Patent Application
20170112792
A joint research agreement was in effect on or before the date the filing of the present application. The parties to the joint research agreement are BETH ISRAEL DEACONESS MEDICAL CENTER and PINTEON, INC.
In general, this invention relates to all-trans retinoic acid (ATRA)-related compounds for modulation of Pin1 and methods of identifying the same. The invention also relates to the treatment of proliferative disorders, autoimmune disorders, and addiction (e.g., disorders, diseases, and conditions characterized by elevated Pin1 marker levels) with retinoic acid compounds.
Immune disorders are characterized by the inappropriate activation of the body's immune defenses. Rather than targeting infectious invaders, the immune response targets and damages the body's own tissues or transplanted tissues. The tissue targeted by the immune system varies with the disorder. For example, in multiple sclerosis, the immune response is directed against the neuronal tissue, while in Crohn's disease the digestive tract is targeted.
Immune disorders affect millions of individuals and include conditions such as asthma, allergic intraocular inflammatory diseases, arthritis, atopic dermatitis, atopic eczema, diabetes, hemolytic anaemia, inflammatory dermatoses, inflammatory bowel or gastrointestinal disorders (e.g., Crohn's disease and ulcerative colitis), multiple sclerosis, myasthenia gravis, pruritis/inflammation, psoriasis, rheumatoid arthritis, cirrhosis, and systemic lupus erythematosus.
A major cellular pathway in the pathogenesis of autoimmunity is the TLR/IRAK1/IRF/IFN pathway. For example, levels of IFNα (type I interferon) are elevated in patients with autoimmune diseases, including systemic lupus erythematosus (SLE), and are central to disease pathogenesis, correlating with autoantibodies and disease development. Recent genetic studies in SLE patients and lupus-prone mice have identified variants in the genes critical for the TLR/IRAK1/IRF/IFN pathways, including TLR7, IRAK1 and IRF5. In addition, several TLR inhibitors are in development for treatment of SLE. Notably, IRAK1 genetic variants have recently been identified in human SLE. IRAK1, a well-established pivotal player in TLRs and inflammation, is located on the X chromosome, which may help account for the fact that SLE is more common in women. Importantly, studies using mouse models, where the IRAK1 gene is removed, have demonstrated a key role for this kinase in the TLR7/9/IRF pathway that produces large quantities of IFNα in response to viral infection. IRAK1 gene deletion prevents TLR dependent activation of IRF5/7 in pDCs, the immune cells responsible for IFNα production. Significantly, autoantibody complexes obtained from SLE patients contain DNA and RNA and are taken up by pDCs to activate TLR7 and TLR9 leading to secretion of cytokines and IFNα. Moreover, TLR activation is known to inhibit activity of glucocorticoids, a frontline drug class used to treat SLE. Although IRAK1 activity is regulated by phosphorylation upon TLR activation, little is known about whether it is subject to further control after phosphorylation and whether such regulation has any role in SLE.
The prevalence of asthma is increasing in the developed world, but the underlying mechanisms are not fully understood, and therapeutic modalities remain limited. Asthma is a chronic inflammatory disease of the airways that is induced by overexpression of multiple proinflammatory genes regulated by various signal pathways in response to exposure to any of numerous allergens. The production of cytokines necessary for the development of adaptive immunity is regulated by upstream signaling pathways, including those initiated by the Toll-like receptor/interleukin-1 receptor (TLR/IL-1R) superfamily of receptors that share structural and functional properties. For example, activated TLR4 induces the secretion of mediators such as interleukin 33 (IL-33), a powerful immune modulator and ligand for IL-1R. IL-33 has been shown to activate IL-1R expressing resident dendritic cells (DC), thus inducing their maturation that is critical for allergic airway inflammation as well as DC-T cell activation and subsequent TH2 polarization. IL-33-activated DCs promote naïve CD4+ T cells to produce IL-5 and IL-13. Moreover, IL-33 prolongs human eosinophil survival, adhesion, and degranulation to directly stimulate mast cells to produce cytokines and to prolong their survival and adhesion, and to stimulate the alveolar macrophages to secrete IL-13. Thus, IL-33 is a pivotal factor in type 2 immunity and allergic asthma. A major regulatory mechanism in these signal pathways and gene activation is Pro-directed phosphorylation (pSer/Thr-Pro), but until recently little was known about whether and how they are regulated following phosphorylation.
Current treatment regimens for immune disorders typically rely on immunosuppressive agents. However, the effectiveness of these agents can vary and their use is often accompanied by adverse side effects. Thus, improved therapeutic agents and methods for the treatment of autoimmune disorders are needed.
In addition, drug addiction affects millions of individuals worldwide. The prevalence of cocaine addiction, for example, is estimated at over one million persons in the United States alone. Dopamine receptor signaling is understood to play a major role in addiction to drugs such as cocaine known to elicit dopamine responses. Dopamine induction is coupled to the phosphorylation of glutamate receptor protein mGluR5, which in turn potentiates NMDA receptor-mediated synaptic plasticity and thus cocaine-induced sensation. MAP Kinase phosphorylates mGluR5 where it binds the adaptor protein Homer and in so doing is thought to create a binding site for proteins that catalyze cis-trans isomerization of a phosphorylated serine-proline bond (pSer/Pro). Despite this recognition, there are presently no FDA-approved medications to treat cocaine addiction. Accordingly, there is a need to identify and develop therapeutic agents for the treatment of cocaine addiction.
The increased number of cancer cases reported in the United States, and, indeed, around the world, is also a significant concern. There are currently only a handful of detection and treatment methods available for some specific types of cancer, and these provide no absolute guarantee of success. In order to be most effective, these treatments require not only an early detection of the malignancy, but a reliable assessment of the severity of the malignancy.
It is apparent that the complex process of tumor development and growth must involve multiple gene products. It is therefore important to define the role of specific genes involved in tumor development and growth and identify those genes and gene products that can serve as targets for the diagnosis, prevention, and treatment of cancers.
In the realm of cancer therapy, it often happens that a therapeutic agent that is initially effective for a given patient becomes, over time, ineffective or less effective for that patient. The very same therapeutic agent may continue to be effective over a long period of time for a different patient. Further, a therapeutic agent that is effective, at least initially, for some patients can be completely ineffective from the outset or even harmful for other patients. Accordingly, it would be useful to identify genes and/or gene products that represent prognostic genes with respect to a given therapeutic agent or class of therapeutic agents. It then may be possible to determine which patients will benefit from a particular therapeutic regimen and, importantly, determine when, if ever, the therapeutic regime begins to lose its effectiveness for a given patient. The ability to make such reasoned predictions would make it possible to discontinue a therapeutic regime that was losing its effectiveness well before its loss of effectiveness becomes apparent by conventional measures.
Recent advances in the understanding of molecular mechanisms of oncogenesis have led to exciting new drugs that target specific molecular pathways. These drugs have transformed cancer treatments, especially for those caused by some specific oncogenic events, such as Herceptin for breast cancer, caused by HER2/Neu, and Gleevec® for chronic myelogenous leukemia caused by Bcr-Abl. However, it has been increasingly evident that, in many individual tumors, there are a large number of mutated genes that disrupt multiple interactive and/or redundant pathways. Thus, intervening in a single pathway may not be effective. Furthermore, cancer resistance to molecularly targeted drugs can develop through secondary target mutation or compensatory activation of alternative pathways, so-called “oncogenic switching.” Thus, a major challenge remains how to simultaneously inhibit multiple oncogenic pathways either using a combination of multiple drugs, with each acting on a specific pathway, or using a single drug that concurrently blocks multiple pathways.
Cancer stem-like cells (CSCs) or tumor-initiating cells (TICs) have been hypothesized to retain the capacity of self-renewal and regeneration of the bulk of a heterogeneous tumor comprised of CSCs and non-stem cells. CSCs have important implications for understanding the molecular mechanisms of cancer progression and developing novel targets for cancer therapeutics because they are thought to be responsible for tumor initiation, progression, metastasis, relapse and drug resistance. A variety of regulators of breast cancer stem-like cells (BCSCs), notably transcription factors including Zeb1 and □-catenin, and miRNAs, have recently been identified. These modulators of transcription and/or translation are further regulated by upstream signaling pathways. For example, Erk signaling has been shown to regulate BCSCs by increasing transcription of Zeb1 and nuclear accumulation of unphosphorylated (active) β-catenin. However, regulatory pathways upstream of Erk signaling that regulates BCSCs are still not fully elucidated.
Among the small GTPase superfamily, Ras has been shown to induce epithelial mesenchymal transition (EMT) and confer CSC traits to breast cells in vitro and in vivo, while the Rho family GTPase Rac1 is involved in the maintenance and tumorigenicity of CSCs in non-small cell lung adenocarcinoma and glioma and is also required for intestinal progenitor cell proliferation and LGR5 intestinal stem cell expansion. Deletion of Rac1 in adult mouse epidermis stimulated stem cells to divide and undergo terminal differentiation. However, the roles of other GTPase family members in CSCs in solid tumors or adult stem cells are yet to be elucidated. For example, Rab2A, a small GTPase mainly localized to the ER-Golgi intermediate compartment (ERGIC), is essential for membrane trafficking between the ER and Golgi apparatus but has no known function in cancer or CSCs. As disclosed herein, we have unexpectedly found that Rab2A is a Pin1 transcriptional target that is activated via its gene amplification or mutation or Pin1 overexpression in breast cancer and promotes BCSC expansion in vitro and in vivo as well as in human primary normal and cancerous breast tissues. Mechanistically, Rab2A directly binds to Erk1/2 via a docking motif that is also used by an Erk1/2 phosphatase, MKP3 (MAP kinase phosphatase 3) to prevent Erk1/2 from being dephosphorylated/inactivated, leading to activation of the known BCSC regulators Zeb1 and □-catenin. We further describe a tight association of Rab2A overexpression with β-catenin or Zeb1 downstream target expression in human breast cancer tissues as well as with poor outcome of breast cancer patients, especially in the most common subtypes, as defined by HER2-negative or non-triple-negative breast cancer. Thus, the Pin1/Rab2A/Erk axis drives BCSC expansion and tumorigenicity, contributing to high mortality in patients. Similarly, Pin1 has also been identified as a critical regulator acting downstream of miR200c.
These and other results disclosed herein suggest that Pin1 inhibitors may have a major impact on treating cancers, especially aggressive and/or drug-resistant cancers. A common and central signaling mechanism in many oncogenic pathways is proline (Pro)-directed phosphorylation (pSer/Thr-Pro). Proline adopts cis and trans conformations, the isomerization of which is catalyzed by prolyl isomerases (PPlases) including Pin1. Phosphorylation on serine/threonine-proline motifs restrains cis/trans prolyl isomerization, and also creates a binding site for the essential protein Pin1. Pin1 binds and regulates the activity of a defined subset of phosphoproteins, as well as participating in the timing of mitotic progression. Both structural and functional analyses have indicated that Pin1 contains a phosphoserine/threonine-binding module that binds phosphoproteins, and a catalytic activity that specifically isomerizes the phosphorylated phosphoserinelthreonine-proline. Both of these Pin1 activities are essential for Pin1 to carry out its function in vivo.
Pin1 has been implicated in autoimmune diseases and conditions such as SLE and asthma and in drug addiction pathways. Further, we and others have shown that Pin1 is prevalently overexpressed in human cancers and that high Pin1 marker levels correlate with poor clinical outcome in many cancers. In contrast, the Pin1 polymorphism that reduces Pin1 expression is associated with reduced cancer risk in humans. Significantly, Pin1 activates at least 32 oncogenes/growth enhancers, including β-catenin, cyclin D1, NF-κB, c-Jun, c-fos, AKT, A1B1, HER2/Neu, MCI-1, Notch, Raf-1, Stat3, c-Myb, Hbx, Tax, and v-rel, and also inactivates at least 19 tumor suppressors/growth inhibitors, including PML, SMRT, FOXOs, RARα, and Smad (
Pin1 is highly conserved and contains active sites including a protein-interacting module, called the WW domain, and a catalytically active peptidyl-prolyl isomerase (PPlase) portion, each of which include at least one binding pocket. Pin1 is structurally and functionally distinct from members of two other well-characterized families of PPlases, the cyclophilins and the FKBPs. PPlases are ubiquitous enzymes that catalyze the typically slow prolyl isomerization of proteins, allowing relaxation of local energetically unfavorable conformational states. Phosphorylation on Ser/Thr residues immediately preceding Pro not only alters the prolyl isomerization rate, but also creates a binding site for the WW domain of Pin1. The WW domain acts as a novel phosphoserine-binding module targeting Pin1 to a highly conserved subset of phosphoproteins. Furthermore, Pin1 displays a unique phosphorylation-dependent PPlase that specifically isomerizes phosphorylated Ser/Thr-Pro bonds and regulates the function of phosphoproteins. The cis-trans isomerization of certain pSer/Thr-Pro motifs can be detected by cis- and trans-specific antibodies.
Taken together, these results indicate that the Pin1 subfamily of enzymes is a diagnostic and therapeutic target for diseases associated with signal pathways involving Pro-directed phosphorylation and characterized by uncontrolled cell proliferation, primarily malignancies.
We have surprisingly found that an approved anticancer reagent with an unknown mechanism, all-trans retinoic acid (ATRA), potently and reversibly binds and inhibits and ultimately induces degradation of active Pin1. The use of all-trans retinoic acid (ATRA) to treat acute promyelocytic leukemia (APL) is described as the first example of targeted therapy in human cancer. ATRA induces leukemia cell differentiation by activating RARα or the oncogene PML/RARα-dependent transcription and induces degradation of PML/RARα. However, the mechanism by which ATRA mediates these anticancer effects is unknown. Though RARα and PML have been described as Pin1 substrates, the link between ATRA and Pin1 is poorly understood. The establishment of the mechanism of interaction between ATRA and Pin1 could facilitate the development and identification of selective Pin1 inhibitors with low toxicity, high cell permeability, and long half-lives for use in the treatment of proliferative and other disorders. Accordingly, there is a need for an improved understanding of the binding interaction between ATRA and Pin1.
The present invention relates to ATRA-related compounds that act as Pin1 substrates and methods of identifying the same. In addition, the invention relates to methods of treating a proliferative disorder, autoimmune disorder, or addiction condition with the retinoic acid compounds of the invention.
Accordingly, in one aspect, the invention provides an all-trans retinoic acid (ATRA)-related compound having a high affinity for an active site of Pin1 (e.g., the PPlase active site) or portion thereof, in which the active site of Pin1 includes a binding pocket comprising K63 and R69 residues, and the ATRA-related compound comprises a carboxyl group which interacts with the K63 and R69 residues. In some embodiments, an ATRA-related compound also comprises a backbone moiety including a carbon chain having one or more double bonds. In certain embodiments, the backbone moiety may be a diterpene moiety such as that of ATRA.
In a related aspect, the invention provides an all-trans retinoic acid (ATRA)-related compound having a high affinity for an active site of Pin1 (e.g., the PPlase active site) or portion thereof, in which the active site of Pin1 includes a binding pocket comprising L122, M130, Q131, and F134 residues, and the ATRA-related compound comprises a cycloalkyl group which interacts with the L122, M130, Q131, and F134 residues, where the cycloalkyl group optionally includes one or more unsaturations (e.g., double bonds) and alkyl substitutions (e.g., methyl or ethyl groups) and is optionally fused to one or more aryl or heteroaryl groups (e.g., a benzene ring). In some embodiments, an ATRA-related compound also comprises a backbone moiety including a carbon chain having one or more double bonds. In certain embodiments, the backbone moiety may be a diterpene moiety such as that of ATRA.
In another related aspect, the invention provides an all-trans retinoic acid (ATRA)-related compound having a high affinity for an active site of Pin1 (e.g., the PPlase active site) or portion thereof, in which the active site of Pin1 includes a binding pocket comprising three or more of K63, R68, R69, S71, S72, D112, and S154 residues, and the ATRA-related compound comprises a backbone moiety which interacts with said residues, wherein said backbone moiety includes a carbon chain having one or more double bonds. In certain embodiments, the backbone moiety may be a diterpene moiety such as that of ATRA.
In a further related aspect, the invention provides an all-trans retinoic acid (ATRA)-related compound having a high affinity for an active site of Pin1 (e.g., the PPlase active site) or portion thereof, in which the active site of Pin1 includes a binding pocket comprising K63 and R69 residues and a binding pocket comprising L122, M130, Q131, and F134 residues, and the ATRA-related compound comprises a carboxyl group which interacts with the K63 and R69 residues and a cycloalkyl group which interacts with the L122, M130, Q131, and F134 residues, where the cycloalkyl group optionally includes one or more unsaturations (e.g., double bonds) and alkyl substitutions (e.g., methyl or ethyl groups) and is optionally fused to one or more aryl or heteroaryl groups (e.g., a benzene ring). In some embodiments, an ATRA-related compound also comprises a backbone moiety including a carbon chain having one or more double bonds. In certain embodiments, the backbone moiety may be a diterpene moiety such as that of ATRA.
In another aspect, the invention provides a co-crystal comprising Pin1 and a retinoic acid compound (e.g., ATRA or an ATRA-related compound). In a particular embodiment, the invention provides a co-crystal comprising Pin1 and ATRA.
In another aspect, the invention provides a method of using a structure of a co-crystal (e.g., obtained using crystallographic methods) comprising Pin1 and a retinoic acid compound (e.g., ATRA or an ATRA-related compound) to identify a Pin1 substrate capable of associating with all or a portion of a Pin1 active site (e.g., the PPlase active site), where the method comprises the steps of
In another aspect, the invention provides a method of identifying a Pin1 substrate capable of associating with all or a portion of a Pin1 active site (e.g., the PPlase active site), in which the Pin1 active site comprises one or more Pin1 binding pockets, the method comprising the steps of:
In some embodiments, one or more Pin1 binding pockets are identified using a three-dimensional model of Pin1. In other embodiments, one or more Pin1 binding pockets are identified using a three-dimensional model generated from a co-crystal structure of Pin1 and ATRA. In some embodiments, the ATRA-related compound is selected for evaluation based on the one or more binding pockets (e.g., based on biochemical and/or physiochemical intuition that a compound with particular groups or features will interact with one or more binding pockets).
In certain embodiments, the method of identifying a Pin1 substrate capable of associating with all or a portion of a Pin1 active site further comprises the steps of
In another aspect, the invention provides a method of designing or identifying a compound capable of associating with all or a portion of a Pin1 active site, in which the active site comprises one or more Pin1 binding pockets, the method comprising
In some embodiments, the method of designing a compound capable of associating with all or a portion of a Pin1 active site further comprises the steps of generating a three-dimensional graphical representation of the association between the ATRA-related compound and the one or more Pin1 binding pockets with a computer using the three-dimensional model of the Pin1 active site and a graphical representation of the ATRA-related compound.
The invention also relates to methods of treating proliferative diseases, autoimmune diseases, and addiction conditions. Thus, in one aspect, the invention provides a method of treating a condition selected from the group consisting of a proliferative disease (e.g., breast cancer), an autoimmune disease (e.g., systemic lupus erythematosus, SLE), or an addiction condition (e.g., cocaine addiction) in a subject having elevated levels of a Pin1 marker, where the method comprises the steps of administering an ATRA-related compound identified by any of the methods described herein to the subject in an amount sufficient to treat the subject. In a related aspect, the invention provides a method of treating a condition selected from the group consisting of proliferative disease, an autoimmune disease, or an addiction condition in a subject comprising determining Pin1 marker levels in a sample from the subject and administering an ATRA-related compound to the subject if the sample is determined to have elevated Pin1 marker levels, where the ATRA-related compound is identified by any of the methods described herein. The invention also provides a method of identifying a candidate for treatment with an ATRA-related compound, where the candidate has a condition selected from the group consisting of a proliferative disease, an autoimmune disease, or an addiction condition and has previously been administered the ATRA-related compound, the method comprising determining whether the candidate has elevated levels of a Pin1 marker, where a candidate for treatment with the ATRA-related compound has elevated levels of a Pin1 marker.
In another aspect, the invention provides a method of treating a condition selected from the group consisting of a proliferative disease (e.g., breast cancer), an autoimmune disease (e.g., systemic lupus erythematosus, SLE), or an addiction condition (e.g., cocaine addiction) in a subject having elevated levels of a Pin1 marker, where the method comprises the steps of administering an ATRA-related compound to the subject in an amount sufficient to treat the subject, where the ATRA-related compound has a high affinity for an active site of Pin1 or a portion thereof, where the Pin1 active site comprises one or more of a binding pocket including K63 and R69 residues; a binding pocket comprising L122, M130, Q131, and F134 residues; and a binding pocket comprising three or more of K63, R68, R69, S71, S72, D112, and S154 residues, and where the ATRA-related compound comprises one or more of a carboxyl group which interacts with said K63 and R69 residues; a cycloalkyl group that optionally comprises one or more double bonds and alkyl substitutions and is optionally fused to one or more aryl or heteroaryl groups which interacts with said L122, M130, Q131, and F134 residues; and a backbone moiety comprising a carbon chain having one or more double bonds which interacts with three or more of K63, R68, R69, S71, S72, D112, and S154 residues. In a related aspect, the invention provides a method of treating a condition selected from the group consisting of a proliferative disease, an autoimmune disease, or an addiction condition in a subject comprising determining Pin1 marker levels in a sample from the subject and administering an ATRA-related compound to the subject if the sample is determined to have elevated Pin1 marker levels, where the ATRA-related compound has a high affinity for an active site of Pin1 or a portion thereof, where the Pin1 active site comprises one or more of a binding pocket including K63 and R69 residues; a binding pocket including L122, M130, Q131, and F134 residues; and a binding pocket comprising three or more of K63, R68, R69, S71, S72, D112, and S154 residues, and where the ATRA-related compound comprises one or more of a carboxyl group which interacts with said K63 and R69 residues; a cycloalkyl group that optionally comprises one or more double bonds and alkyl substitutions and is optionally fused to one or more aryl or heteroaryl groups which interacts with said L122, M130, Q131, and F134 residues; and a backbone moiety comprising a carbon chain having one or more double bonds which interacts with three or more of K63, R68, R69, S71, S72, D112, and S154 residues. The invention also provides a method of identifying a candidate for treatment with an ATRA-related compound, where the candidate has a condition selected from the group consisting of a proliferative disease, an autoimmune disease, or an addiction condition and has previously been administered the ATRA-related compound, the method comprising determining whether the candidate has elevated levels of a Pin1 marker, where a candidate for treatment with the ATRA-related compound has elevated levels of a Pin1 marker, where the ATRA-related compound has a high affinity for an active site of Pin1 or a portion thereof, where the Pin1 active site comprises one or more of a binding pocket including K63 and R69 residues; a binding pocket including L122, M130, Q131, and F134 residues; and a binding pocket comprising three or more of K63, R68, R69, S71, S72, D112, and S154 residues, and where the ATRA-related compound comprises one or more of a carboxyl group which interacts with said K63 and R69 residues; a cycloalkyl group that optionally comprises one or more double bonds and alkyl substitutions and is optionally fused to one or more aryl or heteroaryl groups which interacts with said L122, M130, Q131, and F134 residues; and a backbone moiety comprising a carbon chain having one or more double bonds which interacts with three or more of K63, R68, R69, S71, S72, D112, and S154 residues. In yet another aspect, the invention provides a method of treating a condition selected from the group consisting of a proliferative disease, an autoimmune disease, or an addiction condition in a subject previously treated with a retinoic acid compound (e.g., ATRA or an ATRA-related compound) and having or shown to have Pin1 degradation (e.g., by comparing a Pin1 marker level in a sample obtained from a subject before administration of the retinoic acid compound with a Pin1 marker level in a sample obtained from a subject after administration of the retinoic acid compound), the method comprising administering a retinoic acid compound to the subject in an amount sufficient to treat the subject.
In a related aspect, the invention provides a method of identifying a candidate for treatment with a retinoic acid compound (e.g., ATRA or an ATRA-related compound), in which the candidate has a condition selected from the group consisting of a proliferative disease, an autoimmune disease, or an addiction condition has previously been administered the ATRA-related compound, the method comprising determining whether the candidate has Pin1 degradation, where a candidate for treatment with a retinoic acid compound has Pin1 degradation.
In another aspect, the invention provides a method of treating a condition selected from the group consisting of a proliferative disease, an autoimmune disease, or an addiction condition in a subject by administering an ATRA-related compound of the invention to the subject in an amount sufficient to treat the subject, wherein the subject is determined to have elevated levels of a Pin1 marker (e.g., Ser71 phosphorylation or PML-RARα) prior to the administration.
In another aspect, the invention features a method of treating a condition selected from the group consisting of a proliferative disease, an autoimmune disease, or an addiction condition in a subject by determining Pin1 marker levels (e.g., reduced Ser71 phosphorylation or overexpression of PML-RARα) in a sample (e.g., tumor samples, blood, urine, biopsies, lymph, saliva, phlegm, and pus) from the subject and administering an ATRA-related compound of the invention to the subject if the sample is determined to have elevated Pin1 marker levels. The invention also provides a method of identifying a candidate for treatment with an ATRA-related compound of the invention, where the candidate has a condition selected from the group consisting of a proliferative disease, an autoimmune disease, or an addiction condition and has previously been administered the ATRA-related compound, the method comprising determining whether the candidate has elevated levels of a Pin1 marker, where a candidate for treatment with the ATRA-related compound has elevated levels of a Pin1 marker.
In the methods described herein, a Pin1 marker can be reduced Ser71 phosphorylation of Pin1. In some embodiments, a Pin1 marker is overexpression of PML-RARα. In some embodiments, an elevated Pin1 marker level is due to an inherited trait or somatic mutation.
In certain embodiments, a method of treatment or identifying a candidate for treatment further comprises determining Pin1 marker levels in said sample after said administration of said ATRA-related compound. In particular embodiments, a sample is selected from the group consisting of tumor samples, blood, urine, biopsies, lymph, saliva, phlegm, and pus.
In any of the methods described herein, an ATRA-related compound can be administered in combination with a second therapeutic compound (e.g., any described herein, such as an anti-proliferative, anti-inflammatory, anti-microbial, or anti-viral compound). In some embodiments, a second therapeutic compound is administered at a low dosage or at a different time (e.g., separate administration). In other embodiments, a second therapeutic compound is formulated together with the ATRA-related compound (e.g., in a single formulation). In some embodiments, the second therapeutic compound is formulated as a liposomal formulation or a controlled release formulation. In some embodiments, a second therapeutic compound may be another ATRA-related compound. A second therapeutic compound may be, for example, an anti-proliferative, anti-inflammatory, anti-microbial, or anti-viral compound. In some embodiments, the second therapeutic compound is an anti-proliferative compound (e.g., at a low dosage) or anti-cancer compound (e.g., an anti-angiogenic compound). Examples of anti-proliferative compounds useful in the methods of the invention include, but are not limited to: MK-2206, ON Q13105, RTA 402, BI 2536, Sorafenib, ISIS-STAT3Rx, a microtubule inhibitor, a topoisomerase inhibitor, a platin, an alkylating agent, an anti-metabolite, paclitaxel, gemcitabine, doxorubicin, vinblastine, etoposide, 5-fluorouracil, carboplatin, altretamine, aminoglutethimide, amsacrine, anastrozole, azacitidine, bleomycin, busulfan, carmustine, chlorambucil, 2-chlorodeoxyadenosine, cisplatin, colchicine, cyclophosphamide, cytarabine, cytoxan, dacarbazine, dactinomycin, daunorubicin, docetaxel, estramustine phosphate, floxuridine, fludarabine, gentuzumab, hexamethylmelamine, hydroxyurea, ifosfamide, imatinib, interferon, irinotecan, lomustine, mechlorethamine, melphalen, 6-mercaptopurine, methotrexate, mitomycin, mitotane, mitoxantrone, pentostatin, procarbazine, rituximab, streptozocin, tamoxifen, temozolomide, teniposide, 6-thioguanine, topotecan, trastuzumab, vincristine, vindesine, and/or vinorelbine.
