Structure and dynamics of metallomacrocycles: recognition of zinc xylyl-bicyclam by an HIV coreceptor

As platforms for the design of metal-based therapeutic and diagnostic agents, macrocycles are rigid enough to provide strong metal binding sites and orient functional groups stereoselectively, yet flexible enough to accommodate structural changes required for induced-fit recognition of biological targets. We consider the recognition of the Zn(II) complex of the bis-tetraazamacrocycle xylyl-bicyclam, a potent anti-HIV agent, by the coreceptor CXCR4, a G-protein-coupled receptor used by HIV for membrane fusion and cell entry. NMR studies show that the macrocycles of Zn(II)(2)-xylyl-bicyclam perchlorate exist in aqueous solution as two major configurations, trans-I (nitrogen chirality R,S,R,S), and trans-III (S,S,R,R). Acetate addition induced a major structural change. X-ray crystallography shows that the acetate complex contains the unusual cis-V cyclam configuration (R,R,R,R and folded) with bidentate coordination of acetate to Zn(II) plus second-coordination-sphere double H-bond formation between diagonal NH protons on the opposite cyclam face and acetate carboxylate oxygens. Detailed 1D and 2D NMR studies show that the major configuration of Zn(II)(2)-xylyl-bicyclam acetate in aqueous solution is cis-V/trans-I. Molecular modeling shows that an analogous cis-V site can be formed when Zn(II)(2)-xylyl-bicyclam binds to CXCR4, involving the carboxylate groups of Asp262 (Zn(II) coordination) and Glu288 (double H-bonding). The second cyclam can adopt the trans-I (or trans-III) configuration with Zn(II) binding to Asp171. These interactions are consistent with the known structure-activity relationships for bicyclam anti-HIV activity and receptor mutation. Consideration of the anti-HIV activity of xylyl-bicyclam complexes of other metal ions suggests that affinity for carboxylates, configurational flexibility, and kinetic factors may all play roles in receptor recognition. For example, Pd(II) cyclam complexes interact only weakly with axial ligands and are inflexible and inactive, whereas Co(III) cyclams bind carboxylates strongly, are configurationally flexible, and yet have low activity. Our findings should aid the design of new generations of active macrocycles including highly specific chemokine receptor antagonists.     

Detailed analysis of α,ω-bis(4-hydroxybutyl) poly(dimethylsiloxane) using GPC-MALDI TOF mass spectrometry

In this study the prepolymer alpha,omega-bis(4-hydroxybutyl) poly(dimethylsiloxane), used in the formulation of oxygen permeable films, is evaluated by gel permeation chromatography (GPC) combined with matrix assisted laser desorption ionization (MALDI) time of flight (TOF) mass spectrometry (MS). Two unexpected mass distributions are observed in the mass spectra. Reaction schemes for the formation of these distributions are proposed. A solution phase trimethylsilane end group modification was performed on the prepolymer to determine whether the unexpected mass distributions occur as impurities from synthesis or as artifacts from the MS process. Evaluation of the TMS modified prepolymer indicates the unexpected mass distributions indeed occur as impurities from the synthetic procedure. Average molecular weight values are determined by traditional GPC, direct MALDI-TOF MS, and GPC-MALDI-TOF MS methods and the results are compared.     

Exploring the hydroxylation-dehydrogenation connection: novel catalytic activity of castor stearoyl-ACP Delta(9) desaturase

The novel product profile obtained by incubating chiral fluorinated substrate analogues with castor stearoyl-ACP Delta(9) desaturase has been rationalized through a series of labeling studies. It was found that the introduction of the Z-double bond between C-9 and C-10 of the parent substrate occurs with pro-R enantioselectivity--a result that accounts for the observed stereochemistry of oxidation products derived from (9R)- and (9S)-9-fluorostearoyl-ACP. Oxidation of (9R)-9-fluorostearoyl-ACP occurs via at least two rapidly interchanging substrate conformations in the active site as detected by reaction pathway branching induced by deuteration at C-10 and C-11. Hydroxylation and desaturation of this substrate share the same site of initial oxidative attack.     

GnRH binding RNA and DNA Spiegelmers: a novel approach toward GnRH antagonism

Mirror-image oligonucleotide ligands (Spiegelmers) that bind to the pharmacologically relevant target gonadotropin-releasing hormone I (GnRH) with high affinity and high specificity have been identified using the Spiegelmer technology. GnRH is a decapeptide that plays an important role in mammalian reproduction and sexual maturation and is associated with several benign and malignant diseases. First, aptamers that bind to D-GnRH with dissociation constants of 50-100 nM were isolated out of RNA and DNA libraries. The respective enantiomers of the DNA and RNA aptamers were synthesized, and their binding to L-GnRH was shown. These Spiegelmers bind to L-GnRH with similar affinity to that of the corresponding aptamers that bind to D-GnRH. We further demonstrated dose-dependent inhibition of GnRH-induced Ca(2+) release in Chinese hamster ovary cells that were stably transfected with the human GnRH receptor.     

