CATALYTIC INHIBITOR OF PROTEIN PHOSPHATASE 5 ACTIVATES THE EXTRINSIC APOPTOTIC PATHWAY BY DISRUPTING COMPLEX II
20250360108 ยท 2025-11-27
Inventors
- Mehdi MOLLAPOUR (Syracuse, NY, US)
- Gennady BRATSLAVSKY (Syracuse, NY, US)
- John D Chisholm (Syracuse, NY, US)
- Dimitra Bourdoulia (Syracuse, NY, US)
- Mark R Woodford (Syracuse, NY, US)
Cpc classification
A61K31/625
HUMAN NECESSITIES
A61K31/192
HUMAN NECESSITIES
International classification
A61K31/625
HUMAN NECESSITIES
Abstract
Protein phosphatase 5 (PP5) is a serine/threonine protein phosphatase involved in the maturation and activation of numerous signaling pathways essential for cancer growth. PP5 activity is essential for the survival of clear cell renal cell carcinoma (ccRCC), however the mechanism remains unclear. Data demonstrates that PP5 interacts with caspase-8, FADD, and RIPK1, components of extrinsic apoptotic pathway Complex II. Specifically, PP5 dephosphorylates and inactivates the death effector proteins RIPK1 and FADD, preserving Complex II integrity and regulating extrinsic apoptosis. Protein phosphatases are considered to be undruggable, however we have developed a specific inhibitor of PP5 (P-053) that prevents substrate binding to the active site. Encouragingly, PP5 inhibition using P-53 in VHL-null ccRCC robustly induces extrinsic apoptosis. Taken together, the data suggests that PP5 promotes ccRCC survival by suppressing extrinsic apoptosis, and small molecule inhibition of PP5 presents a viable therapeutic strategy for ccRCC.
Claims
1. A method of treating cancer, comprising: a) providing i) a subject with cancer, ii) one or more protein phosphatase-5 inhibitors, and b) treating said subject with the one or more PP5 inhibitors.
2. The method of claim 1, wherein treating comprises administering a therapeutically effective amount of one or more protein phosphatase-5 inhibitors to the subject.
3. The method of claim 1, wherein the cancer is renal cell carcinoma.
4. The method of claim 3, wherein the renal cancer is clear cell renal cell carcinoma.
5. The method of claim 1, wherein the one or more protein phosphatase-5 inhibitors are characterized as a PP5 specific inhibitor.
6. The method of claim 1, wherein the one or more protein phosphatase-5 inhibitors are selected from the group consisting of: ##STR00072## ##STR00073## ##STR00074## ##STR00075## or a pharmaceutically acceptable salt thereof, and combinations thereof.
7. The method of claim 1, wherein treating the subject with the one or more protein phosphatase-5 inhibitors is sequential.
8. The method of claim 1, wherein treating the subject with the one or more protein phosphatase-5 inhibitors is simultaneous.
9. The method of claim 1, wherein treating with the one or more protein phosphatase-5 inhibitors results in reduced proliferation of at least some of the cancer cells within said subject.
10. A method of treating cancer, comprising: a) providing i) a subject with cancer and one or more compounds of: ##STR00076## or a pharmaceutically acceptable salt thereof, ##STR00077## or a pharmaceutically acceptable salt thereof, and b) treating the subject with the one or more compounds or pharmaceutically acceptable salts thereof.
11. A method of treating cancer, comprising: a) providing i) a subject with cancer and one or more compounds of: ##STR00078## ##STR00079## ##STR00080## ##STR00081## ##STR00082## and b) treating the subject with the one or more compounds or pharmaceutically acceptable salts thereof.
11. A pharmaceutical anticancer composition comprising one or more PP5 inhibitors, or pharmaceutically acceptable salts thereof.
12. The pharmaceutical anticancer composition of claim 11, wherein the composition is characterized as PP5 specific.
13. The pharmaceutical anticancer composition of claim 11, wherein the one or more PP5 inhibitors are selected from the group consisting of: ##STR00083## ##STR00084## ##STR00085## ##STR00086## ##STR00087## or a pharmaceutically acceptable salt thereof, and combinations thereof.
14. A pharmaceutical anticancer composition comprising one or more PP5 inhibitors selected from the group consisting of: ##STR00088## ##STR00089## ##STR00090## ##STR00091## ##STR00092## and combinations thereof.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
[0013] The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
[0014]
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[0020]
[0021]
[0022] It is noted that the drawings of the disclosure are not necessarily to scale. The drawings are intended to depict only typical aspects of the disclosure, and therefore should not be considered as limiting the scope of the disclosure. In the drawings, like numbering represents like elements between the drawings.
Definitions
[0023] As used in the present specification, the following words and phrases are generally intended to have the meanings as set forth below, except to the extent that the context in which they are used indicates otherwise.
[0024] As used herein, the singular forms a, an, and the include plural references unless the context clearly dictates otherwise. Thus, for example, references to a compound include the use of one or more compound(s). A step of a method means at least one step, and it could be one, two, three, four, five or even more method steps.
[0025] As used herein the terms about, approximately, and the like, when used in connection with a numerical variable, generally refers to the value of the variable and to all values of the variable that are within the experimental error (e.g., within the 95% confidence interval [CI 95%] for the mean) or within 10% of the indicated value, whichever is greater.
[0026] As used herein the term alkyl refers to C.sub.1-20 inclusive, linear (i.e., straight-chain), branched, or cyclic, saturated or at least partially and in some cases fully unsaturated (i.e., alkenyl and alkynyl) hydrocarbon chains, including for example, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tert-butyl, pentyl, hexyl, octyl, ethenyl, propenyl, butenyl, pentenyl, hexenyl, octenyl, butadienyl, propynyl, butynyl, pentynyl, hexynyl, heptynyl, and allenyl groups. Branched refers to an alkyl group in which a lower alkyl group, such as methyl, ethyl or propyl, is attached to a linear alkyl chain. Lower alkyl refers to an alkyl group having 1 to about 8 carbon atoms (i.e., a C.sub.1-8 alkyl), e.g., 1, 2, 3, 4, 5, 6, 7, or 8 carbon atoms. Higher alkyl refers to an alkyl group having about 10 to about 20 carbon atoms, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 carbon atoms. In certain embodiments, alkyl refers to C.sub.1-8 straight-chain alkyls. In other embodiments, alkyl refers to C.sub.1-8 branched-chain alkyls. In embodiments, alkyl groups can optionally be substituted (a substituted alkyl) with one or more alkyl group substituents, which can be the same or different. The term alkyl group substituent includes but is not limited to alkyl, substituted alkyl, halo, arylamino, acyl, hydroxyl, aryloxyl, alkoxyl, alkylthio, arylthio, aralkyloxyl, aralkylthio, carboxyl, alkoxycarbonyl, oxo, and cycloalkyl. There can be optionally inserted along the alkyl chain one or more oxygen, sulfur or substituted or unsubstituted nitrogen atoms, wherein the nitrogen substituent is hydrogen, lower alkyl (also referred to herein as alkylaminoalkyl), or aryl. Thus, as used herein, the term substituted alkyl includes alkyl groups, as defined herein, in which one or more atoms or functional groups of the alkyl group are replaced with another atom or functional group, including for example, alkyl, substituted alkyl, halogen, aryl, substituted aryl, alkoxyl, hydroxyl, nitro, amino, alkylamino, dialkylamino, sulfate, and mercapto.
[0027] As used herein, the term heteroalkyl by itself or in combination with another term means, unless otherwise stated, a stable straight or branched chain alkyl group consisting of the stated number of carbon atoms and one or two heteroatoms of O, N, and S, and wherein the nitrogen and sulfur atoms may be optionally oxidized and the nitrogen heteroatom may be optionally quaternized. In embodiments, the heteroatom(s) may be placed at any position of the heteroalkyl group, including between the rest of the heteroalkyl group and the fragment to which it is attached, as well as attached to the most distal carbon atom in the heteroalkyl group. Non-limiting examples include: OCH.sub.2CH.sub.2CH.sub.3, CH.sub.2CH.sub.2CH.sub.2OH, CH.sub.2CH.sub.2CH.sub.2NHCH.sub.3, and CH.sub.2SCH.sub.2CH.sub.3. In embodiments, up to two heteroatoms may be consecutive, such as, for example, CH.sub.2NHOCH.sub.3, or CH.sub.2CH.sub.2SSCH.sub.3. In embodiments, heteroalkyl groups have 1-12 carbons.
[0028] As used herein, the term alkenyl, denotes a monovalent group derived from a hydrocarbon moiety containing at least two carbon atoms and at least one carbon-carbon double bond. In embodiments, the double bond may or may not be the point of attachment to another group. Alkenyl groups (e.g., C.sub.2-C.sub.8-alkenyl) include, but are not limited to, for example, ethenyl, propenyl, prop-1-en-2-yl, butenyl, 1-methyl-2-buten-1-yl, heptenyl, octenyl and the like.
[0029] As used herein the term apoptosis, refers to a form of programmed cell death in multicellular organisms that involves a series of biochemical events that lead to a variety of morphological changes, including blebbing, changes to the cell membrane such as loss of membrane asymmetry and attachment, cell shrinkage, nuclear fragmentation, chromatin condensation, and chromosomal DNA fragmentation. Defective apoptotic processes have been implicated in an extensive variety of diseases; for example, defects in the apoptotic pathway have been implicated in diseases associated with uncontrolled cell proliferations, such as cancer. See e.g. U.S. Patent Publication No. 20200289513 herein entirely incorporated by reference.
[0030] A number of terms herein relate to cancer. Cancer is intended herein to encompass all forms of abnormal or improperly regulated reproduction of cells in a subject.
[0031] The growth of cancer cells (growth herein referring generally to cell division but also to the growth in size of masses of cells) is characteristically uncontrolled or inadequately controlled, as is the death (e.g., apoptosis) of such cells. Local accumulations of such cells result in a tumor. More broadly, and still denoting tumors herein are accumulations ranging from a cluster of lymphocytes at a site of infection to vascularized overgrowths, both benign and malignant. A malignant tumor (as opposed to a benign tumor) herein includes cells that tend to migrate to nearby tissues, including cells that may travel through the circulatory system to invade or colonize tissues or organs at considerable remove from their site of origin in the primary tumor, so-called herein. Metastatic cells are adapted to penetrate blood vessel wells to enter (intravasate) and exit (extravasate) blood vessels. Tumors capable of releasing such cells are also referred to herein as metastatic. The term is used herein also to denote any cell in such a tumor that is capable of such travel, or that is en route, or that has established a foothold in a target tissue. For example, a metastatic breast cancer cell that has taken root in the lung is referred to herein as a lung metastasis. Metastatic cells may be identified herein by their respective sites of origin and destination, such as breast-to-bone metastatic. In the target tissue, a colony of metastatic cells can grow into a secondary tumor, so called herein.
[0032] The terms modified, mutant, and variant (when the context so admits) refer to a gene or gene product that displays modifications in sequence and or functional properties (i.e., altered characteristics) when compared to the wild-type gene or gene product. In some embodiments, the modification includes at least one nucleotide insertion, deletion, or substitution.
[0033] The terms carrier and vehicle as used herein refer to usually inactive accessory substances into which a pharmaceutical substance is suspended. Exemplary carriers include liquid carriers (such as water, saline, culture medium, saline, aqueous dextrose, and glycols) and solid carriers (such as carbohydrates exemplified by starch, glucose, lactose, sucrose, and dextrans, anti-oxidants exemplified by ascorbic acid and glutathione, and hydrolyzed proteins.
[0034] As used herein, the term halo or halogen alone or as part of another substituent means, unless otherwise stated, a fluorine, chlorine, bromine, or iodine atom.
[0035] Cyclic and cycloalkyl refer to a non-aromatic mono- or multicyclic ring system of about 3 to about 10 carbon atoms, e.g., 3, 4, 5, 6, 7, 8, 9, or 10 carbon atoms. In embodiments, a cycloalkyl group can be optionally partially unsaturated. In embodiments, the cycloalkyl group also can be optionally substituted with an alkyl group substituent as defined herein, oxo, and/or alkylene. In embodiments, there can be optionally inserted along the cyclic alkyl chain one or more oxygen, sulfur or substituted or unsubstituted nitrogen atoms, wherein the nitrogen substituent is hydrogen, alkyl, substituted alkyl, aryl, or substituted aryl, thus providing a heterocyclic group. Non-limiting examples of monocyclic cycloalkyl rings include cyclopentyl, cyclohexyl, and cycloheptyl. Non-limiting examples of multicyclic cycloalkyl rings include adamantyl, octahydronaphthyl, decalin, camphor, camphane, and noradamantyl.
[0036] As used herein, the term heterocycloalkyl or heterocyclyl refers to a heteroalicyclic group including one to four ring heteroatoms each selected from O, S, and N. In embodiments, each heterocyclyl group has from 3 to 10 atoms in its ring system, with the proviso that the ring of said group does not contain two adjacent O or S atoms. In embodiments, heterocyclyl substituents may be alternatively defined by the number of carbon atoms, e.g., C.sub.2-C.sub.8-heterocyclyl indicates the number of carbon atoms contained in the heterocyclic group without including the number of heteroatoms. For example, a C.sub.2-C.sub.8-heterocyclyl will include an additional one to four heteroatoms. In embodiments, the heterocyclyl group has less than three heteroatoms. In embodiments, the heterocyclyl group has one to two heteroatoms. In embodiments, the heterocycloalkyl group is fused with an aromatic ring. In embodiments, nitrogen and sulfur heteroatoms may be optionally oxidized, and the nitrogen atom may be optionally quaternized. The heterocyclic system may be attached, unless otherwise stated, at any heteroatom or carbon atom that affords a stable structure.
[0037] As used herein, the term aromatic refers to a carbocycle or heterocycle with one or more polyunsaturated rings and having aromatic character, i.e., having (4n+2) delocalized (pi) electrons, where n is an integer.