Examples of anti-inflammatory compounds useful in the methods of the invention include, but are not limited to: corticosteroids, NSAIDs (e.g., naproxen sodium, diclofenac sodium, diclofenac potassium, aspirin, sulindac, diflunisal, piroxicam, indomethacin, ibuprofen, nabumetone, choline magnesium trisalicylate, sodium salicylate, salicylsalicylic acid (salsalate), fenoprofen, flurbiprofen, ketoprofen, meclofenamate sodium, meloxicam, oxaprozin, sulindac, and tolmetin), COX-2 inhibitors (e.g., rofecoxib, celecoxib, valdecoxib, and lumiracoxib), biologics (e.g., inflixamab, adelimumab, etanercept, CDP-870, rituximab, and atlizumab), small molecule immunomodulators (e.g., VX 702, SCIO 469, doramapimod, RO 30201195, SCIO 323, DPC 333, pranalcasan, mycophenolate, and merimepodib), non-steroidal immunophilin-dependent immunosuppressants (e.g., cyclosporine, tacrolimus, pimecrolimus, and ISAtx247), 5-amino salicylic acid (e.g., mesalamine, sulfasalazine, balsalazide disodium, and olsalazine sodium), DMARDs (e.g., methotrexate, leflunomide, minocycline, auranofin, gold sodium thiomalate, aurothioglucose, and azathioprine), hydroxychloroquine sulfate, and penicillamine. By “corticosteroid” is meant any naturally occurring or synthetic steroid hormone which can be derived from cholesterol and is characterized by a hydrogenated cyclopentanoperhydrophenanthrene ring system. Naturally occurring corticosteroids are generally produced by the adrenal cortex. Synthetic corticosteroids may be halogenated. Functional groups required for activity include a double bond at A4, a C3 ketone, and a C20 ketone. Corticosteroids may have glucocorticoid and/or mineralocorticoid activity. Exemplary corticosteroids include algestone, 6-alpha-fluoroprednisolone, 6-alpha-methylprednisolone, 6-alpha-methylprednisolone 21-acetate, 6-alpha-methylprednisolone 21-hemisuccinate sodium salt, 6-alpha,9-alpha-difluoroprednisolone 21-acetate 17-butyrate, amcinafal, beclomethasone, beclomethasone dipropionate, beclomethasone dipropionate monohydrate, 6-beta-hydroxycortisol, betamethasone, betamethasone-17-valerate, budesonide, clobetasol, clobetasol propionate, clobetasone, clocortolone, clocortolone pivalate, cortisone, cortisone acetate, cortodoxone, deflazacort, 21-deoxycortlsol, deprodone, descinolone, desonide, desoximethasone, dexamethasone, dexamethasone-21-acetate, dichiorisone, diflorasone, diflorasone diacetate, diflucortolone, doxibetasol, fludrocortisone, flumethasone, flumethasone pivalate, flumoxonide, flunisolide, fluocinonide, fluocinolone acetonide, 9-fluorocortisone, fluorohydroxyandrostenedione, fluorometholone, fluorometholone acetate, fluoxymesterone, flupredidene, fluprednisolone, flurandrenolide, formocortal, halcinonide, halometasone, halopredone, hyrcanoside, hydrocortisone, hydrocortisone acetate, hydrocortisone butyrate, hydrocortisone cypionate, hydrocortisone sodium phosphate, hydrocortisone sodium succinate, hydrocortisone probutate, hydrocortisone valerate, 6-hydroxydexamethasone, isoflupredone, isoflupredone acetate, isoprednidene, meclorisone, methylprednisolone, methylprednisolone acetate, methylprednisolone sodium succinate, paramethasone, paramethasone acetate, prednisolone, prednisolone acetate, prednisolone metasulphobenzoate, prednisolone sodium phosphate, prednisolone tebutate, prednisolone-21-hemisuccinate free acid, prednisolone-21-acetate, prednisolone-21 (beta-D-glucuronide), prednisone, prednylidene, procinonide, tralonide, triamcinolone, triamcinolone acetonide, triamcinolone acetonide 21-palmitate, triamcinolone diacetate, triamcinolone hexacetonide, and wortmannin. Desirably, the corticosteroid is fludrocortisone or prednisolone.
Examples of anti-microbial agents useful in the methods of the invention include, but are not limited to: penicillins (e.g., penicillin G, ampicillin, methicillin, oxacillin, and amoxicillin), cephalosporins (e.g., cefadroxil, ceforanid, cefotaxime, and ceftriaxone), tetracyclines (e.g., doxycycline, minocycline, and tetracycline), aminoglycosides (e.g., amikacin, gentamycin, kanamycin, neomycin, streptomycin, and tobramycin), macrolides (e.g., azithromycin, clarithromycin, and erythromycin), fluoroquinolones (e.g., ciprofloxacin, lomefloxacin, and norfloxacin), and other antibiotics including chloramphenicol, clindamycin, cycloserine, isoniazid, rifampin, and vancomycin. Particularly useful formulations contain aminoglycosides, including for example amikacin, gentamicin, kanamycin, neomycin, netilmicin, paromomycin, streptomycin, and tobramycin.
Examples of anti-viral agents useful in the methods of the invention include, but are not limited to: 1-D-ribofuranosyl-1,2,4-triazole-3 carboxamide, 9-[(2-hydroxyethoxy)methyl]guanine, adamantanamine, 5-iodo-2′-deoxyuridine, trifluorothymidine, interferon, adenine arabinoside, protease inhibitors, thymidine kinase inhibitors, sugar or glycoprotein synthesis inhibitors, structural protein synthesis inhibitors, attachment and adsorption inhibitors, and nucleoside analogues such as acyclovir, penciclovir, valacyclovir, and ganciclovir.
By the term “proliferative disorder” is meant a disorder characterized by inappropriate accumulation of a cell population in a tissue (e.g., by abnormal cell growth). This inappropriate accumulation may be the result of a genetic or epigenetic variation that occurs in one or more cells of the cell population. This genetic or epigenetic variation causes the cells of the cell population to grow faster, die slower, or differentiate slower or in a different manner than the surrounding, normal tissue. The cell population includes cells of hematopoietic, epithelial, endothelial, or solid tissue origin.
As used herein, the term “abnormal cell growth” is intended to include cell growth which is undesirable or inappropriate. Abnormal cell growth also includes proliferation which is undesirable or inappropriate (e.g., unregulated cell proliferation or undesirably rapid cell proliferation). Abnormal cell growth can be benign and result in benign masses of tissue or cells, or benign tumors. Many art-recognized conditions are associated with such benign masses or benign tumors including diabetic retinopathy, retrolental fibrioplasia, neovascular glaucoma, psoriasis, angiofibromas, rheumatoid arthritis, hemangiomas, and Karposi's sarcoma. Abnormal cell growth can also be malignant and result in malignancies, malignant masses of tissue or cells, or malignant tumors. Many art-recognized conditions and disorders are associated with malignancies, malignant masses, and malignant tumors including cancer and carcinoma.
As used herein, the term “tumor” is intended to encompass both in vitro and in vivo tumors that form in any organ of the body. Tumors may be associated with benign abnormal cell growth (e.g., benign tumors) or malignant cell growth (e.g., malignant tumors). The tumors which are described herein are preferably sensitive to the Pin1 inhibitors of the present invention. Examples of the types of tumors intended to be encompassed by the present invention include those tumors associated with breast cancer, skin cancer, bone cancer, prostate cancer, liver cancer, lung cancer, brain cancer, cancer of the larynx, gallbladder, pancreas, rectum, parathyroid, thyroid, adrenal, neural tissue, head and neck, colon, stomach, bronchi, kidneys.
The proliferative disorder of any of the foregoing methods can be, but is not limited to: leukemias, polycythemia vera, lymphomas, Waldenstrom's macroglobulinemia, heavy chain disease, and solid tumors. Specifically, proliferative disorders include: acute leukemia, acute lymphocytic leukemia, acute myelocytic leukemia, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, chronic leukemia, chronic myelocytic leukemia, chronic lymphocytic leukemia), Hodgkin's disease, non-Hodgkin's disease, fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma, endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer, ovarian cancer, prostate cancer, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renal cell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma, seminoma, embryonal carcinoma, Wilm's tumor, cervical cancer, uterine cancer, testicular cancer, lung carcinoma, small cell lung carcinoma, bladder carcinoma, epithelial carcinoma, glioma, astrocytoma, medulloblastoma, craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acoustic neuroma, oligodenroglioma, schwannoma, meningioma, melanoma, neuroblastoma, and retinoblastoma. In particular embodiments, a proliferative disease may be selected from the group consisting of leukemias, polycythemia vera, lymphomas, Waldenstrom's macroglobulinemia, heavy chain disease, and solid tumors. In certain embodiments, the proliferative disease is breast cancer.
By the term “immune disorder” is meant a disorder characterized by dysfunction of the immune system. Immune disorders often involve deregulation of Toll like receptor and/or type 1 interferon. By “autoimmune disorder” or “autoimmune disease” is meant any disease, disorder, or condition associated with an immune response against substances normally present in the body (e.g., compounds, polypeptides, nucleic acids, cells, tissues, and organs).
The immune disorder of any of the foregoing methods can, e.g., result from disregulation of Toll-like receptor signaling or type I interferon-mediated immunity. The immune disorder of any of the foregoing methods can be, but is not limited to: acne vulgaris; acute respiratory distress syndrome; Addison's disease; adrenocortical insufficiency; adrenogenital ayndrome; agammagbulinemia; allergic conjunctivitis; allergic rhinitis; allergic intraocular inflammatory diseases; alopecia areata; amyotrophic lateral sclerosis; ANCA-associated small-vessel vasculitis; angioedema; ankylosing spondylitis; antiphospholipid syndrome; antisynthetase syndrome; aphthous stomatitis; arthritis, asthma; atherosclerosis; atopic allergy; atopic dermatitis; autoimmune aplastic anemia; autoimmune cardiomyopathy; autoimmune disease; autoimmune enteropathy; autoimmune hemolytic anemia; autoimmune hepatitis; autoimmune inner ear disease; autoimmune lymphoproliferative syndrome; autoimmune peripheral neuropathy; autoimmune pancreatitis; autoimmune polyendocrine syndrome; autoimmune progesterone dermatitis; autoimmune thrombocytopenic purpura; autoimmune urticaria; autoimmune uveitis; Balo concentric sclerosis; Behcet's disease; Bell's palsy; Berger's disease; berylliosis; Bickerstaff's encephalitis; Blau syndrome; bronchial asthma; bullous herpetiformis dermatitis; bullous pemphigoid; Castleman's disease; carditis; celiac disease; cerebral ischaemia; Chagas disease; chronic bronchitis; chronic inflammatory demyelinating polyneuropathy; chronic obstructive pulmonary disease (COPD); chronic recurrent multifocal osteomyelitis; chronic sinusitis; Churg-Strauss syndrome; cicatricial pemphigold; cirrhosis; Cogan's syndrome; cold agglutinin disease; complement component 2 deficiency; contact dermatitis; cranial arteritis; CREST syndrome; Crohn's disease; Cushing's syndrome; cutaneous leukocytoclastic vasculitis; Dego's disease; Dercum's disease; dermatitis herpetiformis; dermatomyositis; diabetes mellitus type 1; diffuse cutaneous systemic sclerosis; Dressier's syndrome; drug-induced lupus; eczema; encephalomyelitis; discoid lupus erythematosus; endometriosis; enthesitis-related arthritis; eosinophilic fasciitis; eosinophilic gastroenteritis; epicondylitis; epidermolysis bullosa acquisita; erythema nodosum; erythroblastosis fetalis; essential mixed cryoglobulinemia; Evan's syndrome; exfoliative dermatitis; fibrodysplasia ossificans progressive; fibromyalgia; fibrosing alveolitis; focal glomerulosclerosis; gastritis; gastrointestinal pemphigoid; giant cell arteritis; glomerulonephritis; Goodpasture's syndrome; gout; gouty arthritis; graft-versus-host disease; Grave's disease; Guillain-Barre syndrome; hand eczema; Hashimoto's encephalopathy; Hashimoto's thyroiditis; Henoch-Schonlein purpura; herpes gestationis; hidradenitis suppurativa; hirsutism; Hughes-Stovin syndrome; hypersensitivity drug reactions; hypertension; hypogammaglobulinemia; idiopathic cerato-scleritis; idiopathic inflammatory demyelinating diseases; idiopathic pulmonary fibrosis; idiopathic thrombocytopenic purpura; IgA nephropathy; inclusion body myositis; inflammatory bowel or gastrointestinal disorders, inflammatory dermatoses; interstitial cystitis; juvenile idiopathic arthritis; juvenile rheumatoid arthritis; Kawasaki's disease; Lambert-Eaton myasthenic syndrome; laryngeal edema; leukocytoclastic vasculitis; lichen planus; lichen sclerosus; linear IgA disease; Loeffler's syndrome; lupus erythematosus; lupus nephritis; lupus vulgaris; lymphomatous tracheobronchitis; macular edema; Majeed syndrome; Meniere's disease; microscopic polyangiitis; mixed connective tissue disease; morphea; Mucha-Habermann disease; multiple sclerosis; musculoskeletal and connective tissue disorder; myasthenia gravis; myositis; narcolepsy; neuromyelitis optica; neuromyotonia; obstructive pulmonary disease; ocular cicatricial pemphigoid; ocular inflammation; opsoclonus myoclonus syndrome; Ord's thyroiditis; organ transplant rejection; osteoarthritis; palindromic rheumatism; pancreatitis; PANDAS; paraneoplastic cerebellar degeneration; paroxysmal nocturnal hemoglobinuria; Parry Romberg syndrome; Parsonage-Turner syndrome; pars planitis; pemphigoid gestationis; pemphigus vulgaris; pernicious anaemia; perivenous encephalomyelitis; peripheral vascular disease; POEMS syndrome; polyarteritis nodosa; polymyalgia rheumatica; polymyositis; primary adrenocortical insufficiency; primary billiary cirrhosis; primary sclerosing cholangitis; progressive inflammatory neuropathy; pruritus scroti; pruritis/inflammation, psoriasis; psoriatic arthritis; pyoderma gangrenosum; pure red cell aplasia; Rasmussen's encephalitis; raynaud phenomenon; Reiter's disease; relapsing polychondritis; restless leg syndrome; retroperitoneal fibrosis; rheumatic carditis; rheumatic fever; rheumatoid arthritis; rosacea caused by sarcoidosis; rosacea caused by scleroderma; rosacea caused by Sweet's syndrome; rosacea caused by systemic lupus erythematosus; rosacea caused by urticaria; rosacea caused by zoster-associated pain; sarcoldosis; Schnitzler syndrome; scleritis; scleroderma; segmental glomerulosclerosis; septic shock syndrome; serum sickness; shoulder tendinitis or bursitis; Sjogren's syndrome; spondyloarthropathy; stiff person syndrome; Still's disease; stroke-induced brain cell death; subacute bacterial endocarditis; Susac's syndrome; Sweet's disease; sympathetic ophthalmia; systemic dermatomyositis; systemic lupus erythematosus; systemic sclerosis; Takayasu's arteritis; temporal arteritis; thrombocytopenia; thyroiditis; Tolosa-Hunt syndrome; toxic epidermal necrolysis; transverse myelitis; tuberculosis; type-1 diabetes; ulcerative colitis; undifferentiated connective tissue disease; undifferentiated spondyloarthropathy; uveitis; vasculitis; vitiligo; and Wegener's granulomatosis. The autoimmune disorder of any of the foregoing methods can be, but is not limited to: multiple sclerosis (MS); encephalomyelitis; Addison's disease; agammaglbulinemia; alopecia areata; amyotrophic lateral sclerosis; ankylosing spondylitis; antiphospholipid syndrome; antisynthetase syndrome; atopic allergy; atopic dermatitis; autoimmune aplastic anemia; autoimmune cardiomyopathy; autoimmune enteropathy; autoimmunehemolytic anemia; autoimmune hepatitis; autoimmune inner ear disease; autoimmune lymphoproliferative syndrome; autoimmune peripheral neuropathy; autoimmune pancreatitis; autoimmune polyendocrine syndrome; autoimmune progesterone dermatitis; autoimmune thrombocytopenic purpura; autoimmune urticaria; autoimmune uveitis; Balo concentric sclerosis; Behcet's disease; Berger's disease; Bickerstaff's encephalitis; Blau syndrome; bullous pemphigoid; chronic bronchitis; Castleman's disease; Chagas disease; chronic inflammatory demyelinating polyneuropathy; chronic recurrent multifocal osteomyelltis; chronic obstructive pulmonary disease; Churg-Strauss syndrome; cicatricial pemphigoid; Cogan syndrome; cold agglutinin disease; complement component 2 deficiency; contact dermatitis; cranial arteritis; CREST syndrome; Crohn's disease; Cushing's syndrome; cutaneous leukocytoclastic vasculitis; Dego's disease; Dercum's disease; dermatitis herpetiformis; dermatomyositis; diabetes mellitus type 1; diffuse cutaneous systemic sclerosis; Dressler's syndrome; drug-induced lupus; discoid lupus erythematosus; eczema; endometriosis; enthesitis-related arthritis; eosinophilic fasciitis; eosinophilic gastroenteritis; epidermolysis bullosa acquisita; erythema nodosum; erythroblastosis fetalis; essential mixed cryoglobulinemia; Evan's syndrome; fibrodysplasia ossificans progressive; fibrosing alveolitis; gastritis; gastrointestinal pemphigold; giant cell arteritis; glomerulonephritis; Goodpasture's syndrome; Grave's disease; Guillain-Barre syndrome; Hashimoto's encephalopathy; Hashimoto's thyroiditis; Henoch-Schonlein purpura; herpes gestationis; hidradenitis suppurativa; Hughes-Stovin syndrome; hypertension; hypogammaglobulinemia; idiopathic inflammatory demyelinating diseases; idiopathic pulmonary fibrosis; idiopathic thrombocytopenic purpura; IgA nephropathy; inclusion body myositis; chronic inflammatory demyelinating polyneuropathy; interstitial cystitis; juvenile idiopathic arthritis; Kawasaki's disease; Lambert-Eaton myasthenic syndrome; leukocytoclastic vasculitis; lichen planus; lichen scierosus; linear IgA disease; lupus erythematosus; Majeed syndrome; Meniere's disease; microscopic polyangiitis; mixed connective tissue disease; morphea; Mucha-Habermann disease; myasthenia gravis; myositis; narcolepsy; neuromyelitis optica; neuromyotonia; ocular cicatricial pemphigoid; opsoclonus myoclonus syndrome; Ord's thyroiditis; palindromic rheumatism; PANDAS; paraneoplastic cerebellar degeneration; paroxysmal nocturnal hemoglobinuria; Parry Romberg syndrome; Parsonage-Turner syndrome; pars planitis; pemphigus vulgaris; pernicious anaemia; perivenous encephalomyelitis; peripheral vascular disease; POEMS syndrome; polyarteritis nodosa; polymyalgia rheumatic; polymyositis; primary biliary cirrhosis; primary sclerosing cholangitis; progressive inflammatory neuropathy; psoriatic arthritis; psoriasis; pyoderma gangrenosum; pure red cell aplasia; Rasmussen's encephalitis; raynaud phenomenon; relapsing polychondritis; Reiter's syndrome; restless leg syndrome; retroperitoneal fibrosis; rheumatic fever; rheumatoid arthritis; Schnitzler syndrome; scleritis; scieroderma; serum sickness; chronic sinusitis; Sjogren's syndrome; spondyloarthropathy; stiff person syndrome; subacute bacterial endocarditis; Susac's syndrome; Sweet's syndrome; sympathetic ophthalmia; Takayasu's arteritis; temporal arteritis; thrombocytopenia; Tolosa-Hunt syndrome; transverse myelitis; ulcerative colitis; undifferentiated connective tissue disease; undifferentiated spondyloarthropathy; vitiligo; and Wegener's granulomatosis. The invention also features the treatment of immune disorders that increase susceptibility to microbial or viral infection, including HIV. In particular embodiments, the autoimmune disease is lupus erythematosus. In certain embodiments, the autoimmune disease is asthma.
By the term “addiction disorder” or “addiction condition” is meant a compulsive disorder or condition characterized by impulsive behavior. Addiction conditions include substance use disorders, eating disorders, sexual addictions, and other conditions characterized by pathological or compulsive gambling, electronic device use, spending, arson (e.g, pyromania), theft (e.g., kleptomania), hair pulling (e.g., trichotillomania), overworking, overexercising, and other behaviors. In particular embodiments, an addiction condition is a substance use disorder. A substance use disorder may involve dependence or abuse of one or more substances with or without physiological dependence. Such substances include, but are not limited to, alcohol, amphetamines or amphetamine-like substances, inhalants, caffeine, cannabis, cocaine, hallucinogens, inhalants, nicotine, opioids, phencyclidine and phencyclidine-like compounds, sedative-hyptnotics, benzodiazepines, and combinations thereof. In particular embodiments, the methods of the invention are used to treat cocaine addiction. Substance use disorders may encompass drug withdrawal disorders and symptoms including headaches, delirium, perceptual disturbances, mood disorders (e.g., anxiety), sleep disorders (e.g., insomnia), fatigue, sweating, vomiting, diarrhea, nausea, irritability, shaking, difficulty concentrating, and cravings.
As used herein, the term “Pin1 marker” refers to a marker which is capable of being indicative of Pin1 activity levels in a sample of the invention. Pin1 markers include nucleic acid molecules (e.g., mRNA, DNA) which corresponds to some or all of a Pin1 gene, peptide sequences (e.g., amino acid sequences) which correspond to some or all of a Pin1 protein, nucleic acid sequences which are homologous to Pin1 gene sequences, peptide sequences which are homologous to Pin1 peptide sequences, antibodies to Pin1 protein, substrates of Pin1 protein, binding partners of Pin1 protein, and activity of Pin1.
By “elevated levels of a Pin1 marker” is meant a level of Pin1 marker that is altered thereby indicating elevated Pin1 activity. “Elevated levels of a Pin1 marker” include levels at least 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 500%, 1000%, or greater than, or 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100% less than the marker levels measured in a normal, disease fee subject or tissue.
By “Pin1 degradation” is meant a reduction in a level of Pin1 marker. For example, a patient treated with a Pin1 substrate (e.g., catalytic inhibitor) may exhibit a lower level of a Pin1 marker prior to treatment than after treatment, indicating that the substrate degraded Pin1. Pin1 degradation includes changes in a level of a Pin1 marker of less than 5%, or at least 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 40/o, 50%, 60%, 70%, 80%, 90%, 100%, 200%, 500%, 1000%, or 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%.
By “active site” is meant a portion of a protein where a ligand, substrate, or inhibitor associates. For example, Pin1 has at least two active sites including a WW domain and a peptidyl-prolyl isomerase (PPlase) domain that catalyzes the prolyl isomerization of proteins. An active site of Pin1 may include one or more “binding pockets” with which a substrate (e.g., catalytic inhibitor) can interact (e.g., bind, associate, or participate in a chemical reaction or change). For example, a portion of an active site of Pin1 may be a binding pocket. As described herein, the PPlase active site of Pin1 includes multiple Pin1 binding pockets such as a phosphate or carboxyl binding pocket (e.g., a high electron density binding pocket) and a cyclohexenyl or hydrophobic binding pocket. Association of a substrate with Pin1 or a portion thereof (e.g., one or more binding pockets of an active site) may involve non-covalent intermolecular interactions such as electrostatic, van der Waals, hydrogen bonding, and hydrophobic interactions. A substrate having high affinity for Pin1 or a portion thereof may associate strongly and/or efficiently with all or a portion of Pin1 (e.g., with one or more binding pockets of one or more active sites). As used herein, a substrate with a “high affinity” for Pin1 or a portion thereof has a low picomolar to submicromolar Ki and/or Kd value as measured by, for example, a Pin1 fluorescence polarization assay, Pin1 photolabeling, a Pin1 PPlase enzymatic assay, isothermal titration calorimetry, microscale thermophoresis, or a thermal shift assay. Affinity for Pin1 or a portion thereof may also be determined by, for example, a binding energy determined with molecular modeling (e.g., a protein-ligand docking program). Affinities and binding energies determined with molecular modeling may differ from or be the same as or similar to experimental values, though relative values should be similar. For example, a ranking of compounds by affinities or binding energies determined with molecular modeling is likely to be the same as a ranking of the same compounds based on affinities or binding energies determined experimentally, e.g., as described herein. A substrate may alternately be referred to as an inhibitor (e.g., a catalytic inhibitor), binder, or ligand herein.
In the context of the present invention, the term “retinoic acid compound” is a compound that has the general form X—Y—Z, where X is a head group (e.g., a cycloalkyl, cycloalkenyl, aryl, heteroaryl, or heterocyclic ring), Y is a backbone optionally including one or more unsaturations (e.g., an alkene such as a diterpene or a ring), and Z is an end group including one or more electronegative atoms (e.g., a carboxylic acid, alcohol, ester, aldehyde, carbonyl, acyl halide, carbonate, acetal, phosphate, thiol, sulfoxide, sulfinic acid, sulfonic acid, thial, sulfate, sulfonyl, thioketone, thioaldehyde, or amide). For example, a retinoic acid compound may be all-trans retinoic acid (ATRA), 13-cis retinoic acid (13cRA), retinal, or retinol. Any or all of X, Y, and Z or a group or portion thereof may include one or more unsaturations or substitutions (e.g., 1, 2, 3, 4, 5, 6, or more unsaturations or substitutions). An unsaturation may be a multiple bond such as a double bond (alkene) or triple bond (alkyne) or a ring structure. A substitution may be selected from the group consisting of, but not limited to, a halogen atom, a carboxylic acid, an alcohol (e.g., a hydroxyl), an ester, an aldehyde, a carbonyl, an acyl halide, a carbonate, an acetal, a phosphate, a thiol, a sulfoxide, a sulfinic acid, a sulfonic acid, a thial, a sulfate, a sulfonyl, an amide, an azido, a nitro, a cyano, isocyano, acyloxy, an amino, a carbamoyl, a sulfonamide, or another functional group, or an optionally substituted alkyl (e.g., C1-10 alkyl), alkenyl (e.g., C2-10 alkenyl), alkynyl (e.g., C2-10 alkynyl), alkoxy (e.g., C1-10 alkoxy), aryloxy (e.g., C6-10 aryloxy), cycloalkyl (e.g., C3-8 cycloalkyl), cycloalkoxy (e.g., C3-8 cycloalkoxy), aryl (e.g., C6-10 aryl), aryl-alkoxy (e.g, C6-10 aryl-C1-10 alkoxy), heterocyclyl or heterocycloalkyl (e.g., C3-8 heterocycloalkyl), heterocycloalkenyl, (e.g., C4-8 heterocycloalkenyl), or heteroaryl (e.g., C6-10 heteroaryl). In some embodiments, the substituent groups themselves may be further substituted with, for example, 1, 2, 3, 4, 5, or 6 substituents as defined herein. For example, a C1-6 alkyl, aryl, or heteroaryl group may be further substituted with 1, 2, 3, 4, 5, or 6 substituents as described herein.
