Compositions and methods for jamm protein inhibition

A compound suitable for inhibiting the activity of a JAMM metalloprotease domain comprising:

• organic molecule or the pharmaceutically acceptable salt, hydrate, polymorph, solvate thereof or any combination thereof or a mixture thereof with a pharmaceutically acceptable solvent, the organic molecule having a zinc chelating pharmacophore moiety comprised of the fragment S—C—C—N wherein the organic molecule is 8-quinolinethiol, or a derivative thereof, or a dimer of 8-quinolinethiol or a derivative of 8-quinolinethiol dimer;
• wherein,
• the derivative of the 8-quinolinethiol or dimer framework comprises the framework with one or more appended chemical substituents selected from the group consisting of halogen, CN, optionally substituted carboxyl, optionally substituted ester, optionally substituted amine, optionally substituted amide, optionally substituted thioamide, optionally substituted aliphatic or aryl carboxyl, optionally substituted aliphatic or aryl carboxyamide, optionally substituted aminoalkylamine, carboxyl, ester, alkyl aliphatic ester, amine, optionally substituted aliphatic diamine, optionally substituted aminoalkyl carboxyl, optionally substituted amine alkyl ester, amino alkyl amide, halogen, alkyl halogen, alkylheterocycle, alkylaryl, alkylheteroaryl, aminoalkylaryl, aminoalkylheteroaryl, carboxylalkylaryl, carboxylalkylheteroaryl, carboxylalkylcycloalkyl, arylalkoxy, heteroarylalkoxy, cycloalkylalkoxy, the corresponding thio analogs, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted alkthioxy, optionally substituted alkoxalkyl;
• optionally substituted alkoxaryl;
• optionally substituted amino, optionally substituted carbonyl, optionally substituted carboxylic acid, optionally substituted alkoxheteroaryl, optionally substituted alkoxheterocycyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, optionally substituted alkaryl, optionally substituted alkyheteroaryl, optionally substituted alkheterocyclyl, optionally substituted carbocyclyl, optionally substituted alkylcarbocyclyl, carboxyl, ester, alkylcarboxyl, alkyl alkenyl ester, amine, alkylenyl diamine, aminoalkyl carboxyl, amino alkyl ester, amino alkyl amide, halogen, alkyl halogen, alkylheterocycle, alkylaryl, alkylheteroaryl, aminoalkylaryl, aminoalkylheteroaryl, carboxylalkylaryl, carboxylalkylheteroaryl, carboxylalkylcycloalkyl, arylalkoxy, heteroarylalkoxy, cycloalkylalkoxy, the corresponding thio analogs and any combination thereof;
• and,
• the 8-quinolinethiol, the derivative thereof or the dimer of 8-quinolinethiol or of the derivative of 8-quinolinethiol dimer further comprises one or more peptide substituents at the 2, 3, 4, 5, 6 and/or 7 positions of the 8-quinolinethiol framework, the peptide substituent comprising an optionally substituted peptidyl group containing from 1 to 6 natural and/or non-natural amino acid moieties, the peptidyl group being bonded to the 8-quinolinethiol framework through a linker, the linker being an alkyl amide group or an alkyl ester group wherein the amide or ester moiety forms the linking bond to the peptide substituent and the alkyl moiety is directly bonded to the 8-quinolinethiol framework or is bonded to the 8-quinolinethiol framework through an amide group, an ester group, an ether group or an amine group.

A compound suitable for inhibiting the activity of a JAMM metalloprotease domain comprising:

