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A convenient supramolecular strategy for constructing a ratiometric fluorescent chemosensing ensemble, consisting of a macrocyclic host (cucurbit[8]uril CB[8]), and a pyrene-tagged amphiphilic peptide beacon (AP 1), is reported. AP 1 unfolds upon encapsulation of the pyrene termini into the hydrophobic CB[8] cavity. This changes pyrene excimer to monomer emission. Substrates with higher affinity for the CB[8] cavity can displace AP 1 from the ensemble. The released AP 1 folds again to form a pyrene excimer, which allows for the ratiometric fluorescence monitoring of the substrate. In this report, the ensemble capacity for ratiometric fluorescence monitoring of biological substrates, such as amino acid derivatives, specific peptides, and proteins, in aqueous media is demonstrated., (© 2019 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

Pre-equilibrated dynamic combinatorial libraries based on acyl hydrazone interchange of peptide-derived hydrazides and di- and tri-aldehydes have been used to discover potent inhibitors with nanomolar affinities for β-tryptase. To identify potent inhibitors the activity of the full library containing 95 members was compared with those of sub-libraries in which individual building blocks were missing. The most active library members contain a rigid central aromatic scaffold with three cationic peptide arms. The arms of the best inhibitors also contained a tailor-made GCP oxoanion binding motif attached to a lysine side chain. The most potent tri-armed hydrazones with peptide arms GKWR or GKWK(GCP) were shown to inhibit β-tryptase ( K i ca. 10-20 nM) reversibly, non-competitively and selectively (compared to related serine proteases, e.g. trypsin and chymotrypsin), most likely by binding to the protein surface, also in agreement with molecular modelling calculations. These new inhibitors are one order of magnitude more efficient than related tetravalent inhibitors obtained from previous work on a split-mix-combinatorial library and were identified with significantly less effort, demonstrating the usefulness of this approach for the identification of enzyme inhibitors in general.

A series of six new tetravalent ligands (1-6) with two different sets of arms bind to the surface of β-tryptase, a tetrameric enzyme with an A(2)B(2) arrangement of its four monomers and two different binding sites on its protein surface (as suggested by a docking study). Besides proteinogenic amino acids also the guanidiniocarbonyl pyrrole cation (abbreviated as GCP), as an artificial arginine analog, was introduced into the arms of the ligands to investigate its influence on protein surface binding and enzyme inhibition. Furthermore, four ligands (7-10) with four identical arms also containing the GCP group were additionally synthesized to study the influence of the GCP moiety on the inhibition properties compared to related ligands previously identified by us in earlier work. The best ligand from this new series (RWKG)(2)(GCP-LFG)(2) (6) indeed contains the artificial GCP group and with a K(i)-value of 67 nM is two orders of magnitude more efficient than the analogous ligand (RWKG)(2)(RLFG)(2) (1) derived solely from proteinogenic amino acids. Hence, four-armed ligands with two different arms are indeed efficient inhibitors for β-tryptase and the artificial GCP group can improve the binding affinity of this type of ligand to the protein, demonstrating the advantage of tailor-made binding motifs to increase affinity.