As used herein, the term “acyl” represents an alkyl group or hydrogen that is attached to a parent molecular group through a carbonyl group. Examples include formyl, acetyl, and propionyl groups.
As used herein, the term “acyloxy” represents a group of the form —OC(O)R, in which R is a carbon-containing group such as an alkyl group, as defined herein.
As used herein, the term “acetal” represents a group of the form —C(OR′)2R″, in which each OR′ are alkoxy groups, as defined herein, and R′ is a carbon-containing group such as an alkyl group, as defined herein. The alkoxy groups of an acetal group may be the same (e.g., a symmetric acetal) or different (e.g., a mixed acetal).
As used herein, the term “aldehyde” represents an acyl group having the structure —CHO.
As used herein, the term “carbonyl” represents a —C(O)R group, alternatively represented by C═O, in which R is a carbon-containing group such as an alkyl group.
As used herein, the term “alkoxy” represents a group of the formula-OR, where R is an alkyl group of any length (e.g., C1-10 alkyl). Examples include methoxy, ethoxy, propoxy (e.g., n-propoxy and isoproxy) groups. The alkyl portion of an alkoxy group may include any additional substitution as defined herein.
As used herein, the term “alkyl” includes straight chain and branched chain saturated groups including between 1 and 20 carbon atoms, unless otherwise specified. Examples include methyl, ethyl, n-propyl, and isopropyl. An alkyl group may be optionally substituted with one or more substituents as defined herein.
As used herein, the term “alkenyl” represents an alkyl group including one or more double bonds. An alkene or alkenyl group may be a straight or branched alkyl chain with two or more hydrogen atoms removed. Examples include methylene, ethylene, and isopropylene. An alkenyl group may include between 2 and 20 carbon atoms, unless otherwise specified, and may be optionally substituted as defined herein. Alkenyls include both cis and trans isomers. For example, 2-butene includes cis-but-2-ene [(Z)-but-2-ene] and trans-but-2-ene [(E)-but-2-ene].
As used herein, the term “alkynyl” represents an alkyl group including one or more triple bonds. An alkyne or alkynyl group may be a straight or branched alkyl chain with four or more hydrogen atoms removed. Examples include acetylene (ethyne), propyne, and butyne. An alkynyl group may include between 2 and 20 carbon atoms, unless otherwise specified, and may be optionally substituted as defined herein.
As used herein, the term “cycloalkyl” represents a saturated or unsaturated non-aromatic cyclic hydrocarbon group including 3, 4, 5, 6, 7, 8, or more carbon atoms, unless otherwise specified. A cycloalkyl group may optionally include one or more substitutions, as defined herein. Examples include cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, and cyclooctyl groups. In some embodiments, the cycloalkyl is a polycyclic (e.g., adamantyl). A cycloalkyl group including one or more double bonds is referred to as a “cycloalkenyl” group. Examples of cycloalkenyl groups include cyclopentenyl, cyclohexenyl, cycloheptenyl, and cyclooctenyl groups.
As used herein, the term “cycloalkoxy” represents a substituent of the form —OR, where R is a cycloalkyl grup, as defined herein.
As used herein, the term “aryl” represents a mono-, bi-, or multi-cyclic carbocyclic ring system having one or more aromatic rings. For example, an aryl group may be a mono- or bicyclic C6-C14 group with [4n+2] π electrons in conjugation and where n is 1, 2, or 3. Phenyl is an aryl group where n is 1. Aryl groups also include ring systems where the ring system having [4n+2] π electrons is fused to a non-aromatic cycloalkyl or a non-aromatic heterocyclyl. Examples include phenyl, naphthyl, 1,2-dihydronaphthyl, 1,2,3,4-tetrahydronaphthyl, anthracenyl, and indenyl. An aryl group may optionally include one or more substitutions, as defined herein.
As used herein, the term “heterocycloalkyl” or “heterocyclyl” represents a cycloalkyl (e.g., a non-aromatic ring) group including one or more heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur. A heterocycloalkyl group including one or more double bonds is referred to as a “heterocycloalkenyl” group. A heterocyclyl group may be a multicyclic structure (e.g., a bicyclic structure or a bridged multicyclic structure). Examples of heterocycles include piperidinyl, pyrrolidinyl, and tetrahydrofuryl groups. Heterocyclyl groups may be unsubstituted or substituted with, e.g., 1, 2, 3, or 4 substituent groups as defined herein.
As used herein, the term “heteroaryl” represents an aryl (e.g., aromatic) group including one or more heteroatoms independently selected from the group consisting of nitrogen, oxygen, and sulfur. Heteroaryls may be monocycles, bicycles, tricycles, or tetracycles in which any aromatic ring is fused to one, two, or three heterocyclic or carbocyclic rings (e.g., an aryl ring). Examples of heterocyclic aromatic molecules include furan, thiophene, pyrrole, thiadiazole (e.g., 1,2,3-thiadiazole or 1,2,4-thiadiazole), oxadiazole (e.g., 1,2,3-oxadiazole or 1,2,5-oxadiazole), oxazole, isoxazole, isothiazole, pyrazole, thiazole, triazole (e.g., 1,2,4-triazole or 1,2,3-triazole), pyridine, pyrimidine, pyrazine, pyrazine, triazine (e.g, 1,2,3-triazine 1,2,4-triazine, or 1,3,5-triazine), 1,2,4,5-tetrazine, indolyl, quinolinyl, isoquinolinyl, benzimidazolyl, benzothiazolyl, and benzoxazolyl. Heteroaryls may be unsubstituted or substituted with, e.g., 1, 2, 3, or 4 substituents groups as defined herein.
As used herein, the term “fused” refers to one or more chemical elements that are connected to one another by one or more chemical bonds. In particular, two rings (e.g, cycloalkyl or aryl groups) may be fused to one another, as described above. Examples include indolyl, quinolyl, and isoquinolyl groups. As used herein, the term “alkaryl” represents an aryl group, as defined herein, attached to a parent molecular group through an alkyl group, as defined herein.
As used herein, the term “aryl-alkoxy” represents an alkaryl group, as defined herein, attached to a parent molecular group through an oxygen atom.
As used herein, the term “aryloxy” represents a group of the form —OR, where R is an aryl group, as defined herein.
As used herein, the term “halo” represents a halogen selected from the group consisting of bromine, chlorine, iodine, and fluorine.
As used herein, the term “carboxylic acid” or “carboxy” represents a group of the form —C(O)OH, also represented as —CO2H.
As used herein, the term “ester” represents a group of the form —C(O)OR, in which R is a carbon-containing group such as an alkyl group.
As used herein, the term “acyl halide” represents a group of the form —C(O)X, in which X is a halide selected from bromide, fluoride, chloride, and iodide.
As used herein, the term “carbonate” represents a group of the form —OC(O)OR, in which R is a carbon-containing group such as an alkyl group.
As used herein, the term “alcohol” or “hydroxyl” represents a group of the form —OH.
As used herein, the term “phosphate” represents a P(O)43 group.
As used herein, the term “thiol” represents an —SH group.
As used herein, the term “thial” represents a —C(S)H group.
As used herein, the term “sulfoxide” represents an —S(O)R group, in which R is a carbon-containing group such as an alkyl group.
As used herein, the term “sulfonyl” represents an —S(O)2R group, in which R is a carbon-containing group such as an alkyl group.
As used herein, the term “sulfinic acid” represents an —S(O)OH group.
As used herein, the term “sulfonic acid” represents an —S(O)2OH group.
As used herein, the term “sulfate” represents an S(O)42− group.
As used herein, the term “sulfonamide” represents a group of the form —S(O)2NR2 or —N(R)S(O)2R, wherein each R is independently optionally substituted alkyl, aryl, cycloalkyl, cycloaryl, or another group.
As used herein, the term “amide” represents a group of the form —C(O)NR2, or —N(R)C(O)R, wherein each R is independently optionally substituted alkyl, aryl, cycloalkyl, cycloaryl, or another group.
As used herein, the term “amino” represents an —NR2 group, wherein each R is independently optionally substituted alkyl, aryl, cycloalkyl, cycloaryl, or another group.
As used herein, the term “azido” represents an —N3 group.
As used herein, the term “nitro” represents an —NO2 group.
As used herein, the term “cyano” represents a —CN group, while the term “isocyano” represents an —NC group.
As used herein, the term “carbamoyl” represents a group of the form —OC(O)NR2 or —N(R)C(O)OR, wherein each R is independently optionally substituted alkyl, aryl, cycloalkyl, cycloaryl, or another group.
In some embodiments, a retinoic acid compound and/or ATRA-related compound may include one or more isotopic substitutions, including deuterium, tritium, 17O, 18O, 13C, 32P, 15N, and 18F. A retinoic acid compound may have any stereochemistry. All possible isomeric and conformational forms of retinoic acid compounds and/or ATRA-related compounds are contemplated, including diastereomers, enantiomers, and/or conformers of a given structure. Different tautomeric forms are also contemplated. The invention includes protonated, deprotonated, and solvated species, as well as salts of the compounds of the invention.
In some embodiments, the head group X may include one or more rigid or sterically bulky groups such as one or more aryl, heteroaryl, cycloalkyl, cycloalkenyl, heterocycloakyl, or heterocycloalkenyl rings or a fusion thereof. For example, the head group X may include a naphthyl or hydronaphthyl (e.g., di-, tri-, tetra-, penta-, hexa-, hepta-, octa-, nona-, or deca-hydronaphthyl) group. In some embodiments, a head group X may include a single carbon ring including a single double bond (e.g., a cycloalkyl or cycloalkenyl group). For example, the head group X may be an optionally substituted cylcohexene group. In preferred embodiments, substitutions on a ring of the head group X are not sterically bulky. For example, a ring preferably includes one or more short-chain alkyl (e.g., C1-5 alkyl) substituents. In an embodiment, the head group X is a trimethylcyclohexene such as 1,3,3-trimethylcyclohexene.
In some embodiments, the backbone Y is an alkyl chain including one or more rings. For example, the backbone Y may be an alkyl chain fused to an optionally substituted cycloalkyl, cycloalkenyl, heterocycloalkyl, or heterocycloalkenyl group. A backbone Y may include one or more optionally substituted aryl or heteroaryl groups. For example, a backbone Y may include a fused benzene ring. In some embodiments, the backbone Y includes one or more double bonds. In particular embodiments, the backbone Y includes conjugation (e.g., alternating single and double bonds). For example, the backbone Y may be 4-10 carbon chain 2-5 double bonds, such as octa-1,3,5,7-tetraene. In certain embodiments, the backbone Y may include one or more isoprene units and be, e.g., a diterpene. In some embodiments, the backbone Y includes one or more short-chain alkyl (e.g., C1-5 alkyl) substituents. For instance, the backbone may be 2,6-dimethyl-octa-1,3,5,7-tetraene. As described above, all as and trans isomers are contemplated.
In some embodiments, the end group Z includes one or more oxygen atoms and is a group selected from a carboxylic acid, a hydroxyl, an ester, an aldehyde, a carbonyl, an acyl halide, a carbonate, an acetal, a phosphate, a sulfoxide, a sulfone, a sulfinic acid, a sulfonic acid, a sulfate, a sulfonyl, and an amide. In preferred embodiments, the end group Z is selected from a carboxylic acid, a hydroxyl, an ester, an aldehyde, a carbonyl, an acyl halide, a carbonate, and an amide. In particular preferred embodiments, the end group Z is a carboxylic acid.
As used herein, an “all-trans retinoic acid (ATRA)-related compound” refers to a compound that is structurally related to or an analog of ATRA. For example, a compound that is structurally related to or an analog of ATRA may have one or more components (e.g., one or more functional groups or structural motifs) in common with ATRA and/or may have one or more substitutions, elongations, eliminations, additions, or other differences relative to ATRA, e.g., as described herein. An ATRA-related compound may be a retinoic acid compound. An ATRA-related compound may be designed from ATRA. For example, one or more components of ATRA, such as the head group X, the backbone Y, or the end group Z, or a portion thereof, may be modified, replaced, or eliminated, e.g., by adding, changing, or eliminating one or more substitutions, replacing one or more groups (e.g., replacing a carboxyl group with an ester group), and/or increasing or decreasing the size or length of a component of ATRA (e.g., replacing a six-membered ring with a seven-membered ring). An ATRA-related compound may differ from ATRA by as few as one group, element, or feature (e.g., a single isotopic substitution, a single methyl group or absence thereof, etc.). ATRA-related compounds may include isotopically substituted species (e.g., ATRA including one or more isotopic substitutions such as deuterium, tritium, 17O, 18O, 13C, 32P, 15N, and 18F), functionally substituted species (e.g., ATRA with one or more methyl groups eliminated or replaced by one or more other functional groups such as longer chain alkyl groups, hydroxyl groups, cycloalkyl groups, and other groups), and stereoisomers (e.g., ATRA including one or more cis alkene groups along its backbone).
As used herein, ATRA-related compounds do not include: ATRA, 13cRA, retinal, retinol, retinyl acetate, AC-55649, n-carotene, adapalene (e.g., in combination with clindamycin hydrochloride), alitretinoin, bexarotene, isotretinoin, tamibarotene, tazarotene, tretinoin (e.g., in combination with clindamycin phosphate), adapalene (e.g., in combination with benzoyl peroxide), peretinoin, NRX-4204, seocalcitol, 9cUAB-30, RXR agonists (e.g., those described by Okayama University), palovarotene, talarozole, AGN-193174, AGN-194301, AHPN analogs, BMS-181163, E-6060, I-arglitazar, Farnesoid X receptor agonists, GW-0791, HX-600, LG-100754, LG-101506, LG-268, NRX-4310, Ro-13-6307, PA-452, RAR alpha agonists (e.g., those described by Allergan and Eisai), RAR beta agonists (e.g., those described by MD Anderson), RAR-binding retinoids (e.g., those described by Galderma), retinoic acid receptor antagonists (e.g., those described by Allergan), retinoic acid receptor substrates (e.g., those described by Bristol-Myers Squibb), RWJ-23989, RXR modulators (e.g., those described by Ligand/Eli Lilly), SR-11238, amsilarotene, MX-781, SR-11237, acitretin, BMS 194753, AGN 195183, AM580 (CD365), BMS 209641, BMS 238987, AGN-153639, CD586, AC261066, BMS 189981, CD 666, AHPN (CD437), CH55, LGD 1550, TTNPB (R0139410), AGN-194310, BMS 204493, AGN 195109, BMS 206005, Ro 41-5251, BMS 195634, CD2565, or the compounds included in Table 1. Further, ATRA-related compounds of the invention do not include compounds having the structure R1—Ar1-L1Ar2-L2-C(═O)R3 (Formula I), in which Ar1 and Ar2 are, independently, optionally substituted aryl or an optionally substituted heteroaryl; R1 is H, an optionally substituted alkyl group, an optionally substituted alkenyl group, or an optionally substituted alkynyl group; each of L1 and L2 is selected, independently, from a covalent bond, an optionally substituted C1-10 alkylene, an optionally substituted C2-10 alkenylene (e.g., —CH═CH—, —COCH═CH—, —CH═CHCO—, a dienyl group, or a trienyl group), optionally substituted C2-10 alkynylene (e.g., —C≡C—), or —(CHR4)nCONR5—, —NR5CO—, where n is 0 or 1, R4 is H or OH, and R5 is H or optionally substituted alkyl; and R3 is H, OR4, or N(R4)2, where each R4 is selected, independently, from H, optionally substituted alkyl, or optionally substituted heteroalkyl.
In some embodiments, ATRA-related compounds are designed based on the association between ATRA and one or more Pin1 binding pockets as determined from a co-crystal structure including Pin1 and ATRA. For example, one or more groups, elements, features, or components of ATRA may be modified to design a compound with potentially higher potency, selectivity, affinity, or catalytic activity than ATRA with regard to Pin1 association. An ATRA-related compound may be designed to interact more strongly or to fit or otherwise associate better with one or more binding pockets of an active site of Pin1. For example, an ATRA-related compound may include a head group X that differs from that of ATRA by interacting more strongly with the hydrophobic binding pocket with which the head group associates. In other embodiments, an ATRA-related compound is a retinoic acid compound selected from a library or otherwise conceptualized (e.g., through iterative modeling), e.g., not designed based on an association between ATRA and one or more Pin1 binding pockets.
Table 1 includes examples of retinoic acid compounds that are not ATRA-related compounds of the invention.
As used herein, a “co-crystal” is a crystalline solid including two or more components. For example, a co-crystal may include a protein, such as Pin1, and a molecule, such as ATRA or an ATRA-related compound. Without wishing to be bound by theory, components of a co-crystal tend to have one or more hydrogen bonding or solvent-mediated hydrogen bonding interactions, which aids in the formation of the co-crystal. A co-crystal may be formed by, for example, combining a solution containing a first component (e.g., Pin1) with a solution containing a second component (e.g., ATRA), optionally incubating, and performing vapor diffusion (e.g., in a hanging-drop or sitting-drop format).
A co-crystal or portion thereof may be interrogated and characterized with crystallographic methods such as X-ray, neutron, or electron diffraction. An X-ray (e.g., a synchrotron), neutron, or electron source can be used to produce a diffraction pattern from a co-crystal or portion thereof according to methods known in the art. Subsequently, a computer model or program can be used to derive structural coordinates for components of the co-crystal or portion thereof. Derived structural coordinates (e.g., Cartesian or “xyz” coordinates) can be used to generate a three-dimensional visualization or visual or graphical representation of a co-crystal or portion thereof. Such representations can facilitate the identification of binding pockets and to make inferences about the intermolecular forces between the components of the co-crystal (e.g., between Pin1 and ATRA). A three-dimensional visual representation may include an electron density map and may be generated using a computer program, model, or platform, such as those known in the art. Software for generating visual representations from structural coordinates are widely available and include programs such as Mercury, Diamond, CrystalMaker, and VESTA.
The retinoic acid compounds (e.g., ATRA-related compounds) of the invention inhibit Pin1 activity (e.g., as determined by the fluorescence polarization-based displacement assay or PPlase assay as describe herein). This inhibition can be, e.g., greater than 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, or greater.
The term “anti-proliferative compound” is intended to include chemical reagents which inhibit the growth of proliferating cells or tissues wherein the growth of such cells or tissues is undesirable. Chemotherapeutic agents are well known in the art (as well as described herein), and are typically used to treat neoplastic diseases, tumors, and cancers. Anti-proliferative compounds can be, for example, any anti-proliferative compound described herein.
The term “anti-microbial compound” is intended to include agents that inhibit the growth of or kill microorganisms. Anti-microbial compounds may be anti-bacterial compounds (e.g., compounds useful against bacteria), anti-fungal compounds (e.g., compounds useful against fungi), anti-viral compounds, anti-parasitic compounds, disinfectants, and anti-septics. Anti-microbial compounds can be, for example, any anti-microbial compound described herein.
The term “anti-viral compound” is intended to include agents useful for treating viral infections, e.g., by inhibiting the development of a pathogen. Anti-viral compounds can be, for example, any anti-viral compound described herein.
The term “anti-inflammatory compound” is intended to include agents useful for reducing inflammation or swelling. Anti-inflammatory compounds can be, for example, any anti-inflammatory compound described herein.
“Treatment,” as used herein, is defined as the application or administration of a therapeutic agent (e.g., a retinoic acid compound) to a patient (e.g., a subject), or application or administration of a therapeutic agent to an isolated tissue or cell line from a patient, who has a disease, a symptom of disease or a predisposition toward a disease, with the purpose to cure, heal, alleviate, relieve, alter, remedy, ameliorate, improve or affect the disease, the symptoms of disease or the predisposition toward disease, or to slow the progression of the disease.
As used herein, the terms “sample” and “biological sample” include samples obtained from a mammal or a subject containing Pin1 which can be used within the methods described herein, e.g., tissues, cells and biological fluids isolated from a subject, as well as tissues, cells and fluids present within a subject. Typical samples from a subject include tissue samples, tumor samples, blood, urine, biopsies, lymph, saliva, phlegm, pus, and the like.
By a “low dosage” or “low concentration” is meant at least 5% less (e.g., at least 10%, 20%, 50%, 80%, 90%, or even 95%) than the lowest standard recommended dosage or lowest standard recommended concentration of a particular compound formulated for a given route of administration for treatment of any human disease or condition. For example, a low dosage of an anti-proliferative compound formulated for oral administration will differ from a low dosage of an anti-proliferative compound formulated for intravenous administration.
Standard one-letter amino acid abbreviations are used herein. For example, K corresponds to lysine, R corresponds to arginine, L corresponds to leucine, M corresponds to methionine, Q corresponds to glutamine, and F corresponds to phenylalanine. A residue denoted “M130” indicates a methionine at position 130 of an amino acid sequence.
In general, the invention features all-trans retinoic acid (ATRA)-related compounds having high affinities for Pin1 and methods of identifying the same. The invention also features co-crystals of Pin1 and ATRA or ATRA-related compounds. Additionally, the invention includes methods of treating a proliferative disorder, autoimmune disorder, or addiction condition characterized by an elevated Pin1 marker level or Pin1 degradation in a subject by administering a retinoic acid compound. The invention also features methods of treating proliferative disorders, autoimmune disorders, and addiction conditions (e.g., diseases, disorders, and conditions characterized by elevated Pin1 marker levels) by administering a retinoic acid compound in combination with one or more anti-proliferative, anti-microbial, anti-viral, or anti-inflammatory compounds or therapeutic species.
Inhibitors of Pin1 (e.g., retinoic acid compounds) are useful for treating proliferative disorders, autoimmune disorders, and addiction conditions (e.g., diseases, disorders, or conditions characterized by increased Pin1 activity or resulting from disregulation of Toll-like receptor signaling or type I interferon-mediated immunity). Because Pin1 acts in several different oncogenic pathways, Pin1 inhibition would be expected to behave synergistically with many anti-proliferative compounds. Furthermore, because Pin1 associated aberrant IRAK1 activation and type I IFN overproduction occurs in various immune diseases, Pin1 inhibition would be expected to behave synergistically with many anti-inflammatory compounds.
The PPlase active site of Pin1 includes one or more binding pockets or portions that associate with Pin1 catalytic inhibitors. By identifying the one or more binding pockets of the active site, a substrate or catalytic inhibitor capable of associating with all or a portion of the Pin1 active site could be conceptualized, e.g., by using information about the geometric and electrostatic characteristics of the one or more binding sites to design a Pin1 catalytic inhibitor. A Pin1 catalytic inhibitor conceptualized in this manner could be subsequently synthesized and interacted with Pin1 in a binding or inhibition assay in order to determine the affinity and selectivity of the designed catalytic inhibitor for the active site or portion thereof (e.g., one or more binding pockets). The potency and half-life of the catalytic inhibitor and/or protein-inhibitor complex could subsequently be measured in other biological assays. Accordingly, the present invention provides for drug discovery based on structure-activity relationships, and for the design, screening, optimization, and evaluation of Pin1 catalytic inhibitors (e.g., retinoic acid compounds and ATRA-related compounds) for Pin1.
In order to identify one or more binding pockets of the active site, it is useful to examine the structure of the Pin1 active site, e.g., that determined by X-ray crystallographic methods. X-ray crystallographic interrogation of a crystal of a protein provides structural coordinates determined from X-ray diffraction patterns via iterative and widely available computer software such as COOT known to those of skill in the art. These structural coordinates can be evaluated and used to generate a three-dimensional model of a protein (e.g., Pin1) or an active site thereof, for example, using software such as PROCHECK and MolProbity and others described herein. The three-dimensional model may be presented in a variety of formats (e.g., ball and stick, wire frame, portions excluded, etc.) and optimized to provide a visual representation of the one or more binding pockets of an active site of a protein.
As described above, Pin1 includes at least two active sites including the WW domain and the PPlase active site. The amino acid residues involved in the PPlase domain have the following sequence: GKNGQGEPARVRCSHLLVKHSQSRRPSSWRQEKITRTKEEALELINGYIQKIKSGEEDFESLASQFSDCS SAKARGDLGAFSRGQMQKPFEDASFALRTGEMSGPVFTDSGIHIILRTE (SEQ ID NO:1). The PPlase active site includes at least one binding pocket where a Pin1 catalytic inhibitor can interact with one or more amino acid species.
Upon identifying one or more binding pockets of an active site, e.g., of Pin1, a molecule having appropriate characteristics for interaction with one or more of the binding pockets could be conceptualized and subsequently evaluated, as described above. For example, a molecular component capable of forming one or more hydrogen bonds (e.g., a carboxylic acid group) could be designed for a binding pocket consisting of amino acid residues having hydroxyl or amino groups (e.g., lysine, K; arginine, R; and serine, S). Similarly, a molecular component with high hydrophobicity (e.g., consisting primarily of hydrogen and carbon) could be designed for a binding pocket consisting primarily of hydrophobic residues (e.g., leucine, L, and phenylalanine, F). Molecular bridges linking components designed for interaction with different binding groups could be similarly conceptualized. For example, for an active site including two binding pockets spaced approximately 10 Å apart, an alkyl or alkenyl chain approximately 10 Å in length could be designed to link the two associative components. The rigidity of the chain or linker could also be optimized, e.g., by varying the number of unsaturations (e.g., double bonds) in the chain and/or designing an anchor or other component to add bulk at one or more locations between one or more binding pockets. Geometric parameters such as the distance between one or more residues of an active site of a protein could be used to infer the optimal size, geometry, and electrostatics of a molecular component to associate with one or more binding pockets. For example, the distance between hydrogen bonding residues could be used to design an associative molecular component: a carboxyl group may be appropriate for a binding pocket having two hydrogen bonding partners that are relatively close to one another, while a binding pocket having a single hydrogen bonding residue or one or more hydrogen bonding partners diametrically or otherwise distantly positioned may associate more strongly with one or more hydroxyl or other groups. Physico-biochemical interaction models may also be applied to the catalytic inhibitor design process. For example, phosphate groups are generally known to have poor cell permeability. Accordingly, groups such as carboxylic acids, which have electron densities similar to phosphate groups but are more likely to be cell permeable, could be used in place of phosphate groups in electropositive portions of an active site.
Alternatively, iterative drug design could be carried out using crystallographic methods. Analysis of a three-dimensional structure of a crystal or co-crystal structure can provide structural and chemical insight into the activity of a protein and its association with a catalytic inhibitor. Thus, by forming successive protein-compound complexes and then crystallizing each new complex (e.g., as described herein), potential catalytic inhibitors could be screened for their selectivity and affinity for Pin1. High throughput crystallization assays could be used to find new crystallization conditions or to optimize the original protein or complex crystallization condition for a new complex. Pre-formed protein crystals could also be soaked in the presence of a catalytic inhibitor (e.g., an ATRA-related compound), thereby forming a new protein-inhibitor complex and obviating the need to crystallize each individual protein-inhibitor complex. Such an approach could provide insight into the association between the protein and inhibitor of each complex by selecting substrates with inhibitory activity (e.g., as identified in a binding assay) and by comparing the associations (e.g., as measured with modeling, as described herein) and visualizations of the three-dimensional structures of different co-crystals and observing how changes in a substrate (e.g., catalytic inhibitor) affected associations between the protein and substrate. However, this type of optimization process requires extensive lab time as well as significant access to crystallography instrumentation and analytical tools.
