overall vectorial transport of many compounds that are mutual substrates of MDR-ABC and SLC proteins [Kusuhara, H. and Sugiyama, Y., Neuro Rx 2:73-85 (2005)].
Transepithelial transport depends on the polar distribution of proteins and lipids in the plasma membrane of epithelial cells. Typically, one plasma membrane contains a transporter that allows a specific ligand to enter the epithelial cells, and the plasma membrane on the opposite side of the cell contains a transporter that functions to export the ligand from the cell, resulting in net transepithelial transport of the ligand from one side of the epithelium to the other. In general, the substrates for transport by MDR proteins are highly lipophilic, and so enter epithelial cells freely from both surfaces. MDR proteins in the apical plasma membrane could expel substrates across the apical plasma membrane. Thus, ligand entering the cell from the basolateral surface is likely to leave the cell across the apical plasma membrane, whereas ligand entering the cell across the apical plasma membrane is likely to leave the cell across the same plasma membrane, with the result that basolateral to apical flux exceeds apical to basolateral flux. The net effect would be secretion of cytotoxic drugs by each of the epithelia listed above.
The monolayer efflux assay, where the ratio of basolateral-to-apical (B→A) permeability versus apical-to-basolateral (A→B) permeability is compared with a value of 1, is regarded as the standard for identifying MDR substrates because this assay measures efflux in the most direct manner [Polli et al., J Pharmacol Exp Ther 299:620-628 (2001)]. Due to concentration-dependent inhibition of active efflux on the apical side by MDR inhibitors, the B→A permeability decreases whilst A→B permeability increases with ratio approaching unity as the dose of inhibitor increases. The affinity of inhibitor to MDR protein(s) may be studied by calculating the active flux that can be obtained from the B→A fluxes in the absence and presence of MDR inhibitors. Inhibition potency, determined by inhibitor concentration-dependent transport assay, is usually represented as an IC50 value, the concentration that gives 50% of maximum inhibition of a known P-gp substrate. Specificity of the inhibitor to P-gp may be determined by competitive assays, which involve a transport assay of a known substrate in the presence of known inhibitors (specific to various transporters) with and without compounds under test. Thus, appropriate design of competitive inhibition assays using known selected substrates and modulators will show the specificity of the inhibitors towards the efflux pump.
Bacterial multidrug efflux systems are a serious problem in the pharmacological treatment of patients with infectious diseases since the substrate spectra of many multidrug transporters include clinically relevant antibiotics [Putman et al., Microbiol Mol Biol Rev. 64(4):672-693 (2000)]. Multidrug resistant pumps operate via an active efflux mechanism and are typically ATP- or PMF- (proton motive force) dependent. Multidrug transporters are associated with both intrinsic and acquired resistance to antibiotics. For example, homologous to human P-gp ABC-type multidrug transporter LmrA of L. lactis displays very broad antibiotic specificity, demonstrating that ATP-dependent multidrug transporters can seriously affect the efficacy of many antibiotics [van Veen et al., Proc Natl Acad Sci ISA 93:10668-10672 (1996); van Veen et al., Nature 391(6664):291-295 (1998)]. Dyes such as acriflavine, ethidium bromide, rhodamine 6G and pyronin Y are used as substrates for many bacterial efflux pumps and their susceptibility in the presence or absence of efflux pump inhibitors has been used as a screen for the presence of efflux-related resistance mechanisms [DeMarco et al., Antimicrob Agents Chemother. 51:3235-3239 (2007)]. The bacterial multidrug efflux systems transport similar drugs and are sensitive to similar inhibitors as the mammalian multidrug transporter, P-gp [Neyfakh et al., Proc Natl Acad Sci USA. 88:4781-4785 (1991)].
There remains a need for a general non-toxic MDR probe that a) will recognize all three major ABC transporter's types in live cells (unlike the most common MDR probe Calcein AM and other calcium indicator dyes such as Fluo-3 and Fluo-4); b) will be brighter (e.g. possess higher quantum yield and molar extinction coefficient) and more sensitive than common general MDR probes, such as doxorubicin and mitoxantrone; c) could be used in all types of the efflux assays discussed above; d) will require few processing steps and provide a reproducible protocol; and e) will be compatible with other common fluorescent dyes used in flow cytometry and diverse fluorescent proteins expressed in cells.
SUMMARY OF THE INVENTION
This invention relates to a process for determining drug resistance of cells of interest comprising the first step (A) of providing: (i) a clinical or biological sample comprising cells; (ii) at least one xanthene compound that is transportable across a cell membrane by membrane transporters: MDR1, MRP and BCRP; and (iii) one or more membrane transporter inhibitors. In step (B), cells from a first portion of the clinical or biological sample (i) are contacted with at least one xanthene compound (ii) while in step (C), cells from a second portion of the clinical or biological sample (i) are contacted with at least one xanthene compound (ii) and one or more inhibitors (iii). The fluorescent signals generated in steps (B) and (C) are then measured in step (D). By comparing the fluorescent signals measured in step (D), the elevated activities of MDR1, MRP and BCRP, or a combination thereof, are determined, thereby determining the drug resistance of the cells of interest.
This invention also relates to a process for determining drug resistance of cells of interest. In this process, the following are provided in step (A): (i) at least three portions of a clinical or biological sample comprising cells; (ii) at least one xanthene compound that is transportable across a cell membrane by membrane transporters: MDR1, MRP and BCRP; and (iii) one or more membrane transporter inhibitors. Three contacting steps are carried out. In step (B), cells from a first portion of the clinical or biological sample (i) are contacted with at least one xanthene compound (ii) under conditions sufficient to inhibit efflux of the xanthene compound or compounds from the cells. In step (C), cells from a second portion of the clinical or biological sample (i) are contacted with at least one xanthene compound (ii) under conditions sufficient to permit efflux of the xanthene compound or compounds from the cells. In step (D), cells from a third portion of the clinical or biological sample (i) are contacted with at least one xanthene compound (ii) and one or more inhibitors (iii). The fluorescent signals generated in steps (B), (C) and D is then measured in step (E). The fluorescent signals measured in step (D) are then compared in step (F), to determine elevated activities of said MDR1, MRP and BCRP, or a combination thereof, thereby determining the drug resistance of the cells of interest.
This invention also provides a process for determining the effect of a test compound on transport across a cell membrane by the membrane transporters: MDR1, MRP and/or BCRP. In this process, three components are provided in step (A): (i) a clinical or biological sample comprising cells; (ii) at least one xanthene compound that is transportable across a cell membrane by membrane transporters: MDR1, MRP and BCRP; and (iii) one or more test compounds. Two contacting steps are then carried out. These include step (B) of contacting cells from a first portion of the clinical or biological sample (i) with at least one xanthene compound (ii). In step (C), cells from a second portion of the clinical or biological sample (i) are contacted with at least one xanthene compound (ii) and one or more test compounds (iii). The fluorescent signals generated in step (B) and step (C) are measured in step (D). The measured fluorescent signals are then compared in step (E) to determine elevated activities of MDR1, MRP and BCRP, or a combination thereof, thereby determining the effect of the one or more test compounds (iii) on cell membrane transport by the membrane transporters.
The present also provides a process for determining the effect of a test compound on transport across a cell membrane by the membrane transporters: MDR1, MRP and/or BCRP. In step (A) of this process, there are provided (i) at least three portions of a clinical or biological sample comprising cells; (ii) at least one xanthene compound that is transportable across a cell membrane by membrane transporters: MDR1, MRP and BCRP; and (iii) one or more membrane transporter inhibitors. Three contacting steps are then carried out, including step (B) of contacting cells from a first portion of the clinical or biological sample (i) with at least one xanthene compound under conditions sufficient to inhibit efflux of the xanthene compound or compounds from the cells. In a second contacting step, cells from a second portion of the clinical or biological sample (i) are contacted with at least one xanthene compound (ii) under conditions sufficient to permit efflux of the xanthene compound or compounds from the cells. In the third contacting step, cells from a third portion of the clinical or biological sample (i) are contacted with at least one xanthene compound (ii) and one or more inhibitors (iii). In step (E), the fluorescent signals generated in steps (B), (C) and D are measured. The measured fluorescent signals are compared in step (F) to determine elevated activities of MDR1, MRP and BCRP, or a combination thereof, thereby determining the drug resistance of the cells of interest.
This invention additionally provides a kit for determining drug resistance of cells of interest, or detecting and profiling multidrug resistant phenotypes in cells of interest, or determining activity levels of membrane transporters MDR1, MRP and BCRP. The kit comprises in packaged combination: (i) at least one xanthene compound that is transportable across a cell membrane by membrane transporters: MDR1, MRP and BCRP; (ii) one or more membrane transporter inhibitors; and (iii) instructions therefor.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 is a table listing various dyes which have been used in MDR detection.
FIG. 2 is a Venn diagram of fluorescent substrates used for studying MDR-ABC transporter functions.
FIG. 3 are bar graphs of MDR-related chemoresistance of CHO K1 and A549 cell lines toward Doxorubicin (FIG. 3A), Taxol (FIG. 3B), Vincristine (FIG. 3C) and Mitoxantrone (FIG. 3D).
FIG. 4 depicts results of an MDR assay and toxicity in cells treated with two fluorescent probes (Fluo-8TM and Rhod-4TM).
FIG. 5 illustrates results of optimization studies of dye uptake assays.
FIG. 6 illustrates results of optimization studies of dye efflux assays.
FIG. 7 shows results comparing performance of two fluorescent probes (Fluo-8TM and Rhod-4TM dyes) against Calcein AM.
FIG. 8 are results of MDR tests with four different inhibitors comparing Rhod-4TM dye and Fluo-8TM against Doxorubicin and Mitoxantrone.
FIG. 9 illustrate results of MDR tests with four different inhibitors comparing Fluo-8TM and Rhod-4TM against Calcein AM.
FIG. 10 are bar graphs showing results of MDR tests with four different inhibitors in which Fluo-8TM and Rhod-4TM were compared against Calcein AM.



DESCRIPTION OF THE INVENTION
As described above, the three major multidrug resistance ABC proteins are MDR1 (including P-glycoprotein, ABCB1), multidrug resistance associated protein 1 (including MRP1, ABCC1) and ABCG2 (including placenta-specific ABC transporter, ABCP/breast cancer resistance protein, BCRP/mitoxantrone resistance protein and MXR). MDR1 and MRP1 can transport a large variety of hydrophobic drugs, and MRP1 can also extrude anionic drugs or drug conjugates. Other members of the MRP/ABCC family have also been indicated to be involved in cancer multidrug resistance (for details, see [Haimeur et al., Curr Drug Metab 5:21-53 (2004)]). The transport properties of ABCG2 are overlapping with those of both MDR1 and the MRP type proteins; thus these three proteins form a special network in chemo-defense mechanisms (see Table 2 below).







TABLE 1







Substrate and inhibitor specificity of the major multidrug resistance


proteins that belong to the ABC transporter family











MDR
Gene
Substrates of the
Reversal
Probes for


Protein
subfamily
protein
Agents*
Detection*





Pgp
Mdr1/ABCB
Anthracyclines
Verapamil, CsA,
DiOC2(3), Rho 123,




(DOX, DNR),
reserpine, CsD,
DOX, Calcein AM,




colchicines, vinca
quinoline,
JC-1




alkaloids, etoposide,
PK11195




taxanes


MRP
MRP/ABCC
Anthracyclines
Genistein,
Fluo-3, DOX, DNR,




(DOX, DNR),
flavopyridol,
Calcein AM,




camptothecin, vinca
probenecid, MK-
SNARF,




alkaloids,
571, CsA




methotrexate,




etoposide, NOT




TAXANES


BCRP
ABCG
Anthracyclines
Fumitremorgin,
Rho123, JC-1, Mxt,




(DOX, DNR),
Novobiocin,
DNR, BODIPY-




mitoxantrone,
Ko134,
prazozin,




topotecan,
GF120918,
bisantrene,




flavopyridol,
Genistein, CsA,
Hoechst 33342,




methotrexate, NOT
reserpine,
LysotrackerGreen




vinca alkaloids,
tamoxifen,




taxanes
flavopiridol









Dyes have been previously described for MDR detection. Many of these are listed in Table 1, FIG. 1.
The present invention relates to functional detection of multidrug resistant phenotypes in live cells (both suspension and adherent) by measuring the active dye efflux mediated by different ABC transporter proteins using flow cytometry, microplate fluorimetry and/or other device capable of detecting a fluorescence signal.
The suggested application presents a new use for the calcium indicators as described in U.S. Patent Application Publication No. 2008/0254498 A1 (hereby incorporated by reference), in particular Fluo-8TM AM and Rhod-4TM AM (now commercially available from AAT Bioquest) and also offers important advantages over existing functional dye efflux/uptake assays. Unlike the most common MDR probe, Calcein AM, and unlike other calcium indicators such as Fluo-3TM and Fluo-4TM, Fluo-8TM AM and Rhod-4TM AM are capable of detection and distinguishing between all three of the major types of ABC transporters in live cells.
The described application offers a quick, reproducible, specific and relatively simple way for functional detection of ABC transporter proteins that allow high-volume specimen throughput and employs widely available instrumentation. Standard dye uptake and dye efflux protocols include several washing steps, thus being time- and effort consuming. It is demonstrated that the washing step is optional when employing Fluo-8TM AM and Rhod-4TM AM and may be omitted from both uptake and efflux protocols to simplify the assay and make it more user-friendly. If a large number of samples is to be analyzed, however, the excess of dye should be washed away and samples kept on ice until the measurement is performed. Otherwise, samples would have to be analyzed in small batches to avoid artifactual measurements.
Acetate or acetoxy methyl ester (AM) derivatives of Fluo-8TM and Rhod-4TM dyes demonstrate fast internalization, favorable uptake/efflux kinetics and much better sensitivity than commonly used fluorescent substrates of general specificity (such as doxorubicin and mitoxantrone).
With appropriate compensation correction, both probes can be used in combination with propidium iodide or 7-amino-actinomycin D, the common viability dyes employed in flow cytometry. Moreover, their spectral characteristics are compatible with common dyes used in multicolor flow cytometry experiments (such as phycoerythrin), and with different fluorescent proteins such as green fluorescent and red fluorescent proteins (GFP and RFP).
Assays disclosed herein are high-throughput in the sense that these assays may be carried out in a 96-well or higher density format (e.g., 384- or 1536-well plates). Desirably, such assays demonstrate a signal of sufficient intensity that it can be easily measured from a microtiter plate in low volume and have a suitable signal-to-noise ratio and CV determined from the measurements across the entire plate (statistical parameter, Z′, which has an acceptable lower limit of 0.5).
The MDR probes suggested in the present application should also be compatible with clinical samples (both blood and solid tissues), bacterial samples and transwell type of cellular assays.
Fluo-8TM AM and Rhod-4TM AM probes demonstrate performance similar to or better than Calcein AM regarding pH independence and can be used in an operational range of pH 6.0 to 8.0. Despite being calcium indicators, differences in fluorescence intensities of MDR probes Fluo-8TM AM and Rhod-4TM AM in the proposed protocol are solely dependent upon the presence of the ABC transporters and do not depend upon the intracellular Ca2+ concentration (similarly to CalceinTM AM).
It should be appreciated by those skilled in the art that rather than being exclusively confined to Fluo-8TM AM and Rhod-4TM AM, any compound can be employed in the method of the invention that meets the following criteria: it is cell permeable; it is a good substrate for all the three MDR proteins; it gets transformed in the cell by generally present enzymes to a signal generating compound and accumulates within the cell. All those considerations are part of this invention.
DEFINITIONS
By multidrug resistance (MDR) is meant the occurrence of transport protein-mediated cell efflux in a cell(s). Since such a cell efflux typically transports a variety of substances (including chemotherapy drugs) to the outside of the cell membrane, it interferes with the cancer chemotherapy. Tumor cells demonstrating such an efflux are termed “multi-drug resistant”
By fluorophore is meant a component of a molecule which causes a molecule to be fluorescent.
By fluorogenic is meant a process by which fluorescence is generated. In the context of analytical assays, the term refers to a chemical reaction dependent on the presence of a particular analyte that produces fluorescent molecules.
By “MDR probe” is meant an entity, be it a small organic fluorophore, a fluorescent protein, a nanoparticle or a quantum dot, that is useful for monitoring an active and effective transport of a variety of compounds to the exterior of the cell membrane, by one or more transport proteins that are typically over-expressed in the cell.
By “ABC-transporter protein” or “membrane transporter” is meant a membrane bound protein that can transport a given compound through the cell membrane even against the concentration gradient by using the energy obtained through ATP hydrolysis.
By a “transport protein-mediated cell efflux” is meant the active and effective transport of a variety of compounds to the extracellular compartment of the cell, by one or more transport proteins that are typically over-expressed in the cell's plasma membrane.
By an “inhibitor of transport protein-mediated cell efflux” or “transport blocking agent” is meant a compound that can block the active transport of a compound of interest (e.g. Fluo-8TM AM or Rhod-4TM AM) to the outside of the cell membrane by any mechanism of action. A “general inhibitor of efflux” blocks all active transport to the outside of the cell membrane regardless of the type of transport protein expressed in the sample. A “selective inhibitor of efflux” blocks only that transport that is due to a selected transport protein or a selected transport-mediated efflux pathway.
By “MDR1 or P-glycoprotein” is meant a membrane bound protein of  ̃170 kDa molecular weight, functional expression of which causes multi-drug resistance of the given cell.
By “MRP or Multi-drug Resistance protein” is meant a  ̃190 kDa glycoprotein belonging to a family of ABC transporters, functional expression of which confers multi-drug resistance on a given cell by mediating the ATP-dependent membrane transport of glutathione S-conjugates of chemotherapeutic drugs.
By ABCP/MXR/BCRP protein is meant an ABC half-transporter which forms homodimers in the plasma membrane and actively extrudes a wide variety of chemically unrelated compounds from the cells and protects cells against various xenobiotics. This protein participates in stem-cell protection/regulation.
By “MDR activity” is meant the activity of a protein (or membrane transporter) that causes multi-drug resistance. i.e., the activity of an ABC transporter protein or membrane transporter protein.
By a “substrate of an MDR protein” or “substrate of a membrane transporter” is meant a compound that can be extruded from the cell through an MDR mediated active transport mechanism.
By a “cell permeable compound” is meant a usually hydrophobic compound that can enter the cell in a practically unconstrained manner.
By “clinical or biological sample” is meant such biological, clinical and even non-biological samples, including but not limited to blood, urine, feces, saliva, pus, semen, serum, cerebral spinal fluid (CSF) and any other tissue or organ samples, including biopsies.
Sensitivity
Cyclosporin A (noncompetitive broad-spectrum MDR modulator, 5 μM), verapamil (specific Pgp/ABCB1 subfamily inhibitor, 20 μM), probenecid, MK-571 (both are specific MRP/ABCC subfamily inhibitors, 0.2 mM and 50 μM correspondingly), novobiocin and fumitremorgin C (specific for BCRP/ABCG subfamily, 0.5 mM and 100 μM correspondingly) were used in all experiments unless specified differently. Concentrations of the modulators used in the experiments were non-toxic to the cells (based upon standard 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) testing, data not shown). Fluo-8TM was used in all experiments at 5 μM, and Rhod-4TM—at 4 μM final concentrations. Flow cytometry data were analyzed by comparison of median fluorescence or using Kolmogorov-Smirnov statistics [Young, J Histochem Cytochem 25:935-941 (1977)]
Kolmogorov-Smirnov statistics measures the difference between two distribution functions and generates a D value ranging between 0 and 1.0, with higher values indicating a greater difference between the distribution functions. The D value generated by the KS statistics was modified by ascribing a negative value if the fluorescence of a negative control (no inhibitor) was brighter than the fluorescence of the sample with inhibitor. The method was one of those recommended by the First International MDR1Methods Detection Workshop (St. Jude Children's Research Hospital, Memphis, Tenn.).
KS values appear to be a reliable method for accurately measuring of MDR. Intensity staining was categorized as follows (for MRP detection using DiOC2(3) probe):

