A phosphotyrosine-imprinted polymer receptor for the recognition of tyrosine phosphorylated peptides

Fundamentals, Synthetic Strategies and Applications of Non-Covalently Imprinted Polymers

Molecular imprinting has emerged as an important and practical technology to create economical and stable synthetic mimics of antibodies and enzymes. It has already found a variety of important applications, such as affinity separation, chemical/biological sensing, disease diagnostics, proteomics, bioimaging, controlled drug release, and catalysis. In the past decade, significant breakthroughs have been made in non-covalently imprinted polymers, from their synthesis through to their applications. In terms of synthesis, quite a few versatile and facile imprinting approaches for preparing MIPs have been invented, which have effectively solved some key issues in molecular imprinting. Additionally, important applications in several areas, such as sensors, proteomics and bioimaging, have been well demonstrated. In this review, we critically and comprehensively survey key recent advances made in the preparation of non-covalently imprinted polymers and their important applications. We focus on the state-of-art of this technology from three different perspectives: fundamentals, synthetic strategies, and applications. We first provide a fundamental basis for molecular imprinting technologies that have been developed, which is extremely helpful for establishing a sound understanding of the challenges in molecular imprinting. Then, we discuss in particular the major breakthroughs within the last ten years (2014-2024), with emphasis on new imprinting approaches, what strengths the breakthroughs can provide, and which new applications the properties of the prepared non-covalently imprinted polymers are fit for.

Exploring affinity chromatography in proteomics: A comprehensive review

Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.

In situ digestion-assisted multi-template imprinted nanoparticles for efficient analysis of protein phosphorylation

A new general approach called in situ digestion-assisted multi-template imprinting is proposed for preparation of phospho-specific molecularly imprinted nanoparticles. Through the novel templating strategy and controllable imprinting process, imprinted nanoparticles specific to the intact phosphoprotein and its phosphopeptides were synthesized. The prepared imprinted nanoparticles exhibited excellent specificity (cross reactivity < 10%), high affinity (10-6 M), high efficiency (47.5%), and good generality (both intact phosphoprotein and phosphopeptides). We also realized the fine tuning of the recognition at peptide level of the imprinted nanoparticles by adjusting the imprinting time. Based on the selective enrichment of the imprinted nanoparticles, the MS identification of both the intact phosphoprotein (Tau) and phosphopeptides (angiotensin II and peptides of Tau) in real complex samples could be achieved. Therefore, we believe that the in situ digestion-assisted multi-template imprinting strategy holds promising future in both phosphorylation analysis and proteomics applications.

Towards molecularly imprinted polymers that respond to and capture phosphorylated tyrosine epitopes using fluorescent bis-urea and bis-imidazolium receptors

Early detection of cancer is essential for successful treatment and improvement in patient prognosis. Deregulation of post-translational modifications (PTMs) of proteins, especially phosphorylation, is present in many types of cancer. Therefore, the development of materials for the rapid sensing of low abundant phosphorylated peptides in biological samples can be of great therapeutic value. In this work, we have synthesised fluorescent molecularly imprinted polymers (fMIPs) for the detection of the phosphorylated tyrosine epitope of ZAP70, a cancer biomarker. The polymers were grafted as nanometer-thin shells from functionalised submicron-sized silica particles using a reversible addition-fragmentation chain-transfer (RAFT) polymerisation. Employing the combination of fluorescent urea and intrinsically cationic bis-imidazolium receptor cross-linkers, we have developed fluorescent sensory particles, showing an imprinting factor (IF) of 5.0. The imprinted polymer can successfully distinguish between phosphorylated and non-phosphorylated tripeptides, reaching lower micromolar sensitivity in organic solvents and specifically capture unprotected peptide complements in a neutral buffer. Additionally, we have shown the importance of assessing the influence of counterions present in the MIP system on the imprinting process and final material performance. The potential drawbacks of using epitopes with protective groups, which can co-imprint with targeted functionality, are also discussed.

Probing Protein 4'-Phosphopantetheinylation in Single Living Cells

4'-Phosphopantetheinylation (4PPTylation) of proteins, which is derived from the hydrolysis of coenzyme A (CoA), is an essential post-translational modification participating in biosynthetic and metabolic pathways. However, due to the lack of specific recognition ligands as well as the shortage of sensitive analytical tools for single-cell analysis, the in-depth exploration of new cellular functions and mechanisms of protein 4PPTylation has been much hampered. In this study, we rationally engineered CoA-imprinted Raman nanotags for the specific recognition of 4PPTylation and thereby developed a molecularly imprinted polymer (MIP)-based plasmonic immunosandwich assay (PISA) for facile probing the 4PPTylation of ALDH1L1 in single cells. The molecularly imprinted nanotags exhibited excellent binding properties, giving a dissociation constant of 10^-6 M and cross-reactivity values of less than 10%. The MIP-based PISA enabled the specific and sensitive detection of the level of 4PPTylated ALDH1L1 in single living cells. Particularly, monitoring of the fluctuation of 4PPTylated ALDH1L1 in single cells under simulation by an inhibitor (methotrexate) that acts on a different metabolism pathway was achieved, implying possible crosstalk between two different pathways in folate metabolism. Thus, the imprinted Raman nanotags-PISA provides a promising analytical tool with a single-cell resolution for exploring new functions and elucidating their mechanisms of protein 4PPTylation.

