Methods for assaying palmitoyl protein thioesterase 1 and tripeptidyl peptidase activity in dried blood spots for detection of neuronal ceroid lipofuscinoses in newborns
The present disclosure provides assays for lysosomal enzymes, specifically palmitoyl protein thioesterase 1 (PPT1) and tripeptidyl peptidase 1 (TPP1), using, for example, tandem mass spectrometry. The assays involve the detection of enzymatic products obtained through the action of the lysosomal enzymes on new enzyme substrates, and can be used for quantitative enzyme activity measurements. The assays for the enzymes utilize a minimum steps for sample work up and can be run in a simplex format or in a duplex format for the detection of neuronal ceroid lipofuscinoses, or in a multiplex format with other mass spectrometry-based assays for screening of neuronal ceroid lipofuscinoses and other lysosomal storage disorders.
1. A method for assaying for a lysosomal enzyme associated with a lysosomal storage disease, comprising:
(a) contacting a sample with an aqueous solution to provide a solution comprising one or more lysosomal enzymes;
(b) contacting the one or more lysosomal enzymes in solution with one or more lysosomal enzyme substrates, and incubating the substrates with the lysosomal enzymes for a time sufficient to provide a solution comprising one or more enzyme products for the one or more lysosomal enzymes present in the sample,
wherein the enzyme substrate comprises a compound of Formula (TPP1-S1) and/or Formula (PPT1-S1):
wherein in the compound of Formula (TPP1-S1),
P 3 is an achiral amino acid residue, a D-amino acid residue, or a L-amino acid residue;
P 2 is an amino acid residue selected from D-Nle, L-Nle, D-Pro, L-Pro, D-Ala, L-Ala, D-Phe, L-Phe, D-Tyr, L-Tyr, D-Trp, L-Trp, D-Ile, L-Ile, D-Val, L-Val, D-Thr, L-Thr, D-Glu, L-Glu, D-Ser, L-Ser, D-Leu, L-Leu, Gly, D-Gln, L-Gln, D-Lys, L-Lys, D-Asn, L-Asn, D-Asp, L-Asp, D-Arg, L-Arg, D-His, and L-His;
P 1 is an amino acid residue selected from D-Phe, L-Phe, D-Leu, L-Leu, D-Nle, L-Nle, D-Tyr, L-Tyr, D-Glu, L-Glu, D-Trp, L-Trp, D-Asp, L-Asp, D-Gln, L-Gln, D-Ala, L-Ala, D-Ser, L-Ser, D-Lys, L-Lys, D-Arg, L-Arg, D-Asn, L-Asn, D-His, L-His, D-Val, L-Val, D-Ile, L-Ile, D-Thr, L-Thr, Gly, D-Pro, and L-Pro;
wherein P 3 is located at a N-terminus of the P 3 -P 2 -P 1 moiety, P 1 is located at a C-terminus of the P 3 -P 2 -P 1 moiety;
G 1 is a first linker comprising 2-20 carbon atoms in which one or more carbon atoms may be replaced with a heteroatom selected from N, O, and S, and/or one or more of carbon atoms may be substituted with a C 1 -C 6 alkyl group, C 1 -C 6 haloalkyl, halo, or amino;
X A is a first linking functionality linking G 1 to G 2 selected from a bond, amide, thioamide, sulfonamide, ether, sulfide, ureido, thioureido, and ester;
G 2 is a second linker comprising 2-20 carbon atoms in which one or more carbon atoms may be replaced with a heteroatom selected from N, O, and S, and/or one or more of carbon atoms may be substituted with a C 1 -C 6 alkyl group or halogen; and
X B is a second linking functionality linking G 2 to Prot selected from a bond, NH, amide, thioamide, sulfonamide, ether, sulfide, ureido, thioureido, and ester; and
Prot is a protecting group that is capable of fragmenting by one dominant pathway at an efficiency of greater than 5% to provide a residual enzyme product fragment that is detectable by mass spectrometry; and
wherein in the compound of Formula (PPT1-S1),
R A is selected from a peptide, a polymer, a polysaccharide, an aromatic hydrocarbon group, and an aliphatic hydrocarbon group;
W is selected from H and NHCO—C 1 -C 6 alkyl; and
Y is a C 2 -C 19 alkylene; and
(c) determining the quantities of the one or more enzyme products.
2. The method of claim 1 , wherein X A is an amide.
3. The method of claim 1 , wherein X B is selected from NH and an amide.
4. The method of claim 1 , wherein P 3 is selected from D-Ala, L-Ala, D-Arg, L-Arg, D-Asn, L-Asn, D-Asp, L-Asp, D-Cys, L-Cys, D-Glu, L-Glu, D-Gln, L-Gln, Gly, D-His, L-His, D-Ile, L-Ile, D-Leu, L-Leu, D-Lys, L-Lys, D-Met, L-Met, D-Phe, L-Phe, D-Pro, L-Pro, D-Ser, L-Ser, D-Thr, L-Thr, D-Trp, L-Trp, D-Tyr, L-Tyr, D-Val, and L-Val.
