General and Modular Synthesis of Covalent Organic Cages for Efficient Molecular Recognition.

Cage-type structures based on coordination and dynamic covalent chemistry have the characteristics of facile and efficient preparation but poor stability. Chemically stable organic cages, generally involving fragment coupling and multi-step reactions, are relatively difficult to synthesize. Herein, we offer a general and modular strategy to customize covalent organic cages with diverse skeletons and sizes. First, one skeleton (S) module with three extension (E) modules and three reaction (R) modules are connected by one- or two-step coupling to get the triangular monomer bearing three reaction sites. Then one-pot Friedel-Crafts condensation of the monomer and linking module of paraformaldehyde produces the designed organic cages. The cage forming could be regulated by the geometrical configuration of monomeric blocks. The S-E-R angles in the monomer is crucial; only 120o (2,4-dimethoxyphen as reaction module) or 60o (2,5-dimethoxyphen as reaction module) angle between S-E-R successfully affords the resulting cages. By the rational design of the three modules, a series of organic cages have been constructed. In addition, the host-guest properties show that the representative cages could strongly encapsulate neutral aromatic diimine guests driven by solvophobic interactions in polar solvents, giving the highest association constant of (2.58 ± 0.18) × 105 M-1.

Unraveling the Source of Self-Induced Diastereomeric Anisochronism in Chiral Dipeptides.

Mastering of analytical methods for accurate quantitative determinations of enantiomeric excess is a crucial aspect in asymmetric catalysis, chiral synthesis, and pharmaceutical applications. In this context, the phenomenon of Self-Induced Diastereomeric Anisochronism (SIDA) can be exploited in NMR spectroscopy for accurate determinations of enantiomeric composition, without using a chiral auxiliary that could interfere with the spectroscopic investigation. This phenomenon can be particularly useful for improving the quantitative analysis of mixtures with low enantiomeric excesses, where direct integration of signals can be tricky. Here, we describe a novel analysis protocol to correctly determine the enantiomeric composition of scalemic mixtures and investigate the thermodynamic and stereochemical features at the basis of SIDA. Dipeptide derivatives were chosen as substrates for this study, given their central role in drug design. By integrating the experiments with a conformational stochastic search that includes entropic contributions, we provide valuable information on the dimerization thermodynamics, the nature of non-covalent interactions leading to self-association, and the differences in the chemical environment responsible for the anisochrony, highlighting the importance of different stereochemical arrangement and tight association for the distinction between homochiral and heterochiral adducts. An important role played by the counterion was pointed out by computational studies.

Rapid and convenient screening method based on single-chain variable fragments for the detection of restricted monensin in chicken muscle.

A colloidal gold immunochromatographic assay (CGIA) based on single-chain variable fragments (scFvs) has been successfully developed for the detection of monensin (MON). Colloidal gold probes were conjugated to anti-MON scFvs through electrostatic interaction, with the conjugated objects serving as the visual signals. The detection lines were formed by capturing the antibody with MON-OVA. This assay offers a rapid detection time of 15 min, a wide linear range from 2.19 to 10.76 ng mL-1, and boasts high accuracy, precision, and an absence of cross-reactivity. By homology modeling and molecular docking, we predicted the interaction patterns between the scFv and monensin, and the amino acid residues involved in the recognition of MON by the antibody were analyzed. These key amino acid sites are presumed integral to ligand recognition per current interaction models. This hypothesis was confirmed by computer-aided alanine scanning mutation, MM/P(G)BSA molecular dynamics simulation, and in vitro binding experiments. In this study, we successfully developed the scFvs-based CGIA system for rapid and easy quantification of monensin, providing a simple, efficient routine detection of chicken muscle samples.

Langmuir monolayers provide an effective strategy for studying molecular recognition of nucleobases using alkylated nucleotides.