Alternatively, one or more binding pockets of an active site of a protein can be identified by first identifying a molecule (e.g., catalytic inhibitor) capable of associating with the active site of the protein (e.g., with a binding assay) and subsequently examining the active site or portion thereof. For example, a binding assay (e.g., a fluorescence probe high-throughput screen) could be performed to identify one or more molecules (e.g., catalytic inhibitors) capable of associating with all or a portion of an active site. A substrate with particularly high affinity (e.g., with a Z score significantly different than the average, such as a Z score with an absolute value of 2 or greater) for the active site could be selected as a starting point for analysis. Subsequently, the structure of the high affinity substrate (e.g., catalytic inhibitor) could be compared to a three-dimensional model of the active site generated from structural coordinates (e.g., on a computer from data collected by crystallographic methods). Comparison of the structure of the active site and the structure of the high affinity substrate could be performed to identify one or more binding pockets of the active site. In this context, comparison may involve visually inspecting the structure of the active site for grooves, pockets, indentations, folds, or other structural features, and making chemical inferences based on electrostatic, geometric, and steric considerations with regard to the residues occupying or in the vicinity of the active site or a portion thereof (e.g., a groove, pocket, indentation, or the like) to determine how the substrate may associate with the active site of the protein. For example, the Pin1 active site includes a region wherein a lysine residue (K63) and an arginine residue (R69) are in close proximity. Accordingly, if a substrate selected from a binding assay includes a carboxylic acid group, comparison between the structure of the active site and the structure of the substrate and application of chemical intuition would suggest that the carboxylic acid group should associate with the active site in a manner that permits the carboxylic acid group to hydrogen bond with the K63 and R69 residues. A high electron density binding pocket would have thus been identified.
Molecular Modeling Comparison of the structure of an active site of a protein and the structure of a high affinity substrate may also involve performing a fitting operation between the high affinity substrate and all or a portion of the active site. For example, the structure of the high affinity substrate could be optimized (e.g., using force-field optimizations or computational methods such as density functional theory as is well known in the art) and structural coordinates for the substrate obtained. A computer could then be used to position the substrate structure in the vicinity the structure of the active site of the protein. The substrate structure could be initially manually or automatically positioned in the vicinity of the active site structure. Manual positioning may be followed by automated optimization, e.g., using a protein-substrate docking molecular modeling technique. Molecular modeling processes permit prediction of the position and orientation of a substrate relative to the active site of the protein. A modeling process may therefore be used to predict how one or more components of a substrate interact with one or more binding pockets of an active site.
Protein-substrate docking may involve molecular dynamics (MD) simulations (e.g., holding the protein structure rigid while permitting free movement of a substrate and subsequently annealing). While computationally expensive due to the many short energy minimization steps typically involved, MD simulations are often applied in protein-substrate docking. Alternatively, the molecular modeling process may involve shape-complementarity methods. These methods apply descriptors to the protein and substrate that reflect structural and binding complementarity (e.g., geometric parameters such as solvent-accessible surface area, overall shape, geometric constraints, hydrogen bonding interactions, hydrophobic contacts, and van der Waals interactions). Descriptors are provided in the form of structural templates and are interpreted to describe how well a substrate may bind to a protein (e.g., the binding affinity). Such methods may be computationally less expensive than molecular dynamics simulations. Genetic algorithms involving energy optimizations of substrate-protein complexes over large conformational spaces may also be performed. Genetic algorithms are generally temporally expensive due to the size of the conformational space. Commercially available computational docking programs such as AutoDock and Schrödinger's Glide may be used to perform one or more protein-substrate docking methods. Computational docking programs may also quantify the association between a protein and a substrate. For example, a program may generate a “docking score” associated with a given substrate. If multiple substrates are analyzed with molecular modeling, the docking scores of the substrates may be compared to determine which substrate may associate most strongly with a Pin1 active site, for example, in a screening method. Docking score rankings could also readily be compared to the results of binding assays to evaluate the effectiveness and predictiveness of a particular molecular modeling method. A binding energy or binding affinity cutoff could also be used to identify one or more substrates that may be particularly selective or potent Pin1 substrates (e.g., catalytic inhibitors). For example, Pin1 catalytic inhibitors having a deformation energy of binding with a binding pocket of less than −7 kcal/mol could be selected for further analysis (e.g., further computational analysis and/or in vitro assays).
In one aspect, the invention provides such a screening method, in which a compound capable of associating with all or a portion of a Pin1 active site is designed. This method includes the steps of i) utilizing a three-dimensional model of the Pin1 active site including one or more binding pockets (e.g., on a computer, where the model is generated using structural coordinates obtained from crystallographic methods), where one or more Pin1 binding pockets for a substrate (e.g., a retinoic acid compound or an ATRA-related compound) are specified, and where at least one binding pocket includes one or more of H59, K63, S67, R68, R69, S71, S72, W73, Q75, E76, Q77, D112, C113, S114, S115, A116, K117, A118, R119, G120, D121, L122, Q129, M130, Q131, K132, F134, D153, S154, and H157; ii) performing a fitting operation between a first substrate and all or a portion of the one or more Pin1 binding pockets; iii) quantifying the association between the first substrate and all or a portion of the one or more Pin1 binding pockets (e.g., generating docking scores from molecular modeling results or determining a binding affinity or deformation energy of binding); iv) repeating steps i) to iii) with one or more further substrates (e.g., ATRA-related compounds); v) selecting one or more substrates (e.g., ATRA-related compounds) of steps i) to iv) based on the quantified association (e.g., the docking scores), where the quantified association indicates that the one or more substrates are capable of associating with all or a portion of a Pin1 active site; and vi) measuring the catalytic activity of at least one of the substrates (e.g., catalytic inhibitors) selected in step v) using an in vitro assay to classify or determine the potency of the at least one substrate relative to Pin1. In some embodiments, the one or more Pin1 binding pockets are identified using a three-dimensional model of Pin1. In other embodiments, the one or more binding pockets are identified using a three-dimensional model generated from a co-crystal structure of Pin1 and ATRA. In certain embodiments, the first substrate (e.g., ATRA-related compound) is selected for evaluation based on the one or more binding pockets.
Using the method described above, two or more substrates may be screened for their ability to associate with an active site of Pin1 (e.g., their binding affinity). A graphical representation of the association between the substrate (e.g., ATRA-related compound) and one or more Pin1 binding pockets could also be optionally generated using the three-dimensional model of the Pin1 active site and a graphical representation of the substrate to facilitate the identification of the one or more Pin1 binding pockets and, accordingly, the optimization/selection of the substrate (e.g., catalytic inhibitor).
Upon quantifying the association between a high affinity substrate and an active site of a protein, the catalytic activity of a complex of the substrate and protein can be measured. With regard to Pin1, inhibition of catalytic activity is desirable, as inhibition of Pin1 prevents Pin1 from activating oncogenes and inactivating tumor suppressors. The catalytic activity of the protein can be measured using, for example, fluorescence probe, photoaffinity, or PPlase assays, as detailed in the Materials and Methods and Examples sections. The catalytic activity can be classified by, for example, measuring the % decrease in catalytic activity of the protein (e.g., Pin1) at a given concentration (e.g., 5, 10, 15, 20, or 25 μM) of substrate. The degree of decrease in the catalytic activity of Pin1 upon interaction with a given substrate (e.g., catalytic inhibitor) is indicative of the potency of the substrate as an antagonist for Pin1. A substrate with a high affinity and high potency for Pin1 will inactivate Pin1 by inhibiting its ability to isomerize proline residues. Inactive Pin1 is unable to participate in the stimulation of oncogenes and the inactivation of tumor suppressors that characterize its role in cancer. Accordingly, a potent and selective Pin1 substrate (e.g., catalytic inhibitor) may be useful in the treatment of proliferative diseases including cancers (e.g., as described herein). Thus, the present invention provides a method of identifying a Pin1 substrate (e.g., catalytic inhibitor) capable of associating with all or a portion of a Pin1 active site and evaluating the potency of the substrate.
Co-crystal structures of Pin1 and a substrate can be used in methods of identifying Pin1 substrates capable of associating with all or a portion of a Pin1 active site. In some embodiments, the identification of useful Pin1 substrates may involve first obtaining a co-crystal structure including Pin1 and a reference substrate and subsequently generating a three-dimensional model of the Pin1-reference substrate complex using structural coordinates obtained from the co-crystal structure.
Co-crystals are crystalline solid including two or more components. The two components may have distinct physiochemical properties (e.g., structure, melting point, etc.) but are typically solids at room temperature. Co-crystals of the invention include Pin1 and a Pin1 substrate (e.g., catalytic inhibitor) such as ATRA or an ATRA-related compound. In a particular embodiment, a co-crystal includes Pin1 and ATRA. Co-crystals of the invention may additionally include other components including one or more water or other solvent molecules (e.g., DMSO or glycerol) or one or more salts (e.g., ammonium sulfate or sodium citrate) or components thereof (e.g., ammonium, sulfate, sodium, or citrate ions). Without wishing to be bound by theory, the components of a co-crystal may have hydrogen bonding (including water mediated hydrogen bonding), van der Waals, hydrophobic, and other intermolecular interactions. A substrate (e.g., ATRA) of a co-crystal may be positioned at the active site of a protein (e.g., Pin1) of a co-crystal. For example, a substrate (e.g., ATRA) of Pin1 may dock to an active site of Pin1 or a portion thereof based on hydrogen bonding interactions between a component of the substrate (e.g., catalytic inhibitor) and one or more binding pockets of Pin1. The PPlase domain of Pin1 may be phosphorylated or dephosphorylated in a crystal or co-crystal structure.
Methods of forming co-crystals are known to those of skill in the art. In one embodiment, ATRA or a retinoic acid compound (e.g., an ATRA-related compound) may be produced by a well-known method, including synthetic methods such as solid phase, liquid phase, and combinations of solid phase/liquid phase syntheses; recombinant DNA methods, including cDNA cloning, optionally combined with site-directed mutagenesis; and/or purification of a natural product. In one embodiment, co-crystals are prepared by purifying and concentrating Pin1, preparing a substrate solution, combining a solution including purified Pin1 and the substrate solution, and performing vapor diffusion. The mixture of Pin1 and substrate solutions may be incubated at 0° C. for several hours prior to performing vapor diffusion. Pin1 may be derived and purified according to known methods. For example, Pin1 may be overexpressed in E. coli and separated from cells by lysing. The lysate may be subsequently purified with nickel affinity chromatography, dialysed, and incubated with a protease. The protein mixture may be further purified by chromatographic separation with an additional nickel affinity column and subsequent separation by size-exclusion chromatography. The purified Pin1 solution can be combined and incubated with a substrate solution including, in one embodiment, the substrate dissolved in DMSO.
Protein crystallization by vapor diffusion and other methods are well known to those of skill in the art and include hanging-drop, sitting-drop, sandwich-drop, dialysis, and microbatch or microtube batch devices, among others. For example, in a vapor diffusion method, a droplet of the solution including the protein and substrate is permitted to equilibrate with a reservoir including a buffered solution (the “hanging drop” method). Crystallization may be optionally seeded with other crystals (e.g., with apo PPlase domain crystals). Subsequent to their formation, co-crystals may be cryoprotected by adding glycerol and vitrifying with liquid nitrogen.
Co-crystals or portions thereof may be interrogated and characterized using crystallographic methods such as X-ray, neutron, or electron diffraction. In some embodiments, synchrotron (e.g., X-ray) radiation may be used to analyze a co-crystal. Diffraction patterns measured using crystallographic interrogation can be processed using standard software packages (e.g., the CCP4 suite and COOT). Computer software can also be used to evaluate structural determinations (e.g., with programs such as PROCHECK and MolProbity) and to extract structural coordinates from data and to use the structural coordinates to generate a three-dimensional model or visual representation of a protein (e.g., Pin1) and substrate (e.g., ATRA). For example, software including but not limited to QUANTA, O, Sybyl, and RIBBONS can be used to generate three-dimensional structures (e.g., models) of a protein-substrate complex or portion thereof. Certain software programs may imbue a graphical representation with physio-chemical attributes which are known or can be derived from the chemical composition of the molecule including residue charge, hydrophobicity, and torsional or rotational degrees of freedom for a residue or segment, among others. In some embodiments, a three-dimensional graphical representation may include an electron density map or other representation of electron density distribution in the protein-substrate complex. Three-dimensional structural information may be generated by instructions such as a computer program or commands that can generate a three-dimensional structure or graphical representation and may involve measurement of distances between atoms, the calculation of chemical energies for a substrate associating with an active site or portion thereof (e.g., a binding energy of deformation or a binding affinity), the calculation or minimization of energies of association between the substrate (e.g., catalytic inhibitor) and the protein, and other processes. These types of programs and activities are known in the art. Data generated from any such program, activity, or process may be viewed, presented, shared, saved, stored, processed, or transferred in any manner or format known in the art.
Those of skill in the art may understand that a set of structural coordinates for a protein-substrate complex or a portion thereof (e.g., derived from a Pin1-ATRA co-crystal), is a relative set of points that define a shape in three dimensions. Thus, it is possible that an entirely different set of coordinates could define a similar or identical shape. Moreover, slight variations in the individual coordinates will have little effect on overall shape. In terms of binding pockets, these variations would not be expected to significantly alter the nature of substrates (e.g., catalytic inhibitors) that could associate with those pockets. Those of skill in the art will also understand that one or more water molecules may be included in a crystal, co-crystal, and/or a structural representation of a crystal or co-crystal. The number and distribution of water molecules in and/or around a protein-substrate complex is dynamic and may depend on factors including temperature, modeling parameters, and the quality of the crystal or co-crystal.
The variations in coordinates discussed above may be generated as a result of mathematical manipulations of the Pin1 structure coordinates. For example, the structure coordinates could be manipulated by crystallographic permutations of the structure coordinates, fractionalization of the structure coordinates, integer additions or subtractions to sets of the structure coordinates, inversion of the structure coordinates or any combination of the above.
Graphical representations of protein-substrate complexes can be used to identify binding pockets of an active site. For example, a co-crystal of Pin1 and ATRA can be used to generate a graphical representation of a Pin1-ATRA complex that can be visually and/or computationally inspected for one or more binding pockets of Pin's active site. Using a co-crystal structure, distances between atoms and/or functional groups of Pin1 and a substrate can be measured and used to make chemical inferences regarding the natural of an intermolecular interaction between a portion of Pin1 and a substrate or component thereof. For instance, hydrogen bonding between the active site of Pin1 and a substrate can be readily inferred if hydrogen bonding groups (e.g., amines, alcohols, and carboxylic acids) are spaced approximately 2.5 Å apart or less. Hydrophobic interactions can be inferred by, for example, areas of interaction including primarily carbon and hydrogen atoms. These areas of interaction may be classified as binding pockets. Accordingly, visualization of the relative orientations of Pin1 and a Pin1 substrate (e.g., ATRA) can facilitate the identification of one or more binding pockets of the active site of Pin1.
Pin1's PPlase active site includes residues lysine 63 (K63), arginine 69 (R69), leucine 122 (L122), methionine 130 (M130), glutamine 131 (Q131), and phenylalanine 134 (F134), among others. Notably, K63 and R69 are positioned in proximity to one another, while L122, M130, Q131, and F134 are clustered several Angstroms away. The portion of the active site including K63 and R69 also includes serine 71 (S71), the phosphorylation of which inactivates Pin1. Due to the proximity of K63 and R69 to S71, it is likely that inactivation is caused by hydrogen bonding between K63 and R69 and phosphorylated S71. Accordingly, a potent Pin1 substrate should include a molecular component capable of associating with the high electron density binding pocket including the K63, R69, and S71 residues. As phosphate groups are known to be largely cell-impermeable, a carboxylic acid group may be desirable for inclusion in a substrate. Indeed, ATRA includes a carboxylic acid group, and the co-crystal structure of Pin1 and ATRA (
The residues L122, M130, Q131, and F134 form a groove at the surface of Pin1 that readily lends itself to identification as a binding pocket. As these residues are generally hydrophobic, it is reasonable to expect that they would experience a hydrophobic interaction with a molecular component of a substrate. The co-crystal structure of ATRA and Pin1 reveals that the cyclohexene group of ATRA associates with the L122, M130, Q131, and F134 residues. Thus, the residues represent a hydrophobic binding pocket of the active site of Pin1. As shown in
As is evident from the co-crystal structure of Pin1 and ATRA, a narrow groove connects the high electron density and hydrophobic binding pockets of the active site of Pin1. This groove may also be considered a binding pocket of Pin1. In the co-crystal structure of Pin1 and ATRA, the conjugated alkene backbone of ATRA extends along the groove in proximity to (e.g., within 4 Å of) residues K63, R68, R69, S71, S72, D112, and S154 (
By examining the ATRA-Pin1 crystal structure, one or more binding pockets of the PPlase active site can be identified. A binding pocket may include one or more residues that are located within 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 Å of ATRA or another reference molecule (e.g., an ATRA-related compound;
Thus, by examining a graphical representation of a crystal structure of Pin1 or a co-crystal structure including Pin1 and a Pin1 substrate, multiple binding pockets can readily be identified. Additional Pin1 substrates, such as analogs of the reference substrate (e.g., ATRA-related compounds), can be designed based on the information obtained from the co-crystal structure. As the co-crystal structure of Pin1 and ATRA reveals the presence of at least three binding pockets, a substrate including components optimized for association with each binding pocket can be designed using the reference substrate as a starting point. For example, ATRA can be characterized as having three distinct molecular regions: a head group X including a trimethylcyclohexene ring, a backbone Y including a conjugated carbon chain, and an end group Z including a carboxylic acid. Each of these molecular regions or components associates with a different binding pocket of Pin1 (e.g., the hydrophobic pocket, the backbone pocket, or the high electron density pocket). Thus, one or more components of ATRA could be derivatized, substituted, reduced or increased in size, or otherwise changed or optimized to yield an ATRA-related compound.
Though binding pockets of an active site can be defined with reference to one or more substrates, they may also be defined with reference to the active site itself, e.g., by examining the crystal structure of active site and identifying portions thereof where a substrate or portion thereof might conceivably associate or interact. For example,
As is evident from the definitions above, one or more pockets may have one or more residues in common. Potential binding pockets identified by examining the structure of an active site may or may not be identical to those identified by examining a co-crystal structure. A binding pocket identified by the latter method may include one or more potential pockets identified by examining the structure of an active site, or vice versa. For example, the high electron density pocket including residues K63, R69, and S71 shares residues with potential binding pockets P4, P5, and P6. In particular, P4 and P5 both include K63, R69, and S71. Similarly, the hydrophobic binding pocket including residues L122, M130, Q131, and F134 shares residues with P1, P2, P3, and P4. Like binding pockets identified by methods involving one or more reference molecules (e.g., from a co-crystal structure of Pin1 and a substrate such as ATRA), binding pockets identified by examining the structure of an active site (e.g., the PPlase active site of Pin1) can be used, alone or in combination, to identify, select, or design substrates (e.g., catalytic inhibitors) capable of associating with the active site or portion thereof. For instance, potential binding pockets P4 and P5 could be taken together to determine that a substrate should include a group capable of hydrogen bonding. Similar, potential binding pockets P2 and P3 could be taken together to determine that a substrate should include a hydrophobic group. Applying chemical intuition to this structural analysis may result in the design of one or more substrates (e.g., ATRA-related compound) capable of associating with the active site, as described herein.
In addition to being capable of physically and structurally associating (e.g., by means of intermolecular interactions including hydrogen bonding, van der Waals interactions, hydrophobic interactions, and other electrostatic interactions) with all or a portion of a Pin1 active site (e.g., one or more binding pockets of the PPlase active site), a Pin1 substrate must also be able to assume a conformation that allows it to associate with the active site or portion thereof directly. Although certain portions of a substrate may not directly participate in these associations, these portions of the substrate may still influence the overall conformation of the molecule, which may in turn have a significant impact on the potency of the substrate. Such conformational requirements may include the overall three-dimensional structure and orientation of the substrate in relation to all or a portion of the active site or portion thereof (e.g., a binding pocket), or the spacing between functional groups of a substrate including several chemical entities that directly interact with the Pin1 or Pin1-like binding pockets of an active site (e.g., a between a carboxyl group and a cycloalkyl head group that interact with a high electron density binding pocket and a hydrophobic binding pocket, respectively).
A Pin1 substrate may be an ATRA-related compound, which may be a retinoic acid compound. ATRA-related compounds need not be synthetically produced from ATRA. Indeed, many such species are readily commercially available. Instead, ATRA-related compounds could be designed manually, using a computer software package, or via comparison between ATRA and published molecular libraries.
An ATRA-related compound according to the present invention may include one or more components of ATRA, such as the head group X, the backbone Y, or the end group Z, or portions thereof. One or more of these groups or portions thereof may be modified, replaced, or eliminated, e.g., by adding, changing, or eliminating one or more substitutions, replacing one or more groups (e.g., replacing a carboxyl group with an ester group), and/or increasing or decreasing the size or length of a component of ATRA (e.g., replacing a six-membered ring with a seven-membered ring or increasing the length of a carbon chain), to yield an ATRA-related compound, as described herein. In some embodiments, the head group X of an ATRA-related compound may include one or more rigid or sterically bulky groups such as one or more aryl, heteroaryl, cycloalkyl, cycloalkenyl, heterocycloakyl, or heterocycloalkenyl rings or a fusion thereof for interaction with the hydrophobic binding pocket (e.g., a pocket including residues such as L122, M130, Q131, and F134). A cycloalkyl group may optionally include one or more unsaturations (e.g., multiple bonds, such as double bonds, or rings) and alkyl substitutions and may optionally be fused to one or more aryl or heteroaryl groups. In some embodiments, the backbone Y of an ATRA-related compound is an alkyl chain including one or more rings and/or one or more double bonds for association with the groove binding pocket. In certain embodiments, the end group Z includes a group with a high electron density, such as a carboxylic acid group, for interaction with the high electron density binding pocket (e.g., a pocket including residues K63 and R69). Additional modifications are described herein. In particular embodiments, an ATRA-related compound may include molecular components for association with each binding pocket of Pin1 (e.g., pockets P1, P2, P3, P4, P5, and P6 or a hydrophobic pocket, a high electron density pocket, and a backbone pocket). In other embodiments, an ATRA-related compound may include a non-optimized or non-optimal molecular component for association with one or more binding pockets, or may lack a molecular component for association with one or more binding pockets. For example, an ATRA-related compound may include a carboxyl group for association with the high electron density binding pocket and a carbon chain for association with the groove binding pocket and/or may not include a head group for interaction with the hydrophobic binding pocket. In some embodiments, the absence of one or more components may not affect the ability of a substrate to associate with Pin1. For instance, a compound including a group too bulky to strongly associate with a hydrophobic binding pocket may still associate strongly with a high electron density pocket and potentially inactivate the PPlase active site by blocking the phosphorylation site.
In some embodiments, the co-crystal structure of ATRA and Pin1 can be used to identify a Pin1 substrate capable of associating with all or a portion of a Pin1 active site including one or more binding pockets. In certain embodiments, a method of identifying a Pin1 substrate capable of associating with all of a portion of a Pin1 active site includes one or more of the following steps: i) generating, accessing, or otherwise obtaining (e.g., opening, modeling, or calculating) a three-dimensional model of the Pin1-ATRA complex based on the co-crystal structure; ii) identifying one or more Pin1 binding pockets for ATRA, as described herein; and iii) designing or selecting one or more substrates (e.g., ATRA-related compounds) based on the association between ATRA and the one or more Pin1 binding pockets. In some embodiments, a method of identifying a Pin1 substrate capable of associating with all or a portion of a Pin1 active site includes the steps of: i) performing a fitting operation between a substrate (e.g., an ATRA-related compound) and all or a portion of the active site (e.g., one or more binding pockets) using a three-dimensional model (e.g., generated from structural coordinates obtained by crystallographic methods) of the Pin1 active site (e.g., using a molecular modeling program), ii) quantifying the association between the substrate (e.g., ATRA-related compound) and all or a portion of the active site (e.g., with a docking score produced by a molecular modeling program or by determining a binding energy, energy of deformation, or a binding affinity), and viii) measuring the catalytic activity of a complex of Pin1 and the substrate (e.g., using an in vitro assay, such as one of those described herein) to classify or determine the potency of a substrate relative to Pin1. In some embodiments, the one or more binding pockets of Pin1 are identified using a three-dimensional model of Pin1, while in other embodiments the one or more binding pockets are identified using a three-dimensional model generated from a co-crystal structure of Pin1 and ATRA. In certain embodiments, the substrate (e.g., ATRA-related compound) is selected for evaluation based on the one or more Pin1 binding pockets (e.g., based on chemical intuition that a group or feature of a compound will interact with one or more binding pockets). The method may further involve, prior to performing the fitting operation, i) generating a three-dimensional model of Pin1 and ATRA on a computer using structural coordinates obtained from a co-crystal structure of Pin1 and ATRA; ii) utilizing the three-dimensional model to identify one or more Pin1 binding pockets for ATRA; and iii) selecting a substrate (e.g., an ATRA-related compound) for evaluation based on the one or more Pin1 binding pockets.
In some aspects, the present invention pertains to the treatment of proliferative diseases, autoimmune diseases, and addiction conditions identified as coinciding with elevated Pin1 marker levels with retinoic acid compounds (e.g., ATRA-related compounds). In some aspects, the invention features the determination of Pin1 marker levels in a subject; where a retinoic acid compound (e.g., an ATRA-related compound) is administered in subjects where Pin1 marker levels are determined to be elevated. In other aspects, the invention can also feature the measurement of Pin1 marker levels (e.g., Ser71 phosphorylation or Pin1 degradation) subsequent to the administration of a retinoic acid compound in order to evaluate the progress of therapy in treating a proliferative disorder, autoimmune disease, or addiction condition or select a patient population for further treatment.
Accordingly, one aspect of the present invention relates to diagnostic assays for measuring levels of Pin1 marker, as well as Pin1 activity, in the context of a biological sample (e.g., tumor samples, blood, urine, biopsies, lymph, saliva, phlegm, and pus) to thereby determine whether an individual is a candidate for treatment with a retinoic acid compound. The invention features treatment of subjects exhibiting symptoms of a proliferative disorder, autoimmune disorder, or addiction condition; individuals at risk for developing a proliferative disorder, autoimmune disorder, or addiction condition; and subjects demonstrating a response to treatment of a proliferative disorder, autoimmune disorder, or addiction condition (e.g., subjects having Pin1 degradation after administration of a retinoic acid compound).
An exemplary method for detecting the presence or absence of Pin1 protein or nucleic acid in a biological sample involves obtaining a biological sample (e.g., tumor sample, blood, urine, biopsies, lymph, saliva, phlegm, and pus) from a test subject and contacting the biological sample with a compound or an agent capable of detecting Pin1 protein or a nucleic acid (e.g., mRNA, genomic DNA) that encodes Pin1 protein such that the presence of Pin1 protein or nucleic acid is detected in the biological sample. A preferred agent for detecting Pin1 mRNA or genomic DNA is a labeled nucleic acid probe capable of hybridizing to Pin1 mRNA or DNA. The nucleic acid probe can be, for example, a Pin1 nucleic acid or a corresponding nucleic acid such as an oligonucleotide of at least 15, 30, 50, 100, 250 or 500 nucleotides in length which is capable of specifically hybridizing under stringent conditions to Pin1 mRNA or genomic DNA. Other suitable probes for use in the diagnostic assays of the invention are described herein.
