An “OFF–ON–OFF” fluorescence protein-labeling probe for real-time visualization of the degradation of short-lived proteins in cellular systems

The ability to monitor proteolytic pathways that remove unwanted and damaged proteins from cells is essential for understanding the multiple processes used to maintain cellular homeostasis. In this study, we have developed a new protein-labeling probe that employs an ‘OFF–ON–OFF’ fluorescence switch to enable real-time imaging of the expression (fluorescence ON) and degradation (fluorescence OFF) of PYP-tagged protein constructs in living cells. Fluorescence switching is modulated by intramolecular contact quenching interactions in the unbound probe (fluorescence OFF) being disrupted upon binding to the PYP-tag protein, which turns fluorescence ON. Quenching is then restored when the PYP-tag–probe complex undergoes proteolytic degradation, which results in fluorescence being turned OFF. Optimization of probe structures and PYP-tag mutants has enabled this fast reacting ‘OFF–ON–OFF’ probe to be used to fluorescently image the expression and degradation of short-lived proteins.

An “OFF–ON–OFF” fluorescence probe for real-time imaging of the expression (fluorescence ‘OFF’) and degradation (fluorescence ‘ON’) of short lived PYP-tag proteins in cellular systems.     

Biomimetic nanochannels for the discrimination of sialylated glycans via a tug-of-war between glycan binding and polymer shrinkage

Sialylated glycans that are attached to cell surface mediate diverse cellular processes such as immune responses, pathogen binding, and cancer progression. Precise determination of sialylated glycans, particularly their linkage isomers that can trigger distinct biological events and are indicative of different cancer types, remains a challenge, due to their complicated composition and limited structural differences. Here, we present a biomimetic nanochannels system integrated with the responsive polymer polyethyleneimine-g-glucopyranoside (Glc-PEI) to solve this problem. By using a dramatic “OFF–ON” change in ion flux, the nanochannels system achieves specific recognition for N-acetylneuraminic acid (Neu5Ac, the predominant form of sialic acid) from various monosaccharides and sialic acid species. Importantly, different “OFF–ON” ratios of the conical nanochannels system allows the precise and sensitive discrimination of sialylated glycan linkage isomers, α2–3 and α2–6 linkage (the corresponding ion conductance increase ratios are 96.2% and 264%, respectively). Analyses revealed an unusual tug-of-war mechanism between polymer-glycan binding and polymer shrinkage. The low binding affinity of Glc-PEI for the α2–6-linked glycan caused considerable shrinkage of Glc-PEI layer, but the high affinity for the α2–3-linked glycan resulted in only a slight shrinkage. This competition mechanism provides a simple and versatile materials design principle for recognition or sensing systems that involve negatively charged target biomolecules. Furthermore, this work broadens the application of nanochannel systems in bioanalysis and biosensing, and opens a new route to glycan analysis that could help to uncover the mysterious and wonderful glycoworld.

A glycan-responsive polymer-modified nanochannels system enables the precise discrimination of sialylated glycan linkage isomers via the different “OFF–ON” changes resulting from a “tug-of-war” between polymer-glycan binding and polymer shrinkage.     

Electrochemical radical reactions of alkyl iodides: a highly efficient,clean, green alternative to tin reagents

An electrochemical ‘redox-relay’ system has been developed which allows the generation of C-centered radicals. Intermolecular ‘tin-like’ radical reactions can subsequently be conducted under the most benign of conditions. The yields and efficiency of the processes are competitive and even superior in most cases to comparable conditions with tributyltin hydride. The use of air and electricity as the promotor (instead of a tin or other reagent) combined with the aqueous reaction media make this a clean and ‘green’ alternative to these classic C–C bond forming processes.

A ‘green’ and high-yielding electrochemical method for performing tin-free, intermolecular radical reactions (the Giese reaction) has been developed.     

