Search

A conjugated donor−acceptor array composed of two phthalocyanines connected to the bay region of a perylenediimide is assembled by using palladium chemistry. Excitation of the phthalocyanine produces a nanosecond lived charge-separated state. [ABSTRACT FROM AUTHOR]

Staphylococcus aureus is a Gram-positive bacterium that is responsible for severe nosocomial infections. The rise of multidrug-resistant strains, which can pose significant health threats, prompts the development of new treatment interventions, and much attention has been directed at the development of prophylactic and therapeutic vaccination strategies. Capsular polysaccharides (CPs) are key protective elements of the S. aureus cell wall and have been proposed as promising candidate antigens. Thirteen different CP serotypes have been identified to date, of which types 5 and 8 are the most prominent. CP8 is composed of trisaccharide repeating units that are built up from an N -acetyl-4- O -acetyl -β -d-mannosaminuronic acid, that carries a C-4- O -acetyl, an N -acetyl-α-d-fucosamine, and an N -acetyl-α-l-fucosamine. Synthetic oligosaccharides are valuable tools to unravel the immunogenicity of bacterial oligosaccharides at the molecular level. However, the rare monosaccharides, cis -glycosidic linkages, and O -acetylation represent significant challenges for the synthesis of CP8 fragments. Here the stereoselective assembly of well-defined CP8 fragments, comprising a trimer, hexamer, nonamer, and dodecamer, is presented. This is the first time that fragments larger than a single repeating trisaccharide, which has been proven to be insufficient for antigenic activity, have been assembled. Structural studies have revealed a linear conformation for the oligosaccharides, with each trisaccharide repeat tilted ∼90° with respect to the flanking repeats, which is stabilized by the acetyl groups that prevent rotation around the glycosidic linkages. The N -acetyl groups in each repeating unit point in the same direction, generating a hydrophobic flank in the trisaccharide repeats. We applied the oligomers to generate model glycoconjugate vaccine modalities, which we then used to raise anti-CP8 antibodies. The antibody interaction and immunization studies have revealed a clear length dependent structure-activity relationship for the oligosaccharides, with an oligosaccharide of at least three repeating units required for an adequate immune response.

The hydrolysis of glycosides is a biochemical transformation that occurs in all living organisms, catalyzed by a broad group of enzymes, including glycoside hydrolases. These enzymes cleave the glycosidic bond via a transition state with substantial oxocarbenium ion character, resulting in short-lived oxocarbenium ion-like species. While such transient species have been inferred through theoretical studies and kinetic isotope effect measurements, their direct spectroscopic characterization remains challenging. In this study, we exploit a superacid environment to generate, accumulate, and fully characterize nonprotected 2-deoxy glycosyl cations in the d-glucopyranose, d-galactopyranose, and l-arabinofuranose series using low-temperature NMR spectroscopy, supported by DFT calculations. Additionally, QM/MM MD simulations reveal that the properties of these glycosyl cations in superacid closely resemble those within the active sites of glycosidase enzymes, particularly in terms of conformation and anomeric charge distribution. These findings highlight a parallel between the stabilizing effect of counterions in superacid media and the network of multidentate noncovalent interactions within glycosidase active sites, which stabilize transition states with pronounced oxocarbenium ion character.

CH/π bonds are versatile elements for the construction of complex molecular architectures, thus playing key roles in many biomolecular recognition processes. Although seldom acknowledged, aromatic units are inherently bivalent and can participate in CH/π bonds through either face simultaneously, leading to the formation of ternary stacking complexes. This sandwich-like arrangement is by far the most common in natural complexes and could potentially lead to negative cooperativity due to unfavorable polarization or electrostatic effects, especially when polarized CH fragments are involved. To evaluate the energetics of such interaction modes, we selected a biologically relevant model, carbohydrate/aromatic stacking , and conducted an experimental analysis comparing binary CH/π interactions to ternary CH/π/CH stacking. Our approach utilized a dynamic combinatorial strategy, which is well-suited to reveal minor stability differences among aromatic complexes. Our results showed that carbohydrate/aromatic stacking is relatively insensitive to molecular recognition events occurring on the opposite side of the aromatic platform, whether exposed to water or involved in additional CH/π contacts, with free energy fluctuations lower than 10%. Based on these data, for all practical purposes, the two opposing aromatic surfaces can be considered independent, noninteracting binding sites, making aromatic platforms optimal connecting elements for supramolecular cross-linking., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

N -Acetyllactosamine is a common saccharide motif found in various biologically active glycans. This motif usually works as a backbone for additional modifications and thus significantly influences glycan conformational behavior and biological activity. In this work, we have investigated the type-2 N -acetyllactosamine scaffold using the complete series of its monodeoxyfluorinated analogs. These glycomimetics have been studied by molecular mechanics, quantum mechanics, X-ray crystallography, and various NMR techniques, which have provided a comprehensive and complete insight into the role of individual hydroxyl groups in the conformational behavior and lipophilicity of N -acetyllactosamine.

Unsaturated porous media, characterized by the combined presence of several immiscible fluid phases in the pore space, are highly relevant systems in nature, because they control the fate of contaminants and the availability of nutrients in the subsoil. However, a full understanding of the mechanisms controlling solute mixing in such systems is still missing. In particular, the role of saturation in the development of chaotic solute mixing has remained unexplored. Using three-dimensional numerical simulations of flow and transport at the pore scale, built upon X-ray tomograms of a porous medium at different degrees of liquid (wetting)-phase saturation, we show the occurrence of chaotic dynamics in both the deformation of the solute plume, as characterized by computed chaos metrics (Lyapunov exponents), and the mixing of the injected solute. Our results show an enhancement of these chaotic dynamics at lower saturation and their occurrence even under diffusion-relevant conditions over the medium's length, also being strengthened by larger flow velocities. These findings highlight the dominant role of the pore-scale spatial heterogeneity of the system, enhanced by the presence of an immiscible phase (e.g., air), on the mixing efficiency. This represents a stepping stone for the assessment of mixing and reactions in unsaturated porous media.

