Large-scale annotation of small-molecule libraries using public databases

While many large publicly accessible databases provide excellent annotation for biological macromolecules, the same is not true for small chemical compounds. Commercial data sources also fail to encompass an annotation interface for large numbers of compounds and tend to be cost prohibitive to be widely available to biomedical researchers. Therefore, using annotation information for the selection of lead compounds from a modern day high-throughput screening (HTS) campaign presently occurs only under a very limited scale. The recent rapid expansion of the NIH PubChem database provides an opportunity to link existing biological databases with compound catalogs and provides relevant information that potentially could improve the information garnered from large-scale screening efforts. Using the 2.5 million compound collection at the Genomics Institute of the Novartis Research Foundation (GNF) as a model, we determined that approximately 4% of the library contained compounds with potential annotation in such databases as PubChem and the World Drug Index (WDI) as well as related databases such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) and ChemIDplus. Furthermore, the exact structure match analysis showed 32% of GNF compounds can be linked to third party databases via PubChem. We also showed annotations such as MeSH (medical subject headings) terms can be applied to in-house HTS databases in identifying signature biological inhibition profiles of interest as well as expediting the assay validation process. The automated annotation of thousands of screening hits in batch is becoming feasible and has the potential to play an essential role in the hit-to-lead decision making process.     

Temporal Control of Membrane Fusion through Photolabile PEGylation of Liposome Membranes

Membrane fusion results in the transport and mixing of (bio)molecules across otherwise impermeable barriers. In this communication, we describe the temporal control of targeted liposome–liposome membrane fusion and contents mixing using light as an external trigger. Our method relies on steric shielding and rapid, photoinduced deshielding of complementary fusogenic peptides tethered to opposing liposomal membranes. In an analogous approach, we were also able to demonstrate precise spatiotemporal control of liposome accumulation at cellular membranes in vitro.     

High‐Energy Long‐Lived Mixed Frenkel–Charge‐Transfer Excitons: From Double Stranded (AT)n to Natural DNA

The electronic excited states populated upon absorption of UV photons by DNA are extensively studied in relation to the UV‐induced damage to the genetic code. Here, we report a new unexpected relaxation pathway in adenine–thymine double‐stranded structures (AT)_n. Fluorescence measurements on (AT)_n hairpins (six and ten base pairs) and duplexes (20 and 2000 base pairs) reveal the existence of an emission band peaking at approximately 320 nm and decaying on the nanosecond time scale. Time‐dependent (TD)‐DFT calculations, performed for two base pairs and exploring various relaxation pathways, allow the assignment of this emission band to excited states resulting from mixing between Frenkel excitons and adenine‐to‐thymine charge‐transfer states. Emission from such high‐energy long‐lived mixed (HELM) states is in agreement with their fluorescence anisotropy (0.03), which is lower than that expected for π–π* states (≥0.1). An increase in the size of the system quenches π–π* fluorescence while enhancing HELM fluorescence. The latter process varies linearly with the hypochromism of the absorption spectra, both depending on the coupling between π–π* and charge‐transfer states. Subsequently, we identify the common features between the HELM states of (AT)_n structures with those reported previously for alternating (GC)_n: high emission energy, low fluorescence anisotropy, nanosecond lifetimes, and sensitivity to conformational disorder. These features are also detected for calf thymus DNA in which HELM states could evolve toward reactive π–π* states, giving rise to delayed fluorescence.     

Fabrication and thermal analysis of submicron silver tubes prepared from electrospun fiber templates

Submicron silver tubes have been synthesized by a polymer-based template approach. Two different approaches to metallization, electroless deposition and exchange plating, were evaluated within the template approach. Silver films with average thickness approximately 50-100 nm were deposited on polycarbonate fibers approximately 400 nm in diameter by each technique, resulting in tubes with a diameter between 450 and 500 nm after thermal degradation of core fibers. These nanomaterials were characterized by scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), and scanning thermal microscopy. The thermal conductivity of the silver submicron tubes was found to differ depending on the method of preparation, with tubes from electroless plating possessing relative thermal conductivity values that were 1 order of magnitude higher than that from exchange plating, 3000 W/m x K and 660 W/m x K, respectively. Interestingly, these results indicate that silver submicron tubes possess higher thermal conductivity than the bulk metal. This observation is discussed in the context of the continuous conduction path of the tubes and their high surface area-to-volume ratio.     

