Processes and kits for determining multi-drug resistance of cells

1. 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 multidrug resistance associated protein 1 (MDR1), multidrug resistance protein (MRP) and breast cancer resistance protein (BCRP), said 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 selected from

a.

wherein R 1 -R 6 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, NR 9 and CR 10 R 11 ,

wherein X is independently selected from OR 12 , NR 12 R 13 and Z is independently selected from O and NR 16 R 17 , where each R 9 , R 10 , R 11 , R 12 , R 13 , R 16 and R 17 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 OR 14 , SR 15 or NR 12 R 13 , such that at least one of V or W, in combination with NR 7 R 8 , forms a metal chelator, where each R 7 , R 8 , and R 12 -R 15 are independently H, an alkyl having 1-12 carbons, carboxyalkyl, alkoxy or aryloxy; and

b.

wherein A and B are independently hydrogen, alkyl, cycloalkyl, or aryl; or A and B taken in combination are cycloalkyl or aryl;

wherein R 3 , R 4 , 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 R 5 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;

(ii) one or more membrane transporter inhibitors; and

(iii) instructions therefor.

2. The kit of claim 1 , further comprising a buffer (iv).

3. The kit of claim 1 , wherein said kit measures cellular uptake or efflux of said at least one xanthene compound (i).

4. The kit of claim 1 , wherein said at least one or more inhibitors (ii) are provided in an amount sufficient to substantially inhibit transport of the at least one xanthene compound (i) across a cell membrane by one or more of the membrane transporters MDR1, MRP and BCRP.

5. The kit of claim 1 , wherein said at least one xanthene compound ((i)b) has the structure

6. The kit of claim 1 , wherein said one or more inhibitors (ii) comprise general inhibitors, specific inhibitors or a combination of general inhibitors and specific inhibitors.

7. The kit of claim 6 , wherein said 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.

8. The kit of claim 6 , wherein said specific inhibitors comprise valspodar (PSC833), verapamil, vanadate, PAK-104P, MK-571, FTC, Ko134, Elacridar (GF 120918), novobiocin, probenecid, BIB-E, disulfiram, 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.

9. The kit of claim 1 , further comprising at least one viability dye (iv).

10. The kit of claim 9 , wherein said at least one 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 CR 11 R 12 , NR 11 , O, S or Se where R 11 and R 12 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, R 11 and R 12 form a 5 or 6 membered ring;

wherein n can be 0, 1, 2 or 3;

wherein Y is —CR 9 ═CR 10 —;

wherein m and p can have values of 0 or 1 and m+p=1;

wherein at least one of R 1 , R 2 , R 3 , R 4 , R 5 , R 11 or R 12 comprises Q(1) or at least one of R 6 , R 7 , R 8 , R 9 or R 10 comprises Q(2);

wherein Q(1) comprises a sulfonate (SO 3 − ), a sulfonate ester (SO 2 ER 13 ), a sulfoxide (SOR 13 ), a sulfone (SO 2 CR 13 R 14 R 15 ), a sulfonamide (SO 2 NR 13 R 14 ), a phosphate (PO 4 = ), a phosphate monoester (PO 3 − ER 13 ), a phosphate diester (PO 2 ER 13 ER 14 ), a alkyl phosphonate (PO 3 = ) a alkyl phosphonate monoester (PO 2 − ER 13 ) a alkyl phosphonate diester (POER 13 ER 4 ), a thiophosphate (PSO 3 = ), a thiophosphate monoester (PSO 2 − ER 13 ) a thiophosphate diester (PSOER 13 ER 14 ), a thiophosphonate (PSO 2 = ), a thiophosphonate monoester (PSO − ER 13 ) a thiophosphonate diester (PSER 13 ER 14 ), a phosphonamide (PONR 13 R 14 NR 19 R 20 ), its thioanalogue (PSNR 13 R 14 NR 19 R 20 ), a phosphoramide (PONR 13 R 14 NR 15 NR 19 R 20 ), its thioanalogue (PSNR 13 R 14 NR 15 NR 19 R 20 ), a phosphoramidite (PO 2 R 19 NR 13 R 14 ) or its thioanalogue (POSR 19 NR 13 R 14 ) 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 (SOR 13 ), a sulfone (SO 2 CR 13 R 14 R 15 ), a sulfonamide (SO 2 NR 13 R 14 ), a phosphate (PO 4 = ), a phosphate monoester (PO 3 − ER 3 ), a phosphate diester (PO 2 ER 13 ER 14 ), a phosphonate (PO 3 = ) a phosphonate monoester (PO 2 − ER 13 ) a phosphonate diester (POER 13 ER 14 ), a thiophosphate (PSO 3 = ), a thiophosphate monoester (PSO 2 − ER 13 ) a thiophosphate diester (PSOER 13 ER 14 ), a thiophosphonate (PSO 2 = ), a thiophosphonate monoester (PSO − ER 13 ) a thiophosphonate diester (PSER 13 ER 14 ), a phosphonamide (PONR 13 R 14 NR 19 R 20 ), its thioanalogue (PSNR 13 R 14 NR 19 R 20 ), a phosphoramide (PONR 13 R 14 NR 15 NR 19 R 20 ), its thioanalogue (PSNR 13 R 14 NR 15 NR 19 R 20 ), a phosphoramidite (PO 2 R 19 NR 13 R 14 ) or its thioanalogue (POSR 19 NR 13 R 14 ) 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 R 13 , R 14 , R 15 , R 19 and R 20 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 R 13 and R 14 form a five or six membered ring;

