Recognition of proteins and peptides: Rational development of molecular imprinting technology

The creation of tailor-made receptors which are able to recognize molecular targets with high affinity and selectivity has attracted much attention in the field of chemistry, physics, and biology. Molecular imprinting has proved to be an effective technique for generating specific recognition sites in synthetic polymers. The synthesis of molecular imprinted polymers specific for proteins and peptides has been a focus for many scientists working in the area of molecular recognition, since the creation of synthetic polymers that can specifically recognize biomacromolecules is a very challenging but potentially extremely rewarding work. These polymers with specificity for biological macromolecules have considerable potential for applications in the areas of solid phase extraction, catalysis, medicine, clinical analysis, drug delivery, environmental monitoring, and sensors. In this review, the authors discuss the developed approaches associated with the imprinting of peptides and proteins, and provide an overview of the significant progress achieved within this field. Finally, the possible mechanism of the molecular imprinting and recognition has been discussed.     

Capturing molecules with templated materials--analysis and rational design of molecularly imprinted polymers

The creation of synthetic tailor-made receptors capable of recognizing desired molecular targets with high affinity and selectivity is a persistent long-term goal for researchers in the fields of chemical, biological, and pharmaceutical research. Compared to biomacromolecular receptors, these synthetic receptors promise simplified production and processing, less costs, and more robust receptor architectures. During recent decades, molecularly imprinted polymers (MIPs) are widely considered mimics of natural molecular receptors suitable for a diversity of applications ranging from biomimetic sensors, to separations and biocatalysis.A remaining challenge for the next generation of MIPs is the synthesis of deliberately designed and highly efficient receptor architectures suitable for recognizing biologically relevant molecules, for which natural receptors are either not prevalent, or difficult to isolate and utilize. Hence, this review discusses recent advances in synthetic receptor technology for biomolecules (e.g. drugs, amino acids, steroids, proteins, entire cells, etc.) via molecular imprinting techniques. Surface imprinting methods and epitope imprinting approaches have been introduced for protein recognition at imprinted surfaces. Imprinting techniques in aqueous solution or organic-water co-solvents have been introduced avoiding denaturation of biomolecules during MIP synthesis. In addition, improved bioreactivity of entire enzyme or active site mimics generated by molecular imprinting will be highlighted. Finally, the emerging importance of molecular modeling and molecular dynamics studies detailing the intermolecular interactions between the template species, the porogenic solvent molecules, and the involved monomer and cross-linker in the pre-polymerization solution will be addressed yielding a rational approach toward next-generation MIP technology.     

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.     

Design and structure of peptide and peptidomimetic antagonists of protein-protein interaction

Peptides based on the amino acid sequences found at protein-protein interaction sites make excellent leads for antagonist development. A statistical picture of amino acids involved in protein-protein interactions indicates that proteins recognize and interact with one another through the restricted set of specialized interface amino acid residues, Pro, Ile, Tyr, Trp, Asp and Arg. These amino acids represent residues from each of the three classes of amino acids, hydrophobic, aromatic and charged, with one anionic and one cationic residue at neutral pH. The use of peptides as drug leads has been successfully used to search for antagonists of cell-surface receptors. Peptide, peptidomimetic, and non-peptide organic inhibitors of a class of cell surface receptors, the integrins, currently serve as therapeutic and diagnostic imaging agents. In this review, we discuss the structural features of protein-protein interactions as well as the design of peptides, peptidomimetics, and small organic molecules for the inhibition of protein-protein interactions. Information gained from studying inhibitors of integrin functions is now being applied to the design and testing of inhibitors of other protein-protein interactions. Most drug development progress in the past several decades has been made using the enzyme binding-pocket model of drug targets. Small molecules are designed to fit into the substrate-binding pockets of proteins based on a lock-and-key, induced-fit, or conformational ensemble model of the protein binding site. Traditionally, enzymes have been used as therapeutic drug targets because it was easier to develop rapid, sensitive screening assays, and to find low molecular weight inhibitors that blocked the active site. However, for proteins which interact with other proteins, rather than with small substrate molecules, the lack of binding pockets means that this approach will not generally succeed. There exist many diseases in which the inhibition of protein-protein interactions would provide therapeutic benefit, but there are no general methods available to address such problems. The focus of the first part of this review is to discuss the features of protein-protein interactions which may serve as general guidelines for the development and design of inhibitors for protein-protein interactions. In the second part we focus on the design of peptides (lead compounds) and their conversion into peptidomimetics or small organic molecules for the inhibition of protein-protein interactions. We draw examples from the important and emerging area of integrin-based cell adhesion and show how the principles of protein-protein interactions are followed in the discovery, optimization and usage of specific protein interface peptides as drug leads.     