Molecular Recognition in nucleotides is crucial for medicine, underpinning precise interactions in genetic replication and therapy. Alkylated nucleotides, in particular, play a key role in modifying DNA to inhibit cancer cell growth. In this study, we focused on an alkylated nucleotide, PNM2 (3',4',6'-O-tristearoyl uridine or uridine tri-stearate), to investigate the interaction between adenine molecules in the aqueous subphase and PNM2 Langmuir monolayers. Utilizing techniques such as tensiometry, Brewster angle microscopy, infrared spectroscopy, surface potential measurements, and dilatational surface rheology, we found compelling evidence of molecular Recognition between the polar head of the insoluble amphiphile (uridine) in the monolayer and adenine in the aqueous subphase, attributed to hydrogen bonding. These interactions significantly influenced the physicochemical properties of the air-water interface, including monolayer expansion upon molecular recognition, decreased dilatational modulus, increased tensiometric stability of the monolayer when compressed to relevant surface pressures, and decreased surface potential. These findings are noteworthy for drug development, providing crucial insights into the mechanisms of nucleotide interactions.

Levodopa: From Biological Significance to Continuous Monitoring.

A continuous levodopa sensor can improve the quality of life for patients suffering with Parkinson's disease by enhancing levodopa titration and treatment effectiveness; however, its development is currently hindered by the absence of a specific levodopa molecular recognition element and limited insights into how real-time monitoring might affect clinical outcomes. This gap in research contributes to clinician uncertainty regarding the practical value of continuous levodopa monitoring data. This paper examines the current state of levodopa sensing and the inherent limitations in today's methods. Further, these challenges are described, including aspects such as interference from the metabolic pathway and adjunct medications, temporal resolution, and clinical questions, with a specific focus on a comprehensive selection of molecules, such as adjunct medications and structural isomers, as an interferent panel designed to assess and validate future levodopa sensors. We review insights and lessons from previously reported levodopa sensors and present a comparative analysis of potential molecular recognition elements, discussing their advantages and drawbacks.

Solvent Attenuation of London Dispersion in Polycyclic Aromatic Stacking.

Solvent competition for London dispersion attenuates its energetic significance in molecular recognition processes. By varying both the stacked contact area and the solvent, here we experimentally deconvolute solvent attenuation using molecular balances. Experimental stacking energies (phenyl to pyrene) correlated strongly with calculations only when dispersion was considered. Such calculations favoured stacking by up to -27 kJ mol-1 in the gas phase, but it was weakly disfavoured in our solution-phase experiments (+0.5 to +4.6 kJ mol-1). Nonetheless, the propensity for stacking increased with contact area and in solvents with lower bulk polarisabilities that compete less for dispersion. Experimental stacking energies ranged from -0.02 kJ mol-1 Å-2 in CS2, to -0.05 kJ mol-1 Å-2 in CD2Cl2, but were dwarfed by the calculated gas-phase energy of -0.6 kJ mol-1 Å-2. The results underscore the challenge facing the exploitation of dispersion in solution. Solvent competition strongly but imperfectly cancels dispersion at molecular recognition interfaces, making the energetic benefits difficult to realise.

Many locks to one key: N-acetylneuraminic acid binding to proteins.

Sialic acids play crucial roles in cell surface glycans of both eukaryotic and prokaryotic organisms, mediating various biological processes, including cell-cell interactions, development, immune response, oncogenesis and host-pathogen interactions. This review focuses on the ß-anomeric form of N-acetylneuraminic acid (Neu5Ac), particularly its binding affinity towards various proteins, as elucidated by solved protein structures. Specifically, we delve into the binding mechanisms of Neu5Ac to proteins involved in sequestering and transporting Neu5Ac in Gram-negative bacteria, with implications for drug design targeting these proteins as antimicrobial agents. Unlike the initial assumptions, structural analyses revealed significant variability in the Neu5Ac binding pockets among proteins, indicating diverse evolutionary origins and binding modes. By comparing these findings with existing structures from other systems, we can effectively highlight the intricate relationship between protein structure and Neu5Ac recognition, emphasizing the need for tailored drug design strategies to inhibit Neu5Ac-binding proteins across bacterial species.

Molecular mechanism of contactin 2 homophilic interaction.