wherein R 13 and R 14 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 (—OR 25 ), a thioether linkage (—SR 2 ), or an amine linkage (—NR 25 R 26 or —N + R 25 R 26 R 27 ), and wherein R 25 , R 26 and R 27 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, R 25 and R 26 , and R 26 and R 27 independently comprise a five or six membered ring, and wherein any of R 25 , R 26 or R 27 may further comprise said heteroatom containing side chain;

wherein R 16 , R 17 , R 18 and the remaining R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , R 9 , R 10 , R 11 and R 12 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, R 2 and R 3 , R 3 and R 4 , R 4 and R 5 , R 6 and R 7 , and R 7 and R 8 may form a 5 or 6 membered ring; or when taken together R 1 and R 16 , R 11 and R 16 , R 16 and R 17 , R 17 and R 18 , and R 18 and R 9 may form a 5 or 6 membered ring;

wherein Z comprises a carboxyl group (CO 2 − ), a carbonate ester (COER 13 ), a sulfonate (SO 3 − ), a sulfonate ester (SO 2 ER 13 ), a sulfoxide (SOR 13 ), a sulfone (SO 2 CR 13 R 14 R 15 ), a sulfonamide (SO 2 NR 13 R 14 ), a phosphate (PO 4 = ), a phosphate monoester (PO 3 − ER 13 ), a phosphate diester (PO 2 ER 13 ER 14 ), a phosphonate (PO 3 = ) a phosphonate monoester (PO 2 − ER 13 ) a phosphonate diester (POER 13 ER 14 ), a thiophosphate (PSO 3 = ), a thiophosphate monoester (PSO 2 − ER 13 ) a thiophosphate diester (PSOER 13 ER 14 ), a thiophosphonate (PSO 2 = ), a thiophosphonate monoester (PSO − ER 13 ) a thiophosphonate diester (PSER 13 ER 14 ), a phosphonamide (PONR 13 R 14 NR 19 R 20 ), its thioanalogue (PSNR 13 R 14 NR 19 R 20 ), a phosphoramide (PONR 13 R 14 NR 15 NR 19 R 20 ), its thioanalogue (PSNR 13 R 14 NR 15 NR 19 R 20 ), a phosphoramidite (PO 2 R 19 NR 13 R 14 ) or its thioanalogue (POSR 19 NR 13 R 14 ) 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 R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , R 9 or R 10 , R 11 or R 12 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 (—OR 25 ), a thioether linkage (—SR 25 ), or an amine linkage (—NR 25 R 26 or —N + R 25 R 26 R 27 );

wherein R 25 , R 26 and R 27 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, R 25 and R 26 , and R 26 and R 27 independently comprise a five or six membered ring, and wherein any of R 25 , R 26 or R 27 may further comprise said heteroatom containing side chain, and

wherein R 8 may comprise a substituted group capable of forming symmetric or asymmetric polymeric dye.

11. The kit of claim 1 , further comprising at least one non-xanthene dye (v).

12. The kit of claim 11 , wherein said at least one 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 (DIOC 2 (3)] or a dye from Table 2, and a combination of any of the foregoing.

13. The kit of claim 1 , further comprising a quenching reagent (vi) for minimizing extracellular fluorescent signal from said at least one xanthene compound (i).

14. The process of claim 13 , wherein said quenching reagent (vi) comprises Evans Blue, o-tolidine, Trypan Blue, Trypan Red or Brilliant Black, and a combination of the foregoing.

15. The kit of claim 1 , further comprising one or more surfactants (vii) for increasing cellular uptake of said at least one xanthene compound (i).

16. The kit of claim 15 , wherein said one or more surfactants (vii) comprise Pluronic 127, L61, L81, P85 or F108, and a combination of the foregoing.