Molecular Modeling of Histamine Receptors—Recent Advances in Drug Discovery

The recent developments of fast reliable docking, virtual screening and other algorithms gave rise to discovery of many novel ligands of histamine receptors that could be used for treatment of allergic inflammatory disorders, central nervous system pathologies, pain, cancer and obesity. Furthermore, the pharmacological profiles of ligands clearly indicate that these receptors may be considered as targets not only for selective but also for multi-target drugs that could be used for treatment of complex disorders such as Alzheimer’s disease. Therefore, analysis of protein-ligand recognition in the binding site of histamine receptors and also other molecular targets has become a valuable tool in drug design toolkit. This review covers the period 2014–2020 in the field of theoretical investigations of histamine receptors mostly based on molecular modeling as well as the experimental characterization of novel ligands of these receptors.     

Calixarene-based multivalent ligands

Multivalency is a powerful concept which explains the strong binding observed in biological systems and guides the design and synthesis of ligands for self-assembly and molecular recognition in Chemistry. The phenol-formaldehyde cyclic oligomers, called calixarenes, have been used as scaffolds for the synthesis of multivalent ligands thanks to the fact that they have a variable number of reactive positions for attaching the ligating functions, well defined conformational properties and, in some cases, cavities of molecular dimensions eventually able to encapsulate guest species. This tutorial review illustrates the fundamental aspects of multivalency and the properties of calixarene-based multivalent ligands in lectin binding and inhibition, DNA condensation and cell transfection, protein surface recognition, self-assembly, crystal engineering, and nanofabrication.     

Dynamics of membrane adhesion: the role of polyethylene glycol spacers, ligand-receptor bond strength, and rupture pathway

Biological adhesion typically occurs through discrete cross bridges between complementary molecules on adjacent membranes. Here we report quantitative measurements of the binding distance between a lipid membrane functionalized with ligands on flexible polymer tether chains and a second membrane bearing complementary receptors using the surface force apparatus technique. The binding distance is shown to increase as a function of polymer tether length. Upon separation, adhesive failure occurs not at the strong ligand-receptor bond but primarily through the mechanical pullout of cross-bridging polymer tethers from the membrane. We summarize these measurements of complementary membrane adhesion dynamics using an energy-state diagram that encompasses the energetics of the polymer tether, ligand-receptor bond strength, and number of cross bridges formed.     

Novel Approaches To Design Glycan-Based Antibacterial Inhibitors

The interactions between bacterial lectins and carbohydrates on the host cell surface can mediate bacterial adhesion, invasion, and immune evasion. Multivalency plays a key role in these binding events. However, additional molecular mechanisms greatly impact multivalent binding recognition. To develop specific and effective bacterial inhibitors, a deeper understanding of the complex underlying mechanisms of bacterial adhesion processes is necessary. By interfering with bacterial adhesion, synthetic multivalent glycoconjugates do not only have the potential to improve or replace antibiotic treatments, but also represent useful tools to study carbohydrate-pathogen interactions. In this review, we highlight a few recent advances in the synthesis and application of synthetic glycan-based scaffolds to uncover the nature of glycan-bacteria interactions and to design efficient bacterial inhibitors.     

Novel recognition mechanisms in biological adhesion

Molecular recognition is generally thought of in terms of bond formation between unique sites on host and complementary guest molecules, but recent studies have revealed new complexities in biological recognition at cell. Adhesion between cell surfaces similarly involves specific interactions between analogous ligands and receptors. Recent force measurements, however, suggest that cell adhesion proteins may bind via multiple interaction sites that can form in a sequential manner. Other studies further show that in some instances, the principal recognition event may not be receptor–ligand docking, but the assembly of a complex pattern of many receptors and ligands.     