    
    
        Bright (D≧0.30)
        Moderate (0.20≦D≦0.30)
        Dim (0.15≦D<0.20)
        Negative (D<0.15)
        Notably, D-values cut-points may vary slightly (about 10%) based upon staining different proteins with different dyes.
    
    


In various tables below, D-value for each protocol and each inhibitor were compared to MAF values (MDR Activity Factor) that were calculated using the following formula: MAF=100*((MFIinh-MFI0)/MFIinh), where MFIinh and MFI0 are mean fluorescence intensity values measured in the presence and absence of inhibitor. The cut-off values of MAF for Calcein AM that have been adopted in clinical assays are about 20-25.
This invention provides a process for determining drug resistance of cells of interest, the process comprising the steps of: (A) providing: (i) a clinical or biological sample comprising cells; (ii) at least one xanthene compound that is transportable across a cell membrane by membrane transporters: MDR1, MRP and BCRP; and (iii) one or more membrane transporter inhibitors; (B) contacting cells from a first portion of the clinical or biological sample (i) with at least one xanthene compound (ii); (C) contacting cells from a second portion of the clinical or biological sample (i) with at least one xanthene compound (ii) and one or more inhibitors (iii); (D) measuring fluorescent signals generated in step (B) and step (C); and (E) comparing the fluorescent signals measured in step (D) to determine elevated activities of MDR1, MRP and BCRP, or a combination thereof, thereby determining the drug resistance of the cells of interest.
This invention also provides a process for determining the effect of a test compound on transport across a cell membrane by the membrane transporters: MDR1, MRP and/or BCRP, the process comprising the steps of: (A) providing: (i) a clinical or biological sample comprising cells; (ii) at least one xanthene compound that is transportable across a cell membrane by membrane transporters: MDR1, MRP and BCRP; and (iii) one or more test compounds; (B) contacting cells from a first portion of the clinical or biological sample (i) with at least one xanthene compound (ii); (C) contacting cells from a second portion of the clinical or biological sample (i) with at least one xanthene compound (ii) and one or more test compounds (iii); (D) measuring fluorescent signals generated in step (B) and step (C); and (E) comparing the fluorescent signals measured in step (D) to determine elevated activities of said MDR1, MRP and BCRP, or a combination thereof, thereby determining the effect of the one or more test compounds (iii) on cell membrane transport by the membrane transporters.
Other aspects of this process are contemplated by the present invention including carrying out step (D) by measuring cellular uptake of the xanthene compound or compounds (ii). In step (A), the one or more inhibitors (iii) are provided in an amount sufficient to substantially prevent transport of the xanthene compound or compounds (ii) across a cell membrane by one or more of the membrane transporters MDR1, MRP and BCRP.
The xanthene compound (ii) may take a number of forms, including one where it has the structure




wherein R1-R6 are independently H, halogen, carboxy, alkoxy, aryloxy, thiol, alkylthiol, arylthiol, azido, nitro, nitroso, cyano, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl, or heteroaryl; or alkyl, or alkoxy, optionally substituted one or more times by halogen, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl or heteroaryl,
wherein heteroatom Y is independently selected from O, S, Se, NR9 and CR.10R11,
wherein X is independently selected from OR12, NR12R13 and Z is independently selected from O and NR16R17, where each R9, R10, R11, R12, R13, R16 and R17 is independently H, an alkyl having 1-12 carbons, carboxyalkyl, substituted or non-substituted amino alkyl or alkylsulfonate,
wherein T and U are independently selected from alkyl having 1-12 carbons, alkoxy having 1-12 carbons, aryloxy, amino, halogen, cyano, carboxy, carboxyalkyl, carbonyl, sulfonyl, phosphonyl, boronic acid, aryl, and heteroaryl, and
wherein V and W are independently selected from OR14, SR15 or NR12R13, such that at least one of V or W, in combination with NR7R8, forms a metal chelator, where each R7, R8, and R12-R15 are independently H, an alkyl having 1-12 carbons, carboxyalkyl, alkoxy or aryloxy.
In another embodiment, the xanthene compound (ii) has the structure




wherein A and B are independently hydrogen, alkyl, cycloalkyl, or aryl; or A and B taken in combination are cycloalkyl or aryl;
wherein R3, R4, j, k, m, n and V are independently hydrogen, halogen, carboxy, alkoxy, aryloxy, thiol, alkylthiol, arylthiol, azido, nitro, nitroso, cyano, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl, or heteroaryl; or alkyl, or alkoxy that is itself optionally substituted one or more times by halogen, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl or heteroaryl;
wherein each R5 is independently hydrogen, alkyl having 1-9 carbons, acetoxymethyl, or a biologically compatible salt; and
wherein T and U are independently hydrogen, alkyl having 1-12 carbons, alkoxy having 1-12 carbons, aryloxy, amino, halogen, cyano, carboxy, acetoxymethylcarbonyl, carboxyalkyl, carbonyl, sulfonyl, phosphonyl, boronic acid, aryl or heteroaryl; provided that at least one of T and U is not hydrogen.
In yet another embodiment, the xanthene compound (ii) has the structure




With regard to the membrane transporter inhibitors (iii), these may comprise general inhibitors, specific inhibitors or a combination of general inhibitors and specific inhibitors. Among general inhibitors are cyclosporin A, biricodar (VX-710), tariquidar (XR9576), plant polyphenols, curcumin, tRA98006 or imatinib mesylate and a combination of any of the foregoing.
Among specific inhibitors mention should be made of valspodar (PSC833), verapamil, vanadate, PAK-104P, MK-571, FTC, Ko134, Elacridar (GF 120918), novobiocin, probenecid, BIB-E, disulfuram, indomethacin, furocemide, Penicillin G, sulfinpirazole, laniquidar (R101933), zosuquidar (LY335979), ontogeny (ONT-093), isothiocyanates, phytoestrogens, TAG-139, flavenoids, MS-209, NSAIDs, mitotane (NSC-38271), PK11195, cyclosporine D, anthranilamide, pipecolinate, quinoline, OC-144-093, diallyl sulfide, amooranin, agosterol A, siRNA, rifampicin, amiodarone, quinidine, quinine, nifedipine, dexniguldipin, LY455776, V-104, tricyclic izoxazoles, pluronic L61, or fumitremorgin C and a combination of any of the foregoing.
The aforementioned inhibitors, both general and specific inhibitors are listed and described in terms of particular membrane transporter functions in Table 3 below:







TABLE 3







Specificity of MDR Inhibitors.










MRP












Inhibitor
MDR1
MRP1
MRP2
BCRP





Cyclosporine A
+
+
+
+


Valspodar (PSC833)
+

+


Verapamil
+


Vanadate
+


Biricodar (VX-710)
+
+
+
+


PAK-104P
+
+
+


MK571

+
+


FTC



+


Ko143



+


Elacridar (GF120918)
+


+


Probenecid

+


BIB-E



+


Disulfiram
+
+


Indomethacin

+


Furocemide

+


Penicillin G

+


Sulfinpirazole

+


Laniquidar (R101933)
+
?
?
?


Tariquidar (XR9576)
+
+
+
+


Zosuquidar (LY335979)
+


Ontogen (ONT-093)
+


?


Plant polyphenols
+
+
?
+


Curcumin
+
+
?
+


tRA98006
+
+
+
+


Isothiocyanates
+
+
+


Phytoestrogens



+


TAG-139



+


Imatinib Mesylate
+
+

+


flavonoids
+


+


MS-209
+
+


NSAIDs

+


NSC-38271 (mitotane)
+


PK11195
+


Cyclosporine D
+


Anthranilamide
+


Pipecolinate
+


Quinoline
+


OC-144-093
+


Diallyl Sulfide
+


Amooranin
+


Agosterol A
+
+


siRNA
+


Rifampicin

+


Amiodarone
+


Quinidine
+
+


Quinin
+
+


Nifedipine
+


Dexniguldipin
+


LY455776
+
+


V-104
+
+


Tricyclic Izoxazoles

+


Pluronic L61
+









In other aspects, at least one viability dye (iv) can be usefully provided in step (A). Among such viability dyes (iv) are those comprising propidium iodide, 7-amino-actinomycin D (7-AAD), DRAQ7TM, membrane-impermeable form of Nuclear-IDTM Red, membrane-impermeable form of Nuclear-IDTM Green, SYTOX® Green, SYTOX® Orange, SYTOX® Blue, YOYO, TOTO or TO-PRO, or a compound having the structure:




