Identifying a Small Molecule Blocking Antigen Presentation in Autoimmune Thyroiditis

We previously showed that an HLA-DR variant containing arginine at position 74 of the DRβ1 chain (DRβ1-Arg74) is the specific HLA class II variant conferring risk for autoimmune thyroid diseases (AITD). We also identified 5 thyroglobulin (Tg) peptides that bound to DRβ1-Arg74. We hypothesized that blocking the binding of these peptides to DRβ1-Arg74 could block the continuous T-cell activation in thyroiditis needed to maintain the autoimmune response to the thyroid. The aim of the current study was to identify small molecules that can block T-cell activation by Tg peptides presented within DRβ1-Arg74 pockets. We screened a large and diverse library of compounds and identified one compound, cepharanthine that was able to block peptide binding to DRβ1-Arg74. We then showed that Tg.2098 is the dominant peptide when inducing experimental autoimmune thyroiditis (EAT) in NOD mice expressing human DRβ1-Arg74. Furthermore, cepharanthine blocked T-cell activation by thyroglobulin peptides, in particular Tg.2098 in mice that were induced with EAT. For the first time we identified a small molecule that can block Tg peptide binding and presentation to T-cells in autoimmune thyroiditis. If confirmed cepharanthine could potentially have a role in treating human AITD.

Abstract B124: Drugging the undruggable: development of small molecule activators of protein phosphatase 2A for cancer treatment

KRAS is the most common recurrent oncogenomic mutations driving the growth of NSCLC. Patients with KRAS mutations respond poorly to current therapies. Thus, novel therapies, are critically needed, to improve the lives of patients suffering from KRAS driven lung cancers. While oncogenic kinases have proven to be successful targets for cancer treatment, the therapeutic targeting of phosphatases, the key negative regulators of these same pathways, has remained largely unexplored. Through reverse engineering of tricyclic neuroleptic drugs, we developed a first-in-class series of small molecule activators of PP2A activators (SMAPs) molecules, as represented that have favorable pharmaceutic properties directly bind and activate the serine/threonine phosphatase 2A (PP2A). A critical role for PP2A as a tumor suppressor has previously been established, and PP2A inactivation is common feature in human lung cancers. Furthermore, protein phosphatase 2A (PP2A) accounts for the majority of cellular serine/threonine phosphatase activity, and its dominant and best-defined targets are oncogenic protein kinases including ERK and AKT. In this study, we sought to determine both the association of PP2A inactivation in lung cancer with specific molecular genotypes and the biological and functional consequences of PP2A reactivation in lung cancer. To understand the effects of SMAPs on cell viability and survival, we used MTT and colony formation assays in lung cancer cell lines. Apoptosis was evaluated through annexin V staining and cell cycle profile analysis. Additionally, global phosphoproteomic profiling was performed. Effects of SMAPs in vivo were assessed using A549, HH41 and H358 xenograft and Kras LA2 transgenic mouse models. Treatment of lung cancer cell lines with TRC resulted in decreased cell viability, decreased colony formation, and an increase in apoptosis. Global phosphoproteomic analysis of SMAP treated cell lines revealed ERK signaling as a commonly perturbed pathway which was confirmed by western blotting. Single agent SMAP treatment of KRAS GEMM and xenograft mouse models of lung cancer resulted in tumor stasis, induction of tumor cell apoptosis and cell cycle arrest to comparable levels seen with a combination of AKT and MEK inhibitors. Furthermore, combination based therapy with kinase inhibitors and our novel phosphatase activators resulting in marked synergy and tumor regressions in vivo. Importantly, these compounds demonstrate favorable pharmacokinetics and show no overt toxicity both alone or in combination. Taken together, these findings point to therapeutic activation of PP2A as a novel strategy for the treatment of advanced KRAS-mutant NSCLC. While research and clinical effort has largely focused on development of inhibitors of oncogenic kinases, the identification of small molecule activators of tumor suppressor proteins has remained elusive. Activation of such proteins could offer the opportunity to identify novel synergistic strategies for the treatment of a number of cancer types. Nevertheless, translation of a PP2A activation strategy into clinical medicine has required pharmaceutically tractable agents for development. Our studies represent a first step into that new territory and highlight the potential for the development of small molecule activators of other protein phosphatases and tumor suppressor proteins

Citation Format: Jaya Sangodkar, Daniel McQuaid, Janna Kisselar, David Brautigan, Mark Chance, Michael Ohlmeyer, David Kastrinsky, Yiannis Ioannou, Goutham Narla. Drugging the undruggable: development of small molecule activators of protein phosphatase 2A for cancer treatment. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B124.

Abstract C132: Therapeutic reactivation of PP2A for prostate cancer treatment

Several new therapies have recently been approved for patients with castration-resistant prostate cancer (CRPC), however, none are curative and tumors ultimately develop resistance. Advances in the treatment of CRPC require novel approaches and therapies such as those outlined in this study. Most drug development efforts have focused on targeting single oncogenic proteins, an approach limited by the complexity of signaling networks and associated cross talk. Targeting phosphatases, the key negative regulators of signaling proteins, on the other hand, may overcome some of these limitations, particularly if these negative regulators themselves are altered.Through reverse engineering of tricyclic neuroleptic drugs, we have developed a series of small molecule activators of the serine/threonine phosphatase 2A (PP2A), a key negative regulator of numerous oncogenic signaling pathways. PP2A acts as a tumor suppressor and dephosphorylates several critical nodes in prostate cancer pathogenesis including the androgen receptor (AR). Decreased PP2A expression and/or activity have been correlated with castration-resistance in cell culture and human prostate cancer studies. These small molecule activators of PP2A (SMAPs), as represented by TRC-794, TRC-1154, and DT-061, directly bind and activate PP2A and have favorable pharmaceutical properties. In this study we sought to determine the activity of SMAPs in clinically relevant preclinical models of prostate cancer.