Molecular imprinting of peptides and proteins in aqueous media

Molecular imprinting has received significant attention in recent years, as it provides a viable method for creating synthetic receptors capable of selectively recognizing specific target molecules. Despite significant growth within the field, the majority of template molecules studied thus far have been characterized by their low molecular weight and insolubility in aqueous systems. In biological systems, molecular recognition events occur in aqueous media. Therefore, in order to create molecularly imprinted polymers capable of mimicking biological processes, it is necessary to synthesize artificial receptors which can selectively recognize their respective target biological macromolecules such as peptides and proteins in aqueous media. In this review, we discuss the challenges associated with the imprinting of peptides and proteins in aqueous media. In addition, we discuss the significant progress which has been made within the field.     

Calixarenes for Biochemical Recognition and Separation

This review summarizes reference data on the molecular recognition of bioactive molecules by calixarenes. It emphasizes on selectivity, the design principles of the host molecules, and the type of interactions as basis for new analytical and separation methods. The following classes of compounds are discussed: amino acids, peptides and proteins, lectins, enzymes, nucleotides and nucleosides, saccharides, steroids and other guests. Also considered are induced chirality and calixarenes with substituents complementary to biomolecules. Enzyme mimics and amines are briefly discussed.     

Recognition of peptides by antibodies and investigations of affinity using biosensor technology

The study of peptide-antibody interactions has many applications in biology and medicine. Synthetic peptides corresponding to single protein epitopes are used instead of intact proteins as reagents for the diagnosis of viral and autoimmune diseases. Furthermore, antibodies raised against peptides are useful reagents for isolating and characterizing gene products. In this review, methods for analysing the molecular basis of peptide-antibody interactions are described, such as amino acid replacement studies, X-ray crystallography of peptide-antibody complexes and biosensor technology based on surface plasmon resonance. The importance of peptide conformation in antibody recognition is discussed, and the antigenic reactivity of epitopes in synthetic peptides and in cognate, intact proteins is compared.     

Progress in Synthetic Polymers Based on Natural Amino Acids

α-Amino acids are one type of the main building blocks of living systems, being the primary components of all naturally occurring peptides and proteins. They are the simplest optically active compound in the nature and have multiple functional groups, which enable them to be transformed into a wide variety of optically active substances. The resulting materials show a wide variety of functions such as electron transfer, information transfer, photo reactivity and selective catalytic function, which cannot be imitated by synthetic compounds. Functional macromolecular materials using biological chiral resources such as amino acids have been drawing much interest due to their biocompatibility and biodegradability easing the ecological trouble because amino acid residues can be targeted for cleaving by different enzymes. Also, this type of polymer contains nitrogen, which the organism needs for their growth and shows excellent hydrophilic character, reasonably high melting points and good materials properties even at relatively low molecular weights. However, polymers composed of amino acids alone have limited thermal stability and are insoluble in many common organic solvents, which make these materials difficult to fabricate and utilize. Preparation of hybrid systems between conventional synthetic polymers and linear sequences of amino acids are interesting because amino acid segments possess unique properties, such as directional polarity, chirality and their capability to undergo specific noncovalent interactions. These properties can potentially be used for designing novel hierarchical superstructures with tunable material properties for a wide variety of applications. Herein, the synthesis and properties of synthetic macromolecules having natural amino acids are reviewed in details up to now with excluding polypeptides.     

