Search

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 β-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.

Protein–glycan interactions play pivotal roles in numerous biological processes, ranging from cellular recognition to immune response modulation. Understanding the intricate details of these interactions is crucial for deciphering the molecular mechanisms underlying various physiological and pathological conditions. Computational techniques have emerged as powerful tools that can help in drawing, building and visualising complex biomolecules and provide insights into their dynamic behaviour at atomic and molecular levels. This review provides an overview of the main computational tools useful for studying biomolecular systems, particularly glycans, both in free state and in complex with proteins, also with reference to the principles, methodologies, and applications of all-atom molecular dynamics simulations. Herein, we focused on the programs that are generally employed for preparing protein and glycan input files to execute molecular dynamics simulations and analyse the corresponding results. The presented computational toolbox represents a valuable resource for researchers studying protein–glycan interactions and incorporates advanced computational methods for building, visualising and predicting protein/glycan structures, modelling protein–ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein–glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural determinants that govern specific molecular interactions.

Abstract The pH‐dependent assembly of Toll‐like receptors (TLRs), which triggers a threshold‐like response, is a key principle in immune signaling. While crystallography has revealed the intricate structure of these assembly complexes, the mechanisms underlying their pH dependency remain unclear. Herein, constant pH simulations and metadynamics are employed to investigate the pH‐dependent assembly and stability of the TLR3/dsRNA signaling complex. The findings demonstrate that system pH regulates complex assembly and stability by modulating the protonation and charge states of histidines. Histidines in TLR3 act as pH‐dependent, positively charged binding sites that capture negatively charged dsRNA. Additionally, these histidines form a [H682⁺]—[E626⁻] dipole, facilitating the assembly of two TLR3 molecules into an antisymmetric dimer through dipole–dipole interactions. Surprisingly, TLR3 can shift the pKa values of key histidines from their model pKa of 6.5, increasing protonation likelihood and enhancing ligand binding. Notably, the aromatic residue Phe84, located within the dsRNA binding site [His39⁺–His60⁺–Phe84–His108⁺], alters the pKa of His60 through cation‐π interactions with its protonated state. This study offers new insights into the molecular mechanisms underlying pH‐dependent immune signaling via higher‐order assemblies and suggests potential applications for histidine in self‐assembling biomaterials.

Oligonucleotide drugs, an emerging modulator class, hold promise for targeting previously undruggable biomacromolecules. To date, only 18 oligonucleotide drugs, including sought-after antisense oligonucleotides (ASOs) and splice-switching oligonucleotides, have approval from the U.S. Food and Drug Administration. These agents effectively bind mRNA, inducing degradation or modulating splicing. Current oligonucleotide drug design strategies prioritize full Watson-Crick base pair (bp) complementarity, overlooking mRNA target three-dimensional shapes. Given that mRNA conformational diversity can impact hybridization, incorporating mRNA key structural properties into the design may expedite ASO lead discovery. Using atomistic molecular dynamics simulations inspired by experimental data, we demonstrate the advantages of incorporating common triple bps into the design of ASOs targeting RNA hairpin motifs, which are highly accessible regions for interactions. By using an RNA pseudoknot modified into an ASO-hairpin complex, we investigate the effects of ASO length and hairpin loop mutations. Our findings suggest that ASO-mRNA complex stability is influenced by ASO length, number of common triple bps, and the dynamic accessibility of bases in the hairpin loop. Our study offers new mechanistic insights into ASO-mRNA complexation and underscores the value of pseudoknots in constructing training datasets for machine learning models aimed at designing novel ASO leads.

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.

In this work, the authors represent a comprehensive approach for the development and validation of a novel graphite-supported molecularly imprinted poly(methyl methacrylate) electrode for the selective and sensitive detection of aloe emodin (AE) in aloe-based cosmetic products. The electrocatalytic activity of the electrode was evaluated using cyclic voltammetry and differential pulse voltammetry techniques in phosphate buffer saline. Surface morphology, structural characteristics, and imprinting endorsement were investigated using field emission scanning electron microscopy, Fourier-transform infrared spectroscopy, and UV-Vis spectroscopy. Under the optimal conditions, the electrode showed an oxidative differential pulse voltammetry peak at -0.2931±0.011 V (vs. Ag/AgCl, saturated KCl). The current was increased linearly with increasing concentrations of AE from 0.0005 to 350 µM, with a low detection limit of 0.0003 µM. The voltammetric analysis has been validated by reverse-phase high-performance liquid chromatography (RP-HPLC) methods. A partial least square regression model was developed to correlate the results obtained from the proposed system with the reference values obtained by RP-HPLC. The model showed a high prediction accuracy of 95.95 % for the detection of AE in cosmetic samples. The developed electrode provides a low-cost, rapid, easy, and convenient method for the detection of AE in cosmetic products, offering potential benefits for quality control and safety assessment in the cosmetic industry.

Abstract Accurate and efficient molecular recognition plays a crucial role in the fields of molecular detection and diagnostics. Conventional trial‐and‐error‐based molecular recognition approaches have always been challenged in distinguishing minimal differences between targets and non‐targets, such as single nucleotide polymorphisms (SNPs) of oligonucleotides. To address these challenges, here, a novel concept of dynamic addressing analysis is proposed. In this concept, by dissecting the regions of the target and creating a corresponding recognizer, it is possible to eliminate the inaccuracy and inefficiency of recognition. To achieve this concept, a Dynamic Addressing Molecular Robot (DAMR), a DNA‐based dynamic addressing device is developed which is capable of dynamically locating targets. DAMR is designed to first bind to the conserved region of the target while addressing the specific region dynamically until accurate recognition is achieved. DAMR has provided an approach for analyzing low‐resolution targets and has been used for analyzing SNP of miR‐196a2 in both cell and serum samples, which has opened new avenues for effective and efficient molecular recognition.