wherein X comprises CR11R12, NR11, O, S or Se where R11 and R12 independently comprise hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkyl group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R11 and R12 form a 5 or 6 membered ring;
wherein n can be 0, 1, 2 or 3;
wherein Y is —CR9═CR10—;
wherein m and p can have values of 0 or 1 and m+p=1;
wherein at least one of R1, R2, R3, R4, R5, R11 or R12 comprises Q(1) or at least one of R6, R7, R8, R9 or R10 comprises Q(2);
wherein Q(1) comprises a sulfonate (SO3−), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a alkyl phosphonate (PO3=) a alkyl phosphonate monoester (PO2−ER13) a alkyl phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R23), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S and the structures are as described previously;
wherein Q is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof and wherein when Q is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
wherein Q(2) comprises an alkyl, aminoalkyl, substituted aminoalkyl, a benzyl, a substituted benzyl, a sulfoxide (SOR13), a sulfone (SO2CR13R14R16), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S and the structures are as described previously;
wherein Q(2) is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof and wherein when Q′ is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
wherein R13, R14, R15, R19 and R20 can be hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together R13 and R14 form a five or six membered ring;
wherein R13 and R14 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR25), a thioether linkage (—SR25), or an amine linkage (—NR25R26 or N+R25R26R27) and wherein R25, R26 and R27 independently comprise hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five or six membered ring, and wherein any of R25, R26 or R27 may further comprise said heteroatom containing side chain;
wherein R16, R17, R18 and the remaining R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11 and R12 can independently be hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear; substituted or unsubstituted, or when taken together, R2 and R3, R3 and R4, R4 and R5, R6 and R7, and R7 and R8 may form a 5 or 6 membered ring; or when taken together R1 and R16, R11 and R16, R16 and R17, R17 and R18, and R18 and R9 may form a 5 or 6 membered ring;
wherein Z comprises a carboxyl group (CO2−), a carbonate ester (COER13), a sulfonate (SO3−), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSO−ER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphonamide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) where E can be independently O or S and the structures are as described previously;
wherein Z is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof;
wherein any of R1, R2, R3, R4, R5, R6, R7, R8, R9 or R10, R11 or R12 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR25), a thioether linkage (—SR25), or an amine linkage (—NR25R26 or —N+R25R26R27);
wherein R25, R26 and R27 independently comprise hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five or six membered ring, and wherein any of R25, R26 or R27 may further comprise said heteroatom containing side chain; and
wherein R8 may comprise a substituted group capable of forming symmetric or asymmetric polymeric dye.
In carrying out the above process, the cells (i) can be contacted with the viability dye or dyes (iv) before, during or after the contacting steps (B) and (C).
Other non-xanthene dyes can be used in conjunction with the present invention and the xanthenes compounds (ii). Thus, in step (A), there is further provided at least one non-xanthene dye (v) and wherein the non-xanthene dye (v) is included to carry out step (B) and step (C). Among useful non-xanthene dyes (v) are those comprising a nuclear identification stain, calcein AM, Pheophorbide A, Chloromethylfluorescein diacetate (CMFDA), Hoechst 33342, BODIPY-Prazozin, Fura-2 AM, monobromobimane, BODIPY-Taxol or 3,3′-diethyloxacarbocyanine iodide (DIOC2(3)] or a dye from Table 1, FIG. 1, and a combination of any of the foregoing.
A number of different means are available to carrying out measurement of the fluorescent signals. Thus, in said step (D), measuring can be carried out by a means comprising a flow cytometer, a microplate reader, a microscope, a fluorimeter, a high content screening platform, a high-content cell analysis system or a laser-scanning cytometer and a combination of the foregoing. Such means, instruments, apparatus and the like are commercially available.
Useful levels of sensitivity are obtained by the present invention. In one aspect, the MAF value of the elevated levels of MDR1, MRP and BCRP, or a combination thereof, is greater than about 20. In another aspect, the MAF value is greater than about 25.
Quenching reagents are also useful employed in this invention. Such agents eliminate the need to wash cells after incubation with a xanthene compound, especially useful in microplate-based analytical measurements. Thus, in step (A), there may be provided a quenching reagent (vi) for minimizing extracellular fluorescent signal from the xanthene compound or compounds (ii). Among such quenching reagents are those comprising Evans Blue, o-tolidine, Trypan Blue, Trypan Red or Brilliant Black, and a combination of the foregoing.
Also contemplated by the present invention is the use of surfactants which can optionally be included during the dye loading step in order to enhance the uptake of the xanthine dyes of the present invention. For example, Pluronic surfactants (BASF Corporation) are suitable for this application. Pluronic surfactants act to disperse and stabilize water-insoluble dyes in aqueous solution, thereby facilitating their cellular uptake from aqueous dispersions. An example of an especially suitable surfactant would be Pluronic F127. High concentrations of pluronic surfactants will inhibit ABC transporters, so the concentration must be optimized and titrated carefully. See pluronic L61 listed in Table 3 above as an ABC transporter inhibitor. Pluronic L81, P85 and F108 are also listed in this capacity, with the inhibition potency decreasing in the cited series. With respect to dye loading with minimal ABC transporter inhibition, 0.02% to 0.2% (w/v) pluronic acid is roughly the optimal concentration range for most cell types. A concentration of 0.1% (w/v) is an especially suitable concentration for such applications. The uptake of the xanthine dye, as its cell-permeable ester, employing a surfactant, such as pluronic acid F-127 in the incubating solution, can increase dye loading within cells at least 2-fold relative to loading without the surfactant for the same period of time. Employing pluronic can facilitate measurement of ABC transporter activity in cells that are especially difficult to load with xanthine dyes, including plant protoplasts and myotubules. The use of such surfactants can be employed concomitantly or simultaneously with the xanthene compounds to achieve greater cellular uptake of the xanthene compounds. The surfactants are useful in both cellular uptake and efflux processes for determining drug resistance of cells as well as processes for determining the effect of a test compound across a cell membrane by the membrane transporters MDR1, MRP and/or BRCP. Thus, in the processes of the present invention, at least one surfactant (vii) is provided in step (A) for increasing cellular uptake of the xanthene compound or compounds (ii), and such surfactant or surfactants are used in the various contacting steps with the xanthenes compound or compounds (ii).
Determination of drug resistance in cells can also be carried with cellular efflux. Thus, this invention further provides a process for determining drug resistance of cells of interest, the process comprising the steps of: (A) providing: (i) at least three portions of a clinical or biological sample comprising cells; (ii) at least one xanthene compound that is transportable across a cell membrane by membrane transporters: MDR1, MRP and BCRP; and (iii) one or more membrane transporter inhibitors; (B) contacting cells from a first portion of the clinical or biological sample (i) with at least one xanthene compound (ii) under conditions sufficient to inhibit efflux of the xanthene compound or compounds (ii) from the cells; (C) contacting cells from a second portion of the clinical or biological sample (i) with at least one xanthene compound (ii) under conditions sufficient to permit efflux of the xanthene compound or compounds (ii) from the cells; (D) contacting cells from a third portion of the clinical or biological sample (i) with at least one xanthene compound (ii) and one or more inhibitors (iii); (E) measuring fluorescent signals generated in steps (B), (C) and D; and (F) comparing the fluorescent signals measured in step (D) to determine elevated activities of MDR1, MRP and BCRP, or a combination thereof, thereby determining the drug resistance of the cells of interest.
The present invention additionally provides a process for determining the effect of a test compound on transport across a cell membrane by the membrane transporters: MDR1, MRP and/or BCRP, the process comprising the steps of: (A) providing: (i) at least three portions of a clinical or biological sample comprising cells; (ii) at least one xanthene compound that is transportable across a cell membrane by membrane transporters: MDR1, MRP and BCRP; and (iii) one or more membrane transporter inhibitors; (B) contacting cells from a first portion of the clinical or biological sample (i) with at least one xanthene compound (ii) under conditions sufficient to inhibit efflux of the xanthene compound or compounds (ii) from the cells; (C) contacting cells from a second portion of the clinical or biological sample (i) with at least one xanthene compound (ii) under conditions sufficient to permit efflux of the xanthene compound or compounds (ii) from the cells; (D) contacting cells from a third portion of the clinical or biological sample (i) with at least one xanthene compound (ii) and one or more inhibitors (iii); (E) measuring fluorescent signals generated in steps (B), (C) and D; and (F) comparing the fluorescent signals measured in step (D) to determine elevated activities of MDR1, MRP and BCRP, or a combination thereof, thereby determining the drug resistance of the cells of interest.
In the just described processes, one or more inhibitors (iii) are provided in step (A) in an amount sufficient to substantially prevent transport of the xanthene compound (II) across a cell membrane by one or more of the membrane transporters MDR1, MRP and BCRP. Also in these processes, contacting in step (B) is carried out under said conditions wherein temperature is lowered to inhibit efflux. The temperature can be generally in a range from about 4° C. to about 10° C.
In another aspect of these processes, contacting in step (C) is carried out under conditions wherein temperature is raised or brought to a level to permit efflux. Here, the temperature level is in a range from about 15° C. to about 37° C.
The one or more membrane transporter inhibitors (iii) used in these processes may comprise general inhibitors, specific inhibitors or a combination of general inhibitors and specific inhibitors. As previously described above, such general inhibitors comprise cyclosporin A, biricodar (VX-710), tariquidar (XR9576), plant polyphenols, curcumin, tRA98006 or imatinib mesylate and a combination of any of the foregoing. Further, the specific inhibitors comprise valspodar (PSC833), verapamil, vanadate, PAK-104P, MK-571, FTC, Ko134, Elacridar (GF 120918), novobiocin, probenecid, BIB-E, disulfuram, indomethacin, furocemide, Penicillin G, sulfinpirazole, laniquidar (R101933), zosuquidar (LY335979), ontogeny (ONT-093), isothiocyanates, phytoestrogens, TAG-139, flavenoids, MS-209, NSAIDs, mitotane (NSC-38271), PK11195, cyclosporine D, anthranilamide, pipecolinate, quinoline, OC-144-093, diallyl sulfide, amooranin, agosterol A, siRNA, rifampicin, amiodarone, quinidine, quinine, nifedipine, dexniguldipin, LY455776, V-104, tricyclic izoxazoles, pluronic L61, or fumitremorgin C and a combination of any of the foregoing.
As previously described, the xanthene compound (ii) used in these latter processes has the structure of




wherein R1-R6 are independently H, halogen, carboxy, alkoxy, aryloxy, thiol, alkylthiol, arylthiol, azido, nitro, nitroso, cyano, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl, or heteroaryl; or alkyl, or alkoxy, optionally substituted one or more times by halogen, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl or heteroaryl,
wherein heteroatom Y is independently selected from O, S, Se, NR9 and CR10R11,
wherein X is independently selected from OR12, NR12R13 and Z is independently selected from O and NR16 where each R9, R10, R11, R12, R13, R16 and R17 is selected from O and NR independently H, an alkyl having 1-12 carbons, carboxyalkyl, substituted or non-substituted amino alkyl or alkylsulfonate,
wherein T and U are independently selected from alkyl having 1-12 carbons, alkoxy having 1-12 carbons, aryloxy, amino, halogen, cyano, carboxy, carboxyalkyl, carbonyl, sulfonyl, phosphonyl, boronic acid, aryl, and heteroaryl, and
wherein V and W are independently selected from OR14, SR15 or NR12R13, such that at least one of V or W, in combination with NR7R8, forms a metal chelator, where each R7, R8, and R12-R15 are independently H, an alkyl having 1-12 carbons, carboxyalkyl, alkoxy or aryloxy.
In a different embodiment of these processes, the xanthene compound (ii) has the structure




wherein A and B are independently hydrogen, alkyl, cycloalkyl, or aryl; or A and B taken in combination are cycloalkyl or aryl;
wherein R3, R4, j, k, m, n and V are independently hydrogen, halogen, carboxy, alkoxy, aryloxy, thiol, alkylthiol, arylthiol, azido, nitro, nitroso, cyano, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl, or heteroaryl; or alkyl, or alkoxy that is itself optionally substituted one or more times by halogen, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl or heteroaryl;
wherein each R5 is independently hydrogen, alkyl having 1-9 carbons, acetoxymethyl, or a biologically compatible salt; and
wherein T and U are independently hydrogen, alkyl having 1-12 carbons, alkoxy having 1-12 carbons, aryloxy, amino, halogen, cyano, carboxy, acetoxymethylcarbonyl, carboxyalkyl, carbonyl, sulfonyl, phosphonyl, boronic acid, aryl or heteroaryl; provided that at least one of T and U is not hydrogen.
In yet another embodiment, the xanthene compound (ii) has the structure




In a different aspect of these processes, there is further provided in step (A) at least one viability dye (iv). This viability dye (iv) comprises propidium iodide, 7-amino-actinomycin D (7-AAD), DRAQ-7, Nuclear ID Red, Nuclear ID Green, SYTOX Green, SYTOX Orange, SYTOX Blue, YOYO, TOTO or TO-PRO, and a compound having the structure:




wherein X comprises CR11R12, NR11, O, S or Se where R11 and R12 independently comprise hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkyl group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R11 and R12 form a 5 or 6 membered ring;
wherein n can be 0, 1, 2 or 3;
wherein Y is —CR9═CR16—;
wherein m and p can have values of 0 or 1 and m+p=1;

    
    
        wherein at least one of R1, R2, R3, R4, R5, R11 or R12 comprises Q(1) or at least one of R6, R7, R8, R9 or R10 comprises Q(2);
    
    


wherein Q(1) comprises a sulfonate (SO3−), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a alkyl phosphonate (PO3=) a alkyl phosphonate monoester (PO2−ER13) a alkyl phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphonamide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S and the structures are as described previously;
wherein Q is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof and wherein when Q is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
wherein Q(2) comprises an alkyl, aminoalkyl, substituted aminoalkyl, a benzyl, a substituted benzyl, a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S and the structures are as described previously;
wherein Q(2) is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof and wherein when Q′ is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
wherein R13, R14, R15, R19 and R20 can be hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together R13 and R14 form a five or six membered ring;
wherein R13 and R14 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR25), a thioether linkage (—SR25), or an amine linkage (—NR25R26 or —N+R25R26R27), and wherein R25, R26 and R27 independently comprise hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five or six membered ring, and wherein any of R25, R26 or R27 may further comprise said heteroatom containing side chain;
wherein R16, R17, R18 and the remaining R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11 and R12 can independently be hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R2 and R3, R3 and R4, R4 and R5, R6 and R7, and R7 and R8 may form a 5 or 6 membered ring; or when taken together R1 and R16, R11 and R16, R16 and R17, R17 and R18, and R18 and R9 may form a 5 or 6 membered ring;
wherein Z comprises a carboxyl group (CO2−), a carbonate ester (COER13), a sulfonate (SO3−), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) where E can be independently O or S and the structures are as described previously;
wherein Z is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof;
wherein any of R1, R2, R3, R4, R5, R6, R7, R8, R9 or R10, R11 or R12 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR25), a thioether linkage (—SR25), or an amine linkage (—NR25R26 or —N+R25R26R27),
wherein R25, R26 and R27 independently comprise hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five or six membered ring, and wherein any of R25, R26 or R27 may further comprise said heteroatom containing side chain, and
wherein R8 may comprise a substituted group capable of forming symmetric or asymmetric polymeric dye.
Mention should be made that the cells (i) can be contacted with the viability dye (iv) before, during or after contacting steps (B), (C) and (D) in the processes above.
Non-xanthene dyes can also be used in these processes. Thus, in step (A), there is further provided at least one such non-xanthene dye (v) which is included in step (B), step (C) and step (D). As previously described above, the non-xanthene dye (v) comprises a nuclear identification stain, calcein AM, Pheophorbide A, Chloromethylfluorescein diacetate (CMFDA), Hoechst 33342, BODIPY-Prazozin, Fura-2 AM, monobromobimane, BODIPY-Taxol or 3,3′-diethyloxacarbocyanine iodide (DIOC2(3)] or a dye from Table 1, FIG. 1, and a combination of any of the foregoing.
Measuring in these latter processes is done similarly as in other processes above. Thus, in step (E), measuring is carried out by a means comprising a flow cytometer, a microplate reader, a microscope, a fluorimeter, a high content screening platform, a high-content cell analysis system or a laser-scanning cytometer and a combination of the foregoing.
In terms of sensitivity of these processes, the MAF value of the elevated levels of MDR1, MRP and BCRP, or a combination thereof, is greater than 20, and even greater than about 25.
Quenching reagents are also useful in the latter processes. Thus in step (A), there is further provided a quenching reagent (vi) for minimizing extracellular fluorescent signal from the xanthene compound (ii). As described for other processes above, the quenching reagent (vi) comprises Evans Blue, o-tolidine, Trypan Blue, Trypan Red or Brilliant Black, and a combination of the foregoing.
Reagent Kits:
As explained above, multidrug resistance (MDR) relates to the resistance of tumor cells to a variety of chemotherapy drugs with different structures and cellular targets. The phenomenon of multidrug resistance (MDR) is a well-known problem in oncology and thus needs profound consideration in cancer treatment. One of the underlying molecular rationales for MDR is the up-regulation of a family of transmembrane ATB binding cassette (ABC) transporter proteins that are present in practically all living organisms. These proteins cause chemotherapy resistance in cancer by actively extruding a wide range of therapeutic compounds from the malignant cells. The same ABC transporters play an important protective function against toxic compounds in a variety of cells and tissues and at blood-tissue barriers.
Enzo Life Sciences' eFluxx-IDTM Multidrug Resistance Assay Kits have been designed for functional detection and profiling of multidrug resistant phenotypes in live cells (both suspension and adherent) and will be shortly available commercially. The kits include either a green fluorescent or orange fluorescent eFluxx-IDTM Detection Reagent as a major component. Both dyes are excited by a 488 nm laser. Being a substrate for all three main ABC transporter proteins, these reagents serve as indicators of transporter protein activity in cells. The proprietary AM-ester forms of the eFluxx-IDTM Detection Reagents are hydrophobic non-fluorescent compounds that readily penetrate the cell membrane and are subsequently hydrolyzed inside of the cells by intracellular esterases. The resulting probe is a hydrophilic fluorescent dye that is trapped within the cell unless actively pumped out by an ABC transporter. The fluorescence signal of the dye generated within the cells thus depends upon the activity of the ABC transporters. The cells with highly active transporters will demonstrate lower fluorescence because of the active efflux of the reagent from the cell. Application of specific inhibitors of the various ABC transporter proteins, included in the kit, allows differentiation between the three common types of pumps. The activity of a particular MDR transporter is defined by the difference between the amount of the dye accumulated in the presence and in the absence of the inhibitors, respectively
The flow cytometry assay is based upon determining fluorescence intensities of the tested cells after a short in vitro incubation of cell suspensions with the eFluxx-ID Detection Reagent, in the presence or absence of specific ABC transporter inhibitors. The results of the test can be quantified by calculating the MDR activity factor (MAE), which allow comparison of multidrug resistance between the samples or cell lines.
Commercial kits, such as the just-described Enzo's eFluxx-IDTM Multidrug Resistance Assay Kits, are valuable because they eliminate the need for individual laboratories to optimize procedures, saving both time and resources. They also allow better cross-comparison of results generated from different laboratories. The present invention additionally provides reagent kits, i.e., reagent combinations or means, comprising all of the essential elements required to conduct a desired assay method. The reagent system is presented in a commercially packaged form, as a composition or admixture where the compatibility of the reagents will allow, in a test kit, i.e., a packaged combination of one or more containers, devices or the like holding the necessary reagents, and usually written instructions for the performance of the assays. Reagent systems of the present invention include all configurations and compositions for performing the various labeling and staining formats described herein.
The reagent system will contain at least one fluorogenic indicator, generally comprising packaged combinations of the following:
(1) one or more fluorogenic global MDR indicator;
(2) optionally, one or more fluorogenic indicator with selectivity for some sub-class of MDR analyte;
(3) optionally, one or more specific inhibitors of MDR activity; and
(4) instructions for usage of the included reagents;
Generic instructions, as well as specific instructions for the use of the reagents on particular instruments, such as a flow cytometer or microplate-based detection platform may be provided. Recommendations regarding filter sets, monochromator settings and/or illumination sources for optimal performance of the reagents for a particular application also may be provided. Instructions for quantitative assay evaluation also may be provided.
A test kit form designed to directly monitor activity of various ABC transporter proteins in live cells, both pro- and eukaryotic. Such form, for example, can contain an indicator of global MDR activity (e.g. Fluo-8TM AM or Rhod-4TM AM), and additional ancillary chemicals, such as verapamil (Pgp specific inhibitor), MK-571 (MRP1/2 specific inhibitor), novobiocin (BCRP specific inhibitor), assay buffer (e.g. medium), and diluent. In some instances, one or more fluorogenic compound (MDR probes) may be added to a kit form for better specificity of the detection. One or more chemicals serving as inhibitors of MDR activity may be added to a kit form.
The present invention provides a kit for determining drug resistance of cells of interest, or detecting and profiling multidrug resistant phenotypes in cells of interest, or determining activity levels of membrane transporters MDR1, MRP and BCRP, the kit comprising in packaged combination: (i) at least one xanthene compound that is transportable across a cell membrane by membrane transporters: MDR1, MRP and BCRP; (ii) one or more membrane transporter inhibitors; and (iii) instructions therefor.
In one aspect, this kit further comprising buffer (iv). In another aspect, this kit measures cellular uptake or efflux of the xanthene compound or compounds (i). In this kit, the one or more inhibitors (ii) can be provided in an amount sufficient to substantially inhibit transport of the xanthene compound or compounds (i) across a cell membrane by one or more of the membrane transporters MDR1, MRP and BCRP.
Such xanthenes compounds have been described above and can take various forms, including a xanthene compound (i) having the structure of




wherein R1-R6 are independently H, halogen, carboxy, alkoxy, aryloxy, thiol, alkylthiol, arylthiol, azido, nitro, nitroso, cyano, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl, or heteroaryl; or alkyl, or alkoxy, optionally substituted one or more times by halogen, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl or heteroaryl,
wherein heteroatom Y is independently selected from O, S, Se, NR9 and CR.10R11,
wherein X is independently selected from OR12, NR12R13 and Z is independently selected from O and NR16R17, where each R9, R10, R11, R12, R13, R16 and R17 is independently H, an alkyl having 1-12 carbons, carboxyalkyl, substituted or non-substituted amino alkyl or alkylsulfonate,
wherein T and U are independently selected from alkyl having 1-12 carbons, alkoxy having 1-12 carbons, aryloxy, amino, halogen, cyano, carboxy, carboxyalkyl, carbonyl, sulfonyl, phosphonyl, boronic acid, aryl, and heteroaryl, and
wherein V and W are independently selected from OR14, SR15 or NR12R13, such that at least one of V or W, in combination with NR7R8, forms a metal chelator, where each R7, R8, and R12-R15 are independently H, an alkyl having 1-12 carbons, carboxyalkyl, alkoxy or aryloxy.
As also described above, the xanthene compound (i) has the structure




wherein A and B are independently hydrogen, alkyl, cycloalkyl, or aryl; or A and B taken in combination are cycloalkyl or aryl;
wherein R3, R4, j, k, m, n and V are independently hydrogen, halogen, carboxy, alkoxy, aryloxy, thiol, alkylthiol, arylthiol, azido, nitro, nitroso, cyano, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl, or heteroaryl; or alkyl, or alkoxy that is itself optionally substituted one or more times by halogen, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl or heteroaryl;
wherein each R5 is independently hydrogen, alkyl having 1-9 carbons, acetoxymethyl, or a biologically compatible salt; and
wherein T and U are independently hydrogen, alkyl having 1-12 carbons, alkoxy having 1-12 carbons, aryloxy, amino, halogen, cyano, carboxy, acetoxymethylcarbonyl, carboxyalkyl, carbonyl, sulfonyl, phosphonyl, boronic acid, aryl or heteroaryl; provided that at least one of T and U is not hydrogen.
Moreover, the xanthene compound (i) in this kit has the structure




