Sarbecovirus programmed ribosome frameshift RNA element folding studied by NMR spectroscopy and comparative analyses.

The programmed ribosomal frameshift (PRF) region is found in the RNA genome of all coronaviruses and shifts the ribosome reading frame through formation of a three-stem pseudoknot structure, allowing the translation of essential viral proteins. Using NMR spectroscopy, comparative sequence analyses and functional assays we show that, in the absence of the ribosome, a 123-nucleotide sequence encompassing the PRF element of SARS-CoV-2 adopts a well-defined two-stem loop structure that is conserved in all SARS-like coronaviruses. In this conformation, the attenuator hairpin and slippery site nucleotides are exposed in the first stem-loop and two pseudoknot stems are present in the second stem-loop, separated by an 8-nucleotide bulge. Formation of the third pseudoknot stem depends on pairing between bulge nucleotides and base-paired nucleotides of the upstream stem-loop, as shown by a PRF construct where residues of the upstream stem were removed, which formed the pseudoknot structure and had increased frameshifting activity in a dual-luciferase assay. The base-pair switch driving PRF pseudoknot folding was found to be conserved in several human non-SARS coronaviruses. The collective results suggest that the frameshifting pseudoknot structure of these viruses only forms transiently in the presence of the translating ribosome. These findings clarify the frameshifting mechanism in coronaviruses and can have a beneficial impact on antiviral drug discovery.

Urea-Based [2]Rotaxanes as Effective Phase-Transfer Organocatalysts: Hydrogen-Bonding Cooperative Activation Enabled by the Mechanical Bond.

We finely designed a set of [2]rotaxanes with urea threads and tested them as hydrogen-bonding phase-transfer catalysts in two different nucleophilic substitutions requiring the activation of the reactant fluoride anion. The [2]rotaxane bearing a fluorinated macrocycle and a fluorine-containing urea thread displayed significantly enhanced catalytic activity in comparison with the combination of both noninterlocked components. This fact highlights the notably beneficial role of the mechanical bond, cooperatively activating the processes through hydrogen-bonding interactions.

Nanotube-Like Electronic States in [5,5]-C90 Fullertube Molecules.

Fullertubes, that is, fullerenes consisting of a carbon nanotube moiety capped by hemifullerene ends, are emerging carbon nanomaterials whose properties show both fullerene and carbon nanotube (CNT) traits. Albeit it may be expected that their electronic states show a certain resemblance to those of the extended nanotube, such a correlation has not yet been found or described. Here it shows a scanning tunneling microscopy (STM) and spectroscopy (STS) characterization of the adsorption, self-assembly, and electronic structure of 2D arrays of [5,5]-C90 fullertube molecules on two different noble metal surfaces, Ag(111) and Au(111). The results demonstrate that the shape of the molecular orbitals of the adsorbed fullertubes corresponds closely to those expected for isolated species on the grounds of density functional theory calculations. Moreover, a comparison between the electronic density profiles in the bands of the extended [5,5]-CNT and in the molecules reveals that some of the frontier orbitals of the fullertube molecules can be described as the result of the quantum confinement imposed by the hemifullerene caps to the delocalized band states in the extended CNT. The results thus provide a conceptual framework for the rational design of custom fullertube molecules and can potentially become a cornerstone in the understanding of these new carbon nanoforms.

2D Co-Directed Metal-Organic Networks Featuring Strong Antiferromagnetism and Perpendicular Anisotropy.

Antiferromagnetic spintronics is a rapidly emerging field with the potential to revolutionize the way information is stored and processed. One of the key challenges in this field is the development of novel 2D antiferromagnetic materials. In this paper, the first on-surface synthesis of a Co-directed metal-organic network is reported in which the Co atoms are strongly antiferromagnetically coupled, while featuring a perpendicular magnetic anisotropy. This material is a promising candidate for future antiferromagnetic spintronic devices, as it combines the advantages of 2D and metal-organic chemistry with strong antiferromagnetic order and perpendicular magnetic anisotropy.

Delayed immune-related hepatitis after 24 months of pembrolizumab treatment: a case report and literature review.