[0038] The term aryl is used herein to refer to an aromatic substituent that can be a single aromatic ring, or multiple aromatic rings that are fused together, linked covalently, or linked to a common group, such as, but not limited to, a methylene or ethylene moiety. The common linking group also can be a carbonyl, as in benzophenone, or oxygen, as in diphenylether, or nitrogen, as in diphenylamine. In embodiments, the term aryl specifically encompasses heterocyclic aromatic compounds. The aromatic ring(s) can include phenyl, naphthyl, biphenyl, diphenylether, diphenylamine and benzophenone, among others. In particular embodiments, the term aryl means a cyclic aromatic including about 5 to about 10 carbon atoms, e.g., 5, 6, 7, 8, 9, or 10 carbon atoms, and including 5- and 6-membered hydrocarbon and heterocyclic aromatic rings. In embodiments, an aryl group can be optionally substituted (a substituted aryl) with one or more aryl group substituents, which can be the same or different, wherein aryl group substituent includes alkyl, substituted alkyl, aryl, substituted aryl, aralkyl, hydroxyl, alkoxyl, aryloxyl, aralkyloxyl, carboxyl, acyl, halo, nitro, alkoxycarbonyl, aryloxycarbonyl, aralkoxycarbonyl, acyloxyl, acylamino, aroylamino, carbamoyl, alkylcarbamoyl, dialkylcarbamoyl, arylthio, alkylthio, alkylene, and NRR, wherein R and R can each be independently hydrogen, alkyl, substituted alkyl, aryl, substituted aryl, and aralkyl. Thus, as used herein, the term substituted aryl includes aryl groups, as defined herein, in which one or more atoms or functional groups of the aryl group are replaced with another atom or functional group, including for example, alkyl, substituted alkyl, halogen, aryl, substituted aryl, alkoxyl, hydroxyl, nitro, amino, alkylamino, dialkylamino, sulfate, and mercapto. Non-limiting examples of aryl groups include, but are not limited to, cyclopentadienyl, phenyl, furan, thiophene, pyrrole, pyran, pyridine, imidazole, benzimidazole, isothiazole, isoxazole, pyrazole, pyrazine, triazine, pyrimidine, quinoline, isoquinoline, indole, carbazole, and the like.
[0039] As generally discussed herein, a structure represented generally by the formula:
##STR00007##
as used herein refers to a ring structure, for example, but not limited to a 3-carbon, a 4-carbon, a 5-carbon, a 6-carbon, and the like, aliphatic and/or aromatic cyclic compound, including a saturated ring structure, a partially saturated ring structure, and an unsaturated ring structure as defined herein, including a substituent R group. In embodiments, the R group can be present or absent, and when present, one or more R groups can each be substituted on one or more available carbon atoms of the ring structure. The presence or absence of the R group and number of R groups is determined by the value of the integer n. Each R group, if more than one, is substituted on an available carbon of the ring structure rather than on another R group. For example, the structure above where n is 0 to 2 would comprise compound groups including, but not limited to:
##STR00008##
and the like.
[0040] In embodiments, a dashed line representing a bond in a cyclic ring structure indicates that the bond can be either present or absent in the ring. That is a dashed line representing a bond in a cyclic ring structure indicates that the ring structure is one of a saturated ring structure, a partially saturated ring structure, and an unsaturated ring structure.
[0041] In some embodiments, the compounds described by the presently disclosed subject matter contain a linking group. As used herein, the term linking group includes a chemical moiety, such as a furanyl, phenylene, thienyl, and pyrrolyl radical, which is bonded to two or more other chemical moieties, in particular aryl groups, to form a stable structure.
[0042] In embodiments, a named R, or L, group will generally have the structure that is recognized in the art as corresponding to a group having that name, unless specified otherwise herein. These definitions are intended to supplement and illustrate, not preclude, the definitions that would be apparent to one of ordinary skill in the art upon review of the present disclosure.
[0043] As used herein, the term target activity refers to a biological activity capable of being modulated by a selective modulator. Certain exemplary target activities include, but are not limited to, binding affinity, signal transduction, enzymatic activity, tumor growth, inflammation or inflammation-related processes, or amelioration of one or more symptoms associated with a disease or condition such as a disease or condition relating to cancer.
[0044] As used herein, the term target protein refers to a molecule or a portion of a protein capable of being bound by a selective binding compound. For example PP5 is a target protein for the PP5 inhibitor compositions or selective binding compounds of the present disclosure.
[0045] As used herein, the term treatment or treating is defined as the application or administration of a therapeutic agent, i.e., a one or more polycyclic compounds of the present disclosure such as one or more PP5 inhibitors, or pharmaceutically acceptable salts or solvates thereof, (alone or in combination with another pharmaceutical agent, carrier, or vehicle), to a patient, or application or administration of a therapeutic agent.
[0046] A therapeutically effective amount is that amount that will generate the desired therapeutic outcome (i.e., achieve therapeutic efficacy). For example, a therapeutically effective dose of a compound of the present disclosure is an amount that is sufficient to palliate, ameliorate, stabilize, reverse, prevent, slow or delay the progression of the disease state (e.g., cancer). A therapeutically effective amount can be an amount administered in a dosage protocol that includes days or weeks of administration. In certain embodiments, a therapeutically effective dose of a compound is able to improve at least one sign or symptom of a disease state. As used herein, the terms effective amount, and pharmaceutically effective amount, have the same meaning as therapeutically effective amount. In embodiments, a therapeutically effective amount alters the natural state of a subject.
[0047] As used herein, the term patient, individual or subject refers to a human or a non-human mammal. Non-human mammals include, for example, livestock and pets, such as ovine, bovine, porcine, canine, feline and murine mammals. Non-human mammals also include non-human primates, rats, rabbits and camelids. In certain embodiments, the patient, subject, or individual is human.
[0048] As used herein, the phrases selective inhibition or selectively inhibit refer to a molecule's ability to inhibit the activity or expression of a particular protein or protein isoform, or RNA, while being unable to inhibit the protein activity or expression of another protein or protein isoform, or RNA, by more than 5%. In embodiments, the PP5 inhibitors of the present disclosure selectively inhibit PP5.
[0049] As used herein, the term pharmaceutically acceptable refers to a material, such as a carrier or diluent, which does not abrogate the biological activity or properties of the compound, and is relatively non-toxic, i.e., the material may be administered to an individual without causing undesirable biological effects or interacting in a deleterious manner with any of the components of the composition in which it is contained.
[0050] As used herein, the term pharmaceutically acceptable salt refers to derivatives of one or more of the polycyclic compounds of the present disclosure such as PP5 inhibitors, wherein the parent compound is modified by converting an existing acid or base moiety to its salt form. Examples of pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines; alkali or organic salts of acidic residues such as carboxylic acids; and the like. The pharmaceutically acceptable salts of the present disclosure include the conventional non-toxic salts of the parent compound formed, for example, from non-toxic inorganic or organic acids. The pharmaceutically acceptable salts of the present invention can be synthesized from the parent compound which contains a basic or acidic moiety by conventional chemical methods. Generally, such salts can be prepared by reacting the free acid or base forms of these compounds with a stoichiometric amount of the appropriate base or acid in water or in an organic solvent, or in a mixture of the two; generally, nonaqueous media like ether, ethyl acetate, ethanol, isopropanol, or acetonitrile are preferred. Lists of suitable salts are found in Remington's Pharmaceutical Sciences, 17th ed., Mack Publishing Company, Easton, Pa., 1985, p. 1418 and Journal of Pharmaceutical Science, 66, 2 (1977), each of which is incorporated herein by reference in its entirety.
[0051] As used herein, the term solvate refers to complexes of the compounds disclosed herein or salts thereof with solvent molecules, e.g. organic solvent molecules and/or water.
[0052] General methods in molecular and cellular biochemistry can be found in such standard textbooks as Molecular Cloning: A Laboratory Manual, 3rd Ed. (Sambrook et al., Harbor Laboratory Press 2001); Short Protocols in Molecular Biology, 4th Ed. (Ausubel et al. eds., John Wiley & Sons 1999); Protein Methods (Bollag et al., John Wiley & Sons 1996); Nonviral Vectors for Gene Therapy (Wagner et al. eds., Academic Press 1999); Viral Vectors (Kaplift & Loewy eds., Academic Press 1995); Immunology Methods Manual (I. Lefkovits ed., Academic Press 1997); and Cell and Tissue Culture: Laboratory Procedures in Biotechnology (Doyle & Griffiths, John Wiley & Sons 1998), the disclosures of which are incorporated herein by reference. In embodiments, there may be employed conventional molecular biology, microbiology, and recombinant DNA techniques within the skill of the art. Such techniques are explained fully in the literature. See, e.g., Sambrook et al, 2001, Molecular Cloning: A Laboratory Manual; Ausubel, ed., 1994, Current Protocols in Molecular Biology Volumes I-III; Celis, ed., 1994, Cell Biology: A Laboratory Handbook Volumes I-III; Coligan, ed., 1994, Current Protocols in Immunology Volumes I-III; Gait ed., 1984, Oligonucleotide Synthesis; Hames & Higgins eds., 1985, Nucleic Acid Hybridization; Hames & Higgins, eds., 1984, Transcription And Translation; Freshney, ed., 1986, Animal Cell Culture; IRL Press, 1986, Immobilized Cells And Enzymes; Perbal, 1984, A Practical Guide To Molecular Cloning.
[0053] Before embodiments are further described, it is to be understood that this disclosure is not limited to particular embodiments described, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.
[0054] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the invention. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the invention, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the invention.
[0055] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can also be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.
DETAILED DESCRIPTION OF THE EMBODIMENTS
[0056] Throughout the specification and claims, a given chemical formula or name shall encompass all optical and stereoisomers, as well as racemic mixtures where such isomers and mixtures exist.
[0057] The present disclosure provides therapeutic and preventative agents for treating or preventing diseases, disorders and conditions involving cancer. Non-limiting examples of diseases, disorders and conditions involving cancer such as kidney cancer, include one or more renal cell carcinomas (RCC) such as clear cell (ccRCC), papillary, chromophobe, collecting duct, or otherwise unclassified renal cell carcinoma. In embodiments, conditions for treatment include metastasis.
[0058] In embodiments, the present disclosure includes one or more polycyclic compounds, or pharmaceutically acceptable salts or solvates thereof, including: one or more PP5 inhibitors, such as, for example:
##STR00009## ##STR00010##
[0059] In embodiments, the one or more compounds target complex Ila and/or induce the extrinsic apoptotic pathway in cancer cells. For example, the compounds of the present disclosure destabilize complex Ila, which typically includes PP5, FADD, ProCasp8, and RIPK1 constituents.
[0060] Advantages of the present disclosure include compositions and methods for treating, ameliorating, or preventing cancer. In embodiments, compositions are provided that are pharmaceutically acceptable. In embodiments, compositions of the present disclosure target, bind, and/or selectively bind to PP5. In embodiments, compositions of the present disclosure induce the extrinsic apoptotic pathway in cancer cells.
[0061] In embodiments, a compound of the present disclosure is
##STR00011##
or a pharmaceutically acceptable salt or solvate thereof.
[0062] In embodiments, a compound of the present disclosure is
##STR00012##
or a pharmaceutically acceptable salt or solvate thereof.
[0063] In embodiments, a compound of the present disclosure is
##STR00013##
[0064] In embodiments, a compound of the present disclosure is
##STR00014##
or a pharmaceutically acceptable salt or solvate thereof.
[0065] In embodiments, a compound of the present disclosure is
##STR00015##
or a pharmaceutically acceptable salt or solvate thereof.
[0066] In embodiments, a compound of the present disclosure is
##STR00016##
or a pharmaceutically acceptable salt or solvate thereof.
[0067] In embodiments, a compound of the present disclosure is
##STR00017##
or a pharmaceutically acceptable salt or solvate thereof.
[0068] In embodiments, a compound of the present disclosure is
##STR00018##
or a pharmaceutically acceptable salt or solvate thereof.
[0069] In embodiments, a compound of the present disclosure is
##STR00019##
or a pharmaceutically acceptable salt or solvate thereof.
[0070] In embodiments, a compound of the present disclosure is
##STR00020##
or a pharmaceutically acceptable salt or solvate thereof, and combinations thereof.
[0071] In embodiments, one or more compounds or formulas as disclosure herein is provided as a pharmaceutically acceptable salt such as derivatives of one or more of the polycyclic compounds of the present disclosure. In embodiments, a parent compound such as a polycyclic compound of the present disclosure is modified by converting an existing acid or base moiety thereof to a salt form. Examples of pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines; alkali or organic salts of acidic residues such as carboxylic acids; and the like. In embodiments, the pharmaceutically acceptable salts of the present disclosure include the conventional non-toxic salts of the parent compound formed, for example, from non-toxic inorganic or organic acids. The pharmaceutically acceptable salts of the present disclosure can be synthesized from the parent compound which contains a basic or acidic moiety by conventional chemical methods. Generally, such salts can be prepared by reacting the free acid or base forms of these compounds with a stoichiometric amount of the appropriate base or acid in water or in an organic solvent, or in a mixture of the two; generally, nonaqueous media like ether, ethyl acetate, ethanol, isopropanol, or acetonitrile.
[0072] In embodiments, the polycyclic compounds of the present disclosure may possess one or more stereocenters, and each stereocenter may exist independently in either the R or S configuration.
[0073] It is also to be understood that compounds that have the same molecular formula but differ in the nature or sequence of bonding of their atoms or the arrangement of their atoms in space are termed isomers. Isomers that differ in the arrangement of their atoms in space are termed stereoisomers, for example, diastereomers, enantiomers, and atropisomers. Stereoisomers that are not mirror images of one another are termed diastereomers and those that are non-superimposable mirror images of each other are termed enantiomers. When a compound has an asymmetric center, for example, it is bonded to four different groups, a pair of enantiomers is possible. An enantiomer can be characterized by the absolute configuration of its asymmetric center and is described by the R- and S-sequencing rules of Cahn and Prelog, or by the manner in which the molecule rotates the plane of polarized light and designated as dextrorotatory or levorotatory (i.e., as (+) or ()-isomers respectively). A chiral compound can exist as either individual enantiomer or as a mixture thereof. A mixture containing equal proportions of the enantiomers is called a racemic mixture.
[0074] Unless indicated otherwise, the description or naming of a particular compound in the specification and claims is intended to include both individual enantiomers and mixtures, racemic or otherwise, thereof. Within the present disclosure, any open valency appearing on a carbon, oxygen, or nitrogen atom in any structure described herein indicates the presence of a hydrogen atom. Where a chiral center exists in a structure, but no specific stereochemistry is shown for that center, both enantiomers, separately or as a mixture, are encompassed by that structure. The methods for the determination of stereochemistry and the separation of stereoisomers are well-known in the art.