As part of the kit, the one or more inhibitors (ii) comprise general inhibitors, specific inhibitors or a combination of general inhibitors and specific inhibitors. Among such general inhibitors previously described are those comprising cyclosporin A, biricodar (VX-710), tariquidar (XR9576), plant polyphenols, curcumin, tRA98006 or imatinib mesylate and a combination of any of the foregoing. Among specific inhibitors also described previously are those comprising valspodar (PSC833), verapamil, vanadate, PAK-104P, MK-571, FTC, Ko134, Elacridar (GF 120918), novobiocin, probenecid, BIB-E, disulfuram, indomethacin, furocemide, Penicillin G, sulfinpirazole, laniquidar (R101933), zosuquidar (LY335979), ontogeny (ONT-093), isothiocyanates, phytoestrogens, TAG-139, flavenoids, MS-209, NSAIDs, mitotane (NSC-38271), PK11195, cyclosporine D, anthranilamide, pipecolinate, quinoline, OC-144-093, diallyl sulfide, amooranin, agosterol A, siRNA, rifampicin, amiodarone, quinidine, quinine, nifedipine, dexniguldipin, LY455776, V-104, tricyclic izoxazoles, pluronic L61, or fumitremorgin C and a combination of any of the foregoing.
At least one viability dye (iv) may also be incorporated and used as part of the afore-described kit. Such viability dyes (iv) comprise propidium iodide, 7-amino-actinomycin D (7-AAD), DRAQ7TM, membrane impermeable form of Nuclear-IDTM Red, membrane impermeable form of Nuclear-IDTM Green, SYTOX® Green, SYTOX® Orange, SYTOX® Blue, YOYO, TOTO or TO-PRO, and a compound having the structure:




wherein X comprises CR11R12, NR11, O, S or Se where R11 and R12 independently comprise hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkyl group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R11 and R12 form a 5 or 6 membered ring;
wherein n can be 0, 1, 2 or 3;
wherein Y is —CR9═CR16—;
wherein m and p can have values of 0 or 1 and m+p=1;
wherein at least one of R1, R2, R3, R4, R5, R11 or R12 comprises Q(1) or at least one of R6, R7, R8, R9 or R10 comprises Q(2);
wherein Q(1) comprises a sulfonate (SO3−), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a alkyl phosphonate (PO3=) a alkyl phosphonate monoester (PO2−ER13) a alkyl phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S and the structures are as described previously;
wherein Q is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof and wherein when Q is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
wherein Q(2) comprises an alkyl, aminoalkyl, substituted aminoalkyl, a benzyl, a substituted benzyl, a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S and the structures are as described previously;
wherein Q(2) is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof and wherein when Q′ is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
wherein R13, R14, R15, R19 and R20 can be hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together R13 and R14 form a five or six membered ring;
wherein R13 and R14 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR25), a thioether linkage (—SR25), or an amine linkage (—NR25R26 or N+R25R26R27), and wherein R25, R26 and R27 independently comprise hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five or six membered ring, and wherein any of R25, R26 or R27 may further comprise said heteroatom containing side chain;
wherein R16, R17, R18 and the remaining R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11 and R12 can independently be hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R2 and R3, R3 and R4, R4 and R5, R6 and R7, and R7 and R8 may form a 5 or 6 membered ring; or when taken together R1 and R16, R11 and R16, R16 and R17, R17 and R18, and R18 and R9 may form a 5 or 6 membered ring;
wherein Z comprises a carboxyl group (CO2−), a carbonate ester (COER13), a sulfonate (SO3−), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a phosphonate (PO3=) a phosphonate monoester (PO2−ER13), a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) where E can be independently O or S and the structures are as described previously;
wherein Z is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof;
wherein any of R1, R2, R3, R4, R5, R6, R7, R8, R9 or R10, R11 or R12 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR25), a thioether linkage (—SR25), or an amine linkage (—NR25R26 or —N+R25R26R27);
wherein R25, R26 and R27 independently comprise hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five or six membered ring, and wherein any of R25, R26 or R27 may further comprise said heteroatom containing side chain, and
wherein R8 may comprise a substituted group capable of forming symmetric or asymmetric polymeric dye.
As in the case of the variously described processes of the present invention, at least one non-xanthene dye (v) can be incorporated and used in this kit. Such non-xanthene dyes have been described above and comprise a nuclear identification stain, calcein AM, Pheophorbide A, Chloromethylfluorescein diacetate (CMFDA), Hoechst 33342, BODIPY-Prazozin, Fura-2 AM, monobromobimane, BODIPY-Taxol or 3,3′-diethyloxacarbocyanine iodide (DIOC2(3)] or a dye from Table 1, FIG. 1, and a combination of any of the foregoing.
Quenching reagents are also applicable to the kit of the present invention. These quenching reagents minimize extracellular fluorescent signal from the xanthene compound (i). Examples of useful quenching reagents have been given above and include Evans Blue, o-tolidine, Trypan Blue, Trypan Red or Brilliant Black, and a combination of the foregoing.
The examples which follow are set forth to illustrate various aspects of the present invention but are not intended in any way to limit its scope as more particularly set forth and defined in the claims that follow thereafter.
DESCRIPTION OF THE PREFERRED EMBODIMENTS
Example 1
Demonstration of Multidrug Resistance in Mammalian Cell Lines Using MTT Method
Human cervical adenocarcinoma epithelial cell line HeLa (putative MDR negative cell line), human lung carcinoma cell line A549 (over-expression of MPR1 and BCRP) [Sharenberg et al., Blood 99:507-512 (2002); McCollum et al., Cancer Res 68:7419-7427 (2008)]) and hamster ovary CHO K1 cell line (over-expression of all three major ABC transporter proteins) [Ling et al., Cancer Treat Rep 67:869-874 (1983); Gupta et al., Biochem Biophys Res Comm 153:598-605 (1988)]) were obtained from ATCC (Manassas, Va.). HeLa cells were routinely cultured in Eagle's Minimum Essential Medium with low glucose (ATCC), supplemented with 10% fetal bovine serum (ATCC) and 100 U/ml penicillin, 100 ug/ml streptomycin (Sigma-Aldrich, St. Louis, Mo.). A549 and CHO K1 cells were routinely cultured in F-12K medium (ATCC), supplemented with 10% fetal bovine serum (ATCC) and 100 U/ml penicillin, 100 μg/ml streptomycin (Sigma-Aldrich, St. Louis, Mo.). Cell cultures were maintained in a humidified incubator at 37° C., with 5% CO2 atmosphere.
To confirm drug resistance of the above cell lines used as models, cells were seeded in 96-well plates at a density of 5×103 cells/well and 24 h later, treated with increasing doses of different drugs that are commonly used for cancer chemotherapy and are known to be associated with the phenomenon of MDR (taxol, doxorubicin, vincristine, mitoxantrone). A standard 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) viability test was performed 24 and 48 h post-treatment, as described elsewhere [Mosmann T., J Immunol Methods 65(1-2):55-63 (1983)]. Viability was calculated as a ratio of OD595 for treated cells to the OD595 of untreated control cells. Data from the MTT test confirmed higher chemoresistance of CHO K1 and A549 cells compared to HeLa cells toward all toxic compounds used in the study (FIGS. 2A-D). CHO K1 and A549 cell lines were used as model cell lines demonstrating MDR activity in all following studies. No genetically modified cell lines were used as models in the present application since the levels of MDR activity in these cell lines is already much higher compared with standard clinical samples.
Example 2
Minimal Fluo-8TM AM and Rhod-4TM AM Dye Toxicity
Human cervical adenocarcinoma epithelial cell line HeLa (putative MDR negative cell line), human lung carcinoma cell line A549 and hamster ovary CHO K1 cell line were cultured as described in the Example 1. Fluo-8TM AM and Rhod-4TM AM fluorescent probes were dissolved in anhydrous DMSO at the following concentrations: Fluo-8TM AM—1 mM (a 200× stock solution), Rhod-4TM AM—2 mM (a 1000× stock solutions). 1 mM (2000×) stock solution of Calcein AM was prepared for control measurements. Stock solutions of the dyes were aliquoted and stored at −20° C. in the dark.
Three model cell lines (CHO K1, A549 and HeLa cells) were seeded in 96 well plates (5×103 cells/well) and 24 h later were treated with the working concentrations of dyes (0.5 μM of Calcein AM, 5 μM of Fluo-8TM AM, 4 μM of Rhod-4TM AM) used in the MDR assay for 3 h at 37° C. Then reagents were removed and a standard MTT test was performed as described elsewhere [Mosmann T., J Immunol Methods 65(1-2):55-63 (1983)]. Viability was calculated as a ratio of OD595 for treated cells to the OD595 of untreated control cells (FIG. 3). Data presented in FIG. 3 show that Fluo-8TM was not toxic to the cells, and Rhod-4TM shows only minimal toxicity in CHO K1 cell line after prolonged incubation. Standard MDR experimental protocols do not require, however, such long incubation periods with the dye at 37° C.; therefore, in the authentic assay any toxic effect would be much milder than illustrated in this example. Additionally, the concentration of Rhod-4TM AM can be decreased further for particularly sensitive cell lines.
Example 3
Development of the Minimal Step Assay Procedure for the Dye Uptake Flow Cytometry Protocol
Human cervical adenocarcinoma epithelial cell line HeLa (putative MDR negative cell line), human lung carcinoma cell line A549 and hamster ovary CHO K1 cell line were cultured as described in the Example 1. All dyes stocks were prepared as described in Example 2. The following stocks of inhibitors in DMSO were prepared: 5 mM of cyclosporine A (general specificity inhibitor, 1000×), 5 mM of verapamil (MDR-specific inhibitor, 250×), 0.2 M of probenecid (MRP-specific inhibitor, 1000×), 10 mM of MK-571 (MRP-specific inhibitor, 200×), 0.5 M of novobiocin (BCRP-specific inhibitor, 10000×) and 10 mM of fumitremorgin C (BCRP-specific inhibitor, 1000×).
Cells were grown on tissue culture dishes and on the day of assay were trypsinized and washed twice with warm (37° C.) phosphate-buffered saline (PBS). Post-wash, the cells were re-suspended in warm phenol red indicator-free medium at a density of 1×106/ml. For each detection set, sixteen tubes (5 samples in triplicates plus non-stained control for background fluorescence) in numbered tubes each containing 5×105/cells (0.5 ml) were prepared. Warm medium (0.25 mL) containing different inhibitors [4 samples, one general inhibitor (5 μM of cyclosporine A) and three specific inhibitors (20 μM of verapamil, 0.2 mM of probenecid or 0.5 mM of novobiocin)] or vehicle only (1 sample) was added to each designated tube, and cells were mixed thoroughly with gentle pipeting. The non-stained control sample did not receive any inhibitor. After incubation for 5 min at 37° C., 0.25 ml of warm medium with Fluo-8TM AM probe (5 μM final concentration) or Rhod-4TM AM probe (2 μM final concentration) was added to each tube excluding non-stained control that receives plain medium and cells were incubated for 30 min at 37° C. and analyzed immediately by flow cytometry. In the second set of the tubes, the reaction was stopped by rapid centrifugation (1 min) at relatively low speed (200×g). After wash with ice-cold PBS and discarding the supernatant, cells were re-suspended in 0.5 ml of ice-cold medium and kept on ice until flow cytometry analysis. The third set of cells simply was spun down (1 min, 200×g) to remove the excess of the probe, resuspended in ice-cold medium and kept on ice until flow cytometry analysis.
Flow cytometry experiments were performed using a FACS Calibur benchtop flow cytometer (BD Biosciences) equipped with a blue (488 nm) laser, and the signals were registered in the FITC (530/30 filter), PE (585/42 filter) and PerCP (670 LP filter) channels. Fluo-8TM dye fluorescence was measured in the FL1 channel, and Rhod-4TM dye fluorescence—in the FL2 channel. Flow cytometry data were analyzed by comparison of median fluorescence or using Kolmogorov-Smirnov statistics [Young, J Histochem Cytochem 25:935-941 (1977)] or by calculating MAF values (MDR Activity Factor) using the following formula: MAF=100*((MFIinh-MFI0)/MFIinh), where MFIinh and MFI0 are mean fluorescence intensity values measured in the presence and absence of inhibitor [Hollo et al., Biochem Piophys Acta. 1191:384-388 (1994)].
In Table 4 and FIG. 5, the results of a typical experiment with CHO K1 cell line and Fluo-8TM AM probe are presented.







TABLE 4







Optimization of the dye uptake protocol for the MDR assay,


CHO K1 cell line, Fluo-8 TM AM probe.














Cyclosporin
Verap-
Pro-
Novo-


Value
Protocol
A
amil
benecid
biocin















MAP
No Wash
93.0
77.6
85.4
93.5



Spin
91.5
73.0
85.0
92.4



Wash
91.6
73.5
86.2
91.3


D-values
No Wash
0.97
0.81
0.9
0.98



Spin
0.94
0.76
0.9
0.97



Wash
0.94
0.76
0.87
0.94









Experiments with another model cell line (A549) and with other tested probe (Rhod-4TM AM) demonstrated similar results that allow us to conclude that in the novel MDR detection assay, dye uptake protocol may be simplified and used without additional washing steps. In this case, however, the samples must be analyzed within a 30 min interval. If immediate flow cytometry assay is not possible, then washing and storing on ice is recommended, since according to literature reports, most of ABC transporters are inactive at +4° C.
Example 4
Development of the Minimal Step Assay Procedure for the Dye Efflux Flow Cytometry Protocol
Human cervical adenocarcinoma epithelial cell line HeLa (putative MDR negative cell line), human lung carcinoma cell line A549 and hamster ovary CHO K1 cell line were cultured as described in the Example 1. All dyes and inhibitors stocks were prepared as described in Examples 2 and 3.
Cells were grown in tissue culture dishes and on the day of assay they were trypsinized and washed twice with ice-cold PBS. Post-wash, the cells were re-suspended in cold phenol red indicator-free medium at a density of 1×106/ml. For each detection set, eighteen tubes (6 tubes without inhibitor and 3 tubes for each inhibitor tested, in triplicates) each containing 2.5−5×105/cells were prepared. Cells were centrifuged at 200×g for 5 min, and after discarding supernatant, re-suspended at 1×106/ml in ice-cold indicator-free medium containing Fluo-8TM AM or Rhod-4TM AM probes. Additionally, an aliquot of non-stained cells was prepared for background fluorescence measurements. Cells were incubated with the probe(s) on ice for 60 min, than centrifuged at 200×g for 5 min. After discarding the supernatant, cells were either washed twice with PBS or simply were spun down to remove the excess of the probe and resuspended at 5×105 cells/sample in 0.5 ml of following solutions:
1. warm (37° C.) indicator-free medium containing vehicle only (3 tubes)
2. warm (37° C.) indicator-free medium containing inhibitor (3 tubes for each inhibitor tested)
3. ice-cold indicator-free medium (3 tubes)
Tube sets 1 and 2 were immediately transferred to a water bath (37° C.) and incubated for 90 min. Tube set 3 was kept on ice. Post incubation, 4 ml of ice-cold indicator-free medium was added per tube, tubes were centrifuged at 200×g for 5 min, supernatant was discarded, and cell pellet was re-suspended in the cold indicator-free medium and centrifuged again. Finally, cells were re-suspended in 0.5 ml of cold indicator-free medium and maintained on ice until analysis. Alternatively, cells were analyzed without washing. Flow cytometry experiments were performed as described in Example 3.
In Table 5 and FIG. 6, the results of representative experiments in model cell lines with Fluo-8TM AM probe are given.