Terminally Phosphorylated Triblock Polyethers Acting Both as Templates and Pore-Forming Agents for Surface Molecular Imprinting of Monoliths Targeting Phosphopeptides

The novel process reported here described the manufacture of monolithic molecularly imprinted polymers (MIPs) using a terminally functionalized block copolymer as the imprinting template and pore-forming agent. The MIPs were prepared through a step-growth polymerization process using a melamine-formaldehyde precondensate in a biphasic solvent system. Despite having a relatively low imprinting factor, the use of MIP monolith in liquid chromatography demonstrated the ability to selectively target desired analytes. An MIP capillary column was able to separate monophosphorylated peptides from a tryptic digest of bovine serum albumin. Multivariate data analysis and modeling of the phosphorylated and nonphosphorylated peptide retention times revealed that the number of phosphorylations was the strongest retention contributor for peptide retention on the monolithic MIP capillary column.

Combining a hybrid chip and tube microfluidic system with fluorescent molecularly imprinted polymer (MIP) core-shell particles for the derivatisation, extraction, and detection of peptides with N-terminating phosphorylated tyrosine

The reliable identification and quantitation of phosphorylated amino acids, peptides and proteins is one of the key challenges in contemporary bioanalytical research, an area of particular interest when attempting to diagnose and treat diseases at an early stage. We have developed a synthetic probe for targeting phosphorylated amino acids, based on core-shell submicron-sized particles consisting of a silica core, coated with a molecularly imprinted polymer (MIP) shell. The MIP layer contains a fluorescent probe crosslinker which binds selectively to phosphorylated tyrosine (pY) moieties with a significant imprinting factor (IF) and responds with a "light-up" fluorescence signal. The bead-based ratiometric detection scheme has been successfully transferred to a microfluidic chip format and its applicability to rapid assays has been exemplarily shown by discriminating a pY-terminating oligopeptide against its non-phosphorylated counterpart. Such miniaturised devices could lead to an automated pY or pY N-terminated peptide measurement system in the future. The setup combines a modular microfluidic system for amino acid derivatisation, extraction (by micropillar co-flow) and selective adsorption and detection with the fluorescent MIP core-shell particle probes. A miniaturised optical assembly for low-light fluorescence measurements was also developed, based on miniaturised opto-electronic parts and optical fibres. The emission from the MIP particles upon binding of pY or pY N-terminated peptides could be monitored in real-time.

The utility of molecularly imprinted polymers for mass spectrometric protein and proteomics analysis

Selective and efficient sample clean-up is important in mass spectrometric protein- and proteomics analyses from biological matrices. Molecularly imprinted polymers (MIPs), polymers prepared to have tailor-made cavities for capture of target analytes may by such represent an interesting alternative for selective clean-up. The present review aims to give an overview of the utility of MIPs for protein capture from biological matrices prior to mass spectrometry (MS) analysis. The application of MIPs in depletion of abundant proteins, in protein and proteotypic peptide capture as well as in capture of post-translational modifications (PTMs) is described and discussed. In addition, an overview of available MIP formats and their advantages and challenges is given, together with an overview of the mass spectrometric techniques used in protein analysis after MIP capture. Overall, the present literature demonstrates that for many applications MIPs for sample clean-up in mass spectrometric protein and proteomics analysis from biological matrices is still not fully matured. MIPs for proteotypic peptide capture is the most mature approach and a method for routine use may be available within the next few years.

Isoform-specific recognition of phosphopeptides by molecular imprinting nanoparticles with double-binding mode

Phosphorylation is one of the most important post-translational modifications of proteins, but due to the low abundance of phosphopeptides, enrichment is an essential step before mass spectrometric analysis. Although there are a number of enrichment methods developed targeting different forms of proteins phosphorylations, there are few reports on specific recognition and capture of single phosphopeptide. Herein, based on the advantages of dual affinity of TiO₂ and urea to a phosphate group and molecular imprinting towards the peptide sequence, the precise recognition of intact phosphorylated peptides was successfully achieved. The same peptide sequence with different phosphorylation forms (c.a. Ser, Thr and Tyr) were used as templates for proof-of-principle study, and the imprinted particles were successfully synthesized, characterized, and have the capacity to specifically recognize the targeted unique phosphorylation excluding even its isoforms. In addition, the produced molecularly imprinted nanoparticles have numerous important advantages, including strong affinity, high specificity toward single phosphopeptides, tolerance to interferences, fast binding kinetics, substantial binding capacity, excellent stability and reusability, making them an ideal sorbent for specific enrichment of unique phosphopeptides. Finally, different phosphorylation forms were specifically enriched from both standard peptides' mixture and casein/milk digests.