The high standards required for food safety make it necessary to trace unambiguously raw or cooked food products coming from medicated animals. Nevertheless, considering the lability of β-lactams and their degradation, the detection of the presence of antibiotics in meat either raw or submitted to a cooking process is not easily affordable. To achieve this goal, an evaluation of the effect of common domestic cooking procedures, such as boiling and grilling, on the fate of phenoxymethylpenicillin (PENV) residues was performed. Finally, in this work, the penilloic acid from PENV ( MET02) and the corresponding penicilloic acid ( PENV-HYDRO) are suggested as biomarkers. These compounds present the highest relative abundances 5 days after the treatment was stopped ( 5PT ) and show enough thermal stability to be considered suitable biomarker candidates for the pharmacological treatment instead of the parent compound. Nevertheless, the peaks corresponding to MET02 are significantly more intense than those for PENV-HYDRO , which makes preferential the use of MET02 to perform the control of samples.

Systematic structural studies of model oligopeptides revealed important aspects of protein folding and offered design principles to access non-natural materials. In the same way, the rules that regulate glycan folding could be established by studying synthetic oligosaccharide models. However, their analysis is often limited due to the synthetic and analytical complexity. By utilizing a glycan capable of spontaneously folding into a hairpin conformation as a model system, we investigated the factors that contribute to its conformational stability in aqueous solution. The modular design of the hairpin model featured a trisaccharide turn unit and two β-1,4-oligoglucoside stacking strands that allowed for systematic chemical modifications of the glycan sequence, including the introduction of NMR labels and staples. Nuclear magnetic resonance assisted by molecular dynamics simulations revealed that stereoelectronic effects and multiple glycan-glycan interactions are the major determinants of folding stabilization. Chemical modifications in the glycan primary sequence (e.g., strand elongation) can be employed to fine-tune the rigidity of structural motifs distant from the modification sites. These results could inspire the design of other glycan architectures, with implications in glycobiology and material sciences.

The acylation of flavonoids serves as a means to alter their physicochemical properties, enhance their stability, and improve their bioactivity. Compared with natural flavonoid glycosides, the acylation of nonglycosylated flavonoids presents greater challenges since they contain fewer reactive sites. In this work, we propose an efficient strategy to solve this problem based on a first α-glucosylation step catalyzed by a sucrose phosphorylase, followed by acylation using a lipase. The method was applied to phloretin, a bioactive dihydrochalcone mainly present in apples. Phloretin underwent initial glucosylation at the 4'-OH position, followed by subsequent (and quantitative) acylation with C8, C12, and C16 acyl chains employing an immobilized lipase from Thermomyces lanuginosus . Electrospray ionization-mass spectrometry (ESI-MS) and two-dimensional nuclear magnetic resonance spectroscopy (2D-NMR) confirmed that the acylation took place at 6-OH of glucose. The water solubility of C8 acyl glucoside closely resembled that of aglycone, but for C12 and C16 derivatives, it was approximately 3 times lower. Compared with phloretin, the radical scavenging capacity of the new derivatives slightly decreased with 2,2-diphenyl-1-picrylhydrazyl (DPPH) and was similar to 2,2-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS •+ ). Interestingly, C12 acyl-α-glucoside displayed an enhanced (3-fold) transdermal absorption (using pig skin biopsies) compared to phloretin and its α-glucoside.

Human sialic-acid-binding immunoglobulin-like lectin-9 (Siglec-9) is a glycoimmune checkpoint receptor expressed on several immune cells. Binding of Siglec-9 to sialic acid containing glycans (sialoglycans) is well documented to modulate its functions as an inhibitory receptor. Here, we first assigned the amino acid backbone of the Siglec-9 V-set domain (Siglec-9 d1 ), using well-established triple resonance three-dimensional nuclear magnetic resonance (NMR) methods. Then, we combined solution NMR and molecular dynamic simulation methods to decipher the molecular details of the interaction of Siglec-9 with the natural ligands α2,3 and α2,6 sialyl lactosamines (SLN), sialyl Lewis X (sLeX), and 6-O sulfated sLeX and with two synthetically modified sialoglycans that bind with high affinity. As expected, Neu5Ac is accommodated between the F and G β-strands at the canonical sialic acid binding site. Addition of a heteroaromatic scaffold 9 N -5-(2-methylthiazol-4-yl)thiophene sulfonamide (MTTS) at the C9 position of Neu5Ac generates new interactions with the hydrophobic residues located at the G-G' loop and the N-terminal region of Siglec-9. Similarly, the addition of the aromatic substituent (5- N- (1-benzhydryl-1 H- 1,2,3-triazol-4-yl)methyl (BTC)) at the C5 position of Neu5Ac stabilizes the conformation of the long and flexible B'-C loop present in Siglec-9. These results expose the underlying mechanism responsible for the enhanced affinity and specificity for Siglec-9 for these two modified sialoglycans and sheds light on the rational design of the next generation of modified sialoglycans targeting Siglec-9.

