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1.  PDK1 and SGK3 contribute to the growth of BRAF mutant melanomas and are potential therapeutic targets 
Cancer research  2015;75(7):1399-1412.
Melanoma development involves members of the AGC kinase family including AKT, PKC and, most recently, PDK1, as elucidated recently in studies of Braf::Pten mutant melanomas. Here we report that PDK1 contributes functionally to skin pigmentation and to the development of melanomas harboring a wild-type PTEN genotype, which occurs in ~70% of human melanomas. The PDK1 substrate SGK3 was determined to be is an important mediator of PDK1 activities in melanoma cells. Genetic or pharmacological inhibition of PDK1 and SGK3 attenuated melanoma growth by inducing G1 phase cell cycle arrest. In a synthetic lethal screen, pan-PI3K inhibition synergized with PDK1 inhibition to suppress melanoma growth, suggesting that focused blockade of PDK1/PI3K signaling might offer a new therapeutic modality for wild-type PTEN tumors. We also noted that responsiveness to PDK1 inhibition associated with decreased expression of pigmentation genes and increased expression of cytokines and inflammatory genes, suggesting a method to stratify melanoma patients for PDK1-based therapies. Overall, our work highlights the potential significance of PDK1 as a therapeutic target to improve melanoma treatment.
PMCID: PMC4383687  PMID: 25712345
PDK1; SGK; BRAF; PTEN; melanoma; Cyclin D1; MITF
2.  High-throughput screening by Nuclear Magnetic Resonance (HTS by NMR) for the identification of PPIs antagonists 
Current topics in medicinal chemistry  2015;15(20):2032-2042.
In recent years the ever so complex field of drug discovery has embraced novel design strategies based on biophysical fragment screening (fragment-based drug design; FBDD) using nuclear magnetic resonance spectroscopy (NMR) and/or structure-guided approaches, most often using X-ray crystallography and computer modeling. Experience from recent years unveiled that these methods are more effective and less prone to artifacts compared to biochemical high-throughput screening (HTS) of large collection of compounds in designing protein inhibitors. Hence these strategies are increasingly becoming the most utilized in the modern pharmaceutical industry. Nonetheless, there is still an impending need to develop innovative and effective strategies to tackle other more challenging targets such as those involving protein-protein interactions (PPIs). While HTS strategies notoriously fail to identify viable hits against such targets, few successful examples of PPIs antagonists derived by FBDD strategies exist. Recently, we reported on a new strategy that combines some of the basic principles of fragment-based screening with combinatorial chemistry and NMR-based screening. The approach, termed HTS by NMR, combines the advantages of combinatorial chemistry and NMR-based screening to rapidly and unambiguously identify bona fide inhibitors of PPIs. This review will reiterate the critical aspects of the approach with examples of possible applications.
PMCID: PMC4545611  PMID: 25986689
Drug discovery; fragment-based drug design; FBDD; FBLD; HTS by NMR; NMR; PPIs; protein-protein interactions; positional scanning; POS
3.  Genetic inactivation or pharmacological inhibition of Pdk1 delays development and inhibits metastasis of BrafV600E::Pten−/− melanoma 
Oncogene  2013;33(34):4330-4339.
Phosphoinositide-dependent kinase-1 (PDK-1) is a serine/threonine protein kinase that phosphorylates members of the conserved AGC kinase superfamily, including AKT and PKC, and is implicated in important cellular processes including survival, metabolism and tumorigenesis. In large cohorts of nevi and melanoma samples, PDK1 expression was significantly higher in primary melanoma, compared with nevi, and was further increased in metastatic melanoma. PDK1 expression suffices for its activity, due to auto-activation, or elevated phosphorylation by phosphoinositide 3'-OH-kinase (PI 3-K). Selective inactivation of Pdk1 in the melanocytes of BrafV600E::Pten−/− or BrafV600E::Cdkn2a−/−::Pten−/− mice delayed the development of pigmented lesions and melanoma induced by systemic or local administration of 4-HT. Melanoma invasion and metastasis were significantly reduced or completely prevented by Pdk1 deletion. Administration of the PDK1 inhibitor GSK2334470 (PDKi) effectively delayed melanomagenesis and metastasis in BrafV600E::Pten−/− mice. Pdk1−/− melanomas exhibit a marked decrease in the activity of AKT, P70S6K and PKC. Notably, PDKi was as effective in inhibiting AGC kinases and colony forming efficiency of melanoma with Pten WT genotypes. Gene expression analyses identified Pdk1-dependent changes in FOXO3a-regulated genes and inhibition of FOXO3a restored proliferation and colony formation of Pdk1−/− melanoma cells. Our studies provide direct genetic evidence for the importance of PDK1, in part through FOXO3a-dependent pathway, in melanoma development and progression.
