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1.
Bioorg Med Chem Lett ; 100: 129626, 2024 Mar 01.
Article in English | MEDLINE | ID: mdl-38266789

ABSTRACT

Tyrosine phosphatase SHP2 is a proto-oncogenic protein involved in cell growth and differentiation via diverse intracellular signaling pathways. With the scope of identifying new SHP2 allosteric inhibitors, we report here the development and optimization of a high-throughput "Direct-to-Biology" (D2B) workflow including the synthesis and the biological evaluation of the reaction crude, thus eliminating the need for purification. During this labor-saving procedure, the structural diversity was introduced through a SNAr reaction. A wide array of analogues with good chemical purity was generated, allowing the obtention of reliable biological data which validated this efficient technique. This approach enabled the fast evaluation of a variety of structurally diverse fragments leading to nanomolar SHP2 allosteric inhibitors and a new series bearing a novel bicyclo[3.1.0]hexane moiety.


Subject(s)
Enzyme Inhibitors , Signal Transduction , Enzyme Inhibitors/chemistry , Cell Proliferation , Cell Differentiation , Biology
2.
ACS Med Chem Lett ; 14(5): 645-651, 2023 May 11.
Article in English | MEDLINE | ID: mdl-37197453

ABSTRACT

Src homology 2-containing protein tyrosine phosphatase 2 (SHP2) is the first reported nonreceptor oncogenic tyrosine phosphatase connecting multiple signal transduction cascades and exerting immunoinhibitory function through the PD-1 checkpoint receptor. As part of a drug discovery program aimed at obtaining novel allosteric SHP2 inhibitors, a series of pyrazopyrazine derivatives bearing an original bicyclo[3.1.0]hexane basic moiety on the left-hand side region of the molecule were identified. We report herein the discovery process, the in vitro pharmacological profile, and the early developability features of compound 25, one of the most potent members of the series.

3.
ACS Med Chem Lett ; 14(2): 156-162, 2023 Feb 09.
Article in English | MEDLINE | ID: mdl-36793438

ABSTRACT

Protein tyrosine phosphatase SHP2 is an oncogenic protein that can regulate different cytokine receptor and receptor tyrosine kinase signaling pathways. We report here the identification of a novel series of SHP2 allosteric inhibitors having an imidazopyrazine 6,5-fused heterocyclic system as the central scaffold that displays good potency in enzymatic and cellular assays. SAR studies led to the identification of compound 8, a highly potent SHP2 allosteric inhibitor. X-ray studies showed novel stabilizing interactions with respect to known SHP2 inhibitors. Subsequent optimization allowed us to identify analogue 10, which possesses excellent potency and a promising PK profile in rodents.

4.
Commun Biol ; 5(1): 547, 2022 06 06.
Article in English | MEDLINE | ID: mdl-35668202

ABSTRACT

Blocking Plasmodium falciparum human-to-mosquito transmission is essential for malaria elimination, nonetheless drugs killing the pathogenic asexual stages are generally inactive on the parasite transmissible stages, the gametocytes. Due to technical and biological limitations in high throughput screening of non-proliferative stages, the search for gametocyte-killing molecules so far tested one tenth the number of compounds screened on asexual stages. Here we overcome these limitations and rapidly screened around 120,000 compounds, using not purified, bioluminescent mature gametocytes. Orthogonal gametocyte assays, selectivity assays on human cells and asexual parasites, followed by compound clustering, brought to the identification of 84 hits, half of which are gametocyte selective and half with comparable activity against sexual and asexual parasites. We validated seven chemotypes, three of which are, to the best of our knowledge, novel. These molecules are able to inhibit male gametocyte exflagellation and block parasite transmission through the Anopheles mosquito vector in a standard membrane feeding assay. This work shows that interrogating a wide and diverse chemical space, with a streamlined gametocyte HTS and hit validation funnel, holds promise for the identification of dual stage and gametocyte-selective compounds to be developed into new generation of transmission blocking drugs for malaria elimination.


Subject(s)
Anopheles , Malaria , Animals , High-Throughput Screening Assays , Humans , Male , Plasmodium falciparum
5.
Bioorg Med Chem ; 57: 116631, 2022 03 01.
Article in English | MEDLINE | ID: mdl-35123179

ABSTRACT

Zika virus (ZIKV) is a member of the Flaviviridae family that can cause neurological disorders and congenital malformations. The NS2B-NS3 viral serine protease is an attractive target for the development of new antiviral agents against ZIKV. We report here a SAR study on a series of substrate-like linear tripeptides that inhibit in a non-covalent manner the NS2B-NS3 protease. Optimization of the residues at positions P1, P2, P3 and of the N-terminal and C-terminal portions of the tripeptide allowed the identification of inhibitors with sub-micromolar potency with phenylglycine as arginine-mimicking group and benzylamide as C-terminal fragment. Further SAR exploration and application of these structural changes to a series of peptides having a 4-substituted phenylglycine residue at the P1 position led to potent compounds showing double digit nanomolar inhibition of the Zika protease (IC50 = 30 nM) with high selectivity against trypsin-like proteases and the proteases of other flavivirus, such as Dengue 2 virus (DEN2V) and West Nile virus (WNV).