Improving the Identification of Lysine-Acetylated Peptides Using a Molecularly Imprinted Monolith Prepared by a Deep Eutectic Solvent Monomer

To overcome the identification challenge of low-abundance lysine acetylation (Kac), a novel approach based on a molecularly imprinted polymer (MIP) was developed to improve the extraction capacity of Kac peptides in real samples. Green deep eutectic solvents (DESs) were introduced and used as one of the synergistic functional monomers with zinc acrylate (ZnA). Glycine-glycine-alanine-lysine(ac)-arginine (GGAKacR) was chosen as a template and N,N'-methylenbisacrylamide (MBAA) was used as a cross-linker. The obtained GGAKacR-MIP had excellent selectivity for the template with an imprinting factor (IF) of up to 21.4. The histone digest addition experiment demonstrated that GGAKacR-MIP could successfully extract GGAKacR from a complex sample. Finally, the application to the extraction of Kac peptides from mouse liver protein digestion was studied in detail. The number of Kac peptides and Kac proteins identified was 130 and 110, which were 3.71-fold and 3.93-fold higher than those of the untreated sample. In addition, the number of peptides and proteins identified after treatment increased from 5535 and 1092 to 17 149 and 4037 (3.10-fold and 3.70-fold, respectively). The results showed that the obtained MIP may provide an effective technical tool for the identification of Kac-modification and peptide fractionation, as well as a potential approach for simultaneously identifying post-translational-modified proteomic and proteomic information.

Oxoanion Imprinting Combining Cationic and Urea Binding Groups: A Potent Glyphosate Adsorber

The use of polymerizable hosts in anion imprinting has led to powerful receptors with high oxyanion affinity and specificity in both aqueous and non-aqueous environments. As demonstrated in previous reports, a carefully tuned combination of orthogonally interacting binding groups, for example, positively charged and neutral hydrogen bonding monomers, allows receptors to be constructed for use in either organic or aqueous environments, in spite of the polymer being prepared in non-competitive solvent systems. We here report on a detailed experimental design of phenylphosphonic and benzoic acid-imprinted polymer libraries prepared using either urea- or thiourea-based host monomers in the presence or absence of cationic comonomers for charge-assisted anion recognition. A comparison of hydrophobic and hydrophilic crosslinking monomers allowed optimum conditions to be identified for oxyanion binding in non-aqueous, fully aqueous, or high-salt media. This showed that recognition improved with the water content for thiourea-based molecularly imprinted polymers (MIPs) based on hydrophobic EGDMA with an opposite behavior shown by the polymers prepared using the more hydrophilic crosslinker PETA. While the affinity of thiourea-based MIPs increased with the water content, the opposite was observed for the oxourea counterparts. Binding to the latter could however be enhanced by raising the pH or by the introduction of cationic amine- or Na⁺-complexing crown ether-based comonomers. Use of high-salt media as expected suppressed the amine-based charge assistance, whereas it enhanced the effect of the crown ether function. Use of the optimized receptors for removing the ubiquitous pesticide glyphosate from urine finally demonstrated their practical utility.

Specificity recognition for a target protein, cytochrome c using molecularly imprinted hydrogels

Protein imprinted hydrogel, which is one form of protein imprinted molecularly imprinted polymers (MIPs), is an important material for enzyme-linked immunosorbent assay, drug delivery materials, sensors, separation materials, etc. To...

Molecularly imprinted monoliths: Recent advances in the selective recognition of biomacromolecules related biomarkers

Biomarkers are significant indicators to assist the early diagnosis of diseases and assess the therapeutic response. However, due to the low-abundance of biomarkers in complex biological fluids, it is highly desirable to explore efficient techniques to attain their selective recognition and capture before the detection. Molecularly imprinted monoliths integrate the high selectivity of imprinted polymers and the rapid convective mass transport of monoliths, and as a result are promising candidates to achieve the specific enrichment of biomarkers from complex samples. This review summarizes the various imprinting approaches for the preparation of molecularly imprinted monoliths. The state-of-art advances as an effective platform for applications in the selective capture of biomacromolecules related biomarkers were also outlined. This article is protected by copyright. All rights reserved.

Molecularly Imprinted and Cladded Nanoparticles Provide Better Phosphorylation Recognition

Phosphorylation is one of the most frequently occurring post-translation modifications in mammals. Because abnormal protein phosphorylation is related to many diseases, phosphorylation analysis is essential for a sound understanding of protein phosphorylation and its relationship with diseases. Among several types of reagents for phosphorylation recognition, molecularly imprinted polymers (MIPs), as synthetic mimics of antibodies, have exhibited unique strengths that can overcome the drawbacks of biological reagents. However, the performance of current MIPs has remained unideal. Meanwhile, while the currently existing imprinting methods have permitted the production of several material formats, such as crushed particles and mesoporous nanoparticles, a general method allowing for the preparation of monodispersed molecularly imprinted nanoparticles has not been developed yet. Herein, we report a new approach called reverse microemulsion template docking surface imprinting and cladding (RMTD-SIC) for facile preparation of monodispersed imprinted nanoparticles for better phosphorylation recognition. Through rational design and controllable engineering, monodisperse imprinted and cladded nanoparticles specific to general phosphorylation and tyrosine phosphorylation were synthesized, which yield the highest imprinting factors as compared with published studies. The prepared nanomaterials exhibited excellent specificity and affinity, allowing for specific enrichment and improved mass spectrometric identification of target phosphorylated peptides from complex samples containing 100-fold more abundant interfering peptides. Therefore, the RMTD-SIC approach holds great potential for phosphorylation analysis and phosphorylation recognition-based applications.