TABLE 5







Optimization of the dye efflux protocol for the flow cytometry MDR 


assay using Fluo-8 TM AM probe. 


Kolmogorov-Smirnov statistical D-values are presented.















Cyclo-

Proben-
Novobi-
+4° 


Cell Line
Protocol
sporin A
Verapamil
ecid
ocin
C.
















CHO K1
No Wash
0.8
0.21
0.19
0.7
0.78



Wash
0.62
0.34
0.23
0.79
0.76


A549
No Wash
0.83
0.12
0.33
0.57
0.77



Wash
0.71
0.11
0.18
0.46
0.75


HeLa
NoWash
0.12
0.076
0.13
0.13
0.15



Wash
0.14
0.14
0.14
0.16
0.14









Qualitatively and quantitatively, variations of both protocols produce similar results. Additional washing step does not change the results of the assay significantly. For the efflux assay, the washing step increases the difference between control and inhibitor treated sample (probably because there is no dye excess and no passive transport through the membrane during ice incubation.
Example 5
Confirmation of Substrate Specificity of Fluo-8TM AM and Rhodamine-4TM AM Probes in Mammalian Cells Using Flow Cytometry Dye Uptake Protocol
CHO K1, A 549 and HeLa cell lines were cultured as described in Example 1. Stock solutions of the probes and inhibitors were prepared as described in Examples 2 and 3. Additionally, stocks of the following dyes (that have been proven to be specific for particular ABC transporter detection) were made: 20 μg/ml of 3,3′-diethyloxacarbocyanine iodide [DiOC2(3), 1000×], 10 mM of pheophorbide A (2000×) and 5 mM of chloromethylfluorescein diacetate (CMFDA, 1000×).
Cells were grown on tissue culture dishes and on the day of assay were treated according to a dye uptake protocol and analyzed by flow cytometry as described in Example 3. Calcein AM, DiOC2(3), CMFDA and pheophorbide A were used as a control MDR probes with known substrate specificity. The specificity of the probes and D-values obtained as results of the test are listed in Table 5.







TABLE 5







Comparison of MDR activity detection in model cell lines using


MDR probes and inhibitors of different specificity. Average D-


values for three representative experiments are provided.












Cell

Probe
Verap-
Pro-
Fumi-


Line
MDR Probe
Specificity
amil
benecid
tremorgin C















CHO
Calcein AM
Pgp, MRP
0.74
0.77
0.17


K1
Fluo-8 AM

0.84
0.69
0.48



Rhodamine-4

0.80
0.58
0.32



AM



DiOC2(3)
Pgp
0.96
0.01
0



Pheophorbide A
BCRP
0.02
0.03
0.25



CMFDA
MRP
0.19
0.7
0.09


A549
Calcein AM
Pgp, MRP
0.17
0.36
0.04



Fluo-8 AM

0.07
0.26
0.23



Rhodamine-4

0.14
0.21
0.29



AM



DiOC2(3)
Pgp
0.07
0
0.03



Pheophorbide A
BCRP
0.16
0.16
0.35



CMFDA
MRP
0.04
0.29
0.21


HeLa
Calcein AM
Pgp, MRP
0.17
0.06
0.03



Fluo-8 AM

0.10
0
0.15



Rhodamine-4

0
0
0.10



AM



DiOC2(3)
Pgp
0
0.06
0.07



Pheophorbide A
BCRP
0
0
0



CMFDA
MRP
0
0.03
0.12









Comparison of the data from TABLE 5 confirms that both Fluo-8TM AM and Rhodamine-4TM AM can specifically detect particular MDR activity when used with a corresponding modulator of ABC transporter activity. In CHO K1 cell line, Pgp expression was detected by all specific dyes and by Fluo-8TM and Rhodamine-4TM; MRP expression was detected by all specific dyes and by Fluo-8TM and Rhodamine-4TM; BCRP expression was detected by PheA, which is specific for this ABC transporter, and by Fluo-8TM and Rhodamine-4TM. In A549 cell line, Pgp expression was not detected by any specific dye and not by Fluo-8TM and Rhodamine-4TM; MRP expression was detected by all specific dyes and by Fluo-8TM and Rhodamine-4TM; BCRP expression was detected by PheA, which is specific for this ABC transporter, and by FluoForteTM and Rhodamine-4TM. In HeLa cell line, no drug resistance was detected with any dye/inhibitor combination. The data confirmed specificity of FluoForteTM and Rhodamine-4TM for all three major types of ABC transporter proteins.
Example 5A
Profiling of ABC Transporters in Mammalian Cells Using Fluo-8TM AM or Rhodamine-4TM AM Probes in Conjunction with Various Specific MDR Probes Using Flow Cytometry Dye Uptake Protocol
CHO K1, cell line was cultured as described in Example 1. Stock solutions of the probes and inhibitors were prepared as described in Examples 2 and 3. Additionally, stocks of the following dyes (that have been proven to be specific for particular ABC transporter detection) were made: 20 μg/ml of 3,3′-diethyloxacarbocyanine iodide [DiOC2(3), 1000×], 10 mM of pheophorbide A (2000×) and 5 mM of chloromethylfluorescein diacetate (CMFDA, 1000×).
Cells were grown in tissue culture dishes and on the day of assay were treated according to a dye uptake protocol and analyzed by flow cytometry as described in Example 3. Fluo-8TM AM, Rhodamine-4TM AM, DiOC2(3) (MDR1-specific probe), CMFDA (MRP-specific probe) or pheophorbide A (BCRP-specific probe) were added to the cells alone or in combination (general+specific or general+two specific probes) allowing spectral resolution. The concentrations of the probes were as follows: Fluo-8TM AM—5 μM, Rhodamine-4TM AM—2 μM, DiOC2(3)—20 ng/ml, CMFDA—1 μM, Pheophorbide A—5 μM.
Following 30 min incubation at 37° C., cells were analyzing by flow cytometry. Samples were collected as is (uncompensated) and double or triple stained samples were collected second time after compensation correction.
Pheophorbide A, which is specific for BCRP, was used in combination with either green (Fluo-8TM AM) or orange (Rhodamine-4TM AM) MDR general probe. In BCRP-expressing CHO K1 cells, fluorescence decreased in both channels (FL1 and FL3 or FL2 and FL3) if cyclosporin A (general MDR inhibitor) or fumitremorgin C (specific BCRP inhibitor) were not present (Table 6A below). Quantitative characteristics of the changes in fluorescence (expressed as D-values or as MAFs), corresponded to values obtained with single probes. It is important to note that in case of dual probe treatment with Rhodamine-4TM AM, compensation corrections are required to eliminate overlap of the dye spectra. In the cells that are BCRP-negative but positive for other types of ABC transporters, red fluorescence is high, while green or orange fluorescence is dim.







TABLE 6A







Examples of multiplex (dual) probe treatment for MDR activity profiling 


in CHO K1 cell line.


(D-values are provided as characteristics of MDR).











D-values Post Inhibitor Treatment



Detection
(compared to uninhibited cells












Probes
Channel
CsA
Verapamil
MK-571
FTC















Fluo-8 TM AM
FL1
0.94
0.9
0.98
0.56


Pheophorbide
FL3
0.25
0.14
0.15
0.33


A







Rhod-4 TM AM
FL2
0.89
0.94
0.96
0.51


Pheophorbide
FL3
0.25
0.11
0.14
0.34


A







Rhod-4 TM AM
FL2
0.84
0.82
0.96
0.44


DiOC2(3)
FL1
0.94
0.96
0.13
0.16


Rhod-4 TM AM
FL2
0.9
0.94
0.85
0.53


CMFDA
FL1
0.49
0.1
0.91
0.06









If DiOC2(3) is used in combination with Rhodamine-4TM AM, in Pgp expressing cells, both dyes are pumped out in the absence of the inhibitors and cells exhibit less fluorescence in both the FL1 and FL2 channels. In MRP or BCRP expressing cells, only Rhodamine 4TM AM is pumped out in the absence of the inhibitors, and cells show lower fluorescence in the FL2 but not FL1 channel. According to these considerations, when both dyes were used in CHO K1 cell line, orange fluorescence was bright in all cases when cells were treated with the inhibitors, but green fluorescence was bright only in the presence of verapamil (Table 6A).
Chloromethylfluorescein diacetate (CMFDA) could also be used with Rhodamine-4TM AM in a two dye combination. In MRP expressing cells, both dyes would be pumped out in the absence of the inhibitors and cells would demonstrate a decreased fluorescence in both the FL1 and FL2 channels. In Pgp or BCRP expressing cells, only the Rhodamine 4TM AM would be pumped out and fluorescence will go down in the FL2 but not FL1 channel. Accordingly, in CHO K1 cells, orange fluorescence sustained bright when specific inhibitors were used, but green fluorescence was bright only when MRP inhibitor (MK-571) was applied.
For the triplex probe profiling, Rhodamine-4TM AM was employed as a general specificity probe, and DiOC2(3), CMFDA and pheophorbide A was employed as specific probes (Table 6B).







TABLE 6B







Examples of multiplex (triple) probe treatment for MDR activity 


profiling in CHO K1 cell line.


(D-values are provided as characteristics of MDR).











D-values Post Inhibitor Treatment



Detection
(compared to uninhibited cells












Probes
Channel
CsA
Verapamil
MK-571
FTC















DiOC2(3)
FL1
0.98
0.98
0.13
0.11


Rhod-4 TM AM
FL2
0.81
0.91
0.97
0.54


Pheophorbide
FL3
0.4
0.17
0.13
0.41


A







CMFDA
FL1
0.47
0.10
0.89
0.14


Rhod-4 TM AM
FL2
0.93
0.97
0.95
0.64


Pheophorbide
FL3
0.20
0.18
0.09
0.27


A









When DiOC2(3) and pheophorbide A were used in CHO K1 cell line in conjunction with Rhodamine-4TM AM, FL2 (orange) fluorescence stays bright after treatment with all inhibitors used for the experiment. FL1 (green) fluorescence decreased unless cyclosporin A (general MDR inhibitor) or verapamil (MDR1 inhibitor) were present. FL3 (dark red) fluorescence was bright only when cyclosporin A (general MDR inhibitor) or fumitremorgin C (BCRP inhibitor) were present.
Similarly, with the combination of Rhodamine-4TM AM, CMFDA and pheophorbide A, FL2 (orange) fluorescence stays bright after treatment with all inhibitors used for the experiment. FL1 (green) fluorescence decreased unless cyclosporin A (general MDR inhibitor) or MK-571 (MRP inhibitor) were present. FL3 (dark red) fluorescence was bright only when cyclosporin A (general MDR inhibitor) or fumitremorgin C (BCRP inhibitor) were present.
Some additional examples of multiplexed (two or more probes) MDR probes combinations and expected results of the assay are presented in the following Table 6C.







TABLE 6C







Expected results of multiplex probing for MDR activity detection













Decreased Fluorescence in the Absence of the



Fluorogenic

Inhibitors, If cells have active












Set
Probe
Specificity
MDR
MRP
BCRP





A
Fluo-8 TM AM
general
FL1
FL1
FL1 + FL3



Pheophorbide A
BCRP


B
Fluo-8 TM AM
general
FL1 + UV
FL1
FL1 + FL3



Fura-2 AM
Pgp



BODIPY-Prazozin
BCRP


C
Fluo-8 TM AM
general
FL1
FL1
FL1 + UV



Hoechst 33342
BCRP


D
Fluo-8 TM AM
general
FL1
FL1 + FL3
FL1



TMRM
MRP


E
Fluo-8 TM AM
general
FL1
FL1 + UV
FL1 + FL3



monobromobimane
MRP



Pheophorbide A
BCRP


F
Fluo-8 AM
general
FL1 + FL3
FL1
FL1



BODIPY-Taxol
Pgp


G
Rhodamine-4 TM
general
FL2
FL1 + FL2
FL2



AM



CMFDA
MRP


H
Rhodamine-4 TM
general
FL1 + FL2
FL2
FL2



AM



DiOC2(3)
Pgp


I
Rhodamine-4 TM
general
FL1 + FL2
FL2
FL2 + FL3



AM



DiOC2(3)
Pgp



Pheophorbide A
BCRP


J
CMFDA
MRP
FL2
FL1 + FL2
FL2 + FL3



Rhodamine-4 TM
general



AM



Pheophorbide A
BCRP









Example 6
Detection of ABC Transporter Activity in Cancer Cells by Flow Cytometry Using Fluo-8TM AM and Rhod-4TM AM Probes and a Dye Uptake Protocol
CHO K1, A 549 and HeLa cell lines were cultured as described in Example 1. Stock solutions of the probes and inhibitors were prepared as described in Examples 2 and 3. Cells were grown on tissue culture dishes and on the day of assay were treated according to a dye uptake protocol and analyzed by flow cytometry as described in Example 3. Calcein AM was used as a control MDR probe.
In FIG. 7, the results of MDR activity assays using Fluo-8TM AM, Rhod-4TM AM and Calcein AM in model cell lines are presented (representative experiment). Fluorescence profiles for cells treated with inhibitors are shown in bold, and fluorescence profiles for the cells that were untreated are shown as, filled histograms. As shown in FIG. 7, all three dyes detect similar P-gp and MRP levels in CHO K1 cells (Panel A), and detect only MRP but not P-gp in A549 cells (panel B). In contrast to Calcein AM, which is not able to detect BCRP activity, Fluo-8TM AM and Rhod-4TM AM detect significant BCRP activity in both CHO K1 and A549 cell lines. Results obtained with Fluo-8TM and Rhod-4TM dyes correspond to MTT chemoresistance data (FIGS. 3A-D) and to the published data [Ling et al., Cancer Treat Rep 67:869-874 (1983); Scharenberg et al., Blood 99:507-512 (2002); Gupta et al., Biochem Biophys Res Comm 153:598-605 (1988)]. All three probes do not detect any MDR activity in HeLa cells, which are considered to be MDR-negative cells (FIG. 7C).







TABLE 7







Detection of MDR activity by flow cytometry method


(dye uptake) in model cell lines. Activity of


ABC transporters is expressed as D-values.












Cell

Cyclosporine
Verap-
Pro-
Novo-


Line
Probe
A
amil
benecid
biocin















CHO
Calcein AM
0.96
0.93
0.70
0.06


K1
Fluo-8 TM AM
0.96
0.83
0.89
0.78



Rhod-4 TM AM
0.96
0.89
0.74
0.80


A549
Calcein AM
0.47
0.15
0.27
0.03



Fluo-8 TM AM
0.51
0.09
0.49
0.44



Rhod-4 TM AM
0.42
0.12
0.28
0.40


HeLa
Calcein AM
0.14
0.13
0.09
0.09



Fluo-8 TM AM
0.14
0.04
0.15
0.09



Rhod-4 TM AM
0.05
0.04
0.03
0.06









Example 7
Detection of ABC Transporter Activity in Cancer Cells by Flow Cytometry Using a Dye Efflux Protocol
CHO K1, A 549 and HeLa cell lines were cultured as described in Example 1. Stock solutions of the probes and inhibitors were prepared as described in Examples 2 and 3. Cells were grown on tissue culture dishes and on the day of assay were treated according to a dye efflux protocol and analyzed by flow cytometry as described in Example 4. Calcein AM was used as a control MDR probe.







TABLE 8







Detection of MDR activity by flow cytometry method (dye efflux)


in cultured cell lines (representative experiment).