Subject(s)
Antiviral Agents/pharmacology , Peptides/pharmacology , Protease Inhibitors/pharmacology , Viral Nonstructural Proteins/antagonists & inhibitors , Zika Virus/drug effects , Antiviral Agents/chemical synthesis , Antiviral Agents/chemistry , Dengue Virus/drug effects , Dose-Response Relationship, Drug , Humans , Microbial Sensitivity Tests , Molecular Structure , Peptides/chemical synthesis , Peptides/chemistry , Protease Inhibitors/chemical synthesis , Protease Inhibitors/chemistry , RNA Helicases/antagonists & inhibitors , RNA Helicases/metabolism , Serine Endopeptidases/metabolism , Structure-Activity Relationship , Viral Nonstructural Proteins/metabolism , West Nile virus/drug effects , Zika Virus/enzymology
6.
Sci Adv ; 7(23)2021 06.
Article in English | MEDLINE | ID: mdl-34078594

ABSTRACT

H3K9 methylation maintains cell identity orchestrating stable silencing and anchoring of alternate fate genes within the heterochromatic compartment underneath the nuclear lamina (NL). However, how cell type-specific genomic regions are specifically targeted to the NL is still elusive. Using fibro-adipogenic progenitors (FAPs) as a model, we identified Prdm16 as a nuclear envelope protein that anchors H3K9-methylated chromatin in a cell-specific manner. We show that Prdm16 mediates FAP developmental capacities by orchestrating lamina-associated domain organization and heterochromatin sequestration at the nuclear periphery. We found that Prdm16 localizes at the NL where it cooperates with the H3K9 methyltransferases G9a/GLP to mediate tethering and silencing of myogenic genes, thus repressing an alternative myogenic fate in FAPs. Genetic and pharmacological disruption of this repressive pathway confers to FAP myogenic competence, preventing fibro-adipogenic degeneration of dystrophic muscles. In summary, we reveal a druggable mechanism of heterochromatin perinuclear sequestration exploitable to reprogram FAPs in vivo.

7.
J Med Chem ; 63(21): 12957-12977, 2020 11 12.
Article in English | MEDLINE | ID: mdl-33118821

ABSTRACT

Inhibition of glutaminase-1 (GLS-1) hampers the proliferation of tumor cells reliant on glutamine. Known glutaminase inhibitors have potential limitations, and in vivo exposures are potentially limited due to poor physicochemical properties. We initiated a GLS-1 inhibitor discovery program focused on optimizing physicochemical and pharmacokinetic properties, and have developed a new selective inhibitor, compound 27 (IPN60090), which is currently in phase 1 clinical trials. Compound 27 attains high oral exposures in preclinical species, with strong in vivo target engagement, and should robustly inhibit glutaminase in humans.


Subject(s)
Enzyme Inhibitors/chemistry , Glutaminase/antagonists & inhibitors , Triazoles/pharmacokinetics , Administration, Oral , Animals , Cell Line, Tumor , Dogs , Drug Evaluation, Preclinical , Enzyme Inhibitors/metabolism , Enzyme Inhibitors/pharmacokinetics , Glutaminase/genetics , Glutaminase/metabolism , Half-Life , Hepatocytes/cytology , Hepatocytes/drug effects , Hepatocytes/metabolism , Humans , Inhibitory Concentration 50 , Male , Mice , Microsomes/metabolism , Protein Binding , Rats , Rats, Sprague-Dawley , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , Structure-Activity Relationship , Triazoles/chemistry , Triazoles/metabolism
8.
Cell Rep ; 26(2): 469-482.e5, 2019 01 08.
Article in English | MEDLINE | ID: mdl-30625329

ABSTRACT

The plasticity of a preexisting regulatory circuit compromises the effectiveness of targeted therapies, and leveraging genetic vulnerabilities in cancer cells may overcome such adaptations. Hereditary leiomyomatosis renal cell carcinoma (HLRCC) is characterized by oxidative phosphorylation (OXPHOS) deficiency caused by fumarate hydratase (FH) nullizyogosity. To identify metabolic genes that are synthetically lethal with OXPHOS deficiency, we conducted a genetic loss-of-function screen and found that phosphogluconate dehydrogenase (PGD) inhibition robustly blocks the proliferation of FH mutant cancer cells both in vitro and in vivo. Mechanistically, PGD inhibition blocks glycolysis, suppresses reductive carboxylation of glutamine, and increases the NADP+/NADPH ratio to disrupt redox homeostasis. Furthermore, in the OXPHOS-proficient context, blocking OXPHOS using the small-molecule inhibitor IACS-010759 enhances sensitivity to PGD inhibition in vitro and in vivo. Together, our study reveals a dependency on PGD in OXPHOS-deficient tumors that might inform therapeutic intervention in specific patient populations.