CH/π interactions are prevalent among aromatic complexes and represent invaluable tools for stabilizing well-defined molecular architectures. Their energy contributions are exceptionally sensitive to various structural and environmental factors, resulting in a context-dependent nature that has led to conflicting findings in the scientific literature. Consequently, a universally accepted hierarchy for aromatic CH/π interactions has remained elusive. Herein, we present a comprehensive experimental investigation of aromatic CH/π complexes, employing a novel approach that involves isotopically labeled glyco-balances generated in situ . This innovative strategy not only allows us to uncover thermodynamic insights but also delves into the often less-accessible domain of kinetic information. Our analyses have yielded more than 180 new free energy values while considering key factors such as solvent properties, the interaction geometry, and the presence and nature of accompanying counterions. Remarkably, the obtained results challenge conventional wisdom regarding the stability order of common aromatic complexes. While it was believed that cationic CH/π interactions held the highest strength, followed by polarized CH/π, nonpolarized CH/π, and finally anionic CH/π interactions, our study reveals that this hierarchy can be subverted depending on the environment. Indeed, the performance of polarized CH/π interactions can match or even outcompete that of cationic CH/π interactions making them a more reliable stabilization strategy across the entire spectrum of solvent polarity. Overall, our results provide valuable guidelines for the selection of optimal interacting partners in every chemical environment, allowing the design of tailored aromatic complexes with applications in supramolecular chemistry, organocatalysis, and/or material sciences., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

The urgency to find complementary therapies to current SARS-CoV-2 vaccines, whose effectiveness is preserved over time and not compromised by the emergence of new and emerging variants, has become a critical health challenge. We investigate the possibility of jamming the opening of the Receptor Binding Domain (RBD) of the spike protein of SARS-CoV-2 with small compounds. Through in silico screening, we identified two potential candidates that would lock the Receptor Binding Domain (RBD) in a closed configuration, preventing the virus from infecting the host cells. We show that two drugs already approved by the FDA, mithramycin and dihydroergotamine, can block infection using concentrations in the μM range in cell-based assays. Further STD-NMR experiments support dihydroergotamine's direct interaction with the spike protein. Overall, our results indicate that repurposing of these compounds might lead to potential clinical drug candidates for the treatment of SARS-CoV-2 infection., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Bandgap tuning is a crucial characteristic of metal-halide perovskites, with benchmark lead-iodide compounds having a bandgap of 1.6 eV. To increase the bandgap up to 2.0 eV, a straightforward strategy is to partially substitute iodide with bromide in so-called mixed-halide lead perovskites. Such compounds are prone, however, to light-induced halide segregation resulting in bandgap instability, which limits their application in tandem solar cells and a variety of optoelectronic devices. Crystallinity improvement and surface passivation strategies can effectively slow down, but not completely stop, such light-induced instability. Here we identify the defects and the intragap electronic states that trigger the material transformation and bandgap shift. Based on such knowledge, we engineer the perovskite band edge energetics by replacing lead with tin and radically deactivate the photoactivity of such defects. This leads to metal halide perovskites with a photostable bandgap over a wide spectral range and associated solar cells with photostable open circuit voltages., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Bacterial biofilms can form in porous media that are of interest in industrial applications ranging from medical implants to biofilters as well as in environmental applications such as in situ groundwater remediation, where they can be critical locations for biogeochemical reactions. The presence of biofilms modifies porous media topology and hydrodynamics by clogging pores and consequently solutes transport and reactions kinetics. The interplay between highly heterogeneous flow fields found in porous media and microbial behavior, including biofilm growth, results in a spatially heterogeneous biofilm distribution in the porous media as well as internal heterogeneity across the thickness of the biofilm. Our study leverages highly resolved three-dimensional X-ray computed microtomography images of bacterial biofilms in a tubular reactor to numerically compute pore-scale fluid flow and solute transport by considering multiple equivalent stochastically generated internal permeability fields for the biofilm. We show that the internal heterogeneous permeability mainly impacts intermediate velocities when compared with homogeneous biofilm permeability. While the equivalent internal permeability fields of the biofilm do not impact fluid-fluid mixing, they significantly control a fast reaction. For biologically driven reactions such as nutrient or contaminant uptake by the biofilm, its internal permeability field controls the efficiency of the process. This study highlights the importance of considering the internal heterogeneity of biofilms to better predict reactivity in industrial and environmental bioclogged porous systems.

This work combines the wound-healing-related properties of the host defense peptide KR-12 with wood-derived cellulose nanofibrils (CNFs) to obtain bioactive materials, foreseen as a promising solution to treat chronic wounds. Amine coupling through carbodiimide chemistry, thiol-ene click chemistry, and Cu(I)-catalyzed azide-alkyne cycloaddition were investigated as methods to covalently immobilize KR-12 derivatives onto CNFs. The effects of different coupling chemistries on the bioactivity of the KR12-CNF conjugates were evaluated by assessing their antibacterial activities against Escherichia coli and Staphylococcus aureus . Potential cytotoxic effects and the capacity of the materials to modulate the inflammatory response of lipopolysaccharide (LPS)-stimulated RAW 245.6 macrophages were also investigated. The results show that KR-12 endowed CNFs with antibacterial activity against E. coli and exhibited anti-inflammatory properties and those conjugated by thiol-ene chemistry were the most bioactive. This finding is attributed to a favorable peptide conformation and accessibility (as shown by molecular dynamics simulations), driven by the selective chemistry and length of the linker in the conjugate. The results represent an advancement in the development of CNF-based materials for chronic wound care. This study provides new insights into the effect of the conjugation chemistry on the bioactivity of immobilized host defense peptides, which we believe to be of great value for the use of host defense peptides as therapeutic agents.

SARS-CoV-2 viruses engage ACE2 as a functional receptor with their spike protein. The S1 domain of the spike protein contains a C-terminal receptor binding domain (RBD) and an N-terminal domain (NTD). The NTD of other coronaviruses includes a glycan binding cleft. However, for the SARS-CoV-2 NTD, protein-glycan binding was only observed weakly for sialic acids with highly sensitive methods. Amino acid changes in the NTD of variants of concern (VoC) show antigenic pressure, which can be an indication of NTD-mediated receptor binding. Trimeric NTD proteins of SARS-CoV-2, alpha, beta, delta, and omicron did not reveal a receptor binding capability. Unexpectedly, the SARS-CoV-2 beta subvariant strain (501Y.V2-1) NTD binding to Vero E6 cells was sensitive to sialidase pretreatment. Glycan microarray analyses identified a putative 9- O -acetylated sialic acid as a ligand, which was confirmed by catch-and-release ESI-MS, STD-NMR analyses, and a graphene-based electrochemical sensor. The beta (501Y.V2-1) variant attained an enhanced glycan binding modality in the NTD with specificity toward 9- O -acetylated structures, suggesting a dual-receptor functionality of the SARS-CoV-2 S1 domain, which was quickly selected against. These results indicate that SARS-CoV-2 can probe additional evolutionary space, allowing binding to glycan receptors on the surface of target cells.

