One-pot synthesis of phenylphosphonic acid imprinted polymers for tyrosine phosphopeptides recognition in aqueous phase

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.

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.

Imprinted Electrochemical Sensor of Tyrosine Based on Chitosan/β- Cyclodextrin/Multi-walled Carbon Nanotubes Composite Film

Background:

As a vital amino acid in the human body, tyrosine is indispensable in various biological processes, and therefore its accurate and simple determination is of crucial importance. In this work, a facile approach was developed to construct a molecularly imprinted sensor for tyrosine via co-electrodeposition of chitosan, β-cyclodextrin and tyrosine on the surface of indium tin oxide that was pre-coated with multi-walled carbon nanotubes (MWNTs).

Methods:

Benefitting from the excellent film-forming ability and the rich functional groups to form a hydrogen bond with target molecules, chitosan was utilized to form a recognition matrix. MWNTs and β-cyclodextrin were then introduced to enhance the selectivity and sensitivity to tyrosine, due to the subtle electronic, catalytic properties and possible π-π interaction of MWNTs with tyrosine, as well as recognition ability of β-cyclodextrin. The morphology of the imprinted films was characterized by a scanning electron microscope. The electrochemistry and tyrosine sensing performance were investigated in detail by cyclic voltammetry and chronoamperometry.

Results:

Amperometry results showed that the imprinted sensor exhibited a linear range of 1.0×10−6 to 1.0×10−4 M and 1.0×10−4 to 1.0×10−3 M for tyrosine determination, with a detection limit of 6.0 × 10−7 M (S/N=3). Moreover, a satisfactory recovery in the range of 99.0% to 105.1% was obtained with the application of the imprinted sensor in artificial urine samples analysis.

Conclusion:

The imprinted electrode is reusable with satisfactory reproducibility and stability in tyrosine determination.

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.

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.

Construction of Persistent Luminescence-Plastic Antibody Hybrid Nanoprobe for In Vivo Recognition and Clearance of Pesticide Using Background-Free Nanobioimaging

We prepared a specific adsorptive nanocarrier for pesticide due to its challenge to cleanup and low detoxification in the treatment after intake, whether intentional or by mistake. We modified the plastic antibody (molecularly imprinted polymer (MIP)) on the surface of persistent luminescence nanoparticle (La₃Ga₅GeO₁₄: Cr³⁺, Zn²⁺, LGGO) as the specific adsorptive nanocarrier for toxic molecules and realized the nanocarrier was widely distributed for absorbing pesticide and real-time in vivo bioimaging. We used LGGO as the core and trichlorphon as the template to prepare the plastic antibody nanocarrier. After in vivo bioimaging and biodistribution of mice, LGGO@MIP could be distributed evenly in the gastrointestinal tract, circulated in the blood for a long time, and finally excreted to achieve the adsorption and removal of pesticide in the body. The LGGO@MIP nanocarrier prepared in this study opens a new way for the treatment of poisoning.

Advances in the development of molecularly imprinted polymers for the separation and analysis of proteins with liquid chromatography

This review documents recent advances in the design, synthesis, characterization, and application of molecularly imprinted polymers in the form of monoliths and particles/beads for the use in the separation and analysis of proteins with solid-phase extraction or liquid chromatography. The merits of three-dimensional molecular imprinting, whereby the molecular template is randomly embedded in the polymer, and two-dimensional imprinting, in which the template is confined to the surface, are described. Target protein binding can be achieved by either using the entire protein as a template or by using a protein substructure as template, that is, a peptide, as in the "epitope" approach. The intended approach and strategy then determine the choice of polymerization method. A synopsis has been provided on methods used for the physical, chemical, and functional characterizations and associated performance evaluations of molecularly imprinted and nonimprinted control polymers, involving a diverse range of analytical techniques commonly used for low and high molecular mass analytes. Examples of recent applications demonstrate that, due to the versatility of imprinting methods, molecularly imprinted monoliths or particles/beads can be adapted to protein extraction/depletion and separation procedures relevant to, for example, protein biomarker detection and quantification in biomedical diagnostics and targeted proteomics.

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.

