Selective Recognition of Amino Acids and Peptides by Small Supramolecular Receptors

To this day, the recognition and high affinity binding of biomolecules in water by synthetic receptors remains challenging, while the necessity for systems for their sensing, transport and modulation persists. This problematic is prevalent for the recognition of peptides, which not only have key roles in many biochemical pathways, as well as having pharmacological and biotechnological applications, but also frequently serve as models for the study of proteins. Taking inspiration in nature and on the interactions that occur between several receptors and peptide sequences, many researchers have developed and applied a variety of different synthetic receptors, as is the case of macrocyclic compounds, molecular imprinted polymers, organometallic cages, among others, to bind amino acids, small peptides and proteins. In this critical review, we present and discuss selected examples of synthetic receptors for amino acids and peptides, with a greater focus on supramolecular receptors, which show great promise for the selective recognition of these biomolecules in physiological conditions. We decided to focus preferentially on small synthetic receptors (leaving out of this review high molecular weight polymeric systems) for which more detailed and accurate molecular level information regarding the main structural and thermodynamic features of the receptor biomolecule assemblies is available.     

Molecular recognition of carbohydrates with artificial receptors: mimicking the binding motifs found in the crystal structures of protein-carbohydrate complexes

The binding motifs found in the crystal structures of protein-carbohydrate complexes have been successfully mimicked with simple acyclic pyridine- and pyrimidine-based receptors. A full discussion of the recognition motifs observed in the crystal structures of complexes of receptors 1 and 3 with glucopyranosides 4a and 4b is provided. A remarkable similarity of these motifs to those observed in the crystal structures of sugar-binding proteins and those found by molecular modeling is shown. In addition, the recognition properties of the new pyrimidine receptor 3 toward monosaccharides 4-6 are described. This molecule has been established as a highly effective receptor for beta-glucopyranosides.     

Resonance surface plasmon spectroscopy: low molecular weight substrate binding to cytochrome p450

A new detection mechanism has been developed for low molecular weight substrate binding to heme proteins based on resonance localized surface plasmon spectroscopy. Cytochrome P450 has strong electronic transitions in the visible wavelength region. Upon binding of a substrate molecule (e.g., camphor), the absorption band of cytochrome P450 shifts to shorter wavelength. The event of camphor binding to a nanoparticle surface modified with cytochrome P450 protein receptors is monitored using UV-vis spectroscopy. It is observed for the first time that the binding of the substrate molecules to the protein receptor induces a blue-shift in the localized surface plasmon resonance (LSPR) of the nanosensors. The coupling between the molecular resonance of the substrate-free and substrate-bound cytochrome P450 proteins and the nanoparticles' LSPR leads to a highly wavelength-dependent LSPR response. When the LSPR of the nanoparticles is located at a wavelength distant from the cytochrome P450 resonance, an average of approximately 19 nm red-shift is observed upon cytochrome P450 binding to the nanoparticles and a approximately 6 nm blue-shift is observed upon camphor binding However, this response is significantly amplified approximately 3 to 5 times when the LSPR of the nanoparticles is located at a slightly longer wavelength than the cytochrome P450 resonance, that is, a 66.2 nm red-shift upon cytochrome P450 binding and a 34.7 nm blue-shift upon camphor binding. This is the first example of the detection of small molecules binding to a protein modified nanoparticle surface on the basis of LSPR.     

Impact of the Core Chemistry of Self-Assembled Spherical Nucleic Acids on their In Vitro Fate