Treatment of prostate cancer cell lines with SMAPs resulted in decreased cell viability and colony formation, cell cycle arrest, and an increase in apoptosis. Global Phosphoproteomic analysis of TRC-794 treated prostate cancer cells revealed that the AR and MYC were significantly perturbed in drug treated cells compared to controls which was subsequently confirmed by western blotting. Western blot analysis of prostate cancer cells demonstrated dose-dependent degradation of the AR resulting in PSA reduction and changes in canonical AR target gene expression. In order to investigate whether PP2A was mediating SMAP induced AR degradation, LNCAP cells were stably transduced with the SV40 small t antigen (ST), a potent oncoprotein that perturbs PP2A function. SMAPs were unable to degrade AR in LNCAP cells transduced with ST, suggesting that PP2A mediates SMAP induced AR degradation.

SMAPs were evaluated in vivo in xenograft models representing prostate cancers that are sensitive to conventional therapy and resistant to enzalutamide, the current gold standard, due to overexpression of the AR or expression of androgen receptor splice variants (AR-SV). Single agent treatment with DT-1154 or DT-061 in vivo resulted in either significant tumor growth inhibition or tumor regression and induction of tumor cell apoptosis comparable to enzalutamide. Western blot analysis of the tumors demonstrated that the effects on tumor volume correlated strongly with target engagement as evidenced by significant decreases in PSA and AR expression in vivo. Additionally, these compounds demonstrated favorable pharmacokinetics and showed no overt toxicity. Combined these data highlight the potential for PP2A activation for both the treatment of CRPC and potentially for diverse PP2A inactivated tumor types and diseases.

Citation Format: Kim McClinch, Rita Avelar, David Callejas, David Kastrinsky, Michael Ohlmeyer, Stephen Plymate, Matthew Galsky, Goutham Narla. Therapeutic reactivation of PP2A for prostate cancer treatment. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C132.

Reengineered tricyclic anti-cancer agents

The phenothiazine and dibenzazepine tricyclics are potent neurotropic drugs with a documented but underutilized anti-cancer side effect. Reengineering these agents (TFP, CPZ, CIP) by replacing the basic amine with a neutral polar functional group (e.g., RTC-1, RTC-2) abrogated their CNS effects as demonstrated by in vitro pharmacological assays and in vivo behavioral models. Further optimization generated several phenothiazines and dibenzazepines with improved anti-cancer potency, exemplified by RTC-5. This new lead demonstrated efficacy against a xenograft model of an EGFR driven cancer without the neurotropic effects exhibited by the parent molecules. Its effects were attributed to concomitant negative regulation of PI3K-AKT and RAS-ERK signaling.

Abstract SY38-03: Targeting post-translational activation of MYC for the treatment of cancer

The MYC oncoprotein is considered to be one of the most important targets in cancer; however, successful targeting of MYC has not been achieved to date. MYC is a transcription factor, which binds to DNA in target genes as a heterodimer with its partner protein, MAX. While MAX is constitutively expressed, MYC protein expression is tightly regulated at multiple levels, including gene transcription, mRNA stability, protein translation, and post-translational protein stability. In cancer, MYC expression is upregulated through deregulation at many of these levels, resulting in an increase in MYC:MAX heterodimers and MYC-regulated gene expression.

MYC regulated genes are involved in nearly all cellular processes, including cell intrinsic properties such as cell cycle control, cell growth and metabolism, self-renewal, migration and invasion, as well as cell extrinsic programs including angiogenesis, stromal cell expansion, and alterations in immune cell surveillance. MYC is thus a master regulator of cellular phenotype, and its deregulation contributes to tumorigenesis through many mechanisms. Importantly, elegant studies have recently demonstrated the tractability of targeting MYC for cancer therapeutics. Specifically, loss of MYC in adult tissues caused very little toxicity and metronomic expression of a MYC dominant negative protein caused no observable toxicity, but eliminated KRAS-driven pancreatic and lung tumors.

Since targeting MYC directly has proven difficult, we are developing new strategies to target the post-translational activation of MYC. MYC is both stabilized and transcriptionally activated following cell stimulation via receptor tyrosine kinase signaling pathways leading to ERK mediated phosphorylation of Serine 62. We have demonstrated that Serine 62 phosphorylated MYC is upregulated in human cancer cells and that this facilitates its regulation of pro-oncogenic target genes by increasing its DNA binding activity and co-activator recruitment, as well as increasing its protein stability. We have identified Protein Phosphatase 2A (PP2A) as the enzyme responsible for dephosphorylating Serine 62. PP2A is a critical tumor suppressor that is known to inactivate multiple oncogenic signaling pathways, as well as cell cycle drivers and survival factors. Furthermore, inactivation of PP2A has been shown to be critical for the transformation of human cells, and PP2A activity is suppressed in most tested human tumors.

We are utilizing a recently developed small molecule, orally available, allosteric PP2A activator drug. This drug (DTx) is in clinical development by Dual Therapeutics. We have tested this drug, as well as a peptide mimetic PP2A activator, OP449, in cell lines and in mouse models of tumorigenesis. We have observed cytotoxic activity in both breast and pancreas cancer cell lines associated with dephosphorylation of MYC at Serine 62. We have also observed reduced MYC DNA target gene binding and target gene expression with PP2A activation therapy.