Pb(3)F(5)NO(3), a cationic layered material for anion-exchange

Our research involves the development of new cationic materials for anion-based applications. We report the solvothermal synthesis and characterization of Pb(3)F(5)NO(3), a new layered lead fluoride material that, unlike the majority of layered and open-framework materials, is cationic in charge. The structure consists of polyhedral lead centers connected by doubly and triply bridging fluoride groups. We quantitatively exchanged the interlamellar nitrate groups of Pb(3)F(5)NO(3) for dichromate, under ambient aqueous conditions. Nuclear magnetic resonance and UV-vis spectroscopy show the reaction proceeds to 61.0% completion in several days. The material is also stable to 450 degrees C, which is vastly superior to organic resins that are still the standard for anion-exchange. The presence of extraframework anions also opens up other potentially unique anion-based properties, such as new catalytic reactions, anion intercalation, or growth of anionic clusters within the void spaces of the cationic material.     

Synthesis of pyrroloquinolines as indole analogues of flavonols

7-Acetyl-4,6-dimethoxy-3-phenylindole 10 was converted into a range of 7-indolyl chalcones 13 by reaction with aryl aldehydes under basic conditions. Oxidation of the chalcones 13 with alkaline hydrogen peroxide gave the isolable epoxides 14, which were cyclized with further base treatment into the indole flavonols, or 5-hydroxy-6-oxopyrroloquinolines 15. The related compounds 25 and 26, examples of indole flavanones and flavones, respectively, were also synthesized. UV spectroscopic comparisons between flavonoids and indole flavonoids are discussed.     

Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA:RNA hybrids

Locked nucleic acids (LNAs) containing one or more 2'-O,4'-C-methylene-linked bicyclic ribonucleoside monomers possess a number of the prerequisites of an effective antisense oligonucleotide, e.g. unprecedented helical thermostability when hybridized with cognate RNA and DNA. To acquire a detailed understanding of the structural features of LNA giving rise to its remarkable properties, we have conducted structural studies by use of NMR spectroscopy and now report high-resolution structures of two LNA:RNA hybrids, the LNA strands being d(5'-CTGAT(L)ATGC-3') and d(5'-CT(L)GAT(L)AT(L)GC-3'), respectively, T(L) denoting a modified LNA monomer with a thymine base, along with the unmodified DNA:RNA hybrid. In the structures, the LNA nucleotides are positioned as to partake in base stacking and Watson-Crick base pairing, and with the inclusion of LNA nucleotides, we observe a progressive change in duplex geometry toward an A-like duplex structure. As such, with the inclusion of three LNA nucleotides, the hybrid adopts an almost canonical A-type duplex geometry, and thus it appears that the number of modifications has reached a saturation level with respect to structural changes, and that further incorporations would furnish only minute changes in the duplex structure. We attempt to rationalize the conformational steering induced by the LNA nucleotides by suggesting that the change in electronic density at the brim of the minor groove, introduced by the LNA modification, is causing an alteration of the pseudorotational profile of the 3'-flanking nucleotide, thus shifting this sugar equilibrium toward N-type conformation.     

On-line high-performance liquid chromatography/mass spectrometric characterization of native oligosaccharides from glycoproteins

An on-line high-performance liquid chromatography/mass spectrometry (HPLC/MS) method is described for the rapid characterization of any type of oligosaccharide released from glycoproteins. The procedure can be applied without further manipulation to fractions collected from a high-performance anion-exchange chromatography-pulse amperometric detection (HPAEC-PAD) system commonly used for glycosylation mapping of glycoproteins, or to a pool of oligosaccharides directly released from glycoproteins. The system consists of a porous graphitized high-performance chromatography column (Hypercarb) coupled to a quadrupole time-of-flight (TOF) mass spectrometer. Oligosaccharides are eluted from the column with a gradient of ammonium acetate/acetonitrile and directly identified following in-source fragmentation. Some applications of the method are presented, as well as information about the spectra and fragmentation behavior observed for N- and O-linked oligosaccharides released from some recombinant glycoproteins. Low femtomole limits of detection are achieved using proper miniaturization.     

An oligomeric ser-pro dipeptide mimetic assuming the polyproline II helix conformation

A hexapeptide assembled from dipeptide building blocks assumes the secondary structure of the polyproline II (PPII) helix. Side chain-to-backbone hydrogen bonds stabilize peptide torsions next to the fused ring systems. The solution structure of the polyhydroxylated peptide was studied by spectroscopic methods.