Subject(s)
Oxidative Phosphorylation , Phosphogluconate Dehydrogenase/genetics , Synthetic Lethal Mutations , Animals , Cell Line, Tumor , Female , Fumarate Hydratase/genetics , Genomics/methods , Glycolysis , Humans , Loss of Function Mutation , Mice , Mice, Nude
9.
Cancer Res ; 77(14): 3894-3907, 2017 07 15.
Article in English | MEDLINE | ID: mdl-28566332

ABSTRACT

Oncolytic viruses selectively lyse tumor cells, disrupt immunosuppression within the tumor, and reactivate antitumor immunity, but they have yet to live up to their therapeutic potential. Immune checkpoint modulation has been efficacious in a variety of cancer with an immunogenic microenvironment, but is associated with toxicity due to nonspecific T-cell activation. Therefore, combining these two strategies would likely result in both effective and specific cancer therapy. To test the hypothesis, we first constructed oncolytic adenovirus Delta-24-RGDOX expressing the immune costimulator OX40 ligand (OX40L). Like its predecessor Delta-24-RGD, Delta-24-RGDOX induced immunogenic cell death and recruit lymphocytes to the tumor site. Compared with Delta-24-RGD, Delta-24-RGDOX exhibited superior tumor-specific activation of lymphocytes and proliferation of CD8+ T cells specific to tumor-associated antigens, resulting in cancer-specific immunity. Delta-24-RGDOX mediated more potent antiglioma activity in immunocompetent C57BL/6 but not immunodeficient athymic mice, leading to specific immune memory against the tumor. To further overcome the immune suppression mediated by programmed death-ligand 1 (PD-L1) expression on cancer cells accompanied with virotherapy, intratumoral injection of Delta-24-RGDOX and an anti-PD-L1 antibody showed synergistic inhibition of gliomas and significantly increased survival in mice. Our data demonstrate that combining an oncolytic virus with tumor-targeting immune checkpoint modulators elicits potent in situ autologous cancer vaccination, resulting in an efficacious, tumor-specific, and long-lasting therapeutic effect. Cancer Res; 77(14); 3894-907. ©2017 AACR.


Subject(s)
Cancer Vaccines/pharmacology , Neoplasms/therapy , Oncolytic Virotherapy/methods , Oncolytic Viruses/physiology , A549 Cells , Animals , B7-H1 Antigen/antagonists & inhibitors , B7-H1 Antigen/immunology , CD8-Positive T-Lymphocytes/immunology , Cell Line, Tumor , Glioma/immunology , Glioma/therapy , Glioma/virology , HEK293 Cells , Humans , Immunomodulation , Lung Neoplasms/immunology , Lung Neoplasms/therapy , Lung Neoplasms/virology , Melanoma, Experimental/immunology , Melanoma, Experimental/therapy , Melanoma, Experimental/virology , Mice , Mice, Inbred C57BL , Mice, Nude , Neoplasms/immunology , Neoplasms/virology , OX40 Ligand/biosynthesis , OX40 Ligand/genetics , OX40 Ligand/immunology , Oncolytic Viruses/genetics , Oncolytic Viruses/immunology
10.
Sci Signal ; 10(480)2017 May 23.
Article in English | MEDLINE | ID: mdl-28536297

ABSTRACT

Cancers with loss-of-function mutations in BRCA1 or BRCA2 are deficient in the DNA damage repair pathway called homologous recombination (HR), rendering these cancers exquisitely vulnerable to poly(ADP-ribose) polymerase (PARP) inhibitors. This functional state and therapeutic sensitivity is referred to as "BRCAness" and is most commonly associated with some breast cancer types. Pharmaceutical induction of BRCAness could expand the use of PARP inhibitors to other tumor types. For example, BRCA mutations are present in only ~20% of prostate cancer patients. We found that castration-resistant prostate cancer (CRPC) cells showed increased expression of a set of HR-associated genes, including BRCA1, RAD54L, and RMI2 Although androgen-targeted therapy is typically not effective in CRPC patients, the androgen receptor inhibitor enzalutamide suppressed the expression of those HR genes in CRPC cells, thus creating HR deficiency and BRCAness. A "lead-in" treatment strategy, in which enzalutamide was followed by the PARP inhibitor olaparib, promoted DNA damage-induced cell death and inhibited clonal proliferation of prostate cancer cells in culture and suppressed the growth of prostate cancer xenografts in mice. Thus, antiandrogen and PARP inhibitor combination therapy may be effective for CRPC patients and suggests that pharmaceutically inducing BRCAness may expand the clinical use of PARP inhibitors.