Evaluation of the carbohydrate recognition domain of the bacterial adhesin FimH: Design, synthesis and binding properties of mannoside ligands

Fimbriae are proteinogeneous appendages on the surface of bacteria, which mediate bacterial adhesion to the host cell glycocalyx. The so-called type 1 fimbriae exhibit specificity for alpha-d-mannosides and, therefore, they are assumed to mediate bacterial adhesion via the interaction of a fimbrial lectin and alpha-d-mannosyl residues exposed on the host cell surface. This carbohydrate-specific adhesive protein subunit of type 1 fimbriae has been identified as a protein called FimH. The crystal structure of this lectin is known and, based on this information, the molecular details of the interaction of mannoside ligands and FimH are addressed in this paper. Computer-based docking methods were used to evaluate known ligands as well as to design new ones. Then, a series of new mannosides with extended aglycon was synthesized and tested as inhibitors of type 1 fimbriae-mediated bacterial adhesion in an ELISA. The results obtained were compared to the predictions and findings as delivered by molecular modeling. This study led to an improved understanding of the ligand-receptor interactions under investigation.     

Glyco-macroligand microarray with controlled orientation and glycan density

We report a new type of glycan microarray, namely, oriented and density-controlled glyco-macroligand microarray based on end-point immobilization of glycopolymer that was accompanied with boronic acid (BA) ligands in different sizes as detachable "temporary molecular spacers". Briefly, an O-cyanate chain-end functionalized lactose-containing glycopolymer was pre-complexed with polyacrylamide-BA, lysozyme-BA, and bovine serum albumin (BSA)-BA conjugates as macromolecular spacers first and then immobilized onto an amine-functionalized glass slide via isourea bond formation both at pH 10.3, respectively. Subsequently, the macromolecular spacers were detached from the immobilized glycopolymers at pH 7.4 so as to afford the oriented and density controlled glycopolymer microarrays. The spaced glycopolymer microarray showed enhanced lectin (Arachis hypogaea) binding compared to a non-spaced one. Among them, the polyacrylamide-BA spaced glycopolymer showed the highest level of lectin binding compared to lysozyme-BA- and BSA-BA-spaced glycopolymers. Furthermore, SPR results confirmed the same trend of density-dependent lectin binding as the glycoarray. This glyco-macroligand microarray platform permits variations of glycan density in the polymer, glycopolymer density and its orientation on the microarray surface and thus will provide a versatile tool for profiling glycan recognition for both basic biological research and practical applications.     

Optimizing saccharide-directed molecular delivery to biological receptors: design, synthesis, and biological evaluation of glycodendrimer-cyclodextrin conjugates

Dendritic beta-cyclodextrin (betaCD) derivatives bearing multivalent mannosyl ligands have been prepared and assessed for their binding efficiency toward the tetrameric plant lectin concanavalin A (Con A) and a mammalian mannose/fucose specific cell surface receptor from macrophages. The synthetic strategy exploits the reactivity between isothiocyanate and amine functionalities for the high-yielding assembly via thioureido links of the various building blocks, including host, spacer, branching, and carbohydrate ligand elements. The methodology has been applied to the preparation of a series of betaCD-polymannoside scaffolds differing in the ligand valency and geometry. This series allowed us to explore: (i) The effects of the glycodendritic architecture on the binding efficiency; (ii) the mutual influence between the cyclodextrin core and the glycodendritic moieties on the molecular inclusion and lectin-binding properties; and (iii) the consequence of inclusion complex formation, using the anticancer drug docetaxel (Taxotère) as a target guest, on biological recognition. Our results confirm the high drug solubilization capability of this new type of betaCD-dendrimer construct and indicate that subtle changes in the architecture of the conjugate may have important consequences on receptor affinity. Interestingly, the host-guest interaction can be monitored to build up supramolecular dynamic glycoclusters with increased lectin affinity. Alternatively, the information obtained from the structure-lectin-binding avidity-inclusion capability studies has been put forward in the design of very efficient molecular transporters for docetaxel based on glycodendritic CD dimers.     