[0075] In embodiments, the polycyclic compounds may exist as tautomers. All tautomers are included within the scope of the compounds presented herein.
[0076] Compounds described herein also include isotopically-labeled compounds wherein one or more atoms is replaced by an atom having the same atomic number, but an atomic mass or mass number different from the atomic mass or mass number usually found in nature. Non-limiting examples of isotopes suitable for inclusion in the compounds described herein include and are not limited to .sup.2H or deuterium. In one embodiment, isotopically-labeled compounds are useful in drug or substrate tissue distribution studies. In another embodiment, substitution with heavier isotopes such as deuterium affords greater metabolic stability (for example, increased in vivo half-life or reduced dosage requirements).
[0077] In embodiments, the compounds described herein are labeled by other means, including, but not limited to, the use of chromophores or fluorescent moieties, bioluminescent labels, or chemiluminescent labels.
[0078] In embodiments, the compounds described herein, and other related compounds having different substituents are synthesized using techniques and materials described herein and as described, for example, in Fieser and Fieser's Reagents for Organic Synthesis, Volumes 1-17 (John Wiley and Sons, 1991); Rodd's Chemistry of Carbon Compounds, Volumes 1-5 and Supplementals (Elsevier Science Publishers, 1989); Organic Reactions, Volumes 1-40 (John Wiley and Sons, 1991), Larock's Comprehensive Organic Transformations (VCH Publishers Inc., 1989), March, Advanced Organic Chemistry 4.sup.th Ed., (Wiley 1992); Carey and Sundberg, Advanced Organic Chemistry 4th Ed., Vols. A and B (Plenum 2000, 2001), and Green and Wuts, Protective Groups in Organic Synthesis 3rd Ed., (Wiley 1999) (all of which are incorporated by reference for such disclosure). General methods for the preparation of compound as described herein are modified by the use of appropriate reagents and conditions, for the introduction of the various moieties found in the formula as provided herein. See also Sergey I. Filimonov, Mikhail K. Korsakov, Dmitry V. Kravchenko, Mikhail V. Dorogov, Sergey E. Tkachenko, Alexandre V. Ivachtchenko, Convenient Synthesis of Novel 5-Substituted 3-Methylisoxazole-4-sulfonamides, J. Heterocyclic Chem., 43, 663 (2006)(e.g., see the left hand column of page 664, and Scheme 1, step iii shown therein and organic synthesis described therein); Hewings, Fedorov, Filippakopoulos, Martin, Picaud, Tumber, Wells, Olcina, Freeman, Gill, Ritchie, Sheppard, Russell, Hammond, Knapp, Brennan, and Conway, Optimization of 3,5-Dimethylisoxazole Derivatives as Potent Bromodomain Ligands, Journal of Medicinal Chemistry 2013 56 (8), 3217-3227; and A. Alberola, A. M. Gonzalez, M. A. Laguna, F. J. Pulido, Synthesis of 4-Functionalized 2-Isoxazolines by Reduction of the Isoxazole Ring with Complex Metal Hydrides, Synthesis 1983; 1983(5): 413-414 DOI: 10.1055/s-1983-30361 (all of which are entirely incorporated by reference).
[0079] Compounds described herein are synthesized using any suitable procedures starting from compounds that are available from commercial sources or are prepared using procedures described herein.
[0080] In embodiments, the one or more compounds of the present disclosure, or pharmaceutically acceptable salts or solvates thereof of the present disclosure are suitable for use in treating, ameliorating, or preventing diseases, disorders and conditions involving cancer. In embodiments, compositions are provided that are pharmaceutically acceptable, and/or may cross the blood/brain barrier. In embodiments, compositions of the present disclosure target, bind, and/or selectively bind to PP5 to minimize, alleviate or end downstream deleterious aspects associated therewith and/or induce an extrinsic apoptotic pathway. Non-limiting examples of diseases, disorders and conditions involving cancer include those described herein above such as sarcomas and the like.
[0081] Provided herein are methods of treating a medical condition involving cancer in a subject in need thereof by administering to the subject an effective amount of a polycyclic compound of the present disclosure such as those identified above and in the Figures. In embodiments, the medical condition involving cancer include one or more renal cell carcinomas (RCC) such as clear cell (ccRCC), papillary, chromophobe, collecting duct, or otherwise unclassified renal cell carcinoma. Other kidney cancers may include transitional cell carcinoma, Wilms' tumor, or renal sarcoma. In embodiments, conditions for treatment include metastasis.
[0082] In some embodiments, the effective amount is an amount sufficient to block one or more harmful effects of a nonfunctional extrinsic apoptotic pathway in one or more cancer cells. In embodiment, the effective amount is an amount sufficient to enable a nonfunctional extrinsic apoptotic pathway in a cancer cell or tumor. In embodiments, pharmaceutical agents of the present disclosure are provided in a therapeutically acceptable amount, in a form characterized as pharmaceutically acceptable.
[0083] In embodiments, the present disclosure includes a method of inhibiting cancer cells or a tumor by targeting PP5 in a subject in need thereof by administering to the subject a therapeutically effective amount of a polycyclic compound of the present disclosure such as those shown above and in the accompanying figures, or a pharmaceutically acceptable salt or solvate thereof.
[0084] In embodiments, the compositions of the present disclosure are suitable for use in a pharmaceutically acceptable formulation. In embodiments, the present disclosure includes a pharmaceutical formulation including a polycyclic compound of the present disclosure, or a pharmaceutically acceptable salt, and a pharmaceutically acceptable carrier. In embodiments, a polycyclic compound of the present disclosure may be referred to as an active compound. Pharmaceutical formulations including the active compounds also are provided herein. These pharmaceutical formulations include active compounds as described herein, in a pharmaceutically acceptable carrier. Pharmaceutical formulations can be prepared for oral, intravenous, or aerosol administration. Also, the presently disclosed subject matter provides such active compounds that have been lyophilized and that can be reconstituted to form pharmaceutically acceptable formulations for administration, for example, as by intravenous or intramuscular injection. In embodiments, a therapeutically effective dosage of any specific active compound, the use of which is within the scope of embodiments described herein, will vary somewhat from compound to compound, and patient to patient, and will depend upon the condition of the patient and the route of delivery.
[0085] Administration/Dosage/Formulations: In embodiments, provided herein is a pharmaceutical composition including at least one polycyclic compound of the present disclosure, or a pharmaceutically acceptable salt or solvate thereof. Actual dosage levels of the active ingredients in the pharmaceutical compositions of this disclosure may be varied to obtain an amount of the active ingredient that is effective to achieve the desired therapeutic response for a particular patient, composition, and mode of administration, without being toxic to the patient.
[0086] In embodiments, the selected dosage level will depend upon a variety of factors including the activity of the particular compound employed, the time of administration, the rate of excretion of the compound, the duration of the treatment, other drugs, compounds or materials used in combination with the compound, the age, sex, weight, condition, general health and prior medical history of the patient being treated, and like factors well, known in the medical arts.
[0087] A medical doctor, e.g., physician or veterinarian, having ordinary skill in the art may readily determine and prescribe the effective amount of the pharmaceutical composition required. For example, the physician or veterinarian could begin administration of the pharmaceutical composition to dose the polycyclic compound of the present disclosure, at levels lower than that required to achieve the desired therapeutic effect and gradually increase the dosage until the desired effect is achieved.
[0088] In some embodiments, the compounds and salts disclosed herein may be administered as a solvate in a continuous manner. For example, a single dose may be administered to a subject as a solvate (e.g., intravenously or a delayed release capsule) for an administration period of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 30, 45, or 60 minutes. In some embodiments, a single dose may be administered to a subject as a solvate for an administration period of 1-5, 5-10, 10-15, 15-30, 30-45, or 45-60 minutes. In some embodiments, a single dose may be administered to a subject as a solvate for an administration period of 1-60 minutes. In some embodiments a single dose may be administered to a subject for an administration period of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 36, 48, 60, or 72 hours. In some embodiments a single dose may be administered to a subject for an administration period of 1-6, 6-12, 12-24, 24-48, 48-60, 60-72 hours. In some embodiments a single dose may be administered to a subject for an administration period of 1-72 hours.
[0089] In some embodiments, multiple doses of the compounds and salts described herein may be administered to a subject in a pulsatile or intermittent manner. As used herein the term pulsatile dose regimen or intermittent dose regimen refers to a dose administration regimen which includes at least two dosing cycles. Each subsequent dosing cycle is separated by a rest period from the preceding dosing cycle.
[0090] In particular embodiments, it is especially advantageous to formulate the compound in dosage unit form for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suited as unitary dosages for the patients to be treated, each unit containing a predetermined quantity of the polycyclic compound of the present disclosure calculated to produce the desired therapeutic effect in association with the required pharmaceutical vehicle. The dosage unit forms of the disclosure are dictated by and directly dependent on (a) the unique characteristics of the polycyclic compound of the present disclosure and the particular therapeutic effect to be achieved, and (b) the limitations inherent in the art of compounding/formulating such a polycyclic compound of the present disclosure for treatment in a patient.
[0091] In one embodiment, the compounds of the disclosure are formulated using one or more pharmaceutically acceptable excipients or carriers. In one embodiment, the pharmaceutical compositions of the invention comprise a therapeutically effective amount of a polycyclic compound of the present disclosure, and a pharmaceutically acceptable carrier.
[0092] Routes of administration of any of the compositions of the disclosure include oral, nasal, rectal, intravaginal, parenteral, buccal, sublingual or topical. The compounds for use in the disclosure may be formulated for administration by any suitable route, such as for oral or parenteral, for example, transdermal, transmucosal (e.g., sublingual, lingual, (trans)buccal, (trans)urethral, vaginal (e.g., trans- and perivaginally), (intra)nasal and (trans)rectal), intravesical, intrapulmonary, intraduodenal, intragastrical, intrathecal, subcutaneous, intramuscular, intradermal, intra-arterial, intravenous, intrabronchial, inhalation, and topical administration.
[0093] Suitable compositions and dosage forms include, for example, tablets, capsules, caplets, pills, gel caps, troches, dispersions, suspensions, solutions, syrups, granules, beads, transdermal patches, gels, powders, pellets, magmas, lozenges, creams, pastes, plasters, lotions, discs, suppositories, liquid sprays for nasal or oral administration, dry powder or aerosolized formulations for inhalation, compositions and formulations for intravesical administration and the like. It should be understood that the formulations and compositions that would be useful in the present disclosure are not limited to the particular formulations and compositions that are described herein.
[0094] For oral application, particularly suitable are tablets, dragees, liquids, drops, suppositories, or capsules, caplets and gelcaps. The compositions intended for oral use may be prepared according to any method known in the art and such compositions may contain one or more agents selected from the group consisting of inert, non-toxic pharmaceutically excipients that are suitable for the manufacture of tablets. Such excipients include, for example an inert diluent such as lactose; granulating and disintegrating agents such as cornstarch; binding agents such as starch; and lubricating agents such as magnesium stearate. The tablets may be uncoated or they may be coated by known techniques for elegance or to delay the release of the active ingredients. Formulations for oral use may also be presented as hard gelatin capsules wherein the active ingredient is mixed with an inert diluent.
[0095] For parenteral administration, the polycyclic compound of the present disclosure may be formulated for injection or infusion, for example, intravenous, intramuscular or subcutaneous injection or infusion, or for administration in a bolus dose or continuous infusion. Suspensions, solutions or emulsions in an oily or aqueous vehicle, optionally containing other formulatory agents such as suspending, stabilizing or dispersing agents may be used.
[0096] In some embodiments, the present disclosure includes a method of treating cancer, including: a) providing i) a subject with cancer, ii) one or more protein phosphatase-5 inhibitors, and b) treating said subject with the one or more PP5 inhibitors. In embodiments, treating includes administering a therapeutically effective amount of one or more protein phosphatase-5 inhibitors to the subject. In embodiments, the cancer is renal cancer such as renal cell carcinoma. In embodiments, the one or more protein phosphatase-5 inhibitors are characterized as a PP5 specific inhibitor. In embodiments, the one or more protein phosphatase-5 inhibitors are selected from the group consisting of:
##STR00021## ##STR00022## ##STR00023## ##STR00024## ##STR00025##
or a pharmaceutically acceptable salt thereof, and combinations thereof. In some embodiments, treating the subject with the one or more protein phosphatase-5 inhibitors is sequential. In embodiments, treating the subject with the one or more protein phosphatase-5 inhibitors is simultaneous. In embodiments, treating with the one or more protein phosphatase-5 inhibitors results in reduced proliferation of at least some of the cancer cells within said subject.
[0097] In some embodiments, the present disclosure includes a method of treating cancer, including a) providing i) a subject with cancer and one or more compounds of: selected from the group consisting of
##STR00026##
or a pharmaceutically acceptable salt thereof,
##STR00027##
or a pharmaceutically acceptable salt thereof,
##STR00028##
or a pharmaceutically acceptable salt thereof,
##STR00029##
or a pharmaceutically acceptable salt thereof,
##STR00030##
or a pharmaceutically acceptable salt thereof,
##STR00031##
or a pharmaceutically acceptable salt thereof,
##STR00032##
or a pharmaceutically acceptable salt thereof,
##STR00033##
or a pharmaceutically acceptable salt thereof,
##STR00034##
or a pharmaceutically acceptable salt thereof,
##STR00035##
or a pharmaceutically acceptable salt thereof, and combinations thereof, and b) treating the subject with the one or more compounds or pharmaceutically acceptable salts thereof.
[0098] In some embodiments, the present disclosure includes a pharmaceutical anticancer composition including one or more PP5 inhibitors, or pharmaceutically acceptable salts thereof. In embodiments, the composition is characterized as PP5 specific. In embodiments, the one or more PP5 inhibitors are selected from the group consisting of:
##STR00036##
or a pharmaceutically acceptable salt thereof,
##STR00037##
or a pharmaceutically acceptable salt thereof,
##STR00038##
or a pharmaceutically acceptable salt thereof,
##STR00039##
or a pharmaceutically acceptable salt thereof,
##STR00040##
or a pharmaceutically acceptable salt thereof,
##STR00041##
or a pharmaceutically acceptable salt thereof,
##STR00042##
or a pharmaceutically acceptable salt thereof,
##STR00043##
or a pharmaceutically acceptable salt thereof,
##STR00044##
or a pharmaceutically acceptable salt thereof,
##STR00045##
or a pharmaceutically acceptable salt thereof, and combinations thereof.
