Peptide microarrays for the determination of protease substrate specificity

A method is described for the preparation of substrate microarrays that allow for the rapid determination of protease substrate specificity. Peptidyl coumarin substrates, synthesized on solid support using standard techniques, are printed onto glass slides using DNA microarraying equipment. The linkage from the peptide to the slide is formed through a chemoselective reaction, resulting in an array of uniformly displayed fluorogenic substrates. The arrays can be treated with proteases to yield substrate specificity profiles. Standard instrumentation for visualization of microarrays can be used to obtain comparisons of the specificity constants for all of the prepared substrates. The utility of these arrays is demonstrated by the selective cleavage of preferred substrates with trypsin, thrombin, and granzyme B, and by assessing the extended substrate specificity of thrombin using a microarray of 361 different peptidyl coumarin substrates.     

Kinetic evaporation and condensation rates and their coefficients

The origins and properties of evaporation and condensation coefficients are described, and results of their measurement are surveyed for water and liquid metals. Contrasts are drawn as to whether their values are likely to limit practical transfer rates at plane surfaces and on aerosols, and between evaporation and condensation. Existing theories which express condensation and evaporation rates in terms of the coefficients are described. Their failure to satisfy energy and momentum conservation as well as mass conservation at the interface is remedied by constructing a new theory which also starts with vapor molecules in Maxwell-Boltzmann distributions. The resulting rates are shown to be close to those predicted by more accurate theories in which the Boltzmann transport equation is solved.     

Determination of vitamins A (retinol) and E (alpha-tocopherol) in foods by liquid chromatography: collaborative study

A collaborative study was conducted for the determination of vitamins A and E. Existing AOAC liquid chromatographic (LC) methods are suited for specific vitamins A and E analytical applications. This method differs from existing methods in that it can be used to assay samples in all 9 sectors of the food matrix. Standards and test samples are saponified in basic ethanol-water solution, neutralized, and diluted, converting fats to fatty acids and retinol esters and tocopherol esters to retinol and tocopherol, respectively. Retinol and alpha-tocopherol are quantitated on separate LC systems, using UV detection at 313 or 328 nm for retinol, and fluorescence detection (excitation 290 nm, emission 330 nm) for alpha-tocopherol. Vitamin concentrations are calculated by comparison of the peak heights or peak areas of vitamins in test samples with those of standards.     

Pore morphologies in disordered nanoporous thin films

Materials with nanometer size heterogeneities are commonplace in the chemical and biological sciences (e.g, polymer blends, microemulsions, gels) and often exhibit complex morphologies. Although this morphology has a dramatic effect on the materials' properties, it is often difficult to accurately characterize. We describe a method, using small-angle X-ray scattering data, of generating representative three-dimensional morphologies of isotropic two-phase materials where the morphology is disordered, and we apply this to thin films containing nanometer sized pores with a range of porosities (4-44%). These representations provide a visualization of the pore morphology, give the pore size scale and extent of interconnection, and permit the determination of the transitions from closed pore to interconnected pores to bicontinuous morphology.     

ortho-metallation reactions involving some triphenyl phosphite complexes of osmium

Osmium triphenylphosphine complexes, OsH₄(PPh₃)₃, OsH₂ (CO)(PPh₃)₃ and OsHCl(CO)(PPh₃)₃ react with triphenyl phosphite in boiling organic solvents to yield triphenyl phosphite derivatives which subsequently undergo ortho-metallation reactions.     

A novel general route for the preparation of enantiopure imidazolines

A novel procedure for the preparation of enantiopure 1,4-disubstituted 2-imidazolines is reported. Enantiopure beta-amino alcohols are converted into N-hydroxyethylamides, which are reacted with excess thionyl chloride, or with thionyl chloride followed by phosphorus pentachloride to yield N-chloroethylimidoyl chlorides. These intermediates are treated with amines and anilines to produce N-chloroethylamidines, which are converted into imidazolines upon workup with aqueous hydroxide. The method is simple and efficient and has been used to prepare a wide variety of enantiopure imidazolines, in a modular fashion, from readily available amino alcohols.     