The synthesis of polysubstituted spirocyclopropyl oxindoles using a series of rare-earth metal (REM) salts is reported. REMs, in particular Sc(OTf) 3 , allowed access to the target compounds by a multicomponent reaction with high diastereoselectivity (≤94:6:0:0). Density functional theory calculations on the model reaction are consistent with the observed selectivity and revealed that the special coordinating capabilities and the oxophilicity of the metal are key factors in inducing the formation of one main diastereoisomer.

Lectin-glycan interactions are at the heart of a multitude of biological events. Glycans are usually presented in a multivalent manner on the cell surface as part of the so-called glycocalyx, where they interact with other entities. This multivalent presentation allows us to overcome the typical low affinities found for individual glycan-lectin interactions. Indeed, the presentation of glycans may drastically impact their binding by lectins, highly affecting the corresponding binding affinity and even selectivity. In this context, we herein present the study of the interaction of a variety of homo- and heteromultivalent lactose-functionalized glycomacromolecules and their lipid conjugates with two human galectins. We have employed as ligands the glycomacromolecules, as well as liposomes decorated with those structures, to evaluate their interactions in a cell-mimicking environment. Key details of the interaction have been unravelled by NMR experiments, both from the ligand and receptor perspectives, complemented by cryo-electron microscopy methods and molecular dynamics simulations., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Influenza virus infection remains a threat to human health since viral hemagglutinins are constantly drifting, escaping infection and vaccine-induced antibody responses. Viral hemagglutinins from different viruses display variability in glycan recognition. In this context, recent H3N2 viruses have specificity for α2,6 sialylated branched N -glycans with at least three N -acetyllactosamine units (tri-LacNAc). In this work, we combined glycan arrays and tissue binding analyses with nuclear magnetic resonance experiments to characterize the glycan specificity of a family of H1 variants, including the one responsible for the 2009 pandemic outbreak. We also analyzed one engineered H6N1 mutant to understand if the preference for tri-LacNAc motifs could be a general trend in human-type receptor-adapted viruses. In addition, we developed a new NMR approach to perform competition experiments between glycans with similar compositions and different lengths. Our results point out that pandemic H1 viruses differ from previous seasonal H1 viruses by a strict preference for a minimum of di-LacNAc structural motifs., Competing Interests: The authors declare no competing financial interest., (© 2023 The Authors. Published by American Chemical Society.)

Human sialic acid binding immunoglobulin-like lectin-8 (Siglec-8) is an inhibitory receptor that triggers eosinophil apoptosis and can inhibit mast cell degranulation when engaged by specific monoclonal antibodies (mAbs) or sialylated ligands. Thus, Siglec-8 has emerged as a critical negative regulator of inflammatory responses in diverse diseases, such as allergic airway inflammation. Herein, we have deciphered the molecular recognition features of the interaction of Siglec-8 with the mAb lirentelimab (2C4, under clinical development) and with a sialoside mimetic with the potential to suppress mast cell degranulation. The three-dimensional structure of Siglec-8 and the fragment antigen binding (Fab) portion of the anti-Siglec-8 mAb 2C4, solved by X-ray crystallography, reveal that 2C4 binds close to the carbohydrate recognition domain (V-type Ig domain) on Siglec-8. We have also deduced the binding mode of a high-affinity analogue of its sialic acid ligand (9- N -napthylsufonimide-Neu5Ac, NSANeuAc) using a combination of NMR spectroscopy and X-ray crystallography. Our results show that the sialoside ring of NSANeuAc binds to the canonical sialyl binding pocket of the Siglec receptor family and that the high affinity arises from the accommodation of the NSA aromatic group in a nearby hydrophobic patch formed by the N-terminal tail and the unique G - G ' loop. The results reveal the basis for the observed high affinity of this ligand and provide clues for the rational design of the next generation of Siglec-8 inhibitors. Additionally, the specific interactions between Siglec-8 and the N-linked glycans present on the high-affinity receptor FcεRIα have also been explored by NMR., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

The large family of polypeptide GalNAc-transferases (GalNAc-Ts) controls with precision how GalNAc O -glycans are added in the tandem repeat regions of mucins ( e.g. , MUC1). However, the structural features behind the creation of well-defined and clustered patterns of O -glycans in mucins are poorly understood. In this context, herein, we disclose the full process of MUC1 O -glycosylation by GalNAc-T2/T3/T4 isoforms by NMR spectroscopy assisted by molecular modeling protocols. By using MUC1, with four tandem repeat domains as a substrate, we confirmed the glycosylation preferences of different GalNAc-Ts isoforms and highlighted the importance of the lectin domain in the glycosylation site selection after the addition of the first GalNAc residue. In a glycosylated substrate, with yet multiple acceptor sites, the lectin domain contributes to orientate acceptor sites to the catalytic domain. Our experiments suggest that during this process, neighboring tandem repeats are critical for further glycosylation of acceptor sites by GalNAc-T2/T4 in a lectin-assisted manner. Our studies also show local conformational changes in the peptide backbone during incorporation of GalNAc residues, which might explain GalNAc-T2/T3/T4 fine specificities toward the MUC1 substrate. Interestingly, we postulate that a specific salt-bridge and the inverse γ-turn conformation of the PDTRP sequence in MUC1 are the main structural motifs behind the GalNAc-T4 specificity toward this region. In addition, in-cell analysis shows that the GalNAc-T4 isoform is the only isoform glycosylating the Thr of the immunogenic epitope PDTRP in vivo , which highlights the relevance of GalNAc-T4 in the glycosylation of this epitope. Finally, the NMR methodology established herein can be extended to other glycosyltransferases, such as C1GalT1 and ST6GalNAc-I, to determine the specificity toward complex mucin acceptor substrates., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