• an organic molecule or the pharmaceutically acceptable salt, hydrate, polymorph, solvate thereof or any combination thereof or a mixture thereof with a pharmaceutically acceptable solvent, the organic molecule being a derivative of a 3-hydoxyl 4H-pyran-4-thione or 3-hydroxypyridine-4(1H)-thione derivative wherein the derivative comprises the 3-hydroxyl-4H-pyran-4-thione or 3-hydroxylpyridine-4(1H)-thione framework with one or more appended chemical substituents selected from the group consisting of halogen, CN, optionally substituted carboxyl, optionally substituted ester, optionally substituted amine, optionally substituted amide, optionally substituted thioamide, optionally substituted aliphatic or aryl carboxyl, optionally substituted aliphatic or aryl carboxyamide, optionally substituted aminoalkylamine, carboxyl, ester, alkyl aliphatic ester, amine, optionally substituted aliphatic diamine, optionally substituted aminoalkyl carboxyl, optionally substituted amino alkyl ester, amino alkyl amide, halogen, alkyl halogen, alkylheterocycle, alkylaryl, alkylheteroaryl, aminoalkylaryl, aminoalkylheteroaryl, carboxylalkylaryl, carboxylalkylheteroaryl, carboxylalkylcycloalkyl, arylalkoxy, heteroarylalkoxy, cycloalkylalkoxy, the corresponding thio analogs, optionally substituted alkyl optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted alkthioxy, optionally substituted alkoxalkyl, optionally substituted alkoxaryl;
• optionally substituted amino, optionally substituted carbonyl, optionally substituted carboxylic acid, optionally substituted alkoxheteroaryl, optionally substituted alkoxheterocycyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, optionally substituted alkaryl, optionally substituted alkyheteroaryl, optionally substituted alkheterocyclyl, optionally substituted carbocyclyl, optionally substituted alkylcarbocyclyl, carboxyl, ester, alkylcarboxyl, alkyl alkenyl ester, amine, alkylenyl diamine, aminoalkyl carboxyl, amino alkyl ester, amino alkyl amide, halogen, alkyl halogen, alkylheterocycle, alkylaryl, alkylheteroaryl, aminoalkylaryl, aminoalkylheteroaryl, carboxylalkylaryl, carboxylalkylheteroaryl, carboxylalkylcycloalkyl, arylalkoxy, heteroarylalkoxy, cycloalkylalkoxy, the corresponding thio analogs and any combination thereof.

A compound suitable for inhibiting the activity of a JAMM metalloprotease domain comprising:

• an organic molecule or the pharmaceutically acceptable salt, hydrate, polymorph, solvate thereof or any combination thereof or a mixture thereof with a pharmaceutically acceptable solvent, the organic molecule having the formula of a 3-hydroxyl-4H-pyran-4-thione or 3-hydroxypyridine-4(1H)-thione or a derivative thereof and the derivative comprises the 3-hydroxyl-4H-pyran-4-thione or 3-hydroxypyridine-4(1H)-thione framework with one or more appended chemical substituents selected from the group consisting of halogen, CN, optionally substituted carboxyl, optionally substituted ester, optionally substituted amine, optionally substituted amide, optionally substituted thioamide, optionally substituted aliphatic or aryl carboxyl, optionally substituted aliphatic or aryl carboxyamide, optionally substituted aminoalkylamine, carboxyl, ester, alkyl aliphatic ester, amine, optionally substituted aliphatic diamine, optionally substituted aminoalkyl carboxyl, optionally substituted amino alkyl ester, amino alkyl amide, halogen, alkyl halogen, alkylheterocycle, alkylaryl, alkylheteroaryl, aminoalkylaryl, aminoalkylheteroaryl, carboxylalkylaryl, carboxylalkylheteroaryl, carboxylalkylcycloalkyl, arylalkoxy, heteroarylalkoxy, cycloalkylalkoxy, the corresponding thio analogs, optionally substituted alkyl, optionally substituted alkenyl, optionally substituted alkynyl, optionally substituted alkoxy, optionally substituted alkthioxy, optionally substituted alkoxalkyl;
• optionally substituted alkoxaryl;
• optionally substituted amino, optionally substituted carbonyl, optionally substituted carboxylic acid, optionally substituted alkoxheteroaryl, optionally substituted alkoxheterocycyl, optionally substituted aryl, optionally substituted heteroaryl, optionally substituted heterocyclyl, optionally substituted alkaryl, optionally substituted alkyheteroaryl, optionally substituted alkheterocyclyl, optionally substituted carbocyclyl, optionally substituted alkylcarbocyclyl, carboxyl, ester, alkylcarboxyl, alkyl alkenyl ester, amine, alkylenyl diamine, aminoalkyl carboxyl, amino alkyl ester, amino alkyl amide, halogen, alkyl halogen, alkylheterocycle, alkylaryl, alkylheteroaryl, aminoalkylaryl, aminoalkylheteroaryl, carboxylalkyaryl, carboxylalkylheteroaryl, carboxylalkylcycloalkyl, arylalkoxy, heteroarylalkoxy, cycloalkylalkoxy, the corresponding thio analogs and any combination thereof;
• and,
• the 3-hydroxyl-4H-pyran-4-thione or 3-hydroxypyridine-4(1H)-thione or derivative thereof further comprises one or more peptide substituents at the 2, 4, 5 and/or 6 positions of the 3-hydroxyl-4H-pyran-4-thione or 3-hydroxypyridine-4(1H)-thione framework, the peptide substituent comprising an optionally substituted peptidyl group containing from 1 to 6 natural and/or non-natural amino acid moieties, the peptidyl group being bonded to the 3-hydroxyl-4H-pyran-4-thione or 3-hydroxypyridine-4(1H)-thione framework through a linker, the linker being an alkyl amide group or an alkyl ester group wherein the amide or ester moiety forms the linking bond to the peptide substituent and the alkyl moiety is directly bonded to the 3-hydroxyl-4-pyranthione framework or is bonded to the 3-hydroxyl-4-pyridinethione framework through an amide group, an ester group, an ether group or an amine group, the peptide substituent or substituents being capable of interacting with the JAMM metalloprotease domain or a biological complex containing the JAMM metalloprotease domain.