Activity of ABC transporters is expressed as D-values.













Cell

Cyclo-
Verap-
Proben-
Novobi-



Type
MDR Probe
sporin A
amil
ecid
ocin
4° C.
















CHO
Calcein AM
0.31
0.26
0.47
0.13
0.65


K1
Fluo-8 TM AM
0.55
0.28
0.30
0.70
0.72



Rhod-4 TM AM
0.52
0.33
0.21
0.64
0.45


A549
Calcein AM
0.35
0.03
0.40
0.15
0.50



Fluo-8 TM AM
0.5
0.02
0.33
0.57
0.80



Rhod-4 TM AM
0.27
0.1
0.32
0.58
0.65


HeLa
Calcein AM
0.08
0.1
0.62
0.04
0.07



Fluo-8 TM AM
0.13
0.15
0.16
0.15
0.83



Rhod-4 TM AM
0
0
0
0
0.39









Data from the representative experiments included in Tables 7 and 8 demonstrated that the values obtained with Fluo-8TM AM and Rhod-4TM AM are equal to or higher than Calcein AM-based values indicating higher sensitivity of these probes

Example 8
Fluo-8TM AM and Rhod-4TM AM Probes are More Sensitive for MDR Activity Detection than Commonly Used Probes of General Specificity, Such as Mitoxantrone and Doxorubicin
CHO K1, A 549 and HeLa cell lines were cultured as described in Example 1. Stock solutions of the probes and inhibitors were prepared as described in Examples 2 and 3. Additionally, stock solutions of mitoxantrone (10 mM, 1000×) and doxorubicin (5 mM, 1000×) in DMSO were prepared, aliquoted and stored frozen at −20° C. in the dark. Sensitivity and specificity of Fluo-8TM AM, Rhod-4TM AM, mitoxantrone and doxorubicin were analyzed and compared using three model cell lines. Cells were grown in tissue culture dishes and on the day of assay were treated according to a dye uptake protocol and analyzed by flow cytometry, as described in Example 3. The results of the assay are presented in the FIG. 8 (representative experiment) and Table 9 (average D-values from three independent experiments are presented). All four probes are capable of the detection of all three major types of ABC transporters, however the Fluo-8 and Rhod-4 dyes generate higher intensity fluorescence, indicating they are capable of providing more sensitive detection of MDR.







TABLE 9







Sensitivity of MDR probes of general


specificity in the drug uptake assay













Cell

Cyclo-
Verap-

Novobi-



Line
Probe
sporin A
amil
MK-571
ocin
FTC
















CHO
Fluo-8 TM AM
0.89
0.74
0.95
0.68
0.28


K1
Rhod-4 TM AM
0.95
0.75
0.96
0.64
0.32



Mitoxantrone
0.34
0.42
0.18
0.22
0.21



Doxorubicin
0.42
0.27
0.35
0.32
0.22


A549
Fluo-8 TM AM
0.43
0.06
0.61
0.37
0.31



Rhod-4 TM AM
0.35
0.09
0.48
0.41
0.38



Mitoxantrone
0.27
0.12
0.37
0.28
0.28



Doxorubicin
0.14
0.06
0.24
0.28
0.18









Example 9
Testing MDR Activity of Diverse Human Carcinoma Cell Lines Using Fluo-8TM AM and Rhod-4TM AM Probes
Both human ileocecal colorectal carcinoma cell line HCT-8 (reported to over-express P-gp and, to a lesser extent, MRP [Hunter et al., Br J Cancer. 64:437-444 (1991); Collington et al., Biochem Pharmacol 44:417-424 (1992)] and hepatocellular carcinoma Hep G2 (reported to over-express MRP [Roelofsen et al., Gastroenterology 112:511-521 (1997), Cantz et al., Am J Physiol Gastrointest Liver Physiol. 278:G522-G531 (2000)] were obtained from ATCC. HCT-8 cells were routinely cultured in RPMI-1640 Medium with 2 mM L-glutamine, 10 mM HEPES, 1 mM sodium piruvate, 4.5 g/L glucose, 1.5 g/L sodium bicarbonate (ATCC), supplemented with 10% horse serum (ATCC) and 100 U/ml penicillin, 100 ug/ml streptomycin (Sigma-Aldrich, St. Louis, Mo.). Hep G2 cells were routinely cultured in Eagle's Minimum Essential Medium with low glucose (ATCC), supplemented with 10% heat inactivated fetal bovine serum (ATCC) and 100 U/ml penicillin, 100 ug/ml streptomycin (Sigma-Aldrich, St. Louis, Mo.). Cell cultures were maintained in a humidified incubator at 37° C., with 5% CO2 atmosphere. Stock solutions of the probes and inhibitors were prepared, as described in Examples 2 and 3. Cells were grown in tissue culture dishes and on the day of assay were treated according to a dye uptake protocol and analyzed by flow cytometry, as described in Example 3.
According to the data presented in FIG. 9, both FIuo-8TM AM and Rhod-4TM AM probes detect increased P-gp and MRP activity in HCT-8 cells (panel A) and increased MRP activity in Hep G2 cells (panel B). Comparison of D-values confirmed activity of P-gp in HCT-8 cells and of MRP in both cell lines tested.







TABLE 10







Results of detection of MDR activity of HCT-8 and


Hep G2 cancer cell lines. D-values presented.












Cyclosporin
Verap-

Novo-



A
amil
MK-571
biocin
















HCT-8
Fluo-8 TM AM
0.68
0.71
0.34
0.22



Rhod-4 TM AM
0.72
0.51
0.27
0.061



Calcein TM AM
0.31
0.71
0.16
0.44


Hep
Fluo-8 TM AM
0.28
0
0.34
0.13


G2
Rhod-4 TM AM
0.26
0
0.34
0



Calcein TM AM
0.29
0.13
0.29
0.02









Example 10
Compatibility of Fluo-8TM AM and Rhod-4TM AM Probes with Propidium Iodide (PI), the Most Common Dead Cell Indicator Stain
CHO K1 cell line was cultured as described in Example 1. Stock solutions of the probes and inhibitors were prepared as described in Examples 2 and 3. PI stock was made in water (100 μg/mL, 100×). Cells were grown on tissue culture dishes and on the day of assay were treated according to a dye uptake protocol. After 30 min incubation with probe and with/without inhibitors, PI was added to each sample to the final concentration 1 μg/mL and samples were analyzed by flow cytometry as described in Example 3. Single stained samples (PI only, Fluo-8TM AM only and Rhod-4TM only) were made to validate data obtained with two dyes. Data were collected uncompensated, also compensation corrections were performed using unstained cells, PI only stained dead cells and Fluo-8TM AM or Rhod-4TM stained cells (in the presence of cyclosporine A or MK-571 that provide a bright fluorescent signal).







TABLE 11







Compatibility of Fluo-8 TM AM and Rhod-4 TM AM with propidium iodide.


D-values for MDR activity and percentage of PI-positive cells are presented.










Uncompensated data
Compensated Data













Fluo-8 TM,
F8 + PI

R4 + PI
R4 + PI















Inhibitors
D
D-values
% PIpos
Rhod4 TM
D-values
% PIpos
D-values
% PIpos


















Cyclosporin A
0.91
0.96
1.44
0.98
0.98
4.2
0.97
0.59


Verapamil
0.92
0.94
0.83
0.94
0.96
2.75
0.95
0.88


MK-571
0.89
0.92
0.97
.94
0.95
6.72
0.94
1.46


Novobiocin
0.54
0.61
0.83
.64
0.7
1.61
0.66
0.81









Data presented in Table 11, clearly demonstrate that use of PI does not affect MDR detection when AM esters of Fluo-8TM and Rhod-4TM are used as probes. In turn, green or orange fluorescence resulting from the MDR detection does not affect determination of the number of dead cells in the sample. In certain cases (when the combination of Rhod-4TM AM and PI is used, and inhibitor treatment leads to a significant orange fluorescence increase), compensation corrections are needed in order to avoid overestimating dead cell staining.
Example 11
Multiplexed MDR Detection Using by Flow Cytometry in U-2 OS Cells Expressing Green Fluorescent Proteins
U-2 OS human bone osteosarcoma cells were obtained from ATTC, and U-2 OS cells expressing green fluorescent mitochondria were obtained from Marinpharm GmbH, Germany and routinely cultured in McCoy's 5a Modified Medium (ATCC), supplemented with 10% fetal bovine serum heat inactivated (ATCC) and 100 μm! penicillin, 100 ug/ml streptomycin (Sigma-Aldrich). Cell cultures were maintained in an incubator at 37° C., with 5% CO2 atmosphere. All dye and inhibitor stocks were prepared as described in Example 1.
Cells were grown on tissue culture dishes and on the day of assay they were trypsinized and washed twice with warm (37° C.) PBS. Post-wash, the cells were re-suspended in warm indicator-free medium at a density of 1×106/ml. For each detection set, sixteen tubes (5 samples in triplicates plus non-stained control for background fluorescence) in numbered tubes, each containing 5×105/cells (0.5 ml) were prepared. Warm medium (0.25 mL) containing different inhibitors (4 samples, one general inhibitor and three specific inhibitors) of vehicle only (1 sample) was added to each designated tube, and cells were mixed thoroughly with gentle pipeting. Non-stained control cells did not receive any inhibitor. After incubation for 5 min at 37° C., 0.25 ml of warm medium with Fluo-8 AM or Rhod-4TM AM probes (5 μM or 2 μM final concentration, for parental cells) or Rhod-4TM dye (2 μM final concentration, for green mitochondria expressing cells) were added to each tube excluding non-stained control that receives plain medium and cells were incubated for 30 min at 37° C. and analyzed immediately by flow cytometry using FACS Calibur benchtop cytometer (B D Dickinson, CA). To exclude dead cells, propidium iodide (PI) solution was added to the cells during the last 5 min of incubation (final concentration is 1 μg/mL). Fluo-8TM dye fluorescence was measured in the FL1 channel, Rhod-4TM dye fluorescence—in the FL2 channel, and PI fluorescence in the FL3 channel. Single stained samples of parental U-2 OS cells were prepared with each used dye for compensation correction.







TABLE 12







Comparison of the MDR activity data (expressed as MAF values) 


