A new genome-mining tool redefines the lasso peptide biosynthetic landscape.

Ribosomally synthesized and post-translationally modified peptide (RiPP) natural products are attractive for genome-driven discovery and re-engineering, but limitations in bioinformatic methods and exponentially increasing genomic data make large-scale mining of RiPP data difficult. We report RODEO (Rapid ORF Description and Evaluation Online), which combines hidden-Markov-model-based analysis, heuristic scoring, and machine learning to identify biosynthetic gene clusters and predict RiPP precursor peptides. We initially focused on lasso peptides, which display intriguing physicochemical properties and bioactivities, but their hypervariability renders them challenging prospects for automated mining. Our approach yielded the most comprehensive mapping to date of lasso peptide space, revealing >1,300 compounds. We characterized the structures and bioactivities of six lasso peptides, prioritized based on predicted structural novelty, including one with an unprecedented handcuff-like topology and another with a citrulline modification exceptionally rare among bacteria. These combined insights significantly expand the knowledge of lasso peptides and, more broadly, provide a framework for future genome-mining efforts.

Novel sila-amide derivatives of N-acetylcysteine protects platelets from oxidative stress-induced apoptosis.

Oxidative stress-induced platelet apoptosis is one among the many causes for the development and progression of many disorders like cardiovascular diseases, arthritis, Alzheimer's disease and many chronic inflammatory responses. Many studies have demonstrated the less optimal effect of N-acetyl cysteine (NAC) in oxidative stress-induced cellular damage. This could be due to its less lipophilicity which makes it difficult to enter the cellular membrane. Therefore in the present study, lipophilic sila-amide derivatives (6a and 6b) synthesized through the reaction of NAC with 3-Aminopropyltrimethylsilane and aminomethyltrimethylsilane were used to determine their protective property against oxidative stress-induced platelet apoptosis. At a concentration of 10 µM, compound 6a and 6b were able to significantly inhibit Rotenone/H2O2 induced platelet apoptotic markers like reactive oxygen species, intracellular calcium level, mitochondrial membrane potential, cytochrome c release from mitochondrial to the cytosol, caspase-9 and -3 activity and phosphatidylserine externalization. Therefore, the compounds can be extrapolated as therapeutic agents to protect platelets from oxidative stress-induced platelet apoptosis and its associated complications.

Tricin, a flavonoid monomer in monocot lignification.

Tricin was recently discovered in lignin preparations from wheat (Triticum aestivum) straw and subsequently in all monocot samples examined. To provide proof that tricin is involved in lignification and establish the mechanism by which it incorporates into the lignin polymer, the 4'-O-ß-coupling products of tricin with the monolignols (p-coumaryl, coniferyl, and sinapyl alcohols) were synthesized along with the trimer that would result from its 4'-O-ß-coupling with sinapyl alcohol and then coniferyl alcohol. Tricin was also found to cross couple with monolignols to form tricin-(4'-O-ß)-linked dimers in biomimetic oxidations using peroxidase/hydrogen peroxide or silver (I) oxide. Nuclear magnetic resonance characterization of gel permeation chromatography-fractionated acetylated maize (Zea mays) lignin revealed that the tricin moieties are found in even the highest molecular weight fractions, ether linked to lignin units, demonstrating that tricin is indeed incorporated into the lignin polymer. These findings suggest that tricin is fully compatible with lignification reactions, is an authentic lignin monomer, and, because it can only start a lignin chain, functions as a nucleation site for lignification in monocots. This initiation role helps resolve a long-standing dilemma that monocot lignin chains do not appear to be initiated by monolignol homodehydrodimerization as they are in dicots that have similar syringyl-guaiacyl compositions. The term flavonolignin is recommended for the racemic oligomers and polymers of monolignols that start from tricin (or incorporate other flavonoids) in the cell wall, in analogy with the existing term flavonolignan that is used for the low-molecular mass compounds composed of flavonoid and lignan moieties.

Synthesis and structure of m-terphenyl thio-, seleno-, and telluroethers.

Several routes for the synthesis of m-terphenyl thio-, seleno-, and telluroethers were investigated. m-Terphenyl iodides react with diphenyl diselenides or ditellurides (CsOH·H(2)O, DMSO, 110 °C) to give the desired compounds in 19-84% yield which significantly extends the previously reported such reactions because o-benzyne cannot be an intermediate as previously suggested. However, the most general synthetic route was that involving reaction of 2,6-diaryl Grignard reagents with sulfur, selenium, or tellurium electrophiles. The m-terphenyl thio-, seleno-, and telluroethers were characterized spectroscopically and, in one case, by single-crystal X-ray analysis. Certain of these compounds showed atropisomerism and barriers for interconversion of isomers were determined by variable-temperature NMR spectroscopy. The barriers for interconverting the syn and anti atropisomers increase on going from the analogous S to Se to Te compounds. Calculations on this isomerization revealed that the barriers are due to rotation about the aryl-aryl bond and that the barriers for rotation about the aryl-chalcogen bond are much lower.