PMCID: PMC3955742  PMID: 24037523
PDK1; FOXO3a; melanoma; Braf; Pten; GSK2334470
4.  Synthesis and SAR studies of dual AKT/NF-κB inhibitors against melanoma 
Chemical biology & drug design  2013;82(5):520-533.
The AKT and NF-κB pathways are central regulators of cellular signaling events at the basis of tumor development and progression. Both pathways are often up-regulated in different tumor types including melanoma. We recently reported the identification of compound 1 (BI-69A11) as inhibitor of the AKT and the NF-κB pathways. Here we describe SAR studies that led to novel fluorinated derivatives with increased cellular potency, reflected in efficient inhibition of AKT and IKKs. Selected compounds demonstrated effective toxicity on melanoma, breast and prostate cell lines. Finally, a representative derivative showed promising efficacy in an in vivo melanoma xenograft model.
PMCID: PMC3966491  PMID: 23790042
5.  Structure Based Design of Covalent Siah Inhibitors 
Chemistry & biology  2013;20(8):973-982.
The E3 ubiquitin ligase Siah regulates key cellular events that are central to cancer development and progression. A promising route to Siah inhibition is disrupting its interactions with adaptor proteins. However, typical of protein-protein interactions, traditional unbiased approaches to ligand discovery did not produce viable hits against this target, despite considerable effort and a multitude of approaches. Ultimately, a rational structure-based design strategy was successful for the identification of novel Siah inhibitors in which peptide binding drives specific covalent bond formation with the target. X-ray crystallography, mass spectrometry and functional data demonstrate that these peptide-mimetics are efficient covalent inhibitors of Siah and antagonize Siah-dependent regulation of Erk and Hif signaling in cell. The strategy proposed may result useful as a general approach to the design of peptide-based inhibitors of other protein-protein interactions.
PMCID: PMC3763817  PMID: 23891150
6.  Identification of small molecules interfering with H1N1 influenza A viral replication 
ChemMedChem  2012;7(12):2227-2235.
Successful Influenza A viral replication requires both viral proteins and host cellular factors. Here we utilized a cellular assay to screen for small molecules capable of interfering with any of such necessary viral or cellular components. We employed an established reporter assay assessing influenza viral replication by monitoring the activity of co-expressed luciferase. We screened a diverse chemical compound library, resulting in the identification of compound 7, inhibiting a novel yet elusive target. Quantitative real-time PCR studies confirmed the dose dependent inhibitory activity of compound 7 in a viral replication assay. Furthermore, we showed that compound 7 was effective in rescuing high dose influenza infection in an in vivo mouse model. As oseltamivir-resistant influenza strains emerge, compound 7 could be further investigated as a possible novel scaffold for the development of anti-influenza agents acting on novel targets.
PMCID: PMC3769975  PMID: 23139022
Influenza virus; Drug discovery; Ugi reaction; tetrazole formation
7.  Inhibition of melanoma development in the Nras(Q61K)::Ink4a−/− mouse model by the small molecule BI-69A11 
Pigment cell & melanoma research  2012;26(1):136-142.