Epitope-imprinted polymers: Design principles of synthetic binding partners for natural biomacromolecules

Molecular imprinting (MI) has been explored as an increasingly viable tool for molecular recognition in various fields. However, imprinting of biologically relevant molecules like proteins is severely hampered by several problems. Inspired by natural antibodies, the use of epitopes as imprinting templates has been explored to circumvent those limitations, offering lower costs and greater versatility. Here, we review the latest innovations in this technology, as well as different applications where MI polymers (MIPs) have been used to target biomolecules of interest. We discuss the several steps in MI, from the choice of epitope and functional monomers to the different production methods and possible applications. We also critically explore how MIP performance can be assessed by various parameters. Last, we present perspectives on future breakthroughs and advances, offering insights into how MI techniques can be expanded to new fields such as tissue engineering.

Affinity capture in bottom-up protein analysis - Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers

Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.

Spectroscopic and Colorimetric Studies for Anions with a New Urea-Based Molecular Cleft

A new simple urea-based dipodal molecular cleft (L) has been synthesized and studied for its binding affinity for a variety of anions by 1H-NMR, UV-Vis and colorimetric techniques in DMSO-d6 and DMSO, respectively. The results from titration studies suggest that the receptor forms a 1:2 complex with each of the anions used via hydrogen bonding interactions and exhibits strong selectivity for fluoride among halides, showing the binding affinity in the order of fluoride > chloride > bromide > iodide; meanwhile, it displays moderate selectivity for acetate among oxoanions, showing the binding affinity in the order of acetate > dihydrogen phosphate > bicarbonate > hydrogen sulfate > nitrate. Colorimetric studies of L for anions in DMSO reveal that the receptor is capable of detecting fluoride, acetate, bicarbonate and dihydrogen phosphate, displaying a visible color change in the presence of the respective anions.

Molecularly imprinted polymers by epitope imprinting: a journey from molecular interactions to the available bioinformatics resources to scout for epitope templates

The molecular imprinting of proteins is the process of forming biomimetics with entailed protein-recognition by means of a template-assisted synthesis. Protein-imprinted polymers (pMIPs) have been successfully employed in separations, assays, sensors, and imaging. From a technical point of view, imprinting a protein is both costly, for protein expression and purification, and challenging, for the preservation of the protein's structural properties. In fact, the imprinting process needs to guarantee the preservation of the same protein three-dimensional conformation that later would be recognized. So far, the captivating idea to imprint just a portion of the protein, i.e., an epitope, instead of the whole, proved successful, offering reduced costs, compatibility with many synthetic conditions (solvents, pH, temperatures), and fine-tuning of the peptide sequence so to target specific physiological and functional conditions of the protein, such as post-translational modifications. Here, protein-protein interactions and the biochemical features of the epitopes are inspected, deriving lessons to prepare more effective pMIPs. Epitopes are categorized in linear or structured, immunogenic or not, located at the protein's surface or buried in its core and the imprinting strategies are discussed. Moreover, attention is given to freely available online bioinformatics resources that might offer key tools to gain further rationale amid the selection process of suitable epitopes templates.

The Use of Computational Methods for the Development of Molecularly Imprinted Polymers

Recent years have witnessed a dramatic increase in the use of theoretical and computational approaches in the study and development of molecular imprinting systems. These tools are being used to either improve understanding of the mechanisms underlying the function of molecular imprinting systems or for the design of new systems. Here, we present an overview of the literature describing the application of theoretical and computational techniques to the different stages of the molecular imprinting process (pre-polymerization mixture, polymerization process and ligand-molecularly imprinted polymer rebinding), along with an analysis of trends within and the current status of this aspect of the molecular imprinting field.

[Advances in enrichment of phosphorylated peptides and glycopeptides by smart polymer-based materials]

翻译后修饰是蛋白质组学研究的前沿和重点,它不仅调节着蛋白质的折叠、状态、活性、定位以及蛋白质间的相互作用,也能帮助科学家更全面地了解生物体的生命过程,为疾病的预测、诊断和治疗提供更加强大的支撑和依据。翻译后修饰产物(例如磷酸化肽和糖肽)丰度很低,且存在着强烈的背景干扰,很难直接用质谱进行分析,因此迫切需要开发高效的富集材料和技术来选择性富集翻译后修饰产物。近年来,智能聚合物基材料通过外部物理、化学或生物刺激可逆地改变其结构和功能,实现对磷酸化肽和糖肽高度可控的吸附和脱附,进而衍生开发出一系列新颖的富集方法,极大地吸引研究者们的兴趣。一方面,智能聚合物基材料的响应变化包括材料疏水性的增加或减少、形状和形貌的改变、表面电荷的重新分布以及亲和配体的暴露或隐藏等特性。这些特性使得目标物和智能聚合物基材料之间的亲和力可以通过简单改变外部条件(如温度、pH值、溶剂极性和生物分子等)实现更可控和更智能的精细调节。另一方面,智能聚合物基材料为集成功能模块提供了便捷的可扩展平台,例如特定的识别组件,显著提高了目标物质的分离选择性。智能聚合物基材料在分离方面展现出巨大的潜力,这为蛋白质翻译后修饰产物的分析和研究带来了希望。围绕上述主题,该文依据Web of Science近20年来近50篇代表性文献,概述了智能聚合物基材料在磷酸化肽和糖肽分离及富集中的发展方向。

