NONUNIFORMLY AND RANDOMLY SAMPLED SYSTEMS

Problems with missing data, sampling irregularities and randomly sampled systems are the topics covered by this dissertation. The spectral analysis of a series of periodically repeated sampling patterns is developed. Parameter estimation of autoregressive moving average models using partial observations and an algorithm to fill in the missing data are proved and demonstrated by simulation programs. Interpolation of missing data using bandlimiting assumptions and discrete Fourier transform techniques is developed. Representation and analysis of randomly sampled linear systems with independent and identically distributed sampling intervals are studied. The mean, and the mean-square behavior of a multiple-input multiple-output randomly sampled system are found. A definition of and results concerning the power spectral density gain are also given. A complete FORTRAN simulation package is developed and implemented in a microcomputer environment demonstrating the new algorithms

Discovery and Characterization of 2-Anilino-4- (Thiazol-5-yl)Pyrimidine Transcriptional CDK Inhibitors as Anticancer Agents

The main difficulty in the development of ATP antagonist kinase inhibitors is target specificity, since the ATP-binding motif is present in many proteins. We introduce a strategy that has allowed us to identify compounds from a kinase inhibitor library that block the cyclin-dependent kinases responsible for regulating transcription, i.e., CDK7 and especially CDK9. The screening cascade employs cellular phenotypic assays based on mitotic index and nuclear p53 protein accumulation. This permitted us to classify compounds into transcriptional, cell cycle, and mitotic inhibitor groups. We describe the characterization of the transcriptional inhibitor class in terms of kinase inhibition profile, cellular mode of action, and selectivity for transformed cells. A structural selectivity rationale was used to optimize potency and biopharmaceutical properties and led to the development of a transcriptional inhibitor, 3,4-dimethyl-5-[2-(4-piperazin-1-yl-phenylamino)-pyrimidin-4-yl]-3H-thiazol-2-one, with anticancer activity in animal models

Structures of cyclophilin-ligand complexes

No abstract available

Catch the kinase conformer

Protein kinases exist in inactive and active states, but little attention has been paid to which state is or should be the target in drug discovery efforts. In this issue of Chemistry & Biology, Okram et al. [1] tackle this issue and show that inhibitors can be designed specifically to bind to inactive Abl

Volumetric changes to the molecular structure of beta-lactoglobulin processed at high pressure

We measured in-situ the volumetric changes to the molecular structure of the bovine milk protein β-lactoglobulin in a series of high-pressure processing experiments. We used the so-called μPVT device at hydrostatic pressures up to 500 MPa under isothermal conditions of 25 °C, the protein in solution, prepared at both pH 5.0 and 7.0, in a series of compression and decompression cycles. Significant irreversible volumetric changes were found, most notably with a marked step decrease in molar volume of 1.3 litre mol-1 occurring between 10 and 17 MPa. Irreversible molar volume changes of 2.16 litre mol-1 were found when pressures above 17 MPa were applied. This is thought to be due in part to a collapse of the inner calyx. Volume changes were confirmed by measuring the unit-cell volume of the crystalline protein. The effects of pH were indistinguishable. These pressures are considerably less than previously thought necessary for this protein

Strong Binding of C-Glycosylic1,2-Thiodisaccharides to Galectin-3─Enthalpy-Driven Affinity Enhancement by Water-Mediated Hydrogen Bonds

Galectin-3 is involved in multiple pathways of many diseases, including cancer, fibrosis, and diabetes, and it is a validated pharmaceutical target for the development of novel therapeutic agents to address unmet medical needs. Novel 1,2-thiodisaccharides with a C-glycosylic functionality were synthesized by the photoinitiated thiol-ene click reaction of O-peracylated 1-C-substituted glycals and 1-thio-glycopyranoses. Subsequent global deprotection yielded test compounds, which were studied for their binding to human galectin-3 by fluorescence polarization and isothermal titration calorimetry to show low micromolar K d values. The best inhibitor displayed a K d value of 8.0 μM. An analysis of the thermodynamic binding parameters revealed that the binding Gibbs free energy (Δ G) of the new inhibitors was dominated by enthalpy (Δ H). The binding mode of the four most efficient 1,2-thiodisaccharides was also studied by X-ray crystallography that uncovered the unique role of water-mediated hydrogen bonds in conferring enthalpy-driven affinity enhancement for the new inhibitors. This 1,2-thiodisaccharide-type scaffold represents a new lead for galectin-3 inhibitor discovery and offers several possibilities for further development

Solvent Selection for Insoluble Ligands, a Challenge for Biological Assay Development: A TNF-α/SPD304 Study

Many active compounds may be excluded from biological assays due to their low aqueous solubility. In this study, a simple method for the determination of the solubility of compounds containing aromatic rings is proposed. In addition to DMSO, five organic solvents for screening experiments of TNF-α inhibitors were explored. DMSO and PEG3350 were the most suitable for both protein stability and ligand-binding experiments. In addition, glycerol is a promising solvent for the screening of other compounds for which it might provide acceptable solubilization, due to its strong tendency to preserve the protein. Moreover, a fluorescence binding assay was developed using the TNF-α/SPD304 system, and a <i>K</i>_d of 5.36 ± 0.21 μM was determined. The results of this study could be used for the future screening of potential TNF-α inhibitors, while the protocols developed in this work could be applied to other proteins