Immune checkpoint inhibitors targeting the programmed cell death protein 1 (PD-1) pathway have revolutionized cancer immunotherapy by enhancing the immune system's ability to combat cancer cells. However, this innovative approach comes with a distinctive set of challenges, as these therapies can lead to immune-related adverse events (irAEs) due to their mechanism of action. The most common irAEs involve the skin, gastrointestinal tract, liver, endocrine system, and lungs. These events can range from mild skin rashes to severe colitis, pneumonitis, or even autoimmune organ damage. These adverse effects usually appear with an average of 5-15 weeks from the start of treatment depending on the affected organ. This article presents a case report of a delayed related-mediated hepatitis, after 24 months of treatment with pembrolizumab and almost 3 months after its termination, and a review of the scientific literature on cases of delayed immune-related hepatitis caused by anti-PD1. This case highlights the importance of monitoring patients treated with immune checkpoint inhibitors after cessation as a growing number of patients stop treatment due to achieving durable responses.

The low-resolution structural models of hepatitis C virus RNA subdomain 5BSL3.2 and its distal complex with domain 3'X point to conserved regulatory mechanisms within the Flaviviridae family.

Subdomain 5BSL3.2 of hepatitis C virus RNA lies at the core of a network of distal RNA-RNA contacts that connect the 5' and 3' regions of the viral genome and regulate the translation and replication stages of the viral cycle. Using small-angle X-ray scattering and NMR spectroscopy experiments, we have determined at low resolution the structural models of this subdomain and its distal complex with domain 3'X, located at the 3'-terminus of the viral RNA chain. 5BSL3.2 adopts a characteristic 'L' shape in solution, whereas the 5BSL3.2-3'X distal complex forms a highly unusual 'Y'-shaped kissing junction that blocks the dimer linkage sequence of domain 3'X and promotes translation. The structure of this complex may impede an effective association of the viral polymerase with 5BSL3.2 and 3'X to start negative-strand RNA synthesis, contributing to explain the likely mechanism used by these sequences to regulate viral replication and translation. In addition, sequence and shape features of 5BSL3.2 are present in functional RNA motifs of flaviviruses, suggesting conserved regulatory processes within the Flaviviridae family.

On-Surface Synthesis of Non-Benzenoid Nanographenes Embedding Azulene and Stone-Wales Topologies.

The incorporation of non-benzenoid motifs in graphene nanostructures significantly impacts their properties, making them attractive for applications in carbon-based electronics. However, understanding how specific non-benzenoid structures influence their properties remains limited, and further investigations are needed to fully comprehend their implications. Here, we report an on-surface synthetic strategy toward fabricating non-benzenoid nanographenes containing different combinations of pentagonal and heptagonal rings. Their structure and electronic properties were investigated via scanning tunneling microscopy and spectroscopy, complemented by computational investigations. After thermal activation of the precursor P on the Au(111) surface, we detected two major nanographene products. Nanographene Aa-a embeds two azulene units formed through oxidative ring-closure of methyl substituents, while Aa-s contains one azulene unit and one Stone-Wales defect, formed by the combination of oxidative ring-closure and skeletal ring-rearrangement reactions. Aa-a exhibits an antiferromagnetic ground state with the highest magnetic exchange coupling reported up to date for a non-benzenoid containing nanographene, coexisting with side-products with closed shell configurations resulted from the combination of ring-closure and ring-rearragement reactions (Ba-a , Ba-s , Bs-a and Bs-s ). Our results provide insights into the single gold atom assisted synthesis of novel NGs containing non-benzenoid motifs and their tailored electronic/magnetic properties.

Coronene-Based 2D Networks by On-Surface Skeletal Rearrangement of Sumanene Precursors.

The design of novel low-dimensional carbon materials is at the forefront of modern chemistry. Recently, on-surface covalent synthesis has emerged as a powerful strategy to synthesize previously precluded compounds and polymers. Here, we report a scanning probe microscopy study, complemented by theoretical calculations, on the sequential skeletal rearrangement of sumanene-based precursors into a coronene-based organometallic network by stepwise intra- and inter-molecular reactions on Au(111). Interestingly, upon higher annealing, the formed organometallic networks evolve into two-dimensional coronene-based covalently linked patches through intermolecular homocoupling reactions. A new reaction mechanism is proposed based on the role of C-Au-C motifs to promote two stepwise carbon-carbon couplings to form cyclobutadiene bridges. Our results pave avenues for the conversion of molecular precursors on surfaces, affording the design of unexplored two-dimensional organometallic and covalent materials.

Steering Large Magnetic Exchange Coupling in Nanographenes near the Closed-Shell to Open-Shell Transition.