Silicon nanoparticles coated with an epitope-imprinted polymer for fluorometric determination of cytochrome c

The authors describe a composite consisting of silicon nanoparticles that were first coated with SiO₂ and then with a molecularly imprinted polymer (SiNP@SiO₂@MIP). The MIP was generated by dual epitope imprinting such that it can recognize cytochrome c (Cyt c). The MIP on the NPs was prepared from the functional monomer zinc(II) acrylate (ZnA), the crosslinker ethylene glycol dimethacrylate and the initiator 2,2'-azoisobutyronitrile. Dual epitope templates for Cyt c included (a) a C-terminal nonapeptide (AYLKKATNE), and (b) an N-terminal nonapeptide (GDVEKGKKI). The chelation between Zn(II) of ZnA and the amino groups or hydroxy groups of the template nonapeptides warrants good recognition and capture of Cyt c. The fluorescence originating from SiNPs has excitation/emission peaks at 360/480 nm and is quenched by Cyt c in the 0.50-40.0 μM concentration range. The correlation coefficient for the calibration plot of the imprinted NPs is 0.9937. The detection limit is 0.32 ± 0.01 μM, the precisions of six replicate detections at levels of 0.5, 20 and 40 μM Cyt c are 3.2, 2.7 and 2.8%, respectively, and the imprinting factor is 2.43. Compared to single epitope template imprinting, dual epitope imprinting results in improved selectivity. The imprinted nanoparticles can discriminate Cyt c even if one amino acid is mismatched. The method was applied to the determination of Cyt c in spiked diluted human serum and gave recoveries between 94.0 and 107.5%. Graphical Abstract A fluorescent material of the architecture silicon nanoparticle@SiO₂@molecularly imprinted polymer (SiNP@SiO₂@MIP) was fabricated by dual epitope imprinting and a metal-chelating method. The chelation between Zn(II) of the functional monomer zinc(II) acrylate and the amino groups or hydroxy groups of template warrants that the material recognizes and captures cytochrome c well, and this results in fluorescence quenching.

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.

New Opportunities and Challenges of Smart Polymers in Post-Translational Modification Proteomics

Protein post-translational modifications (PTMs), which denote covalent additions of various functional groups (e.g., phosphate, glycan, methyl, or ubiquitin) to proteins, significantly increase protein complexity and diversity. PTMs play crucial roles in the regulation of protein functions and numerous cellular processes. However, in a living organism, native PTM proteins are typically present at substoichiometric levels, considerably impeding mass-spectrometry-based analyses and identification. Over the past decade, the demand for in-depth PTM proteomics studies has spawned a variety of selective affinity materials capable of capturing trace amounts of PTM peptides from highly complex biosamples. However, novel design ideas or strategies are urgently required for fulfilling the increasingly complex and accurate requirements of PTM proteomics analysis, which can hardly be met by using conventional enrichment materials. Considering two typical types of protein PTMs, phosphorylation and glycosylation, an overview of polymeric enrichment materials is provided here, with an emphasis on the superiority of smart-polymer-based materials that can function in intelligent modes. Moreover, some smart separation materials are introduced to demonstrate the enticing prospects and the challenges of smart polymers applied in PTM proteomics.

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.

Selective extraction of proteins and other macromolecules from biological samples using molecular imprinted polymers

The accurate determination of intact macromolecules in biological samples, such as blood, plasma, serum, urine, tissue and feces is a challenging problem. The increased interest in macromolecules both as candidate drugs and as biomarkers for diagnostic purposes means that new method development approaches are needed. This review charts developments in the use of molecularly imprinted polymers first for small-molecular-mass compounds then for proteins and other macromolecules. Examples of the development of molecularly imprinted polymers for macromolecules are highlighted. The two main application areas to date are sensors and separation science, particularly SPE. Examples include peptides and polypeptides, lysozyme, hemoglobin, ovalbumin, bovine serum albumin and viruses.

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.

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.

Template size matched film thickness for effectively in situ surface imprinting: a model study of glycoprotein imprints

For achieving a high imprinting efficiency, the film thickness should be compatible with the geometric size of fixed templates.