5. The method of claim 1 , wherein P 2 is selected from D-Nle, L-Nle, D-Pro, L-Pro, D-Ala, L-Ala, D-Phe, L-Phe, D-Tyr, L-Tyr, D-Trp, L-Trp, D-Ile, L-Ile, D-Val, L-Val, D-Thr, L-Thr, D-Glu, L-Glu, D-Ser, L-Ser, D-Leu, L-Leu, Gly, D-Gln, L-Gln, D-Lys, and L-Lys.
6. The method of claim 1 , wherein P 1 is selected from D-Phe, L-Phe, D-Leu, L-Leu, D-Nle, L-Nle, D-Tyr, L-Tyr, D-Glu, L-Glu, D-Trp, L-Trp, D-Asp, L-Asp, D-Gln, L-Gln, D-Ala, L-Ala, D-Ser, L-Ser, D-Lys, and L-Lys.
7. The method of claim 1 , wherein
P 3 is an amino acid residue selected from L-Ala, L-Arg, L-Asn, L-Asp, L-Cys, L-Glu, L-Gln, Gly, L-His, L-Ile, L-Leu, L-Lys, L-Met, L-Phe, L-Pro, L-Ser, L-Thr, L-Trp, L-Tyr, and L-Val;
P 2 is an amino acid residue selected from L-Nle, L-Pro, L-Ala, L-Phe, and L-Tyr;
P 1 is an amino acid residue selected from L-Phe, L-Leu, L-Nle, and L-Tyr;
G 1 is (CH 2 ) q —Ar,
wherein Ar is selected from a C 5 -C 6 arylene and a C 2 -C 6 heteroarylene, each optionally substituted with 1, 2, 3, or 4 substituents each independently selected from C 1 -C 6 alkyl, C 1 -C 6 haloalkyl, halo, amino; and
q is an integer from 0 to 4;
X A is amide;
G 2 is (CH 2 ) p ,
wherein p is an integer from 3 to 20;
X B is selected from NH and amide; and
Prot is selected from C(O)OC 1 -C 6 alkyl, C 1 -C 6 alkoxy, C 1 -C 6 alkyl, di-C 1 -C 6 alkylamino, and C 1 -C 6 alkylamino.
8. The method of claim 1 , wherein
(a) the substrate of Formula (TPP1-S1) is a compound of Formula (TPP1-S2):
wherein
G 1 is a first linker comprising 2-20 carbon atoms in which one or more carbon atoms may be replaced with a heteroatom selected from N, O, and S, and/or one or more of carbon atoms may be substituted with a C 1 -C 6 alkyl group, C 1 -C 6 haloalkyl, halo, or amino;
X A is a first linking functionality linking G 1 to G 2 selected from a bond, amide, thioamide, sulfonamide, ether, sulfide, ureido, thioureido, and ester; and
G 2 is a second linker comprising 2-20 carbon atoms in which one or more carbon atoms may be replaced with a heteroatom selected from N, O, and S, and/or one or more of carbon atoms may be substituted with a C 1 -C 6 alkyl group or halogen, or
(b) wherein the substrate of Formula (TPP1-S1) is a compound of Formula (TPP1-S3):
Ala-Ala-Phe-NH-G 1 -X A —(CH 2 ) p —X B -Prot (TPP1-S3)
G 1 is a first linker comprising 2-20 carbon atoms in which one or more carbon atoms may be replaced with a heteroatom selected from N, O, and S, and/or one or more of carbon atoms may be substituted with a C 1 -C 6 alkyl group, C 1 -C 6 haloalkyl, halo, or amino;
X A is a first linking functionality linking G 1 to (CH 2 ) p selected from a bond, amide, thioamide, sulfonamide, ether, sulfide, ureido, thioureido, and ester;
X B is a second linking functionality linking (CH 2 ) p to Prot selected from a bond, NH, amide, thioamide, sulfonamide, ether, sulfide, ureido, thioureido, and ester;
Prot is a protecting group that is capable of fragmenting by one dominant pathway at an efficiency of greater than 5% to provide a residual enzyme product fragment that is detectable by mass spectrometry; and
p is an integer from 3 to 20, or
(c) wherein the substrate of Formula (TPP1-S1) is a compound of Formula (TPP1-S4):
wherein Ar is selected from a C 5 -C 6 arylene and a C 2 -C 6 heteroarylene, each optionally substituted with 1, 2, 3, or 4 substituents each independently selected from C 1 -C 6 alkyl, C 1 -C 6 haloalkyl, halo, amino;
R B is selected from H, C 1 -C 6 alkyl, and C 1 -C 6 haloalkyl;
R C is selected from C 1 -C 6 alkoxy, C 1 -C 6 alkyl, di-C 1 -C 6 alkylamino, and C 1 -C 6 alkylamino;
p is an integer from 3 to 6; and
q is an integer from 0 to 4, or
(d) wherein the substrate of Formula (TPP1-S1) is a compound of Formula (TPP1-S5):
wherein Ar is selected from a C 5 -C 6 arylene and a C 2 -C 6 heteroarylene, each optionally substituted with 1, 2, 3, or 4 substituents each independently selected from C 1 -C 6 alkyl, C 1 -C 6 haloalkyl, halo, and amino;
p is an integer from 3 to 6; and
q is an integer from 0 to 4.
