Organic nanotubes created from mesogenic derivatives

A facile route to prepare nanotubes from rod-like mesogens dissolved in typical organic solvents is reported. For selected types of chiral rod-like molecules, nanotubes were formed from both enantiomers and racemic mixtures by slow evaporation from solution, regardless of the solvent, concentration or deposition type. The obtained supramolecular assemblies were studied using AFM, TEM and SEM techniques, and other experimental techniques (IR, UV-Vis spectroscopy and X-ray diffraction) were also applied. The difference in the surface tension at opposite crystallite surfaces is suggested as a possible mechanism for nanotube nucleation. We propose a quite new rolling-up mechanism related to the surface tension difference at opposite crystallite surfaces.

Antimicrobial peptides prevent bacterial biofilm formation on the surface of polymethylmethacrylate bone cement

PURPOSE

Antibiotic-loaded polymethylmethacrylate-based bone cement has been implemented in orthopaedics to cope with implant-related infections associated with the formation of bacterial biofilms. In the context of emerging bacterial resistance to current antibiotics, we examined the efficacy of short antimicrobial peptide-loaded bone cement in inhibiting bacterial adhesion and consequent biofilm formation on its surface.

METHODOLOGY

The ability of α-helical antimicrobial peptides composed of 12 amino acid residues to prevent bacterial biofilm [methicillin-resistant Staphylococcus aureus (MRSA), Staphylococcus epidermidis, Pseudomonas aeruginosa and Escherichia coli] formation on the surface of model implants made from polymethylmethacrylate-based bone cement was evaluated by colony-forming unit (c.f.u.) counting of bacteria released by sonication from the biofilms formed on their surfaces. The biofilms on model implant surfaces were also visualized by light microscopy after staining with tetrazolium dye (MTT) and by scanning electron microscopy.

RESULTS

When incorporated in the implants, these peptides caused a mean reduction in the number of bacterial cells attached to implants' surfaces (by five orders of magnitude), and 88 % of these implants showed no bacterial adhesion after being exposed to growth media containing various bacteria.

CONCLUSION

The results showed that the antibiofilm activity of these peptides was comparable to that of the antibiotics, but the peptides exhibited broader specificity than the antibiotics. Given the rapid development of antibiotic resistance, antimicrobial peptides show promise as a substitute for antibiotics for loading into bone cements.

Identification and Enantiodivergent Synthesis of (5 Z,9 S)-Tetradec-5-en-9-olide, a Queen-Specific Volatile of the Termite Silvestritermes minutus

The queens of social insects differ from sterile colony members in many aspects of their physiology. Besides adaptations linked with their specialization for reproduction and extended lifespan, the queens also invest in the maintenance of their reproductive dominance by producing exocrine chemicals signaling their presence to the nestmates. The knowledge of the chemistry of queen-specific cues in termites is scarce. In addition to the contact recognition based on cuticular hydrocarbons, long-range signals mediated by volatiles are expected to participate in queen signaling, especially in populous colonies of higher termites (Termitidae). In queens of the higher termite Silvestritermes minutus (Syntermitinae), we have detected a previously undescribed volatile. It is present in important quantities on the body surface and in the headspace, ovaries, and body cavity. MS and GC-FTIR data analyses led us to propose the structure of the compound to be a macrolide 10-pentyl-3,4,5,8,9,10-hexahydro-2 H-oxecin-2-one. We performed enantiodivergent syntheses of two possible enantiomers starting from enantiopure ( S)-glycidyl tosylate. The synthetic sequence involved macrolide-closing metathesis quenched with a ruthenium scavenging agent. The absolute and relative configuration of the compound was assigned to be (5 Z,9 S)-tetradec-5-en-9-olide. Identification and preparation of the compound allow for investigation of its biological significance.

Sequence Requirements of Intrinsically Fluorescent G-Quadruplexes

G-Quadruplexes are four-stranded nucleic acid structures typically stabilized by GGGG tetrads. These structures are intrinsically fluorescent, which expands the known scope of nucleic acid function and raises the possibility that they could eventually be used as signaling components in label-free sensors constructed from DNA or RNA. In this study, we systematically investigated the effects of mutations in tetrads, loops, and overhanging nucleotides on the fluorescence intensity and maximum emission wavelength of >500 sequence variants of a reference DNA G-quadruplex. Some of these mutations modestly increased the fluorescence intensity of this G-quadruplex, while others shifted its maximum emission wavelength. Mutations that increased the fluorescence intensity were distinct from those that increased the maximum emission wavelength, suggesting a trade-off between these two biochemical properties. The fluorescence intensity and maximum emission wavelength were also correlated with multimeric state: the most fluorescent G-quadruplexes were monomers, while those with the highest maximum emission wavelengths typically formed dimeric structures. Oligonucleotides containing multiple G-quadruplexes were in some cases more fluorescent than those containing a single G-quadruplex, although this depended on the length and sequence of the spacer linking the G-quadruplexes. These experiments provide new insights into the properties of fluorescent G-quadruplexes and should aid in the development of improved label-free nucleic acid sensors.

