Design and synthesis of conformationally constrained cyclophilin inhibitors showing a cyclosporin-A phenotype in C. elegans

Cyclophilin A (CypA) is a member of the immunophilin family of proteins and receptor for the immunosuppressant drug cyclosporin A (CsA). Here we describe the design and synthesis of a new class of small-molecule inhibitors for CypA that are based upon a dimedone template. Electrospray mass spectrometry is utilised as an initial screen to quantify the protein affinity of the ligands. Active inhibitors and fluorescently labelled derivatives are then used as chemical probes for investigating the biological role of cyclophilins in the nematode Caenorhabditis elegans.     

Semiconductor nanostructure-based photovoltaic solar cells

Substantial efforts have been devoted to design, synthesize, and integrate various semiconductor nanostructures for photovoltaic (PV) solar cells. In this article, we will review the recent progress in this exciting area and cover the material chemistry and physics related to all-inorganic nanostructure solar cells, hybrid inorganic nanostructure-conductive polymer composite solar cells, and dye-sensitized solar cells.     

Binary [Cu2O/MWCNT] and ternary [Cu2O/ZnO/MWCNT] nanocomposites: formation, characterization and catalytic performance in partial ethanol oxidation

Cuprous oxide agglomerates composed of 4-10 nm Cu2O nanoparticles were deposited on multiwalled carbon nanotubes (MWCNTs) and on ZnO/MWCNTs to give binary [Cu2O/MWCNT] and ternary [Cu2O/ZnO/MWCNT] composites. Di-aqua-bis[2-(methoxyimino)propanoato]copper Cu[O2CCCH3NOMe](2)·2H2O 1 in DMF was used as single source precursor for the deposition of nanoscaled Cu2O. The precursor decomposes either in air or under argon to yield CuO2 by in situ redox reaction. Thermogravimetric coupled mass spectroscopic analysis (TG-MS) of 1 revealed that methanol formed during the decomposition of 1 acts as a potential in situ reducing agent. Scanning electron microscopy (SEM) of the binary [Cu2O/MWCNT] nano-composite shows an increase of cuprous oxide loading depending on the precursor amount, along the periphery of the MWCNTs as well as formation of larger particle agglomerates. Transmission electron microscopy (TEM) of the sample shows crystalline domains of size 4-10 nm surrounded by an amorphous region within the larger particles. SEM and TEM of ternary [Cu2O/ZnO/MWCNT] clearly reveal that Cu2O nanoparticles are primarily deposited on ZnO rather than on MWCNTs. The catalytic activities of the [Cu2O/MWCNT] and [Cu2O/ZnO/MWCNT] binary and ternary composites were studied for the selective partial oxidation of ethanol to acetaldehyde with molecular oxygen. While using binary [Cu2O/MWCNT] (13.8 wt% Cu) as catalyst, acetaldehyde was obtained with a yield of 87% at 355 °C (selectivity 96% and conversion 91%). When nanoscale ZnO is present, the resulting [Cu2O/ZnO/MWCNT] composite shows preferential hydrogen and CO2 formation due to the fact that the dehydrogenation and total oxidation pathway is more favoured compared to the binary composite. Significant morphological changes of the catalyst during the catalytic process were observed.     

Photoinduced increase in surfactant solution viscosity using azobenzene dicarboxylate for molecular switching

We provide further insight into the photochemical control of viscoelasticity through the use of azobenzene sodium dicarboxylate for molecular switching. As a photoresponsive molecule, Sodium 3,3'-azobenzene dicarboxylate (3,3'-Azo2Na) was added to a solution of cetyltrimethylammonium bromide (CTAB)/sodium salicylate (NaSal), which is known for inducing the formation of wormlike micelles. This solution maintained a wormlike micellar structure, although a reduction in zero-shear viscosity was observed. When this mixed aqueous solution of CTAB/NaSal/3,3'-Azo2Na (16.7 mM each) was irradiated by ultraviolet light, the 3,3'-Azo2Na exhibited molecular trans-cis photoisomerization. We measured the dynamic viscoelasticity of the sample in the photostationary state and found that the zero-shear viscosity increased approximately sevenfold compared to the preirradiation state. This phenomenon is the opposite of the system wherein viscosity reduced by irradiation, as reported by us. We discuss the mechanism of this viscosity change.     

