Active-metal template clipping synthesis of novel [2]rotaxanes.

Mechanically interlocked molecules (MIMs) have been important synthetic targets in supramolecular chemistry due to their beautiful structures and intriguing properties. We present herein a new synthetic strategy to access [2]rotaxanes, namely active-metal template clipping. We discuss the design of the target [2]rotaxanes, synthesis and characterization of the axle, macrocycle precursors and macrocycles as well as preparation of the final [2]rotaxanes by active template copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) as key step of the synthesis. HRMS and NMR experiments have been performed to confirm the formation of the interlocked structures.

Synthetic Approaches of Epoxysuccinate Chemical Probes.

Synthetic chemical probes are powerful tools for investigating biological processes. They are particularly useful for proteomic studies such as activity-based protein profiling (ABPP). These chemical methods initially used mimics of natural substrates. As the techniques gained prominence, more and more elaborate chemical probes with increased specificity towards given enzyme/protein families and amenability to various reaction conditions were used. Among the chemical probes, peptidyl-epoxysuccinates represent one of the first types of compounds used to investigate the activity of the cysteine protease papain-like family of enzymes. Structurally derived from the natural substrate, a wide body of inhibitors and activity- or affinity-based probes bearing the electrophilic oxirane unit for covalent labeling of active enzymes now exists. Herein, we review the literature regarding the synthetic approaches to epoxysuccinate-based chemical probes together with their reported applications, from biological chemistry and inhibition studies to supramolecular chemistry and the formation of protein arrays.

An attempt to synthesize a terthienyl-based analog of indacenedithiophene (IDT): unexpected synthesis of a naphtho[2,3-b]thiophene derivative.

We report herein our attempt to synthesize an analog of indacenedithiophene (IDT) based on a tetraphenylhexyl substituted, covalently bridged syn-terthienyl unit. Instead of the expected compound the adopted synthetic route led to the formation of an unexpected, new naphtho[2,3-b]thiophene derivative. The structure of this compound was fully characterized by NMR and HRMS as well as single crystal X-ray diffraction and its electronic properties have been analyzed by UV-vis absorption spectroscopy and cyclic voltammetry. A possible mechanism for the formation of this compound is also proposed on the basis of detailed theoretical investigations.

Excess Ascorbate is a Chemical Stress Agent against Proteins and Cells.

Excess ascorbate (as expected in intravenous treatment proposed for COVID-19 management, for example) oxidizes and/or degrades hemoglobin and albumin, as evidenced by UV-vis spectroscopy, gel electrophoresis, and mass spectrometry. It also degrades hemoglobin in intact blood or in isolated erythrocytes. The survival rates and metabolic activities of several leukocyte subsets implicated in the antiviral cellular immune response are also affected. Excess ascorbate is thus an unselective biological stress agent.

A polycarboxylic chelating ligand for efficient resin purification of His-tagged proteins expressed in mammalian systems.

We describe the synthesis of a novel polyamino polycarboxylic ligand, its ability to coordinate metal-ions and attachment to a solid support designed for protein purification through Immobilised Metal-ion Affinity Chromatography (IMAC). The resin was found to be highly efficient for purification of His-tagged HCV E2 glycoproteins expressed in 293T mammalian cells.

A novel adaptive fluorescent probe for cell labelling.

In this study we describe the synthesis and characterisation of a new hydrazone-based fluorescent compound that is able to selectively label the endoplasmic reticulum (ER) in yeast and mammalian living cells. The fluorescence properties of the compound depended on the DMSO/water ratio and on the pH. NMR experiments allowed determination of the conformation adopted in various environments. Apart from the convenient synthetic procedure, our compound displays low cell toxicity and blue emission compatible with filters routinely used in fluorescence microscopy.

A novel profluorescent paramagnetic diaza-crown ether: synthesis, characterization and alkaline metal-ion complexation.