Structural Stability of Peptidic His-Containing Proton Wire in Solution and in the Adsorbed State

Molecular wires are functional molecules applicable in the field of transfer processes in technological and biochemical applications. Besides molecular wires with the ability to transfer electrons, research is currently focused on molecular wires with high proton affinity and proton transfer ability. Recently, proposed peptidic proton wires (H wires) are one example. Their ability to mediate the transport of protons from aqueous solutions onto the surface of a Hg electrode in a catalytic hydrogen evolution reaction was investigated by constant-current chronopotentiometric stripping. However, elucidating the structure of H wires and rationalizing their stability are key requirements for their further research and application. In this article, we focus on the His (H) and Ala (A)-containing peptidic H wire A₃-(H-A₂)₆ in solution and after its immobilization onto the electrode surface in the presence of the secondary structure stabilizer 2,2,2-trifluoroethanol (TFE). We found that the solvent containing more than 25% of TFE stabilizes the helical structure of A₃-(H-A₂)₆ not only in solution but also in the adsorbed state. The TFE efficacy to stabilize α-helical structure was confirmed using high-resolution nuclear magnetic resonance, circular dichroism, and molecular dynamics simulation. Experimental and theoretical results indicated A₃-(H-A₂)₆ to be a high proton-affinity peptidic H wire with an α-helical structure stabilized by TFE, which was confirmed in a comparative study with hexahistidine as an example of a peptide with a definitely disordered and random coil structure. The results presented here could be used for further investigation of the peptidic H wires and for the application of electrochemical methods in the research of proton transfer phenomena in general.

Diquats with Robust Chirality: Facile Resolution, Synthesis of Chiral Dyes, and Application as Selectors in Chiral Analysis

Diquats with extremely high racemization barriers with ΔG^≠_theor of 233 kJ mol^-1 at 180 °C are described. Reported configurational robustness is due to a combination of two structural features: the rigid o-xylylene tether connecting the nitrogen atoms and the presence of two substituents in the bay region of the bipyridinium scaffold. The straightforward synthesis of diquats, plus facile resolution and derivatization make them attractive for chiral application studies. This is demonstrated by: 1) synthesis of the first non-racemic diquat dyes with pronounced chiroptical properties, and 2) capability of diquats to interact stereospecifically with chiral molecules. This suggests potential for diquat derivatives to be used as chiral selectors in separation methods.

Intense redox-driven chiroptical switching with a 580 mV hysteresis actuated through reversible dimerization of an azoniahelicene

Electrochemical reduction of an azoniahelicene affords a dimer, accompanied by a strong change in the electronic circular dichroism. The fast dimerisation event leads to a >500 mV shift of the oxidation potential, affording a large area of bistability, where the chiroptical signal only depends on the redox history.

Multimerization rules for G-quadruplexes

G-quadruplexes can multimerize under certain conditions, but the sequence requirements of such structures are not well understood. In this study, we investigated the ability of all possible variants of the central tetrad in a monomeric, parallel-strand G-quadruplex to form higher-order structures. Although most of these 256 variants existed primarily as monomers under the conditions of our screen, ∼10% formed dimers or tetramers. These structures could form in a wide range of monovalent and divalent metal ions, and folding was highly cooperative in both KCl and MgCl₂. As was previously shown for G-quadruplexes that bind GTP and promote peroxidase reactions, G-quadruplexes that form dimers and tetramers have distinct sequence requirements. Some mutants could also form heteromultimers, and a second screen was performed to characterize the sequence requirements of these structures. Taken together, these experiments provide new insights into the sequence requirements and structures of both homomultimeric and heteromultimeric G-quadruplexes.