Deep learning has been successfully applied to structure-based protein-ligand affinity prediction, yet the black box nature of these models raises some questions. In a previous study, we presented K DEEP , a convolutional neural network that predicted the binding affinity of a given protein-ligand complex while reaching state-of-the-art performance. However, it was unclear what this model was learning. In this work, we present a new application to visualize the contribution of each input atom to the prediction made by the convolutional neural network, aiding in the interpretability of such predictions. The results suggest that K DEEP is able to learn meaningful chemistry signals from the data, but it has also exposed the inaccuracies of the current model, serving as a guideline for further optimization of our prediction tools.

Feature attribution techniques are popular choices within the explainable artificial intelligence toolbox, as they can help elucidate which parts of the provided inputs used by an underlying supervised-learning method are considered relevant for a specific prediction. In the context of molecular design, these approaches typically involve the coloring of molecular graphs, whose presentation to medicinal chemists can be useful for making a decision of which compounds to synthesize or prioritize. The consistency of the highlighted moieties alongside expert background knowledge is expected to contribute to the understanding of machine-learning models in drug design. Quantitative evaluation of such coloring approaches, however, has so far been limited to substructure identification tasks. We here present an approach that is based on maximum common substructure algorithms applied to experimentally-determined activity cliffs. Using the proposed benchmark, we found that molecule coloring approaches in conjunction with classical machine-learning models tend to outperform more modern, graph-neural-network alternatives. The provided benchmark data are fully open sourced, which we hope will facilitate the testing of newly developed molecular feature attribution techniques.

Recently, the activity of heparan sulfate (HS) has led to the discovery of many drug candidates that have the potential to impact both medical science and human health. However, structural diversity and synthetic challenges impede the progress of HS research. Here, we report a library of novel l-iduronic acid (IdoA)-based HS mimics that are highly tunable in conformation plasticity and sulfation patterns to produce many of the functions of native HS oligosaccharides. The NMR analysis of HS mimics confirmed that 4- O -sulfation enhances the population of the 1 C 4 geometry. Interestingly, the 1 C 4 conformer becomes exclusive upon additional 2- O -sulfation. HS mimic microarray binding studies with different growth factors showed that selectivity and avidity are greatly modulated by the oligosaccharide length, sulfation code, and IdoA conformation. Particularly, we have identified 4- O -sulfated IdoA disaccharide ( I-21 ) as a potential ligand for vascular endothelial growth factor (VEGF 165 ), which in a multivalent display modulated endothelial cell proliferation, migration, and angiogenesis. Overall, these results encourage the consideration of HS mimics for therapeutic applications.

Glycerol phosphate (GroP)-based teichoic acids (TAs) are antigenic cell-wall components found in both enterococcus and staphylococcus species. Their immunogenicity has been explored using both native and synthetic structures, but no details have yet been reported on the structural basis of their interaction with antibodies. This work represents the first case study in which a monoclonal antibody, generated against a synthetic TA, was developed and employed for molecular-level binding analysis using TA microarrays, ELISA, SPR-analyses, and STD-NMR spectroscopy. Our findings show that the number and the chirality of the GroP residues are crucial for interaction and that the sugar appendage contributes to the presentation of the backbone to the binding site of the antibody.

Transported chemical reactions in unsaturated porous media are relevant to environmental and industrial applications. Continuum scale models are based on equivalent parameters derived from analogy with saturated conditions and cannot appropriately account for incomplete mixing. It is also unclear how the third dimension controls mixing and reactions. We obtain three-dimensional (3D) images by magnetic resonance imaging using an immiscible nonwetting liquid as a second phase and a fast irreversible bimolecular reaction. We study the impact of phase saturation on the dynamics of mixing and the reaction front. We quantify the temporally resolved effective reaction rate and describe it using the lamellar theory of mixing, which explains faster than Fickian ( t 0.5 ) rate of product formation by accounting for the deformation of the mixing interface between the two reacting fluids. For a given Péclet, although stretching and folding of the reactive front enhance as saturation decreases, enhancing the product formation, the product formation is larger as saturation increases. After breakthrough, the extinction of the reaction takes longer as saturation decreases because of the larger nonmixed volume behind the front. These results are the basis for a general model to better predict reactive transport in unsaturated porous media not achievable by the current continuum paradigm.