In order to test novel therapeutic strategies targeting MYC activity, we have developed new mouse models of Myc-driven tumorigenesis using our ROSA26-LSL-Myc mice that we generated to conditionally express transcriptionally deregulated, physiological levels of Myc in response to Cre recombinase. By crossing these mice with mice expressing other organ specific oncogenic drivers, we have developed mouse mammary tumor models representing HER2+ and Triple Negative breast cancer. We have also developed a novel mouse model of pancreatic tumorigenesis using the same strategy. All of these models appear to molecularly recapitulate the corresponding human disease, and we are using them as pre-clinical testing platforms for our PP2A activation therapy trials. So far, we have seen dramatic tumor growth inhibition and even tumor shrinkage with DTx treatment in all three of these models. This is associated with loss of Serine 62 phosphorylation in the treated tumors. Importantly, we see no signs of toxicity in vivo with this novel compound and pharmacokinetic studies look very promising for bringing this compound to the clinic.

In summary, we believe that targeting pathways that post-translationally activate MYC's oncogenic potential is a promising strategy for targeting this important oncoprotein.

Citation Format: Xiaoyan Wang, Amy Farrell, Mahnaz Janghorban, Brittany Allen-Petersen, Juan Liang, Tyler Risom, Michael Ohlmeyer, Goutham Narla, Rosalie C. Sears. Targeting post-translational activation of MYC for the treatment of cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr SY38-03. doi:10.1158/1538-7445.AM2015-SY38-03

Abstract 5329: Development of small molecule activators of protein phosphatase 2A for the treatment of lung cancer

KRAS is the most common recurrent oncogenomic mutations driving the growth of NSCLC and accounting for ∼25% of patients with advanced NSCLC. Patients with KRAS mutations respond poorly to current therapies. Thus, novel therapies, are critically needed, to improve the lives of patients suffering from KRAS driven lung cancers. While oncogenic kinases have proven to be successful targets for cancer treatment, the therapeutic targeting of phosphatases, the key negative regulators of these same pathways, has remained largely unexplored. Through reverse engineering of tricyclic neuroleptic drugs, we developed a first-in-class series of small molecule activators of PP2A activators (SMAPs) molecules, as represented by TRC-794 and TRC-1154, that have favorable pharmaceutical properties directly bind and activate the serine/threonine phosphatase 2A (PP2A). PP2A accounts for the majority of cellular serine/threonine phosphatase activity, and its dominant and best-defined targets are oncogenic protein kinases including ERK and AKT. In this study, we sought to determine both the association of PP2A inactivation in lung cancer with specific molecular genotypes and the biological and functional consequences of PP2A reactivation in lung cancer. We determined the PP2A activation status by immunohistochemistry for the Y307 PP2A residue, a well documented inactivating site on the phosphatase, in a large cohort of primary lung tumors and identified that KRAS G12C mutant tumors displayed coordinate overexpression of both pERK and PP2A Y307. Global phosphoproteomic analysis of TRC-794 treated KRAS lung cancer cell lines revealed ERK signaling as the only commonly perturbed pathway in drug treated cell lines which was confirmed by western blotting. Treatment of lung cancer cell lines with TRC resulted in decreased cell viability, decreased colony formation, and an increase in apoptosis. Given the marked dephosphorylation of ERK upon treatment of cell lines with TRC-1154, we overexpressed a constitutively active form of MEK (MEKDD) to blunt SMAP mediated ERK dephosphorylation to determine the relevance of ERK inactivation to the biological effects of SMAPs on cellular apoptosis. Overexpression of MEKDD resulted in blunting the apoptotic response to TRC-1154 treatment. Single agent TRC-794 or TRC-1154 treatment of KRAS GEMM and xenograft mouse models of lung cancer resulted in tumor stasis, induction of tumor cell apoptosis and cell cycle arrest to comparable levels seen with a combination of AKT and MEK inhibitors. Western blotting and immunohistochemical analysis of the tumors demonstrated that SMAP treatment resulted in of ERK, AKT, and PP2A-Y307 dephosphorylation in vivo. Additionally, these compounds demonstrate favorable pharmacokinetics and show no overt toxicity. Taken together, these findings point to therapeutic activation of PP2A as a novel strategy for the treatment of advanced KRAS-mutant NSCLC.

Citation Format: Jaya Sangodkar, Sudeh Izadmehr, Sahar Mahzar, Divya Hoon, Shen Yao, David Kastrinsky, Daniela Schlatzer, Neelesh Sharma, Alain C. Borczuk, Michael Ohlmeyer, Yiannis Ioannou, Goutham Narla. Development of small molecule activators of protein phosphatase 2A for the treatment of lung cancer. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5329. doi:10.1158/1538-7445.AM2015-5329

New small molecule agonists to the thyrotropin receptor

BACKGROUND

Novel small molecular ligands (SMLs) to the thyrotropin receptor (TSHR) have potential as improved molecular probes and as therapeutic agents for the treatment of thyroid dysfunction and thyroid cancer.

METHODS

To identify novel SMLs to the TSHR, we developed a transcription-based luciferase-cAMP high-throughput screening system and we screened 48,224 compounds from a 100K library in duplicate.

