ABSTRACT
We synthesized reversible terminators with tethered inhibitors for next-generation sequencing. These were efficiently incorporated with high fidelity while preventing incorporation of additional nucleotides, and we used them to sequence canine bacterial artificial chromosomes in a single-molecule system that provided even coverage for over 99% of the region sequenced. This single-molecule approach generated high-quality sequence data without the need for target amplification and thus avoided concomitant biases.
Subject(s)
Chromosomes, Artificial, Bacterial/chemistry , DNA/chemistry , Nucleotides/chemistry , Sequence Analysis, DNA/methods , Animals , Chromatography, High Pressure Liquid , Chromosomes, Artificial, Bacterial/genetics , Computer Simulation , Dogs , Nucleotides/genetics , Sensitivity and Specificity , Substrate SpecificityABSTRACT
One of the major hurdles in the post-genomic era is to understand the function of genes and the interplay of many different cellular proteins. This is especially important for drug development. Capture compound mass spectrometry (CCMS) addresses this challenge by selectively reducing the complexity of the proteome. Capture compounds are trifunctional molecules: a selectivity function reversibly interacts via affinity with proteins; a reactivity function irreversibly forms a covalent bond outside the affinity binding site; and a sorting/pullout function allows the captured protein(s) to be isolated from cellular lysate for mass spectrometric analysis and characterization by database queries. In the present study, we demonstrate the use of a CCMS capture compound with a sulfonamide drug analog as its selectivity function, isolating an expected target protein from cell lysates containing a large excess of other "non-target" proteins. A future application of CCMS is to define or confirm drug target proteins and their mechanisms of drug action, or to discover off-target proteins that cause side effects, enabling subsequent drug structure optimization.
Subject(s)
Drug Design , Proteins/analysis , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Protein Binding , Sulfonamides/metabolism , Sulfonamides/pharmacologyABSTRACT
The binding affinities at rat A1, A2a, and A3 adenosine receptors of a wide range of heterocyclic derivatives have been determined. Mono-, bi-, tricyclic and macrocyclic compounds were screened in binding assays, using either [3H]PIA or [3H]CGS 21680 in rat brain membranes or [125I]AB-MECA in CHO cells stably transfected with rat A3 receptors. Several new classes of adenosine antagonists (e.g. 5-oxoimidazopyrimidines and a pyrazoloquinazoline) were identified. Various sulfonylpiperazines, 11-hydroxytetrahydrocarbazolenine, 4H-pyrido[1,2-a]pyrimidinone, folic acid, and cytochalasin H and J bound to A3 receptors selectively. Moreover, cytochalasin A, which bound to A1 adenosine receptors with Ki value of 1.9 µM, inhibited adenylyl cyclase in rat adipocytes, but not via reversible A1 receptor binding.