A compound suitable for inhibiting the activity of a JAMM metalloprotease domain, comprising:

• a catechol ketone of the formula:
• (RO)2C6H3—CO—CZ═CHY or (RO)2C6H3—CO—CHC(═O)Y
• or the pharmaceutically acceptable salt, hydrate, polymorpyh, solvate thereof or any combination thereof a mixture thereof with a pharmaceutically acceptable solvent;
• wherein R is H or C1 to C6 alkyl, Z is cyano, nitro, halo or trifluoromethyl and Y is phenyl, substituted phenyl, aminophenyl, 1-indolyl, catecholyl, pyridyl, naphthyl or quinolinyl.

A method for screening for a compound that inhibits the metalloprotease activity of a protein containing a JAMM metalloprotease domain, comprising:

• selecting a candidate from a group of organic molecules;
• testing the selected candidate in a JAMM domain inhibition assay comprising
• combining
• a JAMM enzymatic material selected from the group consisting of a JAMM domain containing protein, a signalosome complex and a 26S proteasome complex containing the JAMM protein,
• and a protein substrate selected from the group consisting of a protein modified by a ubiquitin, a protein modified by a ubiquitin-like modifier and a protein modified by a ubiquitin chain to produce an enzymatic medium
• wherein the protein substrate is modified with a tag that is detectable by measurement of molecular weight, spectroscopic interaction or chromatographic Rf determination,
• conducting a first measurement of the enzymatic medium relative to the protein substrate alone wherein the first measurement is made by a detection of the tag,
• combining the selected candidate with the protein substrate and adding the JAMM enzymatic material to produce a candidate medium,
• conducting a second measurement of the candidate medium relative to the protein substrate alone wherein the second measurement is made by detection of the tag,
• comparing the first and second measurements to identify a candidate that demonstrates at least about a 50% inhibition at a concentration of no more than 500 micromolar in the candidate medium, the difference between the first and second measurements being at least about 50% with the second measurement being greater than the first measurement;
• WHEREIN,
• the organic molecule is selected from the group consisting of subgroups a, b, c, d, e and f, these subgroups being:
• a) an organic molecule having a pharmacophore moiety comprised of the fragment X—C—C—Y wherein:
• X is nitrogen;
• Y is oxygen or sulfur;
• the carbon atoms of the pharmacophore moiety are saturated or unsaturated or a mixture thereof;
• the organic molecule has an aromatic, aliphatic or aliaromatic ring framework with the X group being part of the ring framework and the Y group or the C—Y moiety being a substituent appended to the ring framework, or the organic molecule has an aromatic, aliphatic or aliaromatic ring framework with both or X and Y being substituents appended to the ring framework;
• the framework is a single aromatic or aliphatic 5 or 6 member ring or a 5:5, 5:6, 6:5 or a 6:6 member aromatic, aliphatic or aliaromatic bicyclic ring, the count of members including the carbons and heteroatoms in the ring;
• and
• the ring framework is optionally appended by one or more chemical substituents and optionally includes one or more heteroatoms in the ring framework;
• provided that:
• when X as nitrogen is in the ring framework, it is either a secondary or tertiary nitrogen;
• when X as nitrogen is a substituent appended to the ring framework, it is a primary, secondary or tertiary nitrogen;
• b) the organic molecule is 8-quinolinethiol, or a derivative thereof, or a dimer of 8-quinolinethiol or a derivative of 8-quinolinethiol dimer;
• wherein,
• the derivative of the 8-quinolinethiol or dimer framework comprises the framework with one or more appended chemical substituents;
• and,
• the 8-quinolinethiol, the derivative thereof or the dimer of 8-quinolinethiol or of the derivative of 8-quinolinethiol dimer further comprises one or more peptide substituents at the 2, 3, 4, 5, 6 and/or 7 positions of the 8-quinolinethiol framework, the peptide substituent comprising an optionally substituted peptidyl group containing from 1 to 6 natural and/or non-natural amino acid moieties, the peptidyl group being bonded to the 8-quinolinethiol framework through a linker, the linker being an alkyl amide group or an alkyl ester group wherein the amide or ester moiety forms the linking bond to the peptide substituent and the alkyl moiety is directly bonded to the 8-quinolinethiol framework or is bonded to the 8-quinolinethiol framework through an amide group, an ester group, an ether group or an amine group;
