ABSTRACT
Active or allosteric site arginines can form diverse interactions with ligands including different types of cation-π interactions, H-bond interactions and non-bond, non-canonical interactions. This provides many opportunities for creative structure-based drug design to improve potency, introduce novelty, and modulate MoA (mode of action), and even to achieve selectivity. This digest will use some recent drug targets of interest as examples to illustrate different types of interactions and how these interactions impact on potency, MoA, and selectivity.
Subject(s)
Arginine/chemistry , CREB-Binding Protein/metabolism , Enzyme Inhibitors/metabolism , Methionine Adenosyltransferase/metabolism , Organic Chemicals/metabolism , Polycomb Repressive Complex 2/metabolism , Allosteric Site , Antineoplastic Agents/chemistry , Antineoplastic Agents/metabolism , CREB-Binding Protein/chemistry , Catalytic Domain , Drug Design , Enzyme Inhibitors/chemistry , Humans , Ligands , Methionine Adenosyltransferase/chemistry , Organic Chemicals/chemistry , Polycomb Repressive Complex 2/chemistry , Protein BindingABSTRACT
Protein arginine methyltransferase 5 (PRMT5) is known to symmetrically dimethylate numerous cytosolic and nuclear proteins that are involved in a variety of cellular processes. Recent findings have revealed its potential as a cancer therapeutic target. PRMT5 possesses a cysteine (C449) in the active site, unique to PRMT5. Therefore, covalent PRMT5 inhibition is an attractive chemical approach. Herein, we report an exciting discovery of a series of novel hemiaminals that under physiological conditions can be converted to aldehydes and react with C449 to form covalent adducts, which presumably undergo an unprecedented elimination to form the thiol-vinyl ethers, as indicated by electron density in the co-crystal structure of the PRMT5/MEP50 complex.
ABSTRACT
Protein Arginine Methyltransferase 5 (PRMT5) is known to symmetrically dimethylate numerous cytosolic and nuclear proteins that are involved in a variety of cellular processes. Recent findings have revealed its potential as a cancer therapeutic target. PRMT5 selective inhibitors, GSK3326595, a substrate competitive inhibitor, and JNJ64619178, a SAM (S-adenosyl-l-methionine) mimetic/competitive inhibitor, have entered clinic trials for multiple cancer types. This review focuses on the recent developments in SAM mimetic nucleoside PRMT5 inhibitors, their SAR and structural insight based on published co-crystal structures.
Subject(s)
Enzyme Inhibitors/pharmacology , Protein-Arginine N-Methyltransferases/antagonists & inhibitors , Dose-Response Relationship, Drug , Enzyme Inhibitors/chemistry , Humans , Molecular Structure , Protein-Arginine N-Methyltransferases/metabolism , Structure-Activity RelationshipABSTRACT
High-throughput screening (HTS) hits include compounds with undesirable properties. Many filters have been described to identify such hits. Notably, pan-assay interference compounds (PAINS) has been adopted by the community as the standard term to refer to such filters, and very useful guidelines have been adopted by the American Chemical Society (ACS) and subsequently triggered a healthy scientific debate about the pitfalls of draconian use of filters. Using an inhibitory frequency index, we have analyzed in detail the promiscuity profile of the whole GlaxoSmithKline (GSK) HTS collection comprising more than 2 million unique compounds that have been tested in hundreds of screening assays. We provide a comprehensive analysis of many previously published filters and newly described classes of nuisance structures that may serve as a useful source of empirical information to guide the design or growth of HTS collections and hit triaging strategies.
Subject(s)
Drug Discovery/methods , High-Throughput Screening Assays/methods , Small Molecule Libraries/chemistry , Biological Assay/methodsABSTRACT
A novel series of potent and selective hexokinase 2 (HK2) inhibitors, 2,6-disubstituted glucosamines, has been identified based on HTS hits, exemplified by compound 1. Inhibitor-bound crystal structures revealed that the HK2 enzyme could adopt an "induced-fit" conformation. The SAR study led to the identification of potent HK2 inhibitors, such as compound 34 with greater than 100-fold selectivity over HK1. Compound 25 inhibits in situ glycolysis in a UM-UC-3 bladder tumor cell line via (13)CNMR measurement of [3-(13)C]lactate produced from [1,6-(13)C2]glucose added to the cell culture.
ABSTRACT
A series of novel [3a,4]dihydropyrazolo[1,5a]pyrimidines were identified, which were highly potent and selective inhibitors of PI3Kß. The template afforded the opportunity to develop novel SAR for both the hinge-binding (R3) and back-pocket (R4) substitutents. While cellular potency was relatively modest due to high protein binding, the series displayed low clearance in rat, mouse, and monkey.