Nucleic acid therapeutics (NATs), such as mRNA, small interfering RNA or antisense oligonucleotides are extremely efficient tools to modulate gene expression and tackle otherwise undruggable diseases. Spherical nucleic acids (SNAs) can efficiently deliver small NATs to cells while protecting their payload from nucleases, and have improved biodistribution and muted immune activation. Self-assembled SNAs have emerged as nanostructures made from a single DNA-polymer conjugate with similar favorable properties as well as small molecule encapsulation. However, because they maintain their structure by non-covalent interactions, they might suffer from disassembly in biologically relevant conditions, especially with regard to their interaction with serum proteins. Here, we report a systematic study of the factors that govern the fate of self-assembled SNAs. Varying the core chemistry and using stimuli-responsive disulfide crosslinking, we show that extracellular stability upon binding with serum proteins is important for recognition by membrane receptors, triggering cellular uptake. At the same time, intracellular dissociation is required for efficient therapeutic release. Disulfide-crosslinked SNAs combine these two properties and result in efficient and non-toxic unaided gene silencing therapeutics. We anticipate these investigations will help the translation of promising self-assembled structures towards in vivo gene silencing applications.     

Helical Propensity in an Intrinsically Disordered Protein Accelerates Ligand Binding

Many intrinsically disordered proteins fold upon binding to other macromolecules. The secondary structure present in the well‐ordered complex is often formed transiently in the unbound state. The consequence of such transient structure for the binding process is, however, not clear. The activation domain of the activator for thyroid hormone and retinoid receptors (ACTR) is intrinsically disordered and folds upon binding to the nuclear coactivator binding domain (NCBD) of the CREB binding protein. A number of mutants was designed that selectively perturbs the amount of secondary structure in unbound ACTR without interfering with the intermolecular interactions between ACTR and NCBD. Using NMR spectroscopy and fluorescence‐monitored stopped‐flow kinetic measurements we show that the secondary structure content in helix 1 of ACTR indeed influences the binding kinetics. The results thus support the notion of preformed secondary structure as an important determinant for molecular recognition in intrinsically disordered proteins.     

靶向Toll样受体4的小分子调节剂

Toll样受体(Toll-like receptors,TLRs)是进化保守的天然免疫模式识别受体,能够识别外源的病原菌相关分子模式(Pathogen-associated molecular patterns,PAMPs)、内源的损害相关分子模式(Damage-associated molecular patterns,DAMPs)和异源物相关分子模式(Xenobiotic-associated molecular patterns),诱导炎症免疫反应。 其中,TLR4(Toll-like receptor 4)是目前研究最为广泛的Toll样受体之一,TLR4是脂多糖(lipopoiysaccharide,LPS)的主要受体,LPS激活的TLR4信号通路在炎症信号的传递中发挥着重要作用,而此信号转导需要通过LPS与TLR4及其附属蛋白髓样分化因子2(myeloid differentiation factor 2,MD-2)的相互作用来实现。 因此,TLR4/MD-2成为炎症反应和免疫调控最重要的研究热点。 本文综述靶向TLR4/MD-2的小分子激动剂和抑制剂的研究进展,以进一步理解TLR4小分子调节剂与其相互作用的复杂性,帮助靶向TLR4/MD-2的免疫调节剂药物发现。     

Molecular recognition and fluorescence sensing of monophosphorylated peptides in aqueous solution by bis(zinc(II)-dipicolylamine)-based artificial receptors

The phosphorylation of proteins represents a ubiquitous mechanism for the cellular signal control of many different processes, and thus selective recognition and sensing of phosphorylated peptides and proteins in aqueous solution should be regarded as important targets in the research field of molecular recognition. We now describe the design of fluorescent chemosensors bearing two zinc ions coordinated to distinct dipicolylamine (Dpa) sites. Fluorescence titration experiments show the selective and strong binding toward phosphate derivatives in aqueous solution. On the basis of (1)H NMR and (31)P NMR studies, and the single-crystal X-ray structural analysis, it is clear that two Zn(Dpa) units of the binuclear receptors cooperatively act to bind a phosphate site of these derivatives. Good agreement of the binding affinity estimated by isothermal titration calorimetry with fluorescence titration measurements revealed that these two receptors can fluorometrically sense several phosphorylated peptides that have consensus sequences modified with natural kinases. These chemosensors display the following significant features: (i) clear distinction between phosphorylated and nonphosphorylated peptides, (ii) sequence-dependent recognition, and (iii) strong binding to a negatively charged phosphorylated peptide, all of which can be mainly ascribed to coordination chemistry and electrostatic interactions between the receptors and the corresponding peptides. Detailed titration experiments clarified that the phosphate anion-assisted coordination of the second Zn(II) to the binuclear receptors is crucial for the fluorescence intensification upon binding to the phosphorylated derivatives. In addition, it is demonstrated that the binuclear receptors can be useful for the convenient fluorescent detection of a natural phosphatase (PTP1B) catalyzed dephosphorylation.     