Site-to-site peptide transport on a molecular platform using a small-molecule robotic arm

Peptides attached to a cysteine hydrazide ‘transporter module’ are transported selectively in either direction between two chemically similar sites on a molecular platform, enabled by the discovery of new operating methods for a molecular transporter that functions through ratcheting. Substrate repositioning is achieved using a small-molecule robotic arm controlled by a protonation-mediated rotary switch and attachment/release dynamic covalent chemistry. A polar solvent mixtures were found to favour Z to E isomerization of the doubly-protonated switch, transporting cargo in one direction (arbitrarily defined as ‘forward’) in up to 85% yield, while polar solvent mixtures were unexpectedly found to favour E to Z isomerization enabling transport in the reverse (‘backward’) direction in >98% yield. Transport of the substrates proceeded in a matter of hours (compared to 6 days even for simple cargoes with the original system) without the peptides at any time dissociating from the machine nor exchanging with others in the bulk. Under the new operating conditions, key intermediates of the switch are sufficiently stabilized within the macrocycle formed between switch, arm, substrate and platform that they can be identified and structurally characterized by ¹H NMR. The size of the peptide cargo has no significant effect on the rate or efficiency of transport in either direction. The new operating conditions allow detailed physical organic chemistry of the ratcheted transport mechanism to be uncovered, improve efficiency, and enable the transport of more complex cargoes than was previously possible.

Peptides are transported in either direction between chemically similar sites on a molecular platform, substrate repositioning is achieved using a cysteine hydrazide transporter module and a small-molecule robotic arm controlled by a rotary switch.     

Actinide tetra-N-heterocyclic carbene ‘sandwiches’

Highly-symmetrical, thorium and uranium octakis-carbene ‘sandwich’ complexes have been prepared by ‘sandwiching’ the An(iv) cations between two anionic macrocyclic tetra-NHC ligands, one with sixteen atoms and the other with eighteen atoms. The complexes were characterized by a range of experimental methods and DFT calculations. X-ray crystallography confirms the geometry at the metal centre can be set by the size of the macrocyclic ring, leading to either square prismatic or square anti-prismatic shapes; the geometry of the latter is retained in solution, which also undergoes reversible, electrochemical one-electron oxidation or reduction for the uranium variant. DFT calculations reveal a frontier orbital picture that is similar to thorocene and uranocene, in which the NHC ligands show almost exclusively σ-donation to the metal without π-backbonding.

Highly-symmetrical, thorium and uranium octakis-carbene ‘sandwich’ complexes have been prepared by ‘sandwiching’ the An(iv) cations between two anionic macrocyclic tetra-NHC ligands, one with sixteen atoms and the other with eighteen atoms.     

Sensory Quality Evaluation of Korla Pear from Different Orchards and Analysis of Their Primary and Volatile Metabolites

Metabolites play vital roles in shaping the quality of fresh fruit. In this study, Korla pear fruit harvested from twelve orchards in South Xinjiang, China, were ranked in sensory quality by fuzzy logic sensory evaluation for two consecutive seasons. Then, gas chromatography-mass spectrometry (GC-MS) was applied to determine the primary metabolites and volatile compounds. Sensory evaluation results showed that the panelists were more concerned about ‘mouth feel’ and ‘aroma’ than about ‘fruit size’, ‘fruit shape’ and ‘peel color’. In total, 20 primary metabolites and 100 volatiles were detected in the pear fruit. Hexanal, (E)-2-hexenal, nonanal, d-limonene, (Z)-3-hexen-1-yl acetate and hexyl acetate were identified as the major volatile compounds. Correlation analysis revealed that l-(+)-tartaric acid, hexanoic acid, trans-limonene oxide and 2,2,4-trimethyl-1,3-pentanediol diisobutyrate were negatively correlated with sensory scores. Furthermore, OPLS-DA results indicated that the fruit from three orchards with lower ranks in quality could be distinguished from other samples based on the contents of l-(+)-tartaric acid and other eight metabolites, which were all associated with ‘mouth feel’ and ‘aroma’. This study reveals the metabolites that might be closely associated with the sensory quality attributes of Korla pear, which may provide some clues for promoting the fruit quality in actual production.     