Starting from Kryptofix 22 two different branches were covalently attached through the nitrogen atoms, one containing a fluorescent moiety and the other the stable free radical TEMPO. The novel derivative exhibits fluorescence and paramagnetic properties, while the diaza-crown part ensures the affinity for alkaline metal-ions.

"Click" access to multilayer functionalized Au surface: A terpyridine patterning example.

This work is focused on self-assembled monolayers (SAMs) fabrication, using two types of Au surfaces, by subsequent attachment of different layers in order to develop a stable platform consisting of covalent multilayer functionalized gold surfaces. The key step in the construction of SAMs is the covalent linkage to the gold surface, via an amino-thiol derivative, of a cyclooctyne unit exhibiting strained triple bonds which react fast (catalysts are not needed) and quantitatively with organic azides and enable the introduction of various chemical functionalized entities on the gold surface. The versatility of the system is demonstrated by the reaction of the cyclooctyne decorated gold surface with an azide functionalized terpyridine followed by step by step complexation with Fe(II) and another terpyridine unit resulting into a multilayer covered gold surface. The Au surfaces were characterized by XPS to determine the chemical composition of the resulting SAMs. SPR was applied for real-time monitoring of the molecular interactions that occurred on the Au surface for each deposited layer. DPN was used to direct pattern the terpyridine-ink on a pre-functionalized AuIDE electrode. The AFM topology resulted from DPN and PEIS demonstrated metal-coordinating ligand of Fe(II)-Terpy.

Supramolecular anion recognition by ß-HCH.

The formation of highly ordered supramolecular architectures via cooperative C(aliphatic)-H·anion contacts between ß-HCH and various anions (Cl-, Br-, I- and HSO4-) was investigated by single crystal X-ray diffractometry, molecular modelling, ESI-MS and 1H-NMR titrations.

Exclusive Hydrophobic Self-Assembly of Adaptive Solid-State Networks of Octasubstituted 9,9'-Spirobifluorenes.

An easy and powerful access to 3,3',6,6'-tetrasubstituted 9,9'-spirobifluorene derivatives with tetrahedral orientation of the peripheral groups (i.e., -I, -CN, -NO2, -CH═O, -COOH, -C≡CH, -4-Py) was developed. The NMR and HRMS results are in agreement with the proposed formula and the solid-state molecular structures obtained by single-crystal X-ray diffraction. They form molecular solids self-assembled via exclusive hydrophobic interactions. Solid-state selection and adaptation can be obtained on the basis of variable compact packing of functional groups present on the 9,9'-spirobifluorene backbone.

Selective host molecules obtained by dynamic adaptive chemistry.

Up till 20 years ago, in order to endow molecules with function there were two mainstream lines of thought. One was to rationally design the positioning of chemical functionalities within candidate molecules, followed by an iterative synthesis-optimization process. The second was the use of a "brutal force" approach of combinatorial chemistry coupled with advanced screening for function. Although both methods provided important results, "rational design" often resulted in time-consuming efforts of modeling and synthesis only to find that the candidate molecule was not performing the designed job. "Combinatorial chemistry" suffered from a fundamental limitation related to the focusing of the libraries employed, often using lead compounds that limit its scope. Dynamic constitutional chemistry has developed as a combination of the two approaches above. Through the rational use of reversible chemical bonds together with a large plethora of precursor libraries, one is now able to build functional structures, ranging from quite simple molecules up to large polymeric structures. Thus, by introduction of the dynamic component within the molecular recognition processes, a new perspective of deciphering the world of the molecular events has aroused together with a new field of chemistry. Since its birth dynamic constitutional chemistry has continuously gained attention, in particular due to its ability to easily create from scratch outstanding molecular structures as well as the addition of adaptive features. The fundamental concepts defining the dynamic constitutional chemistry have been continuously extended to currently place it at the intersection between the supramolecular chemistry and newly defined adaptive chemistry, a pivotal feature towards evolutive chemistry.

Luminogenic "clickable" lanthanide complexes for protein labeling.