IR Spectra of n-Bu4M (M = Si, Ge, Sn, Pb), n-BuAuPPh3-d15, and "n-Bu" on a Gold Surface

Observed and DFT-calculated IR spectra of n-Bu₄M (M = Si, Ge, Sn, Pb), (CH₃CH₂CH₂¹³CD₂)₄Sn, and n-BuAuPPh₃-d₁₅ are reported and assigned. The asymmetric CH stretching vibration of the CH₂ group adjacent to the metal atom appears as a distinct shoulder at ∼2934 cm^-1, whereas for other CH₂ groups it is located at ∼2922 cm^-1. The characteristic peak at ∼2899 cm^-1 is attributed to an overtone of a symmetric CH₂ bend at ∼1445 cm^-1. In n-BuAuPPh₃-d₁₅, the CH stretching vibrations of the butyl group are shifted to lower frequencies by ∼10 cm^-1, and two possible rationalizations are offered.

The Role of Cysteine Residues in Catalysis of Phosphoenolpyruvate Carboxykinase from Mycobacterium tuberculosis

Mycobacterium tuberculosis (MTb), the causative agent of tuberculosis, can persist in macrophages for decades, maintaining its basic metabolic activities. Phosphoenolpyruvate carboxykinase (Pck; EC 4.1.1.32) is a key player in central carbon metabolism regulation. In replicating MTb, Pck is associated with gluconeogenesis, but in non-replicating MTb, it also catalyzes the reverse anaplerotic reaction. Here, we explored the role of selected cysteine residues in function of MTb Pck under different redox conditions. Using mass spectrometry analysis we confirmed formation of S–S bridge between cysteines C391 and C397 localized in the C-terminal subdomain. Molecular dynamics simulations of C391-C397 bridged model indicated local conformation changes needed for formation of the disulfide. Further, we used circular dichroism and Raman spectroscopy to analyze the influence of C391 and C397 mutations on Pck secondary and tertiary structures, and on enzyme activity and specificity. We demonstrate the regulatory role of C391 and C397 that form the S–S bridge and in the reduced form stabilize Pck tertiary structure and conformation for gluconeogenic and anaplerotic reactions.

Sensitive Versatile Fluorogenic Transmembrane Peptide Substrates for Rhomboid Intramembrane Proteases

Rhomboid proteases are increasingly being explored as potential drug targets, but their potent and specific inhibitors are not available, and strategies for inhibitor development are hampered by the lack of widely usable and easily modifiable in vitro activity assays. Here we address this bottleneck and report on the development of new fluorogenic transmembrane peptide substrates, which are cleaved by several unrelated rhomboid proteases, can be used both in detergent micelles and in liposomes, and contain red-shifted fluorophores that are suitable for high-throughput screening of compound libraries. We show that nearly the entire transmembrane domain of the substrate is important for efficient cleavage, implying that it extensively interacts with the enzyme. Importantly, we demonstrate that in the detergent micelle system, commonly used for the enzymatic analyses of intramembrane proteolysis, the cleavage rate strongly depends on detergent concentration, because the reaction proceeds only in the micelles. Furthermore, we show that the catalytic efficiency and selectivity toward a rhomboid substrate can be dramatically improved by targeted modification of the sequence of its P5 to P1 region. The fluorogenic substrates that we describe and their sequence variants should find wide use in the detection of activity and development of inhibitors of rhomboid proteases.

Oxahelicene NHC ligands in the asymmetric synthesis of nonracemic helicenes

Oxahelicene NHC ligands were used in Ni-catalysed enantioselective cycloisomerisation of alkynes to obtain helicenes in up to 86% ee.

Silychristin: Skeletal Alterations and Biological Activities

Silychristin is the second most abundant flavonolignan (after silybin) present in the fruits of Silybum marianum. A group of compounds containing silychristin (3) and its derivatives such as 2,3-dehydrosilychristin (4), 2,3-dehydroanhydrosilychristin (5), anhydrosilychristin (6), silyhermin (7), and isosilychristin (8) were studied. Physicochemical data of these compounds acquired at high resolution were compared. The absolute configuration of silyhermin (7) was proposed to be identical to silychristin A (3a) in ring D (10R,11S). The preparation of 2,3-dehydrosilychristin (4) was optimized. The Folin-Ciocalteau reduction and DPPH and ABTS radical scavenging assays revealed silychristin and its analogues to be powerful antioxidants, which were found to be more potent than silybin and 2,3-dehydrosilybin. Compounds 4-6 exhibited inhibition of microsomal lipoperoxidation (IC50 4-6 μM). Moreover, compounds 4-8 were found to be almost noncytotoxic for 10 human cell lines of different histogenetic origins. On the basis of these results, compounds 3-6 are likely responsible for most of the antioxidant properties of silymarin attributed traditionally to silybin (silibinin).