Despite advances in developing specific inhibitors to BRAF mutant melanomas, to date there are no effective therapies for tumors bearing NRAS mutations, present in approximately 15–20% of human melanomas. Here, we extend earlier studies, demonstrating that the small molecule BI-69A11 inhibits the growth of melanoma cell lines in vitro and in vivo. Gene expression microarray analysis of BI-69A11-responsive melanoma cells revealed the induction of interferon- and cell death-related genes that were associated with responsiveness to BI-69A11. Strikingly, the administration of BI-69A11 inhibited melanoma development in genetically modified mice bearing an inducible form of activated Nras and a deletion of the Ink4a gene (Nras(Q61K)::Ink4a−/−). Biweekly administration of BI-69A11 starting at 10 weeks or as late as 24 weeks after the induction of mutant Nras expression inhibited melanoma development (100% and 36%, respectively). BI-69A11 treatment did not inhibit the development of histiocytic sarcomas, which comprise about 50% of the tumors in this model. Immunofluorescent staining analyses of CD45 revealed increased levels of immune cell infiltration in BI-69A11–treated tumors. Gene expression profiling of BI-69A11-resistant Nras(Q61K)::Ink4a−/− tumors revealed the upregulation of functional gene networks associated with the cytoskeleton, DNA damage response, and small molecule transport. The ability to attenuate development of NRAS mutant melanomas by BI-69A11 even when administered at a late stage of the tumor development, support its further development and clinical assessment.
PMCID: PMC3632643  PMID: 23035722
8.  A Disalicylic Acid-Furanyl Derivative Inhibits Ephrin Binding to a Subset of Eph Receptors 
Chemical biology & drug design  2011;78(4):667-678.
Eph receptor tyrosine kinases and ephrin ligands control many physiological and pathological processes, and molecules interfering with their interaction are useful probes to elucidate their complex biological functions. Moreover, targeting Eph receptors might enable new strategies to inhibit cancer progression and pathological angiogenesis as well as promote nerve regeneration. Because our previous work suggested the importance of the salicylic acid group in antagonistic small molecules targeting Eph receptors, we screened a series of salicylic acid derivatives to identify novel Eph receptor antagonists. This identified a disalicylic acid-furanyl derivative that inhibits ephrin-A5 binding to EphA4 with an IC50 of 3 μM in ELISA assays. This compound, which appears to bind to the ephrin-binding pocket of EphA4, also targets several other Eph receptors. Furthermore, it inhibits EphA2 and EphA4 tyrosine phosphorylation in cells stimulated with ephrin while not affecting phosphorylation of EphB2, which is not a target receptor. In endothelial cells, the disalicylic acid-furanyl derivative inhibits EphA2 phosphorylation in response to TNFα and capillary-like tube formation on Matrigel, two effects that depend on EphA2 interaction with endogenous ephrin-A1. These findings suggest that salicylic acid derivatives could be used as starting points to design new small molecule antagonists of Eph receptors.
PMCID: PMC3196665  PMID: 21791013
small molecule; antagonist; dymethylpyrrole derivative; protein tyrosine kinase; angiogenesis; nerve regeneration
9.  Design and characterization of a potent and selective dual ATP- and substrate-competitive sub-nanomolar bi-dentate c-Jun N-terminal Kinase (JNK) inhibitor 
Journal of medicinal chemistry  2011;54(18):6206-6214.
c-Jun N-terminal Kinases (JNKs) represent valuable targets in the development of new therapies. Present on the surface of JNK is a binding pocket for substrates and the scaffolding protein JIP1 in close proximity to the ATP binding pocket. We propose that bi-dentate compounds linking the binding energies of weakly interacting ATP and substrate mimetics could result in potent and selective JNK inhibitors. We describe here a bi-dentate molecule, 19, designed against JNK. 19 inhibits JNK kinase activity (IC50 = 18 nM; Ki = 1.5 nM) and JNK/substrate association in a displacement assay with a substrate peptide (compound 20; IC50 = 46 nM; Ki = 2 nM). Our data demonstrate that 19 targets for the ATP and substrate-binding sites on JNK concurrently. Finally, compound 19 not only inhibits JNK in a variety of cell-based experiments, but it elicits also in vivo activity where it is shown to improve glucose tolerance in diabetic mice.
PMCID: PMC3174326  PMID: 21815634
10.  Functional Specialization in Proline Biosynthesis of Melanoma 
PLoS ONE  2012;7(9):e45190.