RESULTS

We obtained 62 hits using the cut-off criteria of the mean±three standard deviations above the baseline. Twenty molecules with the greatest activity were rescreened against the parent CHO-luciferase cell for nonspecific activation, and we selected two molecules (MS437 and MS438) with the highest potency for further study. These lead molecules demonstrated no detectible cross-reactivity with homologous receptors when tested against luteinizing hormone (LH)/human chorionic gonadotropin receptor and follicle stimulating hormone receptor-expressing cells. Molecule MS437 had a TSHR-stimulating potency with an EC50 of 13×10(-8) M, and molecule MS438 had an EC50 of 5.3×10(-8) M. The ability of these small molecule agonists to bind to the transmembrane domain of the receptor and initiate signal transduction was suggested by their activation of a chimeric receptor consisting of an LHR ectodomain and a TSHR transmembrane. Molecular modeling demonstrated that these molecules bound to residues S505 and E506 for MS438 and T501 for MS437 in the intrahelical region of transmembrane helix 3. We also examined the G protein activating ability of these molecules using CHO cells co-expressing TSHRs transfected with luciferase reporter vectors in order to measure Gsα, Gβγ, Gαq, and Gα12 activation quantitatively. The MS437 and MS438 molecules showed potent activation of Gsα, Gαq, and Gα12 similar to TSH, but neither the small molecule agonists nor TSH showed activation of the Gβγ pathway. The small molecules MS437 and MS438 also showed upregulation of thyroglobulin (Tg), sodium iodine symporter (NIS), and TSHR gene expression.

CONCLUSIONS

Pharmacokinetic analysis of MS437 and MS438 indicated their pharmacotherapeutic potential, and their intraperitoneal administration to normal female mice resulted in significantly increased serum thyroxine levels, which could be maintained by repeated treatments. These molecules can therefore serve as lead molecules for further development of powerful TSH agonists.

Abstract A38: Therapeutic targeting of oncogenic KRAS signaling using a novel small molecule agonist of the PP2A tumor suppressor gene

Metastatic non-small cell lung cancer (NSCLC) is the most common cause of cancer death. Cytotoxic chemotherapy has historically been the mainstay of therapy but is associated with only modest improvements in patient survival. Over the past decade, a better understanding of the pathogenesis of NSCLC, coupled with high throughput genomic technologies applied to patient tumor samples, has led to a molecular classification of NSCLC and a new generation of “precision” therapies. However, the most common recurrent oncogenomic mutation driving the growth of NSCLC, mutant KRAS, accounting for ∼25% of patients with advanced NSCLC, remains without an effective targeted therapy. Mutations in KRAS lead to downstream signaling through ERK, as well as cross talk with the PI3K-Akt pathway, the latter of which is amplified in the presence of inhibition of ERK pathway signaling alone. These findings likely explain, at least in part, why targeting ERK pathway signaling alone in NSCLC has been largely unsuccessful in the clinic, and suggest that coordinate inhibition of both ERK and Akt is necessary for optimal therapy. Approaches to inhibit both of these pathways simultaneously with co-administration of two small molecular kinase inhibitors has shown some promise, but has been limited by both “off-target” treatment-limiting side effects and suboptimal coordinate inhibition of both Akt and ERK signaling. Thus, novel therapies, are critically needed, to improve the lives of patients suffering from KRAS driven lung cancers and while oncogenic kinases have proven to be successful targets for cancer treatment, the therapeutic targeting of phosphatases, the key negative regulators of these same pathways, has remained largely unexplored. Starting with the observation that tricyclic neuroleptic drugs exert anticancer effects in xenograft models, we employed combinatorial chemistry to reverse engineer these drugs into a series of novel compounds that retain the anti-proliferative effects but are devoid of the dose-limiting effects on the central nervous system. We have demonstrated these agents exert potent anti-proliferative effects in both cell culture and in vivo lung cancer models and these effects are functionally linked with simultaneous inhibition of both PI3K-Akt and MAPK signaling. Importantly, these agents that have favorable pharmaceutic properties directly bind and activate the serine/threonine phosphatase 2A (PP2A) and we call these novel first-in-class agents Small Molecule Activators of PP2A (SMAPs). A critical role for PP2A as a tumor suppressor has previously been established, and inhibition and loss-of-function changes in PP2A occur in human lung cancers. Furthermore, protein phosphatase 2A (PP2A) accounts for the majority of cellular serine/threonine phosphatase activity, and its dominant and best defined targets are protein kinases and oncogenic proteins including ERK and AKT. Here we demonstrate for the first time the development and validation of a first-in-class orally bioavailable pharmacological agent that can directly bind and activate PP2A driving coordinate inhibition of both the MAPK and AKT effector pathways in cell culture and both xenograft and genetically engineered mouse models (GEMM) of human lung cancer. Global phosphoproteomic analysis of SMAP treated KRAS lung cancer cell lines reveals ERK signaling as the only commonly perturbed pathway in drug treated cell lines. Single agent SMAP treatment of KRAS GEMM and xenograft mouse models of lung cancer resulted in tumor stasis, induction of tumor cell apoptosis and cell cycle arrest to comparable levels seen with a combination of AKT and MEK inhibitors. Additionally, the compounds demonstrate favorable pharmacokinetics and show no overt toxicity. Taken together, these findings point to therapeutic activation of PP2A as a novel strategy for the treatment of advanced KRAS-mutant NSCLC. While research and clinical effort has largely focused on development of inhibitors of oncogenic kinases, the identification of small molecule activators of tumor suppressor proteins has remained elusive. Activation of such proteins could offer the opportunity to identify novel synergistic strategies for the treatment of a number of cancer types. Nevertheless, translation of a PP2A activation strategy into clinical medicine has required pharmaceutically tractable agents for development. Our studies represent a first step into that new territory and highlight the potential for the development of small molecule activators of other protein phosphatases and tumor suppressor proteins.