Development of lanthanide-based luminescent "switch-on" systems via azide-alkyne [3+2] cycloaddition is described. We used these for non-specific protein labeling and as tags for specific and selective activity-based protein labeling.

Structure of polydopamine: a never-ending story?

Polydopamine (PDA) formed by the oxidation of dopamine is an important polymer, in particular, for coating various surfaces. It is composed of dihydroxyindole, indoledione, and dopamine units, which are assumed to be covalently linked. Although PDA has been applied in a manifold way, its structure is still under discussion. Similarities have been observed in melanins/eumelanins as naturally occurring, deeply colored polymer pigments derived from L-DOPA. Recently, an alternative structure was proposed for PDA wherein dihydroxyindoline, indolinedione, and eventually dopamine units are not covalently linked to each other but are held together by hydrogen bonding between oxygen atoms or π stacking. In this study, we show that this structural proposal is very unlikely to occur taking into account unambiguous results obtained by different analytical methods, among them (13)C CPPI MAS NMR (cross-polarization polarization-inversion magic angle spinning NMR), (1)H MAS NMR (magic angle spinning NMR), and ES-HRMS (electrospray ionization high-resolution mass spectrometry) for the first time in addition to XPS (X-ray photoelectron spectroscopy) and FTIR spectroscopy. The results give rise to a verified structural assignment of PDA wherein dihydroxyindole and indoledione units with different degrees of (un)saturation are covalently linked by C-C bonds between their benzene rings. Furthermore, proof of open-chain (dopamine) monomer units in PDA is provided. Advanced DFT calculations imply the arrangements of several PDA chains preferably by quinone-hydroquinone-type interactions in a parallel or antiparallel manner. From all of these results, a number of hypotheses published before could be experimentally supported or were found to be contradictory, thus leading to a better understanding of the PDA structure.

Unexpected formation of N-(1-(2-aryl-hydrazono)isoindolin-2-yl)benzamides and their conversion into 1,2-(bis-1,3,4-oxadiazol-2-yl)benzenes.

Reaction between ortho-phthalaldehyde and various aroylhydrazines unexpectedly yields N-(1-(2-aryl-hydrazono)isoindolin-2-yl)benzamides as major products along with the predictable 1,2-bis-aroylhydrazones. NMR investigation of the major reaction products indicate the presence of a mixture of geometrical isomers, in various ratios. Single crystal X-ray diffraction confirms the proposed structure and indicates a Z configuration of the C═N double bond substitutents. Optimization of the condensation reaction conditions enabled quantitative isolation of the cyclic isomer. Oxidation of the isomers with bis(trifluoroacetoxy)iodobenzene (PIFA) leads to rapid formation of new highly fluorescent 1,2-bis(5-aryl-1,3,4-oxadiazol-2-yl)benzenes.

A general solid phase method for the synthesis of sequence independent peptidyl-fluoromethyl ketones.

We present here a new, general, solid phase strategy for the synthesis of sequence independent peptidyl-fluoromethyl ketones using standard Fmoc peptide chemistry. Our method is based on the synthesis of bifunctional linkers which allows the incorporation of amino acid fluoromethyl ketone unit at the C-terminal end of peptide sequences. Application of this approach for the synthesis of activity based probes for SENPs is also described.

Glycine fluoromethylketones as SENP-specific activity based probes.

We report here the synthesis and biochemical properties of a new peptidyl activity-based probe 1 for SUMO proteases, SENPs. The activity-based probe has at its C terminus a glycine-derived fluoromethylketone moiety as a reactive group designed to target the active-site cysteine of SENPs. Based on a study of the interactions between SENPs and SUMOs, we introduced further design elements that allow the activity-based probe to selectively target SENPs at low micromolar to high nanomolar concentrations. Moreover, 1 out-competes SUMO1 from the reversible SUMO1-SENP1 complex, thus suggesting that 1 and SUMO1 share a common binding site on SENP1.