Structural basis for the highly selective inhibition of MMP-13

Inhibitors for matrix metalloproteinases (MMPs) are under investigation for the treatment of cancer, arthritis, and cardiovascular disease. Here, we report a class of highly selective MMP-13 inhibitors (pyrimidine dicarboxamides) that exhibit no detectable activity against other MMPs. The high-resolution X-ray structures of three molecules of this series bound to MMP-13 reveal a novel binding mode characterized by the absence of interactions between the inhibitors and the catalytic zinc. The inhibitors bind in the S1' pocket and extend into an additional S1' side pocket, which is unique to MMP-13. We analyze the determinants for selectivity and describe the rational design of improved compounds with low nanomolar affinity.     

Assignments of the Pfr-Pr FTIR difference spectrum of cyanobacterial phytochrome Cph1 using 15N and 13C isotopically labeled phycocyanobilin chromophore

The reversible red and far-red light-induced transitions of cyanobacterial phytochrome Cph1 from Synechocystis PCC 6803 were investigated by Fourier transform infrared (FTIR) difference spectroscopy. High-quality light-induced Pfr-Pr difference FTIR spectra were recorded for the 58 kDa N-terminal domain of Cph1 by repetitive photochemical cycling and signal averaging. The Pfr-Pr difference spectra in H(2)O and D(2)O were very similar to those previously reported for full-length 85 kDa Cph1.(1) Published assignments were extended by analysis of the effects of (13)C and (15)N isotope substitutions at selected sites in the phycocyanobilin chromophore and by (15)N global labeling of the protein. The Pfr-Pr difference spectra were dominated by an amide I peak/trough at 1653 cm(-1)(+)/1631 cm(-1)(-) and a smaller amide II band at 1554 cm(-1). Labeling effects allowed specific chromophore assignments for the C(1)=O (1736 cm(-1)(-)/1724 cm(-1)(+)) and C(19)=O (1704 cm(-1)(-)) carbonyl vibrations, C=C vibrations at 1589 cm(-1)(+), and bands at 1537(-), 1512(+), 1491(-), 1163(+), 1151(-), 1134(+), 1109(-), and 1072(-) cm(-1) that must involve chromophore C-N bonds. A variety of additional changes were insensitive to isotope labeling of the chromophore. Effects of (15)N labeling of the protein were used to tentatively assign some of these to specific amino acid changes. Those insensitive to (15)N labeling included a protonated aspartic or glutamic acid at 1734 cm(-1)(-)/1722 cm(-1)(+) and a cysteine at 2575 cm(-1)(+)/2557 cm(-1)(-). Bands sensitive to (15)N protein labeling at 1487 cm(-1)(+)/1502 cm(-1)(-) might arise from trytophan and bands at 1261 cm(-1)(+)/1244 cm(-1)(-) and 1107 cm(-1)(-)/1095 cm(-1)(+) might arise from a histidine environment or protonation change. These assignments are discussed in light of the 15Z-E photoisomerization model of phototransformation and the associated protein conformational changes.     

Deposition of Oral Bacteria and Polystyrene Particles to Quartz and Dental Enamel in a Parallel Plate and Stagnation Point Flow Chamber

The aim of this paper is to determine to what extent (i) deposition of oral bacteria and polystyrene particles, (ii) onto quartz and dental enamel with and without a salivary conditioning film, (iii) in a parallel plate (PP) and stagnation point (SP) flow chamber and at common Peclet numbers are comparable. All three bacterial strains showed different adhesion behaviors, and even Streptococcus mitis BMS, possessing a similar cell surface hydrophobicity as polystyrene particles, did not mimic polystyrene particles in its adhesion behavior, possibly as a result of the more negative ζ potentials of the polystyrene particles. The stationary endpoint adhesion of all strains, including polystyrene particles, was lower in the presence of a salivary conditioning film, while also desorption probabilities under flow were higher in the presence of a conditioning film than in its absence. Deposition onto quartz and enamel surfaces was different, but without a consistent trend valid for all strains and polystyrene particles. It is concluded that differences in experimental results exist, and the process of bacterial deposition to enamel surfaces cannot be modeled by using polystyrene particles and quartz collector surfaces.     