Proline metabolism is linked to hyperprolinemia, schizophrenia, cutis laxa, and cancer. In the latter case, tumor cells tend to rely on proline biosynthesis rather than salvage. Proline is synthesized from either glutamate or ornithine; both are converted to pyrroline-5-carboxylate (P5C), and then to proline via pyrroline-5-carboxylate reductases (PYCRs). Here, the role of three isozymic versions of PYCR was addressed in human melanoma cells by tracking the fate of 13C-labeled precursors. Based on these studies we conclude that PYCR1 and PYCR2, which are localized in the mitochondria, are primarily involved in conversion of glutamate to proline. PYCRL, localized in the cytosol, is exclusively linked to the conversion of ornithine to proline. This analysis provides the first clarification of the role of PYCRs to proline biosynthesis.
PMCID: PMC3443215  PMID: 23024808
11.  Effective inhibition of melanoma by BI-69A11 is mediated by dual targeting of the AKT and NF-κB pathways 
Pigment cell & melanoma research  2011;24(4):703-713.
In melanoma, the activation of pro-survival signaling pathways, such as the AKT and NF-κB pathways, are critical for tumor growth. We have recently reported that the AKT inhibitor BI-69A11 causes efficient inhibition of melanoma growth. Here, we show that in addition to its AKT inhibitory activity, BI-69A11 also targets the NF-κB pathway. In melanoma cell lines, BI-69A11 inhibited TNF-α-stimulated IKKα/β and IκB phosphorylation as well as NF-κB reporter gene expression. Furthermore, the effective inhibition of melanoma growth by BI-69A11 was attenuated upon NF-κB activation. Mechanistically, reduced NF-κB signaling by BI-69-A11 is mediated by the inhibition of sphingosine kinase 1, identified in a screen of 315 kinases. Significantly, we demonstrate that BI-69A11 is well-tolerated and orally active against UACC 903 and SW1 melanoma xenografts. Our results demonstrate that BI-69A11 inhibits both the AKT and NF-κB pathways and that the dual targeting of these pathways may be efficacious as a therapeutic strategy in melanoma.
Although B-RAF and MEK inhibitors have shown promise in the clinic against melanoma, the development of resistance to these singly targeted agents inevitably results. These observations underscore the plasticity of melanoma to chemotherapeutic agents and further emphasize the need to apply combinatorial targeting of signaling pathways as a strategy to maximize therapeutic response. The PI3K/AKT and NF-κB signaling pathways are altered in melanoma, presenting additional opportunities for target inhibition. Our studies demonstrate that the AKT inhibitor, BI-69A11, also inhibits the NF-κB pathway and that dual inhibition of both pathways is responsible for the anti-tumor efficacy of this molecule.
PMCID: PMC3158838  PMID: 21592316
melanoma; AKT; NF-kB; targeted therapy
12.  Design, synthesis, and structure-activity relationships of 3-ethynyl-1H-indazoles as inhibitors of Phosphatidylinositol 3-kinase signaling pathway 
Journal of medicinal chemistry  2010;53(23):8368-8375.
A new series of 3-ethynyl-1H–indazoles has been synthesized and evaluated in both biochemical and cell-based assays as potential kinase inhibitors. Interestingly, a selected group of compounds identified from this series exhibited low micromolar inhibition against critical components of the PI3K pathway, targeting PI3K, PDK1 and mTOR kinases. Combination of computational modeling and structure-activity relationships studies reveal a possible novel mode for PI3K inhibition, resulting in a PI3Kα isoform specific compound. Hence, by targeting the most oncogenic mutant isoform of PI3K, the compound displays anti-proliferative activity both in monolayer human cancer cell cultures and in three-dimensional tumor models. Because of its favorable physicochemical, in vitro ADME and drug-like properties, we propose that this novel ATP mimetic scaffold could result useful in deriving novel selecting and multi-kinase inhibitors for clinical use.
PMCID: PMC3131451  PMID: 21062009
13.  Design, Synthesis, and Structure-Activity Relationship Studies of Thiophene- 3-carboxamide Derivatives as Dual Inhibitors of the c-Jun N-Terminal Kinase 
Bioorganic & medicinal chemistry  2011;19(8):2582-2588.
We report comprehensive structure activity relationship studies on a novel series of c-Jun N-terminal kinase (JNK) inhibitors. Intriguingly, the compounds have a dual inhibitory activity by functioning as both ATP and JIP mimetics, possibly by binding to both the ATP binding site and to the docking site of the kinase. Several of such novel compounds display potent JNK inhibitory profiles both in vitro and in cell.