Citation Format: Jaya Sangodkar, Sahar Mazhar, Danica Wiredja, Giridharan Gokulrangan, Daniela Schlatzer, David Kastrinsky, Analisa Difeo, Shen Yao, Sudeh Izadmehr, Neelesh Sharma, Yiannis Ioannou, Michael Ohlmeyer, Goutham Narla. Therapeutic targeting of oncogenic KRAS signaling using a novel small molecule agonist of the PP2A tumor suppressor gene. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr A38. doi: 10.1158/1557-3125.RASONC14-A38

Control of embryonic stem cell identity by BRD4-dependent transcriptional elongation of super-enhancer-associated pluripotency genes

Transcription factors and chromatin-remodeling complexes are key determinants of embryonic stem cell (ESC) identity. Here, we demonstrate that BRD4, a member of the bromodomain and extraterminal domain (BET) family of epigenetic readers, regulates the self-renewal ability and pluripotency of ESCs. BRD4 inhibition resulted in induction of epithelial-tomesenchymal transition (EMT) markers and commitment to the neuroectodermal lineage while reducing the ESC multidifferentiation capacity in teratoma as-says. BRD4 maintains transcription of core stem cell genes such as OCT4 and PRDM14 by occupying their super-enhancers (SEs), large clusters of regulatory elements, and recruiting to them Mediator and CDK9, the catalytic subunit of the positive transcription elongation factor b (P-TEFb), to allow Pol-II-dependent productive elongation. Our study describes a mechanism of regulation of ESC identity that could be applied to improve the efficiency of ESC differentiation.

A novel synthetic approach to 11-substituted dibenzo[b,f][1,4]oxazepines

A novel protocol for the synthesis of 11-substituted dibenzo[b,f][1,4]oxazepines is reported. Seven compounds were designed as analogs of the antipsychotic drug loxapine and antidepressant amoxapine. The key transformations include generation of a carbamate intermediate using phenyl chloroformate which avoids the use of harmful phosgene, a microwave-induced transformation of the carbamate intermediate into various urea derivatives, and a subsequent phosphorous oxychloride-induced cyclocondensation. The simple reactions and wide substrate scope enhance the practical application of this methodology.

Structure-guided design of potent diazobenzene inhibitors for the BET bromodomains

BRD4, characterized by two acetyl-lysine binding bromodomains and an extra-terminal (ET) domain, is a key chromatin organizer that directs gene activation in chromatin through transcription factor recruitment, enhancer assembly, and pause release of the RNA polymerase II complex for transcription elongation. BRD4 has been recently validated as a new epigenetic drug target for cancer and inflammation. Our current knowledge of the functional differences of the two bromodomains of BRD4, however, is limited and is hindered by the lack of selective inhibitors. Here, we report our structure-guided development of diazobenzene-based small-molecule inhibitors for the BRD4 bromodomains that have over 90% sequence identity at the acetyl-lysine binding site. Our lead compound, MS436, through a set of water-mediated interactions, exhibits low nanomolar affinity (estimated Ki of 30-50 nM), with preference for the first bromodomain over the second. We demonstrated that MS436 effectively inhibits BRD4 activity in NF-κB-directed production of nitric oxide and proinflammatory cytokine interleukin-6 in murine macrophages. MS436 represents a new class of bromodomain inhibitors and will facilitate further investigation of the biological functions of the two bromodomains of BRD4 in gene expression.

BRD4 sustains melanoma proliferation and represents a new target for epigenetic therapy

Metastatic melanoma remains a mostly incurable disease. Although newly approved targeted therapies are efficacious in a subset of patients, resistance and relapse rapidly ensue. Alternative therapeutic strategies to manipulate epigenetic regulators and disrupt the transcriptional program that maintains tumor cell identity are emerging. Bromodomain and extraterminal domain (BET) proteins are epigenome readers known to exert key roles at the interface between chromatin remodeling and transcriptional regulation. Here, we report that BRD4, a BET family member, is significantly upregulated in primary and metastatic melanoma tissues compared with melanocytes and nevi. Treatment with BET inhibitors impaired melanoma cell proliferation in vitro and tumor growth and metastatic behavior in vivo, effects that were mostly recapitulated by individual silencing of BRD4. RNA sequencing of BET inhibitor-treated cells followed by Gene Ontology analysis showed a striking impact on transcriptional programs controlling cell growth, proliferation, cell-cycle regulation, and differentiation. In particular, we found that, rapidly after BET displacement, key cell-cycle genes (SKP2, ERK1, and c-MYC) were downregulated concomitantly with the accumulation of cyclin-dependent kinase (CDK) inhibitors (p21 and p27), followed by cell-cycle arrest. Importantly, BET inhibitor efficacy was not influenced by BRAF or NRAS mutational status, opening the possibility of using these small-molecule compounds to treat patients for whom no effective targeted therapy exists. Collectively, our study reveals a critical role for BRD4 in melanoma tumor maintenance and renders it a legitimate and novel target for epigenetic therapy directed against the core transcriptional program of melanoma.