A preferred agent for detecting Pin1 marker is an antibody capable of binding to Pin1 protein, preferably an antibody with a detectable label. Antibodies can be polyclonal, or more preferably, monoclonal. An intact antibody, or a fragment thereof (e.g., Fab or F(ab′)2) can be used. The term “labeled,” with regard to the probe or antibody, is intended to encompass direct labeling of the probe or antibody by coupling (i.e., physically linking) a detectable substance to the probe or antibody, as well as indirect labeling of the probe or antibody by reactivity with another reagent that is directly labeled. Examples of indirect labeling include detection of a primary antibody using a fluorescently labeled secondary antibody and end-labeling of a DNA probe with biotin such that it can be detected with fluorescently labeled streptavidin.
With respect to antibody-based detection techniques, one of skill in the art can raise anti-Pin1 antibodies against an appropriate antigen and/or immunogen, such as isolated and/or recombinant Pin1 or a portion or fragment thereof (including synthetic molecules, such as synthetic peptides) using no more than routine experimentation. Synthetic peptides can be designed and used to immunize animals, such as rabbits and mice, for antibody production. The nucleic and amino acid sequence of Pin1 is known (Hunter at al., WO 97/17986 (1997); Hunter et al., U.S. Pat. Nos. 5,952,467 and 5,972,697, the teachings of all of which are hereby incorporated by reference in their entirety) and can be used to design nucleic acid constructs for producing proteins for immunization or in nucleic acid detection methods or for the synthesis of peptides for immunization.
Conditions for incubating an antibody with a test sample can vary depending upon the tissue or cellular type. Incubation conditions can depend on the format employed in the assay, the detection methods employed, and the type and nature of the antibody used in the assay. One skilled in the art will recognize that any one of the commonly available immunological assay formats (such as radioimmunoassays, enzyme-linked immunoadsorbent assays, diffusion based Ouchterlony, or rocket immunofluorescent assays) can readily be adapted to employ the antibodies of the present invention. Examples of such assays can be found in Chard, “An Introduction to Radioimmunoassay and Related Techniques,” Elsevier Science Publishers, Amsterdam, The Netherlands (1986); Bullock et al., “Techniques in Immunocytochemistry,” Academic Press, Orlando, Fla. Vol. 1 (1982), Vol. 2 (1983), Vol. 3 (1985); Tijssen, “Practice and Theory of enzyme Immunoassays: Laboratory Techniques in Biochemistry and Molecular Biology,” Elsevier Science Publishers, Amsterdam, The Netherlands (1985).
The detection method of the invention can be used to detect Pin1 mRNA, protein, or genomic DNA in a biological sample in vitro as well as in vivo. For example, in vitro techniques for detection of Pin1 mRNA include Northern hybridizations and in situ hybridizations. In vitro techniques for detection of Pin1 protein include enzyme linked immunoadsorbent assays (ELISAs), Western blots, immunoprecipitations, immunofluorescence, or quantitative sequencing reactions. In vitro techniques for detection of Pin1 genomic DNA include Southern hybridizations. The detection of genomic mutations in Pin1 (or other genes that effect Pin1 marker levels) can be used to identify inherited or somatic mutations. Furthermore, in vivo techniques for detection of Pin1 protein include introducing into a subject a labeled anti-Pin1 antibody. For example, the antibody can be labeled with a radioactive marker whose presence and location in a subject can be detected by standard imaging techniques.
In another embodiment, the biological sample contains protein molecules from the test subject. Alternatively, the biological sample can contain mRNA molecules from the test subject or genomic DNA molecules from the test subject. A preferred biological sample is a serum sample isolated by conventional means from a subject.
In another embodiment, the methods involve obtaining a control biological sample from a control subject, contacting the control sample with a compound or agent capable of detecting Pin1 marker such that the presence of Pin1 marker is detected in the biological sample, and comparing the presence of Pin1 marker in the control sample with the presence of Pin1 marker in the test sample.
The immunological assay test samples of the present invention may include cells, protein or membrane extracts of cells, blood or biological fluids such as ascites fluid or brain fluid (e.g., cerebrospinal fluid). The test sample used in the above-described method is based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing protein extracts or membrane extracts of cells are well known in the art and can be readily be adapted in order to obtain a sample which is capable with the system utilized. The invention also encompasses kits for detecting the presence of Pin1 in a biological sample. For example, the kit can comprise a labeled compound or agent capable of detecting Pin1 protein or mRNA in a biological sample; means for determining the amount of Pin1 in the sample; and means for comparing the amount of Pin1 in the sample with a standard. The compound or agent can be packaged in a suitable container. The kit can further comprise instructions for using the kit to detect Pin1 protein or nucleic acid.
Pin1 marker levels can also be measured in an assay designed to evaluate a panel of target genes, e.g., a microarray or multiplex sequencing reaction. In the embodiments of the invention described herein, well known biomolecular methods such as northern blot analysis, RNase protection assays, southern blot analysis, western blot analysis, in situ hybridization, immunocytochemical procedures of tissue sections or cellular spreads, and nucleic acid amplification reactions (e.g., polymerase chain reactions) may be used interchangeably. One of skill in the art would be capable of performing these well-established protocols for the methods of the invention. (See, for example, Ausubel, et al., “Current Protocols in Molecular Biology,” John Wiley & Sons, NY, N.Y. (1999)).
Diagnostic assays can be carried out in, e.g., subjects diagnosed with or at risk of a proliferative disorder, autoimmune disease, or addiction condition (e.g., any of those described herein).
The diagnostic methods described herein can furthermore be utilized to identify subjects having or at risk of developing a disease or disorder associated with aberrant Pin1 expression or activity. For example, the assays described herein, such as the preceding diagnostic assays or the following assays, can be utilized to identify a subject having or at risk of developing a disease, disorder, or condition associated with Pin1 marker (e.g., a proliferative disorder, autoimmune disease, or addiction condition). Thus, the present invention provides a method for identifying a disease or disorder associated with aberrant Pin1 expression or activity in which a test sample is obtained from a subject and Pin1 protein or nucleic acid (e.g., mRNA, genomic DNA) is detected, wherein the presence of Pin1 protein or nucleic acid is diagnostic for a subject having or at risk of developing a Pin1-associated disease, disorder, or condition and is, therefore, susceptible to treatment with a retinoic acid compound (e.g., an ATRA-related compound).
Furthermore, the present invention provides methods for determining whether a subject can be effectively treated with a retinoic acid compound (e.g., an ATRA-related compound) for a disorder associated with aberrant Pin1 expression or activity in which a test sample is obtained and Pin1 protein or nucleic acid expression or activity is detected (e.g., wherein the abundance of Pin1 protein or nucleic acid expression or activity is diagnostic for a subject that can be administered the agent to treat a disorder Pin1-associated disorder). The invention also provides for a method of identifying a patient population previously treated with a retinoic acid compound (e.g., an ATRA-related compound) that is susceptible to such treatment (e.g., has Pin1 degradation) and selecting the patient population for additional treatment with the retinoic acid compound.
In one embodiment, the present invention provides methods for determining Pin1 post-translational modifications. For example, phosphorylation of Pin1 on Ser71 in the catalytic active site by the tumor suppressor DAPK1 completely inhibits Pin1 catalytic activity and cell function to promote oncogenesis. More importantly, phosphorylation of Pin1 on Ser71 in the catalytic active site also prevents retinoic acid compounds (e.g., ATRA-related compounds) from binding to Pin1 active site and inducing Pin1 degradation and inhibiting Pin1 function. Therefore, detecting reduced Ser71 phosphorylation using phospho-specific Pin1 antibodies that we have generated is a method of selecting patients for treatments with a retinoic acid compound (e.g., an ATRA-related compound) and explaining why some patients may not respond to treatments with a retinoic acid compound. Because aberrantly proliferating cells exhibit reduced Ser71 phosphorylation, these cells are more sensitive to treatments with a retinoic acid compound compared to normal cells.
The methods of the invention can also be used to detect genetic alterations in a Pin1 gene, thereby determining if a subject with the altered gene is at risk for a disorder associated with the Pin1 gene and, consequently, a candidate for retinoic acid therapy. In preferred embodiments, the methods include detecting, in a sample of cells from the subject, the presence or absence of a genetic alteration characterized by at least one of an alteration affecting the integrity of a gene encoding a Pin1-protein, or the mis-expression of the Pin1 gene. For example, such genetic alterations can be detected by ascertaining the existence of at least one of 1) a deletion of one or more nucleotides from a Pin1 gene; 2) an addition of one or more nucleotides to a Pin1 gene; 3) a substitution of one or more nucleotides of a Pin1 gene, 4) a chromosomal rearrangement of a Pin1 gene; 5) an alteration in the level of a messenger RNA transcript of a Pin1 gene, 6) aberrant modification of a Pin1 gene, such as of the methylation pattern of the genomic DNA, 7) the presence of a non-wild type splicing pattern of a messenger RNA transcript of a Pin1 gene, 8) a non-wild type level of a Pin1-protein, 9) allelic loss of a Pin1 gene, and 10) inappropriate post-translational modification of a Pin1-protein. As described herein, there are a large number of assay techniques known in the art which can be used for detecting alterations in a Pin1 gene. A preferred biological sample is a tissue or serum sample isolated by conventional means from a subject, e.g., a cardiac tissue sample.
In certain embodiments, detection of the alteration involves the use of a probe/primer in a polymerase chain reaction (PCR) (see, e.g., U.S. Pat. Nos. 4,683,195 and 4,683,202), such as anchor PCR or RACE PCR, or, alternatively, in a ligation chain reaction (LCR) (see, e.g., Landegran et al. (1988) Science 241:1077-1080; and Nakazawa et al. (1994) Proc. Natl. Acad. Sci. USA 91:360-364), the latter of which can be particularly useful for detecting point mutations in the Pin1-gene (see Abravaya et al. (1995) Nucleic Acids Res 0.23:675-682). This method can include the steps of collecting a sample from a patient, isolating nucleic acid (e.g., genomic, mRNA or both) from the sample, contacting the nucleic acid sample with one or more primers which specifically hybridize to a Pin1 gene under conditions such that hybridization and amplification of the Pin1-gene (if present) occurs, and detecting the presence or absence of an amplification product, or detecting the size of the amplification product and comparing the length to a control sample. It is anticipated that PCR and/or LCR may be desirable to use as a preliminary amplification step in conjunction with any of the techniques used for detecting mutations described herein.
Alternative amplification methods include: self-sustained sequence replication (Guatelli, J. C. et al., (1990) Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptional amplification system (Kwoh, D. Y. et al, (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta Replicase (Lizardi, P. M. et al. (1988) Bio-Technology 6:1197), or any other nucleic acid amplification method, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. These detection schemes are especially useful for the detection of nucleic acid molecules if such molecules are present in very low numbers.
In an alternative embodiment, mutations in a Pin1 gene from a sample cell can be identified by alterations in restriction enzyme cleavage patterns. For example, sample and control DNA is isolated, amplified (optionally), digested with one or more restriction endonucleases, and fragment length sizes are determined by gel electrophoresis and compared. Differences in fragment length sizes between sample and control DNA indicates mutations in the sample DNA. Moreover, the use of sequence specific ribozymes (see, for example, U.S. Pat. No. 5,498,531) can be used to score for the presence of specific mutations by development or loss of a ribozyme cleavage site.
In other embodiments, genetic mutations in Pin1 can be identified by hybridizing a sample and control nucleic acids, e.g., DNA or RNA, to high density arrays containing hundreds or thousands of oligonucleotide probes (Cronin, M. T. et al. (1996) Human Mutation 7: 244-255; Kozal, M. J. et al. (1996) Nature Medicine 2: 753-759). For example, genetic mutations in Pin1 can be identified in two dimensional arrays containing light-generated DNA probes as described in Cronin, M. T. et al. supra. Briefly, a first hybridization array of probes can be used to scan through long stretches of DNA in a sample and control to identify base changes between the sequences by making linear arrays of sequential overlapping probes. This step allows the identification of point mutations. This step is followed by a second hybridization array that allows the characterization of specific mutations by using smaller, specialized probe arrays complementary to all variants or mutations detected. Each mutation array is composed of parallel probe sets, one complementary to the wild-type gene and the other complementary to the mutant gene.
In yet another embodiment, any of a variety of sequencing reactions known in the art can be used to directly sequence the Pin1 gene and detect mutations by comparing the sequence of the sample Pin1 with the corresponding wild-type (control) sequence. Examples of sequencing reactions include those based on techniques developed by Maxam and Gilbert ((1977) Proc. Natl. Acad. Sci. USA 74:560) or Sanger ((1977) Proc. Natl. Acad. Sci. USA 74:5463). It is also contemplated that any of a variety of automated sequencing procedures can be utilized when performing the diagnostic assays ((1995) Biotechniques 19:448), including sequencing by mass spectrometry (see, e.g., PCT International Publication No. WO 94/16101; Cohen et al. (1996) Adv. Chromatogr. 36:127-162; and Griffin et al. (1993) Appl. Biochem. Biotechnol. 38:147-159).
Other methods for detecting mutations in the Pin1 gene include methods in which protection from cleavage agents is used to detect mismatched bases in RNA/RNA or RNA/DNA heteroduplexes (Myers et al. (1985) Science 230:1242). In general, the art technique of “mismatch cleavage” starts by providing heteroduplexes formed by hybridizing (labeled) RNA or DNA containing the wild-type Pin1 sequence with potentially mutant RNA or DNA obtained from a tissue sample. The double-stranded duplexes are treated with an agent which cleaves single-stranded regions of the duplex such as which will exist due to basepair mismatches between the control and sample strands. For instance, RNA/DNA duplexes can be treated with RNase and DNA/DNA hybrids treated with S1 nuclease to enzymatically digesting the mismatched regions. In other embodiments, either DNA/DNA or RNA/DNA duplexes can be treated with hydroxylamine or osmium tetroxide and with piperidine in order to digest mismatched regions. After digestion of the mismatched regions, the resulting material is then separated by size on denaturing polyacrylamide gels to determine the site of mutation. See, for example, Cotton et al. (1988) Proc. Nat Acad Sci USA 85:4397; Saleeba et al. (1992) Methods Enzymol. 217286-295. In a preferred embodiment, the control DNA or RNA can be labeled for detection.
In still another embodiment, the mismatch cleavage reaction employs one or more proteins that recognize mismatched base pairs in double-stranded DNA (so called “DNA mismatch repair” enzymes) in defined systems for detecting and mapping point mutations in Pin1 cDNAs obtained from samples of cells. For example, the mutY enzyme of E. coli cleaves A at G/A mismatches and the thymidine DNA glycosylase from HeLa cells cleaves T at G/T mismatches (Hsu et al. (1994) Carcinogenesis 15:1657-1662). According to an exemplary embodiment, a probe based on a Pin1 sequence, e.g., a wild-type Pin1 sequence, is hybridized to a cDNA or other DNA product from a test cell(s). The duplex is treated with a DNA mismatch repair enzyme, and the cleavage products, if any, can be detected from electrophoresis protocols or the like. See, for example, U.S. Pat. No. 5,459,039.
In other embodiments, alterations in electrophoretic mobility will be used to identify mutations in Pin1 genes. For example, single strand conformation polymorphism (SSCP) may be used to detect differences in electrophoretic mobility between mutant and wild type nucleic acids (Orita et al. (1989) Proc Natl. Acad. Sci. USA: 86:2766, see also Cotton (1993) Mutat Res 285:125-144; and Hayashi (1992) Genet Anal Tech Appl 9:73-79). Single-stranded DNA fragments of sample and control Pin1 nucleic acids will be denatured and allowed to renature. The secondary structure of single-stranded nucleic acids varies according to sequence; the resulting alteration in electrophoretic mobility enables the detection of even a single base change. The DNA fragments may be labeled or detected with labeled probes. The sensitivity of the assay may be enhanced by using RNA (rather than DNA), in which the secondary structure is more sensitive to a change in sequence. In a preferred embodiment, the subject method utilizes heteroduplex analysis to separate double stranded heteroduplex molecules on the basis of changes in electrophoretic mobility (Keen et al. (1991) Trends Genet. 7:5).
In yet another embodiment the movement of mutant or wild-type fragments in polyacrylamide gels containing a gradient of denaturant is assayed using denaturing gradient gel electrophoresis (DGGE) (Myers et al. (1985) Nature 313:495). When DGGE is used as the method of analysis, DNA will be modified to insure that it does not completely denature, for example by adding a GC clamp of approximately 40 bp of high-melting GC-rich DNA by PCR. In a further embodiment, a temperature gradient is used in place of a denaturing gradient to identify differences in the mobility of control and sample DNA (Rosenbaum and Reissner (1987) Biophys Chem 265:12753).
Examples of other techniques for detecting point mutations include, but are not limited to, selective oligonucleotide hybridization, selective amplification, or selective primer extension. For example, oligonucleotide primers may be prepared in which the known mutation is placed centrally and then hybridized to target DNA under conditions which permit hybridization only if a perfect match is found (Saiki et al. (1986) Nature 324:163); Saiki et al. (1989) Proc. Natl Acad. Sci USA 86:6230). Such allele specific oligonucleotides are hybridized to PCR amplified target DNA or a number of different mutations when the oligonucleotides are attached to the hybridizing membrane and hybridized with labeled target DNA.
Alternatively, allele specific amplification technology which depends on selective PCR amplification may be used in conjunction with the instant invention. Oligonucleotides used as primers for specific amplification may carry the mutation of interest in the center of the molecule (so that amplification depends on differential hybridization) (Gibbs et al. (1989) Nucleic Acids Res. 17:2437-2448) or at the extreme 3′ end of one primer where, under appropriate conditions, mismatch can prevent, or reduce polymerase extension (Prossner et al. (1993) Tibtech 11238). In addition it may be desirable to introduce a novel restriction site in the region of the mutation to create cleavage-based detection (Gasparini et al. (1992) Mol. Cell Probes 6:1). It is anticipated that in certain embodiments amplification may also be performed using Taq ligase for amplification (Barany (1991) Proc. Natl. Acad. Sci USA 88:189). In such cases, ligation will occur only if there is a perfect match at the 3′ end of the 5′ sequence making it possible to detect the presence of a known mutation at a specific site by looking for the presence or absence of amplification.
The methods described herein may be performed, for example, by utilizing pre-packaged diagnostic kits comprising at least one probe nucleic acid or antibody reagent described herein, which may be conveniently used, e.g., in clinical settings to diagnose patients exhibiting symptoms or family history of a disease or illness involving a Pin1 gene.
Furthermore, any cell type or tissue in which Pin1 is expressed may be utilized in the prognostic assays described herein.
As with the diagnostic assay described above, prognostic assays of Pin1 activity can be included as part of a panel of target genes.
Additional methods of detecting Pin1 activity and diagnosing Pin1 related disorders are disclosed in U.S. Patent Application Publication Nos.: 2009/0258352, 2008/0214470, 2006/0074222, 2005/0239095, US2002/0025521, U.S. Pat. No. 6,495,376, and PCT Application Publication No. WO02/065091, each of which is hereby incorporated by reference in its entirety.
The present invention also features methods and compositions to diagnose, treat and monitor the progression of a disorder, disease, or condition described herein (e.g., a cellular proliferation disorder, autoimmune disease, or addiction condition) by detection and measurement of, for example, Pin1 substrates (or any fragments or derivatives thereof) containing a phosphorylated Ser/Thr-Pro motif in a cis or trans conformation, as described in U.S. patent application Ser. No. 13/504,700, which is hereby incorporated by reference in its entirety. The methods can include measurement of absolute levels of the Pin1 substrate (examples of which are listed in Tables 2, 3A, 3B, 3C, and 4 of WO2012125724A1) in a cis or trans conformation as compared to a normal reference, using conformation specific antibodies. For example, a serum level or level in a biopsy of a Pin1 substrate in the cis or trans conformation that is less than 5 ng/ml, 4 ng/ml, 3 ng/ml, 2 ng/ml, or less than 1 ng/ml serum or a biopsy is considered to be predictive of a good outcome in a patient diagnosed with a disorder (e.g., a disorder associated with a deregulation of Pin1 activity). A serum level of the substrate in the cis or trans conformation that is greater than 5 ng/ml, 10 ng/ml, 20 ng/ml, 30 ng/ml, 40 ng/ml, or 50 ng/ml is considered diagnostic of a poor outcome in a subject already diagnosed with a disorder, e.g., associated with a deregulation of Pin1 activity.
For diagnoses based on relative levels of substrate in a particular conformation (e.g., a Pin1 substrate in the cis or trans conformation), a subject with a disorder (e.g., a disorder associated with a deregulation of PPlase activity) will show an alteration (e.g., an increase of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or more) in the amount of the substrate in, for example, the cis conformation. A normal reference sample can be, for example, a prior sample taken from the same subject prior to the development of the disorder or of symptoms suggestive of the disorder, a sample from a subject not having the disorder, a sample from a subject not having symptoms of the disorder, or a sample of a purified reference polypeptide in a given conformation at a known normal concentration (i.e., not indicative of the disorder).
Standard methods may be used to measure levels of the substrate in any bodily fluid, including, but not limited to, urine, blood, serum, plasma, saliva, amniotic fluid, or cerebrospinal fluid. Such methods include immunoassay, ELISA, Western blotting, and quantitative enzyme immunoassay techniques.
For diagnostic purposes, conformation-specific antibodies may be labeled. Labeling of an antibody is intended to encompass direct labeling of the antibody by coupling (e.g., physically linking) a detectable substance to the antibody, as well as indirect labeling the antibody by reacting the antibody with another reagent that is directly labeled. For example, an antibody can be labeled with a radioactive or fluorescent marker whose presence and location in a subject can be detected by standard imaging techniques.
The diagnostic methods described herein can be used individually or in combination with any other diagnostic method described herein for a more accurate diagnosis of the presence or severity of a disorder (e.g., a cellular proliferation disorder, autoimmune disorder, addiction condition, or a neurological disorder). Examples of additional methods for diagnosing such disorders include, e.g., examining a subject's health history, immunohistochemical staining of tissues, computed tomography (CT) scans, or culture growths.
In one embodiment, the present invention features a method for monitoring the effectiveness of treatment of a subject with a retinoic acid compound (e.g., an ATRA-related compound) comprising the steps of (I) obtaining a pre-administration sample from a subject prior to administration of the compound; (ii) detecting the level of expression or activity of a Pin1 protein, Pin1 phosphorylation on Ser71, mRNA, or genomic DNA in the pre-administration sample; (iii) obtaining one or more post-administration samples from the subject after administration of the compound; (iv) detecting the level of expression or activity of the Pin1 protein, mRNA, or genomic DNA in the post-administration samples; (v) comparing the level of expression or activity of the Pin1 protein, mRNA, or genomic DNA in the pre-administration sample with the Pin1 protein, mRNA, or genomic DNA in the post administration sample or samples; and (vi) altering the administration of the retinoic acid compound (e.g., ATRA-related compound) to the subject accordingly. According to such an embodiment, Pin1 expression, phosphorylation or activity may be used as an indicator of the effectiveness of the retinoic acid compound (e.g., ATRA-related compound), even in the absence of an observable phenotypic response.
In another embodiment, the present invention provides a method of selecting a patient population who may derive increased benefit from treatment with a retinoic acid compound (e.g., an ATRA-related compound) comprising the steps of (i) administering a retinoic acid compound to a subject having a proliferative disorder; (ii) detecting whether a subject has Pin1 degradation; and (iii) selecting a subject having Pin1 degradation for additional treatment with a retinoic acid compound. This method may include additional steps such as detecting the level of a Pin1 marker from a sample from a subject prior to the first administration of a retinoic acid compound to a subject; obtaining a sample from a subject after the first administration of a retinoic acid compound for detection of the level of a Pin1 marker; and comparing the levels of Pin1 marker in pre-administration and post-administration samples to determine whether the subject has Pin1 degradation. For example, a subject exhibiting a response to initial treatment with a retinoic acid compound (e.g., an ATRA-related compound) and also showing Pin1 degradation may be a candidate for additional treatment with the retinoic acid compound, whereas a subject not also showing Pin1 degradation may be a candidate for treatment with, e.g., a different retinoic acid compound.
In another embodiment, the diagnostic methods described herein can also be used to measure the levels of, for example, polypeptides (e.g., Pin1 substrates listed in Tables 2, 3A, 3B, 3C, and 4 of WO2012125724A1) with pSer/Thr-Pro motifs in the cis or trans conformation using conformation specific antibodies. The methods can include repeated measurements, using, e.g., conformation specific antibodies, for diagnosing the disorder and monitoring the treatment or management of the disorder. In order to monitor the progression of the disorder in a subject, subject samples can be obtained at several time points and conformation specific antibodies can be used to monitor the levels of cis and trans isomers of Pin1 substrates (e.g., those listed in Tables 2, 3A, 3B, 3C, and 4 of WO2012125724A1). For example, the diagnostic methods can be used to monitor subjects during chemotherapy (e.g., therapy with a retinoic acid compound or other agent described herein). In this example, serum samples from a subject can be obtained before treatment with a chemotherapeutic agent, again during treatment with a chemotherapeutic agent, and again after treatment with a chemotherapeutic agent. In this example, the level of Pin1 substrate with a pSer/Thr-Pro motif in the cis conformation in a subject is closely monitored using the conformation-specific antibodies of the invention and, if the level of Pin1 substrate with a pSer/Thr-Pro motif in the cis conformation begins to increase during therapy, the therapeutic regimen for treatment of the disorder can be modified as determined by the clinician (e.g., the dosage of the therapy may be changed or a different therapeutic may be administered). The monitoring methods of the invention may also be used, for example, in assessing the efficacy of a particular drug or therapy in a subject, determining dosages, or in assessing progression, status, or stage of the disease, disorder, or condition.
The present invention provides for both prophylactic and therapeutic methods of treating a subject at risk of (or susceptible to) or having a proliferative disorder, autoimmune disorder, or addiction condition (e.g., a disorder associated with increased Pin1 expression or activity) with a retinoic acid compound (e.g., an ATRA-related compound).
Certain embodiments of the invention feature formulation of a retinoic acid compound (e.g., an ATRA-related compound) for, e.g., controlled or extended release. Many strategies can be pursued to obtain controlled and/or extended release in which the rate of release outweighs the rate of metabolism of the therapeutic compound. For example, controlled release can be obtained by the appropriate selection of formulation parameters and ingredients (e.g., appropriate controlled release compositions, excipients, formulation types, and coatings). Examples include single or multiple unit tablet or capsule compositions, oil solutions, suspensions, emulsions, microcapsules, microspheres, nanoparticles, patches, films, and liposomes. The release mechanism can be controlled such that the retinoic acid compound and/or a second therapeutic compound used in combination with a retinoic acid compound is released at period intervals, near-simultaneously with administration, or with delay. In a delayed release formulation, one of the agents of the combination could be affected such that a particular agent is released earlier than another agent or both agents could be released at approximately the same time.
Certain embodiments of the invention feature an isotopically substituted (e.g., deuterated) or labeled retinoic acid compound (e.g., ATRA-related compound) that is made by replacing one or all atoms of a given element with an isotope of that element. For example, a fully or partially deuterated retinoic acid compound could be made by replacing some or all hydrogen atoms with deuterium atoms using state of the art techniques (e.g., as described herein and at www.concertpharma.com).
In one aspect, the invention provides a method for preventing a proliferative disorder, autoimmune disorder, or addiction condition in a subject by administering to the subject a retinoic acid compound (e.g., an ATRA-related compound). Subjects at risk for a disease, disorder, or condition which is caused, characterized, or contributed to by aberrant Pin1 expression or activity can be identified by, for example, any or a combination of diagnostic or prognostic assays as described herein. Administration of a retinoic acid compound can occur prior to the manifestation of symptoms characteristic of the Pin1 aberrancy, such that a disease or disorder is prevented or, alternatively, delayed in its progression.