Switchable molecular tweezers are a unique class of molecular switches that, like their macroscopic analogs, exhibit mechanical motion between an open and closed conformation in response to stimuli. Such systems constitute an essential component of artificial molecular machines. This review will present selected examples of switchable molecular tweezers and their potential applications. The first part will be devoted to chemically responsive tweezers, including stimuli such as pH, metal coordination, and anion binding. Then, redox-active and photochemical tweezers will be presented.

Vancomycin is a glycopeptide antibiotic that for decades has been a mainstay of treatment for persistent bacterial infections. However, the spread of antibiotic resistance threatens its continued utility. In particular, vancomycin-resistant enterococci (VRE) have become a pressing clinical challenge. Vancomycin acts by binding and sequestering the intermediate Lipid II in cell-wall biosynthesis, specifically recognizing a D-alanine-D-alanine dipeptide motif within the Lipid II molecule. VRE achieve resistance by remodeling this motif to either D-alanine-D-lactate or D-alanine-D-serine; the former substitution essentially abolishes recognition by vancomycin of Lipid II, whereas the latter reduces the affinity of the antibiotic by roughly one order of magnitude. The complex of vancomycin bound to D-alanine-D-serine has been crystallized, and its 1.20 Å X-ray crystal structure is presented here. This structure reveals that the D-alanine-D-serine ligand is bound in essentially the same position and same pose as the native D-alanine-D-alanine ligand. The serine-containing ligand appears to be slightly too large to be comfortably accommodated in this way, suggesting one possible contribution to the reduced binding affinity. In addition, two flexible hydroxyl groups – one from the serine side chain of the ligand, and the other from a glucose sugar on the antibiotic – are locked into single conformations in the complex, which is likely to contribute an unfavorable entropic component to the recognition of the serine-containing ligand.

The advancement of synthetic host–guest chemistry has played a pivotal role in exploring and quantifying weak non-covalent interactions, unraveling the intricacies of molecular recognition in both chemical and biological systems. Macrocycles, particularly calix[4]resorcinarene-based cavitands, have demonstrated significant utility in receptor design, facilitating the creation of intricately organized architectures. Within the realm of macrocycles, these cavitands stand out as privileged scaffolds owing to their synthetic adaptability, excellent topological structures, and unique recognition properties. So far, extensive investigations have been conducted on various applications of calix[4]resorcinarene-based cavitands. In this review, we will elaborate on their diverse functions, including catalysis, separation and purification, polymeric materials, sensing, battery materials, as well as drug delivery. This review aims to provide a holistic understanding of the multifaceted roles of calix[4]resorcinarene-based cavitands across various applications, shedding light on their contributions to advancing the field of supramolecular chemistry.

Abstract The standard method of receptor activation involves the binding of signals or signal‐loaded solute binding proteins (SBPs) to sensor domains. Many sensor histidine kinases (SHKs), which are activated by SBP binding, are encoded adjacent to their corresponding sbp gene. We examined three SBPs of Pseudomonas aeruginosa PAO1, encoded near the genes for the AgtS (PA0600) and AruS (PA4982) SHKs, to determine how common this arrangement is. Ligand screening and microcalorimetric studies revealed that the SBPs PA0602 and PA4985 preferentially bind to GABA (KD = 2.3 and 0.58 μM, respectively), followed by 5‐aminovalerate (KD = 30 and 1.6 μM, respectively) and ethanoldiamine (KD = 2.3 and 0.58 μM, respectively). In contrast, AgtB (PA0604) exclusively recognizes 5‐aminovaleric acid (KD = 2.9 μM). However, microcalorimetric titrations did not show any binding between the AgtS sensor domain and AgtB or PA0602, regardless of the presence of ligands. Similarly, bacterial two‐hybrid assays did not demonstrate an interaction between PA4985 and the AruS sensor domain. Therefore, sbp and shk genes located nearby are not always functionally linked. We previously identified PA0222 as a GABA‐specific SBP. The presence of three SBPs for GABA may be linked to GABA's role as a trigger for P. aeruginosa virulence.

Bone defects induced by trauma, infection, and tumors present a significant challenge for treatment in clinical trials. Biomaterial-based tissue engineering strategy has shown great promise in bone defect repair. However, multiple functions inherent in the extracellular matrix (ECM) are rarely covered in the design of scaffold materials associated with bone grafting procedures. These deficiencies significantly limit its potential application in pathologic bone defect therapy. In this work, we constructed a hydrogel scaffold mimicking the dynamic features of ECM with the combination of antimicrobial and osteogenic capabilities as well, to investigate its applications in the therapy of infected radial defects. The hydrogel scaffold enables not only minimally invasive implantation but also adaptability and adhesion to irregular defect shapes. Both in vitro and in vivo assays have indicated that the hydrogel scaffold could rapidly eradicate bacteria, restore the infection-induced localized inflammatory microenvironment. Further loading osteogenic growth peptide (OGP) to recruit stem cells promotes osteogenic differentiation and ultimately enhances bone regeneration in the defect region. In summary, our work indicated that hydrogels with ECM-related inherent bioactivities and dynamic inner structures represent a feasible solution as a tissue bionic substitute for the therapy of infected bone defects.

Significant progress has been achieved in the field of solid-state biosensors over the past 50 years. Various sensing devices with high-density integration and flexible configuration, as well as new applications for clinical diagnosis and healthcare, have been developed using blood, serum, and other body fluids such as sweat, tears, and saliva. A high-density array of ion-sensitive field effect transistors was developed by exploiting the advantages of advanced semiconductor technologies and commercialized in combination with an enzymatic primer extension reaction as a DNA sequencer in 2011. Different types of materials such as inorganic materials, metals, polymers, and biomolecules are mixed together on the surface of the gate while maintaining their own functions; therefore, compatibility among different materials has to be optimized so that the best detection performance of solid-state biosensors, including stability and reliability, is achieved as designed. Solid-state biosensors are suitable for the rapid, cost-effective, and noninvasive identification of biomarkers at various timepoints over the course of a disease.