ABSTRACT
A series of 1,2,4-triazolo[1,5-a]pyrimidin-7(3H)-ones with excellent enzyme inhibition, improved isoform selectivity, and excellent inhibition of downstream phosphorylation of AKT has been identified. Several compounds in the series demonstrated potent (â¼ 0.100 µM IC(50)) growth inhibition in a PTEN deficient cancer cell line.
Subject(s)
Phosphoinositide-3 Kinase Inhibitors , Protein Kinase Inhibitors/chemistry , Antineoplastic Agents/chemical synthesis , Antineoplastic Agents/chemistry , Cell Line, Tumor , Cell Proliferation/drug effects , Humans , PTEN Phosphohydrolase/deficiency , Protein Isoforms/antagonists & inhibitors , Pyrimidines , Structure-Activity Relationship , Substrate SpecificityABSTRACT
A series of PI3K-beta selective inhibitors, imidazo[1,2-a]-pyrimidin-5(1H)-ones, has been rationally designed based on the docking model of the more potent R enantiomer of TGX-221, identified by a chiral separation, in a PI3K-beta homology model. Synthesis and SAR of this novel chemotype are described. Several compounds in the series demonstrated potent growth inhibition in a PTEN-deficient breast cancer cell line MDA-MB-468 under anchorage independent conditions.
Subject(s)
Antineoplastic Agents/chemical synthesis , Imidazoles/chemical synthesis , Phosphoinositide-3 Kinase Inhibitors , Protein Kinase Inhibitors/chemical synthesis , Pyrimidinones/chemical synthesis , Antineoplastic Agents/pharmacology , Binding Sites , Breast Neoplasms , Cell Line, Tumor , Drug Screening Assays, Antitumor , Female , Gene Deletion , Humans , Imidazoles/pharmacology , Isoenzymes/antagonists & inhibitors , Isoenzymes/metabolism , Kinetics , Models, Molecular , PTEN Phosphohydrolase/deficiency , PTEN Phosphohydrolase/genetics , Phosphatidylinositol 3-Kinase/metabolism , Protein Binding , Protein Kinase Inhibitors/pharmacology , Pyrimidinones/pharmacology , Structure-Activity RelationshipABSTRACT
A novel thiazolopyrimidinone series of PI3K-beta selective inhibitors has been identified. This chemotype has provided an excellent tool compound, 18, that showed potent growth inhibition in the PTEN-deficient breast cancer cell line MDA-MB-468 under anchorage-independent conditions, and it also demonstrated pharmacodynamic effects and efficacy in a PTEN-deficient prostate cancer PC-3 xenograft mouse model.
ABSTRACT
Drug toxicity is a major cause of late-stage product attrition. During lead identification and optimization phases little information is typically available about which molecules might have safety concerns. A system was built linking chemistry, preclinical and human safety information, enabling scientists to lever safety knowledge across multiple disciplines. The system consists of a data warehouse with chemical structures and chemical and biological properties for â¼80000 compounds and tools to access and analyze clinical data, toxicology, in vitro pharmacology and drug metabolism data. Tapping into this safety knowledge enables rapid clinically focused risk assessments of drug candidates. Use of this strategy adds value to the drug discovery process at GSK via efficient triage of compounds based on their potential for toxicity.
Subject(s)
Drug Design , Drug Discovery/methods , Drug Industry/methods , Animals , Databases, Factual , Drug Evaluation, Preclinical/methods , Drug-Related Side Effects and Adverse Reactions , Humans , Pharmaceutical Preparations/chemistry , Pharmaceutical Preparations/metabolism , Risk Assessment/methods , Toxicology/methodsABSTRACT
Phosphoinositide 3-kinase α (PI3Kα) is a critical regulator of cell growth and transformation, and its signaling pathway is the most commonly mutated pathway in human cancers. The mammalian target of rapamycin (mTOR), a class IV PI3K protein kinase, is also a central regulator of cell growth, and mTOR inhibitors are believed to augment the antiproliferative efficacy of PI3K/AKT pathway inhibition. 2,4-Difluoro-N-{2-(methyloxy)-5-[4-(4-pyridazinyl)-6-quinolinyl]-3-pyridinyl}benzenesulfonamide (GSK2126458, 1) has been identified as a highly potent, orally bioavailable inhibitor of PI3Kα and mTOR with in vivo activity in both pharmacodynamic and tumor growth efficacy models. Compound 1 is currently being evaluated in human clinical trials for the treatment of cancer.