WIDENING THE BOTTLENECK OF PHOSPHOPROTEOMICS: EVOLVING STRATEGIES FOR PHOSPHOPEPTIDE ENRICHMENT

Phosphorylation is a form of protein posttranslational modification (PTM) that regulates many biological processes. Whereas phosphoproteomics is a scientific discipline that identifies and quantifies the phosphorylated proteome using mass spectrometry (MS). This task is extremely challenging as ~30% of the human proteome is phosphorylated; and each phosphoprotein may exist as multiple phospho-isoforms that are present in low abundance and stoichiometry. Hence, phosphopeptide enrichment techniques are indispensable to (phospho)proteomics laboratories. These enrichment methods encompass widely-adopted techniques such as (i) affinity-based chromatography; (ii) ion exchange and mixed-mode chromatography (iii) enrichment with phospho-specific antibodies and protein domains, and (iv) functionalized polymers and other less common but emerging technologies such as hydroxyapatite chromatography and precipitation with inorganic ions. Here, we review these techniques, their history, continuous development and evaluation. Besides, we outline associating challenges of phosphoproteomics that are linked to experimental design, sample preparation, and proteolytic digestion. In addition, we also discuss about the future outlooks in phosphoproteomics, focusing on elucidating the noncanonical phosphoproteome and deciphering the "dark phosphoproteome". © 2020 John Wiley & Sons Ltd.

Combinatorial Design of a Sialic Acid-Imprinted Binding Site

Aberrant glycosylation has been proven to correlate with various diseases including cancer. An important alteration in cancer progression is an increased level of sialylation, making sialic acid one of the key constituents in tumor-specific glycans and an interesting biomarker for a diversity of cancer types. Developing molecularly imprinted polymers (MIPs) with high affinity toward sialic acids is an important task that can help in early cancer diagnosis. In this work, the glycospecific MIPs are produced using cooperative covalent/noncovalent imprinting. We report here on the fundamental investigation of this termolecular imprinting approach. This comprises studies of the relative contribution of orthogonally interacting functional monomers and their synergetic behavior and the choice of different counterions on the molecular recognition properties for the sialylated targets. Combining three functional monomers targeting different functionalities on the template led to enhanced imprinting factors (IFs) and selectivities. This apparent cooperative effect was supported by ¹H NMR and fluorescence titrations of monomers with templates or template analogs. Moreover, highlighting the role of the template counterion use of tetrabutylammonium (TBA) salt of sialic acid resulted in better imprinting than that of sodium salts supported by both in solution interaction studies and in MIP rebinding experiments. The glycospecific MIPs display high affinity for sialylated targets, with an overall low binding of other nontarget saccharides.

Selective Enrichment of Histidine Phosphorylated Peptides Using Molecularly Imprinted Polymers

Protein histidine phosphorylation (pHis) is involved in molecular signaling networks in bacteria, fungi, plants, and higher eukaryotes including mammals and is implicated in human diseases such as cancer. Detailed investigations of the pHis modification are hampered due to its acid-labile nature and consequent lack of tools to study this post-translational modification (PTM). We here demonstrate three molecularly imprinted polymer (MIP)-based reagents, MIP1–MIP3, for enrichment of pHis peptides and subsequent characterization by chromatography and mass spectrometry (LC–MS). The combination of MIP1 and β-elimination provided some selectivity for improved detection of pHis peptides. MIP2 was amenable to larger pHis peptides, although with poor selectivity. Microsphere-based MIP3 exhibited improved selectivity and was amenable to enrichment and detection by LC–MS of pHis peptides in tryptic digests of protein mixtures. These MIP protocols do not involve any acidic solvents during sample preparation and enrichment, thus preserving the pHis modification. The presented proof-of-concept results will lead to new protocols for highly selective enrichment of labile protein phosphorylations using molecularly imprinted materials.

Anion Binding Studies of Urea and Thiourea Functionalized Molecular Clefts

Two rationally designed 4-nitrophenyl-based molecular clefts functionalized with thiourea (L₁) and urea (L₂) have been synthesized and studied for a variety of anions by UV-Vis and colorimetric techniques in DMSO. Results from the binding studies suggest that both L₁ and L₂ bind halides showing the order: fluoride > chloride > bromide > iodide; and oxoanions showing the order: dihydrogen phosphate > hydrogen sulfate > nitrate > perchlorate. Each receptor has been shown to form a 1:1 complex with an anion via hydrogen bonding interactions, displaying distinct color change for fluoride and dihydrogen phosphate in solution. As compared to the urea-based receptor L₂, the thiourea-based receptor L₁ exhibits stronger affinity for anions due the presence of more acidic thiourea functional groups.