Phosphate recognition in structural biology

Drug-discovery research in the past decade has seen an increased selection of targets with phosphate recognition sites, such as protein kinases and phosphatases, in the past decade. This review attempts, with the help of database-mining tools, to give an overview of the most important principles in molecular recognition of phosphate groups by enzymes. A total of 3003 X-ray crystal structures from the RCSB Protein Data Bank with bound organophosphates has been analyzed individually, in particular for H-bonding interactions between proteins and ligands. The various known binding motifs for phosphate binding are reviewed, and similarities to phosphate complexation by synthetic receptors are highlighted. An analysis of the propensities of amino acids in various classes of phosphate-binding enzymes showed characteristic distributions of amino acids used for phosphate binding. This review demonstrates that structure-based lead development and optimization should carefully address the phosphate-binding-site environment and also proposes new alternatives for filling such sites.     

Surface‐Assisted Laser Desorption/Ionization Mass Spectrometric Detection of Biomolecules by Using Functional Single‐Walled Carbon Nanohorns as the Matrix

A surface‐assisted laser desorption/ionization time‐of‐flight mass spectrometric (SALDI‐TOF MS) method was developed for the analysis of small biomolecules by using functional single‐walled carbon nanohorns (SWNHs) as matrix. The functional SWNHs could transfer energy to the analyte under laser irradiation for accelerating its desorption and ionization, which led to low matrix effect, avoided fragmentation of the analyte, and provided high salt tolerance. Biomolecules including amino acids, peptides, and fatty acids could successfully be analyzed with about 3‐ and 5‐fold higher signals than those obtained using conventional matrix. By integrating the advantages of SWNHs and the recognition ability of aptamers, a selective approach was proposed for simultaneous capture, enrichment, ionization, and MS detection of adenosine triphosphate (ATP). This method showed a greatly improved detection limit (1.0 μM ) for the analysis of ATP in complex biological samples. This newly designed protocol not only opened a new application of SWNHs, but also offered a new technique for selective MS analysis of biomolecules based on aptamer recognition systems.     

杯芳烃对生物活性分子的识别性能*

杯芳烃是一类由苯酚和甲醛缩合而成的大环化合物,由于杯芳烃的上沿和下沿容易进行化学修饰及其本身具有一个大小可调节的疏水空腔,使得杯芳烃对客体分子表现出特殊的识别能力.本文就杯芳烃对氨基酸、糖、肽链、蛋白质等生物活性分子及手性药物的分子识别作一综述.     

Short peptides as biosensor transducers

This review deals with short peptides (up to 50 amino acids) as biomimetic active recognition elements in sensing systems. Peptide-based sensors have been developed in recent years according to different strategies. Synthetic peptides have been designed on the basis of known interactions between single or a few amino acids and targets, with attention being paid to the presence of peptide motifs known to allow intermolecular self-organization of the sensing peptides over the sensor surface. Sensitive and sophisticated sensors have been obtained in this way, but the use of designed peptides is limited by severe difficulties in their in silico design. Short peptides from random phage display have been selected in a random way from large, unfocussed, and often preexisting and commercially available phage display libraries, with no design elements. Such peptides often perform better than antibodies, but they are difficult to select when the target is a small molecule because of the need to immobilize it with considerable modifications of its structure. Artificial, miniaturized receptors have been obtained from the reduction of the known sequence of a natural receptor down to a synthesizable and yet stable one. Alternatively, binding sites have been created over a designed, stable peptide scaffold. Short peptides have also been used as active elements for the detection of their own natural receptors: pathogenic bacteria have been detected with antimicrobial and cell-penetrating peptides, but key challenges such as detection of bacteria in real samples, improved sensitivity, and improved selectivity have to be faced. Peptide substrates have been conjugated to fluorescent quantum dots to obtain disposable sensors for protease activity with high sensitivity. Ferrocene–peptide conjugates have been used for electrochemical sensing of protease activity.     