ABSTRACT
A novel series of AKT inhibitors containing 2,3,5-trisubstituted pyridines with novel azaindazoles as hinge binding elements are described. Among these, the 4,7-diazaindazole compound 2c has improved drug-like properties and kinase selectivity than those of indazole 1, and displays greater than 80% inhibition of GSK3beta phosphorylation in a BT474 tumor xenograft model in mice.
Subject(s)
Indazoles/chemistry , Protein Kinase Inhibitors/chemistry , Proto-Oncogene Proteins c-akt/antagonists & inhibitors , Pyrazines/chemistry , Pyridines/chemistry , Animals , Cell Line, Tumor , Glycogen Synthase Kinase 3/antagonists & inhibitors , Glycogen Synthase Kinase 3/metabolism , Glycogen Synthase Kinase 3 beta , Humans , Indazoles/chemical synthesis , Indazoles/pharmacology , Mice , Phosphorylation , Protein Kinase Inhibitors/chemical synthesis , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins c-akt/metabolism , Pyrazines/chemical synthesis , Pyrazines/pharmacology , Pyridines/chemical synthesis , Pyridines/pharmacology , Xenograft Model Antitumor AssaysABSTRACT
2,3,5-Trisubstituted pyridines have been designed as potent AKT inhibitors that are selective against ROCK1 based on the comparison between AKT and ROCK1 structures. Substitution at the 2-position of the core pyridine is the key element to provide selectivity against ROCK1. An X-ray co-crystal structure of 9p in PKA supports the proposed rationale of ROCK1 selectivity.
Subject(s)
Protein Kinase Inhibitors/chemistry , Proto-Oncogene Proteins c-akt/antagonists & inhibitors , Pyridines/chemistry , rho-Associated Kinases/antagonists & inhibitors , Binding Sites , Crystallography, X-Ray , Humans , Protein Kinase Inhibitors/chemical synthesis , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins c-akt/metabolism , Pyridines/chemical synthesis , Pyridines/pharmacology , Structure-Activity Relationship , rho-Associated Kinases/metabolismABSTRACT
The synthesis and evaluation of tetrasubstituted aminopyridines, bearing novel azaindazole hinge binders, as potent AKT inhibitors are described. Compound 14c was identified as a potent AKT inhibitor that demonstrated reduced CYP450 inhibition and an improved developability profile compared to those of previously described trisubstituted pyridines. It also displayed dose-dependent inhibition of both phosphorylation of GSK3beta and tumor growth in a BT474 tumor xenograft model in mice.
Subject(s)
Aminopyridines/chemistry , Cytochrome P-450 Enzyme System/metabolism , Ether-A-Go-Go Potassium Channels/metabolism , Protein Kinase Inhibitors/chemistry , Proto-Oncogene Proteins c-akt/antagonists & inhibitors , Pyrazines/chemistry , Pyridines/chemistry , Aminopyridines/chemical synthesis , Aminopyridines/pharmacokinetics , Animals , Cell Line, Tumor , Dogs , ERG1 Potassium Channel , Glycogen Synthase Kinase 3/antagonists & inhibitors , Glycogen Synthase Kinase 3/metabolism , Glycogen Synthase Kinase 3 beta , Haplorhini , Humans , Mice , Phosphorylation , Protein Kinase Inhibitors/chemical synthesis , Protein Kinase Inhibitors/pharmacokinetics , Proto-Oncogene Proteins c-akt/metabolism , Pyrazines/chemical synthesis , Pyrazines/pharmacokinetics , Rats , Structure-Activity Relationship , Xenograft Model Antitumor AssaysABSTRACT
A pyrrolopyridinyl thiophene carboxamide 7 was discovered as a tractable starting point for a lead optimization effort in an AKT kinase inhibition program. SAR studies aided by a co-crystal structure of 7 in AKT2 led to the identification of AKT inhibitors with subnanomolar potency. Representative compounds showed antiproliferative activity as well as inhibition of phosphorylation of the downstream target GSK3beta.