The mammalian heme enzyme myeloperoxidase (MPO) catalyzes the reaction of Cl(-) to the antimicrobial-effective molecule HOCl. During the catalytic cycle, a reactive intermediate "Compound I" (Cpd I) is generated. Cpd I has the ability to destroy the enzyme. Indeed, in the absence of any substrate, Cpd I decays with a half-life of 100 ms to an intermediate called Compound II (Cpd II), which is typically the one-electron reduced Cpd I. However, the nature of Cpd II, its spectroscopic properties, and the source of the additional electron are only poorly understood. On the basis of DFT and time-dependent (TD)-DFT quantum chemical calculations at the PBE0/6-31G* level, we propose an extended mechanism involving a new intermediate, which allows MPO to protect itself from self-oxidation or self-destruction during the catalytic cycle. Because of its similarity in electronic structure to Cpd II, we named this intermediate Cpd II'. However, the suggested mechanism and our proposed functional structure of Cpd II' are based on the hypothesis that the heme is reduced by charge separation caused by reaction with a water molecule, and not, as is normally assumed, by the transfer of an electron. In the course of this investigation, we found a second intermediate, the reduced enzyme, towards which the new mechanism is equally transferable. In analogy to Cpd II', we named it Fe(II'). The proposed new intermediates Cpd II' and Fe(II') allow the experimental findings, which have been well documented in the literature for decades but not so far understood, to be explained for the first time. These encompass a) the spontaneous decay of Cpd I, b) the unusual (chlorin-like) UV/Vis, circular dichroism (CD), and resonance Raman spectra, c) the inability of reduced MPO to bind CO, d) the fact that MPO-Cpd II reduces SCN(-) but not Cl(-), and e) the experimentally observed auto-oxidation/auto-reduction features of the enzyme. Our new mechanism is also transferable to cytochromes, and could well be viable for heme enzymes in general., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Mammalian (Clade 3) catalases utilize NADPH as a protective cofactor to prevent one-electron reduction of the central reactive intermediate Compound I (Cpd I) to the catalytically inactive Compound II (Cpd II) species by re-reduction of Cpd I to the enzyme's resting state (ferricatalase). It has long been known that ascorbate/ascorbic acid is capable of reducing Cpd I of NADPH-binding catalases to Cpd II, but the mode of this one-electron reduction had hitherto not been explored. We here demonstrate that ascorbate-mediated reduction of Cpd I, generated by addition of peroxoacetic acid to NADPH-free bovine liver catalase (BLC), requires specific binding of the ascorbate anion to the NADPH binding pocket. Ascorbate-mediated Cpd II formation was found to be suppressed by added NADPH in a concentration-dependent manner, for the achievement of complete suppression at a stoichiometric 1:1 NADPH:heme concentration ratio. Cpd I → Cpd II reduction by ascorbate was similarly inhibited by addition of NADH, NADP(+), thio-NADP(+), or NAD(+), though with 0.5-, 0.1-, 0.1-, and 0.01-fold reduced efficiencies, respectively, in agreement with the relative binding affinities of these dinucleotides. Unexpected was the observation that although Cpd II formation is not observed in the presence of NADP(+), the decay of Cpd I is slightly accelerated by ascorbate rather than retarded, leading to direct regeneration of ferricatalase. The experimental findings are supported by molecular mechanics docking computations, which show a similar binding of NADPH, NADP(+), and NADH, but not NAD(+), as found in the X-ray structure of NADPH-loaded human erythrocyte catalase. The computations suggest that two ascorbate molecules may occupy the empty NADPH pocket, preferably binding to the adenine binding site. The biological relevance of these findings is discussed.

A pyrene-functionalized cationic oligopeptide 1 efficiently binds to double-stranded DNA, as shown by different spectrophotochemical studies. Upon binding, the conformation of 1 changes from a folded to an extended form, which leads to a distinct change in the fluorescence properties. Thus, 1 functions as a molecular peptide beacon, and as it is easily taken up by cells, 1 can also be used for imaging of nucleic acids within cells., (© 2012 American Chemical Society)

The 'dipeptide extended' guanidiniocarbonyl pyrrole carboxylate zwitterion GCP-Phe-Phe 1 forms stable dimers in DMSO. However, dimerization is highly stereoselective. Only homochiral dimers are formed and the (L,L)·(L,L) dimer (K(dim) > 10(5) M(-1)) is significantly more stable by a factor of 10(3) than the diastereomeric (D,L)·(D,L) dimer (K(dim) = 120 M(-1)).

The indole based zwitterion 2 forms stable dimers held together by H-bond assisted ion pairs. Dimerisation was confirmed in the solid state and studied in solution using dilution NMR experiments. Even though zwitterion 2 forms very stable dimers even in DMSO, their stability is lower than of an analogous pyrrole based zwitterion 1. As revealed by the X-ray crystal structure the two binding sites in 2 cannot be planar due to steric interactions between the guanidinium group and a neighbouring aromatic CH. Hence the guanidinium moiety is twisted out of planarity from the rest of the molecule forcing the two monomers in dimer 2.2 to interact in a non-ideal orientation. Furthermore, the acidity of the NHs is lower than in 1 (as determined by UV-pH-titration) also leading to less efficient binding interactions.