obtained using Fluo-8 TM AM and 


Rhod-4 TM AM as probes in U-2 OS cells









U-2 OS



Dyes

















R4 + PI 


Inhib-
F8
F8 + PI
R4
R4 + PI
Compens















itors
MAF
MAF
% PIpos
MAF
MAF
% PIpos
MAF
% PIpos


















CsA
68.8
42.6
4.58
44.1
35.8
4.8
47.4
2.04


FTC
5.0
−6.3
2.94
9.9
−9.3
3.19
12.6
2.01


MK
65.4
52.9
4.19
62.8
49.7
4.28
54.5
1.8


Novo
17.9
12.3
3.29
18.7
10.7
2.69
15.1
1.31


Pro
57.5
23.1
4.21
41.2
24.0
3.46
42.4
1.05


Ver
63.4
33.0
3.62
42.5
35.8
3.65
54.1
1.51
















TABLE 12B







Comparison of the MDR activity data (expressed as


MAF values) obtained using Fluo-8 TM AM


and Rhod-4 TM AM as probes in U-2 OS cells expressing GFP









U-2 OS GFP














Dyes
R4
R4 + PI

R4 + PI compens















Inhibitors
MAF
MAF
% PIpos
MAF
% PIpos


















CsA
37.7
42.0
2.2
47.9
2.96



FTC
15.0
25.7
3.18
6.2
3.7



MK
49.6
51.9
3.08
43.3
3.92



Novo
17.9
27.9
2.09
2.8
2.66



Pro
34.0
47.7
2.09
38.5
2.92



Ver
30.4
41.3
2.77
38.0
3.31










Experiment conducted with GFP-expressing U-2 OS cells stained with Rhod-4TM probe and PI demonstrated feasibility of MDR activity detection in such systems. Compensation corrections are needed, however, for correct estimation of PI positive cells. PI fluorescence (red) does not interfere significantly with green and orange signal. Green signal does not affect red fluorescence, either. Orange fluorescence affects PI measurements significantly, however (particularly, when the inhibition of MDR is seen and orange signal increased significantly). These samples stained with Rhod-4TM and PI need compensation correction. Recommendations are to have single stained samples for each dye and unstained cells. Nevertheless, results obtained for the MDR activity do not depend on compensation correction in all cases.
Example 12
Detection of ABC Transporters' Activity in Cancer Cells Using Fluorescence Microplate Reader
CHO K1, A 549 and HeLa cell lines were cultured as described in Example 1. Stock solutions of the probes and inhibitors were prepared as described in Examples 2 and 3. Two protocols (using cells in suspension and using adherent cells) were used. A. For the first protocol (suspension cells), cells in suspension (0.54×105 cells/100 μL) were added to the wells of 96-well black walled microplates where 50 μL of reference or experimental MDR modulators/inhibitors were distributed (PBS was used as a control), mixed and incubated at 37° C. for 15 min. Fifty μL of 20 μM Fluo-8TM AM, 8 μM Rhod-4TM AM or 2 μM Calcein AM (used as a control MDR probe) were added to each well, mixed and incubated at 37° C. for 15 min. After the incubation, plates were centrifuged (5 min, 200×g), the supernatant was removed, the cells were resuspended in 200 μL of cold tissue culture medium and retained fluorescence was measured. Optionally, cells were washed with cold PBS after staining.
B. For the adherent cells, cells were seeded in black walled 96-well microplates (2−5×104 cells/well) and 24 h later were treated with the inhibitors (or vehicle) and stained with the probes (5 μM of Fluo-8TM AM, 2 μM of Rhod-4TM AM or 0.5 μM of Calcein AM final concentration) for 30 min at 37° C. Then the fluorescence was measured immediately or after excess dye(s) was removed by washing with HBSS (inhibitors should be added to the washing buffer to avoid artifacts).
The probe(s) retention was measured using an OPTIMA FluoStar multiplate fluorimeter (BMG Labtech Inc., NC; equipped with 490 and 550 nm excitation filter and 520 and 570 nm emission filters) or SynergyTM Mx multi-mode microplate reader (BioTek Instruments Inc., VT; using 490 and 530 nm excitation and 520 and 555 nm emission settings). The results of the assay were expressed as a ratio of the fluorescence of the inhibitor-treated cells to the fluorescence of the untreated control cells.
Results of measurements of MDR activity using a fluorescence microplate reader are presented in FIGS. 10A and 10B and are similar to the results obtained by flow cytometry methods. There are minor qualitative differences compared to the flow cytometry data. There may be a few reasons accounting for these differences: the method of quantification is different, and the assay has not been optimized.
In addition, using of Fluo-8TM AM and Rhod-4TM AM to detect MDR activity in microplate format also results in a brighter and a more reproducible signal than when Calcein AM is used (FIG. 10C).
Example 13
Determination of Efflux-Mediated Multidrug Resistance in E. coli (or Bacillus subtilis) Using Both Flow Cytometry and Microplate Fluorimetry Method
Flow Cytometry
Flow cytometry experiments were performed using a FACS Calibur benchtop cytometer (BD Biosciences) equipped with a blue (488 nm) laser, and the signals were registered in FITC (530/30 filter), PE (585/42 filter) and PerCP (670 LP filter) channels. Fluo-8TM dye fluorescence was measured in the FL1 channel, and Rhod-4TM dye fluorescence—in the FL2 channel.
(i) Accumulation Assay
E. coli strains were cultured in 10 ml of LB medium at 37° C. and a shaker speed of 220 rpm until an OD600 of 0.6 was achieved. Aliquots of 1.0 ml were centrifuged at 16,000×g for 3 minutes, the supernatant discarded and the pellet washed twice with PBS. The OD600 of the bacterial suspension was adjusted to 0.3 using PBS without glucose. MDR probe was added at a final concentration of 0.5 μM (Fluo-1TM AM) or 2 μM (Rhod-4TM AM), and chlorpromazine (CPZ) was added to a final concentration of 20 μg/ml. Following incubation at 25° C. for 60 minutes, aliquots of 0.5 ml were taken for fluorescence measurements in the FACSCaliburTM flow cytometer. Data were collected for at least 10,000 events per sample.
Since the doses of the probes are not toxic, the net fluorescence of the bacteria is the result of the balance between the probe entry by passive diffusion (influx) and extrusion activity of efflux pump systems. Therefore, the strain that over-expresses efflux systems accumulates the least amount of the dye(s). On the contrary, accumulation of the dyes inside the bacterial cells is increased in the presence of compounds such as phenothiazines (e.g. CPZ), that have been shown to inhibit efflux activity of Gram-negative bacteria [Pages et al. Trends Mol. Med. 11(8):382-389 (2005)]. Thus, these compounds are usually employed for the demonstration of over-expressed efflux pumps of bacteria [Pages et al. Trends Mol. Med. 11(8):382-389 (2005)].
(ii) Efflux Assay
After loading the bacteria with MDR probe (final concentration was 5 μM for Fluo-8TM AM or 2 μM for Rhod-4TM AM) in the presence of chlorpromazine (CPZ, 20 μg/ml), the bacterial suspension was centrifuged at 16,000×g for 3 minutes. The supernatant was removed and the pellet resuspended in dye-free PBS, adjusting the OD600 to 0.3. Efflux was assessed in the presence and absence of glucose at 0.4% (v/v). Aliquots of 0.5 ml were taken after 2.5, 5, 15, 30 and 60 minutes after incubation at 37° C., for fluorescence measurement in the FACSCaliburTM flow cytometer. Analyses were performed with an acquisition of at least 10,000 events per sample.
The on-line visualization of efflux activity by the probe-loaded bacterial cells requires that accumulation of the probes has previously taken place. Therefore, before performing the efflux assays, bacteria are exposed to conditions that promote significant accumulation of the probes(s): a temperature of 25° C., absence of glucose and presence of CPZ (20 μg/ml) for 60 minutes [Viveiros et al., Curr Drug Targets 9(9):760-778 (2008)]. When maximum accumulation has taken place under these conditions, the bacteria are washed free of both probe and inhibitor, and resuspended in fresh buffer with and without glucose. Flow cytometry assay confirms the maximal efflux of the probe occurs within 15 min from the bacterial strain over-expressing efflux pumps. Importantly, restoration of optimum conditions of glucose, noted to prevent accumulation, is required for the extrusion of the dyes. This assay shows that E. coli cells need an energy source for efflux to take place.
Microplate Assay to Estimate Dye Uptake by Mycobacteria.
M. smegmatis was grown to early exponential phase (OD600, 0.6 to 1.0). The cells were pelleted by centrifugation at room temperature, resuspended in uptake buffer (50 mM KH2PO4 [pH 7.0], 5 mM MgSO4), diluted to an OD600 of 0.5, and pre-energized with 25 mM glucose for 5 min. One hundred microliters of cells was added per well of black walled, clear-bottomed 96-well microplates (Greiner Bio-One). Probe was added to a final concentration of 5 μM (Fluo-8TM AM) or 2 μM (Rhod-4TM AM), and its accumulation was measured over 60 min at room temperature in top-reading mode using a Synergy Mx reader (BioTek) and standard FITC (Fluo-8TM) or Rhodamine (Rhod-4TM) filter settings. When required, reserpine was added after 8 min of incubation with probe at a final concentration of 0.1 mM.
It is expected that relative fluorescence that accumulated in the bacterial strains with high expression of the efflux pump will be significantly less compared to the fluorescence accumulated in the non-resistant strain. Addition of the inhibitor (reserpine) will reconstitute fluorescence accumulation in the resistant strain.
Example 14
Bi-Directional Transport Assay in Functionally Polarized Epithelial Cell Monolayer
In the transwell transport assay, polarized pig kidney epithelial cell line LLC-PK1, and its subclones expressing human multidrug resistance proteins (MDR, MRP or BCRP), and the polarized canine kidney cell line MDCK-II, and its multi-drug resistant subclones (described elsewhere) are used. These cell lines are selected for use because they enable direct comparison of their functional behaviors without the confounding effects of multiple transporters expressed in cell lines such as Caco-2.
LLC-PK1 control and transfected cells were grown in complete media consisting of RPMI 1640 medium (ATCC) supplemented with 10% (v/v) fetal calf serum and 1% (v/v) antibiotic-antimycotic and grown at 37° C. in the presence of 5% CO2. Cells were grown in Medium 199 (Invitrogen, Carlsbad, Calif.) supplemented with L-glutamine, 10% (v/v) fetal bovine serum (ATCC), 100 μg of penicillin and streptomycin per ml (Sigma/Aldrich) and grown at 37° C. in the presence of 5% CO2.
Wild-type Madin-Darby canine kidney cells type II (MDCKII/wt) and stable MDCKII transfectants overexpressing hMRP1 (MDCKIIMRP1 cells), hMRP2 (MDCKII-MRP2 cells), hPgp (MDCKII-PGP cells) and hBCRP or mBcrpl (MDCKII-BCRP cells) (all are available from SOLVO Biotechnologies). The MDCKII cell lines were cultured in Dulbecco's modified Eagle's medium (with high glucose and glutamine concentrations, ATCC) supplemented with 10% FBS (ATCC), 1% nonessential amino acids, 100 μg of penicillin and streptomycin per ml (all from Sigma/Aldrich). Cells were incubated at 37° C. in 5% CO2 at 95% humidity and were harvested via trypsinization at 80 to 90% confluence (about 4 days of growth). Studies were performed between the cell passages 6 to 20 from the initial stock.
For the transport assay, wild type and transfected cells were seeded on microporous polycarbonate membrane filters (0.33 cm2 growth area and 0.4-μm pore size Transwell; Costar, Corning, N.Y.) at a density of 1×105 cells/well in 0.2 ml of complete medium. Following seeding, medium was changed daily, and transport studies were performed 4 or 5 days after seeding. Fresh media were added to the cells 1 h before the initiation of the experiment, and transepithelial electrical resistance values were measured with a Millicell-ERS (electrical resistance system) (Millipore, Billerica, Mass.). Bidirectional transport studies were performed at 37° C. in air. Before each experiment, the confluent cell monolayers on Transwell inserts were washed and equilibrated for 30 min with transport media [Hanks' balanced salt solution containing 10 mM HEPES and 10 mM glucose, pH 7.4]. The experiment was initiated by adding a solution containing the 5 μM of Fluo-8TM AM or 2 μM of Rhod-4TM AM in transport media to either the apical (for A-to-B transport) or basolateral (for B-to-A transport) compartment. When applicable, inhibitors were present in the transport medium of the donor side from the pre-incubation period throughout the permeability study. At 30, 60, 120, and 240 min, the sample aliquots (50 μl) of receiving solutions were withdrawn from the basolateral side (for A-to-B transport) or from the apical side (for B-to-A transport) and replaced immediately with an equal amount of fresh transport medium except at the 240-min time point (the end of the incubation). The cell integrity was monitored before and after the transport study to check for leaks in the epithelium by transepithelial electric resistance [Yee, Pharmaceutical Res. 14:763-766 (1997)].
Fluorescence intensity of Fluo-8TM or Rhod-4TM was measured using an OPTIMA FluoStar multiplate fluorimeter (BMG Labtech Inc., NC; equipped with 490 and 550 nm excitation filter and 520 and 570 nm emission filters) or SynergyTM Mx multi-mode microplate reader (BioTek Instruments Inc., VT; using 490 and 530 nm excitation and 520 and 555 nm emission settings). Apparent permeability (Papp) was calculated in the apical-to-basolateral direction (Papp A-->B) and in the basolateral-to-apical direction (Papp B→A) as described previously [Polli et al., J Pharmacol Exp Ther. 299:620-628 (2001)]. Briefly, Papp=(1/(A×C0))×(dQ/dt), where A is the surface area of permeable support, C0 is the initial concentration in the donor compartment, and dQ/dt is the rate of transfer of compound into the acceptor compartment. This ratio of PappB→A/PappA→B was estimated to evaluate all three transporter-mediated directional effluxes. The amount of Fluo-8TM or Rhod-4TM exported was calculated using a calibration curve made with the free dyes. All the data are expressed as mean±S.D. of three individual incubations. Student's two-sided t test was used to evaluate differences between two sets of data. P values<0.05 were considered statistically significant.
In wild type MDCKII and LLC-PK1 cells, Fluo-8TM and Rhod-4TM dye(s) export to the apical and basolateral side should be similar. Dye export should be detected in the transfectants of the epithelial polarized cells, and the nature of this export is dependent on the membrane localization of the particular transporter. When the transporter is localized to the lateral plasma membrane (MRP1), then several-fold increased dye(s) export to the basolateral side is expected. When the transporter is localized to the apical plasma membrane (MRP2 and MDR1), then several-fold increased dye(s) export to the apical side is expected. The increased export of the dye should be blocked in the presence of the corresponding specific inhibitor.
Many obvious variations will no doubt be suggested to those of ordinary skill in the art in light of the above detailed description and examples of the present invention. All such variations are fully embraced by the scope and spirit of the invention as more particularly defined in the claims that now follow.

## Claims

1. A process for determining drug resistance of cells of interest, said process comprising the steps of:
(A) providing:
(i) a clinical or biological sample comprising cells;
(ii) at least one xanthene compound that is transportable across a cell membrane by membrane transporters multidrug resistance 1 (MDR1), multidrug resistance associated protein 1 (MRP) and breast cancer resistant protein (BCRP); and
(iii) one or more membrane transporter inhibitors;

(B) contacting cells from a first portion of said clinical or biological sample with said at least one xanthene compound;
(C) contacting cells from a second portion of said clinical or biological sample (i) with said at least one xanthene compound and said one or more inhibitors;
(D) measuring fluorescent signals generated in step (B) and step (C); and
(E) comparing the fluorescent signals measured in step (D) to determine elevated activities of said MDR1, MRP and BCRP, or a combination thereof, thereby determining the drug resistance of said cells of interest,

wherein said at least one xanthene compound has the structure



wherein
R1-R6 are independently H, halogen, carboxy, alkoxy, aryloxy, thiol, alkylthiol, arylthiol, azido, nitro, nitroso, cyano, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl, or heteroaryl; or alkyl, or alkoxy, optionally substituted one or more times by halogen, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl or heteroaryl,
heteroatom Y is independently selected from O, S, Se, NR9 and CR.10R11,
X is independently selected from OR12, NR12R13 and Z is independently selected from O and NR16R17, where each R9, R10, R11, R12, R13, R16 and R17 is independently H, an alkyl having 1-12 carbons, carboxyalkyl, substituted or non-substituted amino alkyl or alkylsulfonate,

T and U are independently hydrogen, alkyl having 1-12 carbons, alkoxy having 1-12 carbons, aryloxy, amino, halogen, cyano, carboxy, carboxyalkyl, acetoxymethylcarbonyl, carbonyl, sulfonyl, phosphonyl, boronic acid, aryl, and heteroaryl, and
V and W are independently selected from OR14, SR15 or NR12R13, such that at least one of V or W, in combination with NR7R8, forms a metal chelator, where each R7, R8, and R12-R15 are independently H, an alkyl having 1-12 carbons, carboxyalkyl, alkoxy or aryloxy.

2. The process of claim 1, wherein said step (D) measures cellular uptake of said at least one xanthene compound.

3. The process of claim 1, wherein in said step (A), the one or more inhibitors are provided in an amount sufficient to substantially prevent transport of the at least one xanthene compound across a cell membrane by one or more of the membrane transporters MDR1, MRP and BCRP.

4. The process of claim 1, wherein said at least one xanthene compound has the structure



wherein
A and B are independently hydrogen, alkyl, cycloalkyl, or aryl; or A and B taken in combination are cycloalkyl or aryl;
j, k, m and n are independently hydrogen, halogen, carboxy, alkoxy, aryloxy, thiol, alkylthiol, arylthiol, azido, nitro, nitroso, cyano, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl, or heteroaryl; or alkyl, or alkoxy that is itself optionally substituted one or more times by halogen, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl or heteroaryl; and
each R5 is independently hydrogen, alkyl having 1-9 carbons, acetoxymethyl, or a biologically compatible salt.

5. The process of claim 4, wherein said xanthene compound has the structure

6. The process of claim 1, wherein said one or more membrane transporter inhibitors comprise a general inhibitor.

7. The process of claim 6, wherein said general inhibitor is cyclosporin A, biricodar (VX-710), tariquidar (XR9576), a plant polyphenol, curcumin, tRA98006 or imatinib mesylate.

8. The process of claim 6, wherein the general inhibitor is cyclosporin A.

9. The process of claim 1, wherein in said step (A), there is further provided at least one viability dye.

10. The process of claim 9, wherein said at least one viability dye is propidium iodide, 7-amino-actinomycin D (7-AAD), DRAQ-7, Nuclear ID Red, Nuclear ID Green, SYTOX Green, SYTOX Orange, SYTOX Blue, YOYO, TOTO or TO-PRO, or a compound having the structure:



wherein
X comprises CR11R12, NR11, O, S or Se where R11 and R12 independently comprise hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkyl group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R11 and R12 form a 5 or 6 membered ring;
n can be 0, 1, 2 or 3;
Y is —CR9═CR10—;
m and p can have values of 0 or 1 and m+p=1;
at least one of R1, R2, R3, R4, R5, R11 or R12 comprises Q(1) or at least one of R6, R7, R8, R9 or R10 comprises Q(2);
Q(1) comprises a sulfonate (SO3−), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PSO−ER13), a phosphate diester (PO2ER13ER14), a alkyl phosphonate (PO3=) a alkyl phosphonate monoester (PO2−ER13) a alkyl phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S and the structures are as described previously;
Q is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof and wherein when Q is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
Q(2) comprises an alkyl, aminoalkyl, substituted aminoalkyl, a benzyl, a substituted benzyl, a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S and the structures are as described previously;
Q(2) is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof and wherein when Q′ is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
R13, R14, R15, R19 and R20 can be hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together R13 and R14 form a five or six membered ring;
R13 and R14 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR25), a thioether linkage (—SR25), or an amine linkage (—NR25R26 or —N+R25R26R27), and wherein R25, R26 and R27 independently comprise hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five or six membered ring, and wherein any of R25, R26 or R27 may further comprise said heteroatom containing side chain;
R16, R17, R18 and the remaining R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11 and R12 can independently be hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear; substituted or unsubstituted, or when taken together, R2 and R3, R3 and R4, R4 and R5, R6 and R7, and R7 and R8 may form a 5 or 6 membered ring; or when taken together R1 and R16, R11 and R16, R16 and R17, R17 and R18, and R18 and R9 may form a 5 or 6 membered ring;
Z comprises a carboxyl group (CO2—), a carbonate ester (COER13), a sulfonate (SO3−), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) where E can
Z is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof;

any of R1, R2, R3, R4, R5, R6, R7, R8, R9 or R10, R11 or R12 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR25), a thioether linkage (—SR25), Or an amine linkage (—NR25R26 or —N+R25R26R27);
R25, R26 and R27 independently comprise hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five or six membered ring, and wherein any of R25, R26 or R27 may further comprise said heteroatom containing side chain; and
R8 may comprise a substituted group capable of forming symmetric or asymmetric polymeric dye.

11. The process of claim 9, wherein the cells are contacted with said at least one viability dye before said contacting steps (B) and (C).

12. The process of claim 11, wherein said at least one non-xanthene dye is a nuclear identification stain, calcein AM, Pheophorbide A, Chloromethylfluorescein diacetate (CMFDA), Hoechst 33342, BODIPY-Prazozin, Fura-2 AM, monobromobimane, BODIPY-Taxol or 3,3′-diethyloxacarbocyanine iodide (DIOC2(3)].

13. The process of claim 9, wherein said at least one viability dye is propidium iodide.

14. The process of claim 9, wherein the cells are contacted with said at least one viability dye during said contacting steps (B) and (C).

15. The process of claim 9, wherein the cells are contacted with said at least one viability dye after said contacting steps (B) and (C).

16. The process of claim 1, wherein in step (A), there is further provided at least one non-xanthene dye in step (B) and step (C).

17. The process of claim 1, wherein in said step (D), measuring is carried out by a means comprising a flow cytometer, a microplate reader, a microscope, a fluorimeter, a high content screening platform, a high-content cell analysis system or a laser-scanning cytometer.

18. The process of claim 1, wherein in said step (A), there is provided a quenching reagent for minimizing extracellular fluorescent signal from said at least one xanthene compound.

19. The process of claim 18, wherein said quenching reagent comprises Evans Blue, o-tolidine, Trypan Blue, Trypan Red or Brilliant Black.

20. The process of claim 1, wherein in step (A), there is provided one or more surfactants for increasing cellular uptake of said at least one xanthene compound, and wherein said one or more surfactants are used in said contacting steps (B) and (C).

21. The process of claim 20, wherein said one or more surfactants comprise Pluronic 127, L61, L81, P85 or F108.

22. The process of claim 1, wherein said one or more membrane transporter inhibitors comprise a specific inhibitor.

23. The process of claim 22, wherein said specific inhibitor is valspodar (PSC833), verapamil, vanadate, PAK-104P, MK-571, FTC, Ko134, Elacridar (GF 120918), novobiocin, probenecid, BIB-E, disulfuram, indomethacin, furocemide, Penicillin G, sulfinpirazole, laniquidar (R101933), zosuquidar (LY335979), ontogeny (ONT-093), isothiocyanates, phytoestrogens, TAG-139, flavenoids, MS-209, NSAIDs, mitotane (NSC-38271), PK11195, cyclosporine D, anthranilamide, pipecolinate, quinoline, OC-144-093, diallyl sulfide, amooranin, agosterol A, siRNA, rifampicin, amiodarone, quinidine, quinine, nifedipine, dexniguldipin, LY455776, V-104, tricyclic izoxazoles, pluronic L61, or fumitremorgin C.

