Efficient synthesis of tris(4-imidazolyl)methanol derivatives

Biomimetic tris(4-imidazolyl)carbinol derivatives are prepared from imidazole in a short, high-yielding sequence via sulfonamide 1, which is converted to the 2-silylated carbinol 2 by one-pot, sequential 2-functionalization and then 4(5)-functionalization. Alcohol 2 can be transformed either to the parent carbinol 3 or to a desilylated sulfonamide derivative 4. The tripodal alcohol 3 is a convenient precursor to ethers by solvolysis and to metal complexes, as illustrated by the preparation of a bis-tripod complex with iron(III).     

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature

Background  

We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases.     

Asymmetric synthesis of protected 1,2-amino alcohols using tert-butanesulfinyl aldimines and ketimines.

tert-Butanesulfinyl aldimines and ketimines bearing an alpha-benzyloxy or alpha-silyloxy substituent serve as precursors in the synthesis of protected 1,2-amino alcohols in high yields and diastereoselectivities. General protocols are described for the addition of unbranched alkyl, branched alkyl, and aryl organometallic reagents to N-sulfinyl aldimines 1 and 2 and ketimines 5 and 6. Furthermore, the selective N- or O-deprotection of sulfinamide products 3, 4, 7, and 8 is described, enabling further synthetic transformations of the reaction products.     

A synthetic quest for tris(imidazolyl) carboxylates and their metal complexes: active site models for quercetin 2,3-dioxygenases and other non-heme redox metalloenzymes

Synthetic routes to tris(imidazolyl)carboxylate ligands and representative metal complexes are reported, which provide more accurate active site models for several classes of redox metalloenzymes. In the first route a hydroxypivalate ester is converted in four regioselective steps to an imidazole diester 4; this is then converted to tris(imidazolyl)carboxylic acid ligand 9, featuring regiospecific double addition of an N-protected lithio-imidazole to an imidazole diester 8. Ligand 9 forms a Co(III) complex, (9)(9-H)Co (10), characterized by X-ray diffraction, coordinated via two imidazole units and the carboxylate. A second route was developed, which provides more soluble ligands that are less prone to form oligomeric complexes. It utilizes addition of the Grignard reagent from 4-iodo-2-isopropylimidazole 12 to an imidazole diester 13, producing atropisomeric tris(imidazolyl)carbinol esters 15M. Treatment of 15M with [Cu(CH₃CN)₄]PF₆ gives a trinuclear complex 16 having alkoxide bridges between neighboring Cu atoms. A third route avoids the bridging alkoxo groups by reduction of tris(imidazolyl)carbinol 15M to the tris(imidazolyl)methane ester 17, which is hydrolyzed to the tris(imidazolyl)methane carboxylic acid 11a. This ligand reacts with [Cu(CH₃CN)₄]PF₆ to produce dinuclear complex [(11a-H)₂Cu₂](PF₆)₂ (18), whose X-ray crystal structure shows each copper in a distorted square pyramidal geometry with coordination to the three imidazoles and two bridging carboxylate oxygens. Complex 18 is geometrically similar to the active site copper in quercetin 2,3-dioxygenase.     

Molecular recognition of protein surfaces: high affinity ligands for the CBP KIX domain

Potent and specific inhibitors of protein.protein interactions have potential both as therapeutic compounds and biological tools, yet discovery of such molecules remains a challenge. Our laboratory has recently described a strategy, called protein grafting, for the identification of miniature proteins that bind protein surfaces with high affinity and specificity and inhibit the formation of protein.protein complexes. In protein grafting, those residues that comprise a functional alpha-helical binding epitope are stabilized on the solvent-exposed alpha-helical face of the small yet stable protein avian pancreatic polypeptide (aPP). Here we use protein grafting in combination with molecular evolution by phage display to identify phosphorylated peptide ligands that recognize the shallow surface of CBP KIX with high nanomolar to low micromolar affinity. Furthermore, we show that grafting of the CBP KIX-binding epitope of CREB KID onto the aPP scaffold yields molecules capable of high affinity recognition of CBP KIX even in the absence of phosphorylation. Importantly, both classes of designed ligands exhibit high specificity for the target CBP KIX domain over carbonic anhydrase and calmodulin, two unrelated proteins that bind hydrophobic or alpha-helical molecules that might be encountered in vivo.     

