Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis

Based on torsion angle distributions of frequently occurring substructures, conformation preferences of druglike molecules are presented, accompanied by a review of the relevant literature. First, the relevance of the Cambridge Structural Database (CSD) for drug design is demonstrated by comparing substructures present in compounds entering clinical trials with those found in the CSD and protein-bound ligands in the Protein Data Bank (PDB). Next, we briefly highlight preferred conformations of elementary acyclic systems, followed by a discussion of sulfonamide conformations. Due to their central role in medicinal chemistry, we discuss properties of aryl ring substituents in depth, including biaryl systems and systems of two aryl rings connected by two acyclic bonds. For a subset of torsion motifs, we also compare torsion angle histograms derived from CSD structures with those derived from ligands in the PDB. Furthermore, selected properties of some six- and seven-membered ring systems are discussed. The article closes with a section on attractive sulfur-oxygen contacts.     

High-density targeting of a viral multifunctional nanoplatform to a pathogenic, biofilm-forming bacterium

Nanomedicine directed at diagnosis and treatment of infections can benefit from innovations that have substantially increased the variety of available multifunctional nanoplatforms. Here, we targeted a spherical, icosahedral viral nanoplatform to a pathogenic, biofilm-forming bacterium, Staphylococcus aureus. Density of binding mediated through specific protein-ligand interactions exceeded the density expected for a planar, hexagonally close-packed array. A multifunctionalized viral protein cage was used to load imaging agents (fluorophore and MRI contrast agent) onto cells. The fluorescence-imaging capability allowed for direct observation of penetration of the nanoplatform into an S. aureus biofilm. These results demonstrate that multifunctional nanoplatforms based on protein cage architectures have significant potential as tools for both diagnosis and targeted treatment of recalcitrant bacterial infections.     

The PyPES library of high quality semi‐global potential energy surfaces

In this article, we present a Python‐based library of high quality semi‐global potential energy surfaces for 50 polyatomic molecules with up to six atoms. We anticipate that these surfaces will find widespread application in the testing of new potential energy surface construction algorithms and nuclear ro‐vibrational structure theories. To this end, we provide the ability to generate the energy derivatives required for Taylor series expansions to sixth order about any point on the potential energy surface in a range of common coordinate systems, including curvilinear internal, Cartesian, and normal mode coordinates. The PyPES package, along with FORTRAN, C, MATLAB and Mathematica wrappers, is available at http://sourceforge.net/projects/pypes-lib . © 2015 Wiley Periodicals, Inc.     

Elasticity of flexible and semiflexible polymers with extensible bonds in the Gibbs and Helmholtz ensembles

Stretching experiments on single molecules of arbitrary length opened the way for studying the statistical mechanics of small systems. In many cases in which the thermodynamic limit is not satisfied, different macroscopic boundary conditions, corresponding to different statistical mechanics ensembles, yield different force-displacement curves. We formulate analytical expressions and develop Monte Carlo simulations to quantitatively evaluate the difference between the Helmholtz and the Gibbs ensembles for a wide range of polymer models of biological relevance. We consider generalizations of the freely jointed chain and of the worm-like chain models with extensible bonds. In all cases we show that the convergence to the thermodynamic limit upon increasing contour length is described by a suitable power law and a specific scaling exponent, characteristic of each model.     

A step forward in metal nitride and carbide synthesis: from pure nanopowders to nanocomposites

Transition metal nitrides and carbides (MN/MC) are intriguing materials due to their combination of properties that place them between high-performance ceramics and pure metals. Recent progress in easier synthetic routes toward their production as bulk or nanostructured materials explains the current surge in sustained attention such progress has been receiving. After progressing toward easier syntheses of MN/MC nanosystems as pure phases, coupling MN/MC with a second phase for the production of hybrids and nanocomposites is considered a next important step in the development of these nanosystems. The coupled phase can simply be a different nitride or carbide; it also can be a polymer, a poly(ionic liquid) or a carbon phase, just to give a few examples. The combination of these phases with MN/MC nanoparticles could lead to multifunctional materials. The aim of the present review is to show how far the research concerning the production of MN/MC-based nanocomposites has progressed, especially in terms of controlled composition, morphology and properties. We discuss the most intensely investigated systems and related motivations, as well as partially unexplored yet appealing alternative materials.     