[0099] In some embodiments, the present disclosure includes a method of treating cancer, including contacting one or more cancer cells, or a cancerous tumor, with a therapeutically effective amount of one or more protein phosphatase-5 inhibitors. In embodiments, the contacting is characterized as in vivo, and activates an inactivated extrinsic apoptosis pathway.
[0100] In some embodiments, the present disclosure includes a method of treating cancer, including a) providing i) a subject with cancer, ii) one or more protein phosphatase-5 inhibitors, and b) treating said subject with the one or more PP5 inhibitors. In embodiments, treating includes administering a therapeutically effective amount of one or more protein phosphatase-5 inhibitors to the subject. In embodiments, the cancer is renal cancer. In embodiments, the renal cancer is renal cell carcinoma. In embodiments, the one or more protein phosphatase-5 inhibitors are characterized as a PP5 specific inhibitor. In embodiments, the one or more protein phosphatase-5 inhibitors are selected from the group consisting of:
##STR00046## ##STR00047## ##STR00048## ##STR00049##
and combinations thereof. In some embodiments, treating the subject with the one or more protein phosphatase-5 inhibitors is sequential. In embodiments, treating the subject with the one or more protein phosphatase-5 inhibitors is simultaneous. In embodiments, treating with the one or more protein phosphatase-5 inhibitors results in reduced proliferation of at least some of the cancer cells within said subject.
[0101] In embodiments the present disclosure includes a method of treating cancer, including: a) providing i) a subject with cancer and one or more compounds of:
##STR00050##
and b) treating the subject with the one or more compounds. In embodiments, the one or more compounds is provided in a therapeutically acceptable amount.
[0102] In some embodiments, the present disclosure includes a method of treating cancer, including: a) providing i) a subject with cancer and one or more compounds of:
and b) treating the subject with the one or more compounds.
[0103] In embodiments, the present disclosure includes a pharmaceutical anticancer composition including one or more PP5 inhibitors. In embodiments, the composition is characterized as PP5 specific. In embodiments, the one or more PP5 inhibitors are selected from the group consisting of:
##STR00051##
and combinations thereof.
[0104] In embodiments, the present disclosure includes a pharmaceutical anticancer composition including one or more PP5 inhibitors. In embodiments, the composition is characterized as PP5 specific. In embodiments, the one or more PP5 inhibitors are selected from the group consisting of:
##STR00052## ##STR00053## ##STR00054##
and combinations thereof.
[0105] Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation, numerous equivalents to the specific procedures, embodiments, claims, and examples described herein. Such equivalents were considered to be within the scope of this invention and covered by the claims appended hereto. For example, it should be understood, that modifications in reaction conditions, including but not limited to reaction times, reaction size/volume, and experimental reagents, such as solvents, catalysts, pressures, atmospheric conditions, and reducing/oxidizing agents, with art-recognized alternatives and using no more than routine experimentation, are within the scope of the present disclosure.
[0106] It is to be understood that wherever values and ranges are provided herein, all values and ranges encompassed by these values and ranges, are meant to be is encompassed within the scope of the present invention. Moreover, all values that fall within these ranges, as well as the upper or lower limits of a range of values, are also contemplated by the present application.
[0107] The following examples further illustrate aspects of the present disclosure. However, they are in no way a limitation of the teachings or disclosure of the present disclosure as set forth herein.
DETAILED DESCRIPTION OF THE INVENTION
[0108] The serine/threonine protein phosphatase PP5 regulates several signaling cascades that are responsible for tumor initiation, progression and metastasis. Unlike other family members, a single gene encodes PP5, and its regulatory and catalytic domains are all contained within the same polypeptide. PP5 generally has low basal activity due to the interaction of the tetratricopeptide repeat (TPR) motif at its amino-terminus with the J-helix in the carboxy-terminus. This autoinhibitory state prevents substrates from entering the active site of PP5. Additionally, PP5 is a co-chaperone of the molecular chaperone heat shock protein-90 (Hsp90). Binding of PP5's TPR domain Hsp90 releases its autoinhibition and activates PP5. Other cellular factors such as polyunsaturated fatty acids have also been described to activate PP5 in vitro. Furthermore, we have shown that post-translational modifications of PP5 play a major is role in its switching on and off in cells. The Von Hippel-Lindau (VHL) tumor suppressor gene is the recognition subunit of an E3 ubiquitin ligase that canonically recognizes its substrates following an oxygen-dependent prolyl-hydroxylase (PHD) reaction, with hypoxia-inducible factor (HIF) being its most-studied substrate. However, previous studies, including from our group, have demonstrated an oxygen and PHD-independent function for VHL. VHL is involved in multi-monoubiquitination and subsequent proteasomal degradation of PP5 in a hypoxia- and prolyl-hydroxylation-independent manner in normal cells therefore providing an off switch for PP5. The most common type of kidney cancer, clear cell renal cell carcinoma (ccRCC), is closely associated with mutations and inactivation of the VHL tumor suppressor gene. We have previously shown that VHL-deficient renal cancer cell lines and patient-derived ccRCC tumors exhibit elevated PP5 levels. Additionally, casein kinase 1 (CK1)-mediated phosphorylation of T362 in the catalytic domain of PP5 activates this phosphatase. Pharmacological inhibition of CK1 or down-regulation of PP5 induced apoptosis and reduced proliferation in VHL-null ccRCC cells, suggesting a prosurvival role for PP5 in kidney cancer. The mechanism of PP5-dependent cell survival and whether PP5 can be directly targeted, however, remains elusive.
[0109] In this study we used in silico structure-based drug discovery approach and identified a small molecule (P053) that specifically binds and inhibits PP5 activity. Inhibition of PP5 in VHL-null ccRCC cells leads to induction of the extrinsic apoptotic pathway. We found that PP5 interacts with the extrinsic apoptotic complex II members FADD, RIPK1, and caspase 8 and dephosphorylates S194-FADD in an Hsp90 independent manner. Inhibition or down-regulation of PP5 leads to disassociation of this complex, cleavage of caspase 8 and activation of the extrinsic apoptotic pathway in ccRCC.
[0110] Characterization of PP5 specific inhibitors: Since PP5 plays a major role in survival of ccRCC, we sought to design, develop, and test specific small molecule inhibitors of this phosphatase 3. In order to identify small molecule antagonists of PP5 an in silico docking study was initiated using our previously solved X-ray crystal structure of the PP5 active site (PDB:5HPE) 6. The PP5 structure allowed us to employ a virtual screening strategy to identify new inhibitors of PP5 (
[0111] We first treated the ccRCC cell line 786-O with the overlapping hit compound P0 and showed a dose dependent increase in phosphorylation of the known PP5 substrates phospho-S13-Cdc37 and phospho-S211-GR (
[0112] PP5 inhibitors specifically bind to the phosphatase-catalytic domain: We next sought to measure the inhibition of PP5 activity in vitro with P5 and P13. This was done using custom synthesized phospho-S211-glucocorticoid receptor (GR) peptide as a specific substrate and measuring PP5 activity by assessing free phosphate release as a result of PP5-mediated peptide dephosphorylation. As expected, our enzyme kinetics confirmed P5 and P13 to be competitive inhibitors of PP5 (
[0113] We then mutated docking site residues in the active site of PP5 to obtain further insight into the mechanism of P13 binding to PP5. These included H304Q (catalytically inactive), M309C (prevents dephosphorylation of substrate phospho-Ser13-Cdc37), and W386F (hyperactivity against substrates) as well as additional mutants which help coordinate substrate binding based on our previously published work: R275A, R400A and Y451F (
[0114] We next synthesized BODIPY-labelled version of compound P13 (P13-BODIPY) in order to obtain the binding affinity of this inhibitor to PP5 in vitro (
[0115] Design, synthesis and characterization of a more potent PP5 inhibitor: Next used an in silico docking strategy to design series of small molecule inhibitors of PP5 based on the structure of P13 as a starting point. Examination of the docking pose of compound P13 in the active site of PP5 where the isoxazole is coordinating to the metal ions yielded some ideas about modifications that could be beneficial for binding. Neighboring the binding site was a nonpolar pocket near W386 and M309, which might accommodate a tethered nonpolar group off the xylene ring of P13. Additionally, a more polar pocket near R400 and D388 might also be accessible for an alcohol or amide tethered through the sulfonamide nitrogen of P13. Using this model as a guide, a number of sulfonamide analogs were designed and docked into the PP5 active site using Autodock Vina. This docking gave a number of potential new PP5 inhibitors that were predicted to bind to the active site of PP5 with greater affinity than the parent P13 compound. This led to synthesis of a series of compounds: P052 (16), P053 (20), P058 (22), P059 (17), P062 (18), P070 (19), P075 (23) and P129 (21) (
[0116] We next treated the ccRCC cell line 786-O with 10 M of the compounds shown in
[0117] PP5 attenuation induces extrinsic apoptosis in clear cell renal cell cancer: Our data obtained here as well as our previous work showed that pharmacologic inhibition or silencing of PP5 in VHL-null ccRCC induced apoptosis.sup.2. Given this, we asked whether the observed apoptosis resulted from the intrinsic or extrinsic signaling pathway. First, treatment of VHL-null ccRCC lines 786-O with P053 caused increased cleavage of the executioner caspase 3 and the downstream target poly-ADP ribose polymerase (PARP), hallmarks of generalized cell death (
[0118] PP5 dephosphorylates FADD: To determine which aspect of extrinsic apoptosis is regulated by PP5, we examined PP5 association with extrinsic apoptosis proteins Fas-Associated by Death Domain (FADD) and Receptor Interacting Serine/Threonine Kinase 1 (RIPK1). These two proteins, along with caspase 8, comprise complex II of the extrinsic apoptotic pathway (
[0119] Phosphorylation of S194-FADD is important for its pro-apoptotic activity, therefore we hypothesized that PP5 targets and dephosphorylates S194-FADD to suppress apoptosis. Indeed, we found that overexpression of PP5 in 786-O cells led to decreased S194-FADD phosphorylation (
[0120] PP5 associates with intact Complex II: To gain further understanding of the dynamic of PP5 interaction with complex II, we used CRISPR/Cas9 mediated-knockout (KO) of PP5, FADD and RIPK1 in HAP1 cells. These haploid cell lines are a great resource for gene deletion in mammalian cells.sup.36. Immunoprecipitation (IP) of FADD from PP5 KO cells showed FADD interaction with RIPK1 was abrogated (
[0121] We have shown that FADD and RIPK1 interaction is dependent on their death domains. In order to determine whether the death domain (DD) is involved in complex formation with PP5 in a cellular context we created truncated FADD (FADD-DD) (
[0122] Since a vast majority of PP5 substrates are also clients of the molecular chaperone Hsp90, we asked whether RIPK1 and FADD are clients of this chaperone. We therefore performed a time course assay using the Hsp90 inhibitor SNX-2112 (2 M) in HEK293 cells. Upon inhibition of Hsp90 clients such as Tsc2, Akt and phos-Ser473-Akt were destabilized and degraded (
[0123] Discussion: PP5 plays a significant role in proliferation and survival of multiple cancers including kidney cancer. Our previous work has shown that downregulation of PP5 or pharmacologic inhibition of its regulator CK1 caused induction of apoptosis. Here we dissected the induction of this pathway and demonstrated the direct involvement of PP5 in the extrinsic apoptotic pathway. Presence of functional PP5 appears to be important for interaction of FADD and RIPK1. Phosphorylation of S194-FADD has been shown previously to be important for its pro-apoptotic activity and suppresses tumorigenesis. Our data suggest that PP5 mediates dephosphorylation of S194-FADD, independent of Hsp90 and facilitates FADD binding to RIPK1 via their death domains. The presence of active PP5 in complex II appears to maintain suppression of extrinsic apoptosis in VHL-null ccRCC and blocks the cleavage of caspase 8. Downregulation or inhibition of PP5 leads to increased phosphorylation of S194-FADD as well as cleavage of caspase 8 and induction of the extrinsic apoptotic pathway in VHL-null ccRCC. Of note, it has also been shown that many ccRCCs exhibit lower levels of FADD than adjacent normal kidney, however, it is not yet clear whether this may be related to PP5 upregulation and how FADD is functioning in that context. Furthermore, S194-FADD phosphorylation has also been shown to regulate FADD function in cell cycle regulation. PP5 plays a number of roles in cell cycle regulation and this may be in part through FADD.
[0124] There are currently no reports of compounds that specifically inhibit PP5 function within cells. Zhang et al. designed a bifunctional molecule phosphatase recruiting chimera (PHORC) to specifically activate PP5 phosphatase activity toward the substrate Ask1. As PP5 is upregulated in a wide variety of cancers, a similar approach such as using Proteolysis Targeting Chimeras (PROTACs) to specifically degrade PP5 may be beneficial for cancer therapy. Interestingly, LB-100, which has been developed as a specific PP2A inhibitor and is now in both phase 1 and phase 2 clinical trials for various cancers, has also been shown to inhibit PP5 and PP1. There are numerous reports highlighting the role of PP5 in cancer progression and survival due to its functions in cell cycle regulation, DNA damage response, and signaling pathways. These observations suggest a therapeutic benefit of PP5 inhibitors for the clinical treatment of a wide variety cancers. Furthermore, the detailed molecular mechanism of the prosurvival role of PP5 in renal cancer prompted us to screen for and identify a small molecule inhibitor for this phosphatase. We took advantage of available X-ray crystal structures of the PP5 active site and performed threefold docking due to the promiscuity of PP5 to the metal ion in the active site, which can be a Zn, Mn or an Fe ion. We chose residues D271, N303, H304, M309, and W386 to define the active site for docking, as these residues are near the metal ions in the active site of PP5. Our in silico screen and further cell-based assays led us to the identification of two compounds, P5 and P13. We further developed and synthesized the P053 compound based on P13. These inhibitors have high affinity (nM range) towards PP5 and appear to make contact with the active-site residues H304, M309, W386 and R400 within the substrate-binding pocket. We also found these compounds can bind to PP5 from VHL-null ccRCC and cause apoptosis in these cells. Interestingly, although the PP5 active-site residues are conserved in other phosphatases such as PP2A, we did not observe any binding of our compounds to PP2AC, which is the catalytic subunit of PP2A, from cell lysate at the concentration at which they bound PP5.
