Specific recognition of tyrosine-phosphorylated peptides by epitope imprinting of phenylphosphonic acid

Molecularly imprinted electrochemical sensor based on APTES-functionalized indium tin oxide electrode for the determination of sulfadiazine

An electrochemical sensor was developed for the sensitive and selective detection of sulfadiazine (SDZ), based on a molecularly imprinted polymer (MIP) film formed on an indium tin oxide (ITO) electrode through a self-assembly process. The SDZ-imprinted ITO electrode (SDZ-MIP/APTES-ITO) was prepared through in situ polymerization using sulfadiazine, methacrylic acid (MAA), ethylene glycol dimethacrylate (EGDMA), and 2,2'-azobisisobutyronitrile (AIBN) as the template, functional monomer, cross-linker, and initiator respectively. Before polymerization, the ITO electrode was functionalized with 3-aminopropyltriethoxysilane (APTES) to promote covalent attachment of the polymer to the electrode. After polymerization, the template molecule SDZ was removed to create selective recognition sites, forming the molecularly imprinted polymer electrode (MIP/APTES-ITO), which facilitates sulfadiazine detection. The sensor's performance was evaluated using cyclic and differential pulse voltammetry, demonstrating a linear response in the sulfadiazine concentration range 0.1 to 300 μM, with a detection limit of 0.11 μM. The MIP-based sensor exhibited good reproducibility, repeatability, selectivity, and stability in sulfadiazine detection. Its practical applicability was confirmed by the successful quantification of sulfadiazine in spiked milk samples.

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.

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.

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.

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.

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.

Advances in epitope molecularly imprinted polymers for protein detection: a review

Epitope molecularly imprinted polymers (EMIPs) are novel imprinted materials using short characteristic peptides as templates rather than entire proteins. To be specific, the amino acid sequence of the template peptide is the same as an exposed N- or C-terminus of a target protein, or its amino acid composition and sequence replicate a similar conformational arrangement as the same amino acid residues on the surface of the target protein. EMIPs have a good application prospect in protein research. Herein, we focus on classification of epitope imprinting techniques, methods of epitope immobilization on matrix materials including boronate affinity immobilization, covalent bonding immobilization, physical adsorption immobilization and metal ion chelation immobilization, and application of EMIPs in peptides, proteins, target imaging and target therapy fields. Finally, the main problems and future development are summarized.

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.

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.

SH2 Superbinder Modified Monolithic Capillary Column for the Sensitive Analysis of Protein Tyrosine Phosphorylation

In this study, we present a method to specifically capture phosphotyrosine (pTyr) peptides from minute amount of sample for the sensitive analysis of protein tyrosine phosphorylation. We immobilized SH2 superbinder on a monolithic capillary column to construct a microreactor to enrich pTyr peptides. It was found that the synthetic pTyr peptide could be specifically enriched by the microreactor from the peptide mixture prepared by spiking of the synthetic pTyr peptide into the tryptic digests of α-casein and β-casein with molar ratios of 1:1000:1000. The microreactor was further applied to enrich pTyr peptides from pervanadate-treated HeLa cell digests for phosphoproteomics analysis, which resulted in the identification of 796 unique pTyr sites. In contrast, the conventional SH2 superbinder-based method identified 41 pTyr sites for the same sample, only 5.2% of the number achieved by the microreactor. Finally, this microreactor was also applied to analyze the pTyr in Shc1 complex, an immunopurified protein complex, which resulted in the identification of 15 pTyr sites. Together, this technique is best fitted to analyze the pTyr in minute amount of sample and will have broad application in fields where only a limited amount of sample is available.