Sliding on DNA: From Peptides to Small Molecules

Many DNA binding proteins utilize one‐dimensional (1D) diffusion along DNA to accelerate their DNA target recognition. Although 1D diffusion of proteins along DNA has been studied for decades, a quantitative understanding is only beginning to emerge and few chemical tools are available to apply 1D diffusion as a design principle. Recently, we discovered that peptides can bind and slide along DNA—even transporting cargo along DNA. Such molecules are known as molecular sleds. Here, to advance our understanding of structure–function relationships governing sequence nonspecific DNA interaction of natural molecular sleds and to explore the potential for controlling sliding activity, we test the DNA binding and sliding activities of chemically modified peptides and analogs, and show that synthetic small molecules can slide on DNA. We found new ways to control molecular sled activity, novel small‐molecule synthetic sleds, and molecular sled activity in N‐methylpyrrole/N‐methylimidazole polyamides that helps explain how these molecules locate rare target sites.     

Photopolymerization and photostructuring of molecularly imprinted polymers for sensor applications—A review

Biosensors are already well established in modern analytical chemistry, and have become important tools for clinical diagnostics, environmental analysis, production monitoring, drug detection or screening. They are based on the specific molecular recognition of a target molecule by a biological receptor such as an antibody or an enzyme. Synthetic biomimetic receptors like molecularly imprinted polymers (MIPs) have been shown to be a potential alternative to biomolecules as recognition element for biosensing. Produced by a templating process at the molecular level, MIPs are capable of recognizing and binding target molecules with similar specificity and selectivity to their natural analogues. One of the main challenges in MIP sensor development is the miniaturization of MIP structures and their interfacing with the transducer or with a microchip. Photostructuring appears thereby as one of the most suitable methods for patterning MIPs at the micro and nano scale, directly on the transducer surface. In the present review, a general overview on MIPs in biosensing applications is given, and the photopolymerization and photopatterning of MIPs are particularly described.     

Structural Insights into Ligand—Receptor Interactions Involved in Biased Agonism of G-Protein Coupled Receptors

G protein-coupled receptors (GPCRs) are versatile signaling proteins that mediate complex cellular responses to hormones and neurotransmitters. Ligand directed signaling is observed when agonists, upon binding to the same receptor, trigger significantly different configuration of intracellular events. The current work reviews the structurally defined ligand – receptor interactions that can be related to specific molecular mechanisms of ligand directed signaling across different receptors belonging to class A of GPCRs. Recent advances in GPCR structural biology allow for mapping receptors’ binding sites with residues particularly important in recognition of ligands’ structural features that are responsible for biased signaling. Various studies show particular role of specific residues lining the extended ligand binding domains, biased agonists may alternatively affect their interhelical interactions and flexibility what can be translated into intracellular loop rearrangements. Studies on opioid and angiotensin receptors indicate importance of residues located deeper within the binding cavity and direct interactions with receptor residues linking the ortosteric ligand binding site with the intracellular transducer binding domain. Collection of results across different receptors may suggest elements of common molecular mechanisms which are responsible for passing alternative signals from biased agonists.     

A rigid lanthanide binding tag for NMR structural analysis of carbohydrates

The first synthesis of a carbohydrate molecule covalently bound to a rigid lanthanide binding tag is reported. This derivative has been designed as a new tool to provide long-range restraints for structural elucidation and molecular recognition studies of carbohydrates, thus extending the methodology already developed for proteins.     

