Fragment-based lead discovery: challenges and opportunities

Fragment-based lead discovery has undergone remarkable changes over the last 15 years. During this time, the pharmaceutical industry has changed dramatically as well, and continued evolution of the industry is assured. These changes present many challenges but also several opportunities for executing fragment-based drug design. This article will explore some of the more significant changes in the industry and how they may affect future discovery efforts related to fragment-based initiatives.     

Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions

DNA/RNA chromatography presents a versatile platform for the analysis of nucleic acids. Although the mechanism of separation of double stranded (ds) DNA fragments is largely understood, the mechanism by which RNA is separated appears more complicated. To further understand the separation mechanisms of RNA using ion pair reverse phase liquid chromatography, we have analysed a number of dsRNA and single stranded (ss) RNA fragments. The high-resolution separation of dsRNA was observed, in a similar manner to dsDNA under non-denaturing conditions. Moreover, the high-resolution separation of ssRNA was observed at high temperatures (75 °C) in contrast to ssDNA. It is proposed that the presence of duplex regions/secondary structures within the RNA remain at such temperatures, resulting in high-resolution RNA separations. The retention time of the nucleic acids reflects the relative hydrophobicity, through contributions of the nucleic sequence and the degree of secondary structure present. In addition, the analysis of RNA using such approaches was extended to enable the discrimination of bacterial 16S rRNA fragments and as an aid to conformational analysis of RNA. RNA:RNA interactions of the human telomerase RNA component (hTR) were analysed in conjunction with the incorporation of Mg²⁺ during chromatography. This novel chromatographic procedure permits analysis of the temperature dependent formation of dimeric RNA species.     

Isotopic Traceability (13C and 18O) of Greek Olive Oil

In recent years, isotopic analysis has been proven a valuable tool for the determination of the origin of various materials. In this article, we studied the ¹⁸O and ¹³C isotopic values of 210 olive oil samples that were originated from different regions in Greece in order to verify how these values are affected by the climate regime. We observed that the δ¹⁸O isotopic values range from 19.2 ‰ to 25.2 ‰ and the δ¹³C values range from −32.7 ‰ to −28.3 ‰. These differences between the olive oils’ isotopic values depended on the regional temperature, the meteoric water, and the distance from the sea. Furthermore, we studied the ¹³C isotopic values of biophenolic extracts, and we observed that they have same capability to differentiate the geographic origin. Finally, we compared the isotopic values of Greek olive oils with samples from Italy, and we concluded that there is a great dependence of oxygen isotopes on the climatic characteristics of the different geographical areas.     

Structural Insights into the Role of β3 nAChR Subunit in the Activation of Nicotinic Receptors

The β3 subunit of nicotinic acetylcholine receptors (nAChRs) participates in heteropentameric assemblies with some α and other β neuronal subunits forming a plethora of various subtypes, differing in their electrophysiological and pharmacological properties. While β3 has for several years been considered an accessory subunit without direct participation in the formation of functional binding sites, recent electrophysiology data have disputed this notion and indicated the presence of a functional (+) side on the extracellular domain (ECD) of β3. In this study, we present the 2.4 Å resolution crystal structure of the monomeric β3 ECD, which revealed rather distinctive loop C features as compared to those of α nAChR subunits, leading to intramolecular stereochemical hindrance of the binding site cavity. Vigorous molecular dynamics simulations in the context of full length pentameric β3-containing nAChRs, while not excluding the possibility of a β3 (+) binding site, demonstrate that this site cannot efficiently accommodate the agonist nicotine. From the structural perspective, our results endorse the accessory rather than functional role of the β3 nAChR subunit, in accordance with earlier functional studies on β3-containing nAChRs.     

Frequency-switching inversion-recovery for severely hyperfine-shifted NMR: evidence of asymmetric electron relaxation in high-spin Co(II)

A new method for reliably measuring longitudinal relaxation rates for severely hyperfine-shifted NMR signals in aqueous solutions is presented. The method is illustrated for a well-defined cobalt tetracysteinate, with relevance to cobalt-substituted metalloproteins. The relaxation measurements are indicative of asymmetric electronic relaxation of the high-spin Co(II) ion.     