Contactin 2 (CNTN2) is a cell adhesion molecule involved in axon guidance, neuronal migration, and fasciculation. The ectodomains of CNTN1-CNTN6 are composed of six Ig domains (Ig1-Ig6) and four FN domains. Here, we show that CNTN2 forms transient homophilic interactions (KD ∼200 nM). Cryo-EM structures of full-length CNTN2 and CNTN2_Ig1-Ig6 reveal a T-shaped homodimer formed by intertwined, parallel monomers. Unexpectedly, the horseshoe-shaped Ig1-Ig4 headpieces extend their Ig2-Ig3 tips outwards on either side of the homodimer, while Ig4, Ig5, Ig6, and the FN domains form a central stalk. Cross-linking mass spectrometry and cell-based binding assays confirm the 3D assembly of the CNTN2 homodimer. The interface mediating homodimer formation differs between CNTNs, as do the homophilic versus heterophilic interaction mechanisms. The CNTN family thus encodes a versatile molecular platform that supports a very diverse portfolio of protein interactions and that can be leveraged to strategically guide neural circuit development.

Molecular Recognition in Mechanochemistry: Insights from Solid-State NMR Spectroscopy.

Molecular-recognition events are highly relevant in biology and chemistry. In the present study, we investigated such processes in the solid state under mechanochemical conditions using the formation of racemic phases upon reacting enantiopure entities as example. As test systems, α-(trifluoromethyl)lactic acid (TFLA) and the amino acids serine and alanine were used. The effects of ball-milling and resonant acoustic mixing (RAM) on the formation of racemic phases were probed by using solid-state Nuclear Magnetic Resonance (NMR) spectroscopy. In a mixer mill, a highly efficient and fast racemic phase formation occurred for both TFLA and the two amino acids. RAM led to the racemic phase for TFLA also, and this process was facilitated upon employing pre-milled enantiopure entities. In contrast, under comparable conditions RAM did not result in the formation of racemic phases for serine and alanine.

Different roles of the heterodimer architecture of galectin-4 in selective recognition of oligosaccharides and lipopolysaccharides having ABH antigens.

The dimeric architecture of tandem-repeat type galectins, such as galectin-4 (Gal-4), modulates their biological activities, although the underlying molecular mechanisms have remained elusive. Emerging evidence show that tandem-repeat galectins play an important role in innate immunity by recognizing carbohydrate antigens present on the surface of certain pathogens, which very often mimic the structures of the human self-glycan antigens. Herein, we have analyzed the binding preferences of the C-domain of Gal-4 (Gal-4C) toward the ABH-carbohydrate histo-blood antigens with different core presentations and their recognition features have been rationalized by using a combined experimental approach including NMR, solid-phase and hemagglutination assays, and molecular modeling. The data show that Gal-4C prefers A over B antigens (two-fold in affinity), contrary to the N-domain (Gal-4N), although both domains share the same preference for the type-6 presentations. The behavior of the full-length Gal-4 (Gal-4FL) tandem-repeat form has been additionally scrutinized. Isothermal titration calorimetry and NMR data demonstrate that both domains within full-length Gal-4 bind to the histo-blood antigens independently of each other, with no communication between them. In this context, the heterodimeric architecture does not play any major role, apart from the complementary A and B antigen binding preferences. However, upon binding to a bacterial lipopolysaccharide containing a multivalent version of an H-antigen mimetic as O-antigen, the significance of the galectin architecture was revealed. Indeed, our data point to the linker peptide domain and the F-face of the C-domain as key elements that provide Gal-4 with the ability to cross-link multivalent ligands, beyond the glycan binding capacity of the dimer.

Probing the interaction between the metallo-ß-lactamase SMB-1 and ampicillin by multispectral approaches combined with molecular dynamics.