• c) an organic molecule is a derivative of 3-hydoxyl 4-pyrothione or 3-hydroxypyridine-4(H)-thione and the derivative comprises the 3-hydroxyl-4-pyrothione or 3-hydroxypyridine-4(H)-thione framework with one or more appended chemical substituents;
• d) an organic molecule is 5-hydoxyl 4-pyrothione, 3-hydroxypyridine-4(H)-thione or a derivative thereof and the derivative comprises the 3-hydroxyl-4-pyrothione or 3-hydroxypyridine-4(H)-thione framework with one or more appended chemical substituents;
• and,
• the 3-hydoxyl 4-pyrothione, 3-hydroxypyridine-4(H)-thione or derivative thereof further comprises one or more peptide substituents at the 2, 4, 5 and/or 6 positions of the 3-hydroxyl-4-pyrothione or pyrothione or 3-hydroxypyridine-4(H)-thione framework, the peptide substituent comprising an optionally substituted natural or non-natural peptidyl group containing from 2 to 6 amino acid moieties, the peptidyl group being bonded to the 3-hydroxyl-4-pyrothione or 3-hydroxypyridine-4(H)-thione framework through a linker, the linker being an alkyl amide group or an alkyl ester group wherein the amide or ester moiety forms the linking bond to the peptide substituent and the alkyl moiety is directly bonded to the 3-hydroxyl-4-pyrothione framework or is bonded to the 3-hydroxyl-4-pyrothione or 3-hydroxypyridine-4(H)-thione framework through an amide group, an ester group, an ether group or an amine group, the peptide substituent or substituents being capable of interacting with the JAMM metalloprotease domain or a biological complex containing the JAMM metalloprotease domain;
• e) an organic molecule from a group of catechol ketones of the formula:
• (RO)2C6H3—CO—CZ═CHY or (RO)2C6H3—CO—CHZC(═O)Y
• wherein R is hydrogen or alkyl, Z is cyano, nitro, halo or trifluoromethyl and Y is phenyl, substituted phenyl, aminophenyl, 1-indolyl, catecholyl, pyridyl, naphthyl or quinolinyl, and
• f) an organic molecule of group e) with one or more peptide substituents on the Y group or at the 2, 5 and/or 6 positions of the catechol group, the peptide substituent comprising an optionally substituted natural or non-natural peptidyl group containing from 2 to 6 amino acid moieties, the peptidyl group being bonded to the Y group or the catechol group through a linker, the linker being an alkyl amide group or an alkyl ester group wherein the amide or ester moiety forms the linking bond to the peptide substituent and the alkyl moiety is directly bonded to the Y group or the catechol group or is bonded to the Y group or the catechol group through an amide group, an ester group, an ether group or an amine group.

An assay for the determination of inhibition of JAMM metalloprotease domain activity by a potential inhibitory candidate comprising:

• combining
• a JAMM enzymatic material selected from the group consisting of a JAMM domain containing protein, a signalosome complex and a 26S proteasome complex containing the JAMM protein,
• and a protein substrate selected from the group consisting of a protein modified by a ubiquitin, a protein modified by a ubiquitin-like modifier and a protein modified by a ubiquitin chain to produce an enzymatic medium
• wherein the protein substrate is modified with a tag that is detectable by measurement of molecular weight, spectroscopic interaction or chromatographic Rf determination,
• conducting a first measurement of the enzymatic medium relative to the protein substrate alone wherein the first measurement is made by a detection of the tag,
• combining the potential inhibitory candidate with the protein substrate and adding the JAMM enzymatic material to produce a candidate medium,
• conducting a second measurement of the candidate medium relative to the protein substrate alone wherein the second measurement is made by detection of the tag,
• comparing the first and second measurements to identify a candidate that demonstrates at least about a 50% inhibition at a concentration of no more than 500 micromolar in the candidate medium, the difference between the first and second measurements being at least about 50% with the second measurement being greater than the first measurement.