Imaging of Hypochlorous Acid by Fluorescence and Applications in Biological Systems

In recent decades, HOCl research has attracted a lot of scientists from around the world. This chemical species is well known as an important player in the biological systems of eukaryotic organisms including humans. In the human body, HOCl is produced by the myeloperoxidase enzyme from superoxide in very low concentrations (20 to 400 μm ); this species is secreted by neutrophils and monocytes to help fight pathogens. However, in the condition called “oxidative stress”, HOCl has the capability to attack many important biomolecules such as amino acids, proteins, nucleotides, nucleic acids, carbohydrates, and lipids; these reactions could ultimately contribute to a number of diseases such as neurodegenerative diseases (AD, PD, and ALS), cardiovascular diseases, and diabetes. In this review, we discuss recent efforts by scientists to synthesize various fluorophores which are attached to receptors to detect HOCl such as: chalcogen‐based oxidation, oxidation of 4‐methoxyphenol, oxime/imine, lactone ring opening, and hydrazine. These synthetic molecules, involving rational synthetic pathways, allow us to chemoselectively target HOCl and to study the level of HOCl selectivity through emission responses. Virtually all the reports here deal with well‐defined and small synthetic molecular systems. A large number of published compounds have been reported over the past years; this growing field has given scientists new insights regarding the design of the chemosensors. Reversibility, for example is considered important from the stand point of chemosensor reuse within the biological system; facile regenerability using secondary analytes to obtain the initial probe is a very promising avenue. Another aspect which is also important is the energy of the emission wavelength of the sensor; near‐infrared (NIR) emission is favorable to prevent autofluorescence and harmful irradiation of tissue; thus, extended applicability of such sensors can be made to the mouse model or animal model to help image internal organs. In this review, we describe several well‐known types of receptors that are covalently attached to the fluorophore to detect HOCl. We also discuss the common fluorophores which are used by chemist to detect HOCl, Apart from the chemical aspects, we also discuss the capabilities of the compounds to detect HOCl in living cells as measured through confocal imaging. The growing insight from HOCl probing suggests that there is still much room for improvement regarding the available molecular designs, knowledge of interplay between analytes, biological applicability, biological targeting, and chemical switching, which can also serve to further sensor and theurapeutic agent development alike.     

Scope of amino acid recognition by cucurbit[8]uril

This paper describes the molecular recognition of amino acids by cucurbit[8]uril (Q8) and by the 1:1 complex between Q8 and methyl viologen (MV) in purely aqueous solution. These hosts are known to bind aromatic peptides with high affinity and sequence specificity, but prior work has focused on only a small subset of amino acids. In an effort to elucidate the scope and limitations of amino acid recognition by Q8 and Q8?MV, a comprehensive examination of the 20 genetically encoded amino acids was carried out by ¹H NMR spectroscopy and isothermal titration calorimetry. We find that both Q8 and Q8?MV bind measurably to only tryptophan, phenylalanine, and tyrosine. These results demonstrate that Q8 and Q8?MV are highly selective in the context of all genetically encoded amino acids and are therefore promising for the development of recognition-intensive applications involving peptides, proteins, and proteomes.     

Speciation and structural aspects of interactions of Al(III) with small biomolecules

Complexes formed with low molecular mass biomolecules are the ‘dynamic or mobile units’ of Al(III), which may be involved in the absorption and transport processes of this toxic element in organisms. This paper reviews the interactions of Al(III), from speciation and structural aspects, with biologically relevant endogenous and exogenous small biomolecules such as inorganic ligands (hydroxide, fluoride, (oligo)phosphates and silicic acid), amino acids, phosphorylated amino acids, oligopeptides, biophosphates including nucleotides, phosphonates, hydroxamates, and aromatic and aliphatic hydroxycarboxylates. The importance of time in biospeciation is demonstrated on the examples of binary and ternary systems involving Al(III) and citric acid. Examples are also given for the implications of the speciation of Al(III) with such small biomolecules in biology.     