Infected bone fractures remain a major clinical challenge for orthopedic surgeons. From a tissue regeneration perspective, biomaterial scaffolds with antibacterial and osteoinductive activities are highly desired, while advanced materials capable of mimicking the pathological microenvironment during the healing process of infected tissues remain an area deserving more research. Hematoma, the gel-like blood coagulum, plays an essential role in bone fracture repair because of its ability to serve as a dynamic and temporary scaffold with cytokines for both pathogen elimination and tissue healing. In light of this, we designed a dynamic hydrogel with hematoma-like antimicrobial or reparative performance for infected bone fracture repair in this study. The proposed dynamic hydrogel network was based on the reversible recognition of a natural glycopeptide antibiotic vancomycin (Van) and its target dipeptide D-Ala-D-Ala (AA), which could serve as a hematoma-like scaffold for obliterating bacteria in the fracture region and promoting bone repair by introducing an endogenous osteogenic peptide (OGP). In vivo experiments demonstrated that the hydrogel could rapidly eradicate bacteria, improve bone regeneration and restore the local inflammatory microenvironment. Together, findings from this study imply that the use of hematoma-like dynamic hydrogel could lead to a biomimetic revolution in surgical strategies against susceptible bone fractures.

Abstract Background Alzheimer’s disease (AD) is the leading cause of dementia and loss of autonomy in the elderly, implying a progressive cognitive decline and limitation of social activities. The progressive aging of the population is expected to exacerbate this problem in the next decades. Therefore, there is an urgent need to develop quantitative diagnostic methodologies to assess the onset the disease and its progression especially in the initial phases. Results Here we describe a novel technology to extract one of the most important molecular biomarkers of AD (Aβ1−42) from a clinically-relevant volume − 100 µl – therein dispersed in a range of concentrations critical for AD early diagnosis. We demonstrate that it is possible to immunocapture Aβ1−42 on 20 nm wide magnetic nanoparticles functionalized with hyperbranced KVLFF aptamers. Then, it is possible to transport them through microfluidic environments to a detection system where virtually all (~ 90%) the Aβ1−42 molecules are concentrated in a dense plug of ca.50 nl. The technology is based on magnetic actuation by permanent magnets, specifically designed to generate high gradient magnetic fields. These fields, applied through submillimeter-wide channels, can concentrate, and confine magnetic nanoparticles (MNPs) into a droplet with an optimized shape that maximizes the probability of capturing highly diluted molecular biomarkers. These advancements are expected to provide efficient protocols for the concentration and manipulation of molecular biomarkers from clinical samples, enhancing the accuracy and the sensitivity of diagnostic technologies. Conclusions This easy to automate technology allows an efficient separation of AD molecular biomarkers from volumes of biological solutions complying with the current clinical protocols and, ultimately, leads to accurate measurements of biomarkers. The technology paves a new way for a quantitative AD diagnosis at the earliest stage and it is also adaptable for the biomarker analysis of other pathologies.

Multivariate data analysis and machine learning classification have become popular tools to extract features without physical models for complex environments recognition. For electronic noses, time sampling over multiple sensing elements must be a fair compromise between a period sufficiently long to output a meaningful information pattern and sufficiently short to minimize training time for practical applications. Particularly when a reactivity’s kinetics differ from the thermodynamics in sensitive materials, finding the best compromise to get the most from the data is not obvious. Here, we investigate the influence of data acquisition to improve or alter data clustering for molecular recognition on a conducting polymer electronic nose. We found out that waiting for sensing elements to reach their steady state is not required for classification, and that reducing data acquisition down to the first dynamical information suffices to recognize molecular gases by principal component analysis with the same materials. Especially for online inference, this study shows that a good sensing array is not an array of good sensors, and that new figures of merit should be defined for sensing hardware using machine learning pattern recognition rather than metrology.

Toll-like receptors (TLRs) activate innate immunity in response to pathogen-associated molecular patterns (PAMPs). The ectodomain of a TLR directly senses a PAMP and the intracellular TIR domain dimerizes to initiate a signaling cascade. The TIR domains of TLR6 and TLR10, which belong to the TLR1 subfamily, have been structurally characterized in a dimer, whereas those of other subfamilies, including TLR15, have not been explored at the structural or molecular level. TLR15 is a TLR unique to birds and reptiles that responds to virulence-associated fungal and bacterial proteases. To reveal how the TLR15 TIR domain (TLR15TIR) triggers signaling, the crystal structure of TLR15TIR was determined in a dimeric form and a mutational study was performed. TLR15TIR forms a one-domain structure in which a five-stranded β-sheet is decorated by α-helices, as shown for TLR1 subfamily members. TLR15TIR exhibits substantial structural differences from other TLRs at the BB and DD loops and αC2 helix that are involved in dimerization. As a result, TLR15TIR is likely to form a dimeric structure that is unique in its intersubunit orientation and the contribution of each dimerizing region. Further comparative analysis of TIR structures and sequences provides insights into the recruitment of a signaling adaptor protein by TLR15TIR.

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.