Subject(s)
BRCA1 Protein/metabolism , Gene Expression Regulation, Neoplastic/drug effects , Phenylthiohydantoin/analogs & derivatives , Phthalazines/pharmacology , Piperazines/pharmacology , Poly(ADP-ribose) Polymerase Inhibitors/pharmacology , Prostatic Neoplasms, Castration-Resistant/drug therapy , Animals , Apoptosis/drug effects , Benzamides , Cell Proliferation/drug effects , DNA Damage/drug effects , DNA Repair/drug effects , Drug Synergism , Homologous Recombination/drug effects , Humans , Male , Mice , Mice, SCID , Nitriles , Phenylthiohydantoin/pharmacology , Poly(ADP-ribose) Polymerases/chemistry , Prostatic Neoplasms, Castration-Resistant/metabolism , Prostatic Neoplasms, Castration-Resistant/pathology , Receptors, Androgen/chemistry , Tumor Cells, Cultured , Xenograft Model Antitumor Assays
11.
J Biol Chem ; 292(24): 10295-10305, 2017 06 16.
Article in English | MEDLINE | ID: mdl-28468826

ABSTRACT

Neutrophil elastase (NE) can be rapidly taken up by tumor cells that lack endogenous NE expression, including breast cancer, which results in cross-presentation of PR1, an NE-derived HLA-A2-restricted peptide that is an immunotherapy target in hematological and solid tumor malignancies. The mechanism of NE uptake, however, remains unknown. Using the mass spectrometry-based approach, we identify neuropilin-1 (NRP1) as a NE receptor that mediates uptake and PR1 cross-presentation in breast cancer cells. We demonstrated that soluble NE is a specific, high-affinity ligand for NRP1 with a calculated Kd of 38.7 nm Furthermore, we showed that NRP1 binds to the RRXR motif in NE. Notably, NRP1 knockdown with interfering RNA or CRISPR-cas9 system and blocking using anti-NRP1 antibody decreased NE uptake and, subsequently, susceptibility to lysis by PR1-specific cytotoxic T cells. Expression of NRP1 in NRP1-deficient cells was sufficient to induce NE uptake. Altogether, because NRP1 is broadly expressed in tumors, our findings suggest a role for this receptor in immunotherapy strategies that target cross-presented antigens.


Subject(s)
Absorption, Physiological , Breast Neoplasms/metabolism , Cross-Priming , Leukocyte Elastase/metabolism , Neoplasm Proteins/metabolism , Neuropilin-1/metabolism , Amino Acid Motifs , Antibodies, Blocking/metabolism , Breast Neoplasms/immunology , Breast Neoplasms/pathology , CRISPR-Cas Systems , Cell Line, Tumor , Female , Humans , Kinetics , Leukocyte Elastase/chemistry , Leukocyte Elastase/immunology , Ligands , Neoplasm Proteins/antagonists & inhibitors , Neoplasm Proteins/chemistry , Neoplasm Proteins/genetics , Neuropilin-1/antagonists & inhibitors , Neuropilin-1/chemistry , Neuropilin-1/genetics , Peptide Fragments/chemistry , Peptide Fragments/genetics , Peptide Fragments/metabolism , Protein Interaction Domains and Motifs , RNA Interference , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Solubility , T-Lymphocytes, Cytotoxic/immunology , T-Lymphocytes, Cytotoxic/metabolism
12.
Nature ; 542(7641): 362-366, 2017 02 16.
Article in English | MEDLINE | ID: mdl-28178232

ABSTRACT

Malignant neoplasms evolve in response to changes in oncogenic signalling. Cancer cell plasticity in response to evolutionary pressures is fundamental to tumour progression and the development of therapeutic resistance. Here we determine the molecular and cellular mechanisms of cancer cell plasticity in a conditional oncogenic Kras mouse model of pancreatic ductal adenocarcinoma (PDAC), a malignancy that displays considerable phenotypic diversity and morphological heterogeneity. In this model, stochastic extinction of oncogenic Kras signalling and emergence of Kras-independent escaper populations (cells that acquire oncogenic properties) are associated with de-differentiation and aggressive biological behaviour. Transcriptomic and functional analyses of Kras-independent escapers reveal the presence of Smarcb1-Myc-network-driven mesenchymal reprogramming and independence from MAPK signalling. A somatic mosaic model of PDAC, which allows time-restricted perturbation of cell fate, shows that depletion of Smarcb1 activates the Myc network, driving an anabolic switch that increases protein metabolism and adaptive activation of endoplasmic-reticulum-stress-induced survival pathways. Increased protein turnover renders mesenchymal sub-populations highly susceptible to pharmacological and genetic perturbation of the cellular proteostatic machinery and the IRE1-α-MKK4 arm of the endoplasmic-reticulum-stress-response pathway. Specifically, combination regimens that impair the unfolded protein responses block the emergence of aggressive mesenchymal subpopulations in mouse and patient-derived PDAC models. These molecular and biological insights inform a potential therapeutic strategy for targeting aggressive mesenchymal features of PDAC.