[0125] The role of PP5 in cancer cell proliferation and survival as well as its unique structure make it an attractive therapeutic target. Important next steps for further evaluation of these PP5 inhibitors are to examine their pharmacokinetic and pharmacodynamic parameters as well as their effect on VHL-null ccRCC xenograft models. Examination in other cancers in which PP5 has been seen to play a pro-tumorigenic role is also warranted. Further refinement may be needed to optimize their on-target effects, but ultimately this work reveals a potential for small molecule PP5 inhibition in the clinic.
[0126] Limitations of the study: The PP5 inhibitors designed in this study bind specifically to and inhibit PP5 in vitro at nM range. However, in the cellular context, we used these PP5 inhibitors at low M in order to achieve apoptosis in ccRCC cell lines. Although we do not currently have experimental evidence, there are a number of reasons that can potentially explain this phenomenon. For instance, these drugs must cross the plasma membrane to enter the cell and inhibit the target, and therefore higher amounts are needed to achieve a potent inhibitory effect. Additionally, the PP5 protein used in our biochemical analysis was expressed and purified from bacteria, and therefore it is devoid of any posttranslational modifications. However, PP5 targeted in ccRCC cells is subjected to various posttranslational modifications and this may potentially impact the binding affinity to the small molecule inhibitors of PP5.
[0127] Significance: Protein phosphatase 5 is a serine/threonine phosphatase and a co-chaperone of Hsp90 that helps regulate an array of cellular functions including stress response, proliferation, apoptosis, and DNA repair.sup.3. PP5 plays a significant role in survival and propagation of multiple cancers, which makes it a promising target for cancer therapy. Though there are several naturally occurring phosphatase inhibitors, none are specific for PP5. Additionally, the detailed molecular mechanism of PP5 prosurvival role in cancer has remained elusive. In this manuscript we have addressed these two overarching gaps in our knowledge. We previously solved the X-ray crystal structure of PP5 bound to its substrate peptide Cdc37.sup.6. We used this information as well as other X-ray crystal structures of PP5 to conduct an in silico drug screen. This led to identification and development of a selective and competitive inhibitors of PP5. To our knowledge, this is the first known compound that specifically targets only the PP5 phosphatase. The second part of this story focuses on dissecting the molecular mechanism of PP5 in cancer cell survival. We previously reported the prosurvival role of PP5 in kidney cancer 2. In this study we provide a mechanistic understanding of PP5 role in cells. We demonstrated that PP5 interacts with FADD, RIPK1 and caspase 8, components of the extrinsic apoptotic pathway complex II. Specifically, PP5 dephosphorylates and inactivates the death effector protein FADD in an Hsp90 independent manner, therefore preserving complex II integrity and regulating extrinsic apoptosis. Small molecule inhibition of PP5 activates this pathway, presenting a viable therapeutic strategy for renal cancer.
[0128] Experimental Model And Subject Details Cell lines: Cultured human embryonic kidney (HEK293) and human kidney 2 (HK2) cells were grown in Dulbecco's Modified Eagle Medium (DMEM, Sigma-Aldrich), 786-O cells in Roswell Park Memorial Institute (RPMI)1640 Medium (Sigma-Aldrich), A498 cells in Minimum Essential Medium (MEM, Sigma-Aldrich), Caki-1 and Caki-2 cells in McCoy's 5A Medium (Sigma-Aldrich) and wild-type (WT) HAP1 and knock-out (KO) cells in Isocove's Modified Dulbecco's Medium (IMDM, Gibco), all supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich). WT-HAP1 and KO cell lines were acquired from Horizon Discovery. All other cell lines were obtained from (American Type Culture Collection, ATCC). Cells were maintained in a CellQ incubator (Panasonic Healthcare) at 37 C. in an atmosphere containing 5% CO.sub.2.
[0129] Plasmids: For mammalian expression, pcDNA3-PP5-FLAG and the M309C and W386F point mutations were created previously. Site-directed mutagenesis was performed to mutate R275A, H304Q, R400A, and Y451 F residues (see Table S1) and confirmed by DNA sequencing. The pcDNA3-FLAG-FADD and pcDNA3-HA-RIPK1 were purchased from Addgene. FLAG-FADD-ADD as well as HA-RIPK1-ADD constructs were subcloned using the primers listed in Table S1. For bacterial expression, we used our previously reported human PP5 gene in pGEX6P1 plasmid with an N-terminal GST tag and C-terminal His.sub.6 tag.
[0130] Method Details Cell Transfection and Treatment: Cultured cells were split and then transfected the following day when about 40% confluent with each construct using Mirus TranslT-2020 (MirusBio) according to manufacturer's protocol. Cells were incubated at 37 C. and then extracted or collected for analysis after 24 hrs (HEK293) or 72 hrs (ccRCC cell lines). Short interfering RNA (siRNA) scramble control and PPP5C (PP5) targeting duplexes were purchased from OriGene (SKU: SR321403A, SR321403B, and SR321403C). Indicated cells were transiently transfected with the siRNA using Mirus TranslT-2020. For PP5 knock-down, either 30 nM of control siRNA or 10 nM of each PP5 siRNA duplex (A, B and C) were mixed prior to transfection. Cells were incubated at 37 C. for 72 hrs, then harvested for protein extraction. To inhibit PP5 activity, 786-O cells were incubated with indicated amount of IC261 (Abcam) for 16 hrs. Blockage of caspase activity was performed by treatment with 10 M of z-VAD-fmk (Enzo Life Sciences) for 1 hr followed by IC261 treatment with the indicated amount for 16 hrs. Cells were then harvested for protein extraction.
[0131] Protein Extraction, Immunoprecipitation and Immunoblotting: Protein extraction from mammalian cells was carried out using methods previously described. Cell lysates were quantified using 1 Bradford reagent (Biorad). For immunoprecipitation, cell lysates were incubated with anti-FLAG antibody conjugated beads (Sigma) or anti-HA conjugated beads (ThermoFisher Scientific) at 4 C. for 2 hrs. Endogenous IPs were achieved by incubating lysate with anti-PP5 antibody (Cell Signaling), anti-FADD antibody (Cell Signaling), or anti-RIPK1 antibody (Cell Signaling) overnight followed by protein G agarose (Invitrogen) at 4 C. for 2 hrs. Immunopellets were washed 4 times with fresh lysis buffer (20 mM Tris-HCl (pH 7.4), 100 mM NaCl, 1 mM MgCl.sub.2, 0.1% NP40, protease inhibitor cocktail (Roche), and PhosSTOP (Roche)) and eluted in 5 Laemmli buffer. Precipitated proteins were separated by SDS-PAGE and transferred to nitrocellulose membranes. Co-immunoprecipitated proteins or proteins from cell lysate were detected with antibodies recognizing FLAG, 6-His (ThermoFisher Scientific), GAPDH (ENZO Life Sciences), Cdc37 (StressMarq), GR, phospho-GR (S211), PP5, caspase-3, cleaved caspase-3, caspase-8, cleaved caspase-8, cleaved caspase-7, cleaved-PARP, phospho-RIPK1 (S166), phospho-FADD (S194), PP2A-C, VHL (Cell Signaling), phospho-RIPK1 (S161) (Invitrogen), PP5 and phospho-Cdc37 (S13) (Abcam). Secondary antibodies raised against mouse and rabbit (Cell Signaling) were used (See Key Resources Table).
[0132] Bacterial Expression and Protein Purification of PP5: Human PPP5c was cloned into pGEX6P1 with an N-terminal GST tag and C-terminal His.sub.6 tag. Transformed cells were grown at 37 C. in LB with 100 mg/L ampicillin until OD.sub.600=0.6 and induced with 1 mM IPTG. Cells were harvested by centrifugation and lysed by sonication in lysis buffer (50 mM Hepes (pH 8.0), 150 mM NaCl, 0.5 mM TCEP and EDTA-free protease inhibitor cocktail tablet (Roche)). Lysate was incubated with talon resin (Takara Bio) for 1 hr at 4 C. The resin was washed three times with lysis buffer and PP5 was eluted with lysis buffer containing 250 mM imidazole. Precision protease was added to the elution overnight to cleave the GST tag and the sample was then mixed with Glutathione Sepharose resin (Cytiva) to remove the free GST and un-cleaved protein. The sample was applied to a Superdex S75 16/60 size exclusion column (GE Healthcare) and eluted in 100 mM NaCl, 20 mM Hepes pH 8, 02 mM TCEP.
[0133] Cell Viability Assay: Renal cancer cell lines 786-O, Caki-2, Caki-1, and A498 as well as the normal renal cell line HK-2 were plated at 10,000 cells per well in 96-well plates. Cells were treated with different amounts of inhibitors (P075, P059, P058, P13, P053) and DMSO was used as control (0 M). After 24 or 48 hrs, cell viability assay was performed using the Quick Cell Proliferation Kit Plus (BioVision) according to the manufacturer's protocol. The absorbance at 450 nm was measured on a Tecan Infinite M200 Pro and proliferation rate was calculated.
[0134] In silico Docking: Virtual high throughput docking simulations were carried out using Dockblaster with the Zinc library of drug like compounds (3.7 million compounds). PDB structures of PP5 (PDB:3H60 and 3H66) were used as receptor structures. In preparation for docking the water molecules were eliminated, and any missing hydrogens and charges were added to the system to generate the receptor input file. The active site residues of D271, N303, H304, M309 and W386 were chosen to define the active site for docking, as these residues are nearby the active site. Once biological activity was of an inhibitor was confirmed, docking was performed again using Autodock Vina (.sup.57 to generate docking poses which were used to guide synthetic efforts. The Autodock docking calculation was carried out using a grid per map with 404040 points of (PDB: 3H60) in addition to a grid-point spacing of 0.375 , which was centered on the metals in the active site.
[0135] Synthesis of Small Molecules: General experimental information for the synthesis of small molecules: All anhydrous reactions were run under a positive pressure of argon. Dichloromethane (DCM) was dried by passage through an alumina column. 1,2-Dichloroethane (DCE) was freshly distilled from calcium hydride before use. Tetrahydrofuran (THF) was freshly distilled from Na/benzophenone still before use. DMF was distilled from calcium hydride under reduced pressure. Ethyl acetate (EA) and hexanes were purchased from commercial sources and used as received. Silica gel column chromatography was performed using 60 silica gel (230-400 mesh). Melting points were obtained on crystalline compounds and are uncorrected. The BODIPY acid 13 was prepared as reported previously.
##STR00055##
[0136] Methyl 3-aminobenzoate 2 (4.23 g, 28.1 mmol) was dissolved in 52 mL DMF and cooled to 0 C. Pyridine (4.1 mL, 51 mmol) was then added and the mixture stirred for 10 minutes. 3,5-Dimethyl-isoxazole-4-sulfonyl chloride 1 (5.00 g, 25.5 mmol) was then added in portions over one hour. The reaction was then allowed to warm to room temperature (RT) and stirred for 16 hrs. The reaction was quenched by adding 1 M HCl until the pH remained below 2 (60 mL). The reaction mixture was then taken up in EA (400 mL) and washed with 1 M HCl (2200 mL) and brine (2200 mL). The organic layer was dried (MgSO.sub.4) and concentrated to give a yellow solid. Purification using silica gel chromatography (50% EA/50% hexanes) provided pure 3 (5.65 g, 72%) as a yellow solid.
[0137] Methyl m-(3,5-dimethyl-4-isoxazolylsulfonylamino)benzoate 3 (P5). mp=140-142 C.; TLC Rf=0.45 (50% EA/50% hexanes); IR (ATR) 3226, 2970, 2359, 2341, 1692, 1588, 1339, 1306 cm.sup.1; .sup.1H NMR (400 MHz, CDCl.sub.3) 7.84-7.81 (m, 2H), 7.79 (bs, 1H), 7.43-7.36 (m, 2H), 3.93 (s, 3H), 2.52 (s, 3H), 2.30 (s, 3H); .sup.13C NMR (100 MHz, CDCl.sub.3) 174.4, 166.6, 157.6, 136.5, 131.5, 129.9, 126.8, 125.7, 122.3, 115.4, 52.8, 12.7, 10.8; HRMS (ESI+) m/z calculated (calcd) for C.sub.13H.sub.14N.sub.2O.sub.5S [M+Na].sup.+: 333.0516, found: 333.0515.
##STR00056##
[0138] Potassium hydroxide (8.5 g, 152 mmol) was dissolved in 40 mL of water and MeOH (160 mL) was added. The ester 3 (P5) (5.2 g, 16.9 mmol) was then added and the reaction mixture was stirred for 16 hrs at RT. The reaction mixture was then quenched by slowly adding 1M HCl until the pH remained below 2 (180 mL). The methanol was then removed in vacuo and the residue was taken up in water (200 mL). This mixture was extracted with EA (3150 mL), and the combined organic extracts were dried (MgSO.sub.4) and concentrated to provide carboxylic acid 4 (4.82 g, 96%) as an off white solid which was used without further purification.
[0139] m-(3,5-Dimethyl-4-isoxazolylsulfonylamino)benzoic acid 4. mp=184-187 C.; TLC Rf=0.51 (100% EA); IR (ATR) 3157, 2980, 2359, 1694, 1590, 1408, 1118 cm.sup.1; .sup.1H NMR (400 MHz, CD.sub.3OD) 7.80-7.78 (m, 2H), 7.42-7.38 (m, 1H), 7.33-7.30 (m, 1H), 2.49 (s, 3H), 2.26 (s, 3H); .sup.13C NMR (100 MHz, CD.sub.3OD) 175.3, 168.8, 158.9, 138.6, 133.2, 130.6, 127.4, 126.7, 123.1, 116.8, 12.5, 10.7.