Exploring the peptide retention mechanism in molecularly imprinted polymers

Molecularly imprinted polymers (MIPs) have been used as useful sorbents in solid-phase extraction for a wide range of molecules and sample matrices. Their unique selectivity can be fine-tuned in the imprinting process and is crucial for the extraction of macromolecules from complex matrices such as serum. A relevant example of this is the application of MIPs to peptides in diagnostic assays. In this article the selectivity of MIPs, previously implemented in a quantitative mass-spectrometric assay for the biomarker pro-gastrin-releasing peptide, is investigated. Partial least squares regression was used to generate models for the evaluation and prediction of the retention mechanism of MIPs. A hypothesis on interactions of MIPs with the target peptide was verified by ad hoc experiments considering the relevant peptide physicochemical properties highlighted from the multivariate analysis. Novel insights into and knowledge of the driving forces responsible for the MIP selectivity have been obtained and can be directly used for further optimization of MIP imprinting strategies. Graphical Abstract Applied analytical strategy: the Solid Phase Extraction (SPE) of digested Bovin Serum Albumin (BSA), using Molecularly Imprinted Polymers (MIP), is followed by the liquid chromatography-mass spectrometry (LC-MS) analysis for the identification of the retained peptides. The further application of multivariate analysis allows setting up a Partial Least Square (PLS) model, which describes the peptide retention into the MIP and gives additional knowledge to be used in the optimization of the MIP and the whole SPE method.

Hierarchically templated beads with tailored pore structure for phosphopeptide capture and phosphoproteomics

Phosphotyrosine selective beads prepared by polymer templating at two length scales results in improved capture of larger sized peptide fragments from tryptic protein digests.

Preparation of High-Efficiency Cytochrome c-Imprinted Polymer on the Surface of Magnetic Carbon Nanotubes by Epitope Approach via Metal Chelation and Six-Membered Ring

A novel epitope molecularly imprinted polymer on the surface of magnetic carbon nanotubes (MCNTs@EMIP) was successfully fabricated to specifically recognize target protein cytochrome c (Cyt C) with high performance. The peptides sequences corresponding to the surface-exposed C-terminus domains of Cyt C was selected as epitope template molecule, and commercially available zinc acrylate and ethylene glycol dimethacrylate (EGDMA) were employed as functional monomer and cross-linker, respectively, to synthesize MIP via free radical polymerization. The epitope was immobilized via metal chelation and six-membered ring formed between the functional monomer and the hydroxyl and amino groups of the epitope. The resulting MCNTs@EMIP exhibited specific recognition ability toward target Cyt C including more satisfactory imprinting factor (about 11.7) than that of other reported imprinting methods. In addition, the MCNTs@EMIP demonstrated a high adsorption amount (about 780.0 mg g(-1)) and excellent selectivity. Besides, the magnetic property of the support material made the processes easy and highly efficient by assistance of an external magnetic field. High-performance liquid chromatography analysis of Cyt C in bovine blood real sample and protein mixture indicated that the specificity was not affected by other competitive proteins, which forcefully stated that the MCNTs@EMIP had potential to be applied in bioseparation area. In brief, this study provided a new protocol to detect target protein in complex sample via epitope imprinting approach and surface imprinting strategy.

Thermoresponsive Epitope Surface-Imprinted Nanoparticles for Specific Capture and Release of Target Protein from Human Plasma

Among various artificial antibodies, epitope imprinted polymer has been paid increasingly attention. To modulate the "adsorption and release" behavior by environment stimuli, N-isopropylacrylamide, was adopted to fabricate the thermoresponsive epitope imprinted sites. The prepared imprinted materials could adsorb 46.6 mg/g of target protein with the imprinting factor of 4.0. The template utilization efficiency could reach as high as 8.21%. More importantly, in the real sample, the materials could controllably capture the target protein from the human plasma at 45 °C and release it at 4 °C, which demonstrated the "on-demand" application potentials of such materials in the biomolecule recognition field.

Surface protein imprinted magnetic nanoparticles for specific recognition of bovine hemoglobin

Magnetic molecular imprinting for recognition of bovine hemoglobin was prepared by combining the surface imprinting technique with two-stage core–shell sol–gel polymerization.

Molecularly imprinted polymers for separating and sensing of macromolecular compounds and microorganisms

The present review article focuses on gathering, summarizing, and critically evaluating the results of the last decade on separating and sensing macromolecular compounds and microorganisms with the use of molecularly imprinted polymer (MIP) synthetic receptors. Macromolecules play an important role in biology and are termed that way to contrast them from micromolecules. The former are large and complex molecules with relatively high molecular weights. The article mainly considers chemical sensing of deoxyribonucleic acids (DNAs), proteins and protein fragments as well as sugars and oligosaccharides. Moreover, it briefly discusses fabrication of chemosensors for determination of bacteria and viruses that can ultimately be considered as extremely large macromolecules.