The Search for Peptide Epitopes for Molecular Imprinting Through Bioinformatics

Epitope imprinting is an effective strategy to prepare molecularly imprinted polymers (MIPs) for protein recognition. Indeed, the idea to use as a template just a fragment of the protein of interest, called the epitope, instead of the whole protein, presents some key advantages for the imprinting process, in particular: cutting the costs for MIP production and avoiding protein unfolding during the imprinting process, so to ultimately improve the quality of the stamped binding sites. How to select an epitope for the imprinting is the strategic question. Here, the bioinformatics tools to search for suitable epitopes for the imprinting process and rational tools to select the most suitable epitope are briefly introduced along with protocols for their practical use.

Combinatorial design of a sialic acid imprinted binding site exploring a dual ion receptor approach

Dual-ion imprinting of sialic acid via cooperatively acting ureido- and crown ether functionalities leads to charge neutral sialic acid receptors with strong sialoglycopeptide affinity.

Stoichiometric molecular imprinting using polymerisable urea and squaramide receptors for the solid phase extraction of organo-arsenic compound roxarsone

The design, preparation and evaluation of molecularly imprinted polymers for roxarsone (4-hydroxy-3-nitrophenylarsonic acid), an organo-arsenic swine and poultry feed additive, using bi-substituted ureas and squaramide receptors as the functional monomers, are demonstrated. Pre-polymerisation studies of the template-monomer complexation performed by ¹H NMR experiments show that squaramide-based monomers provide association equilibrium constant values higher than urea-based monomers. Equilibrium rebinding experiments in methanol show that two squaramide-based materials have good molecular recognition properties towards roxarsone, with high affinity (K_eq = 16.85 × 10³ L mol^-1 and 14.65 × 10³ L mol^-1, respectively), high imprinting factors (4.73 and 3.64 respectively) and good selectivity towards two roxarsone-related compounds, acetarsone (3-acetamido-4-hydroxyphenylarsonic acid) and nitarsone (4-nitrophenylarsonic acid). Polymer MIP-SQ2 was successfully used to setup an experimental protocol for the direct solid phase extraction of roxarsone from surface water samples. The method gives clean HPLC traces, with recoveries between 91% and 95% at concentration levels of 5.0, 10, and 25 mg L^-1. Sample preconcentration with good recoveries between 87% and 97%, are shown, confirming that it is possible to employ the developed materials to measure roxarsone down to 1 μg L^-1 in water samples.

Urea-Based Imprinted Polymer Hosts with Switchable Anion Preference

The design of artificial oxyanion receptors with switchable ion preference is a challenging goal in host–guest chemistry. We here report on molecularly imprinted polymers (MIPs) with an external phospho-sulpho switch driven by small molecule modifiers. The polymers were prepared by hydrogen bond-mediated imprinting of the mono- or dianions of phenyl phosphonic acid (PPA), phenyl sulfonic acid (PSA), and benzoic acid (BA) using N-3,5-bis-(trifluoromethyl)-phenyl-Ń-4-vinylphenyl urea (1) as the functional host monomer. The interaction mode between the functional monomer and the monoanions was elucidated by ¹H NMR titrations and ¹H–¹H NMR NOESY supported by molecular dynamic simulation, which confirmed the presence of high-order complexes. PPA imprinted polymers bound PPA with an equilibrium constant K_eq = 1.8 × 10⁵ M^–1 in acetonitrile (0.1% 1,2,2,6,6-pentamethylpiperidine) and inorganic HPO₄^2– and SO₄^2– with K_eq = 2.9 × 10³ M^–1 and 4.5 × 10³ M^–1, respectively, in aqueous buffer. Moreover, the chromatographic retentivity of phosphonate versus sulfonate was shown to be completely switched on this polymer when changing from a basic to an acidic modifier. Mechanistic insights into this system were obtained from kinetic investigations and DSC-, MALDI-TOF-MS-, ¹H NMR-studies of linear polymers prepared in the presence of template. The results suggest the formation of template induced 1–1 diad repeats in the polymer main chain shedding unique light on the relative contributions of configurational and conformational imprinting.

High salt compatible oxyanion receptors by dual ion imprinting

Imprinting of an ion-pair in presence of mutually compatible anion and cation host monomers leads to polymers showing enhanced ion uptake in competitive high ionic strength buffers.

Epitope Imprinting Technology: Progress, Applications, and Perspectives toward Artificial Antibodies

Epitope imprinting is a promising tool to generate antibody-like specific recognition sites. Recently, because of the ease of obtaining templates, the flexibility in selecting monomers, their resistance to harsh environments, and the high specificity toward targets, epitope-imprinted materials have attracted much attention in various fields, such as bioanalysis, clinical therapy, and pharmacy. Here, the discussion is focused on the current representative epitope imprinting technologies, including epitope bulk imprinting and epitope surface imprinting. Moreover, the application of epitope-imprinted materials to the recognition of peptides, proteins, and cells is reviewed. Finally, the remaining challenges arising from the intrinsic properties of epitope imprinting are discussed, and future development in the field is prospected.