Dye-sensitized solar cells under ambient light powering machine learning: towards autonomous smart sensors for the internet of things

The field of photovoltaics gives the opportunity to make our buildings ‘‘smart’’ and our portable devices “independent”, provided effective energy sources can be developed for use in ambient indoor conditions. To address this important issue, ambient light photovoltaic cells were developed to power autonomous Internet of Things (IoT) devices, capable of machine learning, allowing the on-device implementation of artificial intelligence. Through a novel co-sensitization strategy, we tailored dye-sensitized photovoltaic cells based on a copper(ii/i) electrolyte for the generation of power under ambient lighting with an unprecedented conversion efficiency (34%, 103 μW cm⁻² at 1000 lux; 32.7%, 50 μW cm⁻² at 500 lux and 31.4%, 19 μW cm⁻² at 200 lux from a fluorescent lamp). A small array of DSCs with a joint active area of 16 cm² was then used to power machine learning on wireless nodes. The collection of 0.947 mJ or 2.72 × 10¹⁵ photons is needed to compute one inference of a pre-trained artificial neural network for MNIST image classification in the employed set up. The inference accuracy of the network exceeded 90% for standard test images and 80% using camera-acquired printed MNIST-digits. Quantization of the neural network significantly reduced memory requirements with a less than 0.1% loss in accuracy compared to a full-precision network, making machine learning inferences on low-power microcontrollers possible. 152 J or 4.41 × 10²⁰ photons required for training and verification of an artificial neural network were harvested with 64 cm² photovoltaic area in less than 24 hours under 1000 lux illumination. Ambient light harvesters provide a new generation of self-powered and “smart” IoT devices powered through an energy source that is largely untapped.

Indoor light harvesters enable machine learning on fully autonomous IoT devices at 2.72 × 10¹⁵ photons per inference.     

Nature of the copper-nitrosyl intermediates of copper nitrite reductases during catalysis

The design and synthesis of copper complexes that can reduce nitrite to NO has attracted considerable interest. They have been guided by the structural information on the catalytic Cu centre of the widespread enzymes Cu nitrite reductases but the chemically novel side-on binding of NO observed in all crystallographic studies of these enzymes has been questioned in terms of its functional relevance. We show conversion of NO₂⁻ to NO in the crystal maintained at 170 K and present ‘molecular movies’ defining events during enzyme turnover including the formation of side-on Cu-NO intermediate. DFT modelling suggests that both true {CuNO}¹¹ and formal {CuNO}¹⁰ states may occur as side-on forms in an enzymatic active site with the stability of the {CuNO}¹⁰ side-on form governed by the protonation state of the histidine ligands. Formation of a copper-nitrosyl intermediate thus needs to be accommodated in future design templates for functional synthetic Cu-NiR complexes.

Observation of side-on copper-nitrosyl intermediate and its confirmation by DFT during catalysis of copper nitrite reductases.     

Stealth nanorods via the aqueous living crystallisation-driven self-assembly of poly(2-oxazoline)s

The morphology of nanomaterials critically influences their biological interactions. However, there is currently a lack of robust methods for preparing non-spherical particles from biocompatible materials. Here, we combine ‘living’ crystallisation-driven self-assembly (CDSA), a seeded growth method that enables the preparation of rod-like polymer nanoparticles, with poly(2-oxazoline)s (POx), a polymer class that exhibits ‘stealth’ behaviour and excellent biocompatibility. For the first time, the ‘living’ CDSA process was carried out in pure water, resulting in POx nanorods with lengths ranging from ∼60 to 635 nm. In vitro and in vivo study revealed low immune cell association and encouraging blood circulation times, but little difference in the behaviour of POx nanorods of different length. The stealth behaviour observed highlights the promising potential of POx nanorods as a next generation stealth drug delivery platform.

Triggered by heating, a poly(2-alkyl-2-oxazoline) block copolymer undergoes seeded growth in water forming length tuneable nanorods. Morphology and composition combine to impart low immune cell association and promising blood circulation lifetimes.     

Correction: Click activated protodrugs against cancer increase the therapeutic potential of chemotherapy through local capture and activation

Correction for ‘Click activated protodrugs against cancer increase the therapeutic potential of chemotherapy through local capture and activation’ by Kui Wu et al., Chem. Sci., 2021, 12, 1259–1271, DOI: 10.1039/D0SC06099B.

The authors regret that the reference to the bond-breaking bioorthogonal chemistry, termed ‘click-to-release’ was omitted from the original article. In addition, we would like to include a reference describing the synthesis of compound 1, which is an intermediate to the protodrugs described in the original article. These references are listed below as ref. 1 and 2.The Royal Society of Chemistry apologizes for these errors and any consequent inconvenience to authors and readers.     