Solid-state equilibrium relations in the Ternary Systems TeO2?MoO3?MoO2 and TeO2?MoO3?Te

In a study of the solid-state reactions in the ternary systems TeO₂? MoO₃? MoO₂ and TeO₂? MoO₃? Te, approximately 70 selected compositions were sintered at 550°C to attain equilibrium conditions, and solid-state equilibrium relations were characterized by x-ray diffraction. In a large composition range, the interaction of TeO₂ and MoO₃ with the reducing agents MoO₂ or Te leads to the reduced ternary oxide TeMo₄O₁₃ (m. p. 748°C), in addition to Te₂MoO₇, Te and (intermediate) molybdenum oxides. The compatibility relations for the binary systems TeO₂? MoO₂ and MoO₃? Te are presented for the first time. In the TeO₂? MoO₂ system, three-phase regions are found: (Te₂MoO₇? TeO₂? Te) on the TeO₂? and (TeMo₄O₁₃? MoO₂? Te) on the MoO₂-rich sides with (TeMo₄O₁₃? Te₂MoO₇? Te) in the intermediate region. In the MoO₃? Te system, three-phase regions (TeMo₄O₁₃? MoO₂? Te), (TeMo₄O₁₃? Mo₄O₁₁? MoO₂) and (TeMo₄O₁₃? MoO₃? Mo₄O₁₁) were detected. TeMo₄O₁₃ presents two allotropic forms (α′ for T < 450°C, α for T > 450°C). Both structures have been characterized by I.R. and optical reflectance spectroscopy. Unit cell dimensions are also given.     

Effect of the segmental mobility restriction on the thermoset chemical kinetics

The cure kinetics of an epoxy–amine commercial thermoset system have been investigated with the isothermal differential scanning calorimetry technique. In particular, a kinetic study has been performed in the glass–transition zone, in which diffusion phenomena compete with the chemical transformations and the overall reaction rate is partially slowed by the reduced segmental chain mobility. A generalized form of the Vogel equation has been formulated to account for the effect of the increasing glass–transition temperature on the chain mobility and, therefore, on the overall reaction rate. The kinetic model has been expressed with two factors representing the chemical reaction rate and the segmental mobility reduction. As the main result, the activation energy relative to the diffusion phenomena has been found to be very low, having a value of 42.5 K ≈ 0.356 kJ/mol, which is compatible only with the small‐angle rotation of the reactive unit. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 3757–3770, 2002     

The spiropiperidine-3,3′-oxindole scaffold: a type II β-turn peptide isostere

An unprecedented chiral spiropiperidine oxindole system was synthesized starting from enantiopure quaternary 3-aminooxindole and relying on a ring closing metathesis as the key step. This compound acts as an highly constrained Freidinger γ-lactam, adopting a type II β-turn conformation in solution, as assessed by modelling and spectroscopical studies.     

A Universal DNA Aptamer that Recognizes Spike Proteins of Diverse SARS-CoV-2 Variants of Concern

We report on a unique DNA aptamer, denoted MSA52, that displays universally high affinity for the spike proteins of wildtype SARS-CoV-2 as well as the Alpha, Beta, Gamma, Epsilon, Kappa, Delta and Omicron variants. Using an aptamer pool produced from round 13 of selection against the S1 domain of the wildtype spike protein, we carried out one-round SELEX experiments using five different trimeric spike proteins from variants, followed by high-throughput sequencing and sequence alignment analysis of aptamers that formed complexes with all proteins. A previously unidentified aptamer, MSA52, showed K_d values ranging from 2 to 10 nM for all variant spike proteins, and also bound similarly to variants not present in the reselection experiments. This aptamer also recognized pseudotyped lentiviruses (PL) expressing eight different spike proteins of SARS-CoV-2 with K_d values between 20 and 50 pM, and was integrated into a simple colorimetric assay for detection of multiple PL variants. This discovery provides evidence that aptamers can be generated with high affinity to multiple variants of a single protein, including emerging variants, making it well-suited for molecular recognition of rapidly evolving targets such as those found in SARS-CoV-2.     

Polyphenolic Composition and Antioxidant Activity (ORAC,EPR and Cellular) of Different Extracts of Argylia radiata Vitroplants and Natural Roots

Plant biochemistry studies have increased in recent years due to their potential to improve human health. Argylia radiata is an extremophile plant with an interesting polyphenolic profile. However, its biomass is scarce and occasionally available. Argylia in vitro biomass was obtained from tissue culture and compared with in vivo roots regarding its polyphenolic and flavonoid content. Different solvents were used to prepare extracts from the in vitro tissue of callus and aerial plant organs and in vivo roots. UPLC-MS/MS was used to assess the chemical composition of each extract. ORAC-FL and scavenging of free radicals (DPPH and OH) methods were used to determine the antioxidant capacity of extracts. Furthermore, the biological activity of the extracts was established using the cellular antioxidant activity method. The vitroplants were a good source of polyphenols (25–68 mg GAE/100 g tissue FW), and methanol was the most efficient solvent. Eight polyphenolic compounds were identified, and their antioxidant properties were investigated by different chemical methods with EPR demonstrating its specific scavenging activity against free radicals. All extracts showed cellular dose-dependent antioxidant activity. The methanolic extract of vitroplants showed the highest cellular antioxidant activity (44.6% and 51%) at 1 and 10 µg/mL of extract, respectively. Vitroplants of A. radiata are proposed as a biotechnological product as a source of antioxidant compounds with multiple applications.