Characterization of unusual alkenones and alkyl alkenoates by electron ionization gas chromatography/mass spectrometry

Unusual long-chain, diunsaturated alkenones and alkyl alkenoates exhibiting double bonds separated by three methylene units instead of the more usual five were characterized by electron ionization (EI) gas chromatography/mass spectrometry. In a first step, the positions of the double bonds of these compounds (isolated from Holocene Black Sea sediments) were confirmed after OsO4 treatment and silylation. Mass spectra of the resulting tetratrimethylsilyloxy derivatives allowed unambiguous determination of the positions of unsaturations. The EI mass spectra of the non-derivatized compounds were then compared with those of the alkenones and alkyl alkenoates having double bonds separated by five methylene units. Specific fragment ions resulting from gamma-H rearrangements were found to be prominent in EI mass spectra of these unusual 'Black Sea' diunsaturated alkenones and alkyl alkenoates. These fragment ions can be used to characterize these compounds in natural samples without the need for laborious derivatization treatments.     

Dynamic Interchanging Native States of Lymphotactin Examined by SNAPP-MS

The human chemokine lymphotactin (Ltn) is a remarkable protein that interconverts between two unrelated native state structures in the condensed phase. It is possible to shift the equilibrium toward either conformation with selected sequence substitutions. Previous results have shown that a disulfide-stabilized variant preferentially adopts the canonical chemokine fold (Ltn10), while a single amino acid change (W55D) favors the novel Ltn40 dimeric structure. Selective noncovalent adduct protein probing (SNAPP) is a recently developed method for examining solution phase protein structure. Herein, it is demonstrated that SNAPP can easily recognize and distinguish between the Ltn10 and Ltn40 states of lymphotactin in aqueous solution. The effects of organic denaturants, acid, and disulfide bond reduction and blocking were also examined using SNAPP for the CC3, W55D, and wild type proteins. Only disulfide reduction was shown to significantly perturb the protein, and resulted in considerably decreased adduct formation consistent with loss of tertiary/secondary structure. Cold denaturation experiments demonstrated that wild-type Ltn is the most temperature sensitive of the three proteins. Examination of the higher charge states in all experiments, which are presumed to represent transition state structures between Ltn-10 and Ltn-40, reveals increased 18C6 attachment relative to the more folded structures. This observation is consistent with increased competitive intramolecular hydrogen bonding, which may guide the transition. Experiments examining the gas phase structures revealed that all three proteins can be structurally distinguished in the gas phase. In addition, the gas phase experiments enabled identification of preferred adduct binding sites.     

A triangular palladium(II) supramolecular coordination complex based on 1,4‐bis(1H‐imidazol‐1‐yl)benzene and (2,2′‐bipyridyl)palladium(II) nitrate: synthesis and crystal structure

The self‐assembly of ditopic bis(1H‐imidazol‐1‐yl)benzene ligands ( L ^H) and the complex (2,2′‐bipyridyl‐κ²N,N′)bis(nitrato‐κO)palladium(II) affords the supramolecular coordination complex tris[μ‐bis(1H‐imidazol‐1‐yl)benzene‐κ²N³:N^3′]‐triangulo‐tris[(2,2′‐bipyridyl‐κ²N,N′)palladium(II)] hexakis(hexafluoridophosphate) acetonitrile heptasolvate, [Pd₃(C₁₀H₈N₂)₃(C₁₂H₁₀N₄)₃](PF₆)₆·7CH₃CN, 2 . The structure of 2 was characterized in acetonitrile‐d₃ by ¹H/¹³C NMR spectroscopy and a DOSY experiment. The trimeric nature of supramolecular coordination complex 2 in solution was ascertained by cold spray ionization mass spectrometry (CSI–MS) and confirmed in the solid state by X‐ray structure analysis. The asymmetric unit of 2 comprises the trimetallic Pd complex, six PF₆^? counter‐ions and seven acetonitrile solvent molecules. Moreover, there is one cavity within the unit cell which could contain diethyl ether solvent molecules, as suggested by the crystallization process. The packing is stabilized by weak inter‐ and intramolecular C—H…N and C—H…F interactions. Interestingly, the crystal structure displays two distinct conformations for the L ^H ligand (i.e. syn and anti), with an all‐syn‐[Pd] coordination mode. This result is in contrast to the solution behaviour, where multiple structures with syn/anti‐ L ^H and syn/anti‐[Pd] are a priori possible and expected to be in rapid equilibrium.     

The effect of CpG-ODN on antigen presenting cells of the foal

Background  

Cytosine-phosphate-guanosine oligodeoxynucleotide (CpG-ODN) has been used successfully to induce immune responses against viral and intracellular organisms in mammals. The main objective of this study was to test the effect of CpG-ODN on antigen presenting cells of young foals.