Subject(s)
Mesoderm/pathology , Pancreatic Neoplasms/pathology , Animals , Carcinoma, Pancreatic Ductal/drug therapy , Carcinoma, Pancreatic Ductal/metabolism , Carcinoma, Pancreatic Ductal/pathology , Deoxycytidine/analogs & derivatives , Deoxycytidine/pharmacology , Deoxycytidine/therapeutic use , Endoplasmic Reticulum Stress/genetics , Female , Genes, myc , Genes, ras , Humans , MAP Kinase Kinase 4/metabolism , MAP Kinase Signaling System , Male , Mesoderm/metabolism , Mice , Mosaicism , Oncogene Protein p55(v-myc)/metabolism , Pancreatic Neoplasms/drug therapy , Pancreatic Neoplasms/metabolism , Proteolysis , Proto-Oncogene Proteins p21(ras)/genetics , Proto-Oncogene Proteins p21(ras)/metabolism , SMARCB1 Protein/deficiency , SMARCB1 Protein/metabolism , Transcriptome/genetics , Gemcitabine
13.
Oncotarget ; 7(26): 39595-39608, 2016 Jun 28.
Article in English | MEDLINE | ID: mdl-27167191

ABSTRACT

PURPOSE: Though the efficacy of MEK inhibitors is being investigated in KRAS-mutant colorectal cancers (CRC), early clinical trials of MEK inhibitor monotherapy did not reveal significant antitumor activity. Resistance to MEK inhibitor monotherapy developed through a variety of mechanisms converging in ERK reactivation. Since ERK increases cyclin D expression and increases entry into the cell cycle, we hypothesized that the combination of MEK inhibitors and CDK4/6 inhibitors would have synergistic antitumor activity and cause tumor regression in vivo. RESULTS: The combination of MEK and CDK4/6 inhibitors synergistically inhibited cancer cell growth in vitro and caused tumor regression in vivo in cell line and patient-derived xenograft models. Combination therapy markedly decreased levels of phosphorylated ribosomal protein S6 both in vitro and in vivo and decreased Ki67 staining in vivo. EXPERIMENTAL DESIGN: We performed in vitro proliferation, colony formation, apoptosis, and senescence assays, and Western blots, on a panel of 11 KRAS mutant CRC cell lines treated with the MEK inhibitor MEK162, the CDK4/6 inhibitor palbociclib, or the combination. We also treated 4 KRAS mutant CRC cell line and patient-derived xenografts with the MEK inhibitor trametinib, the CDK4/6 inhibitor palbociclib, or the combination, and performed immunohistochemical and reverse phase protein array analysis. CONCLUSIONS: Combined inhibition of both MEK and CDK4/6 is effective in preclinical models of KRAS mutant CRC and justifies a planned phase II clinical trial in patients with refractory KRAS-mutant CRC.Efficacy of the combination of MEK and CDK4/6 inhibitors in vitro and in vivo in KRAS mutant colorectal cancer models.


Subject(s)
Antineoplastic Agents/pharmacology , Colorectal Neoplasms/drug therapy , Cyclin-Dependent Kinase 4/antagonists & inhibitors , Cyclin-Dependent Kinase 6/antagonists & inhibitors , MAP Kinase Kinase Kinase 1/antagonists & inhibitors , Animals , Cell Line, Tumor , Cell Proliferation , Clinical Trials as Topic , Colorectal Neoplasms/genetics , Disease Models, Animal , Extracellular Signal-Regulated MAP Kinases/metabolism , Female , Genes, ras , Humans , Mice , Mice, Nude , Mutation , Neoplasm Transplantation , Phosphorylation , Piperazines/pharmacology , Pyridines/pharmacology , Treatment Outcome
14.
Bioorg Med Chem Lett ; 26(6): 1503-1507, 2016 Mar 15.
Article in English | MEDLINE | ID: mdl-26898335

ABSTRACT

Structure based design of a novel class of aminopyrimidine MTH1 (MutT homolog 1) inhibitors is described. Optimization led to identification of IACS-4759 (compound 5), a sub-nanomolar inhibitor of MTH1 with excellent cell permeability and good metabolic stability in microsomes. This compound robustly inhibited MTH1 activity in cells and proved to be an excellent tool for interrogation of the utility of MTH1 inhibition in the context of oncology.