Electrochemical and chemical oxidation of dithia-, diselena-, ditellura-, selenathia-, and tellurathiamesocycles and stability of the oxidized species.

The diverse electrochemical and chemical oxidations of dichalcogena-mesocycles are analyzed, broadening our understanding of the chemistry of the corresponding radical cations and dications. 1,5-Diselenocane and 1,5-ditellurocane undergo reversible two-electron oxidation with inverted potentials analogous to 1,5-dithiocane. On the other hand, 1,5-selenathiocane and 1,5-tellurathiocane undergo one-electron oxidative dimerization. The X-ray crystal structures of the Se-Se dimer of the 1,5-selenathiocane one-electron oxidized product and the monomeric two-electron oxidized product (dication) of 1,5-tellurathiocane are reported. 1,5-Dithiocanes and 1,5-diselenocanes with group 14 atoms as ring members undergo irreversible oxidation, unlike the reversible two-electron oxidation of the corresponding silicon-containing 1,5-ditellurocanes. These results demonstrate the chemical consequences of the dication stabilities Te(+)-Te(+) > Se(+)-Se(+) > S(+)-S(+), as well as Se(+)-Se(+) > Se(+)-S(+) and Te(+)-Te(+) > Te(+)-S(+).

2-{[(4-Methoxy-phen-yl)dimethyl-silyl]meth-yl}isoindoline-1,3-dione.

In the course of our studies of silicon-containing anti-cancer compounds, the title compound, C(18)H(19)NO(3)Si, was synthesized. The mol-ecular geometry including bond distances and angles involving the Si atoms are typical. Torsion angles associated with the isoindoline ring and the silyl group [C-N-C(methyl-ene)-Si = 90.5 (2) and -93.1 (2)°] indicate that there is no inter-action between the O and Si atoms despite silicon's high affinity for oxygen.

2-[2-(Trimethyl-silyl)eth-yl]isoindoline-1,3-dione.

In the course of our studies of silicon-containing anti-cancer compounds, the title compound, C(13)H(17)NO(2)Si, was synthesized. The geometrical parameters including the geometry about the Si atom are typical. The mol-ecules form dimers via a weak C-H⋯O inter-action described by the graph set R(2) (2)(10). The dimers are assembled in rows stacked in the crystallographic b-axis direction via π-π inter-actions with a 3.332 (3) Šseparation between the rows.

2-[3-(Methyl-diphenyl-silyl)prop-yl]isoindoline-1,3-dione.

In the title compound, C(24)H(23)NO(2)Si, the dihedral angle between the planes of the phenyl rings attached to the Si atom is 80.78 (10)°. In the crystal, the mol-ecules form sheets lying perpendicular to [101] via C-H⋯O inter-actions. These sheets are stacked and linked in a three-dimensional framework by additional C-H⋯O inter-actions in the [10] direction.

Silicon containing ibuprofen derivatives with antioxidant and anti-inflammatory activities: An in vivo and in silico study.

There are many chronic diseases related with inflammation. The chronic inflammation can produce other problems as cancer. Therefore, it is necessary to design drugs with better anti-inflammatory activity than those in the clinic. Likewise, these could be used in chronic treatments with minimum adverse effects. The amide or ester functionality in combination with the insertion of a silyl alkyl moiety is able to improve some drug properties. In this context, the evaluation of a group of silicon containing ibuprofen derivatives (SCIDs) as antioxidants and anti-inflammatory agents is reported. Antioxidant activity was evaluated by the 2,2-Diphenyl-1-picrylhydrazyl (DPPH⨪), 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic) acid (ABTS•+) and the Fe(II) chelating ability methods. The anti-inflammatory activity was determined by using the carrageenan induced rat paw edema. The gastrotoxic profile of the SCIDs that displayed significant anti-inflammatory activity was determined by the indomethacin induced ulceration method. The SCIDs performed better than ibuprofen as chelating agents for Fe(II) and as scavengers for the free radicals DPPH• and ABTS•+. On the anti-inflammatory test, compound 4a inhibited the edema up to 87%, while 4d &10b achieved significant inflammation inhibition at a lower effective dose 50 (ED50) than ibuprofen´s. None of the SCIDs endowed with anti-inflammatory activity, showed significant gastrotoxic effects with respect to those displayed by ibuprofen. Based on the experimental results and aided by the theoretical docking approach, it was possible to rationalize how the SCIDs may bind to cyclooxygenase isoforms and helped to explain their reduced gastrotoxicity. The evaluated effects were improved in SCIDs with respect to ibuprofen.

Methotrexate Promotes Platelet Apoptosis via JNK-Mediated Mitochondrial Damage: Alleviation by N-Acetylcysteine and N-Acetylcysteine Amide.

