Efficient Access to Peptidyl‐RNA Conjugates for Picomolar Inhibition of Non‐ribosomal FemXWv Aminoacyl Transferase

Peptidyl–RNA conjugates have various applications in studying the ribosome and enzymes participating in tRNA‐dependent pathways such as Fem transferases in peptidoglycan synthesis. Herein a convergent synthesis of peptidyl–RNAs based on Huisgen–Sharpless cycloaddition for the final ligation step is developed. Azides and alkynes are introduced into tRNA and UDP‐MurNAc‐pentapeptide, respectively. Synthesis of 2′‐azido RNA helix starts from 2′‐azido‐2′‐deoxyadenosine that is coupled to deoxycytidine by phosphoramidite chemistry. The resulting dinucleotide is deprotected and ligated to a 22‐nt RNA helix mimicking the acceptor arm of Ala‐tRNA^Ala by T4 RNA ligase. For alkyne UDP‐MurNAc‐pentapeptide, meso‐cystine is enzymatically incorporated into the peptidoglycan precursor and reduced, and L ‐Cys is converted to dehydroalanine with O‐(mesitylenesulfonyl)hydroxylamine. Reaction of but‐3‐yne‐1‐thiol with dehydroalanine affords the alkyne‐containing UDP‐MurNAc‐pentapeptide. The Cu^I‐catalyzed azide alkyne cycloaddition reaction in the presence of tris[(1‐hydroxypropyl‐1H‐1,2,3‐triazol‐4‐yl)methyl]amine provided the peptidyl‐RNA conjugate, which was tested as an inhibitor of non‐ribosomal FemX_Wv aminoacyl transferase. The bi‐substrate analogue was found to inhibit FemX_Wv with an IC₅₀ of (89±9) pM , as both moieties of the peptidyl–RNA conjugate contribute to high‐affinity binding.     

Stability Enhancement of a Dimeric HER2-Specific Affibody Molecule through Sortase A-Catalyzed Head-to-Tail Cyclization

Natural backbone-cyclized proteins have an increased thermostability and resistance towards proteases, characteristics that have sparked interest in head-to-tail cyclization as a method to stability-enhance proteins used in diagnostics and therapeutic applications, for example. In this proof-of principle study, we have produced and investigated a head-to-tail cyclized and HER2-specific Z_HER2:342 Affibody dimer. The sortase A-mediated cyclization reaction is highly efficient (>95%) under optimized conditions, and renders a cyclic Z_HER3:342-dimer with an apparent melting temperature, T_m, of 68 °C, which is 3 °C higher than that of its linear counterpart. Circular dichroism spectra of the linear and cyclic dimers looked very similar in the far-UV range, both before and after thermal unfolding to 90 °C, which suggests that cyclization does not negatively impact the helicity or folding of the cyclic protein. The cyclic dimer had an apparent sub-nanomolar affinity (K_d ~750 pM) to the HER2-receptor, which is a ~150-fold reduction in affinity relative to the linear dimer (K_d ~5 pM), but the anti-HER2 Affibody dimer remained a high-affinity binder even after cyclization. No apparent difference in proteolytic stability was detected in an endopeptidase degradation assay for the cyclic and linear dimers. In contrast, in an exopeptidase degradation assay, the linear dimer was shown to be completely degraded after 5 min, while the cyclic dimer showed no detectable degradation even after 60 min. We further demonstrate that a site-specifically DyLight 594-labeled cyclic dimer shows specific binding to HER2-overexpressing cells. Taken together, the results presented here demonstrate that head-to-tail cyclization can be an effective strategy to increase the stability of an Affibody dimer.     

Synthesis of a C(sp2)-bridged Phosphine-Borane by Ionic Coupling

The vinyl carbenoid H₂C=CBr(Li) has been used as key precursor to prepare a geminal C(sp²)-bridged phosphine-borane. Starting from bromoethene, two sequences of lithiation/electrophilic trapping, with ClPiPr₂ and FBMes₂ respectively, affords iPr₂P–C(=CH₂)–BMes₂ 3 [Mes = 2,4,6-(H₃C)₃C₆H₂]. This new phosphine-borane 3 was characterized by multi-nuclear NMR and mass spectroscopy. It adopts a monomeric open structure without P→B interaction. A few crystals of a secondary product 4 were analyzed by X-ray diffraction, revealing an unusual dimeric structure.     

Emerging Bottom-Up Strategies for the Synthesis of Graphene Nanoribbons and Related Structures

The solution-phase synthesis is one of the most promising strategies for the preparation of well-defined graphene nanoribbons (GNRs) in large scale. To prepare high quality, defect-free GNRs, cycloaromatization reactions need to be very efficient, proceed without side reaction and mild enough to accommodate the presence of various functional groups. In this Minireview, we present the latest synthetic approaches for the synthesis of GNRs and related structures, including alkyne benzannulation, photochemical cyclodehydrohalogenation, Mallory and Pd- and Ni-catalyzed reactions.     