Carbohydrates (glycans, saccharides, and sugars) are essential molecules in all domains of life. Research on glycoscience spans from chemistry to biomedicine, including material science and biotechnology. Access to pure and well-defined complex glycans using synthetic methods depends on the success of the employed glycosylation reaction. In most cases, the mechanism of the glycosylation reaction is believed to involve the oxocarbenium ion. Understanding the structure, conformation, reactivity, and interactions of this glycosyl cation is essential to predict the outcome of the reaction. In this Account, building on our contributions on this topic, we discuss the theoretical and experimental approaches that have been employed to decipher the key features of glycosyl cations, from their structures to their interactions and reactivity.We also highlight that, from a chemical perspective, the glycosylation reaction can be described as a continuum, from unimolecular S N 1 with naked oxocarbenium cations as intermediates to bimolecular S N 2-type mechanisms, which involve the key role of counterions and donors. All these factors should be considered and are discussed herein. The importance of dissociative mechanisms (involving contact ion pairs, solvent-separated ion pairs, solvent-equilibrated ion pairs) with bimolecular features in most reactions is also highlighted.The role of theoretical calculations to predict the conformation, dynamics, and reactivity of the oxocarbenium ion is also discussed, highlighting the advances in this field that now allow access to the conformational preferences of a variety of oxocarbenium ions and their reactivities under S N 1-like conditions.Specifically, the ground-breaking use of superacids to generate these cations is emphasized, since it has permitted characterization of the structure and conformation of a variety of glycosyl oxocarbenium ions in superacid solution by NMR spectroscopy.We also pay special attention to the reactivity of these glycosyl ions, which depends on the conditions, including the counterions, the possible intra- or intermolecular participation of functional groups that may stabilize the cation and the chemical nature of the acceptor, either weak or strong nucleophile. We discuss recent investigations from different experimental perspectives, which identified the involved ionic intermediates, estimating their lifetimes and reactivities and studying their interactions with other molecules. In this context, we also emphasize the relationship between the chemical methods that can be employed to modulate the sensitivity of glycosyl cations and the way in which glycosyl modifying enzymes (glycosyl hydrolases and transferases) build and cleave glycosidic linkages in nature. This comparison provides inspiration on the use of molecules that regulate the stability and reactivity of glycosyl cations.

Graph neural networks are able to solve certain drug discovery tasks such as molecular property prediction and de novo molecule generation. However, these models are considered "black-box" and "hard-to-debug". This study aimed to improve modeling transparency for rational molecular design by applying the integrated gradients explainable artificial intelligence (XAI) approach for graph neural network models. Models were trained for predicting plasma protein binding, hERG channel inhibition, passive permeability, and cytochrome P450 inhibition. The proposed methodology highlighted molecular features and structural elements that are in agreement with known pharmacophore motifs, correctly identified property cliffs, and provided insights into unspecific ligand-target interactions. The developed XAI approach is fully open-sourced and can be used by practitioners to train new models on other clinically relevant endpoints.

Molecular recognition of carbohydrates is a key step in essential biological processes. Carbohydrate receptors can distinguish monosaccharides even if they only differ in a single aspect of the orientation of the hydroxyl groups or harbor subtle chemical modifications. Hydroxyl-by-fluorine substitution has proven its merits for chemically mapping the importance of hydroxyl groups in carbohydrate-receptor interactions. 19 F NMR spectroscopy could thus be adapted to allow contact mapping together with screening in compound mixtures. Using a library of fluorinated glucose (Glc), mannose (Man), and galactose (Gal) derived by systematically exchanging every hydroxyl group by a fluorine atom, we developed a strategy combining chemical mapping and 19 F NMR T 2 filtering-based screening. By testing this strategy on the proof-of-principle level with a library of 13 fluorinated monosaccharides to a set of three carbohydrate receptors of diverse origin, i.e. the human macrophage galactose-type lectin, a plant lectin, Pisum sativum agglutinin, and the bacterial Gal-/Glc-binding protein from Escherichia coli , it became possible to simultaneously define their monosaccharide selectivity and identify the essential hydroxyls for interaction.

The dynamic adaptability of tetragonal prismatic nanocapsule 1 8+ in the selective separation of fullerenes and endohedral metallofullerenes (EMFs) remains unexplored. Therefore, the essential molecular details of the fullerene recognition and binding process into the coordination capsule and the origins of fullerene selectivity remain elusive. In this work, the key steps of fullerene recognition and binding processes have been deciphered by designing a protocol which combines 1 H- 1 H exchange spectroscopy (2D-EXSY) NMR experiments, long time-scale Molecular Dynamics (MD) and accelerated Molecular Dynamics (aMD) simulations, which are combined to completely reconstruct the spontaneous binding and unbinding pathways from nanosecond to second time-range. On one hand, binding ( k ' on ) and unbinding ( k off ) rate constants were extracted from 1 H- 1 H exchange spectroscopy (EXSY) NMR experiments for both C 60 and C 70 . On the other hand, MD and aMD allowed monitoring the molecular basis of the encapsulation and guest competition processes at a very early stage under nonequilibrium conditions. The receptor capsule displays dynamical adaptability features similar to those observed in the process of biomolecular recognition in proteins. In addition, the encapsulation of bis-aza[60]fullerene (C 59 N) 2 within a supramolecular coordination capsule has been studied for the first time, showcasing the pros and cons of the dumbbell-shaped guest in the dynamics of the encapsulation process and in the stability of the final bound adduct. The powerful combination of NMR, MD, and aMD methodologies allows to obtain a precise picture of the subtle events directing the encapsulation and is thus a predictive tool for understanding host-guest encapsulation and interactions in numerous supramolecular systems.

A method for the detection and quantification of nanoplastics (NPTs) at environmentally relevant concentrations was developed. It is based on conjugating nanoplastics with functionalized metal (Au)-containing nanoparticles (NPs), thus making them detectable by highly sensitive inductively coupled plasma mass spectrometry (ICP-MS) operated in single particle (SP) mode. The selectivity of the method was achieved by the coupling of negatively charged carboxylate groups present at the surface of nanoplastics with a positively charged gelatin attached to the custom-synthesized AuNPs. The adsorbed Au produced a SP-ICP-MS signal allowing the counting of individual nanoplastic particles, and hence their accurate quantification (<5% error). Polystyrene (PS) particle models with controlled surface functionalization mimicking the nanoplastics formed during natural degradation of plastic debris were used for the method development. The nanoplastic number concentration quantification limit was calculated at 8.4 × 10 5 NPTs L -1 and the calibration graph was linear up to 3.5 × 10 8 NPTs L -1 . The method was applied to the analysis of nanoplastics of up to 1 μm in drinking, tap, and river water. The minimum detectable and quantifiable size depended on the degree of functionalization and the surface available for labeling. For a fully functionalized nanoplastic, the lower size detectable by this strategy is reported as 135 nm. In this study, authors use the recommendation for the definition of nanoplastics as plastic particles with sizes ranging between 1 nm and 1 μm, although it has not been accepted by a dedicated organization.