Anti-proliferative and other anti-cancer compounds (e.g., those described herein, including anti-angiogenic compounds), anti-viral compounds, anti-microbial compounds, anti-inflammatory compounds, and other therapeutic species are useful for treating proliferative disorders, autoimmune diseases, and addiction conditions in combination with the retinoic acid compounds of the invention. With regard to anti-proliferative compounds, the ability of a compound to inhibit the growth of a neoplasm can be assessed using known animal models.
Compounds which are known to interact with other proteins implicated in Pin1 signaling pathways can also be useful in combination with a retinoic acid compound (see, e.g., the targets and compounds in Table 5 of WO2012125724A1). Such compounds can act synergistically with a retinoic acid compound (e.g., an ATRA-related compound). Additionally, co-administration with a retinoic acid compound may result in the efficacy of the therapeutic agent at lower (and thus safer) doses (e.g., at least 5%, 10%, 20%, 50%, 80%, 90%, or even 95%) less than when the therapeutic agent is administered alone.
Therapy according to the invention may be performed alone or in conjunction with another therapy and may be provided at home, a doctor's office, a clinic, a hospital's outpatient department, or a hospital. Treatment optionally begins at a hospital so that the doctor can observe the therapy's effects closely and make any adjustments that are needed, or it may begin on an outpatient basis. The duration of the therapy depends on the type of disease, disorder, or condition being treated; the age and condition of the patient; the stage and type of the patient's disease; and how the patient responds to the treatment. Additionally, a person having a greater risk of developing a proliferative or autoimmune disease may receive treatment to inhibit or delay the onset of symptoms.
Routes of administration for the various embodiments include, but are not limited to, topical, transdermal, transmucosal, transepithelial, nasal, and systemic administration (such as, intravenous, intramuscular, subcutaneous, cutaneous, injection, infusion, infiltration, irrigation, intra-articular, intra-tumoral, inhalation, rectal, buccal, vaginal, intraperitoneal, intraarticular, ophthalmic, otic, or oral administration). As used herein, “systemic administration” refers to all nondermal routes of administration, and specifically excludes topical and transdermal routes of administration. Depending on the intended use, a retinoic acid compound or salt thereof, optionally in combination with one or more additional therapeutic agents, may be prepared in any useful manner and with any useful components such as pharmaceutical excipients, coatings, fillers, bulking agents, viscosity enhancers/reducers, chelating agents, adjuvants, disintegrants, lubricants, glidants, binders, stabilizers, buffers, solubilizers, solvents, dispersion media, diluents, dispersion aids, suspension aids, granulating aids, liquid vehicles, buffers, propellants, tonicity modifiers, isotonic agents, thickening or emulsifying agents, surfactants, surface altering agents, flavoring or taste-masking agents, preservatives, coloring agents, perfuming agents, oils, waxes, carbohydrates, polymers, permeability enhancers, or other components. Such species are well known in the art (see for example Remington's The Science and Practice of Pharmacy, 21st Edition, A. R. Gennaro; Lippincott, Williams & Wilkins, Baltimore, Md., 2006). Conventional excipients and accessory ingredients, including those approved for use in humans and/or for veterinary use, may be used in any pharmaceutical composition of the invention, except insofar as any conventional excipient or accessory ingredient may be incompatible with a retinoic acid compound of the invention. An excipient or accessory ingredient may be incompatible with a component of a retinoic acid compound if its combination with the compound may result in any undesirable biological effect or otherwise deleterious effect Excipients and other useful components may make up any total mass or volume of a pharmaceutical composition including a retinoic acid compound, including greater than 40%, 50%, 60%, 70%, 80%, 90%, or 95% of a composition. Similarly, a pharmaceutical composition may include any useful amount of retinoic acid compound, e.g., between 0.1% and 100% (wt/wt) of a pharmaceutical composition. Pharmaceutical compositions including retinoic acid compounds of the invention and/or for use in the methods of the invention may be prepared, packaged, and/or sold in bulk, as single unit doses, and/or as a plurality of single unit doses, where a “unit dose” is a discrete amount of a pharmaceutical composition including a predetermined amount of a retinoic acid compound.
A retinoic acid compound may be preparing in any useful form of a pharmaceutical composition suitable for a variety of routes of administration. For example, pharmaceutical compositions of the invention may be prepared in liquid dosage forms (e.g., emulsions, microemulsions, nanoemulsions, solutions, suspensions, syrups, and elixirs), injectable forms, solid dosage forms (e.g., capsules, tablets, pills, powders, films, and granules), dosage forms for topical and/or transdermal administration (e.g., liniments, ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants, and patches), suspensions, powders, and other forms.
In combination therapy (e.g., administration of a retinoic acid compound with a second therapeutic agent), the dosage and frequency of administration of each component of the combination can be controlled independently. For example, one compound may be administered three times per day, while the second compound may be administered once per day. Alternatively, one compound may be administered earlier and the second compound may be administered later. Combination therapy may be given in on-and-off cycles that include rest periods so that the patient's body has a chance to recover from any as yet unforeseen side effects induced by one or more therapeutic agents. The compounds may also be formulated together, e.g., as described herein, such that one administration delivers both compounds.
Each compound of the combination may be formulated in a variety of ways that are known in the art. For example, the first and second anti-proliferative agents may be formulated together or separately. Desirably, the first and second anti-proliferative agents are formulated together for the simultaneous or near simultaneous administration of the agents. Such co-formulated compositions can include the two drugs together in the same pill, ointment, cream, foam, capsule, liquid, etc. It is to be understood that, when referring to the formulation of combinations of the invention, the formulation technology employed is also useful for the formulation of the individual agents of the combination, as well as other combinations of the invention. By using different formulation strategies for different agents, the pharmacokinetic profiles for each agent can be suitably matched.
The individually or separately formulated agents can be packaged together as a kit. Non-limiting examples include kits that contain, e.g., two pills, a pill and a powder, a suppository and a liquid in a vial, two topical creams, ointments, foams etc. The kit can include optional components that aid in the administration of the unit dose to patients, such as vials for reconstituting powder forms, syringes for injection, customized IV delivery systems, inhalers, etc. Additionally, the unit dose kit can contain instructions for preparation and administration of the compositions. The kit may be include one or more single-use unit doses or multiple-use doses for a particular patient (e.g., at a constant dose or in which the individual compounds may vary in potency as therapy progresses). Alternatively, the kit may contain multiple doses suitable for administration to multiple patients (“bulk packaging”). The kit components may be assembled in cartons, blister packs, bottles, tubes, and the like.
In the experiments described below, 293T, HeLa, AU565, BT474, HCC1937, MCF7, MDA-MB-231, MDA-MB-468, SKBR3 and T47D cells (originally obtained from ATCC and maintained in our laboratory) were cultured in Dulbecco's modified Eagle's medium (DMEM), while NB4 cells (obtained from the Pandolfi lab at BIDMC) was cultured in RPMI-1640 and immortalized human mammary epithelial cells (HMLE) and MCF10A cells were cultured in F12/DMEM medium. RARα, β, γ triple KO MEFs were from Dr. Hugues de Thé (Unversité Paris Diderot). HMLE cells and transformed HMLE cells (HMLE-Ras) were kindly provided by Dr. Robert A. Weinberg, and maintained as described (Elenbaas et al. (2001) Genes Dev. 15:50-65). HeLa and HEK293 cells were maintained in DMEM with 10% FBS. Freshly isolated primary normal human MEC or breast cancer cells were cultured in MEGM with supplements (Keller et al. (2012) Proc. Natl. Acad. Sci. USA 1092772-2777).
All mediums were supplemented with 10% fetal bovine serum (FBS) and all of the cells were cultured at 37° C. in a humidified incubator containing 5% CO2. HA-Pin1 was previously described. 13cRA, ATRA, EGCG and Juglone were from purchased from Sigma. ATRA-releasing pellets were from Innovative Research of America. All mutations were generated by site-directed mutagenesis. Antibodies against various proteins were obtained from the following sources: mouse monoclonal antibodies: Pin1 as described by Liou et al. (2002) Proc. Natl. Acad. Sci. USA 99:1335-40; α-tubulin, β-actin, Flag from Sigma; cyclin D1 from Santa Cruz Biotechnology; rabbit antibodies: HER2, ERα, PML (immunostaining), RARα (Immunoblotting) from Santa Cruz Biotechnology. Antibodies against pS71 Pin1 were described by Lee et al. (2011) Mol. Cell. 22:147-159. AC-93253, Ro-415253 and DAPK1 inhibitor were purchased from Sigma Aldrich.
In Examples 27-36, the DC2.4 cell line, derived from C57BL/6 bone marrow, was kindly provided by Dr. Kenneth Rock (University of Massachusetts Medical Center, Worcester, Mass.). Cells were grown in complete media comprised of DMEM, supplemented with 10% FBS, 10 mM HEPES, 2 mM L-glutamine and 50 μg/ml gentamicin. DC2.4 cells were maintained at 37° C. in a humidified incubator with 5% CO2. Cells were maintained via weekly passage and utilized for experimentation at 60-80% confluency. Anti IRAKM was purchased from Sigma (catalog number SAB3500193). Anti Pin1 was purchased from EPITOMICS (catalog number S2707). Recombinant mouse IL-33 was purchased from BioLegend. IL6 ELISA KIT Ready-Set-Go was from eBioscience. shRNA for IRAKM was purchased from DANA Farber siRNA core facility.
The PPlase activity on GST-Pin1, GST-FKBP12, or GST-cyclophilin in response to 13cRA or ATRA were determined using the chymotrypsin coupled PPlase activity assay with the substrate Suc-Ala-pSer-Pro-Phe-pNA, Suc-Ala-Glu-Pro-Phe-pNA or Suc-Ala-Ala-Pro-Phe-pNA (50 mM) in a buffer containing 35 mM HEPES (pH 7.8), 0.2 mM DTT, and 0.1 mg/ml BSA, at 10° C. Compounds were preincubated with enzymes for 0.5 to 2 hours at 4° C. Ki values obtained from PPlase assays are derived from the Cheng-Prusoff equation:
where Km is the Michaelis constant for the used substrate, S is the initial concentration of the substrate in the assay, and the IC50 value is of the inhibitor.
For cell growth assays described below, cells were seeded in a density of 3000 cells per well in 96-well flat-bottomed plates, and incubated for 24 h in 10% FBS-supplemented DMEM culture medium. Cells were then treated with ATRA alone or in combination with other drugs. Control cells received DMSO at a concentration equal to that in drug-treated cells. After 72 hours, the number of cells was counted after trypsin digestion, or medium containing 0.5 mg/ml 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide was added to each well for 2 hours of incubation at 37° C., followed by removal of the media before the addition of 200 μl DMSO. Absorbance was determined at 570 nm.
DC2.4 cell line were either treated with 100 ng/ml IL-33 for indicate time (0, 5, and 15 min). The cells were harvested and homogenized in a reaction buffer containing 100 mM NaCl, 50 mM HEPES, pH 7, 2 mM DTT, and 0.04 mg/ml BSA. The lysates were cleared by centrifugation at 12,000 g for 10 minutes (4° C.). PPlase activity was measured using equal amounts of parathyroid cytoplasmic lysates and α-chymotrypsin using a synthetic tetrapeptide substrate Suc-Ala-Glu-Pro-Phe-pNa (Peptides International). Absorption at 390 nM was measured using an Ultrospec 2000 spectrophotometer. The results are expressed as the mean of 3 measurements from a single experiment and are representative of 3 independent experiments.
For immunoprecipitation and immunoblotting in the examples below, cells were polyethylenimine (PEI)- or lipofemamine-transfected with 8 μg of various plasmids, incubated in 10 cm dishes for 24 hours, and subsequently treatment with drugs as needed. When harvesting, cells were lysed for 30 minutes at 4° C. in an IP lysis buffer (50 mM HEPES, pH7.4, 150 mM NaCl, 1% Tritin X-100, and 10% glycerol) with freshly added phosphatase and protease inhibitors consisting of 100 μM 4-(2-aminoethyl)-benzenesulfonyl fluoride, 80 nM aprotinin, 5 μM bestatin, 1.5 μM E-64 protease inhibitor, 2 μM leupeptin, 1 μM pepstatin A, 2 mM imidazole, 1 mM sodium fluoride, 1 mM sodium molybdate, 1 mM sodium orthovanadate, and 4 mM sodium tartrate dihydrate. After centrifugation at 13,000 g for 10 minutes, one tenth of the supernatant was stored as input, and the remainder was incubated 12 hours with M2 Flag agarose (Sigma). After brief centrifugation, immunoprecipitates were collected, extensively washed with the aforementioned lysis buffer twice, suspended in 2×SDS sample buffer (100 mM Tris-HCl, pH 6.8, 4% SDS, 5% β-mercaptoethanol, 20% glycerol, and 0.1% bromphenol blue), boiled for 10 minutes, and subjected to immunoblotting analysis. Equal amounts of protein were resolved in 15% SDS-polyacrylamide gels. After electrophoresis, gel was transferred to nitrocellulose membranes using a semidry transfer cell. The transblotted membrane was washed twice with Tris-buffered saline containing 0.1% Tween 20 (TBST). After blocking with TBST containing 5% bovine serum albumin (BSA) for 1 hour, the membrane was incubated with the appropriate primary antibody (diluted 1:1000) in 2% BSA-containing TBST at 4° C. overnight. After incubation with the primary antibody, the membrane was washed three times with TBST for a total of 30 minutes followed by incubation with horseradish peroxidase (HRP)-conjugated goat anti-rabbit or anti-mouse IgG (diluted 1:2500) for 1 hour at room temperature. After three extensive washes with TBST for a total of 30 minutes, the immunoblots were visualized by enhanced chemiluminescence.
In Examples 27-36, glutathione-Sepharose 4B (Amersham) coupled with glutathione S-transferase (GST) or GST-Pin1 and washed with 150 mM NaCl, 20 mM Tris-HCl (pH 8), 1 mM MgCl2, and 0.1% NP-40 was mixed with 1 mg of total protein extract for 3 hours at 4° C. The beads were then washed extensively, and the protein was eluted with 20 mM reduced glutathione. The proteins were resolved by SDS-PAGE and visualized by Western analysis or autoradiography. For tandem mass spectrometry analysis the eluted protein were further immunopercipited for IRAKM. In this case, the eluted proteins were incubated with pre incubated immobilized rProtein A agarose beads (RepliGen) premixed with IRAKM antibody, for three hours. The beads were extensively washed with lysis buffer containing 150 mM NaCl, 1% NP-40, 0.5% deoxycholate, 0.1% SDS, 50 mM Tris-HCl (pH 7.7), 1 mM phenylmethylsulfonyl fluoride (PMSF), 1 mM dithiothreitol, and protease inhibitors before elution in SDS sample buffer.
Co-immunoprecipitation described in Examples 27-36 proceeded as follows: cells from one 10-cm dish were homogenized in lysis buffer containing 150 mM NaCl, 1% NP-40, 0.5% deoxycholate, 0.1% SDS, 50 mM Tris-HCl (pH 7.7), 1 mM phenylmethylsulfonyl fluoride (PMSF), 1 mM dithiothreitol, and protease inhibitors. Clarified supernatants were incubated with pre incubated immobilized beads rProtein A agarose beads (RepliGen) premixed with Pin1, GFP or IRAKM antibody or, as a control, IgG overnight at 4° C. The beads were washed extensively with lysis buffer before elution in SDS sample buffer.
Human APL samples were kindly provided by Dr. Eduardo Rego from Brazil. Tissue samples were washed with PBS and fixed with 4% paraformaldehyde at room temperature for 20 minutes, followed by permeabilization and blocking with PBS containing 0.1% Triton X-100 and 5% FBS for 1 hour. After another wash with PBS, immunostaining was performed by incubating the cells with mouse anti-Pin1 (1:1000), or rabbit anti-PML (Santa Cruz; 1:100) primary antibodies at 4° overnight. Primary antibodies were diluted in PBS containing 0.1% Triton X-100, 0.2% BSA, 0.5 mM PMSF, and 1 mM dithiothreitol. After washing with PBS, secondary Alexa Fluor 488-conjugated goat anti-mouse antibodies or Alexa Fluor 564-conjugated goat anti-rabbit antibodies (Invitrogen; 1200) were added at room temperature for 2 hours. Samples were nuclear counterstained with 4,6-diamidino-2-phenylindole (DAPI), mounted and visualized with a LSM510 confocal imaging system. For centrosome duplication assays, NIH3T3 cells were used. Cells were synchronized in G1/S phase by adding 10 μg/ml aphidicolin for 24 hours, then fixed with 4% paraformaldehyde at room temperature for 20 minutes. Cells were then stained for centrosomes with anti-γ-tubulin antibodies (Sigma; 1:100) and analyzed by confocal microscopy.
For xenograft experiments, 2×106 of MDA-MB-231 parent cells or expressing Pin1 or control vectors were injected subcutaneously into flank of 8 weeks-old BALB/c nude mice (Jackson Laboratories). After one week, when tumor growth was just notable, mice were randomly selected to receive ATRA treatment. For intraperitoneal injection, vehicle or 12.5 mg/kg ATRA were administered three times a week for 8 weeks. For implantation, placebo, 5 or 10 mg 21 day ATRA-releasing pellets (Innovative Research of America) were implanted one week after injection in the back of nude mice. Tumor sizes were recorded weekly by a caliber for up to 8 weeks and tumor volumes were calculated using the formula L×W2×0.52, where L and W represent length and width, respectively. For NB4 cells transplantation, 8 weeks-old NOD.Cg-prkdcscid II2rgtm1Wjl/SzJ (termed NSG) were used as transplant recipients after sublethal irradiation at 350 Gy. Each mouse was transplanted with 5×105 NB4 cells stably expressing Tet-on shPin1 via retro-orbital injection. Five days later, mice were randomly selected to receive regular or doxycycline food and survival curve was recorded. For PML-RARα transgenic cells transplantation, each C57BL/6 mice were given 350 Gy irradiation followed by transplantation with 1×106 APL cells from hCG-PML-RARα transgenic mice. After 5 days, mice were randomly selected to receive placebo (21 days placebo-releasing pills), ATRA (5 mg of 21 days ATRA-releasing pills) or EGCG (12.5 mg/kg/day, intraperitoneal), Juglone (1 mg/kg/day, intravenous). Mice were sacrificed 3 weeks after when APL blastic cells appeared in peripheral blood smear of placebo mice. Spleen weight was measured and bone marrow was collected for immunoblotting detection on PML-RARα and Pin1.
In Examples 27-36 below, male mice in each group, 3-5 months old were amnestied using Iso flurane. The mice were treated intranasal with 200 ng/mice/day for four continues days. By the fifth day the mice were sacrificed and bronchial alveolar lavage fluid (BALF) was extracted using PBS. The lungs were extracted and fixed using 10% para formaldehyde. Immunofluresence of slide sections was performed. Slides were analyzed using anti-Pin1 antibodies and anti-IRAKM antibodies or IgG as control and were counterstained using DAPI. In some cases, cells obtained from BALF were cytospined and the cells were fixed and stained in the same manner. For staining of the cells, Diff-Quick (Diff-Quik) Staining Protocol were used. For ATRA pretreatment, 3 months old male mice were randomly selected to receive placebo (21 days placebo-releasing pills) or ATRA (10 mg of 21 days ATRA-releasing pills) for 14 days. The mice were treated with IL-33 as before, before they were sacrificed for further analysis.
All animal work was carried out in compliance with the ethical regulations approved by the Animal Care Committee, Beth Israel Deaconess Medical Center, Boston, Mass., USA.
Bone marrow aspirates were obtained with informed consent from the iliac crest of patients in whom the diagnosis of acute promyelocytic leukemia was suspected based on the morphological evaluation of peripheral blood smear. Immediately after the procedure, therapy with ATRA was started. Second bone marrow aspirate samples were obtained on day 3 or 10 of ATRA therapy in order to complement the laboratorial investigation of the cases. Samples tested positive for the PML/RARα rearrangement by RT-PCR. The human sample collection has been approved by the Institutional Review Board at University of São Paulo (HCRP #13496/2005) or at Tor Vergata University (IRB #12/07).
For overexpression, Pin1 and RAB2A CDS were subcloned into the pBabe retroviral vector or pBybe lentiviral vector. To overexpress Rab2A and the Q58H mutant using lentivirus-mediated gene expression at levels similar to or 3 times over the endogenous level, less optimal Kozak sequences were introduced into the vector, namely GCCTTT and GCCGCC, respectively. Specific point mutations were introduced using the Quickchange kit (Stratagene) and sequences were verified. All lentiviral shRNA constructs were provided by Dr. William C. Hahn. The target sequence of Pin1 shRNA is CCACCGTCACACAGTATTTAT (SEQ ID NO:2). The target sequences of Rab2A shRNAs are GCTCGAATGATAACTATTGAT SEQ ID NO:3) and CCAGTGCATGACCTTACTATT (SEQ ID NO:4). The production of retroviruses or lentiviruses as well as the infection of target cells was described previously (Stewart et al. (2003) RNA 9:493-501). Following infection, the cells were selected using puromycin, hygromycin or blasticidin. Cells were used immediately following selection and for up to one month after selection.
RNA from Lin MECs and neuron cells of Pin1 KO and WT mice was extracted with the total RNA isolation mini kit (Agilent). Microarray expression profiles were collected using the Affymetrix GeneChip Mouse Expression Array 430A. Affymetrix .CEL files were analyzed with BRB-ArrayTools (Simon et al. (2007) Cancer Inform. 3:493-501) (http://linus.nci.nih.gov/BRB-ArrayTools.html). Microarray data have been deposited in NCBI Gene Expression Omnibus with series accession number GSE49971. Genes that expressed lower in KO cells than in WT cells with fold change<0.8 (P<0.05) were selected as “downregulated” ones. Two datasets obtained from NCBI's Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) with GEO Series accession numbers GSE3711 (Stingl et al. (2006) Nature 439:993-997) and GSE8863 (Zhang et al. (2008) Cancer Res. 68:4674-4682) were reanalyzed together with our raw data. In GSE3711, mammary stem cells (MaSC, defined as lineage− CD49f++CD24+) were compared to myoepithellal cells (MYO, defined as lineage− CD49f+CD24+) and colony-forming progenitor cells (CFC, defined as lineage-CD49f+CD24++). Genes that expressed higher in MaSC than in both MYO and CFC with fold change>1.5 (P<0.05) were selected as “upregulated” ones. In GSE8863, the Lin-CD29HighCD24High subpopulation of CSCs was compared to the Lin-CD29LowCD24Low subpopulation of non-CSCs. Genes that expressed higher in CSC than in non-CSC with fold change>1.5 (P<0.05) were selected as “upregulated” ones. When comparing the upregulated gene list in these two datasets (SC/non-SC>1.5, P<0.05) with the downregulated gene list in Pin1 KO cells (KO/WT<0.8, P<0.05), 14 genes were repeatedly found in the two gene lists and were identified as candidate genes.
Primary monoclonal Pin1 antibody (1:5000), polyclonal RAB2A antibody (1:1000) (Proteintech Group), polyclonal Erk1/2 (1:4000) and pErk antibody (1:2000) (Cell Signaling Technology), monoclonal unphosphorylated β-catenin antibody (1:2000) (Millipore), monoclonal M2 antibody for Flag tag (1:2000) (Sigma), and monoclonal Actin antibody (1:5000) (Sigma) were used in Western blots.
RNA from cells was extracted with the Total RNA isolation mini kit (Agilent). cDNA was prepared with transcriptor first strand cDNA synthesis kit (Roche) and PCR was carried out with iQ SYBR Green Supermix (Bio-Rad) or SYBR Green PCR Master Mix (Applied Blosystems). 1 μl cDNA was used for each RT-PCR reaction. Samples were run on the QIAGEN Rotor-Gene Q real-time cycler or the Applied Biosystems StepOnePlus Real Time PCR instrument. GAPDH was used as an internal control. Analysis was performed with the ΔΔCt method. The following primers were used:
Additional primers' sequences were designed using the rpimer3 tool (http://bioinfo.ut.ee/primer3-0.4.0/primer3/). Expression value of the targeted gene in a given sample was normalized to the corresponding expression of Actin.
For the reporter assay of RAB2A promoter, two deletion luciferase reporter constructs of RAB2A were generated. The promoter sequences from −1310 and −904, which contain the −1293 and −890 AP-1 binding sites, respectively, were subcloned into pGL3 vector. HEK293 cells were plated in 12-well plates for 24 hr and transfected with luciferase reporter constructs, pRL-tk renilla luciferase and Flag-Pin1 or control vector. Increasing dose of Flag-Pin1 or control vector plasmid were add as 0.15, 0.5 1.5 μg. Cells were harvested and luciferase activity was measured 48 hr later using the Dual-Luciferase Reporter Assay System (Promega).
ChIP assay was performed according to the manufacturer's instruction (Upstate Biotechnology). Monoclonal Pin1 antibody (generated by our lab) or polyclonal c-Jun antibody (Abcam) were used to precipitate the chromatin-protein complexes. Re-ChIP assay was performed as described (Petruk et al. (2012) Cell 150:922-933). Real-time PCR primers for the −1293 locus were CCTGTGGTCTTTTTGAACAGAG (SEQ ID NO:45) and CAACTGGAGGCCCTGTATGT (SEQ ID NO:46), and for the −890 locus were ACACACACATAAACAGATCATCTCGG (SEQ ID NO:47) and AGTCTCTGAACCTGTCCTGGTTCTG (SEQ ID NO:48).
Mammosphere culture was performed as described (Dontu et al. (2003) Genes Dev. 17:1253-1270). A single-cell suspension was plated on ultra-low attachment plates (Corning, Costar) in DMEM/F-12 HAM medium containing bFGF, EGF, heparin and B-27 supplement. The mammospheres were cultured for two weeks. Then the mammospheres with diameter>75 μm were counted.
Soft agar assays were done by seeding cells at a density of 103 in 60 mm culture dishes containing 0.3% top low-melt agarose and 0.5% bottom low-melt agarose, as described (Ryo et al. (2001) Nat. Cell Biol. 3:793-801). Cells were fed every 4 days, and colonies were stained with 0.2% p-iodonitrotetrazolium violet and counted after 3 weeks.
For wound healing assays, cells were grown to confluence and then wounded using a yellow pipette tip, and migration was visualized by time-lapse imaging. The rate of wound closure was calculated by a ratio of the average distance between the two wound edges and the total duration of migration.
Transwell migration assay were performed as previously described (Luo et al. (2006) Cancer Res. 66:11690-11699). Assay media with EGF (5 ng/ml) was added to the bottom chamber. Cells (5×104/100 μl) were added to the top chamber of cell culture inserts (8 mm pore size) (Corning, Costar). After 12 hours of incubation, cells that migrated to the bottom surface of the insert were fixed with methanol and stained with 0.4% crystal violet. The number of cells that had migrated was quantified by counting ten random distinct fields using a microscope.
Rab2A GTPase hydrolysis assay were performed as described (Davis et al. (2013) Proc. Natl. Acad. Sci. USA 110:912-917) with small modifications. GST-Rab2A or GST-Rab2A Q58H (100 nM) was incubated in 20 mM Tris-HCl (pH 7.5), 50 mM NaCl, 10 mM MgCl2, 0.5 uM GTP and 3 μmol of [α-32P] GTP at room temperature for the indicated time. The Rab2a-bound nucleotides were eluted with elution buffer (2 mM EDTA, 0.2% sodium dodecyl sulfate, 1 mM GDP, 1 mM GTP). 1 μL of the reaction mixture was spotted onto polyethyleneimine-cellulose sheets. Chromatograms were developed in 0.75M KH2PO4 (pH 3.4). GTP and GDP resolved by thin-layer chromatography were visualized by autoradiography film exposure.