Abstract A10: BRD4 is a new therapeutic target in melanoma

Metastatic melanoma remains a mostly incurable disease. Although newly approved targeted therapies are efficacious in a subset of patients, resistance and relapse rapidly ensue. Alternative therapeutic strategies to manipulate epigenetic regulators and disrupt the transcriptional program that maintains tumor cell identity are emerging. Bromodomain and extraterminal domain (BET) family of proteins consists of BRD2, BRD3, BRD4, and testis- specific BRDT, and are epigenome readers known to exert key roles at the interface between chromatin remodeling and transcriptional regulation. We investigated the role of BET proteins in melanoma tumor maintenance and assessed their value as therapeutic targets. Data mining of our previously published gene expression profile of melanoma cell lines and immunostaining of melanoma tissue microarray revealed that BRD4 is significantly upregulated in primary and metastatic melanoma tissues compared to melanocytes and nevi, thus suggesting a potential role for BET family proteins in promoting melanoma tumorigenesis. Treatment with BET inhibitors impaired melanoma cell proliferation and colony formation in vitro. Moreover, tumor growth and metastatic behavior assessed by a xenograft model also revealed impairment of melanoma proliferation in vivo. These effects were mostly recapitulated by individual silencing of BRD4, and not of other BET family members. RNA sequencing of BET inhibitor-treated cells followed by gene ontology analysis showed a striking impact on transcriptional programs controlling cell growth, proliferation, cell-cycle regulation and differentiation. In particular, we found that, rapidly after BET displacement, key cell cycle genes (SKP2, ERK1 and c-MYC) were downregulated concomitantly with the accumulation of CDK inhibitors (p21, p27), followed by melanoma cell cycle arrest. However, single genetic manipulation of these cell cycle genes did not rescue the cytostatic effect of BET inhibition, suggesting that BET inactivation leads to a non-redundant, simultaneous regulation of multiple cell cycle effectors. Interestingly, SKP2 and ERK1 mRNA levels directly correlated with those of BRD4 in a panel of melanoma tissues, suggesting that these two factors may be direct BRD4 targets. Importantly, the effects of the BET inhibitor were not influenced by BRAF or NRAS mutational status, opening the possibility of using these small molecule compounds to treat patients for whom no effective targeted therapy currently exists. Collectively, our results strongly support a critical role for BRD4 in melanoma tumor maintenance, and render it a legitimate and novel target for epigenetic therapy directed against the core transcriptional program of melanoma.

Citation Format: Barbara Fontanals-Cirera, Miguel F. Segura, Avital Gaziel-Sovran, Maria V. Guijarro, Doug Hanniford, Pilar Gonzalez-Gomez, Weijia Zhang, Guantao Zhang, Farbod Darvishian, Michael Ohlmeyer, Iman Osman, Ming-Ming Zhou, Eva Hernando. BRD4 is a new therapeutic target in melanoma. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr A10.

Targeting BET proteins in melanoma: A novel treatment approach

9091

Background: Manipulation of key epigenetic regulators in melanoma proliferation is emerging as a new therapeutic strategy. Bromodomain-containing proteins such as the extraterminal domain (BET) family are components of transcription factor complexes and determinants of epigenetic memory. We investigated the expression of BRD4, a BET family member in melanoma cell lines and tissues, and the effects of its inhibition with the small molecule compounds MS436 and MS417 in in vitro and in vivo models of melanoma. Methods: BRD2 and BRD4 expression were analyzed by immunohistochemistry. We tested the effects of pharmacological or RNAi-mediated inhibition of BRD4 in melanoma cells using crystal violet-based assays for proliferation/colony formation and flow-cytometry for cell cycle analysis. The molecular effects of BRD4 suppression were examined using RNA sequencing, Real-Time quantitative PCR and western blots for p27, p21, MYC, ERK1 and SKP2. In the in vivo xenograft experiments NOD/SCID/IL2γR-/-mice were injected with melanoma cells and treated with MS417. Statistical significance was determined by unpaired t-test (GraphPad). Results: BRD4 was found significantly upregulated in primary and metastatic melanoma tissues compared to melanocytes and nevi (p<0.001). Treatment with BET inhibitors impaired melanoma cell proliferation in vitro and tumor growth and metastatic behavior in vivo, effects that were mostly recapitulated by individual silencing of BRD4. Rapidly after BET displacement, key cell cycle genes (SKP2, ERK1 and c-MYC) were downregulated concomitantly with the accumulation of CDK inhibitors (p21, p27), followed by melanoma cell cycle arrest. BET inhibitor efficacy was not influenced by BRAF or NRAS mutational status. Conclusions: Our results demonstrate for the first time a role for BRD4 in melanoma maintenance and support the role of BET proteins as novel targets in melanoma. Further investigation in the clinical setting is warranted.

Identification of a novel binding site between HIV type 1 Nef C-terminal flexible loop and AP2 required for Nef-mediated CD4 downregulation

HIV-1 Nef is an accessory protein necessary for HIV-1 virulence and rapid AIDS development. Nef promotes viral replication and infection by connecting CD4 and several other cell surface receptors to the clathrin adaptor protein AP2, resulting in the internalization and degradation of the receptors interacting with Nef. We investigated how Nef can mediate constitutive receptor endocytosis through the interaction of the dileucine motif in its C-terminal flexible loop (C-loop) with AP2, whereas AP2 binding of the transmembrane receptors usually results in an equilibrated (recycled) endocytosis. Our results indicated that in addition to the dileucine motif, there is a second motif in the Nef C-loop involved in the Nef-AP2 interaction. Nef-mediated CD4 downregulation was impaired when the residue in the hydrophobic region in the Nef C-loop (LL165HPMSLHGM173) was mutated to a basic residue K/R or an acidic residue E/D or to the rigid residue P, or when M168L170, L170H171, or G172M173 was mutated to AA. A pull-down assay indicated that AP2 was not coprecipitated with Nef mutants that did not downregulate CD4. Molecular modeling of the Nef C-terminal flexible loop in complex with AP2 suggests that M168L170 occupies a pocket in the AP2 σ2 subunit. Our data suggest a new model in the Nef-AP2 interaction in which the hydrophobic region in the Nef C-loop with the dileucine (L164L165) motif and M168L170 motif binds to AP2(σ2), while the acidic motif E174 and D175 binds to AP2(α), which explains how Nef through the flexible loop connects CD4 to AP2 for constitutive CD4 downregulation.