The main aim of this study is to figure out how well cryptand-2.2.1 (C 2.2.1) and cryptand-2.1.1 (C 2.1.1) macrocyclic compounds (MCs) work as novel extractants for scandium (Sc) by using an artificial neural network (ANN) models in MATLAB software. Moreover, C2.2.1 and C2.1.1 have never been evaluated to recover Sc. The independent variables impacting the extraction process (concentration of MC, concentration of Sc, pH, and time), and a nonlinear autoregressive network with exogenous input (NARX) and feed-forward neural network (FFNN) models were used to estimate their optimum values. The greatest obstacle in the selective recovery process of the REEs is the similarity in their physicochemical properties, specifically their ionic radius. The recovery of Sc from the aqueous solution was experimentally evaluated, then the non-linear relationship between those parameters was predictively modeled using (NARX) and (FFNN). To confirm the extraction and stripping efficiency, an atomic absorption spectrophotometer (AAS) was employed. The results of the extraction investigations show that, for the best conditions of 0.008 mol/L MC concentration, 10 min of contact time, pH 2 of the aqueous solution, and 75 mg/L Sc initial concentration, respectively, the C 2.1.1 and C 2.2.1 extractants may reach 99 % of Sc extraction efficiency. Sc was recovered from a multi-element solution of scandium (Sc), yttrium (Y), and lanthanum (La) under these circumstances. Whereas, at a concentration of 0.3 mol/L of hydrochloric acid, the extraction of Sc was 99 %, as opposed to Y 10 % and La 7 %. The Levenberg-Marquardt training algorithm had the best training performance with an mean-squared-error, MSE, of 5.232x10−6 and 6.1387x10−5 for C 2.2.1 and C 2.1.1 respectively. The optimized FFNN architecture of 4-10-1 was constructed for modeling recovery of Sc. The extraction process was well modeled by the FFNN with an R2 of 0.999 for the two MC, indicating that the observed Sc recovery efficiency consistent with the predicted one.

Abstract Dinuclear copper complexes have been designed for molecular recognition in order to selectively bind to two neighboring phosphate moieties in the backbone of double strand DNA. Associated biophysical, biochemical and cytotoxic effects on DNA were investigated in previous works, where atomic force microscopy (AFM) in ambient conditions turned out to be a particular valuable asset, since the complexes influence the macromechanical properties and configurations of the strands. To investigate and scrutinize these effects in more depth from a structural point of view, cutting-edge preparation methods and scanning force microscopy under ultra-high vacuum (UHV) conditions were employed to yield submolecular resolution images. DNA strand mechanics and interactions could be resolved on the single base pair level, including the amplified formation of melting bubbles. Even the interaction of singular complex molecules could be observed. To better assess the results, the appearance of treated DNA is also compared to the behavior of untreated DNA in UHV on different substrates. Finally, we present data from a statistical simulation reasoning about the nanomechanics of strand dissociation. This sort of quantitative experimental insights paralleled by statistical simulations impressively shade light on the rationale for strand dissociations of this novel DNA interaction process, that is an important nanomechanistic key and novel approach for the development of new chemotherapeutic agents.

SARS‐CoV‐2 aptamer is a favorable candidate for the recognition and detection of SARS‐CoV‐2, owing to its small size and easy synthesis. However, the issue of compromised binding affinities in real samples and targeting mutant SARS‐CoV‐2 hinder wide applications of the aptamer. In this study, it is discovered that molecular crowding could increase binding affinity of CoV2‐6C3 aptamer against RBD (Receptor Binding Domain) of SARS‐CoV‐2 via increasing the absolute value of the enthalpy change. The values of the equilibrium dissociation constant in molecular crowding decrease by 70% and 150%, respectively, against wild‐type and mutant RBD compared with those in buffer without crowding. Moreover, the detection limit of SARS‐CoV‐2 pseudovirus is up to 5 times lower under molecular crowding compared to dilute conditions. The discovery deepens the understanding of aptamer‐target interaction mechanisms in crowding conditions and provides an effective way to apply SARS‐CoV‐2 aptamer for virus recognition and detection.

Various functional groups have been considered as acceptors for halogen bonds, but the oxime functionality has received very little attention in this context. In this study, we focus on the analysis of the hydrogen and halogen bond preferences observed in the crystal structures of 5-halogeno-1H-isatin-3-oximes. These molecules can be involved in various non-covalent interactions, and the competition between these interactions has a decisive influence on their self-organization. In particular, we were interested to see whether the crystal structures of 5-halogeno-1H-isatin-3-oximes, especially bromine- and iodine-substituted ones, are characterized by the presence of halogen bonds formed with the oxime functionality. The oxime group proved its ability to compete with the other strong donor and acceptor sites by participating in the formation of cyclic hydrogen-bonded heterosynthons oxime∙∙∙amide and Ooxime∙∙∙Br/I halogen bonds.

Molecular recognition elements like enzymes, antibodies, and nucleic acids, which are involved in specific binding, are important components in biosensing technologies. These biomolecular recognition elements are based on molecular interactions such as hydrogen bonding, van der Waals forces, and hydrophobic interactions. However, these interactions are often affected by the solution environment such as pH, temperature, and salt concentration, which are the rate-limiting factors for biosensing applications. In this study, we focused on molecular recognition using photocrosslinkable artificial nucleic acids. Photocrosslinkable artificial nucleic acids can form covalent bonds with target nucleic acids upon photoirradiation after hybridization. The covalent bonds formed are stronger than those in conventional molecular recognition and are not affected by the solution environment. Herein, we propose a biosensing system that combines molecular recognition by photocrosslinkable artificial nucleic acids, isothermal amplification by hybridization chain reaction, and electrochemical detection of miR-21 as the target molecule, which has recently attracted attention as a cancer biomarker. This technology eliminates non-specific binding and enables biosensing measurements with a suppressed background.

A synthetic route to 1,4,6,10-tetraazaadamantanes (TAADs) bearing free and protected amino groups at the bridge N-atoms has been developed via intramolecular cyclotrimerization of C=N units in the corresponding tris(hydrazonoalkyl)amines. In a similar fashion, unsymmetrically substituted TAADs having both amino and hydroxy groups at the bridge N-atoms were prepared via a hitherto unknown co-trimerization of oxime and hydrazone groups. The use of N-TAAD derivatives as potential ligands and receptors was showcased through forming boron chelates and host–guest complexes with water and simple alcohols.