Synthesis and Langmuir studies of bivalent and monovalent alpha-D-mannopyranosides with lectin Con A

Highly avid interaction between carbohydrate ligands and lectin receptors nominally requires the ligand presentation in a clustered form. We present herein an approach involving Langmuir monolayer formation of the sugar ligands and the assessment of their lectin binding at the air-water interface. Bivalent alpha-D-mannopyranoside containing the glycolipid ligand was used to study its binding profiles with lectin Con A, in comparison to the corresponding monovalent glycolipid. In addition to the bivalent and monovalent nature of the glycolipid ligands at the molecular level, the ligand densities at the monolayer level were varied with the aid of a nonsugar lipid molecule so as to obtain mixed monolayers with various sugar-nonsugar ratios. Lectin binding of bivalent and monovalent ligands at different ratios was monitored by differential changes in the surface area per molecule of the mixed monolayer, with and without the lectin. The present study shows that maximal binding of the lectin to the bivalent ligand occurs at lower sugar densities at the interface ( approximately 10% sugar in the mixed monolayer) than for that of the monovalent ligand ( approximately 20% sugar in the mixed monolayer). It is observed that complete coverage of the monolayer with only the sugar ligands does not allow all of the sugars to be functionally active.     

Anticalins versus antibodies: made-to-order binding proteins for small molecules

Engineering proteins to bind small molecules presents a challenge as daunting as drug discovery, for both hinge upon our understanding of receptor-ligand molecular recognition. However, powerful techniques from combinatorial molecular biology can be used to rapidly select artificial receptors. While traditionally researchers have relied upon antibody technologies as a source of new binding proteins, the lipocalin scaffold has recently emerged as an adaptable receptor for small molecule binding. 'Anticalins', engineered lipocalin variants, offer some advantages over traditional antibody technology and illuminate features of molecular recognition between receptors and small molecule ligands.     

利用表面上的小分子控制细胞黏附

细胞黏附是重要的生理过程,多细胞生物体中大部分种类的细胞都依赖于在表面的黏附而进行其正常生理活动。细胞的黏附需要固定在表面的有机分子（例如蛋白质或多肽）作配体。我们利用表面小分子模拟蛋白质或多肽作为配体,通过与细胞膜上受体结合,促进细胞黏附到表面。聚乙二醇（PEG）可以抵抗细胞在表面的黏附,我们利用含有PEG的表面小分子来调节细胞黏附。细胞表面的受体与胞外基质表面的配体结合是一个动态过程,在适宜时间和空间发生的时候,细胞就会产生运动和迁移,细胞的迁移也是重要的生理过程。本文主要介绍近年来利用小分子的表面化学和微纳米结构控制细胞在表面的黏附和迁移。     

Multivalent gold glycoclusters: high affinity molecular recognition by bacterial lectin PA-IL

Multivalent protein-carbohydrate interactions are involved in the initial stages of many fundamental biological and pathological processes through lectin-carbohydrate binding. The design of high affinity ligands is therefore necessary to study, inhibit and control the processes governed through carbohydrate recognition by their lectin receptors. Carbohydrate-functionalised gold nanoclusters (glyconanoparticles, GNPs) show promising potential as multivalent tools for studies in fundamental glycobiology research as well as biomedical applications. Here we present the synthesis and characterisation of galactose functionalised GNPs and their effectiveness as binding partners for PA-IL lectin from Pseudomonas aeruginosa. Interactions were evaluated by hemagglutination inhibition (HIA), surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) assays. Results show that the gold nanoparticle platform displays a significant cluster glycoside effect for presenting carbohydrate ligands with almost a 3000-fold increase in binding compared with a monovalent reference probe in free solution. The most effective GNP exhibited a dissociation constant (K(d)) of 50 nM per monosaccharide, the most effective ligand of PA-IL measured to date; another demonstration of the potential of glyco-nanotechnology towards multivalent tools and potent anti-adhesives for the prevention of pathogen invasion. The influence of ligand presentation density on their recognition by protein receptors is also demonstrated.     

