Methods of identifying compounds that modulate IL-4 receptor-mediated IgE synthesis utilizing a c-MYC protein
View Patent ↗The present provides compounds capable of modulating IL-4 receptor-mediated IgE production, as well as IL-4 induced processes associated therewith, methods and kits for identifying such compounds that utilize a c-Myc protein as a surrogate analyte and methods of using the compounds in a variety of in vitro, in vitro and ex vivo contexts.
1. A method of identifying a compound that inhibits IL-4 receptor-mediated IgE production or a compound that inhibits IL-4 induced transcription from a germline epsilon promoter, comprising determining whether the compound binds a mammalian c-Myc protein, and determining the ability of the compound to inhibit IL-4 induced IgE production or inhibit IL-4 induced transcription from a germline epsilon promoter.
2. The method of claim 1 in which the compound identified inhibits IL-4 receptor-mediated IgE production.
3. The method of claim 1 in which the compound identified inhibits IL-4 receptor-mediated isotype switching of B-cells.
4. The method of claim 1 in which the mammalian c-Myc protein is a human c-Myc protein.
5. The method of claim 1 in which determining whether the compound binds the c-Myc protein is in a competitive binding assay.
6. The method of claim 5 in which the compound competes for binding the c-Myc protein with an active BR10A1 compound of the formula:
Z 1 —X 1 ˜X 2 ˜X 3 ˜X 4 ˜X 5 ˜X 6 ˜X 7 ˜X 8 ˜X 9 ˜X 10 ˜X 11 ˜X 12 ˜X 13 ˜X 14 ˜X 15 ˜X 16 ˜X 17 ˜X 18 ˜X 19 ˜X 20 ˜X 21 ˜X 22 ˜X 23 —Z 2
wherein:
X 1 is a non-polar amino acid residue;
X 2 is a polar amino acid residue or an alanine;
X 3 is a basic or an aliphatic amino acid residue;
X 4 is a basic or an aliphatic amino acid residue;
X 5 is an acidic or an aliphatic amino acid residue;
X 6 is a hydroxyl-containing or an aliphatic amino acid residue;
X 7 is a cysteine-like amino acid residue or an alanine;
X 8 is an aliphatic amino acid residue;
X 9 is a hydroxyl-containing or an aliphatic amino acid residue;
X 10 is a basic or an aliphatic amino acid residue;
X 11 is a hydroxyl-containing amino acid residue;
X 12 is an aliphatic amino acid residue;
X 13 is an acidic or an aliphatic amino acid residue;
X 14 is an acidic or an aliphatic amino acid residue;
X 15 is an aliphatic amino acid residue;
X 16 is a hydrophobic amino acid residue;
X 17 is an aliphatic amino acid residue;
X 18 is an aliphatic amino acid residue;
X 19 is a hydrophobic amino acid residue;
X 20 is a hydrophobic amino acid residue;
X 21 is an aliphatic amino acid residue;
X 22 is an aliphatic amino acid residue;
X 23 is a conformationally constrained amino acid residue;
Z 1 is RRN—, RC(O)NR—, RS(O) 2 NR— or an amino-terminal blocking group;
Z 2 is —C(O)OR, —C(O)O—, —C(O)NRR or a carboxyl-terminal blocking group;
each R is independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, aryl, substituted aryl, arylalkyl, substituted arylalkyl, heteroaryl, substituted heteroaryl, heteroarylalkyl and substituted heteroarylalkyl;
each “˜” independently represents an amide, a substituted amide or an isostere of an amide;
each “—” represents a bond, or a 1 to 10 residue peptide, peptide with a substituted amide linkage, or peptide isostere; and
wherein one or more of X 1 , X 2 , X 3 , X 21 , X 22 , or X 23 may be absent.
7. The method of claim 6 in which the active BR10A1 compound is selected from the group consisting of BR10A1wt (SEQ ID NO:1); BR10A1CI (SEQ ID NO:2); BR10A1TR (SEQ ID NO:3); BR10A1MQ (SEQ ID NO:4); BR10A1RR (SEQ ID NO:5); BR10A1EE (SEQ ID NO:6); BR10A1GW (SEQ ID NO:7); BR10A1GL (SEQ ID NO:8); BR10A1FY (SEQ ID NO:9); BR10A1STOP (SEQ ID NO:10); BR10A1ES (SEQ ID NO:11); and BR10A1CIGW (SEQ ID NO:12) and a peptide analog thereof in which one or more of the amide linkages are replaced with an isostere of an amide.
8. The method of claim 1 which is carried out in a cell-free system.
9. The method of claim 1 in which the compound is a small organic compound.
10. The method of claim 9 in which the small organic compound has a molecular weight in the range of about 100-2500 dalton.