Molecular imprinting polymers (MIPs) have been widely used to produce stable polymeric materials due to their highly selective binding sites to determine the analyte (target molecule) in food products. MIPs begin with a complex compound between the template molecule and the functional monomers that can be polymerized when there is a closely crossed link. MIPs left specific cavities after the removal of templates during washing, which complements the size and shape of the templates. The use of MIPs has contributed to novel advances in materials science, polymer science, natural science, and other multi-disciplinary systems. Optical chemical sensor is an exciting field in MIPs today due to comprehend the unique affirmation limit of associated polymers giving stable polymers with high molecular recognition capabilities. MIPs display a wide extent of relevance, incredible flexibility, security, and high selectivity; their internal affirmation districts can be explicitly gotten together with design molecules to achieve specific affirmation. This review covers the various achievements of sensors used in laboratory analyses. The advancement in the development of MIPs is evaluated with an accentuation on the preparation principle, the discovery process, the molecular recognition mechanism and future perspectives and challenges for MIPs in building an optical chemical sensor.

Abstract Among the 1,3,5-trisubstituted 2,4,6-triethylbenzenes bearing pyrazolyl groups, the compounds with 3,5-dimethylpyrazolyl moieties were found to be effective receptors for ammonium ions (NH4 +). The current study investigated the extent to which the incorporation of an additional alkyl group in the 4-position of the pyrazole ring affects the binding properties of the new compounds. 1H NMR spectroscopic titrations and investigations using isothermal titration calorimetry revealed that this small structural variation leads to a significant increase in the binding strength towards NH4 + and also improves the binding preference for NH4 + over K+. In addition to the studies in solution, crystalline complexes of the new triethyl- and trimethylbenzene derivatives, bearing 3,4,5-trialkylpyrazolyl groups, with NH4 +PF6 − were obtained and analyzed in detail. It is noteworthy that two of the crystal structures discussed in this work are characterized by the presence of two types of ammonium complexes. Studies focusing on the development of new artificial ammonium receptors are motivated, among other things, by the need for more selective ammonium sensors than those based on the natural ionophore nonactin.

In this work, molecular dynamics (MD) simulations and time-dependent density functional theory (TD-DFT) calculations were applied to study the formation of binary and ternary complexes between cucurbit[8]uril (CB8) and three tryptophan-containing tripeptides (WGG, GWG, and GGW), as well as heteroternary complexes of the tripeptides in the presence of methyl viologen (MV) as an auxiliary ligand. All complexes were stable in water, and exhibited encapsulation of the indole moiety of W. Analysis of the MD trajectories of the homoternary complexes revealed π-π stacking within the CB8 cavity between the indole rings. MM-PBSA analysis indicated higher binding energy for tripeptides containing W residue at the N-terminus. The heteroternary complexes showed two binding modes, one with MV fully included (and π-π stacked with the indole ring) and the other with MV mostly excluded. The computed UV–Visible spectra of the free guests and their heteroternary complexes exhibited new bands emerged in the spectra of the complexes, which resulted from the transitions from HOMO and HOMO–1 to LUMO related to W–MV charge transfer (CT) complexes.

Abstract Understanding dynamic systems is a crucial step toward the design of complex matter. Here, we aim to study the behavior of Constitutional Dynamic Networks (CDNs) in conditions of dynamic competition, taking cryptands and metal cations as a test bed. The CDNs of cryptates were analyzed by NMR spectroscopy. The experimental results were complemented by extensive numerical simulations, based on a large amount of thermodynamic and kinetic data available in the literature for cryptates. Although the CDN′s output is a result of the interplay between the individual stability constants of the complexes in a mixture, the overall effect may be governed by only one – the most thermodynamically stable member of a network. Significantly, these findings indicate that an increase in complexity (multiplicity and connectivity) of a system may, in conditions of dynamic competition, result in “simplexity”, i. e. a simplification of the output of the system.

Accurate modeling of nonbonded interactions between protein kinases and their small molecule inhibitors is essential for structure-based drug design. Quantum chemical methods such as density functional theory (DFT) hold significant promise for quantifying the strengths of these key protein–ligand interactions. However, the accuracy of DFT methods can vary substantially depending on the choice of exchange–correlation functionals and associated basis sets. In this study, a comprehensive benchmarking of nine widely used DFT methods was carried out to identify an optimal approach for quantitative modeling of nonbonded interactions, balancing both accuracy and computational efficiency. From a database of 2139 kinase-inhibitor crystal structures, a diverse library of 49 nonbonded interaction motifs was extracted, encompassing CH–π, π–π stacking, cation–π, hydrogen bonding, and salt bridge interactions. The strengths of nonbonded interaction energies for all 49 motifs were calculated at the advanced CCSD(T)/CBS level of theory, which serve as references for a systematic benchmarking of BLYP, TPSS, B97, ωB97X, B3LYP, M062X, PW6B95, B2PLYP, and PWPB95 functionals with D3BJ dispersion correction alongside def2-SVP, def2-TZVP, and def2-QZVP basis sets. The RI, RIJK, and RIJCOSX approximations were used for selected functionals. It was found that the B3LYP/def2-TZVP and RIJK RI-B2PLYP/def2-QZVP methods delivered the best combination of accuracy and computational efficiency, making them well-suited for efficient modeling of nonbonded interactions responsible for molecular recognition of protein kinase inhibitors in their targets.