Noscapine is a natural alkaloid that is used as an antitussive medicine. However, it also acts as a weak anticancer agent in certain in vivo models through a mechanism that is largely unknown. Here, we performed structural studies and show that the cytotoxic agent 7A- O -demethoxy-amino-noscapine (7A-aminonoscapine) binds to the colchicine site of tubulin. We suggest that the 7A-methoxy group of noscapine prevents binding to tubulin due to a steric clash of the compound with the T5-loop of α-tubulin. We further propose that the anticancer activity of noscapine arises from a bioactive metabolite that binds to the colchicine site of tubulin to induce mitotic arrest through a microtubule cytoskeleton-based mechanism.

Pluripotent stem cells maintain the property of self-renewal and differentiate into all cell types under clear environments. Though the gene regulatory mechanism for pluripotency has been investigated in recent years, it is still not completely understood. Here, we show several signaling pathways involved in the maintenance of pluripotency. To investigate whether AMPK is involved in maintaining the pluripotency in mouse embryonic stem cells (mESCs) and elucidating the possible molecular mechanisms, implicated D3 and R1/E mESC lines were used in this study. Cells were cultured in the absence or presence of LIF and treated with 1 mM and 0.5 mM 5-aminoimidazole-4-carboxamide-1-β-d-ribofuranoside (AICAR), 2 mM metformin, compound C, and the PI3K inhibitor LY294002 for 24, 72, and 120 h. The levels of Nanog, Oct3/4, and REX1 and Brachyury, Notch2, and Gata4 mRNAs and Nanog or OCT3/4 protein levels were analyzed. Alkaline phosphatase and the cellular cycle were determined. The pGSK3β, GSK3β, p-β-catenin, and β-catenin protein levels were also investigated. We found that AMPK activators such as AICAR and metformin increase mRNA expression of pluripotency markers and decrease mRNA expression of differentiation markers in R1/E and D3 ES cells. AICAR increases phosphatase activity and arrests the cellular cycle in the G1 phase in these cells. We describe that AICAR effects were mediated by AMPK activation using a chemical inhibitor or by silencing this gene. AICAR effects were also mediated by PI3K, GSK3β, and β-catenin in R1/E ES cells. According to our findings, we provide a mechanism by which AICAR increases and maintains a pluripotency state through enhanced Nanog expression, involving AMPK/PI3K and p-GSK3β Ser21/9 pathways backing up the AICAR function as a potential target for this drug controlling pluripotency. The highlights of this study are that AICAR (5-aminoimidazole-4-carboxamied-1-b-riboside), an AMP protein kinase (AMPK) activator, blocks the ESC differentiation and AMPK is a key enzyme for pluripotency and shows valuable data to clarify the molecular pluripotency mechanism., Competing Interests: The authors declare no competing financial interest., (Copyright © 2020 American Chemical Society.)

Glycosylations promoted by triflate-generating reagents are widespread synthetic methods for the construction of glycosidic scaffolds and glycoconjugates of biological and chemical interest. These processes are thought to proceed with the participation of a plethora of activated high energy intermediates such as the α- and β-glycosyl triflates, or even increasingly unstable glycosyl oxocarbenium-like species, among which only α-glycosyl triflates have been well characterized under representative reaction conditions. Interestingly, the remaining less accessible intermediates, yet to be experimentally described, seem to be particularly relevant in α-selective processes, involving weak acceptors. Herein, we report a detailed analysis of several paradigmatic and illustrative examples of such reactions, employing a combination of chemical, NMR, kinetic and theoretical approaches, culminating in the unprecedented detection and quantification of the true β-glycosyl triflate intermediates within activated donor mixtures. This achievement was further employed as a stepping-stone for the characterization of the triflate anomerization dynamics, which along with the acceptor substitutions, govern the stereochemical outcome of the reaction. The obtained data conclusively show that, even for highly dissociative reactions involving β-close ion pair (β-CIP) species, the formation of the α-glycoside is necessarily preceded by a bimolecular α → β triflate interconversion, which under certain circumstances becomes the rate-limiting step. Overall, our results rule out the prevalence of the Curtin-Hammett fast-exchange assumption for most glycosylations and highlight the distinct reactivity properties of α- and β-glycosyl triflates against neutral and anionic acceptors.

The presence of anthropogenic nanoparticles (NPs) in the aquatic environment has become an emerging concern in terms of environmental and health safety. In the present study, we assessed the presence of Ag-bearing, Ti-bearing, and Ce-bearing NPs in the Barcelona catchment area, including the Besòs River basin and the Barcelona coast, and in the Ebro River Delta, using single particle inductively coupled plasma mass spectrometry (sp-ICP-MS). Ti-NPs and Ce-NPs were ubiquitously detected in surface waters, and their presence was related to a high natural background. Concentrations of Ti-NPs ranged from 23.2 × 10 6 to 298 × 10 6 Ti-NPs/L, with high concentrations being detected in areas with little anthropogenic pressure, while the presence of nanosilver (17.9 × 10 6 to 45.1 × 10 6 Ag-NPs/L) in the analyzed rivers was limited to certain hotspots close to wastewater treatment plants discharge points. The concentrations of Ce-NPs in the river ranged from 18.1 × 10 6 to 278 × 10 6 NPs/L, and they were related to the natural occurrence of the mineral Monazite-(Ce). Overall, the concentrations of these nanomaterials in the Barcelonan coast were significantly attenuated by river-sea environmental dilution. Nevertheless, Ce-NPs were eventually detected in some seawater samples with low levels of lanthanum-NPs, suggesting anthropogenic inputs of nanoCeO 2 , probably from atmospheric deposition.