X-ray structures of the 13 different monofunctional heme catalases published to date were scrutinized in order to gain insight in the mechanism by which NADPH in Clade 3 catalases may protect the reactive ferryloxo intermediate Compound I (Cpd I; por (*+)Fe (IV)O) against deactivation to the catalytically inactive intermediate Compound II (Cpd II; porFe (IV)O). Striking similarities in the molecular network of the protein subunits encompassing the heme center and the surface-bound NADPH were found for all of the Clade 3 catalases. Unique features in this region are the presence of a water molecule (W1) adjacent to the 4-vinyl group of heme and a serine residue or a second water molecule hydrogen-bonded to both W1 and the carbonyl group of a threonine-proline linkage, with the proline in van der Waals contact with the dihydronicotinamide group of NADPH. A mechanism is proposed in which a hydroxyl anion released from W1 undergoes reversible nucleophilic addition to the terminal carbon of the 4-vinyl group of Cpd I, thereby producing a neutral porphyrin pi-radical ferryloxo (HO-por (*)Fe (IV)O) species of reduced reactivity. This structure is suggested to be the elusive Cpd II' intermediate proposed in previous studies. An accompanying proton-shifting process along the hydrogen-bonded network is believed to facilitate the NADPH-mediated reduction of Cpd I to ferricatalase and to serve as a funnel for electron transfer from NADPH to the heme center to restore the catalase Fe (III) resting state. The proposed reaction paths were fully supported as chemically reasonable and energetically feasible by means of density functional theory calculations at the (U)B3LYP/6-31G* level. A particularly attractive feature of the present mechanism is that the previously discussed formation of protein-derived radicals is avoided.

Non-heme iron(III) complexes of 14-membered tetraaza macrocycles have previously been found to catalytically decompose hydrogen peroxide to water and molecular oxygen, like the native enzyme catalase. Here the mechanism of this reaction is theoretically investigated by DFT calculations at the (U)B3LYP/6-31G* level, with focus on the reactivity of the possible spin states of the FeIII complexes. The computations suggest that H2O2 decomposition follows a homolytic route with intermediate formation of an iron(IV) oxo radical cation species (L.+FeIV==O) that resembles Compound I of natural iron porphyrin systems. Along the whole catalytic cycle, no significant energetic differences were found for the reaction proceeding on the doublet (S=1/2) or on the quartet (S=3/2) hypersurface, with the single exception of the rate-determining O--O bond cleavage of the first associated hydrogen peroxide molecule, for which reaction via the doublet state is preferred. The sextet (S=5/2) state of the FeIII complexes appears to be unreactive in catalase-like reactions.

Acyclic receptors containing neutral hydrogen bonding sites, such as amino-pyridine groups and a crown unit, perform effective recognition of neutral sugar molecules through multiple interactions. Receptor 1 has been shown to be a particularly effective and highly selective receptor for beta-glucopyranoside.

The effect of pressure on the oxidation of hydroarenes 3-9 with 2,3-dichloro-5,6-dicyano-1,4-quinone (DDQ; 1 a) or o-chloranil (10), leading to the corresponding arenes, has been investigated. The activation volumes were determined from the pressure dependence of the rate constants of these reactions monitored by on-line UV/Vis spectroscopic measurements in an optical high-pressure cell (up to 3500 bar). The finding that they are highly negative and only moderately dependent on the solvent polarity (DeltaV( not equal ) = -13 to -25 in MTBE and -15 to -29 cm(3) mol(-1) in MeCN/AcOEt, 1:1) rules out the formation of ionic species in the rate-determining step and is good evidence for a hydrogen atom transfer mechanism leading to a pair of radicals in the rate-determining step, as was also suggested by kinetic measurements, studies of kinetic isotope effects, and spin-trapping experiments. The strong pressure dependence of the kinetic deuterium isotope effect for the reaction of 9,10-dihydroanthracene 5/5-9,9,10,10-D(4) with DDQ (1 a) can be attributed to a tunneling component in the hydrogen transfer. In the case of formal 1,3-dienes and enes possessing two vicinal C--H bonds, which have to be cleaved during the dehydrogenation, a pericyclic hydrogen transfer has to considered as one mechanistic alternative. The comparison of the kinetic deuterium isotope effects determined for the oxidation of tetralin 9/9-1,1,4,4-D(4)/9-2,2,3,3-D(4)/9-D(12) either with DDQ (1 a) or with thymoquinone 1 c indicates that the reaction with DDQ (1 a) proceeds in a stepwise manner through hydrogen atom transfer, analogously to the oxidations of 1,4-dihydroarenes, whereas the reaction with thymoquinone 1 c is concerted, following the course of a pericyclic hydrogen transfer. The difference in the mechanistic courses of these two reactions may be explained by the effect of the CN and Cl substituents in 1 a, which stabilize a radical intermediate better than the alkyl groups in 1 c. The mechanistic conclusions are substantiated by DFT calculations.