##STR00057##
[0140] Carboxylic acid 4 (1.0 g, 3.37 mmol) was dissolved in 25 mL DMF and EDCI (0.79 g, 5.05 mmol), HOBt (80%, 0.95 g, 6.31 mmol) and diisopropylethylamine (0.88 mL, 5.05 mmol) were added. After aging for 30 min, tert-butyl piperazine-1-carboxylate (0.94 g, 5.05 mmol) was then added in one portion. The reaction mixture was stirred at RT for 3 hrs, and then quenched by the addition of brine (30 mL). The mixture was then taken up in EA (100 mL) and washed with water (260 mL) and brine (260 mL). The organic layer was then dried (MgSO.sub.4) and concentrated. Purification of the residue using silica gel chromatography (60% EA/40% hexanes) gave amide 5 as a white solid (1.62 g, 94%).
[0141] tert-Butyl 4-[m-(3,5-dimethyl-4-isoxazolylsulfonylamino)benzoyl]-1-piperazine carboxylate 5. mp=187-189 C.; TLC Rf=0.61 (80% EA/20% hexanes); IR (ATR) 3080, 2974, 2359, 2341, 1618, 1614, 1165, 1120 cm.sup.1; .sup.1H NMR (400 MHz, CDCl.sub.3) 8.59 (bs, 1H), 7.32-7.30 (m, 2H), 7.15-7.12 (m, 2H), 3.76-3.37 (m, 8H), 2.49 (s, 3H), 2.28 (s, 3H), 1.47 (s, 9H); .sup.13C NMR (100 MHz, CDCl.sub.3) 173.7, 169.7, 157.6, 154.5, 137.1, 136.2, 129.5, 123.8, 123.3, 121.4, 115.6, 80.6, 47.7, 47.6, 43.5, 42.5, 28.4, 12.6, 10.8.
##STR00058##
[0142] The Boc protected amine 5 (0.95 g, 20.43 mmol) was dissolved in 1:1 DCM:TFA (60 mL) and stirred for 1 hr. The solvent was then evaporated, and the crude TFA salt was used in the next step without further purification. Biotin (1.01 g, 2.19 mmol), EDCI (0.51 g, 3.3 mmol), HOBt (0.62 g, 4.1 mmol) were dissolved in 20 mL of DMF and diisopropylethylamine (0.77 mL, 4.4 mmol) was then added. After stirring for 10 min the crude TFA salt (0.80 g) was then added to the reaction mixture in portions. The reaction was then stirred for 16 hrs at RT. The reaction mixture was then taken up in brine (30 mL) and extracted with EA (330 mL). The combined organic layers were washed with water (230 mL) and brine (230 mL), dried (MgSO.sub.4) and concentrated. Purification using silica gel chromatography (5% MeOH/95% DCM) gave the biotin-P5 6 as a white solid (0.53 g, 40%).
[0143] N-[3-(4-(4-[(3aS,4S,6aR)-2-Oxo-hexahydro-1H-thieno[3,4-d]imidazol-4-yl]butanoyl) piperazine-1-carbonyl)phenyl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide 6 (biotin-P5). TLC Rf=0.40 (30% EA/70% toluene); IR (ATR) 3083, 2978, 2359, 2341, 1686, 1614, 1406, 1120 cm.sup.1; .sup.1H NMR (400 MHz, CDCl.sub.3) 7.43 (t, J=7.9 Hz, 1H), 7.27-7.24 (m, 2H), 7.19-7.18 (m, 1H), 4.49 (dd, J=7.8, 4.7 Hz, 1H), 4.31 (dd, J=7.8, 4.4 Hz, 1H), 3.67-3.37 (m, 8H), 3.24-3.20 (m, 3H), 2.93 (dd, J=12.7, 4.9 Hz, 1H), 2.70 (d, J=12.7 Hz, 1H), 2.48-2.47 (m, 5H), 2.25 (s, 3H), 1.78-1.57 (m, 4H), 1.51-1.46 (m, 2H); .sup.13C NMR (100 MHz, CDCl.sub.3) 175.2, 174.2, 171.5, 166.0, 158.9, 138.7, 137.7, 131.0, 125.0, 124.5, 116.9, 63.3, 61.6, 57.0, 46.4, 46.3, 42.8, 42.6, 41.0, 33.6, 29.8, 29.5, 26.2, 12.6, 10.8; HRMS (ESI+) m/z calcd for C.sub.26H.sub.34N.sub.6O.sub.6S.sub.2 [M+Na].sup.+: 613.1879, found: 613.1872.
##STR00059##
[0144] 3,4-Dimethylaniline 7 (1.36 g, 11.2 mmol) was dissolved in 20 mL DMF and cooled to 0 C. Pyridine (1.7 mL, 20.4 mmol) was then added and the mixture stirred for 10 min. 3,5-Dimethyl-isoxazole-4-sulfonyl chloride 1 (2.00 g, 10.2 mmol) was then added in portions over one hour. The reaction was then allowed to warm to RT and stirred for 16 hrs. The reaction was quenched by adding 1 M HCl until the pH remained below 2 (25 mL). The reaction mixture was then taken up in EA (80 mL) and washed with 1 M HCl (250 mL) and brine (250 mL). The organic layer was then dried with MgSO.sub.4. Filtration and evaporation of solvent yielded a red-brown solid which was further purified using silica gel chromatography (40% EA/60% hexanes) to provide sulfonamide 8 as a beige solid (2.04 g, 73%).
[0145] (3,5-Dimethyl-4-isoxazolylsulfonyl)(3,4-xylyl)amine 8 (P13). mp=90-92 C.; TLC Rf=0.48 (50% EA/50% hexanes); IR (ATR) 3250, 2920, 1591, 1327, 1118 cm.sup.1; .sup.1H NMR (400 MHz, CDCl.sub.3) 7.06-7.01 (m, 2H), 6.87-6.86 (m, 1H), 6.81 (dd, J=8.0, 2.4 Hz, 1H), 2.42 (s, 3H), 2.27 (s, 3H), 2.20 (s, 3H), 2.19 (s, 3H); .sup.13C NMR (100 MHz, CDCl.sub.3) 174, 157.8, 138.2, 135.3, 133, 130.6, 124.4, 120.5, 115.5, 19.8, 19.3, 12.6, 10.9. HRMS (ESI+) m/z calcd for C.sub.13H.sub.16N.sub.2O.sub.3S [M+H].sup.+: 281.0954, found: 281.0955.
##STR00060##
[0146] The sulfonamide 8 (P13) (1.80 g, 6.42 mmol) and K.sub.2CO.sub.3 (1.95 g, 14.12 mmol) were suspended in 22 mL DMF and stirred for 15 min at RT. 3-Chloropropyl p-toluenesulfonate (2.39 g, 9.63 mmol) was then added and the reaction was heated to 80 C. (oil bath temperature). After 20 hrs, the reaction mixture was allowed to cool to RT and 30 mL water was added. The reaction mixture was then extracted with EA (330 mL). The combined organic layers were washed with brine (100 mL), dried with MgSO.sub.4 and filtered. After evaporating the solvent, the residue was purified using silica gel chromatography (5% EA/95% hexanes) to provide alkyl chloride 9 as a pale yellow solid (1.89 g, 83%).
[0147] (3-Chloropropyl)(3,5-dimethyl-4-isoxazolylsulfonyl)(3,4-xylyl)amine 9. mp=90-93 C.; TLC Rf=0.68 (30% EA/70% hexanes); IR (ATR) 2923, 2358, 1587, 1346, 1121, 689 cm.sup.1; .sup.1H NMR (400 MHz, CDCl.sub.3) 7.09 (d, J=8.0 Hz, 1H), 6.94 (d, J=2.0 Hz, 1H), 6.85 (dd, J=8.4, 2.4 Hz, 1H), 3.75 (t, J=6.7 Hz, 2H), 3.57 (t, J=6.3 Hz, 2H), 2.27 (s, 3H), 2.26 (s, 3H), 2.23 (s, 3H), 1.96-1.90 (m, 2H); .sup.13C NMR (100 MHz, CDCl.sub.3) 173.6, 158, 138.1, 137.5, 135.5, 130.5, 129.9, 125.6, 114.8, 47.7, 41.6, 31.2, 19.8, 19.4, 12.5, 11.0.
##STR00061##
[0148] The alkyl chloride 19 (0.85 g, 2.2 mmol) was dissolved in 7 mL of DMF. Sodium azide (0.4 g, 6.6 mmol) was then added and the reaction mixture was heated to 80 C. (oil bath temperature). After 16 hrs the mixture was allowed to cool to RT and 30 mL water was added. The reaction mixture was then extracted with EA (250 mL). The combined the organic layers were washed with brine (100 mL), dried with MgSO.sub.4, filtered and concentrated in vacuo. This gave azide 10 as a yellow foam (0.80 g, 92%) which was used without further purification.
[0149] (3-Azidopropyl)(3,5-dimethyl-4-isoxazolylsulfonyl)(3,4-xylyl)amine 10. TLC Rf=0.46 (30% EA/70% hexanes); IR (ATR) 2938, 2358, 2096, 1587, 1346, 1180 cm.sup.1; .sup.1H NMR (400 MHz, CDCl.sub.3) 7.09 (d, J=8.0 Hz, 1H), 6.93 (d, J=2.1 Hz, 1H), 6.83 (dd, J=10.2, 2.2 Hz, 1H), 3.68 (t, J=6.6 Hz, 2H), 3.38 (t, J=6.6 Hz, 2H), 2.25-2.24 (m, 6H), 2.22 (s, 3H), 2.09 (s, 3H), 1.79-1.72 (m, 2H); .sup.13C NMR (100 MHz, CDCl.sub.3) 173.6, 158, 138.2, 137.6, 135.4, 130.5, 129.8, 125.6, 114.9, 48.4, 47.6, 27.8, 19.7, 19.4, 12.5, 11.0.
##STR00062##
[0150] The azide 10 (1.00 g, 2.75 mmol) was dissolved in 20 mL of THF. Water (4 mL) was then added followed by triphenyl phosphine (0.79 g, 3.03 mmol). After 16 hrs at RT the solvent was evaporated and excess triphenyl phosphine was removed by passing the residue through a short plug of silica gel (20% EA/80% hexanes). This provided the amine product containing some triphenyl phosphine oxide, which was used without further purification. Biotin (1.32 g, 5.4 mmol), EDCI (0.84 g, 5.4 mmol) and diisopropylethylamine (0.95 mL, 5.4 mmol) were dissolved in 27 mL of DMF and stirred for 10 min. The crude amine (0.91 g) was then added to the reaction mixture. After 16 hrs at RT brine (30 mL) was added and the reaction mixture was extracted with EA (330 mL). The combined organic layers washed with water (130 mL) and brine (230 mL), dried (MgSO.sub.4), filtered and concentrated. The residue was purified using silica gel chromatography (15% MeOH/85% DCM) to provide the amide 11 (biotin-P13) as a waxy yellow solid (0.30 g, 20%).
[0151] 4-[(3aS,4S,6aR)-2-Oxo-hexahydro-1H-thieno[3,4-d]imidazol-4-yl]-N-(3-[N-(3,4-dimethylphenyl)3,5-dimethyl-1,2-oxazole-4-sulfonamido]propyl}butanamide 11 (biotin-P13). TLC Rf=0.32 (10% MeOH/90% DCM); IR (ATR) 3208, 2923, 2359, 2341, 1696, 1641, 1342, 1116, 688 cm.sup.1; .sup.1H NMR (400 MHz, CDCN.sub.3) 7.14 (d, J=8.4 Hz, 1H), 7.00-6.99 (m, 1H), 6.92 (dd, J=8.0, 2.2 Hz, 1H), 6.47 (bs, 1H), 5.55 (bs, 1H). 5.23 (bs, 1H), 4.42-4.39 (m, 1H), 4.23-4.20 (m, 1H), 3.61 (t, J=5.1 Hz, 2H), 3.17-3.12 (m, 3H), 2.87 (dd, J=12.7, 4.9 Hz, 1H), 2.63 (d, J=12.7 Hz, 1H), 2.27 (s, 3H), 2.25 (s, 3H), 2.21 (s, 3H), 2.08 (t, J=7.4 Hz, 3H), 1.99 (s, 3H), 1.71-1.48 (m, 6H), 1.39-1.31 (m, 2H); .sup.13C NMR (100 MHz, CDCN.sub.3) 174.7, 173.7.9, 163.9, 158.8, 138.8, 138.3, 136.5, 131.0, 130.7, 127.0, 115.5, 62.3, 60.7, 56.3, 48.7, 41.1, 36.9, 36.3, 29, 28.9, 28.8, 26.4, 19.7, 19.4, 12.8, 11.1; HRMS (ESI+) m/z calcd for C.sub.26H.sub.37N.sub.5O.sub.5S.sub.2 [M+Na].sup.+: 586.2134, found: 586.2119.
##STR00063##
[0152] The azide 12 (1.00 g, 2.75 mmol) was dissolved in 20 mL of THF. Water (4 mL) was then added followed by triphenyl phosphine (0.79 g, 3.03 mmol). After 16 hrs at RT the solvent was evaporated and excess triphenyl phosphine was removed by passing the residue through a short plug of silica gel (20% EA/80% hexanes). This provided the amine product containing some triphenyl phosphine oxide, which was used without further purification. 4,4-Difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-propionic acid (BODIPY Acid 13) (0.043 g, 0.148 mmol) was dissolved in DMF (2 mL) and HATU (0.112 g, 0.296 mmol) was added. After 5 min the amine from the previous step (0.050 g, 0.148 mmol) was added followed by addition of diisopropylethylamine (0.05 mL, 0.296 mmol). The reaction mixture was stirred at RT for 16 hrs, and was then quenched by addition of sat. NH.sub.4Cl (10 mL) and then extracted with DCM (35 mL). The combined organic layers washed with water (15 mL) and brine (25 mL), dried (MgSO.sub.4), filtered and concentrated. Purification of the residue by column chromatography (30% DCM/EA) yielded the amide 14 (BODIPY-P13) as dark red crystals (0.078 g, 87%).