水相识别分子印迹技术

在各种基于超分子方法的仿生识别体系中,分子印迹聚合物已经证明是一种有潜力的合成受体,受到了广泛的关注。传统的分子印迹技术通常是在有机溶剂中制备对小分子具有选择性的印迹聚合物,而在水相中制备及识别生物大分子的研究仍具有相当的挑战性。从小分子到生物大分子、从有机相到水相,反映了分子印迹技术的发展趋势。本文对最近几年分子印迹在水相制备与识别方面的最新进展进行了总结与评述,探讨了水相识别印迹聚合物的设计策略与制备方法;着重介绍了水相识别技术在固相萃取、色谱固定相、药物控释、中药有效成份提取以及生物分子识别等方面的应用;指出了提高水相识别选择性的途径并对其将来的发展进行了建议与展望。     

Secondary Structures in Synthetic Poly(Amino Acids): Homo- and Copolymers of Poly(Aib), Poly(Glu), and Poly(Asp)

The secondary structure of poly(amino acids) is an excellent tool for controlling and understanding the functionality and properties of proteins. In this perspective article the secondary structures of the homopolymers of oligo- and poly-glutamic acid (Glu), aspartic acid (Asp), and α-aminoisobutyric acid (Aib) are discussed. Information on external and internal factors, such as the nature of side groups, interactions with solvents and interactions between chains is reviewed. A special focus is directed on the folding in hybrid-polymers consisting of oligo(amino acids) and synthetic polymers. Being part of the SFB TRR 102 “Polymers under multiple constraints: restricted and controlled molecular order and mobility” this overview is embedded into the cross section of protein fibrillation and supramolecular polymers. As polymer- and amino acid folding is an important step for the utilization and design of future biomolecules these principles guide to a deeper understanding of amyloid fibrillation.     

Installing Reduction Responsiveness into Biomolecules by Introducing Nitroaryl Groups

Artificially synthesized stimuli-responsive biomolecules are attractive as molecular tools for monitoring and modulating biological systems. In biological systems, redox stimuli are common, and their dysregulation is typically linked to various abnormal or disease states. In this Concept article, the molecular design of reduction-responsive biomolecules, such as peptides, nucleic acids, and saccharides, which are produced by introducing nitroaryl groups into them, is reviewed with a special emphasis on simple 4-nitrobenzene-based motifs.     

Na和Cl对CDI活化的酸性及碱性氨基酸聚合反应的高效促进效应

含有Na⁺（K⁺）及Cl^-等无机离子的水溶液是所有生化反应的反应体系，因而也是地球上最重要的反应体系。目前科学界对这一体系中上述离子与离子之间、离子与水分子之间、离子与生物分子之间的弱相互作用的了解还非常有限，很多离子特异性现象的机理至今仍不清楚。结合我们近期发现在水溶液中Na⁺（K⁺）及Cl^-等简单离子对带相反电荷氨基酸成肽的高效促进效应，本文希望强调水溶液体系中Na⁺（K⁺）及Cl^-等简单离子与多肽及蛋白之间的弱静电相互作用对蛋白及多肽结构及功能的重要性。本文还讨论了水溶液中的这些弱静电相互作用在生命起源及生命现象中的意义。     

Molecular Recognition of Zwitterions with Artificial Receptors

Many biomolecules exist as internal ion pairs or zwitterions within a biologically relevant pH range. Despite their importance, the molecular recognition of this type of systems is specially challenging due to their strong solvation in aqueous media, and their trend to form folded or self‐assembled structures by pairing of charges of different sign. In this Minireview, we will discuss the molecular recognition of zwitterions using non‐natural, synthetic receptors. This contribution does not intend to make a full in‐depth revision of the existing research in the field, but a personal overview with selected representative examples from the recent literature.