Subject(s)
Drug Discovery , Protein Kinase Inhibitors/chemical synthesis , Proto-Oncogene Proteins c-akt/antagonists & inhibitors , Pyridines/chemical synthesis , Pyridines/pharmacology , Thiophenes/chemistry , Animals , Crystallography, X-Ray , Drug Discovery/methods , Humans , Mice , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins c-akt/metabolism , Thienopyridines , Thiophenes/chemical synthesis , Thiophenes/pharmacologyABSTRACT
Eltrombopag is a first-in-class, orally bioavailable, small-molecule, nonpeptide agonist of the thrombopoietin receptor (TpoR), which is being developed as a treatment for thrombocytopenia of various etiologies. In vitro studies have demonstrated that the activity of eltrombopag is dependent on expression of TpoR, which activates the signaling transducers and activators of transcription (STAT) and mitogen-activated protein kinase signal transduction pathways. The objective of this preclinical study is to determine if eltrombopag interacts selectively with the TpoR to facilitate megakaryocyte differentiation in platelets. Functional thrombopoietic activity was demonstrated by the proliferation and differentiation of primary human CD34(+) bone marrow cells into CD41(+) megakaryocytes. Measurements in platelets in several species indicated that eltrombopag specifically activates only the human and chimpanzee STAT pathways. The in vivo activity of eltrombopag was demonstrated by an increase of up to 100% in platelet numbers when administered orally (10 mg/kg per day for 5 days) to chimpanzees. In conclusion, eltrombopag interacts selectively with the TpoR without competing with Tpo, leading to the increased proliferation and differentiation of human bone marrow progenitor cells into megakaryocytes and increased platelet production. These results suggest that eltrombopag and Tpo may be able to act additively to increase platelet production.
Subject(s)
Benzoates/pharmacology , Cell Differentiation/drug effects , Hydrazines/pharmacology , Pyrazoles/pharmacology , Receptors, Thrombopoietin/agonists , Animals , Antigens, CD34/metabolism , Benzoates/administration & dosage , Blotting, Western , Bone Marrow Cells/cytology , Bone Marrow Cells/drug effects , Bone Marrow Cells/metabolism , Caspase 3/metabolism , Caspase 7/metabolism , Cell Line , Cell Proliferation/drug effects , Cells, Cultured , Electrophoretic Mobility Shift Assay , Humans , Hydrazines/administration & dosage , Megakaryocytes/cytology , Megakaryocytes/metabolism , Mice , Molecular Structure , Pan troglodytes , Platelet Membrane Glycoprotein IIb/metabolism , Pyrazoles/administration & dosage , Receptors, Thrombopoietin/chemistry , Signal Transduction/drug effectsABSTRACT
[reaction: see text] A novel and practical synthesis of 3-substituted 3H-pyrimidin-4-ones is described. The key step involves the cyclization of enamide esters, derived from readily available beta-keto esters, with trimethylaluminum and various primary amines.
ABSTRACT
Granulocyte colony-stimulating factor regulates neutrophil production by binding to a specific receptor, the granulocyte colony-stimulating factor receptor, expressed on cells of the granulocytic lineage. Recombinant forms of granulocyte colony-stimulating factor are used clinically to treat neutropenias. As part of an effort to develop granulocyte colony-stimulating factor mimics with the potential for oral bioavailability, we previously identified a nonpeptidyl small molecule (SB-247464) that selectively activates murine granulocyte colony-stimulating factor signal transduction pathways and promotes neutrophil formation in vivo. To elucidate the mechanism of action of SB-247464, a series of cell-based and biochemical assays were performed. The activity of SB-247464 is strictly dependent on the presence of zinc ions. Titration microcalorimetry experiments using a soluble murine granulocyte colony-stimulating factor receptor construct show that SB-247464 binds to the extracellular domain of the receptor in a zinc ion-dependent manner. Analytical ultracentrifugation studies demonstrate that SB-247464 induces self-association of the N-terminal three-domain fragment in a manner that is consistent with dimerization. SB-247464 induces internalization of granulocyte colony-stimulating factor receptor on intact cells, consistent with a mechanism involving receptor oligomerization. These data show that small nonpeptidyl compounds are capable of selectively binding and inducing productive oligomerization of cytokine receptors.
Subject(s)
Receptors, Granulocyte Colony-Stimulating Factor/chemistry , Receptors, Granulocyte Colony-Stimulating Factor/metabolism , Animals , Benzimidazoles/pharmacology , Bone Marrow Cells/metabolism , Calorimetry , Cell Line , Circular Dichroism , Cytokines/metabolism , Dimerization , Dose-Response Relationship, Drug , Edetic Acid/pharmacology , Guanidines/pharmacology , Ions , Ligands , Mice , Models, Chemical , Peptides/chemistry , Protein Binding , Protein Structure, Tertiary , Recombinant Fusion Proteins/metabolism , Signal Transduction , Transfection , Ultracentrifugation , ZincABSTRACT
High-throughput screening has resulted in the discovery of thiosemicarbazone thrombopoietin mimics. A shared pharmacophore hypothesis between this series and a previously identified class, the pyrazol-4-ylidenehydrazines, led to the rapid optimization of both potency and efficacy of the thiosemicarbazones. The application of high-throughput chemistry and purification techniques allowed for the rapid elucidation of structure-activity relationships.