[0153] 12-[2-((3-[N-(3,4-Dimethylphenyl)3,5-dimethyl-1,2-oxazole-4-sulfonamido]propyl}carbamoyl)ethyl]-2,2-difluoro-4,6-dimethyl-1.sup.5,3-diaza-2-boratricyclo[7.3.0.0.sup.3,7]dodeca 1(12), 4,6,8,10-pentaen-1-ylium-2-uide 14 (BODIPY-P13). mp=175-177 C.; TLC Rf=0.68 (30% DCM/EA); .sup.1H NMR (400 MHz, CDCl.sub.3) 7.08 (s, 1H), 7.06 (s, 1H), 6.91 (s, 1H), 6.85 (d, J=3.7 Hz, 1H), 6.81 (d, J=7.9 Hz, 1H), 6.27 (d, J=3.7 Hz, 1H), 6.13 (s, 1H), 5.99 (bs, 1H), 3.57 (t, J=6.4 Hz, 2H), 3.33-3.24 (m, 4H), 2.62 (t, J=7.5 Hz, 2H), 2.56 (s, 3H), 2.26 (s, 3H), 2.24 (s, 6H), 2.22 (s, 3H), 2.06 (s, 3H), 1.61-1.54 (m, 2H); .sup.13C NMR (100 MHz, CDCl.sub.3) 173.4, 171.8, 160.3, 158, 157.4, 143.9, 138, 137.4, 135.3, 135.1, 133.3, 130.4, 129.9, 128.1, 125.7, 123.8, 120.4, 117.4, 115, 47.8, 36, 35.9, 27.8, 24.8, 19.8, 19.4, 14.9, 12.5, 11.3, 11.0.
##STR00064##
[0154] 4-Phenoxy aniline 15 (1.00 g, 5.4 mmol) was dissolved in 15 mL DMF and cooled to 0 C. Pyridine (0.90 mL, 10.8 mmol) was then added. After 10 min, 3,5-dimethyl-isoxazole-4-sulfonyl chloride 1 (1.16 g, 5.94 mmol) was added in portions over 15 min. After the addition was complete the ice bath was removed and the reaction mixture was allowed to warm to RT. After 16 hrs the reaction was quenched by adding 1M HCl until the pH remained below 2 (15 mL). The reaction mixture was then extracted with EA (220 mL). The combined organic layers were washed with 1M HCl (220 mL) and brine (220 mL), dried (MgSO4) and concentrated. The residue was purified using silica gel chromatography (40% EA/60% hexanes) that provided sulfonamide 16 as an off-white powder (1.58 g, 91%).
[0155] (3,5-Dimethyl-4-isoxazolylsulfonyl)(p-phenoxyphenyl)amine 16 (P052). mp=106-109 C.; TLC Rf=0.30 (50% EA/hexanes); .sup.1H NMR (400 MHz, CDCl.sub.3) 7.35 (t, J=7.5 Hz, 2H), 7.14 (t, J=7.4 Hz, 1H), 7.05 (d, J=7.4, 2H), 6.98 (d, J=8.3 Hz, 2H), 6.93 (d, J=9.0 Hz, 2H), 6.44 (bs, 1H), 2.42 (s, 3H), 2.29 (s, 3H); .sup.13C NMR (100 MHz, CDCl.sub.3) 173.9, 157.6, 156.6, 156.5, 129.9, 129.8, 126, 123.9, 119.4, 119.2, 115.2, 12.5, 10.8; Anal. Calcd for C.sub.17H.sub.16N.sub.2O.sub.4S: C, 59.29; H, 4.68; N, 8.13. Found: C, 59.23; H, 4.78; N, 8.17.
##STR00065##
[0156] The sulfonamide 16 (0.2 g, 0.58 mmol) and K.sub.2CO.sub.3 (0.24 g, 1.74 mmol) were suspended in 25 mL of MeCN and stirred for 15 min at rt. 3-Chloropropyl p-toluenesulfonate (0.29 g, 1.16 mmol (prepared as described in .sup.59) was then added and the reaction mixture warmed to reflux. After 20 hrs the reaction was allowed to cool to RT and 30 mL water was added. The reaction mixture was the extracted with EA (3 is 30 mL). The combined organic extracts were washed with brine (100 mL), dried (MgSO.sub.4), filtered and concentrated. Purification of the residue using silica gel chromatography (50% EA/50% hexanes) gave alkyl chloride 17 as an off-white powder (0.190 g, 77%).
[0157] (3-Chloropropyl)(3,5-dimethyl-4-isoxazolylsulfonyl)(p-phenoxyphenyl)amine 17 (P059). mp=95-98 C.; TLC Rf=0.21 (50% DCM/hexanes); .sup.1H NMR (400 MHz, CDCl.sub.3) 7.38 (t, J=7.8 Hz, 2H), 7.17 (t, J=7.4 Hz, 1H), 7.11 (d, J=8.8 Hz, 2H), 7.01 (d, J=7.8 Hz, 2H), 6.96 (d, J=8.8 Hz, 1H), 3.77 (t, J=6.8 Hz, 2H), 3.59 (t, J=6.3 Hz, 2H), 2.32 (s, 3H), 2.15 (s, 3H), 2.00-1.94 (m, 2H); .sup.13C NMR (100 MHz, CDCl.sub.3) 173.7, 157.9, 156, 132.5, 130.2, 130, 124.3, 119.5, 118.9, 114.7, 47.9, 41.5, 31.3, 12.5, 11.0; Anal. Calcd for C.sub.20H.sub.21ClN.sub.2O.sub.4S: C, 57.07; H, 5.03; N, 6.66. Found: C, 56.98; H, 5.10; N, 6.60.
##STR00066##
[0158] The alkyl chloride 17 (0.100 g, 0.24 mmol) was dissolved in 1 mL of DMF. Sodium azide (0.050 g, 0.71 mmol) was then added and the reaction mixture was warmed to 80 C. After 16 hrs the reaction mixture was allowed to cool to RT and 10 mL water was added. The reaction mixture was extracted with EA (35 mL). The combined organic extracts were washed with brine (10 mL), dried (MgSO.sub.4), filtered and concentrated. This provided the azide 18 a tan solid (0.090 g, 87%).
[0159] (3-Azidopropyl)(3,5-dimethyl-4-isoxazolylsulfonyl)(p-phenoxyphenyl)amine 18 (P062). mp=72-76 C.; TLC Rf=0.63 (30% EA/70% hexanes); IR (ATR) 3076, 2935, 2091, 1585, 1484, 1345 cm.sup.1; .sup.1H NMR (400 MHz, CDCl.sub.3) 7.37 (t, J=7.7 Hz, 2H), 7.17 (t, J=7.4 Hz, 1H), 7.11 (d, J=8.8 Hz, 2H), 7.01 (d, J=8.2 Hz, 2H), 6.97 (d, J=8.7 Hz, 2H), 3.71 (t, J=6.7 Hz, 2H), 3.34 (t, J=6.6 Hz, 2H), 2.31 (s, 3H), 2.15 (s, 3H), 1.79-1.72 (m, 2H); .sup.13C NMR (100 MHz, CDCl.sub.3) 173.6, 157.9, 157.8, 156, 132.4, 130.2, 130, 124.3, 119.5, 118.9, 114.7, 48.4, 47.8, 27.9, 12.5, 11.0; Anal. Calcd for C.sub.20H.sub.21N.sub.5O.sub.4S: C, 56.19; H, 4.95; N, 16.38. Found: C, 56.15; H, 4.87; N, 16.45.
##STR00067##
[0160] The azide 18 (0.55 g, 1.29 mmol) was dissolved in 10 mL of THF and water (2 mL) was added followed by triphenyl phosphine (0.38 g, 1.42 mmol). After 16 hrs at RT the solvent was evaporated and the residue was put through a plug of silica gel (20% EA/80% hexanes). This gave the amine product containing small amounts of triphenyl phosphine oxide. This amine (0.05 g, 0.12 mmol) was dissolved in 0.5 mL of DCM and cooled to 0 C. Pyridine (0.06 mL, 0.07 mmol) was then added, followed by acetic anhydride (0.013 mL, 0.14 mmol). After 3 hrs at RT 5 mL water was added and the reaction mixture was extracted with DCM (35 mL). The combined organic extracts were washed with sat. aq. NaHCO.sub.3 (5 mL) and brine (5 mL), dried (MgSO.sub.4), filtered and concentrated. Purification of the residue using silica gel chromatography (10% MeOH/DCM) provided acetamide 19 as a white foam (0.040 g, 73%).
[0161] 1-(3-[(3,5-Dimethyl-4-isoxazolylsulfonyl)(p-phenoxyphenyl)amino]propylamino)-1-ethanone 19 (P070). TLC Rf=0.44 (100% EA); IR (ATR) 3265, 3097, 2936, 1629, 1502, 1343, 1246 cm.sup.1; .sup.1H NMR (400 MHz, CDCl.sub.3) 7.36 (t, J=7.6 Hz, 2H), 7.16 (t, J=7.4 Hz, 1H), 7.36 (d, J=8.8 Hz, 2H), 6.93 (d, J=7.8 Hz, 2H), 6.95 (d, J=8.8 Hz, 1H), 3.67 (t, J=6.3 Hz, 2H), 3.36 (q, J=6.2 Hz, 2H), 2.30 (s, 3H), 2.14 (s, 3H), 1.99 (s, 3H), 1.69-1.62 (m, 2H); .sup.13C NMR (100 MHz, CDCl.sub.3) 173.5, 170.5, 157.9, 157.7, 156, 132, 130.3, 130, 124.3, 119.6, 118.9, 114.8, 47.9, 36, 27.5, 23.2, 12.5, 11.0; Anal. Calcd for C.sub.22H.sub.25N.sub.3O.sub.5S: C, 59.58; H, 5.68; N, 9.47. Found: C, 59.63; H, 5.74; N, 9.26.
##STR00068##
[0162] 4-Benzylaniline (0.5 g, 2.73 mmol) was dissolved in 10 mL of DMF and cooled to 0 C. Pyridine (0.44 mL, 5.46 mmol) was then added. After 10 min, 3,5-dimethyl-isoxazole-4-sulfonyl chloride 1 (0.59 g, 3 mmol) was added in portions over 15 min. After 16 hrs the reaction was quenched by adding 1 M HCl until the pH was maintained below 2. The reaction mixture was then taken up in EA (50 mL) and washed with 1 M HCl (220 mL) and brine (220 mL). The organic layer was then dried (MgSO.sub.4), filtered and concentrated. The residue was purified using silica gel chromatography (10% EA/90% hexanes) to obtain sulfonamide 20 as a light brown foam (0.482 g, 47%).
[0163] (3,5-Dimethyl-4-isoxazolylsulfonyl)(p-benzylphenyl)amine 20 (P053). mp=111-115 C.; IR (ATR) 3227, 2951, 1588, 1490, 1337, 1179 cm.sup.1; .sup.1H NMR (400 MHz, CDCl.sub.3) 7.28 (t, J=7.2 Hz, 2H), 7.20 (t, J=7.3 Hz, 1H), 7.14-7.11 (m, 4H), 6.99 (d, J=8.4 Hz, 2H), 6.8 (bs, 1H), 3.94 (s, 2H), 2.39 (s, 3H), 2.25 (s, 3H); .sup.13C NMR (100 MHz, CDCl.sub.3) 173.9, 157.6, 140.4, 140.1, 133.2, 130, 128.8, 128.6, 126.3, 123.6, 115.3, 41.3, 12.5, 10.7; Anal. Calcd for C.sub.18H.sub.18N.sub.2O.sub.3S: C, 63.14; H, 5.30; N, 8.18. Found: C, 63.19; H, 5.27; N, 7.99.
##STR00069##
[0164] The sulfonamide 16 (0.2 g, 0.58 mmol) and K.sub.2CO.sub.3 (0.18 g, 1.28 mmol) were suspended in 2.5 mL of MeCN and stirred for 15 min at RT. 3-Chloropropanol (0.082 g, 0.087 mmol) was then added and the reaction mixture was heated to reflux. After 20 is hrs the reaction mixture was allowed to cool to RT and 30 mL water was added. The reaction mixture was extracted with EA (310 mL) and the combined organic layers were washed with brine (20 mL), dried (MgSO.sub.4), filtered and concentrated. Purification of the residue using silica gel chromatography (10% EA/90% hexanes) yielded alcohol 21 as a white powder (0.09 g, 39%).
[0165] 3-[(3,5-Dimethyl-4-isoxazolylsulfonyl)(p-phenoxyphenyl)amino]propanol 21 (P129). TLC Rf=0.90 (50% EA/50% hexanes); .sup.1H NMR (400 MHz, CDCl.sub.3) 7.37 (t, J=7.6 Hz, 2H), 7.17 (t, J=7.4 Hz, 1H), 7.12 (d, J=9.1 Hz, 2H), 6.96 (d, J=8.9 Hz, 2H), 3.79-3.75 (m, 4H), 2.33 (s, 3H), 2.16 (s, 3H), 1.72-1.66 (m, 4H); .sup.13C NMR (100 MHz, CDCl.sub.3) 173.5, 157.8, 157.7, 156.1, 132.4, 130.4, 130, 124.2, 119.5, 118.9, 114.9, 58.8, 47.3, 30.7, 12.6, 11.1; Anal. Calcd for C.sub.20H.sub.22N.sub.2O.sub.5S: C, 59.69; H, 5.51; N, 6.96. Found: C, 59.61; H, 5.63; N, 6.79.
##STR00070##
[0166] The sulfonamide 16 (0.2 g, 6.42 mmol) and K.sub.2CO.sub.3 (0.24 g, 1.74 mmol) were dissolved in 20 mL of MeCN and stirred for 15 min at RT. 1-Bromobutane (0.12 mL, 1.16 mmol) was then added and the reaction was heated to 80 C. After 20 hrs, 30 mL water was added and reaction mixture was extracted with EA (310 mL). The combined organic layers were washed with brine (50 mL) dried (MgSO.sub.4), filtered and concentrated. Purification of the residue with silica gel chromatography (10% EA/90% hexanes) gave sulfonamide 22 as an off-white foam (0.19 g, 83%).