表面分子印迹聚合物纳米线用于蛋白质的特异性识别

手性配体交换色谱是拆分手性化合物,特别是氨基酸和羟基酸对映体的一种有效方法,通常以光活性氨基酸或其衍生物为手性选择子,可通过键合及涂渍制备手性固定相,也可作为流动相添加剂来实现手性配体交换色谱分离分析,配体交换键合固定相需要完成载体和手性选择子之间的偶联,键合量因受到载体和制备条件的影响而较难控制,且柱效较低。     

基于银增强金标记物的阳极溶出伏安免疫分析用于补体第三成分的测定

分子印迹是制备对特定分子具有专一性结合能力的聚合物的技术,所制备的聚合物被称为分子印迹聚合物（Molecularly imprinted polymers,MIPs）,此类聚合物在分离提纯、模拟酶和传感器等方面均显示出广阔的应用前景,迄今,小分子化合物的印迹技术已经十分成熟。     

二酰胺吡啶修饰杯[4]芳烃与脂肪二羧酸主客体相互作用的理论研究

本文用分子力学和分子动力学方法对二酰胺吡啶修饰杯[4]芳烃与脂肪二羧酸的主客体相互作用进行了研究.     

Spectrophotometric and calorimetric titration studies on molecular recognition of camphor and borneol by nucleobase-modified beta-cyclodextrins

A series of modified beta-cyclodextrins with nucleobase substituents, that is, mono(6-ade-6-deoxy)-beta-cyclodextrin (2) and mono(6-ura-6-deoxy)-beta-cyclodextrin (3) as well as mono(6-thy-6-deoxy)-beta-cyclodextrin (4), were selected as molecular receptors to investigate their conformation and inclusion complexation behaviors with some chiral molecules, that is, (+)-camphor, (-)-camphor, (+)-borneol, and (-)-borneol, by spectrophotometric and microcalorimetric titrations in aqueous phosphate buffer solution (pH 7.2) at 298.15 K. Circular dichroism and NMR studies demonstrated that these nucleobase-modified beta-cyclodextrins adopted a co-inclusion mode upon complexation with guest molecules; that is, the originally self-included nucleobase substituents of the host did not move out from the beta-cyclodextrin cavity, but coexisted with guest molecule in the beta-cyclodextrin cavity upon inclusion complexation. Significantly, these nucleobase-modified beta-cyclodextrins efficiently enhanced the molecular binding ability and the chiral recognition ability of native beta-cyclodextrin, displaying enantioselectivity up to 3.7 for (+)-camphor/(-)-camphor pair by 2 and 3.5 for (-)-borneol/(+)-borneol pair by 3. The enhanced molecular/chiral recognition abilities of 2-4 toward (+/-)-camphor were mainly attributed to the increased entropic gains due to the extensive desolvation effects, while the favorable enthalpic gains originating from the good size-fit relationship as well as the hydrogen bond interactions between host and guest result in the enhanced molecular/chiral recognition abilities of 2-4 toward (+/-)-borneol.     

Cholesteric liquid crystal displays as optical sensors of barbiturate binding

The influence on the optical properties of cholesteric liquid crystal displays (LCDs) was examined for neutral molecule binding by mesogen/receptors in the mesomorphic phase. The motivation was to prepare neutral molecule sensors that use a colour change to signal analyte binding. A receptor that binds barbiturate analytes was modified with two or one cholesteryl groups to yield compounds 2 and 3, respectively. LCDs were prepared by incorporating one of the receptor/mesogen compounds into a cholesteric LC blend along with a potential H-bonding guest. The optical properties of the LCDs were then determined by measuring the absorbance of the displays. For various LCDs, the colour of the display depended upon several factors: the amount of guest molecule used, the number of cholesteryl side chains on the receptor and the mole concentration of receptor/mesogen in the blend. In particular, complementary host/guest binding of H-bonding analytes by the bis(cholesteryl) receptor 2 in a cholesteric LCD caused a change of up to +70 nm, which was observed by the naked eye as a blue-to-orange colour change. Control experiments confirm that the colour of an LCD is a consequence of molecular recognition in the mesomorphic phase.     