Irreversible changes in protein conformation due to interaction with superparamagnetic iron oxide nanoparticles

The understanding of the interactions between nanomaterials and proteins is of extreme importance in medicine. In a biological fluid, proteins can adsorb and associate with nanoparticles, which can have significant impact on the biological behavior of the proteins and the nanoparticles. We report here on the interactions of iron saturated human transferrin protein with both bare and polyvinyl alcohol coated superparamagnetic iron oxide nanoparticles (SPIONs). The exposure of human transferrin to SPIONs results in the release of iron, which changes the main function of the protein, which is the transport of iron among cells. After removal of the magnetic nanoparticles, the original protein conformation is not recovered, indicating irreversible changes in transferrin conformation: from a compact to an open structure.     

Mechanism of cytotoxicity and cellular uptake of lipophilic inert dinuclear polypyridylruthenium(II) complexes

The accumulation, uptake mechanism, cytotoxicity, cellular localisation of—and mode of cell death induced by—dinuclear ruthenium(II) complexes ΔΔ/ΛΛ‐[{Ru(phen)₂}₂{μ‐bb_n}]⁴⁺ (Rubb_n), where phen is 1,10‐phenanthroline, bb_n is bis[4(4′‐methyl‐2,2′‐bipyridyl)]‐1,n‐alkane (n=2, 5, 7, 10, 12 or 16), and the corresponding mononuclear complexes containing the bb_n ligands, were studied in L1210 murine leukaemia cells. Cytotoxicity increased with linker chain length, and the ΔΔ‐Rubb₁₆ complex displayed the highest cytotoxicity of the series, with an IC₅₀ value of 5 μM , similar to that of carboplatin in the L1210 murine leukaemia cell line. Confocal microscopy and flow cytometry studies indicated that the complexes accumulate in the mitochondria of L1210 cells, with the magnitude of cellular uptake and accumulation increasing with linking chain length in the bb_n bridge of the metal complex. ΔΔ‐Rubb₁₆ entered the L1210 cells by passive diffusion (with a minor contribution from protein‐mediated active transport), inducing cell death via apoptosis. Additionally, metal‐complex uptake in leukaemia cells was approximately 16‐times that observed in healthy B cells highlighting that the bb_n series of complexes may have potential as selective anticancer drugs.     

Inhibition of galectins with small molecules

Evidence that the galectin family of proteins plays crucial roles in cancer, inflammation, and immunity has accumulated over the last decade. The galectins have consequently emerged as interesting drug targets. A majority of galectin functions occurs by means of cross-linking glycoproteins and by doing so controlling glycoprotein cellular localization and residence times. The glycoprotein cross-linking occurs when galectin dimers or multimers, or galectins with two binding sites, bind galactose-containing glycans of the glycoproteins. Such galectin-glycan interactions have been successfully blocked with compounds having multivalent presentation of galactose, lactose, or N-acetyllactosamine, with peptides, and with small carbohydrate (galactose) derivatives. This review summarizes and analyzes attempts to develop efficient and selective small-molecule galectin inhibitors through derivatization of monosaccharides, mainly galactosides, with non-carbohydrate structures that protrude into subsites adjacent to the core-conserved galactose-recognizing site of the galectins.     

Glycoinformatics: data mining-based approaches

Carbohydrates or glycans are major cellular macromolecules, working for a variety of vital biological functions. Due to long-term efforts by experimentalists, the current number of structurally different, determined carbohydrates has exceeded 10,000 or more. As a result data mining-based approaches for glycans (or trees in a computer science sense) have attracted attention and have been developed over the last five years, presenting new techniques even from computer science viewpoints. This review summarizes cutting-edge techniques for glycans in each of the three categories of data mining: classification, clustering and frequent pattern mining, and shows results obtained by applying these techniques to real sets of glycan structures.     