24. The process of claim 22, wherein said one or more membrane transporter inhibitors comprise more than one specific inhibitors.

25. The process of claim 22, wherein said specific inhibitor is verapamil, probenecid or novobiocin.

26. The process of claim 1, wherein said one or more membrane transporter inhibitors comprise both a general inhibitor and a specific inhibitor.

27. A process for determining drug resistance of cells of interest, said process comprising the steps of:
(A) providing:
(i) at least three portions of a clinical or biological sample comprising cells;
(ii) at least one xanthene compound that is transportable across a cell membrane by membrane transporters MDR1, MRP and BCRP; and
(iii) one or more membrane transporter inhibitors;

(B) contacting cells from a first portion of said clinical or biological sample with said at least one xanthene compound under conditions sufficient to inhibit efflux of said at least one xanthene compound from said cells;
(C) contacting cells from a second portion of said clinical or biological sample with said at least one xanthene compound under conditions sufficient to permit efflux of said at least one xanthene compound from said cells;
(D) contacting cells from a third portion of said clinical or biological sample with said at least one xanthene compound and said one or more inhibitors;
(E) measuring fluorescent signals generated in steps (B), (C) and (D); and
(F) comparing the fluorescent signals measured in step (E) to determine elevated activities of said MDR1, MRP, BCRP, or a combination thereof, thereby determining the drug resistance of said cells of interest,

wherein said at least one xanthene compound has the structure



wherein
R1-R6 are independently H, halogen, carboxy, alkoxy, aryloxy, thiol, alkylthiol, arylthiol, azido, nitro, nitroso, cyano, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl, or heteroaryl; or alkyl, or alkoxy, optionally substituted one or more times by halogen, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl or heteroaryl,
heteroatom Y is independently selected from O, S, Se, NR9 and CR.10R11,
X is independently selected from OR12, NR12R13 and Z is independently selected from O and NR16R17, where each R9, R10, R11R12, R13, R16 and R17 is independently H, an alkyl having 1-12 carbons, carboxyalkyl, substituted or non-substituted amino alkyl or alkylsulfonate,
T and U are independently hydrogen, alkyl having 1-12 carbons, alkoxy having 1-12 carbons, aryloxy, amino, halogen, cyano, carboxy, carboxyalkyl, acetoxymethylcarbonyl, carbonyl, sulfonyl, phosphonyl, boronic acid, aryl, and heteroaryl, and
V and W are independently selected from OR14, SR15 or NR12R13, such that at least one of V or W, in combination with NR7R8, forms a metal chelator, where each R7, R8, and R12-R15 are independently H, an alkyl having 1-12 carbons, carboxyalkyl, alkoxy or aryloxy.

28. The process of claim 27, wherein in said step (A), the one or more inhibitors are provided in an amount sufficient to substantially prevent transport of the at least one xanthene compound (II) across a cell membrane by one or more of the membrane transporters MDR1, MRP and BCRP.

29. The process of claim 27, wherein step (B), contacting is carried out under conditions wherein temperature is lowered to inhibit efflux.

30. The process of claim 29, wherein said lowered temperature is in a range from about 4° C. to about 10° C.

31. The process of claim 27, wherein in step (C), contacting is carried out under said conditions wherein temperature is raised to permit efflux.

32. The process of claim 31, wherein said raised temperature is from about 15° C. to about 37° C.

33. The process of claim 27, wherein said one or more membrane transporter inhibitors comprise a general inhibitor.

34. The process of claim 33, wherein said general inhibitor is cyclosporin A, biricodar (VX-710), tariquidar (XR9576), a plant polyphenol, curcumin, tRA98006 or imatinib mesylate.

35. The process of claim 27, wherein said at least one xanthene compound has the structure



wherein
A and B are independently hydrogen, alkyl, cycloalkyl, or aryl; or A and B taken in combination are cycloalkyl or aryl;
j, k, m and n are independently hydrogen, halogen, carboxy, alkoxy, aryloxy, thiol, alkylthiol, arylthiol, azido, nitro, nitroso, cyano, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl, or heteroaryl; or alkyl, or alkoxy that is itself optionally substituted one or more times by halogen, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl or heteroaryl; and
each R5 is independently hydrogen, alkyl having 1-9 carbons, acetoxymethyl, or a biologically compatible salt.

36. The process of claim 35, wherein said at least one xanthene compound has the structure

37. The process of claim 27, wherein said step (A), there is further provided at least one viability dye.

38. The process of claim 37, wherein said at least one viability dye is propidium iodide, 7-amino-actinomycin D (7-AAD), DRAQ-7, Nuclear ID Red, Nuclear ID Green, SYTOX Green, SYTOX Orange, SYTOX Blue, YOYO, TOTO or TO-PRO, or a compound having the structure:



wherein
X comprises CR11R12, NR11, O, S or Se where R11 and R12 independently comprise hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkyl group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R11 and R12 form a 5 or 6 membered ring;
n can be 0, 1, 2 or 3;
Y is —CR9═CR10—
m and p can have values of 0 or 1 and m+p=1;
at least one of R1, R2, R3, R4, R5, R11 or R12 comprises Q(1) or at least one of R6, R7, R8, R9 or R10 comprises Q(2);
Q(1) comprises a sulfonate (SO3−), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a alkyl phosphonate (PO3=) a alkyl phosphonate monoester (PO2−ER13) a alkyl phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S and the structures are as described previously;
Q is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof and wherein when Q is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;

Q(2) comprises an alkyl, aminoalkyl, substituted aminoalkyl, a benzyl, a substituted benzyl, a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) wherein any of E can independently comprise O or S and the structures are as described previously;
Q(2) is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof and wherein when Q′ is a sulfonamide, it does not comprise a terminal reactive group or a linker joining the dye to a target molecule;
R13, R14, R15, R19 and R20 can be hydrogen, a halogen, an amino group, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together R13 and R14 form a five or six membered ring;
R13 and R14 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR25), a thioether linkage (—SR25), or an amine linkage (—NR25R26 or —N+R25R26R27), and wherein R25, R26 and R27 independently comprise hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five or six membered ring, and wherein any of R25, R26 or R27 may further comprise said heteroatom containing side chain;

R16, R17, R18 and the remaining R1, R2, R3, R4, R5, R6, R7, R8, R9, R10, R11 and R12 can independently be hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group wherein said alkoxy group is saturated or unsaturated, branched or linear; substituted or unsubstituted, or when taken together, R2 and R3, R3 and R4, R4 and R5, R6 and R7, and R7 and R8 may form a 5 or 6 membered ring; or when taken together R1 and R16, R11 and R16, R16 and R17, R17 and R18, and R18 and R9 may form a 5 or 6 membered ring;
Z comprises a carboxyl group (CO2−), a carbonate ester (COER13), a sulfonate (SO3−), a sulfonate ester (SO2ER13), a sulfoxide (SOR13), a sulfone (SO2CR13R14R15), a sulfonamide (SO2NR13R14), a phosphate (PO4=), a phosphate monoester (PO3−ER13), a phosphate diester (PO2ER13ER14), a phosphonate (PO3=) a phosphonate monoester (PO2−ER13) a phosphonate diester (POER13ER14), a thiophosphate (PSO3=), a thiophosphate monoester (PSO2−ER13) a thiophosphate diester (PSOER13ER14), a thiophosphonate (PSO2=), a thiophosphonate monoester (PSO−ER13) a thiophosphonate diester (PSER13ER14), a phosphonamide (PONR13R14NR19R20), its thioanalogue (PSNR13R14NR19R20), a phosphoramide (PONR13R14NR15NR19R20), its thioanalogue (PSNR13R14NR15NR19R20), a phosphoramidite (PO2R19NR13R14) or its thioanalogue (POSR19NR13R14) where E can be independently O or S and the structures are as described previously;
Z is attached directly, or indirectly through a linker arm comprising carbon, sulfur, oxygen, nitrogen, and any combinations thereof and wherein said linker arm may be saturated or unsaturated, linear or branched, substituted or unsubstituted and any combinations thereof;
any of R1, R2, R3, R4, R5, R6, R7, R8, R9 or R10, R11 or R12 may further comprise a heteroatom containing side chain wherein said side chain is joined to the R group by a linkage which comprises an ether linkage (—OR25), a thioether linkage (—SR25), Or an amine linkage (—NR25R26 or —NR25R26R27);
R25, R26 and R27 independently comprise hydrogen, Z, an alkyl group wherein said alkyl group is saturated or unsaturated, linear or branched, substituted or unsubstituted, an alkoxy group that is saturated or unsaturated, branched or linear, substituted or unsubstituted, or when taken together, R25 and R26, and R26 and R27 independently comprise a five or six membered ring, and wherein any of R25, R26 or R27 may further comprise said heteroatom containing side chain; and
R8 may comprise a substituted group capable of forming symmetric or asymmetric polymeric dye.

39. The process of claim 37, wherein the cells are contacted with said at least one viability dye before contacting steps (B), (C) and (D).

40. The process of claim 37, wherein the cells are contacted with said at least one viability dye during contacting steps (B), (C) and (D).

41. The process of claim 37, wherein the cells are contacted with said at least one viability dye after contacting steps (B), (C) and (D).

42. The process of claim 27, wherein in step (A), there is further provided at least one non-xanthene dye in step (B), step (C) and step (D).

43. The process of claim 42, wherein said at least one non-xanthene dye is a nuclear identification stain, calcein AM, Pheophorbide A, Chloromethylfluorescein diacetate (CMFDA), Hoechst 33342, BODIPY-Prazozin, Fura-2 AM, monobromobimane, BODIPY-Taxol or 3,3′-diethyloxacarbocyanine iodide (DIOC2(3)].

44. The process of claim 27, wherein in step (E), measuring is carried out by a means comprising a flow cytometer, a microplate reader, a microscope, a fluorimeter, a high content screening platform, a high-content cell analysis system or a laser-scanning cytometer.

45. The process of claim 27, wherein said step (A), wherein in said step (A), there is provided a quenching reagent for minimizing extracellular fluorescent signal from said at least one xanthene compound.

46. The process of claim 45, wherein said quenching reagent comprises Evans Blue, o-tolidine, Trypan Blue, Trypan Red or Brilliant Black.

47. The process of claim 27, wherein in step (A), there is provided one or more surfactants for increasing cellular uptake of said at least one xanthene compound, and wherein said one or more surfactants are used in said contacting steps (B), (C) and (D).

48. The process of claim 47, wherein said one or more surfactants comprise Pluronic 127, L61, L81, P85 or F108.

49. The process of claim 27, wherein said one or more membrane transporter inhibitors comprise a specific inhibitor.

50. The process of claim 49, wherein said one or more membrane transporter inhibitors comprise more than one specific inhibitor.

51. The process of claim 49, wherein said specific inhibitor is valspodar (PSC833), verapamil, vanadate, PAK-104P, MK-571, FTC, Ko134, Elacridar (GF 120918), novobiocin, probenecid, BIB-E, disulfuram, indomethacin, furocemide, Penicillin G, sulfinpirazole, laniquidar (R101933), zosuquidar (LY335979), ontogeny (ONT-093), isothiocyanates, phytoestrogens, TAG-139, flavenoids, MS-209, NSAIDs, mitotane (NSC-38271), PK11195, cyclosporine D, anthranilamide, pipecolinate, quinoline, OC-144-093, diallyl sulfide, amooranin, agosterol A, siRNA, rifampicin, amiodarone, quinidine, quinine, nifedipine, dexniguldipin, LY455776, V-104, tricyclic izoxazoles, pluronic L61, or fumitremorgin C.

52. The process of claim 27, wherein said one or more membrane transporter inhibitors comprise both a general inhibitor and a specific inhibitor.

53. A process for determining the effect of a test compound on transport across a cell membrane by the membrane transporters MDR1, MRP and BCRP, said process comprising the steps of:
(A) providing:
(i) a clinical or biological sample comprising cells;
(ii) at least one xanthene compound that is transportable across a cell membrane by membrane transporters MDR1, MRP and BCRP; and
(iii) one or more test compounds;

(B) contacting cells from a first portion of said clinical or biological sample with said at least one xanthene compound;
(C) contacting cells from a second portion of said clinical or biological sample with said at least one xanthene compound and said one or more test compounds;
(D) measuring fluorescent signals generated in step (B) and step (C); and
(E) comparing the fluorescent signals measured in step (D) to determine elevated activities of said MDR1, MRP and BCRP, or a combination thereof, thereby determining the effect of said one or more test compounds on cell membrane transport by said membrane transporters,

wherein said at least one xanthene compound has the structure



wherein
R1-R6 are independently H, halogen, carboxy, alkoxy, aryloxy, thiol, alkylthiol, arylthiol, azido, nitro, nitroso, cyano, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl, or heteroaryl; or alkyl, or alkoxy, optionally substituted one or more times by halogen, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl or heteroaryl,
heteroatom Y is independently selected from O, S, Se, NR9 and CR.10R11,
X is independently selected from OR12, NR12R13 and Z is independently selected from O and NR16R17, where each R9, R10, R11R12, R13, R16 and R17 is independently H, an alkyl having 1-12 carbons, carboxyalkyl, substituted or non-substituted amino alkyl or alkylsulfonate,
T and U are independently hydrogen, alkyl having 1-12 carbons, alkoxy having 1-12 carbons, aryloxy, amino, halogen, cyano, carboxy, carboxyalkyl, acetoxymethylcarbonyl, carbonyl, sulfonyl, phosphonyl, boronic acid, aryl, and heteroaryl, and
V and W are independently selected from OR14, SR15 or NR12R13, such that at least one of V or W, in combination with NR7R8, forms a metal chelator, where each R7, R8, and R12-R15 are independently H, an alkyl having 1-12 carbons, carboxyalkyl, alkoxy or aryloxy.

54. A process for determining the effect of a test compound on transport across a cell membrane by the membrane transporters MDR1, MRP and/or BCRP, said process comprising the steps of:
(A) providing:
(i) at least three portions of a clinical or biological sample comprising cells;
(ii) at least one xanthene compound that is transportable across a cell membrane by membrane transporters MDR1, MRP and BCRP; and
(iii) one or more membrane transporter inhibitors;

(B) contacting cells from a first portion of said clinical or biological sample with said at least one xanthene compound under conditions sufficient to inhibit efflux of said at least one xanthene compound from said cells;
(C) contacting cells from a second portion of said clinical or biological sample with said at least one xanthene compound under conditions sufficient to permit efflux of said at least one xanthene compound from said cells;
(D) contacting cells from a third portion of said clinical or biological sample with said at least one xanthene compound (II) and said one or more inhibitors;
(E) measuring fluorescent signals generated in steps (B), (C) and D; and
(F) comparing the fluorescent signals measured in step (D) to determine elevated activities of said MDR1, MRP and BCRP, or a combination thereof, thereby determining the drug resistance of said cells of interest,

wherein said at least one xanthene compound has the structure



wherein
R1-R6 are independently H, halogen, carboxy, alkoxy, aryloxy, thiol, alkylthiol, arylthiol, azido, nitro, nitroso, cyano, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl, or heteroaryl; or alkyl, or alkoxy, optionally substituted one or more times by halogen, amino, hydroxy, phosphonyl, sulfonyl, carbonyl, boronic acid, aryl or heteroaryl,
heteroatom Y is independently selected from O, S, Se, NR9 and CR.10R11,
X is independently selected from OR12, NR12R13 and Z is independently selected from O and NR16R17, where each R9, R10, R11, R12, R13, R16 and R17 is independently H, an alkyl having 1-12 carbons, carboxyalkyl, substituted or non-substituted amino alkyl or alkylsulfonate,
T and U are independently hydrogen, alkyl having 1-12 carbons, alkoxy having 1-12 carbons, aryloxy, amino, halogen, cyano, carboxy, carboxyalkyl, acetoxymethylcarbonyl, carbonyl, sulfonyl, phosphonyl, boronic acid, aryl, and heteroaryl, and
V and W are independently selected from OR14, SR15 or NR12R13, such that at least one of V or W, in combination with NR7R8, forms a metal chelator, where each R7, R8, and R12-R15 are independently H, an alkyl having 1-12 carbons, carboxyalkyl, alkoxy or aryloxy.