[0167] N-Butyl(3,5-dimethyl-4-isoxazolylsulfonyl)(p-phenoxyphenyl)amine 22 (P058). TLC Rf=0.61 (30% EA/70% hexanes); IR (ATR) 3065, 2951, 2868, 1588, 1503, 1340, 1180 cm.sup.1; .sup.1H NMR (400 MHz, CDCl.sub.3) 7.41 (t, J=7.6 Hz, 2H), 7.19 (t, J=7.4 Hz, 1H), 7.12 (d, J=8.9 Hz, 2H), 7.04 (d, J=7.7 Hz, 2H), 6.98 (d, J=8.9 Hz, 2H), 3.63 (t, J=6.8 Hz, 2H), 2.32 (s, 3H), 2.18 (s, 3H), 1.50-1.34 (m, 4H), 0.92 (t, J=7.2 Hz, 2H); .sup.13C NMR (100 MHz, CDCl.sub.3) 173.4, 157.9, 157.6, 156.2, 132.6, 130.4, 130, 124.1, 119.4, 118.8, 115.0, 50.1, 30.2, 19.5, 13.5, 12.5, 11.0; Anal. Calcd for C.sub.21H.sub.24N.sub.2O.sub.4S: C, 62.98; H, 6.04; N, 6.99. Found: C, 62.90; H, 6.14; N, 6.85.
##STR00071##
[0168] Alkyl chloride 17 (0.70 g, 1.67 mmol) was dissolved in DMF (15 mL) and NaCN (0.25 g, 5 mmol) was added. The reaction was then heated to 85 C. (oil bath temperature). After 18 hrs the reaction mixture was allowed to cool to RT and poured into water (50 mL). The resulting mixture was extracted with EA (330 mL). The combined organic extracts were washed with water (50 mL) and brine (250 mL), dried (MgSO.sub.4), filtered and concentrated. The residue was purified using silica gel chromatography (30% EA/70% hexanes) to obtain nitrile 23 as an off-white crystalline solid (0.62 g, 91%).
[0169] 4-[(3,5-Dimethyl-4-isoxazolylsulfonyl)(p-phenoxyphenyl)amino]butyronitrile 23 (P075). mp=78-83 C.; TLC Rf=0.32 (30% EA/70% hexanes); IR (ATR) 3384, 3225, 2938, 2246, 1732, 1586, 1487 cm.sup.1; .sup.1H NMR (400 MHz, CDCl.sub.3) 7.41 (t, J=7.6 Hz, 2H), 7.20 (t, J=7.4 Hz, 1H), 7.13 (d, J=8.9 Hz, 2H), 7.04 (d, J=7.7 Hz, 2H), 6.99 (d, J=8.9 Hz, 1H), 3.76 (t, J=6.5 Hz, 2H), 2.51 (t, J=7.3 Hz, 2H), 2.33 (s, 3H), 2.16 (s, 3H), 1.93-1.87 (m, 2H); .sup.13C NMR (100 MHz, CDCl.sub.3) 173.8, 158.1, 157.8, 155.9, 132, 130.2, 130, 124.4, 119.7, 118.9, 118.7, 114.5, 49.2, 24.5, 14.4, 12.5, 11.0; Anal. Calcd for C.sub.21H.sub.21N.sub.3O.sub.4S: C, 61.30; H, 5.14; N, 10.21. Found: C, 61.25; H, 5.17; N, 10.06.
[0170] Binding Measurements and Anisotropy: Recombinant PP5-His.sub.6 at the indicated concentrations was incubated on ice in 100 mM NaCl, 20 mM HEPES pH 8.0, 1% glycerol, 0.2 mM tris(2-carboxyethyl)phosphine (TCEP) and 0.5 mM MnCl2 with 10 nM BODIPY-labeled P13 in 2% DMSO for 30 min in opaque black 96 well plates (Corning). Uncalibrated fluorescence anisotropy was then measured using a SpectraMax i3 equipped with fluorescein anisotropy module (Molecular Devices). Curves were fit to a one-site binding equation using GraphPad Prism version 9.5.0. y=y.sub.0+A*x/(K.sub.d+x) where y is measured uncalibrated anisotropy, y.sub.0 is the y intercept, A is the amplitude of the curve, x is the concentration of PP5 used, and K.sub.d is the measured dissociation constant. Data are presented as meanSEM.
[0171] PP5 Phosphatase Activity and Inhibition Assay: The phosphatase activity of the recombinant PP5-His.sub.6 was measured using the PiPer Phosphate Assay Kit (Thermo Fisher Scientific) as described in the manufacturer's protocol. Standard curve with linear fit line was created from 0-1 nM Pifinal concentration reactions. 1 nM of PP5-His.sub.6 was added to each reaction with indicated amounts of custom synthesized substrate phospho-S211-glucocorticoid receptor (PhosS211-GR) peptide (see Key Resources Table) as specific substrate (Thermo Fisher Scientific). Reactions were run in triplicate and incubated at 37 C. for over 10 min. Reaction was also performed in the presence of different amounts (100-1200 nM) of PP5 inhibitors (P5, P13 and P053). Enzyme kinetics were calculated and plotted using Lineweaver Burk plot and web-based tool (https://www.aatbio.com/tools/ic50-calculator) for calculating IC.sub.50 and (https://bioinfo-abcc.ncifcrf.gov/IC50_Ki_Converter/index.php) for converting IC.sub.50 to K.sub.i values for inhibitors of enzyme activity and ligand binding.
[0172] Flow Cytometric Analysis: Fluorescence-activated cell sorting (FACS) analysis was performed according to the protocol in the Annexin V:FITC kit (Bio-Rad). In brief, cells were plated in 10 cm dish at 0.510.sup.6 and incubated at 37 C. for 18 hrs. Cells were subsequently treated with compound P053 at the indicated concentrations for 18 hrs. Cells were trypsinized, collected and washed once with 1 binding buffer (included in the kit). Propidium iodide was added, then the cells were immediately run on a Becton Dickinson LSRFortessa instrument (BD Biosciences). Data were analyzed using FlowJo software version 10.7.1 for Windows (BD Biosciences).
[0173] Biotin-P5 and biotin-P13 Pulldown: HEK293 cells were transiently transfected with PP5-FLAG or active site point mutants and protein lysate extracted. Lysate was incubated with 0.01-10 M biotin-P5 or biotin P-13 as indicated at 4 C. for 1 hr then added to streptavidin-conjugated agarose and incubated at 4 C. for 1 hr. Following three washes with fresh extraction buffer bound proteins were eluted in 5 Laemmli buffer and analyzed by Western blot. Competition experiment with P053 was conducted with protein lysate from untreated 786-O cells. Lysate was incubated with 1 M biotin-P5 or biotin-P13 for 1 hr followed by competition with 1 M P053 at 4 C. for 30 min This was then incubated with streptavidin-conjugated agarose at 4 C. for 1 hr prior to washing 3 with fresh extraction buffer and elution in 5 Laemmli buffer. Samples were run by SDS PAGE, transferred to nitrocellulose membrane, and analyzed by Western blot.
[0174] Quantification, statistical analysis and reproducibility: The data presented are representative of three biological replicates, unless otherwise specified. All statistics were performed using GraphPad Prism version 9.5.0 for Windows (GraphPad Software at graphpad.com). Statistical significance was ascertained between individual samples using a parametric unpaired t-test. Significance is denoted by asterisks in each figure: *P<0.05; **P<0.01; ***P<0.001; ****P<0.0001. Error bars represent the standard deviation for three independent experiments, unless otherwise indicated.
Resources Table:
TABLE-US-00001 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit anti-FLAG tag Thermo Scientific Cat# PA1-984B; RRID: AB_347227 Rabbit anti-HA tag (C29F4) Cell Signaling Cat# 3724; RRID: AB_1549585 Technology Mouse anti-6x-His Thermo Scientific Cat# MA1-21315; epitope tag (HIS.H8) RRID: AB_557403 Mouse anti-GAPDH (1D4) Enzo Life Sciences Cat# ADI-CSA-335; RRID: AB_10617247 Rabbit anti-PP5 Cell Signaling Cat# 2289; RRID: AB_2168757 Technology Mouse anti-PP5 (2E12) Abcam Cat# ab123919; RRID: AB_10976136 Rabbit anti-FADD Cell Signaling Cat# 2782; RRID: AB_2100484 Technology Rabbit anti-phos-Ser194- Cell Signaling Cat# 2781; RRID: AB_2100485 FADD Technology Rabbit anti-RIPK1 Cell Signaling Cat# 3493; RRID: AB_2305314 Technology Rabbit anti-phos-Ser161- Invitrogen Cat# PA5-105640; RIPK1 RRID: AB_2817068 Rabbit anti-phos-Ser166- Cell Signaling Cat# 44590; RRID: AB_2799268 RIPK1 Technology Rabbit anti-phos-Ser13- Abcam Cat# ab108360; Cdc37 (EPR4979) RRID: AB_10859480 Rabbit anti-Cdc37 StressMarq Cat# SPC-142; Biosciences RRID: AB_2570605 Rabbit anti-GR (D6H2L) Cell Signaling Cat# 12041; RRID: AB_2631286 Technology Mouse anti-GR (D4X9S) Cell Signaling Cat# 47411; RRID: AB_2799324 Technology Rabbit anti-phospho-GR S211 Cell Signaling Cat# 4161; RRID: AB_2155797 Technology Rabbit anti-cleaved-PARP Cell Signaling Cat# 5625; RRID: AB_10699459 Technology Rabbit anti-caspase-3 Cell Signaling Cat# 9665; RRID: AB_2069872 Technology Rabbit anti-cleaved caspase-3 Cell Signaling Cat# 9664; RRID: AB_2070042 Technology Rabbit anti-cleaved caspase-7 Cell Signaling Cat# 9491; RRID: AB_2068144 Technology Mouse anti-caspase-9 Cell Signaling Cat# 9508; RRID: AB_2068620 Technology Mouse anti-caspase-8 Cell Signaling Cat# 9746; RRID: AB_2275120 Technology Rabbit anti-cleaved Cell Signaling Cat# 9496; RRID: AB_561381 caspase-8 Technology Rabbit anti-PP2A C Subunit Cell Signaling Cat# 2038; RRID: AB_2169495 Technology Rabbit anti-VHL Cell Signaling Cat# 68547; RRID: AB_2716279 Technology Rabbit anti-phospho-Akt S473 Cell Signaling Cat# 2289; RRID: AB_2315049 (D9E) Technology Mouse anti-Akt (2H10) Cell Signaling Cat# 2967; RRID: AB_331160 Technology Rabbit Tuberin/TSC2 Cell Signaling Cat# 4308; RRID: AB_10547134 (D93F12) Technology XP Rat anti-Hsp90 (16F1) Enzo Life Sciences Cat# ADI-SPA-835; RRID: AB_11181205 Anti-mouse secondary Cell Signaling Cat# 7076; RRID: AB_330924 Technology Anti-rabbit secondary Cell Signaling Cat# 7074; RRID: AB_2099233 Technology Bacterial and Virus Strains BL21(DE3) EMD Millipore Cat# 69450 DH5-alpha Goldbio Cat# CC-203 Electrocompetent E coli Biological Samples Chemicals, Peptides, and Recombinant Proteins IC261 Abcam Cat# ab145189 Z-VAD-FMK pan- Enzo Life Sciences Cat# ALX-260-020-M001 caspase Inhibitor PP5 (PPP5C) Human OriGene Technologies Cat# SR321403; SKU# siRNA Oligo Duplex SR321403A; SKU# SR321403B; SKU# SR321403C Universal scrambled negative OriGene Technologies Cat# SR30004 control siRNA duplex Compound P0-P13 This Paper Biotin-P5 This Paper Biotin-P13 This Paper BODIPY-P13 This Paper P13 derivatives This Paper Phos-Ser211-GR peptide ThermoFisher This paper ([NH2]PGKETNE[pS]PWRSDL Scientific custom L[COOH]) synthesized SNX2112 Duke University; CAS# 908112-43-6 Dr. Timothy Haystead 61 Critical Commercial Assays Mirus TransIT-2020 MirusBio Cat# MIR5405 Anti-FLAG M2 affinity gel Sigma-Aldrich Cat# A2220 Protein G agarose ThermoFisher Cat# 15-920-010 Scientific Pierce Anti-HA Agarose ThermoFisher Cat# PI26182 Scientific Ni-NTA Agarose ThermoFisher Cat# 88221 Scientific Quick Cell Proliferation Kit BioVision Cat# K302-500; CAS# 150849- Plus 52-8 PiPer Phosphate Assay Kit ThermoFisher Cat# P22061 Scientific ANNEXIN V: FITC assay Kit BIO-RAD Cat# ANNEX300F Experimental Models: Cell Lines 786-O ATCC Cat# CRL-1932 A498 ATCC Cat# HTB-44 WT HAP-1 Horizon Discovery Cat# C631 PP5 HAP-1 KO Horizon Discovery Cat# HZGHC003163c001 FADD HAP-1 KO Horizon Discovery Cat# HZGHC002596c006 RIPK1 HAP1-KO Horizon Discovery Cat# HZGHC000060c015 HEK293 ATCC Cat# CRL-1573 HK-2 ATCC Cat# CRL-2190 Caki-1 ATCC Cat# HTB-46 Caki-2 ATCC Cat# HTB-47 Experimental Models: Organisms/Strains Oligonucleotides DNA primers Eurofins Genomics See Supplemental Table S1 Recombinant DNA pcDNA3-PP5-FLAG 2 n/a pcDNA3-HA-RIPK1 38 Addgene plasmid # 78834; RRID: Addgene_78834 pcDNA3-FLAG-FADD 31 Addgene plasmid # 78802; RRID: Addgene_78802 pcDNA3-PP5-FLAG-M309C 5 n/a pcDNA3-PP5-FLAG-W386F 5 n/a pGEX6P1-PP5 5 n/a Software and Algorithms Biorender https://biorender.com/ PyMOL version 2.5.4 for https://pymol.org/2/ windows GraphPad Prism version GraphPad Software, La Jolla, 9.5.0 for windows California, USA, www.graphpad.com FlowJo 10.7.1 for windows https://www.flowjo.com/ Chemdraw 20.1 https://perkinelmerinformatics.com/ products/research/chemdraw
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[0176] The entire disclosure of all applications, patents, and publications cited herein are herein incorporated by reference in their entirety. While the foregoing is directed to embodiments of the present disclosure, other and further embodiments of the disclosure may be devised without departing from the basic scope thereof.