Subject(s)
DNA Repair Enzymes/antagonists & inhibitors , Enzyme Inhibitors/pharmacology , Phosphoric Monoester Hydrolases/antagonists & inhibitors , DNA Repair Enzymes/metabolism , Dose-Response Relationship, Drug , Enzyme Inhibitors/chemical synthesis , Enzyme Inhibitors/chemistry , Humans , Models, Molecular , Molecular Structure , Phosphoric Monoester Hydrolases/metabolism , Structure-Activity Relationship , Substrate Specificity
15.
J Med Chem ; 59(4): 1440-54, 2016 Feb 25.
Article in English | MEDLINE | ID: mdl-26061247

ABSTRACT

The bromodomain containing proteins TRIM24 (tripartite motif containing protein 24) and BRPF1 (bromodomain and PHD finger containing protein 1) are involved in the epigenetic regulation of gene expression and have been implicated in human cancer. Overexpression of TRIM24 correlates with poor patient prognosis, and BRPF1 is a scaffolding protein required for the assembly of histone acetyltransferase complexes, where the gene of MOZ (monocytic leukemia zinc finger protein) was first identified as a recurrent fusion partner in leukemia patients (8p11 chromosomal rearrangements). Here, we present the structure guided development of a series of N,N-dimethylbenzimidazolone bromodomain inhibitors through the iterative use of X-ray cocrystal structures. A unique binding mode enabled the design of a potent and selective inhibitor 8i (IACS-9571) with low nanomolar affinities for TRIM24 and BRPF1 (ITC Kd = 31 nM and ITC Kd = 14 nM, respectively). With its excellent cellular potency (EC50 = 50 nM) and favorable pharmacokinetic properties (F = 29%), 8i is a high-quality chemical probe for the evaluation of TRIM24 and/or BRPF1 bromodomain function in vitro and in vivo.


Subject(s)
Adaptor Proteins, Signal Transducing/antagonists & inhibitors , Adaptor Proteins, Signal Transducing/metabolism , Benzimidazoles/chemistry , Benzimidazoles/pharmacology , Carrier Proteins/antagonists & inhibitors , Carrier Proteins/metabolism , Drug Design , Nuclear Proteins/antagonists & inhibitors , Nuclear Proteins/metabolism , Adaptor Proteins, Signal Transducing/chemistry , Animals , Benzimidazoles/pharmacokinetics , Carrier Proteins/chemistry , DNA-Binding Proteins , Female , Humans , Methylation , Mice , Molecular Docking Simulation , Nuclear Proteins/chemistry , Protein Binding
16.
Article in English | MEDLINE | ID: mdl-26396593

ABSTRACT

BACKGROUND: Proteins that 'read' the histone code are central elements in epigenetic control and bromodomains, which bind acetyl-lysine motifs, are increasingly recognized as potential mediators of disease states. Notably, the first BET bromodomain-based therapies have entered clinical trials and there is a broad interest in dissecting the therapeutic relevance of other bromodomain-containing proteins in human disease. Typically, drug development is facilitated and expedited by high-throughput screening, where assays need to be sensitive, robust, cost-effective and scalable. However, for bromodomains, which lack catalytic activity that otherwise can be monitored (using classical enzymology), the development of cell-based, drug-target engagement assays has been challenging. Consequently, cell biochemical assays have lagged behind compared to other protein families (e.g., histone deacetylases and methyltransferases). RESULTS: Here, we present a suite of novel chromatin and histone-binding assays using AlphaLISA, in situ cell extraction and fluorescence-based, high-content imaging. First, using TRIM24 as an example, the homogenous, bead-based AlphaScreen technology was modified from a biochemical peptide-competition assay to measure binding of the TRIM24 bromodomain to endogenous histone H3 in cells (AlphaLISA). Second, a target agnostic, high-throughput imaging platform was developed to quantify the ability of chemical probes to dissociate endogenous proteins from chromatin/nuclear structures. While overall nuclear morphology is maintained, the procedure extracts soluble, non-chromatin-bound proteins from cells with drug-target displacement visualized by immunofluorescence (IF) or microscopy of fluorescent proteins. Pharmacological evaluation of these assays cross-validated their utility, sensitivity and robustness. Finally, using genetic and pharmacological approaches, we dissect domain contribution of TRIM24, BRD4, ATAD2 and SMARCA2 to chromatin binding illustrating the versatility/utility of the in situ cell extraction platform. CONCLUSIONS: In summary, we have developed two novel complementary and cell-based drug-target engagement assays, expanding the repertoire of pharmacodynamic assays for bromodomain tool compound development. These assays have been validated through a successful TRIM24 bromodomain inhibitor program, where a micromolar lead molecule (IACS-6558) was optimized using cell-based assays to yield the first single-digit nanomolar TRIM24 inhibitor (IACS-9571). Altogether, the assay platforms described herein are poised to accelerate the discovery and development of novel chemical probes to deliver on the promise of epigenetic-based therapies.