Metallo-ß-lactamases (MßLs) hydrolyze and inactivate ß-lactam antibiotics, are a pivotal mechanism conferring resistance against bacterial infections. SMB-1, a novel B3 subclass of MßLs from Serratia marcescens could deactivate almost all ß-lactam antibiotics including ampicillin (AMP), which has posed a serious threat to public health. To illuminate the mechanism of recognition and interaction between SMB-1 and AMP, various fluorescence spectroscopy techniques and molecular dynamics simulation were employed. The results of quenching spectroscopy unraveled that AMP could make SMB-1 fluorescence quenching that mechanism was the static quenching; the synchronous and three-dimensional fluorescence spectra validated that the microenvironment and conformation of SMB-1 were altered after interaction with AMP. The molecular dynamics results demonstrated that the whole AMP enters the binding pocket of SMB-1, even though with a relatively bulky R1 side chain. Loop1 and loop2 in SMB-1 undergo significant fluctuations, and α2 (71-73) and local α5 (186-188) were turned into random coils, promoting zinc ion exposure consistent with circular dichroism spectroscopy results. The binding between them was driven by a combination of enthalpy and entropy changes, which was dominated by electrostatic force in agreement with the fluorescence observations. The present study brings structural insights and solid foundations for the design of new substrates for ß-lactamases and the development of effective antibiotics that are resistant to superbugs.

Crystal structure and characterization of monascin from the extracts of Monascus purpureus-fermented rice.

We present a novel solid form of monascin, an azaphilonoid derivative extracted from Monascus purpureus-fermented rice. The crystal structure, C21H26O5, was characterized by single-crystal X-ray diffraction and belongs to the orthorhombic space group P212121. To gain insight into the electronic properties of the short contacts in the crystalline state of monascin, we utilized the Experimental Library of Multipolar Atom Model 2 (ELMAM2) database to transfer the electron density of monascin in its crystalline state. Hirshfeld surface analysis, fingerprint analysis, electronic properties and energetic characterization reveal that intermolecular C-H...O hydrogen bonds play a crucial role in the noncovalent bonding interactions by connecting molecules into two- and three-dimensional networks. The molecular electrostatic potential (MEP) map of the monascin molecule demonstrates that negatively charged regions located at four O atoms are favoured binding sites for more positively charged amino acid residues during molecular recognition. In addition, powder X-ray diffraction confirms that no transformation occurs during the crystallization of monascin.

Porous Supramolecular Crystalline Probe that Detects Non-Covalent Interactions Involved in Molecular Recognition of Furanic Compounds.

Selective separation and conversion of furan-based biomass-derived compounds, which are closely related to biorefineries, is currently an important issue. To improve their performance, it is important to deepen the understanding of non-covalent interactions that act on the molecular recognition of furanic compounds on separation or catalyst matrices. Here, a new method is reported to comprehensively visualize such intermolecular interactions using a porous supramolecular crystalline probe with polar and non-polar binding sites within a low-symmetric nanochannel consisting of four isomeric PdII 3-macrocycles. Single-crystal X-ray diffraction analysis of the crystals including 5-hydroxymethylfurfural, furfural, furfuryl alcohol, or 2-acetylfuran reveals a variety of interactions involving their furan rings and polar substituents. It is also found that cooperative and competitive effects between guest and solvent molecules significantly change their recognition mode.

Selective Solid-Liquid Extraction of Lithium Cation Using Tripodal Sulfate-Binding Receptors Driven by Electrostatic Interactions.

Owing to the important role of and increasing demand for lithium resources, lithium extraction is crucial. The use of molecular extractants is a promising strategy for selective lithium recovery, in which the interaction between lithium and the designed extractant can be manipulated at the molecular level. Herein, we demonstrate that anion receptors of tripodal hexaureas can selectively extract Li2SO4 solids into water containing DMSO (0.8% water) compared to other alkali metal sulfates. The hexaurea receptor with terminal hexyl chains displays the best Li+ extraction selectivity at 2-fold over Na+ and 12.5-fold over K+. The driving force underpinning selective lithium extraction is due to the combined interactions of Li+-SO42- electrostatics and the ion-dipole interaction of the lithium-receptor (carbonyl groups and N atoms); the latter was found to be cation size dependent, as supported by computational calculations. This work indicates that anion binding receptors could drive selective cation extraction, thus providing new insights into the design of receptors for ion recognition and separation.

Discovery of periplasmic solute binding proteins with specificity for ketone bodies: ß-hydroxybutyrate binding proteins.