11. The method of claim 1 in which the compound is a peptide.
12. A method of identifying compounds that inhibit IL-4 receptor-mediated IgE production, comprising the step of contacting a compound from pool of candidate compounds with a mammalian c-Myc protein and identifying those compounds of the pool that bind the c-Myc protein, and determining whether the compounds inhibit IL-4 receptor-mediated IgE production.
13. The method of claim 12 which is carried out in the presence of a compound known to bind the c-Myc protein such that those compounds of the pool that competitively bind the c-Myc protein are identified and wherein the compound known to bind the c-Myc protein is an active BR10A1 compound of the formula:
Z 1 —X 1 ˜X 2 ˜X 3 ˜X 4 ˜X 5 ˜X 6 ˜X 7 ˜X 8 ˜X 9 ˜X 10 ˜X 11 ˜X 12 ˜X 13 ˜X 14 ˜X 15 ˜X 16 ˜X 17 ˜X 18 ˜X 19 ˜X 20 ˜X 21 ˜X 22 ˜X 23 —Z 2
wherein:
X 1 is a non-polar amino acid residue;
X 2 is a polar amino acid residue or an alanine;
X 3 is a basic or an aliphatic amino acid residue;
X 4 is a basic or an aliphatic amino acid residue;
X 5 is an acidic or an aliphatic amino acid residue;
X 6 is a hydroxyl-containing or an aliphatic amino acid residue;
X 7 is a cysteine-like amino acid residue or an alanine;
X 8 is an aliphatic amino acid residue;
X 9 is a hydroxyl-containing or an aliphatic amino acid residue;
X 10 is a basic or an aliphatic amino acid residue;
X 11 is a hydroxyl-containing amino acid residue;
X 12 is an aliphatic amino acid residue;
X 13 is an acidic or an aliphatic amino acid residue;
X 14 is an acidic or an aliphatic amino acid residue;
X 15 is an aliphatic amino acid residue;
X 16 is a hydrophobic amino acid residue;
X 17 is an aliphatic amino acid residue;
X 18 is an aliphatic amino acid residue;
X 19 is a hydrophobic amino acid residue;
X 20 is a hydrophobic amino acid residue;
X 21 is an aliphatic amino acid residue;
X 22 is an aliphatic amino acid residue;
X 23 is a conformationally constrained amino acid residue;
Z 1 is RRN—, RC(O)NR—, RS(O) 2 NR— or an amino-terminal blocking group;
Z 2 is —C(O)OR, —C(O)O—, —C(O)NRR or a carboxyl-terminal blocking group;
each R is independently selected from the group consisting of hydrogen, alkyl, substituted alkyl, aryl, substituted aryl, arylalkyl, substituted arylalkyl, heteroaryl, substituted heteroaryl, heteroarylalkyl and substituted heteroarylalkyl;
each “˜” independently represents an amide, a substituted amide or an isostere of an amide;
each “-” represents a bond, or a 1 to 10 residue peptide, peptide with a substituted amide linkage or peptide isostere; and
wherein one or more of X 1 , X 2 , X 3 , X 21 , X 22 , or X 23 may be absent.
14. The method of claim 13 in which the active BR10A1 compound is selected from the group consisting of BR10A1wt (SEQ ID NO:1); BR10A1CI (SEQ ID NO:2); BR10A1TR (SEQ ID NO:3); BR10A1MQ (SEQ ID NO:4); BR10A1RR (SEQ ID NO:5); BR10A1EE (SEQ ID NO:6); BR10A1GW (SEQ ID NO:7); BR10A1GL (SEQ ID NO:8); BR10A1FY (SEQ ID NO:9); BR10A1STOP (SEQ ID NO:10); BR10A1ES (SEQ ID NO:11); and BR10A1CIGW (SEQ ID NO:12) and a peptide analog thereof in which one or more of the amide linkages are replaced with an isostere of an amide.
15. The method of claim 12 in which the candidate compounds are peptides or small organic compounds.
16. The method of claim 15 in which the pool of candidate compounds is a phage display library.
17. The method of claim 15 in which the candidate compounds are immobilized on a substrate or a plurality of substrates.
18. The method of claim 12 in which the compound or c-Myc protein is labeled with a detectable label.
19. The method of claim 12 in which the c-Myc protein is immobilized on a substrate.
20. The method according to claim 1 or claim 12 in which the c-Myc protein is a polypeptide comprising the amino acid sequence selected from the group consisting of the sequence of SEQ ID NO:20 and the sequence of SEQ ID NO:21.