17.
Cancer Res ; 75(18): 3865-3878, 2015 Sep 15.
Article in English | MEDLINE | ID: mdl-26139243

ABSTRACT

The SWI/SNF multisubunit complex modulates chromatin structure through the activity of two mutually exclusive catalytic subunits, SMARCA2 and SMARCA4, which both contain a bromodomain and an ATPase domain. Using RNAi, cancer-specific vulnerabilities have been identified in SWI/SNF-mutant tumors, including SMARCA4-deficient lung cancer; however, the contribution of conserved, druggable protein domains to this anticancer phenotype is unknown. Here, we functionally deconstruct the SMARCA2/4 paralog dependence of cancer cells using bioinformatics, genetic, and pharmacologic tools. We evaluate a selective SMARCA2/4 bromodomain inhibitor (PFI-3) and characterize its activity in chromatin-binding and cell-functional assays focusing on cells with altered SWI/SNF complex (e.g., lung, synovial sarcoma, leukemia, and rhabdoid tumors). We demonstrate that PFI-3 is a potent, cell-permeable probe capable of displacing ectopically expressed, GFP-tagged SMARCA2-bromodomain from chromatin, yet contrary to target knockdown, the inhibitor fails to display an antiproliferative phenotype. Mechanistically, the lack of pharmacologic efficacy is reconciled by the failure of bromodomain inhibition to displace endogenous, full-length SMARCA2 from chromatin as determined by in situ cell extraction, chromatin immunoprecipitation, and target gene expression studies. Furthermore, using inducible RNAi and cDNA complementation (bromodomain- and ATPase-dead constructs), we unequivocally identify the ATPase domain, and not the bromodomain of SMARCA2, as the relevant therapeutic target with the catalytic activity suppressing defined transcriptional programs. Taken together, our complementary genetic and pharmacologic studies exemplify a general strategy for multidomain protein drug-target validation and in case of SMARCA2/4 highlight the potential for drugging the more challenging helicase/ATPase domain to deliver on the promise of synthetic-lethality therapy.


Subject(s)
Azabicyclo Compounds/pharmacology , Chromatin Assembly and Disassembly/drug effects , Chromosomal Proteins, Non-Histone/deficiency , DNA Helicases/antagonists & inhibitors , Molecular Targeted Therapy , Neoplasm Proteins/antagonists & inhibitors , Neoplasms/drug therapy , Nuclear Proteins/antagonists & inhibitors , Pyridines/pharmacology , Transcription Factors/antagonists & inhibitors , Transcription Factors/deficiency , Binding, Competitive , Catalysis , Cell Line, Tumor , Chromatin/metabolism , Chromosomal Proteins, Non-Histone/genetics , DNA Helicases/chemistry , DNA Helicases/deficiency , DNA, Complementary/genetics , Gene Knockout Techniques , Genetic Complementation Test , Humans , Lung Neoplasms/pathology , Microarray Analysis , Neoplasms/genetics , Nuclear Proteins/chemistry , Nuclear Proteins/deficiency , Protein Structure, Tertiary , RNA Interference , RNA, Small Interfering/pharmacology , Rhabdoid Tumor/genetics , Rhabdoid Tumor/pathology , Sarcoma, Synovial/genetics , Sarcoma, Synovial/pathology , Transcription Factors/chemistry , Transcription Factors/genetics
18.
Cancer Discov ; 5(8): 860-77, 2015 Aug.
Article in English | MEDLINE | ID: mdl-26069186

ABSTRACT

UNLABELLED: The molecular underpinnings that drive the heterogeneity of KRAS-mutant lung adenocarcinoma are poorly characterized. We performed an integrative analysis of genomic, transcriptomic, and proteomic data from early-stage and chemorefractory lung adenocarcinoma and identified three robust subsets of KRAS-mutant lung adenocarcinoma dominated, respectively, by co-occurring genetic events in STK11/LKB1 (the KL subgroup), TP53 (KP), and CDKN2A/B inactivation coupled with low expression of the NKX2-1 (TTF1) transcription factor (KC). We further revealed biologically and therapeutically relevant differences between the subgroups. KC tumors frequently exhibited mucinous histology and suppressed mTORC1 signaling. KL tumors had high rates of KEAP1 mutational inactivation and expressed lower levels of immune markers, including PD-L1. KP tumors demonstrated higher levels of somatic mutations, inflammatory markers, immune checkpoint effector molecules, and improved relapse-free survival. Differences in drug sensitivity patterns were also observed; notably, KL cells showed increased vulnerability to HSP90-inhibitor therapy. This work provides evidence that co-occurring genomic alterations identify subgroups of KRAS-mutant lung adenocarcinoma with distinct biology and therapeutic vulnerabilities. SIGNIFICANCE: Co-occurring genetic alterations in STK11/LKB1, TP53, and CDKN2A/B-the latter coupled with low TTF1 expression-define three major subgroups of KRAS-mutant lung adenocarcinoma with distinct biology, patterns of immune-system engagement, and therapeutic vulnerabilities.