The cycloaddition of thiobenzophenone S-methylide to thiobenzophenone, an experimentally well-known reaction, was studied, using (U)HF/3-21G* for finding stationary points and (U)B3LYP/6-31G*//(U)HF/3-21G* single-point calculations for energies. Some optimizations were performed by (U)B3LYP/ 6-31G* to check the reliability of the calculations. The comparison of the concerted pathways and stepwise reactions via C,C-biradicals and C,S-zwitterions showed that the formation of a tetraphenyl-substituted C,C-biradical and its ring closure to 4,4,5,5-tetraphenyl-1,3-dithiolane constitutes the energetically most probable pathway of product formation, despite the fact that the regioisomeric 2,2,4,4-tetraphenyl-substituted product is more favorable by 17 kcal mol(-1). Model calculations on bond dissociation energies showed that (U)B3LYP with various basis sets overestimates radical stabilization, whereas CBS-QB3 closely reproduced experimental values. Results with the BLYP functional are similar to those with B3LYP. The consequences of the overestimation of radical stability for the cycloaddition mechanism involving biradicals are discussed. Thiobenzophenone S-methylide, if not captured by a dipolarophile, dimerizes to 2,2,3,3-tetraphenyl-1,4-dithiane. Calculation disclosed likewise a tetraphenyl-substituted C,C-biradical as intermediate.

The mechanisms of cycloaddition of thioformaldehyde S-methylide and thioacetone S-methylide, as models for an alkyl-substituted ylide, to thioformaldehyde and thioacetone, as well as to ethene as a model for a C=C double bond have been studied by ab initio calculations. Restricted and unrestricted B3LYP/6-31G* calculations were performed for the geometries of ground states, transition structures, and intermediates. Although basis sets with more polarization functions were tested, the 6-31G* basis set was applied throughout. Single-point CASPT2 calculations are reported for analysis of the unsubstituted system. The stabilities of structures with high biradical character seem to be overestimated by DFT methods in comparison to CASPT2. The general trends of the results are independent of the level of theory. Thioformaldehyde adds to thioformaldehyde S-methylide without activation energy, and the activation energies for two-step biradical pathways to 1,3-dithiolane are low. C,S biradicals are more stable than C,C biradicals. The two-step cycloaddition is not competitive with the concerted cycloaddition. Methyl substitution in the 1,3-dipole and the dipolarophile does not change the mechanistic relationships. TSs for the concerted formation of the regioisomeric cycloadducts of thioacetone Smethylide and thioacetone were located. Concerted addition remains the preferred reaction. The reactivity of the C=S double bond is high relative to that of the C=C double bond.

[structure: see text] New effective, acyclic, pyridine-based receptors 1-3 show remarkable alpha/beta binding selectivity in the recognition of monosaccharides. They are able to participate in cooperative and bidentate hydrogen bonds with sugar hydroxyls as well as in CH-pi interactions with CH's of sugar molecules.

The synthesis and binding properties for carbohydrates of several artificial, acyclic receptors containing two or three heterocyclic recognition units covalently attached to a phenyl spacer is described. These host molecules having uncharged hydrogen-bonding sites were used in a systematic study towards the evaluation of recognition motifs for carbohydrates. A novel effective, acyclic hydrogen-bonding receptor possessing naphthyridine-amide moieties as heterocyclic recognition units has been developed.

Despite their acyclic structure, the simple host molecules 1 and 2 can effectively hydrogen bond to monosaccharides. They show marked binding affinities to glucopyranosides in chloroform, and they are able to participate in three-dimensional recognition of monosaccharides.