In silico approaches were employed to examine the characteristics of interactions between human mitochondrial thioredoxin 2 (HsTrx2) and its 38 previously identified mitochondrial protein ligands. All interactions appeared driven mainly by electrostatic forces. The statistically significant residues of HsTrx2 for interactions were characterized as “contact hot spots”. Since these were identical/adjacent to putative thermodynamic hot spots, an energy network approach identified their neighbors to highlight possible contact interfaces. Three distinct areas for binding emerged: (i) one around the active site for covalent interactions, (ii) another antipodal to the active site for strong non-covalent interactions, and (iii) a third area involved in both kinds of interactions. The contact interfaces of HsTrx2 were projected as respective interfaces for Escherichia coli Trx1 (EcoTrx1), 2, and HsTrx1. Comparison of the interfaces and contact hot spots of HsTrx2 to the contact residues of EcoTx1 and HsTrx1 from existing crystal complexes with protein ligands supported the hypothesis, except for a part of the cleft/groove adjacent to Trp30 preceding the active site. The outcomes of this study raise the possibility for the rational design of selective inhibitors for the interactions of HsTrx2 with specific protein ligands without affecting the entirety of the functions of the Trx system.

The GABAA receptor (GABAAR) is a target channel for the loss of awareness of general anesthesia. General anesthetic (GA) spans a wide range of chemical structures, such as monatomic molecules, barbital acids, phenols, ethers, and alkanes. GA has a weak binding affinity, and the affinity has a characteristic that correlates with the solubility in olive oil rather than the molecular shape. The GA binding site of GABAAR is common to GAs and exists in the transmembrane domain of the GABAAR intersubunit. In this study, the mechanism of GA binding, which allows binding of various GAs with intersubunit selectivity, was elucidated from the hydration analysis of the binding site. Regardless of the diverse GA chemical structures, a strong correlation was observed between the binding free energy and total dehydration number of the binding process. The GA binding free energy was more involved in the binding dehydration and showed molecular recognition that allowed for the binding of various GA structures via binding site hydration. We regarded the GA substitution for the interfacial water molecule of the binding site as a dissolution into the interfacial hydration layer. The elucidation of the GA binding mechanism mediated by hydration at the GABAAR common binding site provides a rationale for the combined use of anesthetics in medical practice and its combination adjustments via drug interactions.

Integrins in the cell surface interact with functional motifs found in the extracellular matrix (ECM) that queue the cell for biological actions such as migration, adhesion, or growth. Multiple fibrous proteins such as collagen or fibronectin compose the ECM. The field of biomechanical engineering often deals with the design of biomaterials compatible with the ECM that will trigger cellular response (e.g., in tissue regeneration). However, there are a relative few number of known integrin binding motifs compared to all the possible peptide epitope sequences available. Computational tools could help identify novel motifs, but have been limited by the challenges in modeling the binding to integrin domains. We revisit a series of traditional and novel computational tools to assess their performance in identifying novel binding motifs for the I-domain of the α2β1 integrin.

Calixarenes are host molecules that can form complexes with one or more guest molecules, and molecular recognition in calixarenes can be affected by many factors. With a view to establishing molecular recognition rules, the host p-tert-butylcalix[6]arene (TBC6) was crystallized with different guest molecules (cyclohexane, anisole, heptane, toluene, benzene, methyl acetate, ethyl acetate, dichloromethane, tetrahydrofuran and pyridine) and the obtained structures were characterized by X-ray diffraction. With most solvents, 1:1 and/or 1:3 host–guest complexes were formed, although other stoichiometries were also observed with small guest molecules, and crystallization from ethyl acetate produced the unsolvated form. The calculated fill percentage of the TBC6 cavity was ∼55% for apolar guests and significantly lower for polar solvents, indicating that polar molecules can bind to apolar cavities with significantly lower packing coefficients. The most stable crystals were formed by 1:1 host–guest inclusion complexes. The ratio between the apolar surface area and the volume was used to predict the formation of inclusion versus exclusion complexes, with inclusion complexes observed at ratios

The paper is a self-review of works on development of new approaches to formation of mimics of receptor and catalytic sites of biological macromolecules in the structure of highly cross-linked polymer membranes and thin films. The general strategy for formation of the binding sites in molecularly imprinted polymer (MIP) membranes and thin films was described. A selective recognition of a number of food toxins, endocrine disruptors and metabolites is based on the results of computational modeling data for the prediction and optimization of their structure. A strategy proposed for the design of the artificial binding sites in MIP membranes was supported by the research performed by the authors on development of a number of the MIP membrane-based affinity and catalytic biosensors for selective and sensitive measurement (detection limits 0.3–100 nM) of the target analytes. Novel versatile approaches aimed at improving sensitivity of the developed biosensor systems were discussed.

Catalysis in pharma manufacturing processes is typically homogeneous, expensive and with hard catalyst recovery/regeneration. Herein an enzyme-inspired dry-powder molecularly imprinted polymeric (MIP) system was designed for fast, selective oxidation of a cholesterol derivative and easy catalyst regeneration. The strategy involved the synthesis of a template-monomer (T:M) complex followed by the crosslinked polymerization in supercritical carbon dioxide (scCO2). A 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO)-MIP catalyst is obtained after the template cleavage from the matrix, and the oxidation of the NH groups turns available TEMPO moieties within the MIP. The oxidation of benzyl alcohol, 5α-cholestan-3β-ol and cholic acid was fast, in high yield and with selective oxidation capacity.

This study aims to introduce a fluorescence-based chemosensing method for Zn2+ in aqueous suspensions and untreated surface waters, conditions which generally hinder the application of conventional optochemical sensing platforms. A macrocyclic fluoroionophore was covalently bonded to a silica-coated magnetic nanoparticle and applied according to a predetermined protocol for analyzing trace amounts of Zn2+ under rarely investigated conditions. Utilizing the reversible complexation of the immobilized fluoroionophore, rapid regeneration was carried out via simple acidification after the magnetic-assisted solid-phase extraction of the particles. Forming inclusion complexes with Zn2+ with the receptor units of the particles leads to a significant enhancement in fluorescence intensity at 370 nm, above the detection limit of 5 ppb, with a dynamic linear range of quantification of 15–3000 ppb in a pH range of 5.5–7.5. Practical applicability was confirmed by analyzing untreated river water and an aqueous suspension of pumpkin seed flour as real and relevant heterogeneous multicomponent samples of predetermined sample composition and natural Zn2+ content. Our practical approach aims to broaden the applicability range of optochemical sensing platforms for Zn2+.