Macromolecular Diffusion in Self-Assembling Biodegradable Thermosensitive Hydrogels

Hydrogel formation triggered by a change in temperature is an attractive mechanism for in situ gelling biomaterials for pharmaceutical applications such as the delivery of therapeutic proteins. In this study, hydrogels were prepared from ABA triblock polymers having thermosensitive poly(N-(2-hydroxypropyl) methacrylamide lactate) flanking A-blocks and hydrophilic poly(ethylene glycol) B-blocks. Polymers with fixed length A blocks (~22 kDA) but differing PEG-midblock lengths (2, 4 and 10 kDa) were synthesized and dissolved in water with dilute fluorescein isothiocyanate (FITC)-labeled dextrans (70 and 500 kDA). Hydrogels encapsulating the dextrans were formed by raising the temperature. Fluorescence recovery after photobleaching (FRAP) studies showed that diffusion coefficients and mobile fractions of the dextran dyes decreased upon elevating temperatures above 25 °C. Confocal laser scanning microscopy and cryo-SEM demonstrated that hydrogel structure depended on PEG block length. Phase separation into polymer-rich and water-rich domains occurred to a larger extent for polymers with small PEG blocks compared to polymers with a larger PEG block. By changing the PEG block length and thereby the hydrogel structure, mobility of FITC-dextran could be tailored. At physiological pH the hydrogels degraded over time by ester hydrolysis, resulting in increased mobility of the encapsulated dye. Since diffusion can be controlled according to polymer design and concentration, plus temperature, these biocompatible hydrogels are attractive as potential in situ gelling biodegradable materials for macromolecular drug delivery.     

A semigroup characterization of well-posed linear control systems

We study the well-posedness of a linear control system Σ(A,B,C,D) with unbounded control and observation operators. To this end we associate to our system an operator matrix $\mathcal{A}$ on a product space $\mathcal{X}^{p}$ and call it p-well-posed if $\mathcal{A}$ generates a strongly continuous semigroup on $\mathcal{X}^{p}$ . Our approach is based on the Laplace transform and Fourier multipliers. The results generalize and complement those of Curtain and Weiss (Int. Ser. Numer. Math. vol. 91. Birkhäuser, Basel, 1989), Staffans and Weiss (Trans. Am. Math. Soc. 354:3229–3262, 2002) and are illustrated by a heat equation with boundary control and point observation.     

Direct potentiometric immunoelectrodes

A method is described to determine Atrazine and its cross-reacting relatives in water, using a previously described graphite based one-way immunoelectrode and any standard millivoltmeter with low input bias current. The new procedure separates the potential measuring step from the incubation step. In this way, the conditions for highly stable potential measurements and for a most effective formation of the hapten (Atrazine) antibody complex can be optimized separately and all imponderable influence from ions in the analyte water is excluded. The limit of detection of such an electrode is some nanogram per liter.Part III: see [4]     

Determination of the impurity profile of ethyl-2-(4-[(5R)-3[4-(methoxycarboxamidoiminomethyl)-phenyl]-2- oxo-5-oxazolidinylmethyl]-1-piperazinyl) acetate, citrate, a highly active platelet aggregation inhibitor, by liquid chromatography-mass spectrometry.

Ethyl-2-(4-[(5R)-3-[4-(methoxycarboxamidoiminomethyl)-phenyl] -2-oxo-5-oxazolidinylmethyl]-1-piperazinyl) acetate, a glycoprotein IIb/IIIa antagonist, is a drug substance of the oxazolidinone type from Merck's research to be developed for the chronic oral treatment of thrombotic disorders. For the separation of the byproducts in the bulk drug substance, a reversed-phase HPLC gradient separation was developed. The eluent consisting of a nonvolatile phosphate buffer system had to be changed to a volatile acetate buffer system in order to perform on-line LC-MS coupling.With a triple quadrupole system it was possible to characterize most of the unknown byproducts occuring during synthesis and during scale-up to kg amounts of the bulk drug substance.