Docking, synthesis, and NMR studies of mannosyl trisaccharide ligands for DC-SIGN lectin

DC-SIGN, a lectin, which presents at the surface of immature dendritic cells, constitutes nowadays a promising target for the design of new antiviral drugs. This lectin recognizes highly glycosylated proteins present at the surface of several pathogens such as HIV, Ebola virus, Candida albicans, Mycobacterium tuberculosis, etc. Understanding the binding mode of this lectin is a topic of tremendous interest and will permit a rational design of new and more selective ligands. Here, we present computational and experimental tools to study the interaction of di- and trisaccharides with DC-SIGN. Docking analysis of complexes involving mannosyl di- and trisaccharides and the carbohydrate recognition domain (CRD) of DC-SIGN have been performed. Trisaccharides Manalpha1,2[Manalpha1,6]Man 1 and Manalpha1,3[Manalpha1,6]Man 2 were synthesized from an orthogonally protected mannose as a common intermediate. Using these ligands and the soluble extracellular domain (ECD) of DC-SIGN, NMR experiments based on STD and transfer-NOE were performed providing additional information. Conformational analysis of the mannosyl ligands in the free and bound states was done. These studies have demonstrated that terminal mannoses at positions 2 or 3 in the trisaccharides are the most important moiety and present the strongest contact with the binding site of the lectin. Multiple binding modes could be proposed and therefore should be considered in the design of new ligands.     

Progress in DNA Aptamers as Recognition Components for Protein Functional Regulation

Proteins play a central role in all domains of life, and precise regulation of their activity is essential for understanding the related biological processes and therapeutic functions. Nucleic acid aptamers, the molecular recognition components derived from systematic evolution of ligands by exponential enrichment(SELEX), can specifically identify proteins with antibody-like recognition characteristics and help to regulate their activity. This minireview covers the SELEX-based selection of protein-binding aptamers, membrane protein analytical techniques based on aptamer-mediated target recognition, aptamer-mediated functional regulation of proteins, including membrane receptors and non-membrane proteins(thrombin as a model), as well as the potential challenges and prospects regarding aptamer-mediated protein manipulation, aiming to supply some useful information for researchers in this field.     

Coupling a natural receptor protein with an artificial receptor to afford a semisynthetic fluorescent biosensor

An artificial receptor and a signal transducer have been engineered on a lectin (saccharide-binding protein) surface by a post-photoaffinity labeling modification method. Saccharide binding can be directly and selectively read out by the fluorescence changes of the fluorophore via photoinduced electron transfer (PET) mode. Fluorescence titration with various saccharides reveals that molecular recognition by the artificial receptor is successfully coupled to the native binding site of the lectin, producing a novel fluorescent saccharide biosensor showing modulated specificity and enhanced affinity. Designed cooperativity between artificial and native molecular recognition modules was quantitatively demonstrated by the comparison of the binding affinities, and it represents a new strategy in molecular recognition. By using appropriate artificial receptors and various native lectins, this approach may provide many new semisynthetic biosensors for saccharide derivatives such as glycolipids and glycopeptides/proteins. An extended library of lectin-based biosensors is envisioned to be useful for glycome research, a newly emerging field of the post-genomic era.     

Influencing receptor-ligand binding mechanisms with multivalent ligand architecture

Multivalent ligands can function as inhibitors or effectors of biological processes. Potent inhibitory activity can arise from the high functional affinities of multivalent ligand-receptor interactions. Effector functions, however, are influenced not only by apparent affinities but also by alternate factors, including the ability of a ligand to cluster receptors. Little is known about the molecular features of a multivalent ligand that determine whether it will function as an inhibitor or effector. We envisioned that, by altering multivalent ligand architecture, ligands with preferences for different binding mechanisms would be generated. To this end, a series of 28 ligands possessing structural diversity was synthesized. This series provides the means to explore the effects of ligand architecture on the inhibition and clustering of a model protein, the lectin concanavalin A (Con A). The structural parameters that were varied include scaffold shape, size, valency, and density of binding elements. We found that ligands with certain architectures are effective inhibitors, but others mediate receptor clustering. Specifically, high molecular weight, polydisperse polyvalent ligands are effective inhibitors of Con A binding, whereas linear oligomeric ligands generated by the ring-opening metathesis polymerization have structural properties that favor clustering. The shape of a multivalent ligand also influences specific aspects of receptor clustering. These include the rate at which the receptor is clustered, the number of receptors in the clusters, and the average interreceptor distance. Our results indicate that the architecture of a multivalent ligand is a key parameter in determining its activity as an inhibitor or effector. Diversity-oriented syntheses of multivalent ligands coupled with effective assays that can be used to compare the contributions of different binding parameters may afford ligands that function by specific mechanisms.     