(Amino)cyclotriphosphazenes have been used as new scaffolds for the synthesis of silver(I) metallomesogens. Two cyclotriphosphazenes, [N 3 P 3 (NHCy) 6 ] ( phos-1 ) and nongem-trans- [N 3 P 3 (NHCy) 3 (NMe 2 ) 3 ] ( phos-2 ), were reacted with the silver complex having a pro-mesogenic ligand, [Ag(OTf)L] (L = CNC 6 H 4 {OC(O)C 6 H 2 (3,4,5-(OC 10 H 21 ) 3 )}-4; OTf = OSO 2 CF 3 ), in different molar ratios, 1:1, 1:2, or 1:3, to give two series of cationic metallophosphazenes, [N 3 P 3 (NHCy) 6 {AgL} n ](TfO) n ( phos-1. n ) and nongem-trans- [N 3 P 3 (NHCy) 3 (NMe 2 ) 3 {AgL} n ](TfO) n ( phos-2. n ) with n = 1, 2, or 3. The chemical structure of these compounds, deduced from spectroscopic techniques, was in accordance with coordination of the silver fragments "AgL" to nitrogen atoms of the phosphazene ring, whereby their number n depends on the molar ratio used. Despite the presence of the bulky substituents on the core N atoms, cyclotriphosphazenes coordinated to three "AgL" units exhibited mesomorphism at room temperature. The mesophase was characterized as columnar hexagonal according to the optical microscopy and X-ray diffraction studies. A model based on an intermolecular association in pairs of the metallocyclotriphosphazenes having three AgL units has been proposed in order to explain the mesomorphic columnar arrangement in these materials. Starting silver complex, [Ag(OTf)L], also exhibited a columnar hexagonal mesophase at room temperature.

Transthyretin (TTR) modulates the deposition, processing, and toxicity of Abeta (Aβ) peptides. We have shown that this effect is enhanced in mice by treatment with small molecules such as iododiflunisal (IDIF, 4 ), a good TTR stabilizer. Here, we describe the thermodynamics of the formation of binary and ternary complexes among TTR, Aβ(1-42) peptide, and TTR stabilizers using isothermal titration calorimetry (ITC). A TTR/Aβ(1-42) (1:1) complex with a dissociation constant of K d = 0.94 μM is formed; with IDIF ( 4 ), this constant improves up to K d = 0.32 μM, indicating the presence of a ternary complex TTR/IDIF/Aβ(1-42). However, with the drugs diflunisal ( 1 ) or Tafamidis ( 2 ), an analogous chaperoning effect could not be observed. Similar phenomena could be recorded with the shorter peptide Aβ(12-28) ( 7 ). We propose the design of a simple assay system for the search of other chaperones that behave like IDIF and may become potential candidate drugs for Alzheimer's disease (AD).

A new family of chiral C 2 symmetric tetraazamacrocycles, coined ISAC for IminoSugar Aza-Crown, incorporating two iminosugars adopting a 4 C 1 conformation is disclosed. Multinuclear NMR experiments on the corresponding Cd 2+ complex show that the ISAC is a strong chelator in water and its tetramine cavity adopts a conformation similar to that of the parent Cd-cyclam complex. Similar behavior is observed with Cu 2+ in solution, with enhanced stability compared to the Cu-cyclam complex.

The reactivity of the multisite (amino)cyclotriphosphazene ligands, [N 3 P 3 (NHCy) 6 ] and [N 3 P 3 (NHCy) 3 (NMe 2 ) 3 ], has been explored in order to obtain silver(I) metallophosphazene complexes. Two series of cationic silver(I) metallophosphazenes were obtained and characterized: [N 3 P 3 (NHCy) 6 {AgL} n ](TfO) n [ n = 2, L = PPh 3 ( 2 ), PPh 2 Me ( 4 ); n = 3, L = PPh 3 ( 3 ), PPh 2 Me ( 5 ), TPA (TPA = 1,3,5-triaza-7-phosphaadamantane, 6 )] and nongem - trans -[N 3 P 3 (NHCy) 3 (NMe 2 ) 3 {AgL} n ](TfO) n [ n = 2, L = PPh 3 ( 7 ), PPh 2 Me ( 9 ); n = 3, L = PPh 3 ( 8 ), PPh 2 Me ( 10 )]. 5 , 7 , and 9 have also been characterized by single-crystal X-ray diffraction, thereby allowing key bonding information to be obtained. Compounds 2 - 6 , 9 , and 10 were screened for in vitro cytotoxic activity against two tumor human cell lines, MCF7 (breast adenocarcinoma) and HepG2 (hepatocellular carcinoma), and for antimicrobial activity against five bacterial species including Gram-positive, Gram-negative, and Mycobacteria strains. Both the IC 50 and MIC values revealed excellent biological activity for these metal complexes, compared with their precursors and cisplatin and also AgNO 3 and silver sulfadiazine, respectively. Both IC 50 and MIC values are among the lowest values found for any silver derivatives against the cell lines and bacterial strains used in this work. The structure-activity relationships were clear. The most cytotoxic and antimicrobial derivatives were those with the triphenylphosphane and [N 3 P 3 (NHCy) 6 ] ligands. A significant improvement in the activity was also observed upon a rise in the number of silver atoms linked to the phosphazene ring.

The use of C 60 as an interfacial layer between TiO 2 and methylammonium lead iodide perovskite is probed to reduce the current-voltage hysteresis in perovskite solar cells (PSCs) and, in turn, to impact the interfacial carrier injection and recombination processes that limit solar cell efficiencies. Detailed kinetic analyses across different time scales, that is, from the femtoseconds to the seconds, reveal that the charge carrier lifetimes as well as the charge injection and charge recombination dynamics depend largely on the presence or absence of C 60 . In addition, we corroborate that C 60 is applicable in hot carrier PSCs as it is capable of extracting hot carriers generated throughout the early time scales following photoexcitation.