The design of open-shell carbon-based nanomaterials is at the vanguard of materials science, steered by their beneficial magnetic properties like weaker spin-orbit coupling than that of transition metal atoms and larger spin delocalization, which are of potential relevance for future spintronics and quantum technologies. A key parameter in magnetic materials is the magnetic exchange coupling (MEC) between unpaired spins, which should be large enough to allow device operation at practical temperatures. In this work, we theoretically and experimentally explore three distinct families of nanographenes (NGs) (A, B, and C) featuring majority zigzag peripheries. Through many-body calculations, we identify a transition from a closed-shell ground state to an open-shell ground state upon an increase of the molecular size. Our predictions indicate that the largest MEC for open-shell NGs occurs in proximity to the transition between closed-shell and open-shell states. Such predictions are corroborated by the on-surface syntheses and structural, electronic, and magnetic characterizations of three NGs (A[3,5], B[4,5], and C[4,3]), which are the smallest open-shell systems in their respective chemical families and are thus located the closest to the transition boundary. Notably, two of the NGs (B[4,5] and C[4,3]) feature record values of MEC (close to 200 meV) measured on the Au(111) surface. Our strategy for maximizing the MEC provides perspectives for designing carbon nanomaterials with robust magnetic ground states.

Stoichiometry-Directed Two-Level Hierarchical Growth of Lanthanide-Based Supramolecular Nanoarchitectures.

The design of a well-ordered arrangement of atoms on a solid surface has long been sought due to the envisioned applications in many different fields. On-surface synthesis of metal-organic networks is one of the most promising fabrication techniques. Hierarchical growth, which involves coordinative schemes with weaker interactions, favours the formation of extended areas with the desired complex structure. However, the control of such hierarchical growth is in its infancy, particularly for lanthanide-based architectures. Here the hierarchical growth of a Dy-based supramolecular nanoarchitecture on Au(111) is described. Such an assembly is based on a first hierarchical level of metallo-supramolecular motifs, which in a second level of hierarchy self-assemble through directional hydrogen bonds, giving rise to a periodic two-dimensional supramolecular porous network. Notably, the size of the metal-organic based tecton of the first level of hierarchy can be tailored by modifying the metal-ligand stoichiometric ratio.

Chained Deep Learning Using Generalized Cross-Entropy for Multiple Annotators Classification.

Supervised learning requires the accurate labeling of instances, usually provided by an expert. Crowdsourcing platforms offer a practical and cost-effective alternative for large datasets when individual annotation is impractical. In addition, these platforms gather labels from multiple labelers. Still, traditional multiple-annotator methods must account for the varying levels of expertise and the noise introduced by unreliable outputs, resulting in decreased performance. In addition, they assume a homogeneous behavior of the labelers across the input feature space, and independence constraints are imposed on outputs. We propose a Generalized Cross-Entropy-based framework using Chained Deep Learning (GCECDL) to code each annotator's non-stationary patterns regarding the input space while preserving the inter-dependencies among experts through a chained deep learning approach. Experimental results devoted to multiple-annotator classification tasks on several well-known datasets demonstrate that our GCECDL can achieve robust predictive properties, outperforming state-of-the-art algorithms by combining the power of deep learning with a noise-robust loss function to deal with noisy labels. Moreover, network self-regularization is achieved by estimating each labeler's reliability within the chained approach. Lastly, visual inspection and relevance analysis experiments are conducted to reveal the non-stationary coding of our method. In a nutshell, GCEDL weights reliable labelers as a function of each input sample and achieves suitable discrimination performance with preserved interpretability regarding each annotator's trustworthiness estimation.

Exploring the HIV-1 Rev Recognition Element (RRE)-Rev Inhibitory Capacity and Antiretroviral Action of Benfluron Analogs.

Human immunodeficiency virus-type 1 (HIV-1) remains one of the leading contributors to the global burden of disease, and novel antiretroviral agents with alternative mechanisms are needed to cure this infection. Here, we describe an exploratory attempt to optimize the antiretroviral properties of benfluron, a cytostatic agent previously reported to exhibit strong anti-HIV activity likely based on inhibitory actions on virus transcription and Rev-mediated viral RNA export. After obtaining six analogs designed to modify the benzo[c]fluorenone system of the parent molecule, we examined their antiretroviral and toxicity properties together with their capacity to recognize the Rev Recognition Element (RRE) of the virus RNA and inhibit the RRE-Rev interaction. The results indicated that both the benzo[c] and cyclopentanone components of benfluron are required for strong RRE-Rev target engagement and antiretroviral activity and revealed the relative impact of these moieties on RRE affinity, RRE-Rev inhibition, antiviral action and cellular toxicity. These data provide insights into the biological properties of the benzo[c]fluorenone scaffold and contribute to facilitating the design of new anti-HIV agents based on the inhibition of Rev function.