Thrombocytopenia in methotrexate (MTX)-treated cancer and rheumatoid arthritis (RA) patients connotes the interference of MTX with platelets. Hence, it seemed appealing to appraise the effect of MTX on platelets. Thereby, the mechanism of action of MTX on platelets was dissected. MTX (10 µM) induced activation of pro-apoptotic proteins Bid, Bax and Bad through JNK phosphorylation leading to ΔΨm dissipation, cytochrome c release and caspase activation, culminating in apoptosis. The use of specific inhibitor for JNK abrogates the MTX-induced activation of pro-apoptotic proteins and downstream events confirming JNK phosphorylation by MTX as a key event. We also demonstrate that platelet mitochondria as prime sources of ROS which plays a central role in MTX-induced apoptosis. Further, MTX induces oxidative stress by altering the levels of ROS and glutathione cycle. In parallel, the clinically approved thiol antioxidant N-acetylcysteine (NAC) and its derivative N-acetylcysteine amide (NACA) proficiently alleviate MTX-induced platelet apoptosis and oxidative damage. These findings underpin the dearth of research on interference of therapeutic drugs with platelets, despite their importance in human health and disease. Therefore, the use of antioxidants as supplementary therapy seems to be a safe bet in pathologies associated with altered platelet functions.

Interaction of C-Si, C-Sn, and Si-Si sigma-bonds with chalcogen lone pairs.

The ability of neighboring C-Si, C-Sn, and Si-Si groups in conformationally constrained cyclic molecules to reduce the lowest ionization energies of sulfur, selenium, and tellurium compounds has been determined by charge-transfer spectroscopy of complexes with tetracyanoethylene. For selected compounds, ionization energies were determined by gas-phase photoelectron spectroscopy. The lowest ionization energies measured by photoelectron spectroscopy, with one exception, correlate with the charge-transfer spectroscopic data. In addition, theoretical analysis has provided insight into the photoelectron spectra and the geometry-dependent interaction between C-Si or C-Sn bonds and chalcogen lone pairs. Substantial lowering of ionization energies is found which is anticipated to have important consequences in the chemistry of these and related species.

Hydrogen generation from weak acids: electrochemical and computational studies of a diiron hydrogenase mimic.

Extended investigation of electrocatalytic generation of dihydrogen using [(mu-1,2-benzenedithiolato)][Fe(CO)3]2 has revealed that weak acids, such as acetic acid, can be used. The catalytic reduction producing dihydrogen occurs at approximately -2 V for several carboxylic acids and phenols resulting in overpotentials of only -0.44 to -0.71 V depending on the weak acid used. This unusual catalytic reduction occurs at a potential at which the starting material, in the absence of a proton source, does not show a reduction peak. The mechanism for this process and structures for the intermediates have been discerned by electrochemical and computational analysis. These studies reveal that the catalyst is the monoanion of the starting material and an ECEC mechanism occurs.

The Si-Si effect on ionization of beta-disilanyl sulfides and selenides.

The ionization energies of conformationally constrained, newly synthesized beta-disilanyl sulfides and selenides were determined by photoelectron spectroscopy. These ionization energies reflect substantial (0.53-0.75 eV) orbital destabilizations. The basis for these destabilizations was investigated by theoretical calculations, which reveal geometry-dependent interaction between sulfur or selenium lone pair orbitals and sigma-orbitals, especially Si-Si sigma-orbitals. These results presage facile redox chemistry for these compounds and significantly extend the concept of sigma-stabilization of electron-deficient centers.

Synthesis, gas-phase photoelectron spectroscopic, and theoretical studies of stannylated dinuclear iron dithiolates.

Stannylated dinuclear iron dithiolates (mu-SSnMe(2)CH(2)S)[Fe(CO)(3)](2), (mu-SCH(2)SnMe(2)CH(2)S) [Fe(CO)(3)](2), and (mu-SCH(2)SnMe(3))(2)[Fe(CO)(3)](2), which are structurally similar to the active site of iron-only hydrogenase, were synthesized and studied by gas-phase photoelectron spectroscopy. The orbital origins of ionizations were assigned by comparison of He I and He II photoelectron spectra and with the aid of hybrid density functional electronic structure calculations. Stannylation lowers the ionization energy of sulfur lone pair orbitals in these systems owing to a geometry-dependent interaction. The Fe-Fe sigma bond, which is the HOMO in all these systems, is also substantially destabilized by stannylation due to a previously unrecognized geometry-dependent interaction between axial sulfur lone pair orbitals and the Fe-Fe sigma bond. Since cleaving the Fe-Fe sigma bond is a key step in the mechanism of action of iron-only hydrogenase, these newly recognized geometry-dependent interactions may be utilized in designing biologically inspired hydrogenase catalysts.