ABSTRACT
Chemical- and enzyme-coated beads (ChemBeads and EnzyBeads) were introduced recently as a universal strategy for the accurate dispensing of various solids in submilligram quantities using automated instrumentation or manual dispensing. The coated beads are prepared using a resonant acoustic mixer (RAM)-an instrument that may be available only to well-established facilities. In this study, we evaluated alternative coating methods for preparing ChemBeads and EnzyBeads without the use of a RAM. We also evaluated the effects of bead sizes on loading accuracy using 4 coating methods and 12 solids (9 chemicals and 3 enzymes) as test subjects. While our original RAM coating method is the most versatile for the broadest range of solids, high-quality ChemBeads and EnzyBeads that are suitable for high-throughput experimentation can be prepared using alternative methods. These results should make ChemBeads and EnzyBeads readily accessible as the core technology for setting up high-throughput experimentation platforms.
ABSTRACT
Eg5 is a kinesin motor protein that is responsible for bipolar spindle formation and plays a crucial role during mitosis. Loss of Eg5 function leads to the formation of monopolar spindles, followed by mitotic arrest, and subsequent cell death. Several cell-permeable small molecules have been reported to inhibit Eg5 and some have been evaluated as anticancer agents. We now describe the design, synthesis, and biological evaluation of photoswitchable variants with five different pharmacophores. Our lead compound Azo-EMD is a cell permeable azobenzene that inhibits Eg5 more potently in its light-induced cis form. This activity decreased the velocity of Eg5 in single-molecule assays, promoted formation of monopolar spindles, and led to mitotic arrest in a light dependent way.
Subject(s)
Azo Compounds/pharmacology , Kinesins/antagonists & inhibitors , Mitosis/drug effects , Azo Compounds/chemical synthesis , Azo Compounds/chemistry , Humans , Kinesins/metabolism , Photochemical Processes , Spindle Apparatus/drug effectsABSTRACT
Photoswitchable lipids are emerging tools for the precise manipulation and study of lipid function. They can modulate many aspects of membrane biophysics, including permeability, fluidity, lipid mobility and domain formation. They are also very useful in lipid physiology and enable optical control of a wide array of lipid receptors, such as ion channels, G protein-coupled receptors, nuclear hormone receptors, and enzymes that translocate to membranes. Enzymes involved in lipid metabolism often process them in a light-dependent fashion. Photoswitchable lipids complement other functionalized lipids widely used in lipid chemical biology, including isotope-labeled lipids (lipidomics), fluorescent lipids (imaging), bifunctional lipids (lipid-protein crosslinking), photocaged lipids (photopharmacology), and other labeled variants.
Subject(s)
Lipids/chemistry , Lipid Metabolism , Molecular Structure , Photochemical ProcessesABSTRACT
Spleen tyrosine kinase (SYK) is a non-receptor cytosolic kinase. Due to its pivotal role in B cell receptor and Fc-receptor signaling, inhibition of SYK has been targeted in a variety of disease areas. Herein, we report the optimization of a series of potent and selective SYK inhibitors, focusing on improving metabolic stability, pharmacokinetics and hERG inhibition. As a result, we identified 30, which exhibited no hERG activity but unfortunately was poorly absorbed in rats and mice. We also identified a SYK chemical probe, 17, which exhibits excellent potency at SYK, and an adequate rodent PK profile to support in vivo efficacy/PD studies.
Subject(s)
Indazoles/pharmacology , Protein Kinase Inhibitors/pharmacology , Syk Kinase/antagonists & inhibitors , Animals , Binding Sites , Caco-2 Cells , Crystallography, X-Ray , ERG1 Potassium Channel/antagonists & inhibitors , Humans , Indazoles/chemical synthesis , Indazoles/metabolism , Indazoles/pharmacokinetics , Mice , Microsomes, Liver/metabolism , Molecular Structure , Protein Binding , Protein Kinase Inhibitors/chemical synthesis , Protein Kinase Inhibitors/metabolism , Protein Kinase Inhibitors/pharmacokinetics , Rats, Wistar , Structure-Activity Relationship , Syk Kinase/chemistry , Syk Kinase/metabolismABSTRACT
Cyclin-dependent kinase (CDK) 12 knockdown via siRNA decreases the transcription of DNA-damage-response genes and sensitizes BRCA wild-type cells to poly(ADP-ribose) polymerase (PARP) inhibition. To recapitulate this effect with a small molecule, we sought a potent, selective CDK12 inhibitor. Crystal structures and modeling informed hybridization between dinaciclib and SR-3029, resulting in lead compound 5 [(S)-2-(1-(6-(((6,7-difluoro-1H-benzo[d]imidazol-2-yl)methyl)amino)-9-ethyl-9H-purin-2-yl)piperidin-2-yl)ethan-1-ol]. Further structure-guided optimization delivered a series of selective CDK12 inhibitors, including compound 7 [(S)-2-(1-(6-(((6,7-difluoro-1H-benzo[d]imidazol-2-yl)methyl)amino)-9-isopropyl-9H-purin-2-yl)piperidin-2-yl)ethan-1-ol]. Profiling of this compound across CDK9, 7, 2, and 1 at high ATP concentration, single-point kinase panel screening against 352 targets at 0.1â µm, and proteomics via kinase affinity matrix technology demonstrated the selectivity. This series of compounds inhibits phosphorylation of Ser2 on the C-terminal repeat domain of RNA polymeraseâ II, consistent with CDK12 inhibition. These selective compounds were also acutely toxic to OV90 as well as THP1 cells.
Subject(s)
Benzimidazoles/chemistry , Bridged Bicyclo Compounds, Heterocyclic/chemistry , Cyclin-Dependent Kinases/antagonists & inhibitors , Piperidines/chemical synthesis , Purines/chemistry , Pyridinium Compounds/chemistry , Benzimidazoles/pharmacology , Bridged Bicyclo Compounds, Heterocyclic/pharmacology , Cell Line , Cell Survival/drug effects , Crystallization , Cyclic N-Oxides , Cyclin-Dependent Kinase 9/antagonists & inhibitors , Drug Design , Humans , Indolizines , Kinetics , Phosphorylation , Piperidines/pharmacology , Protein Binding , Purines/pharmacology , Pyridinium Compounds/pharmacology , RNA Polymerase II/metabolism , Stereoisomerism , Structure-Activity RelationshipABSTRACT
Cyclization of 1,6-diynes promoted by stoichiometric Ga(III) halides produces vinyl halides in good to excellent yields. Under acidic conditions, initially formed iodocyclization products undergo in situ Friedel-Crafts cyclizations, giving access to iodoindenopyridines. Application of the vinyl halides in cross-coupling reactions has been explored, and mechanistic aspects of the cyclization are discussed.