A novel chemical biology and computational approach to expedite the discovery of new-generation polymyxins against life-threatening Acinetobacter baumannii

Multidrug-resistant Gram-negative bacteria represent a major medical challenge worldwide. New antibiotics are desperately required with ‘old’ polymyxins often being the only available therapeutic option. Here, we systematically investigated the structure–activity relationship (SAR) of polymyxins using a quantitative lipidomics-informed outer membrane (OM) model of Acinetobacter baumannii and a series of chemically synthesized polymyxin analogs. By integrating chemical biology and all-atom molecular dynamics simulations, we deciphered how each residue of the polymyxin molecule modulated its conformational folding and specific interactions with the bacterial OM. Importantly, a novel designed polymyxin analog FADDI-287 with predicted stronger OM penetration showed improved in vitro antibacterial activity. Collectively, our study provides a novel chemical biology and computational strategy to expedite the discovery of new-generation polymyxins against life-threatening Gram-negative ‘superbugs’.

Multidrug-resistant Gram-negative bacteria have been an urgent threat to global public health. Novel antibiotics are desperately needed to combat these ''superbugs''.     

Redox Electrochemistry of Silicon Dioxide Gel Films Containing 1:12 Molybdosilicate Acid and Its Electrocatalytic Activity toward the Reduction of Nitrite Ions

Silicon dioxide gel films containing 1:12 molybdosilicate acid were achieved on the surface of a glassy carbon electrode by sol–gel technique. The electrochemical behavior of the modified electrode was studied in detail. The new chemically modified electrode was shown to exhibit an excellent electrocatalytic activity toward the reduction of nitrite ions in 0.5 M sulfuric acid and possesses several attractive features, such as simple preparation, fast response, good chemical, mechanical stability, and excellent reproducibility.     

Harnessing sulfur and nitrogen in the cobalt(iii)-catalyzed unsymmetrical double annulation of thioamides: probing the origin of chemo- and regio-selectivity

An unconventional cobalt(iii)-catalyzed one-pot domino double annulation of aryl thioamides with unactivated alkynes is presented. Sulfur (S), nitrogen (N), and o,o′-C–H bonds of aryl thioamides are involved in this reaction, enabling access to rare 6,6-fused thiopyrano-isoquinoline derivatives. A reverse ‘S’ coordination over a more conventional ‘N’ coordination of thioamides to the Co-catalyst specifically regulates the formation of four [C–C and C–S at first and then C–N and C–C] bonds in a single operation, a concept which is uncovered for the first time. The power of the N-masked methyl phenyl sulfoximine (MPS) directing group in this annulation sequence is established. The transformation is successfully developed, building a novel chemical space of structural diversity (56 examples). In addition, the late-stage annulation of biologically relevant motifs and drug candidates is disclosed (17 examples). The preliminary photophysical properties of thiopyrano-isoquinoline derivatives are discussed. Density functional theory (DFT) studies authenticate the participation of a unique 6π-electrocyclization of a 7-membered S-chelated cobaltacycle in the annulation process.

A Co-catalyzed one-pot double annulation of sulfoximine bearing thioamides with alkynes for the synthesis of [6,6]-fused thiopyrano-isoquinolines is disclosed. The annulation involves a 6π-electrocyclization of 7-membered S-chelated cobaltacycle.     

Broad-band spectroscopy of a vanadyl porphyrin: a model electronuclear spin qudit

We explore how to encode more than a qubit in vanadyl porphyrin molecules hosting a S = 1/2 electronic spin coupled to a I = 7/2 nuclear spin. The spin Hamiltonian and its parameters, as well as the spin dynamics, have been determined via a combination of electron paramagnetic resonance, heat capacity, magnetization and on-chip magnetic spectroscopy experiments performed on single crystals. We find low temperature spin coherence times of micro-seconds and spin relaxation times longer than a second. For sufficiently strong magnetic fields (B > 0.1 T, corresponding to resonance frequencies of 9–10 GHz) these properties make vanadyl porphyrin molecules suitable qubit realizations. The presence of multiple equispaced nuclear spin levels then merely provides 8 alternatives to define the ‘1’ and ‘0’ basis states. For lower magnetic fields (B < 0.1 T), and lower frequencies (<2 GHz), we find spectroscopic signatures of a sizeable electronuclear entanglement. This effect generates a larger set of allowed transitions between different electronuclear spin states and removes their degeneracies. Under these conditions, we show that each molecule fulfills the conditions to act as a universal 4-qubit processor or, equivalently, as a d = 16 qudit. These findings widen the catalogue of chemically designed systems able to implement non-trivial quantum functionalities, such as quantum simulations and, especially, quantum error correction at the molecular level.