γ-H2AX kinetics as a novel approach to high content screening for small molecule radiosensitizers

BACKGROUND

Persistence of γ-H2AX after ionizing radiation (IR) or drug therapy is a robust reporter of unrepaired DNA double strand breaks in treated cells.

METHODS

DU-145 prostate cancer cells were treated with a chemical library ±IR and assayed for persistence of γ-H2AX using an automated 96-well immunocytochemistry assay at 4 hours after treatment. Hits that resulted in persistence of γ-H2AX foci were tested for effects on cell survival. The molecular targets of hits were validated by molecular, genetic and biochemical assays and in vivo activity was tested in a validated Drosophila cancer model.

RESULTS

We identified 2 compounds, MS0019266 and MS0017509, which markedly increased persistence of γ-H2AX, apoptosis and radiosensitization in DU-145 cells. Chemical evaluation demonstrated that both compounds exhibited structurally similar and biochemical assays confirmed that these compounds inhibit ribonucleotide reductase. DNA microarray analysis and immunoblotting demonstrates that MS0019266 significantly decreased polo-like kinase 1 gene and protein expression. MS0019266 demonstrated in vivo antitumor activity without significant whole organism toxicity.

CONCLUSIONS

MS0019266 and MS0017509 are promising compounds that may be candidates for further development as radiosensitizing compounds as inhibitors of ribonucleotide reductase.

Targeting the FOXO1/KLF6 axis regulates EGFR signaling and treatment response

EGFR activation is both a key molecular driver of disease progression and the target of a broad class of molecular agents designed to treat advanced cancer. Nevertheless, resistance develops through several mechanisms, including activation of AKT signaling. Though much is known about the specific molecular lesions conferring resistance to anti-EGFR-based therapies, additional molecular characterization of the downstream mediators of EGFR signaling may lead to the development of new classes of targeted molecular therapies to treat resistant disease. We identified a transcriptional network involving the tumor suppressors Krüppel-like factor 6 (KLF6) and forkhead box O1 (FOXO1) that negatively regulates activated EGFR signaling in both cell culture and in vivo models. Furthermore, the use of the FDA-approved drug trifluoperazine hydrochloride (TFP), which has been shown to inhibit FOXO1 nuclear export, restored sensitivity to AKT-driven erlotinib resistance through modulation of the KLF6/FOXO1 signaling cascade in both cell culture and xenograft models of lung adenocarcinoma. Combined, these findings define a novel transcriptional network regulating oncogenic EGFR signaling and identify a class of FDA-approved drugs as capable of restoring chemosensitivity to anti-EGFR-based therapy for the treatment of metastatic lung adenocarcinoma.

Down-regulation of NF-κB transcriptional activity in HIV-associated kidney disease by BRD4 inhibition

NF-κB-mediated inflammation is the major pathology in chronic kidney diseases, including HIV-associated nephropathy (HIVAN) that ultimately progresses to end stage renal disease. HIV infection in the kidney induces NF-κB activation, leading to the production of proinflammatory chemokines, cytokines, and adhesion molecules. In this study, we explored selective inhibition of NF-κB transcriptional activity by small molecule blocking NF-κB binding to the transcriptional cofactor BRD4, which is required for the assembly of the productive transcriptional complex comprising positive transcription elongation factor b and RNA polymerase II. We showed that our BET (Bromodomain and Extra-Terminal domain)-specific bromodomain inhibitor MS417, designed to block BRD4 binding to the acetylated NF-κB, effectively attenuates NF-κB transcriptional activation of proinflammatory genes in kidney cells treated with TNFα or infected by HIV. MS417 ameliorates inflammation and kidney injury in HIV-1 transgenic mice, an animal model for HIVAN. Our study suggests that BET bromodomain inhibition, targeting at the proinflammatory activity of NF-κB, represents a new therapeutic approach for treating NF-κB-mediated inflammation and kidney injury in HIVAN.

Abstract 1885: Targeting the FOXO1/KLF6 transcriptional network to modulate response to anti-EGFR based therapy

Epidermal growth factor receptor (EGFR) activation is both a key molecular driver of disease progression and the target of a broad class of molecular agents designed to treat advanced cancer. Nevertheless, resistance develops through several mechanisms including constitutive activation of AKT signaling. Additional molecular characterization of the downstream mediators of EGFR signaling may lead to the development of new classes of targeted molecular therapies to treat resistant disease. Here we identify a transcriptional network involving the KLF6 and FOXO1 tumor suppressor genes that negatively regulate activated EGFR signaling and that can be reactivated using the combination of two FDA approved agents in both cell culture and in vivo models of the disease. In both murine models and patient derived lung adenocarcinoma samples, EGFR activation is associated with FOXO1 mislocalization and decreased KLF6 expression. Furthermore, in a Kras driven mouse model, KLF6 expression is not significantly changed whereas AKT activation seen in the Pten/Mmac1+/− heterozygous mouse model results in FOXO1 mislocalization and decreased KLF6 expression. Consistent with these findings, inhibition of AKT signaling promotes increase in nuclear FOXO1 resulting in transactivation of the KLF6 tumor suppressor gene in lung adenocarcinoma cell lines. Correspondingly, the EGFRL858R mouse model demonstrates spontaneous tumor regression when treated with the anti-EGFR based therapy, erlotinib, an FDA-approved small-molecule inhibitor of EGFR signaling. We analyzed L858R mouse tumors samples treated with erlotinib and found increased KLF6 expression following EGFR inhibition. Conversely, targeted reduction of KLF6 resulted in decreased erlotinib response in both cell culture and in vivo models of disease suggesting a direct link between KLF6 upregulation and the induction of apoptosis by anti-EGFR based therapy. Therefore, we hypothesized that acquired resistance to anti-EGFR based therapies could be overcome by restoring downstream function of the FOXO1/KLF6 transcriptional network. Here we demonstrate that an FDA-approved drug, trifluoperazine hydrochloride (TFP), which has been shown to inhibit FOXO1 nuclear export, restores sensitivity to AKT-driven erlotinib-resistance through modulation of the KLF6/FOXO1 signaling cascade in both cell culture and xenograft models. Furthermore, silencing of FOXO1 blunts apoptosis mediated through combination erlotinib and TFP treatment suggesting that this transcriptional network is important for negatively regulating AKT signaling. Combined, these studies define a novel transcriptional network regulating oncogenic EGFR signaling and identify a class of FDA-approved drugs with the potential for rapid clinical translation to restore chemosensitivity to anti-EGFR-based therapy for the treatment of metastatic lung adenocarcinoma.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1885. doi:1538-7445.AM2012-1885