Emerging Bottom‐Up Strategies for the Synthesis of Graphene Nanoribbons and Related Structures

The solution‐phase synthesis is one of the most promising strategies for the preparation of well‐defined graphene nanoribbons (GNRs) in large scale. To prepare high quality, defect‐free GNRs, cycloaromatization reactions need to be very efficient, proceed without side reaction and mild enough to accommodate the presence of various functional groups. In this Minireview, we present the latest synthetic approaches for the synthesis of GNRs and related structures, including alkyne benzannulation, photochemical cyclodehydrohalogenation, Mallory and Pd‐ and Ni‐catalyzed reactions.     

In-Situ Synthesis and Characterization of Nanocomposites in the Si-Ti-N and Si-Ti-C Systems

The pyrolysis (1000 °C) of a liquid poly(vinylmethyl-co-methyl)silazane modified by tetrakis(dimethylamido)titanium in flowing ammonia, nitrogen and argon followed by the annealing (1000–1800 °C) of as-pyrolyzed ceramic powders have been investigated in detail. We first provide a comprehensive mechanistic study of the polymer-to-ceramic conversion based on TG experiments coupled with in-situ mass spectrometry and ex-situ solid-state NMR and FTIR spectroscopies of both the chemically modified polymer and the pyrolysis intermediates. The pyrolysis leads to X-ray amorphous materials with chemical bonding and ceramic yields controlled by the nature of the atmosphere. Then, the structural evolution of the amorphous network of ammonia-, nitrogen- and argon-treated ceramics has been studied above 1000 °C under nitrogen and argon by X-ray diffraction and electron microscopy. HRTEM images coupled with XRD confirm the formation of nanocomposites after annealing at 1400 °C. Their unique nanostructural feature appears to be the result of both the molecular origin of the materials and the nature of the atmosphere used during pyrolysis. Samples are composed of an amorphous Si-based ceramic matrix in which TiN_xC_y nanocrystals (x + y = 1) are homogeneously formed “in situ” in the matrix during the process and evolve toward fully crystallized compounds as TiN/Si₃N₄, TiN_xC_y (x + y = 1)/SiC and TiC/SiC nanocomposites after annealing to 1800 °C as a function of the atmosphere.     

Nonlinear normal modes and band zones in granular chains with no pre-compression

We study standing waves (nonlinear normal modes—NNMs) and band zones in finite granular chains composed of spherical granular beads in Hertzian contact, with fixed boundary conditions. Although these are homogeneous dynamical systems in the notation of Rosenberg (Adv. Appl. Mech. 9:155–242, 1966), we show that the discontinuous nature of the dynamics leads to interesting effects such as separation between beads, NNMs that appear as traveling waves (these are characterized as pseudo-waves), and localization phenomena. In the limit of infinite extent, we study band zones, i.e., pass and stop bands in the frequency–energy plane of these dynamical systems, and classify the essentially nonlinear responses that occur in these bands. Moreover, we show how the topologies of these bands significantly affect the forced dynamics of these granular media subject to narrowband excitations. This work provides a classification of the coherent (regular) intrinsic dynamics of one-dimensional homogeneous granular chains with no pre-compression, and provides a rigorous theoretical foundation for further systematic study of the dynamics of granular systems, e.g., the effects of disorders or clearances, discrete breathers, nonlinear localized modes, and high-frequency scattering by local disorders. Moreover, it contributes toward the design of granular media as shock protectors, and in the passive mitigation of transmission of unwanted disturbances.     

Monte carlo estimates of domain-deformation sensitivities

It is shown that, when a Monte Carlo algorithm is used for estimation of any physical quantity A, a simple and fast additional procedure can be implemented that simultaneously estimates the sensitivity of A to any problem parameter. The proposed approach is general and systematic in the sense that: (i) it includes domain-deformation sensitivities, i.e., cases where a change in the parameter modifies the domain over which the sampled random variables are defined and (ii) a simple generic procedure is presented to address all remaining free choices in terms of variance minimization.     

Phosphine-mediated [4 + 2] annulation of bis(enones): a Lewis base catalyzed "mock Diels-Alder" reaction

Lewis-base-catalyzed cycloisomerization of bis(enones) to decalins has been demonstrated as an alternative to the traditional Lewis acid catalyzed Diels-Alder cycloaddition. In this process, a trialkylphosphine mediates both bond formation steps in two distinct catalytic cycles. The single-pot operation generates two carbon-carbon bonds and up to five contiguous stereocenters in one step, starting from achiral, aliphatic substrates; eight examples are provided. [reaction: see text]