Subject(s)
Adenocarcinoma/genetics , Adenocarcinoma/pathology , Genetic Variation , Genomics , Lung Neoplasms/genetics , Lung Neoplasms/pathology , Mutation , ras Proteins/genetics , AMP-Activated Protein Kinase Kinases , AMP-Activated Protein Kinases/metabolism , Adenocarcinoma/immunology , Adenocarcinoma/metabolism , Adenocarcinoma/mortality , Adenocarcinoma/therapy , Adenocarcinoma of Lung , Cell Line, Tumor , Cluster Analysis , DNA-Binding Proteins/genetics , Gene Expression , Gene Expression Profiling , Genomics/methods , Humans , Inflammation/genetics , Inflammation/immunology , Inflammation/pathology , Lung Neoplasms/immunology , Lung Neoplasms/metabolism , Lung Neoplasms/mortality , Lung Neoplasms/therapy , Oxidative Stress , Prognosis , Protein Serine-Threonine Kinases/genetics , Protein Serine-Threonine Kinases/metabolism , Signal Transduction , Transcription Factors , Tumor Suppressor Proteins/genetics
19.
Cancer Res ; 75(6): 1091-101, 2015 Mar 15.
Article in English | MEDLINE | ID: mdl-25736685

ABSTRACT

Mutated KRAS (KRAS*) is a fundamental driver in the majority of pancreatic ductal adenocarcinomas (PDAC). Using an inducible mouse model of KRAS*-driven PDAC, we compared KRAS* genetic extinction with pharmacologic inhibition of MEK1 in tumor spheres and in vivo. KRAS* ablation blocked proliferation and induced apoptosis, whereas MEK1 inhibition exerted cytostatic effects. Proteomic analysis evidenced that MEK1 inhibition was accompanied by a sustained activation of the PI3K-AKT-MTOR pathway and by the activation of AXL, PDGFRa, and HER1-2 receptor tyrosine kinases (RTK) expressed in a large proportion of human PDAC samples analyzed. Although single inhibition of each RTK alone or plus MEK1 inhibitors was ineffective, a combination of inhibitors targeting all three coactivated RTKs and MEK1 was needed to inhibit proliferation and induce apoptosis in both mouse and human low-passage PDAC cultures. Importantly, constitutive AKT activation, which may mimic the fraction of AKT2-amplified PDAC, was able to bypass the induction of apoptosis caused by KRAS* ablation, highlighting a potential inherent resistance mechanism that may inform the clinical application of MEK inhibitor therapy. This study suggests that combinatorial-targeted therapies for pancreatic cancer must be informed by the activation state of each putative driver in a given treatment context. In addition, our work may offer explanative and predictive power in understanding why inhibitors of EGFR signaling fail in PDAC treatment and how drug resistance mechanisms may arise in strategies to directly target KRAS.


Subject(s)
Mitogen-Activated Protein Kinase Kinases/antagonists & inhibitors , Pancreatic Neoplasms/drug therapy , Protein Kinase Inhibitors/therapeutic use , Proto-Oncogene Proteins p21(ras)/genetics , Receptor Protein-Tyrosine Kinases/antagonists & inhibitors , Animals , Disease Models, Animal , Humans , MAP Kinase Signaling System , Mice , Pancreatic Neoplasms/genetics , Phosphatidylinositol 3-Kinases/physiology , Proto-Oncogene Proteins c-akt/physiology , Signal Transduction/physiology , TOR Serine-Threonine Kinases/physiology
20.
J Med Chem ; 58(8): 3302-14, 2015 Apr 23.
Article in English | MEDLINE | ID: mdl-25761096

ABSTRACT

Poly(ADP-ribose) polymerases (PARPs) are involved in DNA repair following damage by endogenous or exogenous processes. It has become clear over the past decade that inhibition of PARP in the context of defects in other DNA repair mechanisms provide a tumor specific way to kill cancer cells. We describe the rationale for this approach and the design and discovery of niraparib, a potent PARP-1/2 inhibitor with good cell based activity, selectivity for cancer over normal cells, and oral bioavailability. Niraparib was characterized in a number of preclinical models before moving to phase I clinical trials, where it showed excellent human pharmacokinetics suitable for once a day oral dosing, achieved its pharmacodynamic target for PARP inhibition, and had promising activity in cancer patients. It is currently being tested in phase 3 clinical trials as maintenance therapy in ovarian cancer and as a treatment for breast cancer.


Subject(s)
Enzyme Inhibitors/therapeutic use , Homologous Recombination/drug effects , Indazoles/therapeutic use , Neoplasms/drug therapy , Piperidines/therapeutic use , Poly(ADP-ribose) Polymerase Inhibitors , Animals , BRCA1 Protein/genetics , BRCA1 Protein/metabolism , BRCA2 Protein/genetics , BRCA2 Protein/metabolism , Drug Discovery , Enzyme Inhibitors/chemistry , Enzyme Inhibitors/pharmacology , Humans , Indazoles/chemistry , Indazoles/pharmacology , Models, Molecular , Neoplasms/enzymology , Neoplasms/genetics , Neoplasms/metabolism , Piperidines/chemistry , Piperidines/pharmacology , Poly(ADP-ribose) Polymerases/metabolism
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