We show that a sizeable electronuclear entanglement of the S = 1/2 and I = 7/2 spins of a vanadyl porphyrin provides the conditions to act as a universal 4-qubit processor, and thus implement quantum error correction at the molecular level.     

Programmed catalysis within stimuli-responsive mechanically unlocked nanocavities in DNA origami tiles

The assembly of reversible stimuli-responsive locked DNA origami tiles being unlocked, in the presence of appropriate triggers, to form nanocavities in the origami rafts, is introduced. In the presence of ATP, K⁺-ion-stabilized G-quadruplexes or pH-responsive T-A·T triggers and appropriately engineered “helper units”, the origami rafts are unlocked to form nanocavities. By the application of appropriate counter-triggers, the nanocavities are relocked, thus establishing the switchable and reversible “mechanical” opening and closure mechanism of the nanocavities. The interconnection of the stimuli-responsive origami tiles into dimer structures enables the programmed triggered unlocking of each of the origami tiles, or both of the origami tiles, to yield dictated nanocavity-containing tiles. In addition, the functionalization of the opposite faces of the origami tiles with Mg²⁺-ion-dependent DNAzyme subunits leads, upon the triggered unlocking of the nanocavities, to the self-assembly of the active DNAzymes in the confined cavities. By the cyclic opening and closure of the cavities the reversible “ON”/“OFF” activation of the Mg²⁺-ion-dependent DNAzyme is demonstrated. Furthermore, upon the tethering of different Mg²⁺-ion-dependent subunits to the opposite faces of stimuli-responsive dimer origami tiles, the triggered programmed catalytic operation of different Mg²⁺-ion-dependent DNAzymes in the confined nanocavities, associated with the origami tiles, is demonstrated.

Programmed unlocking of nanocavities in origami dimer structures using different auxiliary triggers.     

Terroir Effect on the Phenolic Composition and Chromatic Characteristics of Mencía/Jaen Monovarietal Wines: Bierzo D.O. (Spain) and Dão D.O. (Portugal)

‘Mencía’/‘Jaen’ it’s an important red grape variety, exclusive of the Iberian Peninsula, used in wine production namely in Bierzo D.O. and Dão D.O., respectively. This work evaluates the effect of the two different “terroirs” on the phenolic composition and chromatic characteristics of ‘Mencía’/‘Jaen’ monovarietal wines produced at an industrial scale in the same vintage. Using Principal Component Analysis (PCA), Partial Least Squares-Discrimination Analysis (PLS-DA), and Orthogonal PLS-DA (OPLS-DA) it was found that peonidin-3-coumaroylglucoside, petunidin-3-glucoside, malvidin-3-coumaroylglucoside, peonidin-3-glucoside, malvidin-3-acetylglucoside, malvidin-3-glucoside, and ferulic acid were the phenolic compounds with the highest differences between the two regions. PLS regression allowed to correlate the differences in lightness (L*) and redness (a*) of wines from ‘Jaen’ and ‘Mencía’ to differences in colored anthocyanins, polymeric pigments, total pigments, total anthocyanins, cyanidin-3-acetylglucoside, delphinidin-3-acetylglucoside, delphinidin-3-glucoside, peonidin-3-coumaroylglucoside, petunidin-3-glucoside and malvidin-3-glucoside in wines, and the colorless ferulic, caffeic, and coutaric acids, and ethyl caffeate. The wines a* values were more affected by colored anthocyanins, ferulic acid, total anthocyanins, delphinidin-3-acetylglucoside, delphinidin-3-glucoside and petunidin-3-acetylglucoside, and catechin. The positive influence of ferulic acid in the a* values and ferulic, caffeic, coutaric acids, and ethyl caffeate on the L* values can be due to the co-pigmentation phenomena. The higher dryness and lower temperatures during the September nights in this vintage might explain the differences observed in the anthocyanin content and chromatic characteristics of the wines.