Altered biochemical specificity of G-quadruplexes with mutated tetrads

A fundamental motif in canonical nucleic acid structure is the base pair. Mutations that disrupt base pairs are typically destabilizing, but stability can often be restored by a second mutation that replaces the original base pair with an isosteric variant. Such concerted changes are a way to identify helical regions in secondary structures and to identify new functional motifs in sequenced genomes. In principle, such analysis can be extended to non-canonical nucleic acid structures, but this approach has not been utilized because the sequence requirements of such structures are not well understood. Here we investigate the sequence requirements of a G-quadruplex that can both bind GTP and promote peroxidase reactions. Characterization of all 256 variants of the central tetrad in this structure indicates that certain mutations can compensate for canonical G-G-G-G tetrads in the context of both GTP-binding and peroxidase activity. Furthermore, the sequence requirements of these two motifs are significantly different, indicating that tetrad sequence plays a role in determining the biochemical specificity of G-quadruplex activity. Our results provide insight into the sequence requirements of G-quadruplexes, and should facilitate the analysis of such motifs in sequenced genomes.

Functional and Structural Characterization of Novel Type of Linker Connecting Capsid and Nucleocapsid Protein Domains in Murine Leukemia Virus

The assembly of immature retroviral particles is initiated in the cytoplasm by the binding of the structural polyprotein precursor Gag with viral genomic RNA. The protein interactions necessary for assembly are mediated predominantly by the capsid (CA) and nucleocapsid (NC) domains, which have conserved structures. In contrast, the structural arrangement of the CA-NC connecting region differs between retroviral species. In HIV-1 and Rous sarcoma virus, this region forms a rod-like structure that separates the CA and NC domains, whereas in Mason-Pfizer monkey virus, this region is densely packed, thus holding the CA and NC domains in close proximity. Interestingly, the sequence connecting the CA and NC domains in gammaretroviruses, such as murine leukemia virus (MLV), is unique. The sequence is called a charged assembly helix (CAH) due to a high number of positively and negatively charged residues. Although both computational and deletion analyses suggested that the MLV CAH forms a helical conformation, no structural or biochemical data supporting this hypothesis have been published. Using an in vitro assembly assay, alanine scanning mutagenesis, and biophysical techniques (circular dichroism, NMR, microcalorimetry, and electrophoretic mobility shift assay), we have characterized the structure and function of the MLV CAH. We provide experimental evidence that the MLV CAH belongs to a group of charged, E(R/K)-rich, single α-helices. This is the first single α-helix motif identified in viral proteins.

Antimicrobial Peptide from the Wild Bee Hylaeus signatus Venom and Its Analogues: Structure-Activity Study and Synergistic Effect with Antibiotics

Venoms of hymenopteran insects have attracted considerable interest as a source of cationic antimicrobial peptides (AMPs). In the venom of the solitary bee Hylaeus signatus (Hymenoptera: Colletidae), we identified a new hexadecapeptide of sequence Gly-Ile-Met-Ser-Ser-Leu-Met-Lys-Lys-Leu-Ala-Ala-His-Ile-Ala-Lys-NH2. Named HYL, it belongs to the category of α-helical amphipathic AMPs. HYL exhibited weak antimicrobial activity against several strains of pathogenic bacteria and moderate activity against Candida albicans, but its hemolytic activity against human red blood cells was low. We prepared a set of HYL analogues to evaluate the effects of structural modifications on its biological activity and to increase its potency against pathogenic bacteria. This produced several analogues exhibiting significantly greater activity compared to HYL against strains of both Staphylococcus aureus and Pseudomonas aeruginosa even as their hemolytic activity remained low. Studying synergism of HYL peptides and conventional antibiotics showed the peptides act synergistically and preferentially in combination with rifampicin. Fluorescent dye propidium iodide uptake showed the tested peptides were able to facilitate entrance of antibiotics into the cytoplasm by permeabilization of the outer and inner bacterial cell membrane of P. aeruginosa. Transmission electron microscopy revealed that treatment of P. aeruginosa with one of the HYL analogues caused total disintegration of bacterial cells. NMR spectroscopy was used to elucidate the structure-activity relationship for the effect of amino acid residue substitution in HYL.