Abstract A218: Simultaneous inhibition of both the PI3K-AKT and MAPK-ERK pathways using a single small molecule based approach for the treatment of advanced cancer

Background: Activation of the PI3K-AKT and MAPK-ERK signaling pathways drives a significant percentage of human cancer and serve as the target for multiple drug development efforts and clinical trials. Due to defined molecular crosstalk, dual inhibition of both pathways is necessary for optimal therapeutic efficacy, and therefore, combinations of PI3K-AKT and MAPK-ERK specific drug therapies are being evaluated. In this study, we have identified compounds that are capable of simultaneously inhibiting both the PI3K-AKT and MAPK-ERK pathway to induce apoptosis both in vitro and in mouse models of the disease. Moreover, we have performed additional derivatization of these small molecules to limit their toxicity and significantly improve their therapeutic window in cell culture and in vivo.

Methods: Our new series of molecules are derived from the phenothiazine, exemplified by trifluoperazine(TFP), and dibenzazepine structural backbones, exemplified by clomipramine(CIP). While the antiproliferative properties of neuroleptic tricyclics have been identified, previous clinical trials failed due to dose limiting CNS toxicities related to their potent antidopaminergic properties. We rendered the pendant amine non-basic to attempt to abolish the antidopaminergic effects of this class of drugs. We screened 100 of these novel compounds in the PTEN-null, EGFR-activated H1650 cell line. Subsequently, we determined the effect of two candidate molecules on the PI3K-AKT and MAPK-ERK pathways and their ability to induce apoptosis in vitro and in vivo.

Results: Through multiple rounds of SAR (structure activity relationship) analysis, we sequentially derivatized the parent compounds and identified two potent small molecule candidates that efficiently decouple the dose limiting CNS toxicity from the anti-proliferative and anti-tumorigenic properties of this class of FDA approved drugs. Treatment of a panel of lung adenocarcinoma cancer cell lines with these compounds, DBK-368 and DBK-382, led to a decrease in cell viability through the induction of spontaneous apoptosis. These compounds specifically induce caspase-dependent apoptosis as indicated by ZVAD-mediated inhibition of Annexin V staining. Upon mechanistic analysis, DBK-368 and DBK-382 display the ability to directly inhibit AKT and ERK downstream of PI3K and MEK, efficiently and potently decoupling the crosstalk between these two signaling pathways. Furthermore, in a transgenic inducible EGFR-activated mouse model of lung adenocarcinoma, we demonstrated that the novel derivative compounds inhibit AKT and ERK signaling and induce apoptosis in vivo. Lastly, in vivo toxicology studies demonstrated that while TFP exhibited dose limiting CNS toxicities at 15 mg/kg, DBK-368 and DBK-382 displayed no significant effects up to 60 mg/kg.

Conclusions: We have identified a series of novel small molecules through a reverse engineering effort of the tricyclic class of FDA approved drugs. Specifically, DBK-368 and DBK-382 appear to be promising monotherapy for advanced cancer as they exhibit dual functionality in the inhibiting both the PI3K-AKT and MAPK-ERK pathways simultaneously, both in vitro and in vivo.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A218.

Integration of small-molecule discovery in academic biomedical research

Rapid advances in biomedical sciences in recent years have drastically accelerated the discovery of the molecular basis of human diseases. The great challenge is how to translate the newly acquired knowledge into new medicine for disease prevention and treatment. Drug discovery is a long and expensive process, and the pharmaceutical industry has not been very successful at it, despite its enormous resources and spending on the process. It is increasingly realized that academic biomedical research institutions ought to be engaged in early-stage drug discovery, especially when it can be coupled to their basic research. To leverage the productivity of new-drug development, a substantial acceleration in validation of new therapeutic targets is required, which would require small molecules that can precisely control target functions in complex biological systems in a temporal and dose-dependent manner. In this review, we describe a process of integration of small-molecule discovery and chemistry in academic biomedical research that will ideally bring together the elements of innovative approaches to new molecular targets, existing basic and clinical research, screening infrastructure, and synthetic and medicinal chemistry to follow up on small-molecule hits. Such integration of multidisciplinary resources and expertise will enable academic investigators to discover novel small molecules that are expected to facilitate their efforts in both mechanistic research and new-drug target validation. More broadly academic drug discovery should contribute new entities to therapy for intractable human diseases, especially for orphan diseases, and hopefully stimulate and synergize with the commercial sector.