On-Surface Design of a 2D Cobalt-Organic Network Preserving Large Orbital Magnetic Moment.

The design of antiferromagnetic nanomaterials preserving large orbital magnetic moments is important to protect their functionalities against magnetic perturbations. Here, we exploit an archetype H6HOTP species for conductive metal-organic frameworks to design a Co-HOTP one-atom-thick metal-organic architecture on a Au(111) surface. Our multidisciplinary scanning probe microscopy, X-ray absorption spectroscopy, X-ray linear dichroism, and X-ray magnetic circular dichroism study, combined with density functional theory simulations, reveals the formation of a unique network design based on threefold Co+2 coordination with deprotonated ligands, which displays a large orbital magnetic moment with an orbital to effective spin moment ratio of 0.8, an in-plane easy axis of magnetization, and large magnetic anisotropy. Our simulations suggest an antiferromagnetic ground state, which is compatible with the experimental findings. Such a Co-HOTP metal-organic network exemplifies how on-surface chemistry can enable the design of field-robust antiferromagnetic materials.

Interplay between π-Conjugation and Exchange Magnetism in One-Dimensional Porphyrinoid Polymers.

The synthesis of novel polymeric materials with porphyrinoid compounds as key components of the repeating units attracts widespread interest from several scientific fields in view of their extraordinary variety of functional properties with potential applications in a wide range of highly significant technologies. The vast majority of such polymers present a closed-shell ground state, and, only recently, as the result of improved synthetic strategies, the engineering of open-shell porphyrinoid polymers with spin delocalization along the conjugation length has been achieved. Here, we present a combined strategy toward the fabrication of one-dimensional porphyrinoid-based polymers homocoupled via surface-catalyzed [3 + 3] cycloaromatization of isopropyl substituents on Au(111). Scanning tunneling microscopy and noncontact atomic force microscopy describe the thermal-activated intra- and intermolecular oxidative ring closure reactions as well as the controlled tip-induced hydrogen dissociation from the porphyrinoid units. In addition, scanning tunneling spectroscopy measurements, complemented by computational investigations, reveal the open-shell character, that is, the antiferromagnetic singlet ground state (S = 0) of the formed polymers, characterized by singlet-triplet inelastic excitations observed between spins of adjacent porphyrinoid units. Our approach sheds light on the crucial relevance of the π-conjugation in the correlations between spins, while expanding the on-surface synthesis toolbox and opening avenues toward the synthesis of innovative functional nanomaterials with prospects in carbon-based spintronics.

Electrically Tunable Reactivity of Substrate-Supported Cobalt Oxide Nanocrystals.

First-row transition metal oxides are promising materials for catalyzing the oxygen evolution reaction. Surface sensitive techniques provide a unique perspective allowing the study of the structure, adsorption sites, and reactivity of catalysts at the atomic scale, which furnishes rationalization and improves the design of highly efficient catalytic materials. Here, a scanning probe microscopy study complemented by density functional theory on the structural and electronic properties of CoO nanoislands grown on Au(111) is reported. Two distinct phases are observed: The most extended displays a Moiré pattern (α-region), while the less abundant is 1Co:1Au coincidental (ß-region). As a result of the surface registry, in the ß-region the oxide adlayer is compressed by 9%, increasing the unoccupied local density of states and enhancing the selective water adsorption at low temperature through a cobalt inversion mechanism. Tip-induced voltage pulses irreversibly transform α- into ß-regions, thus opening avenues to modify the structure and reactivity of transition metal oxides by external stimuli like electric fields.

Engineering Periodic Dinuclear Lanthanide-Directed Networks Featuring Tunable Energy Level Alignment and Magnetic Anisotropy by Metal Exchange.

The design of lanthanide multinuclear networks is an emerging field of research due to the potential of such materials for nanomagnetism, spintronics, and quantum information. Therefore, controlling their electronic and magnetic properties is of paramount importance to tailor the envisioned functionalities. In this work, a multidisciplinary study is presented combining scanning tunneling microscopy, scanning tunneling spectroscopy, X-ray absorption spectroscopy, X-ray linear dichroism, X-ray magnetic circular dichroism, density functional theory, and multiplet calculations, about the supramolecular assembly, electronic and magnetic properties of periodic dinuclear 2D networks based on lanthanide-pyridyl interactions on Au(111). Er- and Dy-directed assemblies feature identical structural architectures stabilized by metal-organic coordination. Notably, despite exhibiting the same +3 oxidation state, there is a shift of the energy level alignment of the unoccupied molecular orbitals between Er- and Dy-directed networks. In addition, there is a reorientation of the easy axis of magnetization and an increment of the magnetic anisotropy when the metallic center is changed from Er to Dy. Thus, the results show that it is feasible to tune the energy level alignment and magnetic anisotropy of a lanthanide-based metal-organic architecture by metal exchange, while preserving the network design.