A series of mono- and dicationic 1,3,5-trisubstituted 2,4,6-triethylbenzenes containing pyridinium groups in combination with aminopyrimidine-/aminopyridine-based recognition units were synthesized and crystallographically studied. The combination of neutral and ionic building blocks represents a promising strategy for the development of effective and selective artificial receptors for anionic substrates. In the crystalline state, the investigated compounds show a tendency to bind the counterion PF6− in the cavity formed by the three functionalized side-arms. The intermolecular interactions with the PF6− ion comprise N-H∙∙∙F and C-H∙∙∙F bonds. Detailed analysis of various supramolecular motifs, including interactions with solvent molecules, provides deeper insights into the processes of molecular recognition. The information obtained is useful in the development of new receptor molecules for anions and in the selection of the most appropriate counterion.

It is of great importance to have sensitive and accurate detection of cis-diol-containing biologically related substances because of their important functions in the research fields of metabolomics, glycomics, and proteomics. Boronic acids can specifically and reversibly interact with 1,2- or 1,3-diols to form five or six cyclic esters. Based on this unique property, boronic acid-based materials have been used as synthetic receptors for the specific recognition and detection of cis-diol-containing species. This review critically summarizes the recent advances with boronic acid-based materials as recognition elements and signal labels for the detection of cis-diol-containing biological species, including ribonucleic acids, glycans, glycoproteins, bacteria, exosomes, and tumor cells. We also address the challenges and future perspectives for developing versatile boronic acid-based materials with various promising applications.

Reactions in water between the Cu2(µ-EGTA) chelate (EGTA = ethylene-bis(oxyethyleneimino)tetraacetate(4-) ion) and Hdap in molar ratios 1:1 and 1:2 yield only blue crystals of the ternary compound [Cu4(μ-EGTA)2(μ-H(N3)dap)2(H2O)2]·7H2O (1), which has been studied via single-crystal X-ray diffraction and various physical methods (thermal stability, spectral and magnetic properties), as well as DFT theoretical calculations. In the crystal, uncoordinated water is disordered. The tetranuclear complex molecule also has some irrelevant disorder in an EGTA-ethylene moiety. In the complex molecule, both bridging organic molecules act as binucleating ligands. There are two distorted five- and two six-coordinated Cu(II) centers. Each half of EGTA acts as a tripodal tetradentate Cu(II) chelator, with a mer-NO2 + O(ether, distal) conformation. Hdap exhibits the tautomer H(N3)dap, with the dissociable H-atom on its less basic N-heterocyclic atom. These features favor the efficient cooperation between Cu-N7 or Cu-N9 bonds with appropriate O-EGTA atoms, as N6-H···O or N3-H···O interligand interactions, respectively. The bridging role of both organics determines the tetranuclear dimensionality of the complex. In this crystal, such molecules associate in zig-zag chains built by alternating π–π interactions between the five- or six-atom rings of Hdap ligands of adjacent molecules. DFT theoretical calculations (using two different theoretical models and characterized by the quantum theory of “atoms in molecules”) reveal the importance of these π–π interactions between Hdap ligands, as well as those corresponding to the referred hydrogen bonds in the contributed tetranuclear molecule.

Specific identification and monitoring of senescent cells are essential for the in-depth understanding and regulation of senescence-related life processes and diseases. Fluorescent sensors providing real-time and in situ information with spatiotemporal resolution are unparalleled tools and have contributed greatly to this field. This review focuses on the recent progress in fluorescent sensors for molecularly targeted imaging and real-time tracking of cellular senescence. The molecular design, sensing mechanisms, and biological activities of the sensors are discussed. The sensors are categorized by the types of markers and targeting ligands. Accordingly, their molecular recognition and fluorescent performance towards senescence biomarkers are summarized. Finally, the perspective and challenges in this field are discussed, which are expected to assist future design of next-generation sensors for monitoring cellular senescence.

MarR family proteins regulate the transcription of multiple antibiotic-resistance genes and are widely found in bacteria and archaea. Recently, a new MarR family gene was identified by genome analysis of the psychrophilic bacterium Paenisporosarcina sp. TG-14, which was isolated from sediment-laden basal ice in Antarctica. In this study, the crystal structure of the MarR protein from Paenisporosarcina sp. TG-14 (PaMarR) was determined at 1.6 Å resolution. In the crystal structure, a novel lipid-type compound (palmitic acid) was found in a deep cavity, which was assumed to be an effector-binding site. Comparative structural analysis of homologous MarR family proteins from a mesophile and a hyperthermophile showed that the DNA-binding domain of PaMarR exhibited relatively high mobility, with a disordered region between the β1 and β2 strands. In addition, structural comparison with other homologous complex structures suggests that this structure constitutes a conformer transformed by palmitic acid. Biochemical analysis also demonstrated that PaMarR binds to cognate DNA, where PaMarR is known to recognize two putative binding sites depending on its molar concentration, indicating that PaMarR binds to its cognate DNA in a stoichiometric manner. The present study provides structural information on the cold-adaptive MarR protein with an aliphatic compound as its putative effector, extending the scope of MarR family protein research.