Polyhydroxyalkanoates are a class of biodegradable, thermoplastic polymers which represent a major carbon source for various bacteria. Proteins which mediate the translocation of polyhydroxyalkanoate breakdown products, such as ß-hydroxybutyrate (BHB)-a ketone body which in humans serves as an important biomarker, have not been well characterized. In our investigation to screen a solute-binding protein (SBP) which can act as a suitable recognition element for BHB, we uncovered insights at the intersection of bacterial metabolism and diagnostics. Herein, we identify SBPs associated with putative ATP-binding cassette transporters that specifically recognize BHB, with the potential to serve as recognition elements for continuous quantification of this analyte. Through bioinformatic analysis, we identified candidate SBPs from known metabolizers of polyhydroxybutyrate-including proteins from Cupriavidus necator, Ensifer meliloti, Paucimonas lemoignei, and Thermus thermophilus. After recombinant expression in Escherichia coli, we demonstrated with intrinsic tryptophan fluorescence spectroscopy that four candidate proteins interacted with BHB, ranging from nanomolar to micromolar affinity. Tt.2, an intrinsically thermostable protein from Thermus thermophilus, was observed to have the tightest binding and specificity for BHB, which was confirmed by isothermal calorimetry. Structural analyses facilitated by AlphaFold2, along with molecular docking and dynamics simulations, were used to hypothesize key residues in the binding pocket and to model the conformational dynamics of substrate unbinding. Overall, this study provides strong evidence identifying the cognate ligands of SBPs which we hypothesize to be involved in prokaryotic cellular translocation of polyhydroxyalkanoate breakdown products, while highlighting these proteins' promising biotechnological application.

Tailoring Metallosupramolecular Glycoassemblies for Enhancing Lectin Recognition.

Multivalency is a fundamental principle in nature that leads to high-affinity intermolecular recognition through multiple cooperative interactions that overcome the weak binding of individual constituents. For example, multivalency plays a critical role in lectin-carbohydrate interactions that participate in many essential biological processes. Designing high-affinity multivalent glycoconjugates that engage lectins results in systems with the potential to disrupt these biological processes, offering promising applications in therapeutic design and bioengineering. Here, a versatile and tunable synthetic platform for the synthesis of metallosupramolecular glycoassemblies is presented that leverages subcomponent self-assembly, which employs metal ion templates to generate complex supramolecular architectures from simple precursors in one pot. Through ligand design, this approach provides precise control over molecular parameters such as size, shape, flexibility, valency, and charge, which afforded a diverse family of well-defined hybrid glyconanoassemblies. Evaluation of these complexes as multivalent binders to Concanavalin A (Con A) by isothermal titration calorimetry (ITC) demonstrates the optimal saccharide tether length and the effect of electrostatics on protein affinity, revealing insights into the impact of synthetic design on molecular recognition. The presented studies offer an enhanced understanding of structure-function relationships governing lectin-saccharide interactions at the molecular level and guide a systematic approach towards optimizing glyconanoassembly binding parameters.

From X-ray crystallographic structure to intrinsic thermodynamics of protein-ligand binding using carbonic anhydrase isozymes as a model system.

Carbonic anhydrase (CA) was among the first proteins whose X-ray crystal structure was solved to atomic resolution. CA proteins have essentially the same fold and similar active centers that differ in only several amino acids. Primary sulfonamides are well defined, strong and specific binders of CA. However, minor variations in chemical structure can significantly alter their binding properties. Over 1000 sulfonamides have been designed, synthesized and evaluated to understand the correlations between the structure and thermodynamics of their binding to the human CA isozyme family. Compound binding was determined by several binding assays: fluorescence-based thermal shift assay, stopped-flow enzyme activity inhibition assay, isothermal titration calorimetry and competition assay for enzyme expressed on cancer cell surfaces. All assays have advantages and limitations but are necessary for deeper characterization of these protein-ligand interactions. Here, the concept and importance of intrinsic binding thermodynamics is emphasized and the role of structure-thermodynamics correlations for the novel inhibitors of CA IX is discussed - an isozyme that is overexpressed in solid hypoxic tumors, and thus these inhibitors may serve as anticancer drugs. The abundant structural and thermodynamic data are assembled into the Protein-Ligand Binding Database to understand general protein-ligand recognition principles that could be used in drug discovery.