Aryl Crown Ethers Based on d-Glucose Scaffold – Highly Selective Receptors of Amino Acid Ester Hydrochlorides

Amino acids are important biomolecules with a broad scope of applications in chemical and biological sciences. Their functions and properties depend on their absolute configuration. Therefore, methods for chiral recognition and separation of amino acids are highly sought after. For the purposes of diagnostic and medicinal applications chiral recognition of amino acids in water is particularly relevant. However synthetic receptors for enantioselective binding of amino acids in aqueous media are rare. Recently we reported a d -glucose-based crown ether for chiral recognition of amino acid esters in water. We achieved enantioselectivities towards amino acids with hydrophobic sidechains which were among the highest ever reported for a small molecule receptor. The binding affinities were however moderate. Herein we disclose analogs of that receptor, containing aryl functionalities in the crown ether fragment. The new receptors show considerably improved binding affinities for amino acid ester hydrochlorides in water, while retaining high enantio- or chemoselectivities.     

Chemocavity: specific concavity in protein reserved for the binding of biologically functional small molecules

The idea that there should be a specific site on a protein for a particular functional small molecule is widespread. It is, however, usually not so easy to understand what characteristics of the site determine the binding ability of the functional small molecule. We have focused on the concurrence rate of the 20 standard amino acids at such binding sites. In order to correlate the concurrence rate and the specific binding site, we have analyzed high-quality X-ray structures of complexes between proteins and small molecules. A novel index characterizing the binding site based on the concurrency rate has been introduced. Using this index we have identified that there is a specific concavity designated as a chemocavity where a specific group of small molecules, i.e., canonical molecular group, is highly inclined to be bound. This study has demonstrated that a chemocavity is reserved for a specific canonical molecular group, and the prevalent idea has been confirmed.     

间苯二甲酰腙分子钳的合成及阴离子识别研究

设计合成了3种新型间苯二甲酰腙类化合物,利用UV-Vis及¹H NMR考察了其与F^-、Cl^-、Br^-、I^-、CH₃COO^-、HSO₄^-、H₂PO4-、ClO4-阴离子的相互作用。结果表明,主体分子4a(双对硝基苯并呋喃甲醛间苯二甲酰腙)在DMSO溶液中对F-和CH₃COO-有显著识别效果,溶液颜色由黄色变为深黄色和棕红色。通过¹H NMR滴定及质子溶剂效应进一步证明,主体分子与阴离子之间是以氢键作用方式相结合。Job曲线表明,主客体间形成1：1型氢键络合物。基于实验结果,探讨了主客体间形状和大小匹配对识别能力的影响以及主客体之间的识别模式。     

Identification of small molecule binding sites within proteins using phage display technology

Affinity selection of peptides displayed on phage particles was used as the basis for mapping molecular contacts between small molecule ligands and their protein targets. Analysis of the crystal structures of complexes between proteins and small molecule ligands revealed that virtually all ligands of molecular weight 300 Da or greater have a continuous binding epitope of 5 residues or more. This observation led to the development of a technique for binding site identification which involves statistical analysis of an affinity-selected set of peptides obtained by screening of libraries of random, phage-displayed peptides against small molecules attached to solid surfaces. A random sample of the selected peptides is sequenced and used as input for a similarity scanning program which calculates cumulative similarity scores along the length of the putative receptor. Regions of the protein sequence exhibiting the highest similarity with the selected peptides proved to have a high probability of being involved in ligand binding. This technique has been employed successfully to map the contact residues in multiple known targets of the anticancer drugs paclitaxel (Taxol), docetaxel (Taxotere) and 2-methoxyestradiol and the glycosaminoglycan hyaluronan, and to identify a novel paclitaxel receptor [1]. These data corroborate the observation that the binding properties of peptides displayed on the surface of phage particles can mimic the binding properties of peptides in naturally occurring proteins. It follows directly that structural context is relatively unimportant for determining the binding properties of these disordered peptides. This technique represents a novel, rapid, high resolution method for identifying potential ligand binding sites in the absence of three-dimensional information and has the potential to greatly enhance the speed of development of novel small molecule pharmaceuticals.