9. The method of claim 1 , wherein R A is N-acetyl-Ala-Ala-Ala-Pro-Phe-Gly-Cys, and S in Formula (PPT1-S1) is a sulfur on the Cys side chain.
10. The method of claim 1 , wherein W is NHCO—C 1 -C 6 alkyl.
11. The method of claim 1 , wherein Y is a C 3 -C 11 alkylene.
12. The method of claim 1 , wherein the one or more of the enzyme products comprise a compound of Formula (TPP1-P1) and/or (PPT1-P1),
wherein in the compound of Formula (TPP1-P1),
G 1 is a first linker comprising 2-20 carbon atoms in which one or more carbon atoms may be replaced with a heteroatom selected from N, O, and S, and/or one or more of carbon atoms may be substituted with a C 1 -C 6 alkyl group, C 1 -C 6 haloalkyl, halo, or amino;
X A is a first linking functionality linking G 1 to G 2 selected from a bond, amide, thioamide, sulfonamide, ether, sulfide, ureido, thioureido, and ester;
G 2 is a second linker comprising 2-20 carbon atoms in which one or more carbon atoms may be replaced with a heteroatom selected from N, O, and S, and/or one or more of carbon atoms may be substituted with a C 1 -C 6 alkyl group or halogen;
X B is a second linking functionality linking G 2 to Prot selected from a bond, NH, amide, thioamide, sulfonamide, ether, sulfide, ureido, thioureido, and ester; and
Prot is a protecting group that is capable of fragmenting by one dominant pathway at an efficiency of greater than 5% to provide a residual enzyme product fragment that is detectable by mass spectrometry; and
wherein in the compound of Formula (PPT1-P1),
W is selected from H and NHCO—C 1 -C 6 alkyl; and
Y is a C 2 -C 19 alkylene.
13. The method of claim 1 , wherein the one or more lysosomal enzymes comprises an enzyme selected from tripeptidyl peptidase 1 and palmitoyl protein thioesterase 1.
14. The method of claim 1 , wherein in step (b), the one or more lysosomal enzyme substrates further comprises a compound having a carbohydrate moiety and an aglycone moiety and having Formula (MPS-S):
wherein S is the carbohydrate moiety that when covalently coupled to the aglycone moiety provides a substrate for an enzyme selected from the group consisting of:
(i) alpha-L-iduronidase;
(ii) iduronate 2-sulfatase;
(iii) heparan N-sulfatase;
(iv) N-acetyl-alpha-D-glucosaminidase;
(v) N-acetylgalactosamine 6-sulfate-sulfatase;
(vi) N-acetylgalactosamine 4-sulfate-sulfatase; and
(vii) beta-glucuronidase;
L 2 is a linker comprising 1-20 carbon atoms in which one or more carbon atoms may be replaced with a heteroatom selected from N, O, and S, and/or one or more of carbon atoms may be substituted with a C 1 -C 6 alkyl group or halogen;
L 3 is a linker comprising 1-20 carbon atoms in which one or more carbon atoms may be replaced with a heteroatom selected from N, O, or S, and/or one or more of carbon atoms may be substituted with a C 1 -C 6 alkyl group or halogen;
L 4 is optional and when present is a linker comprising 1-20 carbon atoms in which one or more carbon atoms may be replaced with a heteroatom selected from N, O, or S), and/or one or more of carbon atoms may be substituted with a C 1 -C 6 alkyl group or halogen;
R 1 is a C 1 -C 10 alkyl group or a C 1 -C 10 alkoxy group;
R 2 at each occurrence is independently selected from a C 1 -C 10 alkyl group, a C 1 -C 10 alkoxy group, halogen, nitro, C(═O)NHR, and C(═O)OR, where R is C 1 -C 8 alkyl group;
R 3 is a C 1 -C 10 alkyl group or a substituted or unsubstituted C 6 -C 10 aryl group; and
n is 0, 1, 2, 3, or 4.
15. The method of claim 14 , further comprising contacting the one or more enzyme products with a glycohydrolase to provide glycohydrolase enzyme products.
16. The method of claim 1 , further comprising adding an inhibitor to block endogenous glycohydrolase enzymatic activity that acts on a substrate for one or more of an enzyme selected from the group consisting of:
(a) N-acetylgalactosamine 6-sulfate-sulfatase; and
(b) N-acetylgalactosamine 4-sulfate-sulfatase.
17. The method of claim 1 , further comprising adding an internal standard for each lysosomal enzyme to be analyzed before, after, or simultaneously with contacting the lysosomal enzymes with the one or more substrates.
18. The method of claim 1 wherein the sample is a blood or tissue sample.
19. The method of claim 1 , wherein determining the quantities of the one or more enzyme products comprises mass spectrometric analysis or fluorescence analysis.
20. The method of claim 1 , further comprising using the quantities of the one or more enzyme products to determine whether the sample is from a candidate for treatment for a condition associated with one or more lysosomal storage diseases.