Under the Influence of Water: Molecular Recognition of Organic Hydrophilic Molecules in Water with a Prismarene Host Driven by Hydration Effects.

A water-soluble prism[5]arene host can form endo-cavity complexes with hydrophilic organic substances in water by displacing frustrated water molecules from its deep cavity. Water molecules structured at both rims of the prismarene host can mediate hydrogen bonding interactions with the guest. Water-mediated hydrogen bonding interactions were invoked here to elucidate the elevated binding affinities and selectivity of the prismarene host toward hydrophilic organic guests. We show that water at the interface of a host-guest complex can act as an extension of the host structure, facilitating the accommodation of neutral guests within the binding site. This study highlights the crucial role of water in facilitating supramolecular interactions between a deep-cavity prismarene host and organic hydrophilic guests in aqueous medium.

Detection of Tumor-Associated Autoantibodies in the Sera of Pancreatic Cancer Patients Using Engineered MUC1 Glycopeptide Nanoparticle Probes.

Pancreatic cancer is one of the deadliest cancers worldwide, mainly due to late diagnosis. Therefore, there is an urgent need for novel diagnostic approaches to identify the disease as early as possible. We have developed a diagnostic assay for pancreatic cancer based on the detection of naturally occurring tumor associated autoantibodies against Mucin-1 (MUC1) using engineered glycopeptides on nanoparticle probes. We used a structure-guided approach to develop unnatural glycopeptides as model antigens for tumor-associated MUC1. We designed a collection of 13 glycopeptides to bind either SM3 or 5E5, two monoclonal antibodies with distinct epitopes known to recognize tumor associated MUC1. Glycopeptide binding to SM3 or 5E5 was confirmed by surface plasmon resonance and rationalized by molecular dynamics simulations. These model antigens were conjugated to gold nanoparticles and used in a dot-blot assay to detect autoantibodies in serum samples from pancreatic cancer patients and healthy volunteers. Nanoparticle probes with glycopeptides displaying the SM3 epitope did not have diagnostic potential. Instead, nanoparticle probes displaying glycopeptides with high affinity for 5E5 could discriminate between cancer patients and healthy controls. Remarkably, the best-discriminating probes show significantly better true and false positive rates than the current clinical biomarkers CA19-9 and carcinoembryonic antigen (CEA).

Harnessing Cooperative Multivalency in Thioguanine for Surface-Enhanced Raman Scattering (SERS)-Based Differentiation of Polyfunctional Analytes Differing by a Single Functional Group.

Small-molecule receptors are increasingly employed to probe various functional groups for (bio)chemical analysis. However, differentiation of polyfunctional analogs sharing multiple functional groups remains challenging for conventional mono- and bidentate receptors because their insufficient number of binding sites limits interactions with the least reactive yet property-determining functional group. Herein, we introduce 6-thioguanine (TG) as a supramolecular receptor for unique tridentate receptor-analyte complexation, achieving ≥97 % identification accuracy among 16 polyfunctional analogs across three classes: glycerol derivatives, disubstituted propane, and vicinal diols. Crucially, we demonstrate distinct spectral changes induced by the tridentate interaction between TG's three anchoring points and all the analyte's functional groups, even the least reactive ones. Notably, hydrogen bond (H-bond) networks formed in the TG-analyte complexes demonstrate additive effects in binding strength originating from good bond linearity, cooperativity, and resonance, thus strengthening complexation events and amplifying the differences in spectral changes induced among analytes. It also enhances spectral consistency by selectively forming a sole configuration that is stronger than the respective analyte-analyte interaction. Finally, we achieve 95.4 % accuracy for multiplex identification of a mixture consisting of multiple polyfunctional analogs. We envisage that extension to other multidentate non-covalent interactions enables the development of interference-free small molecule-based sensors for various (bio)chemical analysis applications.