Mixed-metal cluster chemistry Part 20. Syntheses, crystal structures and electrochemical studies of W2Ir2(μ-L)(CO)8(η-C5H4Me)2 (L=dppe, dppf)

The 60-electron tetrahedral clusters W₂Ir₂(μ-L)(CO)₈(η⁵-C₅H₄Me)₂ [L=dppe (2), dppf (3)] have been prepared from reaction between W₂Ir₂(CO)₁₀(η⁵-C₅H₄Me)₂ (1) and the corresponding diphosphine in 52 and 66% yields, respectively. A structural study of 2 reveals that three edges of a WIr₂ face are spanned by bridging carbonyls, that the iridium-ligated diphosphine coordinates diaxially and that the tungsten-bound methylcyclopentadienyls coordinate axially and apically with respect to the plane of bridging carbonyls. A structural study of 3 reveals that the dppf ligand bridges an Ir---Ir bond which is also spanned by a bridging carbonyl; tungsten-ligated methylcyclopentadienyl ligands and terminal carbonyls result in electronic asymmetry (17e and 19e iridium atoms) in the electron-precise cluster. Both clusters show two reversible one-electron oxidation processes and an irreversible two-electron reduction; the dppf-containing cluster 3 has a further, irreversible, one-electron oxidation process. UV–vis-NIR spectroelectrochemical studies of the 2→2⁺→2²⁺ progression reveal the appearance of a low-energy transition on oxidation to 2⁺ which persists on further oxidation to 2²⁺.     

Syntheses and conformational analyses of some 3-amino-2,5-dioxo-2,3,4,5-tetrahydro-1H-1-benzazepine derivatives: X-ray crystal structure of 35–3-[[(1,1-dimethylethoxy)carbonyl]amino]-2,5-dioxo-2,3,4,5-tetrahydro-1H-1-benzazepine

The constrained dipeptide mimic 1 was synthesized from 2 in three steps with 65% overall yield. Analyses of the ¹H nmr data of a number of 3-amino-2,5-dioxo-2,3,4,5-tetrahydro-1H-1-benzazepine derivatives led to the conclusion that these compounds adopt a similar conformation and that this ring system is rigid. X-ray crystallography was used to define the structure of 3 , and computer-aided energy minimization of 6 gave a preferred conformation similar to that observed in the crystal of 3 .     

Synthesis of a diverse library of mechanism-based cysteine protease inhibitors

We report improvements of our method for the solid-phase synthesis of mechanism-based mercaptomethyl ketone inhibitors of cysteine proteases (Lee, A.; Huang, L.; Ellman, J. A. J. Am. Chem. Soc. 1999, 121, 9907-9914). Specifically, Fmoc-protected chloromethyl ketones were used, rather than the Alloc-protected counterparts. In addition, we further demonstrated that diverse polar functionality can be incorporated at the R1', R1, and R2 sites, in contrast to our previous efforts, where primarily hydrophobic groups were incorporated at these positions. On the basis of these results, a 2016-membered library of potential mercaptomethyl ketone inhibitors was prepared that incorporated diverse functionality. The library was screened against cathepsin B, which is implicated in cancer, resulting in the identification of single-digit nanomolar inhibitors. Because of the diverse functionality incorporated in this library, it should be a rich source of potent inhibitors against many other cysteine proteases.     

Macrocycle synthesis strategy based on step-wise “adding and reacting” three components enables screening of large combinatorial libraries

Macrocycles provide an attractive modality for drug development, but generating ligands for new targets is hampered by the limited availability of large macrocycle libraries. We have established a solution-phase macrocycle synthesis strategy in which three building blocks are coupled sequentially in efficient alkylation reactions that eliminate the need for product purification. We demonstrate the power of the approach by combinatorially reacting 15 bromoacetamide-activated tripeptides, 42 amines, and 6 bis-electrophile cyclization linkers to generate a 3780-compound library with minimal effort. Screening against thrombin yielded a potent and selective inhibitor (K_i = 4.2 ± 0.8 nM) that efficiently blocked blood coagulation in human plasma. Structure–activity relationship and X-ray crystallography analysis revealed that two of the three building blocks acted synergistically and underscored the importance of combinatorial screening in macrocycle development. The three-component library synthesis approach is general and offers a promising avenue to generate macrocycle ligands to other targets.

Combination of three efficient chemical reactions allows for solution-phase synthesis of 3780 macrocycles and identification of potent thrombin inhibitor.