Multivalent Gold Glycoclusters: High Affinity Molecular Recognition by Bacterial Lectin PA‐IL

Multivalent protein‐carbohydrate interactions are involved in the initial stages of many fundamental biological and pathological processes through lectin–carbohydrate binding. The design of high affinity ligands is therefore necessary to study, inhibit and control the processes governed through carbohydrate recognition by their lectin receptors. Carbohydrate‐functionalised gold nanoclusters (glyconanoparticles, GNPs) show promising potential as multivalent tools for studies in fundamental glycobiology research as well as biomedical applications. Here we present the synthesis and characterisation of galactose functionalised GNPs and their effectiveness as binding partners for PA‐IL lectin from Pseudomonas aeruginosa. Interactions were evaluated by hemagglutination inhibition (HIA), surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) assays. Results show that the gold nanoparticle platform displays a significant cluster glycoside effect for presenting carbohydrate ligands with almost a 3000‐fold increase in binding compared with a monovalent reference probe in free solution. The most effective GNP exhibited a dissociation constant (K_d) of 50 nM per monosaccharide, the most effective ligand of PA‐IL measured to date; another demonstration of the potential of glyco‐nanotechnology towards multivalent tools and potent anti‐adhesives for the prevention of pathogen invasion. The influence of ligand presentation density on their recognition by protein receptors is also demonstrated.     

Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes

Despite its central role in structure based drug design the determination of the binding mode (position, orientation and conformation in addition to protonation and tautomeric states) of small heteromolecular ligands in protein:ligand complexes based on medium resolution X-ray diffraction data is highly challenging. In this perspective we demonstrate how a combination of molecular dynamics simulations and free energy (FE) calculations can be used to correct and identify thermodynamically stable binding modes of ligands in X-ray crystal complexes. The consequences of inappropriate ligand structure, force field and the absence of electrostatics during X-ray refinement are highlighted. The implications of such uncertainties and errors for the validation of virtual screening and fragment-based drug design based on high throughput X-ray crystallography are discussed with possible solutions and guidelines.     

Biophysical approaches to G protein-coupled receptors: Structure, function and dynamics

G protein-coupled receptors (GPCR) represent a large family of drug targets for which there is no high-resolution structural information. In order to understand the mechanisms of ligand recognition and receptor activation, there is a strong need for novel biophysical methods. In this Perspective we provide an overview of recent experimental approaches used to explore the molecular architecture and dynamics of GPCR and their interactions with ligands and G proteins using biophysical, non-crystallographic, methods.     

Non-carbohydrate inhibitors of the lectin DC-SIGN

The C-type lectin dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin (DC-SIGN) is found on the surface of dendritic cells. It can mediate adhesion between dendritic cells and T lymphocytes and facilitate antigen capture and presentation. Many pathogens can exploit DC-SIGN binding for nefarious purposes. For example, DC-SIGN can facilitate the dissemination of viruses, like HIV-1. Alternatively, some microbes (e.g., Mycobacterium tuberculosis) use their ability to interact with DC-SIGN to evade immune detection. The diverse roles attributed to DC-SIGN provide impetus to identify ligands that can be used to explore its different functions. Such compounds also could serve as therapeutic leads. Most of the DC-SIGN ligands studied previously are mannose- or fucose-derived monosaccharides or oligosaccharides with inhibitory constants in the range of 0.1-10 mM. To identify monovalent ligands with more powerful DC-SIGN blocking properties, we devised a high-throughput fluorescence-based competition assay. This assay afforded potent non-carbohydrate, small molecule inhibitors (IC50 values of 1.6-10 microM). These compounds block not only DC-SIGN-carbohydrate interactions but also DC-SIGN-mediated cell adhesion. Thus, we anticipate that these non-carbohydrate inhibitors can be used to illuminate the role of DC-SIGN in pathogenesis and immune function.