Aliquots of indicated numbers of cells were injected into 5-week-old BALB/c nude mice (Jackson Laboratories), as described (Mani et al. (2008) Cell 133:704-715). The tumor incidence was monitored by palpation and determined at two months after injection, with the same tumor incidence at 6 months postinjection. After tumors were detected, tumor size was measured every three days.
Human mammary reduction plasty tissues and breast cancer tissues were mechanically disaggregated and then digested with 200 U/ml collagenase (Sigma) and 100 U/ml hyaluronidase (Sigma), as described (Al-Hajj et al. (2003) Proc. Natl. Acad. Sci. USA 100:3983-3988). The resultant organoids were further digested in 0.25% trypsin-EDTA and Dispase/DNasel, and then filtered through a 40 μm mesh.
Lin−CD24−CD44+ cells were sorted from eight breast cancer specimens and cultured as single cell suspension in ultra-low attachment dishes, and then infected with lentivirus expressing control vector or Rab2A shRNA. After one week of puromycin selection, 2,000 transduced cells from each patient were injected into the mammary fat pads of 5-week-old nude mice. For serial passaging, cells from the primary tumors were sorted again for Lin−CD24−CD44+ cells. Among the 6 primary tumors formed in the shCtrl group, four tumors were randomly selected and passaged into eight mice (two mice per tumor). For the one tumor formed from 2,000 shRab2A cells, this tumor cells were injected into eight mice for serial passaging. The same procedure was applied to the second passage of xenograft cells. The size of tumors was measured every 3 d by calipers, and tumor volumes were calculated as Volume (mm3)=L×W2×0.4, as described (Yu et al. (2007) Cell 131:1109-1123). All studies involving human subjects were approved by the Institutional Review Board at Beth Israel Deaconess Medical Center or Sun Yat-Sen Memorial Hospital. All studies involving mice were approved by the Institutional Animal Care and Use Committee at Beth Israel Deaconess Medical Center and performed in accordance with the relevant protocols.
Formalin-fixed and paraffin-embedded tissue microarrays of human breast tissue were purchased from Imgenex (IMH-364 and 371). Rab2A (Proteintech Group) and ALDH1 (BD biosciences) staining was performed following the manufacturer's protocol. Immunolabeling was visualized with a mixture of DAB solution (Vector Laboratories), followed by counterstaining with hematoxylin. Microscopic analysis was assessed in a blinded manner. Immunostaining results were scored using percentage (P) x intensity (I), as described (Ginestier et al. (2002) Am. J. Pathol. 161:1223-1233). In brief, percentage of positive cells ranged from 0 to 100, and intensity was categorized into three groups as 1 (negative or weak), 2 (moderate) and 3 (strong). Expression levels are scored as low (0<P×I≦100), medium (100<P×I≦200) and high (200<P×I≦300). For ALDH1, only the intensity was estimated, because the percentages of positive cells were low. Intensity in foci with maximum staining was scored as low, medium and high, as described (Kunju et al. (2011) Mod. Pathol. 24:786-793).
ELISA measurements carried out using eBioscience ELISA Ready-Set-Go system according to manufacture protocol.
In Examples 27-36 below, lungs were digested using Kollagenase D and dispase and the dendritic cells populations ((CD11c+ CD205+ CD11 b+) were determined by staining the cells using the following antibodies: PE anti mouse CD11c, APC anti mouse CD205, FITC anti mouse CD11b. For T cell (CD3+ CD4+) population isolation, the cells were stained with APC anti mouse CD3+, FITC anti mouse CD4+ before the cells were cell sorted. Human BALF samples were stained with FITC anti human CD15 or FITC anti human CD205. All antibodies were purchased from Biolegend. Cells were analyzed using LSRII flow cytometer and FlowJo software. For cytospin the cells were spun onto glass slides, air dried and fixed using 4% PFA and stained with the indicated antibodies.
For mass spectrometry (MS) experiments described below, IRAK3 immunoprecipitates were separated using SDS-PAGE, the gel was stained with Coomassie blue, and the IRAK3 band was excised. Samples were subjected to reduction with DTT, alkylation with iodoacetamide, and in-gel digestion with trypsin overnight at pH 8.3, followed by reversed-phase microcapillary/tandem mass spectrometry (LC-MS/MS). LC-MS/MS was performed using an EASY-nLC II nanoflow HPLC (Thermo Scientific) with a self-packed 75 μm id×15 cm C18 column connected to a high resolution Orbitrap Elite mass spectrometer (Thermo Scientific) in the data-dependent acquisition and positive ion mode at 300 nL/min. MS/MS spectra collected via CID were searched against the concatenated target and decoy (reversed) Swiss-Prot protein database using Mascot 2.4 (Matrix Science, Inc.) with differential modifications for Ser/Thr/Tyr phosphorylation (+79.97) and the sample processing artifacts Met oxidation (+15.99), deamidation of Asn and Gin (+0.984) and Cys alkylation (+57.02). Phosphorylated and non-phosphorylated peptide sequences were accepted as valid if they passed a 1.0% false discovery rate (FDR) threshold. Passing MS/MS spectra were then manually inspected to be sure that all b- and y-fragment ions aligned with the assigned sequence and putative phosphorylation sites. Determination of the exact sites of phosphorylation was aided using Scaffold 4 and ScaffoldP™ software (Proteome Software, Inc.).
Gene expression described in Examples 27-36 was assessed using Affymetrix (Santa Clara, Calif.) GeneChip® Mouse Genome 430 2.0 arrays. 15 μg cRNA was fragmented and hybridized to arrays' according to the manufacturer's protocols. The quality of scanned array images were determined on the basis of background values, percent present calls, scaling factors, and 3′/5′ ratio of 3-actin and GAPDH. Data were extracted from CEL files and normalized using RMAexpress (http://rmaexpress.bmbolstad.com/) and annotated using MeV software (http://www.tm4.org/mev.html). Differentially expressed genes between different conditions were determined using a fold change threshold of 2. The data discussed in this publication have been deposited in NCBI's Gene Expression Omnibus, and are accessible through GEO Series accession number GSE66431.
Pathway and Functional analyses of the differentially expressed genes described in Examples 27-36 were performed using the commercial systems biology oriented package, Ingenuity Pathways Analysis (www.ingenuity.com). IPA provides a framework by which the lists of genes identified by large microarray experiments can be annotated in terms of functional relationships to understand the underlying biological mechanisms. It calculates the p-value using Fisher's Exact Test for each pathway and functions according to the fit of user's data to IPA databases. The p-value measures how likely the observed association between a specific pathway/function and the dataset would be if it were only due to random chance, by also considering the total number of Functions/Pathways/Lists of eligible genes in the dataset and the Reference Set of genes (those which potentially could be significant in the dataset). In case of interactive networks, all the identified genes were mapped to genetic networks available in the ingenuity database and were ranked by the score. The Score (−log p-value) is calculated using Fisher's Exact Test and indicates the likelihood a gene will be found in a network due to random chance. For example, if a network achieves a score of 2, it has at least 99% confidence of not being generated by chance alone.
The 15N-labeled Pin1 WW domain (Pin1 residues 1-50) was expressed and purified. The Pin1 WW domain was expressed in E. coli (BL21(DE3)) using M9 minimal media containing 15N—NH4Cl (Cambridge Isotope Laboratories, Inc.). Cells were induced at OD600 of 0.6˜0.8 by adding 1 mM final concentration of Isopropy β-D-1-thiogalactopyranoside (IPTG) at 37° C., and harvested at OD600 of 2.0. The Pin1 gene was inserted into a pET28 vector with Kanamycin resistance as a fusion protein with an N-terminal His6-tag. Pin1 was expressed in LB culture. The cells were induced at OD600 of 0.6˜0.8 by adding 1 mM of final concentration of IPTG at 16° C. for 20 hours. Synthetic peptides pSer110 (comprised of IRAKM residues 103-124 with Ser110 phosphorylated, TNYGAVL(pS)PSEKSYQEGGFPNI), and IRAKM S110E (IRAKM residues 103-124 with the S110E substitution), were purchased from Tufts University, Core Facility, Boston, Mass.
Nuclear magnetic resonance (NMR) experiments were performed on a Varian Inova 600-MHz spectrometer at 25° C. NMR spectra were processed and analyzed using NMRPipe and Sparky software. The composite chemical shift change in the 2D 1H-15N HSQC was monitored during NMR titration experiments and was fit to the standard bimolecular binding equation as described. To fit the data to the standard bimolecular binding equation solver function in Excel (Microsoft) was used.
To quantify the binding affinity between the Pin1 WW domain and peptides, the 15N labeled Pin1 WW domain was titrated with the each of the synthetic peptides, pSer110 and IRAKM S110E. A reverse titration method was used, where the 15N labeled protein was mixed with high concentration synthetic peptide for the first sample. Subsequent samples were a serial dilution of this sample with one part derived from the previous sample and one part from a stock solution of the 15N labeled Pin1 WW domain at the same concentration as the 15N labeled Pin1 WW domain in the first sample. This resulted in a titration where the concentration of the 15N Pin1 WW domain was constant, and the concentration of synthetic peptide decreased by a factor of ½ in each successive sample. For each of the pSer110 and IRAKM S110E peptides, a 1H-15N HSQC of each titration point was acquired on a Varian Inova 600-MHz spectrometer at 25° C., and the resulting chemical shift perturbations were used to determine the KD value as described above.
For the quantification of Pin1 isomerization of peptides pSer110 and IRAKM S110E, homonuclear 2D rotating-frame overhauser effect spectroscopy (ROESY) NMR experiments were performed. For Pin1 catalysis of pSer110, 13.8 μM of Pin1 was added to 4.44 mM of pSer110, and ROESY experiments were acquired with 0 ms, 4 ms, 8 ms, 20 ms, 40 ms, 60 ms, 80 ms, 100 ms, and 150 ms mixing times. For Pin1 catalysis of IRAKM S110E, 20 μM of Pin1 was added to 4.18 mM of IRAKM S110E, and ROESY experiments were acquired with 0 ms, 16 ms, 20 ms, 40 ms, 60 ms, 80 ms, 100 ms, and 150 ms mixing times. For the appropriate controls, each of pSer110 and IRAKM S110E were detected by ROESY without Pin1. The ratios trans to as were measured by Total Correlation Spectroscopy (TOCSY) for both pS110 and IRAKM S110E. The intensity ratios of cross peaks to diagonal peaks for as and trans conformation in the ROESY spectra were fit using the equations:
R2,c and R2,t are the transverse relaxation rates of magnetization in cis and trans, tm is the mixing time, kctcat and ktccat represent the exchange rates between as and trans, and Icc(0) and Itt(0) are the diagonal peak intensities of the cis and trans at states at time tm=0.
For human subject study described in Example 35, non-smokers with a history of mild asthma with an FEV1 greater than 70% of predicted, using only intermittent beta-agonists for treatment, who were between the ages of 18 and 55 were recruited to undergo segmental allergen challenge via bronchoscopy. Subjects were selected on the basis of both a positive methacholine PC20<8 mg/mL and a positive skin prick test to Dermatophgoides pternyssinus (DerP1). A positive intradermal that yielded a reaction at or below the concentration threshold of 0.1 AU/mL following the methods set forth in Parulekar et al. (2013) Am. J. Respir. Crit. Care Med. 187:494-501 was also required, although only the DerP1 antigen was used.
All subjects were enrolled at Brigham and Women's Hospital (BWH) in Boston, Mass. and all procedures were performed at BWH. Institutional Review Board approval was obtained at the site and each participant provided written informed consent. The study was registered with ClinicalTrials.gov (NCT01691612). For further analysis the human samples were de-identified. The following criteria were applied:
After recoding baseline vitals, PO2, FEV1, PEFR, appropriate anesthetic medication was administered. Then, a fiberoptic bronchoscope with bronchoalveolar lavage (BAL) was performed by sequential instillation and removal of 5 aliquots of 50 mL normal saline in the lingula. Brushings and biopsies were taken after the BAL. The bronchoscope was then re-wedged on the contra lateral side (right middle lobe) in a readily identifiable sub-segment. A safety dose (100×the minimum dose that caused reaction during the intradermal) of 5 mL of allergen in a prefilled syringe was instilled followed by 5 mL of air and the wedge was maintained for 5 minutes. Subject's safety parameters were assessed after administration of the sub-threshold allergen dose. If the investigator determined the subject had well tolerated the safety dose, full dose of allergen (1000×the minimum dose that caused reaction during the intradermal) in a pre-filled syringe was administered followed by 5 ml of air and the wedge was maintained for 5 min. Antigen lot to lot consistency was maintained between the subjects intradermal skin test and segmental challenge. Subjects were monitored for safety until 2 hours after the procedure. After allergen challenge, if the subject developed systemic allergic reaction such as diffuse urticaria, angioedema, stridor, hypotension, syncope or any other serious adverse event, subject would be dropped from the study and only be followed up for safety reasons.
Subjects were not allowed to leave for home until their condition was stable as assessed by the study physician.
Pre-bronchoscopy and bronchoscopy eligibility procedures were followed as detailed above prior 25 to 2nd bronchoscopy. Specimens taken were BAL first, followed by brushings, and finally biopsies. These were taken where the segmental allergen challenge was placed (right middle lobe). Drug and post-procedure follow up and monitoring were followed as detailed above. Details of participants are summarized in Table 3.
The experiments described herein were routinely repeated at least three times, and the repeat number was increased according to effect size or sample variation. We estimated the sample size considering the variation and mean of the samples. No statistical method was used to predetermine sample size. No animals or samples were excluded from any analysis. Animals were randomly assigned groups for in vivo studies; no formal randomization method was applied when assigning animals for treatment. Group allocation and outcome assessment was not done in a blinded manner, including for animal studies. All data are presented as the means±SD, followed by determining significant differences using the two-tailed student t test or ANOVA test, where *P<0.05, **P<0.01, ***P<0.001. Limiting dilution data were analyzed by the single-hit Poisson model using a complementary log-log generalized linear model with L-Calc Software (Stemcell Technologies). Correlations of Rab2A expression with other gene expression were analyzed with the Pearson correlation test. For survival analysis, Kaplan-Meier analysis, univariate and multivariate Cox regression analysis were used.
As described above, phosphorylation of Pin1 on S71 inhibits Pin1 catalytic activity and oncogenic function by blocking a phosphorylated substrate from entering the PPlase active site (see, for example,
We have previously shown that phosphorylation (e.g., inactivation) prevents Pin1 from binding to species with high affinity for Pin1. One such species is pTide (Bth-D-phos.Thr-Pip-Nal), a substrate-mimicking inhibitor that selectively binds Pin1 at its PPlase domain and does not bind to the WW domain of Pin1 or to FKBP12 (
The N-terminal HiLyte™ Fluor 488-, fluorescein- or TAMRA-labeled peptide had a 4 residue sequence core structure of pTide, which was synthesized by a commercial company (Anaspec). This sequence was optimized for solubility and binding to GST-PPI. For the screening assay, a solution containing 250 nM GST-Pin1, 5 nM labeled peptide, 10 μg/mL bovine serum albumin, 0.01% Tween-20 and 1 mM DTT in a buffer composed of 10 mM HEPES, 10 mM sodium chloride, and 1% glycerol at pH 7.4 was used. Measurements of fluorescence polarization and fluorescence absorbance were made in black 384-well plates (Corning) using a Synergy II plate reader. Compounds were transferred to plates using a custom-built Seiko pin-transfer robot at the Institute for Chemistry and Cell Biology at Harvard Medical School. The assay can tolerate up to 10%/o DMSO.
Molecules that compete with pTide for binding to the active site, e.g., Pin1 substrates, were detected under equilibrium conditions. A Z score was used to identify and rank those molecules that were most competitive with pTide (e.g., that have higher binding affinity). A Z score is defined as Z=(x−μ)/σ, where x is a raw score, μ is the mean of the population, and σ is the standard deviation of the population. Molecules with the most negative Z scores represent those with the highest Pin1 binding affinity. The Z′ value for this assay was around 0.70 and was consistent for day-to-day performance, with a coefficient of variation in the range of 4-5%.
The structure of 13cRA and its isomer ATRA are shown in
in which Kd [M] is the equilibrium dissociation constant of the probe, EC50 [M] is obtained from the FP assay, Lo [M] is the probe concentration in the FP assay, Lb [M] is the concentration of the probe that binds to the target protein (85% of the total probe concentration), and Ro [M] is the Pin1 concentration in the assay. Additional details are available in Auld et al., Assay Guidance Manual (Bethesda (Md.), 2004). A lower value of Ki is indicative of higher association and, accordingly, higher affinity of the substrate to the protein.
As shown in
Photoaffinity labeling of Pin1 with radiolabeled ATRA was performed to provide further confirmation of the direct binding between ATRA and Pin1. 10 μmol of Pin1 was incubated in microcentrifuge tubes with a series of concentrations of all-trans-[11,12-3H]-retinoic acid (PerkinElmer, 43.7 Ci/mmol) in 20 μl of the FP assay buffer at 23° C. with agitation for 2 hours in the dark. The caps of the microcentrifuge tubes were opened, and the samples were placed on ice and exposed to an Electrophoresis System 365/254 nm UV hand lamp (Fisher Scientific) suspended 6 cm above the surface of the liquid for 15 minutes. The samples were boiled in SDS sample buffer and subsequently separated on standard SDS/PAGE gels. The gels were dried and then used for fluorography at −80° C. for 5 days and quantified using Quantity One from BioRad.
Binding detected using SDS-containing gels confirms the direct binding of ATRA and Pin1 (
Having determined ATRA to be a potent and selective Pin1 substrate, we compared the binding activity of ATRA to several ATRA-related compounds to investigate the structural features important to the association of the substrate with Pin1. These structures are presented in
To understand how ATRA inhibits Pin1 catalytic activity, we determined the co-crystal structure of ATRA and the Pin1 PPlase domain. Pin1 PPlase domain (residue 51-163) was cloned into a pET28a derivative vector with an N-terminal hexahistidine tag followed by recognition sequences by thrombin and PreScission 3C proteases and then the recombinant gene. Mutations of K77Q, K82Q were created by QuikChange™ site directed mutagenesis.
The PPlase K77/82Q was purified by overexpression in E. coli BL21 (DE3) strain with isopropyl-β-D-thiogalactopyranoside (IPTG) and induction at 16° C. overnight. Cell lysate was first purified with nickel affinity chromatography. The elution was dialysed in a buffer of pH 8 including 20 mM HEPES, 100 mM NaCl, and 8 mM A-Mercaptoethanol while the protein was treated with PreScission Protease (GE) over night at 4° C. After His tag removal, Pin1 PPlase K77/82Q was separated from untruncated protein by a second round of nickel affinity chromatography, and subsequently purified by size exclusion chromatography columns Superdex 75 (GE Healthcare).
Purified PPlase K77/82Q was concentrated to 15 mg/mL ATRA dissolved in DMSO at the concentration of 1 mM was mixed with the protein solution and the mixture incubated on ice for 3 hours before setting up trays. Incubated protein was co-crystallized by vapor diffusion using a hanging drop of 1 μL protein-ATRA plus 1 μL well solution. The complex formed crystals in 0.2 M ammonium sulfate, 0.1 M HEPES, and 0.9 M-1.4 M sodium citrate in pH 7-8.5 solutions after micro-seeding using apo PPlase domain crystals. The crystals were cryoprotected by adding 30% glycerol in mother liquor and vitrifying in liquid nitrogen before data collection.
X-ray diffraction was performed using synchrotron radiation at beamline 5.0.2 of the Advanced Light Source (Berkeley, Calif.) with 3×3 CCD array detectors (ADSC Q315R). Data were processed and scaled using the HKL2000 software suite. Data collection statistics are summarized in the tables below.
The structure of PPlase K77/82Q bound with ATRA was determined by molecular replacement with PPlase K77/82Q (PDB: 3IKG) as the search model using program Phaser from the CCP4 package suite. The structure was refined with the Refmac5 program from CCP4 package and iterative model building in COOT. The final structure was evaluated by both PROCHECK and MolProbity. Refinement statistics are summarized in Table 5 above. The Pin1-ATRA structure was deposited into the Worldwide Protein Data Bank with the PDB code of 4TNS.
The co-crystal structure of ATRA and Pin1 is presented in
To determine whether ATRA inhibits Pin1 in vivo, we first compared its anti-proliferative effects on Pin1 KO (Pin1−/−) and wild-type (WT, Pin1+/+) mouse embryonic fibroblasts (MEFs). Although relatively high concentrations of ATRA were required to inhibit the growth of Pin1 WT MEFs, Pin1 knockout (KO) cells were much more resistant to ATRA (
In order to determine the mechanism of down-regulation of Pin1, ATRA's effect on Pin1 mRNA levels (
To determine whether ATRA inhibits Pin1 oncogenic function in vitro, we examined the effects of ATRA on the well-documented oncogenic phenotypes induced by Pin1 overexpression, such as inducing centrosome amplification, activating the cyclin D1 promoter, and enhancing foci formation. These phenotypes are all inhibited by DAPK1-mediated S71 phosphorylation in Pin1. Indeed, ATRA dose-dependently and fully inhibited the ability of Pin1 overexpression to induce centrosome amplification (
ATRA activates RARs to induce acute promyelocytic leukemia (APL) cell differentiation and also causes PML-RARα degradation to inhibit APL stem cells. Though ATRA has been approved for APL therapy, the mechanism of its activity is unknown. The ability of ATRA to activate RARα can be decoupled from its ability to induce PML-RARα degradation and to treat APL. Thus, the drug target(s) of ATRA for the latter effects remain elusive.