Epitope-imprinted mesoporous silica nanoparticles for specific recognition of tyrosine phosphorylation

Tyrosine phosphorylation regulates the upstream signaling pathway but accounts for less than 0.1% of total phosphorylation in human cells. Herein, molecularly imprinted mesoporous materials were first synthesized to recognize the phosphorylated tyrosine residue from other phosphorylated residues.

Molecularly Imprinted Materials for Selective Biological Recognition

Molecular imprinting is an approach of generating imprinting cavities in polymer structures that are compatible with the target molecules. The cavities have memory for shape and chemical recognition, similar to the recognition mechanism of antigen-antibody in organisms. Their structures are also called biomimetic receptors or synthetic receptors. Owing to the excellent selectivity and unique structural predictability of molecularly imprinted materials (MIMs), practical MIMs have become a rapidly evolving research area providing key factors for understanding separation, recognition, and regenerative properties toward biological small molecules to biomacromolecules, even cell and microorganism. In this review, the characteristics, morphologies, and applicability of currently popular carrier materials for molecular imprinting, especially the fundamental role of hydrogels, porous materials, hierarchical nanoparticles, and 2D materials in the separation and recognition of biological templates are discussed. Moreover, through a series of case studies, emphasis is given on introducing imprinting strategies for biological templates with different molecular scales. In particular, the differences and connections between small molecular imprinting (bulk imprinting, "dummy" template imprinting, etc.), large molecular imprinting (surface imprinting, interfacial imprinting, etc.), and cell imprinting strategies are demonstrated in detail. Finally, future research directions are provided.

Precision Imprinting of Glycopeptides for Facile Preparation of Glycan-Specific Artificial Antibodies

Antibodies specific to glycans are essential in many areas for many important fields, including disease diagnostics, therapeutics, and fundamental researches. However, due to their low immunogenicity and poor availability, glycans pose serious challenges to antibody development. Although molecular imprinting has developed into important methodology for creating antibody mimics with low cost and better stability, glycan-specific molecularly imprinted polymers (MIPs) still remain rather rare. Herein, we report a new strategy, precision imprinting with alternative templates, for the facile preparation of glycan-specific MIPs. Glycopeptides with desirable peptide length immobilized on a boronate affinity substrate were first prepared as alternative templates through in situ dual enzymatic digestion. A thinlayer was then produced to cover the glycans to an appropriate thickness through precision imprinting. With glycoproteins containing only N-glycans as well as both N- and O-glycans as glycan source, this approach was proved to be widely applicable and efficient. The strategy is particularly significant for the recognition of O-glycans, because enzymes that can release O-glycans from O-linked glycoproteins are lacking. The MIPs exhibited excellent glycan specificity. Specific extraction of glycopeptides and glycoproteins containing certain glycans from complex samples was demonstrated. This strategy opened a new avenue for the facile preparation of glycan-specific MIPs, facilitating glycan-related applications and research.

Role of Counterions in Molecularly Imprinted Polymers for Anionic Species

Small-molecule oxoanions are often imprinted noncovalently as carboxylates into molecularly imprinted polymers (MIPs), requiring the use of an organic counterion. Popular species are either pentamethylpiperidine (PMP) as a protonatable cation or tetraalkylammonium (TXA) ions as permanent cations. The present work explores the influence of the TXA as a function of their alkyl chain length, from methyl to octyl, using UV/vis absorption, fluorescence titrations, and HPLC as well as MD simulations. Protected phenylalanines (Z-l/d-Phe) served as templates/analytes. While the influence of the counterion on the complex stability constants and anion-induced spectral changes shows a monotonous trend with increasing alkyl chain length at the prepolymerization stage, the cross-imprinting/rebinding studies showed a unique pattern that suggested the presence of adaptive cavities in the MIP matrix, related to the concept of induced fit of enzyme-substrate interaction. Larger cavities formed in the presence of larger counterions can take up pairs of Z-x-Phe and smaller TXA, eventually escaping spectroscopic detection. Correlation of the experimental data with the MD simulations revealed that counterion mobility, the relative distances between the three partners, and the hydrogen bond lifetimes are more decisive for the response features observed than actual distances between interacting atoms in a complex or the orientation of binding moieties. TBA has been found to yield the highest imprinting factor, also showing a unique dual behavior regarding the interaction with template and fluorescent monomer. Finally, interesting differences between both enantiomers have been observed in both theory and experiment, suggesting true control of enantioselectivity. The contribution concludes with suggestions for translating the findings into actual MIP development.