On cyclic strings avoiding a pattern

We count the number of cyclic strings over an alphabet that avoid a single pattern under two different assumptions. In the first case, we assume that the symbols of the alphabet are on numbered positions on a circle, while in the second case we assume that the symbols can be freely rotated on the circle (i.e., we deal with necklaces). In each case, we provide a generating function, and we explain how these two cases are related. For the situation of avoiding more than one pattern, we formulate a general conjecture for the first case, and a conditional result for the second case. We also explain the differences between our theory and the theory of Edlin and Zeilberger (2000) by emphasizing how we modified the definition of the enumeration of cyclic strings that avoid one or more patterns when their lengths are less than the length of the longest pattern.     

PHOTOSENSITIZATION BY ANTITUMOR AGENTS—1. PRODUCTION OF SINGLET OXYGEN DURING IRRADIATION OF ANTHRAPYRAZOLES WITH VISIBLE LIGHT

Abstract— Oxygen consumption, photoinduced by visible light, and sensitized by novel anthrapyrazole antitumor agents has been observed. Generation of singlet oxygen upon irradiation of ethanolic solutions of the drugs with visible light (480–520 nm) was demonstrated using a specific ¹O₂ acceptor, 2.5-dimethylfuran and a quencher, sodium azide. An electron paramagnetic resonance method was employed to measure the rate of oxygen consumption. Significant differences were found in the sensitizing properties among the anthrapyrazoles studied. Intramolecular hydrogen bonding within the chro-mophore is one of the structural factors that determine the efficacy of a given anthrapyrazole in ¹O₂ generation     

A Unified Mechanism for the PhCOCOOH-mediated Photochemical Reactions: Revisiting its Action and Comparison to Known Photoinitiators

Since 2014, we have introduced in literature the use of phenylglyoxylic acid (PhCOCOOH), a small and commercially available organic molecule, as a potent promoter in a variety of photochemical processes. Although PhCOCOOH has a broad scope of photochemical reactions that can promote, the understanding of its mode of action in our early contributions was moderate. Herein, we are restudying and revisiting the mechanism of action of PhCOCOOH in most of these early contributions, providing a unified mechanism of action. Furthermore, the understanding of its action as a photoinitiator opened a new comparison study with known and commercially available photoinitiators.     

Heterogeneous nucleation and growth of calcium carbonate on calcite and quartz

The precipitation of calcium carbonate as a binding salt for the consolidation of loose sand formations is a promising approach. The heterogeneous nucleation and growth of calcite were investigated in supersaturated solutions. The ionic activities in the solutions tested were selected so that they included both supersaturations in which crystal growth took place only following the introduction of seed particles and supersaturations in which precipitation occurred spontaneously past the lapse of induction times. In the latter case the supersaturation conditions were sufficiently low to allow the measurement of induction times preceding the onset of precipitation. The stability domain of the calcium carbonate system was established at pH 8.50, 25 degrees C, measuring the induction times in the range between 30 min and 2 h. The rates of precipitation following the destabilization of the solutions were measured from the pH and/or concentration-time profiles. The induction times were inversely proportional and rates proportional to the solution supersaturation as expected. The high-order dependence of the rates of precipitation on the solution supersaturation suggested a polynuclear growth mechanism. Fitting of the induction time-supersaturation data according to this model yielded a value of 64 mJ/m2 for the surface energy of the calcite nucleus. In the concentration domain corresponding to stable supersaturated solutions, seeded growth experiments at constant supersaturation showed a second-order dependence on the rates of crystal growth of calcite seed crystals. Inoculation of the stable supersaturated solutions with quartz seed crystals failed to induce nucleation. Raising supersaturation to reach the unstable domain showed interesting features: calcite seed crystals yielded crystal growth kinetics compatible with the polynuclear growth model, without any induction time. The presence of quartz seed crystals reduced the induction times and resulted in nucleation in the bulk solution. The kinetic data in the latter case were consistent with the polynuclear growth model and the surface energy for the newly forming embryo was calculated equal to 31.1 mJ/m2, because of the dominantly heterogeneous nature of the process.