To examine the role of RARs in ATRA-directed degradation of PML-RARα, we used a pan-RARs agonist, AC-93253, and a pan-RARs inhibitor, Ro-415253, each structurally distinct from ATRA (
ATRA-induced PML-RARα degradation is associated with phosphorylation on the Ser581-Pro motif, which corresponds to the Pin1 binding site pSer77-Pro in RARα. Since Pin1 binds to and increases protein stability of numerous oncogenes (
Because Pin1 regulates many transcriptional factors (
Clustering analysis revealed that ATRA-treated cells and Pin1 KD cells have striking similarities. 528 genes were identified to be differentially expressed, with 304 upregulated and 224 downregulated including many growth-stimulators (e.g., CCL2, SPP1, IL1 B, and IL8) and growth-suppressors (e.g., PDCD4 and SORL1) and no-coding RNAs both in Pin1 KD cells and ATRA-treated cells (
Immunodeficient NOD-SCID-Gamma (NSG) mice transplanted with NB4 cells stably expressing an inducible Tet-on shPin1 after sublethal irradiation were used to corroborate the findings of in vitro studies that Pin1 KD can cause PML-RARα degradation. When doxycycline-containing food was given to the mice 5 days post-transplantation and throughout the course of the experiment, doxycycline-induced Pin1 KD also drastically reduced PML-RARα in the bone marrow (
Based on the results presented herein, ATRA effectively binds, inhibits, and ablates Pin1 and thereby induces PML-RARα degradation to treat APL. This idea was further investigated by comparing ATRA to three less potent and specific and structurally distinct Pin1 inhibitors: PiB, EGCG, and Juglone. Like ATRA, these agents all dose-dependently reduced PML-RARα in APL cells. However, in contrast to ATRA, the non-ATRA species inhibited Pin1 without degrading it (
To examine the effects of these Pin1 inhibitors on APL phenotypes in an in situ APL mouse model, sublethal irradiated B6 mice were engrafted for 5 days with APL cells isolated from hCG-PML-RARα transgenic mice and treated with EGCG or Juglone, or with ATRA-releasing pellets (5 mg 21 day). After 20 days, again, ATRA, but neither EGCG nor Juglone, induced APL cell differentiation in mice (
An ultimate question is whether ATRA treatment might lead to degradation of Pin1 and PML-RARα in APL patients. We used double immunostaining with antibodies against Pin1 and PML to detect Pin1 and PML-RARα levels and their localization in the bone marrow of normal controls or APL patients before or after the treatment with ATRA for 3 or 10 days or APL patients in complete remission (
Given that ATRA potently ablates Pin1, which regulates numerous cancer-driving molecules in solid tumors (
To explore this range of ATRA sensitivity in breast cell lines, we first analyzed Pin1 levels. Compared with normal MCF10 and HMLE cells, Pin1 was overexpressed in all breast cancer cells (
To examine whether the inhibitory effects of ATRA on breast cancer cell growth are related to RARs activation, we again used Ro-415253 and AC-93253 (
We next examined whether ATRA would affect protein levels of a select set of oncogenes and tumor suppressors whose protein stability has been shown to be regulated by Pin1 in breast cancer. Indeed, ATRA caused dose-dependent protein reduction in Pin1 and its substrate oncogenes, including cyclin D1, HER2, ERα, Akt, NFκB/p65, c-Jun, and PKM2, as well as protein induction in its substrate tumor suppressors such as Smad2/3 or SMRT, in all three sensitive cancer cell lines (
The ability of ATRA to inhibit breast tumor growth in vivo was investigated using MDA-MB-231 and MDA-MB-468 cells in mouse xenograft models. Both cell types are associated with human triple negative breast cancer, which has the worst prognosis and fewest treatment options. In pilot experiments, MDA-MB-231 cells were subcutaneously injected into female nude mice in the flank. ATRA was subsequently administered in the flank or vehicle intraperitoneally 3 times a week for 8 weeks. ATRA had only modest antitumor activity (
In order to circumvent the short half-life, we implanted ATRA-releasing or placebo pills into mice to maintain a constant drug level for 8 weeks after cells were injected into nude mice for 1 week. ATRA potently and dose-dependently inhibited tumor growth, as well as reduced both Pin1 and its substrate cyclin D1 in tumors derived from MDA-MB-231 cells (
Schemes summarizing the activities of ATRA and Pin1 are presented in
We previously demonstrated a fundamental role of the unique prolyl isomerase Pin1 in driving the expansion, invasiveness and tumorigenicity of BCSCs, as well as the abundance and repopulating capability of mouse mammary stem cells (MaSCs) (Luo et al. (2014) Cancer Res. 71:3603-3616). To elucidate the underlying molecular mechanisms, we analyzed the effects of Pin1 KO on gene expression in mouse mammary epithelial cells (MECs). Global expression profiling of Lin−MECs isolated from two pairs of virgin Pin1 KO and WT littermates identified 1723 genes that were downregulated in both Pin1 KO mice (
To validate these candidate genes, we used qRT-PCR to determine the effects of Pin1 knockdown (KD) on their expression in six human breast cell lines. Rab2A was down-regulated after Pin1 KD in all 6 breast cancer cell lines examined, and Lamp2 and Magi3 were downregulated in 5 of 6 cell lines (
Pin1 regulates its target function directly by isomerizing pSer/Thr-Pro motifs in the substrate or indirectly via regulating gene transcription. Rab2A does not have any Ser/Thr-Pro motif, but has two putative AP-1 binding sites (−1293 and −890) in its promoter region (
To confirm that Pin1 regulates Rab2A transcription through AP-1, we first examined whether Pin1 binds to Rab2A promoter by the chromatin immunoprecipitation (ChIP) using cells transfected with Pin1 expression plasmid. Compared to control IgG, anti-Pin1 antibodies showed appreciable binding to the −1293 locus, as assayed by quantitative real-time PCR using primers flanking the −1293 and −890 loci (
To investigate whether Rab2A is a functional downstream target of Pin1, we knocked down Rab2A in control or Pin1-overexpressing HMLE cells to examine whether Rab2A mediates the action of Pin1 in BCSCs (
We recently showed that Pin1 overexpression induces EMT in HMLE cells. Strikingly, Rab2A KD in Pin1-overexpressing cells reverted the EMT phenotype. After Rab2A KD, Pin1-overexpressing HMLE cells changed to epithelial morphology (
Given that Rab2A KD suppresses BCSC expansion, we next sought to determine more directly the role of Rab2A in breast cancer. We first checked Rab2A gene alterations in cancers in the cBio Cancer Genomics Portal (Cerami et al. (2012) Cancer Discov. 2:401-404). Significantly, Rab2A gene amplification occurs in a wide range of human cancers, with the highest amplification frequency of ˜9.5% (72 of 760) in invasive breast carcinoma patients (
We overexpressed Rab2A in control shRNA or Pin1 KD HMLE cells (
To further investigate whether Rab2A is sufficient to induce HMLE cell transformation, we performed soft agar colony formation assay on Rab2A-overexpressing and control vector cells. Whereas control cells could hardly form colonies, Rab2A-overexpressing cells robustly formed colonies (
To evaluate the impact of Rab2A on tumor initiation, we assessed the effects of Rab2A overexpression on tumor formation by limiting dilution transplantation assays in nude mice. We used HMLER cells, HMLE cells transformed with V12H-Ras, which is needed to enable Snail or Twist-overexpressing HMLE cells to form tumors in nude mice. When 1×104 Rab2A-expressing HMLER cells were inoculated into nude mice, 3 of 6 mice generated tumors. All animals injected with 10- or 100-fold more cells developed tumors. By contrast, no mice inoculated with 1×104 control HMLER cells developed tumors, while tumors developed in only 2 of 8 mice inoculated with 105 control cells and 3 of 6 mice injected with 106 control cells (
During our investigation into the clinical relevance of Rab2A genomic alterations in human cancer, we also noted that several Rab2A missense mutations have been identified in the cBio Cancer Genomics Portal (Cerami et al. (2012) Cancer Discov. 2:401-404) and the COSMIC database (Forbes et al. (2011) Nucleic Acids Res. 29:D945-950). Notably, the Rab2A Q58H mutation has been identified in a lung squamous cell carcinoma and a lung adenocarcinoma. Given that 058 is highly conserved in Rab2A genes across species (
To understand how Rab2A drives BCSC expansion, we examined whether Rab2A activates Erk1/2 (extracellular signal-regulated kinases 1/2)-MAP kinase pathway, which is crucial for Ras to induce EMT and increase the BCSC-enriched CD24−CD44+ population. First, we tested whether Rab2A activates Erk1/2 signaling. After serum starvation and EGF stimulation, Rab2A overexpression significantly increased Erk1/2 activation monitored by p-Erk1/2 in a time-dependent manner and also increased expression of Zeb1 (
Next, to examine whether Erk1/2 activation is required for mediating Rab2A's action in BCSCs, we silenced the expression of Erk1 or 2 in Rab2A-overexpressing HMLE cells. Since Erk2, but not Erk1, is required to induce EMT and CD24−CD44+ population, we knocked down Erk1 or Erk2 separately using lentiviral shRNA vector (
To elucidate how Rab2A overexpression or its Q58H mutation activates Erk1/2, we first examined whether Rab2A co-localized with Erk1/2. HMLE cells were starved and then stimulated by EGF to induce Erk1/2 phosphorylation. As compared with the vector control, overexpressing WT Rab2A not only activated Erk1/2, but also surprisingly colocalized with activated Erk1/2 at the perinuclear region at five minutes (
The unexpected findings that Rab2A or its Q58H mutant colocalizes with activated Erk1/2 at the ERGIC suggested that Rab2A might directly interact with Erk1/2 to initiate Erk1/2 signaling. To test this possibility, we first examined whether Rab2A and Erk1/2 might form stable complexes given their colocalization. We detected co-immunoprecipitation of the endogenous Rab2A with Erk1/2 in HMLE cells by reciprocal co-immunoprecipitation (co-IP) experiments (
Interestingly, the conserved docking motif described in Example 22 is also found in MKP3, a phosphatase that binds and dephosphorylates Erk, leading to Erk inactivation, and MEK1, a kinase that binds and phosphorylates Erk, leading to Erk activation. To examine whether Rab2A and MKP3 or MEK1 compete with each other to interact with Erk, HEK293 cells were co-transfected with decreasing doses of myc-MKP3 or the constitutively active HA-MEK1 and a constant dose of Flag-Rab2A. With decreasing amounts of MKP3 expressed, more Erk1/2 were immunoprecipitated by Rab2A using Flag antibody in a dose-dependent manner (
The above results suggest that Rab2A might prevent the dephosphorylation of Erk1/2 by competing with MKP3 for Erk1/2 binding. To examine this possibility, we transfected HEK293 cells with MKP3 and the constitutively active MEK1 mutant as well as different amounts of epitope-tagged Rab2A, followed by assaying Erk phosphorylation. Expression of the active MEK1 induced Erk1/2 phosphorylation even in serum-starved cells and this was largely reversed by myc-MKP3 expression (
To further demonstrate whether this Rab2A-Erk interaction is functionally important for Rab2A to regulate BCSC, we infected HMLE cells with Flag-tagged wild-type Rab2A or its mutants defective in binding to Erk, followed by comparing their effects on BCSC (
As Erk1/2 signaling is known to increase the nuclear accumulation of unphosphorylated (active) β-catenin, a known regulator of CSCs, and Pin1 is known to have a similar effect on β-catenin in breast cancer cells, we examined whether Pin1/Rab2A/p-Erk signaling regulates nuclear β-catenin levels. Confocal analysis showed that most unphosphorylated β-catenin localized at the plasma membrane in starved HMLE cells, but translocated into the nucleus, along with increased p-Erk1/2 6 hr after EGF stimulation (
The above results demonstrate that Rab2A drives the expansion, invasiveness and tumorigenicity of BCSCs in human breast cell lines. To extend our findings to primary human cells, we first examined whether Rab2A or the Q58H mutant might confer BCSC properties to normal human primary MECs. As shown in
We next assessed whether Rab2A is also important for tumorigenesis of BCSCs in primary breast cancers. To this end, we sorted Lin−CD24−CD44+ cells from freshly isolated human breast cancer cells of eight patients (
Given that Rab2A was highly expressed in the BCSC-enriched population, we tested whether endogenous Rab2A was required to maintain the BCSC population in the primary breast cancers by transducing Lin−CD24−CD44+ primary breast cancer cells with a lentivirus expressing Rab2A shRNA. Rab2A was efficiently silenced after three days of puromycin selection (
We finally investigated whether Rab2A was required for the tumorigenicity of the BCSC-enriched Lin−CD24−CD44+ population. We injected 2,000 control or Rab2A shRNA-transduced Lin−CD24− CD44+ cells, or Lin−non-CD24−CD44+ cells isolated from eight breast cancer patients into nude mice, using the same procedure as described previously (Yu et al. (2007) Cell 131:1109-1123). While no tumors developed in mice injected with the cells that were not CD24−CD44+, 2,000 control Lin−CD24−CD44+ cells generated six tumors in eight injected mice (
To assess whether the experimental findings of Rab2A expression and activity in BCSCs are relevant to human breast cancer patients in the clinic, we asked whether Rab2A might also be overexpressed in human breast cancer tissues and whether its expression might correlate with clinical outcome. We first analyzed expression of Rab2A, Pin1 and ALDH1, a marker for stem and progenitor cells as well as BCSCs, in normal and cancerous breast tissue arrays using immunohistochemistry. Pin1 and Rab2A were undetectable or low in all 24 human normal breast tissues, but their expression was dramatically increased in many of 65 human breast cancer tissues (
To expand our immunohistochemistry findings on limited samples, we studied multiple independent breast cancer datasets from Oncomine (Rhodes et al. (2007) Neoplasia 9:166-180), which collectively link clinical data with Rab2A mRNA expression in about 3,000 patients. Rab2A overexpression was closely associated with advanced stage in the Bittner dataset, with metastasis in the Schmidt dataset, and with death at 3 or 5 years in the Bild, Bittner, Kao and Schmidt breast datasets (Bild et al. (2006) Nature 439:353-357; Kao et al. (2011) BMC Cancer 11:143; Schmidt et al. (2008) Cancer Res. 68:5405-5413) (
Giving that the microarray experiments and the methods to normalize data vary among different datasets making it difficult to pool the data from different datasets, we chose to further analyze the Curtis dataset, which has over 2,000 patients (Curtis et al. (2012) Nature 486:346-352). When treated as a continuous variable, Rab2A mRNA level was a strong prognostic factor for survival by univariate Cox regression analysis (
We next analyzed Rab2A expression in the PAM50 intrinsic subtypes (Parker et al. (2009) J. Clin. Oncol. 27:1160-1167) and integrative subgroups (Curtis et al., supra). Strikingly, high Rab2A mRNA levels were found in the poor prognosis subtypes, defined as PAM50 intrinsic subtypes, luminal B, HER2-enriched and basal-like, and in the IntClust5, IntClust6, IntClust9 and IntClust10 integrative subgroups (
TLR/IL-1R signaling is known to regulate the production of cytokines necessary for the development of adaptive TH2 immunity and IgG class switching, goblet cell metaplasia, and airway eosinophilia, hallmarks of allergic asthma. TLR4, for examples, secretes the cytokine IL-33, which prolongs eosinophil survival, adhesion, and degranulation and stimulates both mast cells and alveolar macrophages. Proline-directed phosphorylation accelerated by Pin1 is an important mechanism in these signaling pathways. Indeed, Pin1 is abnormally activated in eosinophils in asthmatic airways and increases key cytokine production necessary for eosinophils survival and activation by stabilizing their mRNA half life. Pin1 inhibition thus attenuates pulmonary eosinophils and bronchial remodeling.
Pin1 enzymatic activity is highly regulated and affected by external stimuli. To examine whether IL-33 signaling affects Pin1 enzymatic activity, the dendritic cell line DC2.4 was treated with IL-33, followed by Pin1 enzymatic activity assay (
To assess the role of Pin1 in the IL-33 signaling pathway, mouse embryonic fibroblasts (MEFs) derived from Pin1 wild-type (WT, +/+) or knockout (KO, −/−) mice were treated with increasing concentrations of IL-33, followed by measuring IL-6 production (
To test whether the involvement of Pin1 in asthma is restricted to the IL-33/IL-1R pathway or extends to other allergy-inducing pathways, we evaluated the same parameters as above in an ovalbumin (OVA) induced model of allergic asthma. In a similar manner, OVA-challenged Pin1 KO mice showed reduced lung inflammation (
It has been reported that IL-33 induces TH2 polarization and IL-5 and IL-13 secretion from naive CD4+ cells co-cultured with dendritic cells. To examine whether Pin1 is required for IL-33-induced TH2 polarization, we evaluated the effects of Pin1 KO derived dendritic cells in IL-33-induced TH2 polarization by co-culturing bone marrow dendritic cells (BMDCs) derived from WT or Pin1 KO mice with WT naïve CD4+ cells. The cells were treated with IL-33 and resultant IL-5 and IL-13 were measured. The naive CD4+ cells were stimulated to secrete high levels of IL-5 and -13 when they were co-cultured with BMDCs in the presence of IL-33 (
Dendritic cells are among the predominant cell types reacting to IL-33 stimulation and are necessary for IL-33 dependent allergic asthma induction. To identify possible protein targets regulated by Pin1 upon IL-33 induction, the dendritic cell line DC 2.4 was treated with IL-33 or LPS for 1 hour before cell lysates were subjected to GST-Pin1 pull down to identify Pin1-binding proteins, a technique that has been used to identify almost all Pin1 substrates. Our focus on interleukin receptor associated kinase (IRAK) family members stemmed from the fact that: i) we have shown that IRAK1 activity is regulated by Pin1 and ii) IL-33 has been shown to activate the IRAK dependent pathway.
We identified a specific interaction between Pin1 and IRAKM (
To identify which of the two Pin1 domains mediate the Pin1-IRAKM interaction, HEK293 cells expressing the ST2 were co-overexpressed with IRAKM along with GFP, GFP-Pin1, GFP-WW (GFP fused to the Pin1 WW domain that mediates binding to pS/T-P motifs) or GFP-PPlase (GFP fused the Pin1 peptidyl-prolyl cis-trans isomerase (PPlase) domain). These cells were treated with IL-33 before they were subjected to CO-IP for GFP (
To directly observe the Pin1-IRAKM interaction, two dimensional (2D) nuclear magnetic resonance (NMR) spectroscopy was employed. In the 2D 1H-15N Heteronuclear Single Quantum Coherence (HSQC) spectrum of a 15N-labeled protein, each backbone NH group gives rise to a peak at a specific position that reflects the average chemical environment of that NH group. Individual peaks in this spectrum thereby serve as sensors to detect and quantify ligand binding. When uniformly 15N-labeled Pin1 WW domain (15N-Pin1-WW) was titrated with unlabeled IRAKM phosphopeptide (IRAKM-pS110) or the corresponding phosphomimetic mutant IRAKM-S110E (
To determine whether Pin1 catalyzes isomerization of the IRAKM-pS110 and IRAKM-S110E peptides, homonuclear 2D rotating-frame Overhauser effect spectroscopy (ROESY) NMR experiments were performed. In the absence of Pin1, no exchange cross-peaks were observed between cis and trans isomers in ROESY spectra of either IRAKM-pS110 or IRAKM-S110E peptides (
The as/trans conformational changes catalyzed by Pin1 have profound effects on the function of Pin1 target proteins, notably regulating nuclear translocation and stability and activity of many transcription factors. IRAKM can shuttle between the cytoplasm and nucleus in pro-monocytic THP-1 cells upon TLR2 activation and is associated with chromatin remodeling in lung macrophages during sepsis. To see whether IL-33 affects IRAKM-Pin1 localization as well, DC2.4 cells were treated with IL-33 before immunostaining for IRAKM and Pin1 (
To examine whether Pin1 might affect IRAKM stability and/or transcription, IRAKM was co-overexpressed in WT and Pin1 KO MEFs with GFP as a control, followed by assaying IRAKM protein stability using the cyclohexamide chase. Absence of Pin1 reduced the IRAKM half-life by more than 50% (
To examine whether the effects of Pin1 on IRAKM protein stability are dependent on the pS110-P motif in IRAKM, we generated S110A or P111A IRAKM mutants (to abolish interaction with Pin1), as well as the S110E IRAKM mutant (to mimic S110 phosphorylation). IRAKM or each mutant was overexpressed in WT MEFs and the stability of each protein was assessed. While the S110A and P111A mutations decreased IRAKM protein stability by ˜50%, the S110E mutation rendered IRAKM completely resistant to degradation (
IRAKM is expressed in bronchial epithelial cells and resident immune cells of the lung. To assess IRAKM protein levels in the lung after IL-33 stimulation and the effects of Pin1 KO on IRAKM protein levels, WT and Pin1 KO mice were treated with intranasal administration of IL-33 (
To avoid the possibility that Pin1 germline KO could potentially affect the development of some immune cells, we utilized Pin1 chemical inhibitors. It has previously been reported that Pin1 inhibition using Juglone in a rat model of asthma selectively reduces eosinophilic pulmonary inflammation and airway remodeling, while ATRA inhibits type 2 responses in asthma. Notably, most of the available Pin1 inhibitors, including Juglone, exhibit low specificity and/or high toxicity. These observations prompted us to investigate the effects of ATRA on IL-33-induced asthma, and the effects of Pin1 inhibition on IRAKM levels. WT mice were implanted with either 10 mg, 21 day ATRA-releasing pellets or placebo in their backs, 14 days prior to intranasal IL-33 or PBS administration. Intranasal IL-33 administration in the placebo group induced massive inflammation and airway remodeling, which were further corroborated by a substantial increase of total cells, eosinophils, neutrophils, lymphocytes and macrophages in BALF as compared with the PBS-administered group (
To further determine the effects of ATRA on TH1 and TH2 cytokine production upon IL-33 induction, BALF IL-5, -13, -12 and TNF-α levels were assessed. Intranasal IL-33 in the placebo group induced high levels of IL-13 and -5 in compared with those in the PBS-treated control group (
To further support the above findings, we directly evaluate the effects of ATRA on Pin1 and IRAKM protein levels in the lung because ATRA selectively degrades active Pin1 and also because Pin1 involvement in IRAKM protein stability (
To further support this model, we also evaluated whether IL-33 or ATRA altered IRAKM localization in vivo. When cells obtained from BALF of treated mice were cytospinned and stained for IRAKM and CD205, a dendritic/monocyte marker, IRAKM localization was predominantly cytoplasmic in PBS-treated mice (
To assess the role of IRAKM and Pin1 in IL-33 as well other stimuli signaling pathways, BMDCs derived from WT, Pin1 KO and IRAKM KO mice were treated with different stimulants and the levels of IL-6 were measured as a proxy for degree of immune response (
We have further confirmed these different responses in DC2.4 cells where IRAKM was stably overexpressed (
The above results demonstrate a crucial role of IRAKM in IL-33-induced asthma. A critical question is what its downstream mediators are. Our data showing IRAKM nuclear localization upon IL-33 stimulation and combined with the previous findings that IRAKM is crucial for NF-κB activation in IRAK1 and IRAK2 double KO mice prompted us to investigate changes in the gene expression profile of DC2.4 cells following IL-33 exposure and the involvement of IRAKM in this process. Control pLKO-expressing DC2.4 cells, IRAKM KD cells (
Differential expression of these genes was validated by RT-PCR. Notably, upon IL-33 treatment, there was up-regulation in expression of all four of these genes in pLKO control cells, which was attenuated or blocked by IRAKM KD. In contrast, stable overexpression of IRAKM dramatically elevated the expression of these genes, compared to control DC2.4 cells. These findings were consistently recapitulated in IL-33-challenged DC2.4 cells (
Next we explored the effects of IRAKM mutations at the S110 site on the expression of these four target genes. We hypothesized that if the expression of these genes is regulated by IRAKM, and mediated by Pin1 isomerization of the S110 site, Pin1 inhibition would have minimal effect on expression of these genes when employing IRAKM mutants that do not contain the necessary S-T/P site for Pin1 interaction. To this end, we treated DC2.4 cells stably expressing IRAKM or two mutants (S110E or P111A) with two different doses of ATRA (5 and 10 μM) before IL-33 treatment. S110E elevated the expression of these target genes comparable to IRAKM expressing cells (
To confirm these findings, we measured expression of these target genes following IL-33 stimulation in IRAKM-expressing cells that are also Pin1 KD (
It has been previously demonstrated that IRAKM KO derived BMDCs tend to produce higher levels of pro inflammatory TH1 cytokines compared to WT derived BMDCs upon different TLR activation, indicating skewing toward TH1 polarization. To elucidate any effect that IRAKM might have in dendritic cells on TH2 cell polarization upon IL-33 stimulation, we repeated the co-culturing experiment as described in
We identified a crucial role of IRAKM and its target genes in asthma using IL-33-induced asthma in cell and mouse models. To address the clinical significance of our findings, we assessed levels of IRAKM protein and its target genes expression in asthmatic patients using a segmental allergen Derp1 challenge, a well-known induction of allergic asthma in humans. Briefly, non-smokers with a history of mild asthma were recruited to undergo bronchoscopy with segmental allergen installation with DerP1, followed by repeat bronchoscopy with bronchoalveolar lavage, brushing, and endobronchial biopsy of the challenged segment as described in material and methods. For further sample analysis, all asthmatic human samples were de-identified.
Derp1 treatment caused a massive immunological reaction, which was evident by the infiltration of granulocytes into the lung tissue and hyperreactivity of the bronchia epithelial cells, which was evident by PAS tissue staining (
To evaluate the expression of IRAKM target genes in these samples, BALF cellular RNA was extracted and the genes expression were monitored (
The above results show that allergenic challenges activate the Pin1/IRAKM axis, which in turn is necessary for the expression of IL-6, CXCL2, CSF3 and CCL5. To examine the effect of Pin1 KO or IRAKM KO on IL-33 induce allergic asthma and the expression of its downstream target genes upon challenge, we treated WT, Pin1 KO and IRAKM KO mice with intranasal IL-33 treatment, followed by examining lung pathology, BALF cellular content and TH2 cytokines.
As expected, WT mice exhibited high inflammation, which was evident by the high presence of inflammatory cells surrounding the bronchoalveolar space as well as the high PAS staining of the bronco epithelial cells (
We also examined the expression levels of IRAKM downstream targets IL-6, CXCL2, CSF3 and CCL5, in the lung tissues of treated mice and their differences among different groups (
It has been reported that IL-33 activated dendritic cells are necessary for airway inflammation26. To see whether Pin1 KO or IRAKM KO had any effect on dendritic cell activation in lungs upon IL-33 stimulation, WT, Pin1 KO and IRAKM KO mice were treated as before and surface expression of CD11c, CD11b, and CD205 was monitored (
The results summarized in Examples 27-35 in cellular, animal, and human models demonstrate for the first time that Pin1 regulates type 2 immune responses in asthma by activating IRAKM and suggest that Pin1 inhibitors such as ATRA or an ATRA-related compound or a longer half-life ATRA might be used to treat asthma. Pin1 and its substrate IRAKM are crucial factors for IL-33 signaling in dendritic cells and asthma induction, and their inhibition by KO or inhibitor dramatically inhibits a set of pro-inflammatory cytokine and asthma phenotype upon allergenic challenge. This observation might be due to the fact that deletion of IRAKM or Pin1 in BMDCs potently suppresses TH2 polarization and induction, a hallmark of asthma pathogenesis as shown by co-culturing experiments where IRAKM KO and Pin1 KO derived BMDCs induce less TH2 polarization of naïve CD4+ cells, which could be account for the lack of IL-33 based asthma induction in these mice. Therefore, our results identify a novel role of Pin1 in regulating upstream signaling pathways in asthma, but also further support potential use of Pin1 inhibitors such as longer half-life ATRA in treating asthma.
In order to demonstrate the cellular and serological role of Pin1 on systemic lupus erythematosus (SLE), phenotypes of lupus prone mouse models were identified. Deletion of Pin1 in the lupus-prone mice may result in suppression of lupus parameters, such as IFN-α, which is crucial for the development of disease in MRL/lpr mice as well as IRAK1 for Sle1 and Sle3 mice. Further procedures may include the examination of cell specific contribution of Pin1 deletion to lupus phenotype using a conditional Pin1 knock out (KO). This cell-type conditional Pin1 KO model may demonstrate the relative cell specific contribution of Pin1 to the lupus phenotype, for example in B cells, T cells or DCs.
Pin1 is an essential regulator of TLR signaling, a pathway known to play a major role in SLE. The prevention or suppression of autoimmunity with regard to Pin1 was examined in B6.MRL/lpr lupus prone mice in which Pin1 was removed. This lupus prone mouse model may be homozygous for lymphoproliferation spontaneous mutation (Faslpr) and may develop systemic autoimmunity, massive lymphadenopathy associated with proliferation of aberrant T cells, arthritis, and immune complex glomerulonephrosis, recapitulating many aspects of human SLE. Subsequently, B6.Pin1−/− mice were crossed with lupus-prone mice (B6.lpr, B6.Sle1 and B6.Sle3). B6.lpr::Pin1−/−, B6.Sle1::Pin−/− and B6.Sle3::Pin1−/− mice, along with control mice, were followed between 9 and 20 months. The effects of Pin1 deficiency on the lupus-related phenotypes, including fur loss (butterfly rash area), skin inflammation, and lymphoid hyperplasia, in these mice were evaluated and compared with Pin1 WT controls (
In further studies, ATRA was shown to potently suppress the expression of autoimmunity in MRL/lpr lupus prone mice. To test the effects of inhibiting Pin1 on lupus-related phenotypes in a mouse models, ATRA was used to treat six pairs of MRL/lpr mice at 8 weeks with 5 mg ATRA or a placebo for 8 weeks to examine whether ATRA would prevent the development of lupus-related phenotypes in this mouse model, which usually occur at 12 weeks. It was strikingly observed that ATRA drastically suppressed visual lupus-related phenotypes in all six treated mice, including fur loss (butterfly rash area), skin inflammation, and lymphoid hyperplasia, as compared with placebo-treated controls (
Additional in vivo studies as well as other studies involving models including in vitro and human models may provide further insight into the efficacy of ATRA and ATRA-related compounds in the treatment of SLE.
Dopamine receptor and group I mGluR signaling may be cofunctional, and MAP Kinase phosphorylates mGluR5(S1126) within the sequence that is bound by Homer (TPPSPF). D1 dopamine receptors activate MAP Kinase, and phosphorylation of mGluR5(S1126) increasing Homer binding avidity and influences mGluR signaling. In addition, phosphorylation of mGluR5(S1126) also creates a binding site for the prolyl isomerase Pin1, where Pin1 accelerates rotation of the phosphorylated S/T-P bond in target proteins, and acts as a molecular switch. It is believed that Pin1 may be co-functional with Homer in controlling mGluR1/5 signaling.
It has been demonstrated (Park et al., 2013) that Pin1 catalyzes isomerization of phosphorylated mGluR5 at the pS1126-P site and consequently enhances mGluR5-dependent gating of NMDA receptor channels. The immediate early gene (IEG) Homer1a, induced in response to neuronal activity, plays an essential role by interrupting Homer cross-linking and therefore facilitating Pin1 catalysis. Mutant mice that constrain Pin1-dependent mGluR5 signaling fail to exhibit normal motor sensitization, implicating this mechanism in cocaine-induced behavioral adaptation. Subsequently, in vivo studies confirmed that Pin1 co-immunoprecipitates with mGluR5 from mouse brain. Consistent with the notion that cross-linking Homer proteins compete with Pin1 for mGluR5 binding, Pin1 co-immunoprecipitation with mGluR5 increased in brains of mice lacking Homer (Homer1−/−Homer2−/−Homer3−/−, Homer triple knockout, HTKO), and increased in parallel with mGluR5(S1126) phosphorylation induced by acute administration of cocaine. An increase of Pin1 binding in WT mice was not detected. This could challenge the notion that Pin1 is a natural signaling partner of mGluR5(S1126), but since Homer1a protein levels in vivo are many fold less than constitutively expressed Homer proteins, the possibility that effects of Homer1a may be restricted to a minority of mGluR5(S1126) that are not easily detected in biochemical assays was considered. Overall, the data indicate that the IEG isoform Homer1a facilitates the binding of Pin1 to mGluR5 that has been phosphorylated in response to cocaine and/or dopamine receptor stimulation (Park et al., 2013). Accordingly, administration to a subject affected by cocaine addition of a Pin1 inhibitor such as an ATRA-related compound may be efficacious in the treatment of the addiction condition.
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each independent publication or patent application was specifically and individually indicated to be incorporated by reference.
While the invention has been described in connection with specific embodiments thereof, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure that come within known or customary practice within the art to which the invention pertains and may be applied to the essential features hereinbefore set forth, and follows in the scope of the claims.
Other embodiments are within the claims.
This invention was made with government support under grant numbers NIH CA122434, NIH CA167677, NIH AG039405, NIH R03DA031663, and NIH R01HL111430. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US15/21522 | 3/19/2015 | WO | 00 |
| Number | Date | Country | |
|---|---|---|---|
| 61968862 | Mar 2014 | US | |
| 62177419 | Mar 2015 | US |