Structure and function analysis of the essential 3'X domain of hepatitis C virus.

The 3'X domain of hepatitis C virus has been reported to control viral replication and translation by modulating the exposure of a nucleotide segment involved in a distal base-pairing interaction with an upstream 5BSL3.2 domain. To study the mechanism of this molecular switch, we have analyzed the structure of 3'X mutants that favor one of the two previously proposed conformations comprising either two or three stem-loops. Only the two-stem conformation was found to be stable and to allow the establishment of the distal contact with 5BSL3.2, and also the formation of 3'X domain homodimers by means of a universally conserved palindromic sequence. Nucleotide changes disturbing the two-stem conformation resulted in poorer replication and translation levels, explaining the high degree of conservation detected for this sequence. The switch function attributed to the 3'X domain does not occur as a result of a transition between two- and three-stem conformations, but likely through the sequestration of the 5BSL3.2-binding sequence by formation of 3'X homodimers.

Comprehensive and systematic characterization of multi-functionalized cisplatin nano-conjugate: from the chemistry and proteomic biocompatibility to the animal model.

BACKGROUND: Nowadays, nanoparticles (NPs) have evolved as multifunctional systems combining different custom anchorages which opens a wide range of applications in biomedical research. Thus, their pharmacological involvements require more comprehensive analysis and novel nanodrugs should be characterized by both chemically and biological point of view. Within the wide variety of biocompatible nanosystems, iron oxide nanoparticles (IONPs) present mostly of the required features which make them suitable for multifunctional NPs with many biopharmaceutical applications. RESULTS: Cisplatin-IONPs and different functionalization stages have been broadly evaluated. The potential application of these nanodrugs in onco-therapies has been assessed by studying in vitro biocompatibility (interactions with environment) by proteomics characterization the determination of protein corona in different proximal fluids (human plasma, rabbit plasma and fetal bovine serum),. Moreover, protein labeling and LC-MS/MS analysis provided more than 4000 proteins de novo synthetized as consequence of the nanodrugs presence defending cell signaling in different tumor cell types (data available via ProteomeXchanges with identified PXD026615). Further in vivo studies have provided a more integrative view of the biopharmaceutical perspectives of IONPs. CONCLUSIONS: Pharmacological proteomic profile different behavior between species and different affinity of protein coating layers (soft and hard corona). Also, intracellular signaling exposed differences between tumor cell lines studied. First approaches in animal model reveal the potential of theses NPs as drug delivery vehicles and confirm cisplatin compounds as strengthened antitumoral agents.

Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy.

The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5' end, the ribosomal frameshift segment and the 3'-untranslated region (3'-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.

Effective bioremediation of soil from the Burgan oil field (Kuwait) using compost: A comprehensive hydrocarbon and DNA fingerprinting study.

An innovative combination of metagenomic profiling of microbial communities and GC-MS & Pyrolysis-GC-MS fingerprinting methods were used to assess the biodegradation of contaminated soil from the Burgan oil field in Kuwait. The soil was treated with (sludge) compost in microcosms to evaluate the feasibility of this material for bioremediation purposes. The most favourable trial showed a > 80% decrease in TPH, thereby indicating strong potential for full-scale application using a cost-effective technology and thus in line with the principles of the circular economy. The microbial study showed that compost addition enhanced the organic matter and nutrient content of the soil. However, the microorganisms in the compost did not seem to play a relevant role in bioremediation, meaning that compost amendments serve as a biostimulation rather than a bioaugmentation approach. The chemical study of the distinct oil fractions revealed rapidly biodegraded compounds (alkanes, alkyl-aromatics, etc.) and others that were much more refractory (hopanes, benzohopanes, etc.). Of note, although heavy fractions are usually considered recalcitrant to biodegradation, we observed incipient degradation of the asphaltene fraction by means of double-shot thermodesorption and pyrolysis. Finally, chemical fingerprinting also revealed that the treated soil contained some of the compounds found in the compost, such as coprostanol, cholesterol, and plant sterols. This observation would support the use of these compounds as proxies to monitor the effects of compost and to adjust dosages in real-scale bioremediation treatments.