Isolation of viable type I and II methanotrophs using cell-imprinted polyurethane thin films

Studies on methanotrophs utilizing methane as sole source of carbon and energy are meaningful for governing global warming; although, the isolation of methanotrophs from nature is challenging. Here, surface imprinted polyurethane films were fabricated to selectively capture living methanotrophs from paddy soil. Two tracks of molecularly imprinted film based on polyurethane (PU-MIF1 and PU-MIF2) were imprinted using type I or II methanotrophs as template, respectively, and then reacted with polyethylene glycol, castor oil, and hexamethylene diisocyanate. Results demonstrated these PU-MIFs hold low water absorption rate and superior biocompatibility, which was highly demanded for maintaining cell viability. Superior selectivity and affinity of PU-MIFs toward their cognate methanotroph cells was observed by fluorescent microscopy. Atomic force microscopy revealed the adhesion force of PU-MIFs with its cognate cells was much stronger in comparison with noncognate ones. Using the as-prepared PU-MIFs, within 30 min, methanotroph cells could be separated from rice paddy efficiently. Therefore, the PU-MIFs might be used as an efficient approach for cell sorting from environmental samples.

A "turn-on" fluorescent receptor for detecting tyrosine phosphopeptide using the surface imprinting procedure and the epitope approach

A new strategy for the manufacture of a turn-on fluorescent molecularly imprinted polymer (CdTe/SiO2/MIP) receptor for detecting tyrosine phosphopeptide (pTyr peptide) was proposed. The receptor was prepared by the surface imprinting procedure and the epitope approach with silica-capped CdTe quantum dots (QDs) as core substrate and fluorescent signal, phenylphosphonic acid (PPA) as the dummy template, 1-[3-(trimethoxysilyl) propyl] urea as the functional monomer, and octyltrimethoxysilane as the cross-linker. The synthetic CdTe/SiO2/MIP was able to selectively capture the template PPA and corresponding target pTyr peptide with fluorescence enhancement via the special interaction between them and the recognition cavities. The receptor exhibited the linear fluorescence enhancement to pTyr peptide in the range of 0.5-35μM, and the detection limit was 0.37μM. The precision for five replicate detections of pTyr peptide at 20μM was 2.60% (relative standard deviation). Combining the fluorescence property of the CdTe QDs with the merits of the surface imprinting technique and the epitope approach, the receptor not only owned high recognition site accessibility and good binding affinities for target pTyr peptide, but also improved the fluorescence selectivity of the CdTe QDs, as well revealed the feasibility of fabrication of a turn-on fluorescence probe using the surface imprinting procedure and the epitope approach.

Combination of surface imprinting and immobilized template techniques for preparation of core-shell molecularly imprinted polymers based on directly amino-modified Fe3O4 nanoparticles for specific recognition of bovine hemoglobin

In this work, the core-shell bovine hemoglobin (BHb)-imprinted superparamagnetic nanoparticles (Fe₃O₄@BHb-MIPs) were synthesized by combining for the first time a surface imprinting technique and a two-step immobilized template strategy. Initially, amino-functionalized Fe₃O₄ nanoparticles (Fe₃O₄@NH₂) were synthesized directly through a facile one-pot hydrothermal method. Next, BHb was immobilized on the surface of Fe₃O₄@NH₂ through non-covalent interactions. Then, siloxane co-polymerization on the Fe₃O₄@NH₂-protein complex surface resulted in a polymeric network molded around BHb which then became further immobilized. Finally, a thin polymer layer with specific recognition cavities for BHb was formed on the surface of Fe₃O₄@NH₂ after the removal of the template protein. The morphology and structure property of the prepared magnetic nanoparticles were characterized by transmission electronic microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), X-ray diffractometer (XRD), and vibrating sample magnetometer (VSM). To obtain the best selectivity and binding performance, the polymerization and adsorption conditions were investigated in detail. Under the optimized conditions, the Fe₃O₄@BHb-MIPs exhibited fast adsorption kinetics, large binding capacity, significant selectivity, and favorable reproducibility. The resultant Fe₃O₄@BHb-MIPs could not only specifically extract BHb from a mixed standard protein mixture, but also selectively enriched BHb from a real bovine blood sample. In addition, the synthetic process was quite simple and the stability and regeneration of the Fe₃O₄@BHb-MIPs were also satisfactory.