Modern pathology: protein mis-folding and mis-processing in complex disease

Electrostatic and electrochemical properties of bio-molecules, such as proteins, are governed by energy parameters that are, in part dependent on its folding. Disruption of this process can lead to the development of complex, multisystem diseases whose presentation may be organ-dependent. Examples include cystic fibrosis, alpha-1 antitrypsin deficiency, and Alzheimer disease. In addition to explaining exotic pathologic syndromes, an understanding of protein folding mechanisms may facilitate the understanding of less complex diseases and allow the development of novel therapeutic approaches.     

A study of the interactions between carboplatin and blood plasma proteins using size exclusion chromatography coupled to inductively coupled plasma mass spectrometry

To study the carboplatin–protein interaction, a sensitive method using size exclusion chromatography coupled to inductively coupled plasma mass spectrometry (SEC–ICP–MS) was developed. The complexes formed between plasma proteins and carboplatin were monitored and identified with this method. Composite blood plasma samples from patients who were undergoing chemotherapy were analyzed, and carboplatin was found to bind plasma proteins. In addition, blank plasma samples were spiked with carboplatin and were analyzed as a time course study, and the results confirmed that carboplatin formed complexes with plasma proteins, primarily albumin and γ-globulin. To further substantiate the study, these two proteins were incubated with carboplatin. The binding between carboplatin and these proteins was then characterized qualitatively and quantitatively. In addition to a one-to-one binding of Pt to protein, protein aggregation was observed. The kinetics of the binding process of carboplatin to albumin and γ-globulin was also studied. The initial reaction rate constant of carboplatin binding to albumin was determined to be 0.74 M⁻¹ min⁻¹, while that for γ-globulin was 1.01 M⁻¹ min⁻¹, which are both lower than the rate constant of the cisplatin–albumin reaction previously reported.     

A perylenedicarboxamide linker for DNA hairpins

The synthesis and properties of a perylenediamide diol linker and several DNA hairpins possessing this linker are described. The diol linker absorbs and fluoresces strongly in the visible. Hairpins having poly(dA)-poly(dT) stems have fluorescence quantum yields and decay times similar to those of the linker, indicating that hole injection does not occur from the singlet excited linker into the base pair domain. Fluorescence quenching by dG or dZ bases is observed when these bases are located near the linker. The strong distance dependence of fluorescence quenching is consistent with a superexchange mechanism for electron transfer. Failure to observe formation of the linker anion radical by means of femtosecond time resolved absorption spectroscopy is attributed to fast charge recombination. The properties and behavior of the perylene linker and its hairpins are compared to those of other arenedicarboxamide linkers.     

Synthesis and polymerisation of α,ω-bis(3-pyrrolyl)alkanes

The synthesis, characterisation and polymerisation studies of a homologous series of α,ω-bis(pyrrolyl)alkanes are described. These α,ω-bis(pyrrolyl)alkanes were produced using Friedel-Crafts acylation followed by reduction of the carbonyl group using Red-Al^®. Chemical polymerisation of the resultant dimers using FeCl₃ produced poly(α,ω-bis(pyrrolyl)alkane) films, which were characterised by SEM, FTIR and tested for conductivity.     

Sensitivity in Supramolecular Architectures of Polyaromatic Salts Containing Two Singly‐Pimerized Bipyridines

Three novel supramolecular arrays of zigzag polyaromatic salts are reported. Both the conformation and disposition of the dications are subjected to various noncovalent interactions. Thus, the presence or absence of the π‐π interacting enclathrated molecules, the efficient packing and the involved hydrogen bonding interactions of anions, as well as the increased hydrophobic property of the dications themselves exert influence.