A series of porphyrin dimers have been prepared and characterized in order to form inclusion complexes with Lindqvist-type polyoxometallates. The synthesis of the porphyrin dimer has been optimized and can serve general purposes. The formation of inclusion complexes has been monitored using spectroscopic methods and moderate affinities with $\log \, K_{\mathrm{assoc}}$ varying from 2.6 to 4.2 have been determined and the parameters governing the formation of the complexes have been examined.

A widely used class of synthetic receptors are resorcin[4]arene-based cavitands. A collection of the most representative studies in this field is reported here, from organic-soluble receptors to those that are water-soluble. Intermolecular forces involved in complex formation – hydrogen bonds, halogen bonds and solvophobic interactions – are discussed with emphasis on the relationship between guest conformation and reactivity in the cavity. The applications of hosts as reaction vessels, chaperones, templates and protecting groups in organic and aqueous media are explored, highlighting how synthetic receptors are modern tools to explore the behavior of molecules in confined spaces.

In this work, a sialic acid (SA)-imprinted thermo-responsive hydrogel layer was prepared for selective capture and release of cancer cells. The SA-imprinting process was performed at 37 °C using thermo-responsive functional monomer, thus generating switchable SA-recognition sites with potent SA binding at 37 °C and weak binding at a lower temperature (e.g., 25 °C). Since SA is often overexpressed at the glycan terminals of cell membrane proteins or lipids, the SA-imprinted hydrogel layer could be used for selective cancer cell recognition. Our results confirmed that the hydrogel layer could efficiently capture cancer cells from not only the culture medium but also the real blood samples. In addition, the captured cells could be non-invasively released by lowing the temperature. Considering the non-invasive processing mode, considerable capture efficiency, good cell selectivity, as well as the more stable and durable SA-imprinted sites compared to natural antibodies or receptors, this thermo-responsive hydrogel layer could be used as a promising and general platform for cell-based cancer diagnosis.

Hexahexyloxycalix[6]arene 2b leads to the endo-cavity complexation of linear and branched alkylammonium guests showing a conformational adaptive behavior in CDCl3 solution. Linear n-pentylammonium guest 6a+ induces the cone conformation of 2b at the expense of the 1,2,3-alternate, which is the most abundant conformer of 2b in the absence of a guest. In a different way, branched alkylammonium guests, such as tert-butylammonium 6b+ and isopropylammonium 6c+, select the 1,2,3-alternate as the favored 2b conformation (6b+/6c+⊂2b1,2,3-alt), but other complexes in which 2b adopts different conformations, namely, 6b+/6c+⊂2bcone, 6b+/6c+⊂2bpaco, and 6b+/6c+⊂2b1,2-alt, have also been revealed. Binding constant values determined via NMR experiments indicated that the 1,2,3-alternate was the best-fitting 2b conformation for the complexation of branched alkylammonium guests, followed by cone > paco > 1,2-alt. Our NCI and NBO calculations suggest that the H-bonding interactions (+N–H···O) between the ammonium group of the guest and the oxygen atoms of calixarene 2b are the main determinants of the stability order of the four complexes. These interactions are weakened by increasing the guest steric encumbrance, thus leading to a lower binding affinity. Two stabilizing H-bonds are possible with the 1,2,3-alt- and cone-2b conformations, whereas only one H-bond is possible with the other paco- and 1,2-alt-2b stereoisomers.

Biosensors show promising prospects in the assays of various targets due to their advantages of high sensitivity, good selectivity and rapid response. Molecular recognition is a key event of biosensors, which usually involves the interaction of antigen–antibody, aptamer–target, lectin–sugar, boronic acid–diol, metal chelation and DNA hybridization. Metal ions or complexes can specifically recognize phosphate groups in peptides or proteins, obviating the use of biorecognition elements. In this review, we summarized the design and applications of biosensors with metal ion–phosphate chelation interaction for molecular recognition. The sensing techniques include electrochemistry, fluorescence, colorimetry and so on.

The development of supramolecular chemistry has always been accompanied by the innovation of macrocyclic hosts. The synthesis of novel macrocycles with unique structures and functions will bring new development opportunities for supramolecular chemistry. As a new generation of macrocyclic hosts, biphenarenes have customizable cavity sizes and diverse backbones, overcoming the limitation that the cavities of traditionally popular macrocyclic hosts are generally smaller than 10 Å. These features undoubtedly endow biphenarenes with distinguished host–guest properties, which have attracted more and more attention. In this review, the structural characteristics and molecular recognition properties of biphenarenes are summarized. In addition, the applications of biphenarenes in adsorption and separation, drug delivery, fluorescence sensing and other fields are introduced. Hopefully, this review will provide a reference for the study of macrocyclic arenes, especially biphenarenes.

The paper describes the use of native β-cyclodextrin (CD) for the modification of silver nanoparticles (AgNPs) in order to improve the determination of the anticancer drug methotrexate (MTX) using surface-enhanced Raman spectroscopy (SERS). A control experiment with unmodified AgNPs showed that the strong SERS signal of MTX can only be achieved in alkaline media. However, competitive interactions and the strong background signal of human body fluid components significantly challenge MTX determination in real samples. While previous reports propose the use of thorough sample pretreatment (e.g., solid phase extraction), the application of CD-modified AgNPs increases the SERS signal of MTX in neutral media by seven times which enables simplifying the analysis and improving its accuracy by reducing the influence of endogenous components of body fluids. A detailed study of the synthesis conditions (CD concentration and reaction time) and SERS registration conditions (pH, NaCl concentration, dilution of urine samples) was performed to maximize the analytical signal and signal-to-noise ratio. The final assay was tested for MTX determination in artificially spiked samples of real human urine. The results demonstrated that MTX can be determined within the concentration range suitable for therapeutic drug monitoring (20–300 μg mL−1) with satisfactory precision (6–15% RSD), accuracy (95–111% apparent recovery), and limit of detection (0.3 μg mL−1).