Phosphate-imprinted magnetic nanoparticles using phenylphosphonic acid as a template for excellent recognition of tyrosine phosphopeptides

The tyrosine phosphorylation of proteins and peptides plays a vital role in cell signal transduction pathways, and it is very important to assay them for understanding their action mechanism. Due to the low levels of the tyrosine phosphopeptides (pTyr) in cells, it is a challenge to enrich them with traditional sorbents, therefore, development of specific and selective sorbents is urgent and necessary. In this work, the phosphate-imprinted magnetic nanoparticles (PMNPs) to enrich the pTyr with high efficiency and selectivity have been fabricated using the phenylphosphonic acid as a template for the "epitope" of pTyr. The magnetic nanoparticles have been functionalized with TiO₂ and then the imprinting silica shells have been coated on the surface of the functional core to obtain the PMNPs sorbents. The PMNPs can obviously shorten the enrichment time and improve the adsorption efficiency for pTyr, and the epitope imprinting films provide an excellent selective recognition ability to target. The recognition capability of PMNPs for pTyr is 90.3 μg/mg and the imprinting factor of the sorbents can reach 24.4. The results indicate that the PMNPs can enrich the pTyr from the tryptic digest of β-casein samples with high specificity, and the spiking recoveries of the pTyr range from 85.1% to 93.8% with the RSD from 0.04 to 3.73. With the high adsorption capacity, rapid separation, excellent specificity and recyclability, the PMNPs sorbents show great potential for analysis of the phosphorylation of peptides in biological and medical fields.

Ratiometric Fluorescence Detection of Phosphorylated Amino Acids Through Excited-State Proton Transfer by Using Molecularly Imprinted Polymer (MIP) Recognition Nanolayers

A 2,3-diaminophenazine bis-urea fluorescent probe monomer (1) was developed. It responds to phenylphosphate and phosphorylated amino acids in a ratiometric fashion with enhanced fluorescence accompanied by the development of a redshifted emission band arising from an excited-state proton transfer (ESPT) process in the hydrogen-bonded probe/analyte complex. The two urea groups of 1 form a cleft-like binding pocket (K_b >10¹⁰  L²  mol^-2 for 1:2 complex). Imprinting of 1 in presence of ethyl ester- and fluorenylmethyloxycarbonyl (Fmoc)-protected phosphorylated tyrosine (Fmoc-pTyr-OEt) as the template, methacrylamide as co-monomer, and ethyleneglycol dimethacrylate as cross-linker gave few-nanometer-thick molecularly imprinted polymer (MIP) shells on silica core microparticles with excellent selectivity for the template in a buffered biphasic assay. The supramolecular recognition features were established by spectroscopic and NMR studies. Rational screening of co-monomers and cross-linkers allowed to single out the best performing MIP components, giving significant imprinting factors (IF>3.5) while retaining ESPT emission and the ratiometric response in the thin polymer shell. Combination of the bead-based detection scheme with the phase-transfer assay dramatically improved the IF to 15.9, allowing sensitive determination of the analyte directly in aqueous media.

Molecularly Imprinted Porous Monolithic Materials from Melamine-Formaldehyde for Selective Trapping of Phosphopeptides

Thirty-five melamine-formaldehyde (MF) monolithic materials with bimodal pore distributions were synthesized in fused silica capillaries by catalyst-free polycondensation, starting with an aqueous MF precondensate, using acetonitrile as the macroporogen and a variety of aliphatic polyethers and triblock copolymeric surfactants as porogens and mesoporogens, respectively. By varying the prepolymer composition and the type and molecular weight of the polymeric porogen components, a library of porous monolithic materials was produced, covering a range of meso- and macroporous properties. A multivariate evaluation revealed that the amount of surfactant was the strongest contributor to specific surface area and pore volume and to the inversely related mesopore size, whereas the macropore dimensions were controlled mainly by the amount of aliphatic polyether porogen. One of these capillary monoliths, chosen based on the combination of meso- and macropores providing optimal percolative flow and accessible surface area, was synthesized in the presence of N-Fmoc and O-Et protected phosphoserine and phosphotyrosine to prepare molecularly imprinted monoliths with surface layers selective for phosphopeptides. These imprinted monoliths were characterized alongside nonimprinted monoliths by a variety of techniques and finally evaluated by liquid chromatography-mass spectrometry in the capillary format to assess their abilities to trap and release phosphorylated amino acids and peptides from partly aqueous media. Selective enrichment of phosphorylated targets was demonstrated, suggesting that these materials could be useful as trapping media in affinity-based phosphoproteomics.

Automated Protein Biomarker Analysis: on-line extraction of clinical samples by Molecularly Imprinted Polymers

Robust biomarker quantification is essential for the accurate diagnosis of diseases and is of great value in cancer management. In this paper, an innovative diagnostic platform is presented which provides automated molecularly imprinted solid-phase extraction (MISPE) followed by liquid chromatography-mass spectrometry (LC-MS) for biomarker determination using ProGastrin Releasing Peptide (ProGRP), a highly sensitive biomarker for Small Cell Lung Cancer, as a model. Molecularly imprinted polymer microspheres were synthesized by precipitation polymerization and analytical optimization of the most promising material led to the development of an automated quantification method for ProGRP. The method enabled analysis of patient serum samples with elevated ProGRP levels. Particularly low sample volumes were permitted using the automated extraction within a method which was time-efficient, thereby demonstrating the potential of such a strategy in a clinical setting.