Flexizymes: their evolutionary history and the origin of catalytic function

Transfer RNA (tRNA) is an essential component of the cell's translation apparatus. These RNA strands contain the anticodon for a given amino acid, and when "charged" with that amino acid are termed aminoacyl-tRNA. Aminoacylation, which occurs exclusively at one of the 3'-terminal hydroxyl groups of tRNA, is catalyzed by a family of enzymes called aminoacyl-tRNA synthetases (ARSs). In a primitive translation system, before the advent of sophisticated protein-based enzymes, this chemical event could conceivably have been catalyzed solely by RNA enzymes. Given the evolutionary implications, our group attempted in vitro selection of artificial ARS-like ribozymes, successfully uncovering a functional ribozyme (r24) from an RNA pool of random sequences attached to the 5'-leader region of tRNA. This ribozyme preferentially charges aromatic amino acids (such as phenylalanine) activated with cyanomethyl ester (CME) onto specific kinds of tRNA. During the course of our studies, we became interested in developing a versatile, rather than a specific, aminoacylation catalyst. Such a ribozyme could facilitate the preparation of intentionally misacylated tRNAs and thus serve a convenient tool for manipulating the genetic code. On the basis of biochemical studies of r24, we constructed a truncated version of r24 (r24mini) that was 57 nucleotides long. This r24mini was then further shortened to 45 nucleotides. This ribozyme could charge various tRNAs through very simple three-base-pair interactions between the ribozyme's 3'-end and the tRNA's 3'-end. We termed this ribozyme a "flexizyme" (Fx3 for this particular construct) owing to its flexibility in addressing tRNAs. To devise an even more flexible tool for tRNA acylation, we attempted to eliminate the amino acid specificity from Fx3. This attempt yielded an Fx3 variant, termed dFx, which accepts amino acid substrates having 3,5-dinitrobenzyl ester instead of CME as a leaving group. Similar selection attempts with the original phenylalanine-CME and a substrate activated by (2-aminoethyl)amidocarboxybenzyl thioester yielded the variants eFx and aFx (e and a denote enhanced and amino, respectively). In this Account, we describe the history and development of these flexizymes and their appropriate substrates, which provide a versatile and easy-to-use tRNA acylation system. Their use permits the synthesis of a wide array of acyl-tRNAs charged with artificial amino and hydroxy acids. In parallel to these efforts, we initiated a crystallization study of Fx3 covalently conjugated to a microhelix RNA, which is an analogue of tRNA. The X-ray crystal structure, solved as a co-complex with phenylalanine ethyl ester and U1A-binding protein, revealed the structural basis of this enzyme. Most importantly, many biochemical observations were consistent with the crystal structure. Along with the predicted three regular-helix regions, however, the flexizyme has a unique irregular helix that was unexpected. This irregular helix constitutes a recognition pocket for the aromatic ring of the amino acid side chain and precisely brings the carbonyl group to the 3'-hydroxyl group of the tRNA 3'-end. This study has clearly defined the molecular interactions between Fx3, tRNA, and the amino acid substrate, revealing the fundamental basis of this unique catalytic system.     

Toward the discovery of novel anti-HIV drugs. Second-generation inhibitors of the cellular ATPase DDX3 with improved anti-HIV activity: synthesis, structure-activity relationship analysis, cytotoxicity studies, and target validation

A hit optimization protocol applied to the first nonnucleoside inhibitor of the ATPase activity of human DEAD-box RNA helicase DDX3 led to the design and synthesis of second-generation rhodanine derivatives with better inhibitory activity toward cellular DDX3 and HIV-1 replication. Additional DDX3 inhibitors were identified among triazine compounds. Biological data were rationalized in terms of structure-activity relationships and docking simulations. Antiviral activity and cytotoxicity of selected DDX3 inhibitors are reported and discussed. A thorough analysis confirmed human DDX3 as a valid anti-HIV target. The compounds described herein represent a significant advance in the pursuit of novel drugs that target HIV-1 host cofactors.