PMCID: PMC3089059  PMID: 21458276
14.  Synthesis and optimization of thiadiazole derivatives as a novel class of substrate competitive c-Jun N-terminal kinase inhibitors 
A series of thiadiazole derivatives has been designed as potential allosteric, substrate competitive inhibitors of the protein kinase JNK. We report on the synthesis, characterization and evaluation of a series of compounds that resulted in the identification of potent and selective JNK inhibitors targeting its JIP-1 docking site.
PMCID: PMC2818674  PMID: 20045647
15.  BI-69A11-mediated inhibition of AKT leads to effective regression of xenograft melanoma 
Pigment cell & melanoma research  2009;22(2):187-195.
The AKT/PKB pathway plays a central role in tumor development and progression and is often up-regulated in different tumor types, including melanomas. We have recently reported on the in silico approach to identify putative inhibitors for AKT/PKB. Of the reported hits, we selected BI-69A11, a compound which was shown to inhibit AKT activity in in vitro kinase assays. Analysis of BI-69A11 was performed in melanoma cells, a tumor type that commonly exhibits up-regulation of AKT. Treatment of the UACC903 human melanoma cells, har-boring the PTEN mutation, with BI-69A11 caused efficient inhibition of AKT S473 phosphorylation with concomitant inhibition of AKT phosphorylation of PRAS40. Treatment of melanoma cells with BI-69A11 also reduced AKT protein expression, which coincided with inhibition of AKT association with HSP-90. BI-69A11 treatment not only caused cell death of melanoma, but also prostate tumor cell lines. Notably, the effect of BI-69A11 on cell death was more pronounced in cells that express an active form of AKT. Significantly, intra-peritoneal injection of BI-69A11 caused effective regression of melanoma tumor xenografts, which coincided with elevated levels of cell death. These findings identify BI-69A11 as a potent inhibitor of AKT that is capable of eliciting effective regression of xenograft melanoma tumors.
PMCID: PMC2860277  PMID: 19175524
AKT; melanoma; BI-69A11; HSP90; Pten; PI3K
16.  Design, Synthesis, and Structure-Activity Relationship of Substrate Competitive, Selective, and in Vivo Active Triazole and Thiadiazole inhibitors of the c-Jun N-Terminal Kinase 
Journal of medicinal chemistry  2009;52(7):1943-1952.
We report comprehensive structure activity relationship studies on a novel series of c-Jun N-terminal kinase (JNK) inhibitors. The compounds are substrate competitive inhibitors that bind to the docking site of the kinase. The reported medicinal chemistry and structure-based optimizations studies resulted in the discovery of selective and potent thiadiazole JNK inhibitors that displays promising in vivo activity in mouse models of insulin insensitivity.
PMCID: PMC2667321  PMID: 19271755
17.  Discovery of 2-(5-nitrothiazol-2-ylthio)benzo[d]thiazoles as novel c-Jun N-terminal kinase inhibitors 
Bioorganic & medicinal chemistry  2009;17(7):2712-2717.
A new series of 2-thioether-benzothiazoles has been synthesized and evaluated for JNK inhibition. The SAR studies led to the discovery of potent, allosteric JNK inhibitors with selectivity against p38.
PMCID: PMC2828351  PMID: 19282190
JNK1; JNK2; JIP1; DJNKI; Allosteric kinase inbhibitors
18.  Development of Paramagnetic Probes for Molecular Recognition Studies in Protein Kinases 
Journal of medicinal chemistry  2008;51(12):3460-3465.
We report on the synthesis and evaluation of an indazole-spin-labeled compound that was designed as an effective chemical probe for second site screening against the protein kinase JNK using NMR-based techniques. We demonstrate the utility of the derived compound in detecting and characterizing binding events at the protein kinase docking site. In addition, we report on the NMR-based design and synthesis of a bidentate compound spanning both the ATP site and the docking site. We show that the resulting compound has nanomolar affinity for JNK despite the relatively weak affinities of the individual fragments that constitute it. The approach demonstrates that targeting the docking site of protein kinases represents a valuable yet unexplored avenue to obtain potent kinase inhibitors with increased selectivity.
PMCID: PMC2825083  PMID: 18494454

Results 1-18 (18)