Tag-Specific Affinity Purification of Recombinant Proteins by Using Molecularly Imprinted Polymers

Imprinted Polymers on the Route to Plastibodies for Biomacromolecules (MIPs), Viruses (VIPs), and Cells (CIPs)

Around 30% of the scientific papers published on imprinted polymers describe the recognition of proteins, nucleic acids, viruses, and cells. The straightforward synthesis from only one up to six functional monomers and the simple integration into a sensor are significant advantages as compared with enzymes or antibodies. Furthermore, they can be synthesized against toxic substances and structures of low immunogenicity and allow multi-analyte measurements via multi-template synthesis. The affinity is sufficiently high for protein biomarkers, DNA, viruses, and cells. However, the cross-reactivity of highly abundant proteins is still a challenge.

Rational Supramolecular Strategy via Halogen Bonding for Effective Halogen Recognition in Molecular Imprinting

Halogen bonding is a highly directional interaction and a potential tool in functional material design through self-assembly. Herein, we describe two fundamental supramolecular strategies to synthesize molecularly imprinted polymers (MIPs) with halogen bonding-based molecular recognition sites. In the first method, the size of the σ-hole was increased by aromatic fluorine substitution of the template molecule, enhancing the halogen bonding in the supramolecule. The second method involved sandwiching hydrogen atoms of a template molecule between iodo substituents, which suppressed competing hydrogen bonding and enabled multiple recognition patterns, improving the selectivity. The interaction mode between the functional monomer and the templates was elucidated by ¹H NMR, ¹³C NMR, X-ray absorption spectroscopy, and computational simulation. Finally, we succeeded in the effective chromatographic separation of diiodobenzene isomers on the uniformly sized MIPs prepared by multi-step swelling and polymerization. The MIPs selectively recognized halogenated thyroid hormones via halogen bonding and could be applied to screening endocrine disruptors.

Molecularly Imprinted Polymers as Synthetic Antibodies for Protein Recognition: The Next Generation

Molecularly imprinted polymers (MIPs) are chemical antibody mimics obtained by nanomoulding the 3D shape and chemical functionalities of a desired target in a synthetic polymer. Consequently, they possess exquisite molecular recognition cavities for binding the target molecule, often with specificity and affinity similar to those of antigen-antibody interactions. Research on MIPs targeting proteins began in the mid-90s, and this review will evaluate the progress made till now, starting from their synthesis in a monolith bulk format through surface imprinting to biocompatible soluble nanogels prepared by solid-phase synthesis. MIPs in the latter format will be discussed more in detail because of their tremendous potential of replacing antibodies in the biomedical domain like in diagnostics and therapeutics, where the workforce of antibodies is concentrated. Emphasis is also put on the development of epitope imprinting, which consists of imprinting a short surface-exposed fragment of a protein, resulting in MIPs capable of selectively recognizing the whole macromolecule, amidst others in complex biological media, on cells or tissues. Thus selecting the 'best' peptide antigen is crucial and in this context a rational approach, inspired from that used to predict peptide immunogens for peptide antibodies, is described for its unambiguous identification.

Core-Shell Magnetic Imprinted Polymers for the Recognition of FLAG-Tagpeptide

FLAG^® tag (DYKDDDDK) is a small epitope peptide employed for the purification of recombinant proteins such as immunoglobulins, cytokines, and gene regulatory proteins. It provides superior purity and recoveries of fused target proteins when compared to the commonly used His-tag. Nevertheless, the immunoaffinity-based adsorbents required for their isolation are far more expensive than the ligand-based affinity resin used in combination with the His-tag. In order to overcome this limitation we report herein the development of molecularly imprinted polymers (MIPs) selective to the FLAG^® tag. The polymers were prepared by the epitope imprinting approach using a four amino acids peptide, DYKD, including part of the FLAG^® sequence as template molecule. Different kinds of magnetic polymers were synthesised in aqueous and organic media also using different sizes of magnetite core nanoparticles. The synthesised polymers were used as solid phase extraction materials with excellent recoveries and high specificity for both peptides. The magnetic properties of the polymers confer a new, effective, simple, and fast method in the purification using FLAG^® tag.

Current Trends in Molecular Imprinting: Strategies, Applications and Determination of Target Molecules in Spain

Over the last decades, an increasing demand for new specific molecular recognition elements has emerged in order to improve analytical methods that have already been developed in order to reach the detection/quantification limits of target molecules. Molecularly imprinted polymers (MIPs) have molecular recognition abilities provided by the presence of a template molecule during their synthesis, and they are excellent materials with high selectivity for sample preparation. These synthetic polymers are relatively easy to prepare, and they can also be an excellent choice in the substitution of antibodies or enzymes in different kinds of assays. They have been properly applied to the development of chromatographic or solid-phase extraction methods and have also been successfully applied as electrochemical, piezoelectrical, and optical sensors, as well as in the catalysis process. Nevertheless, new formats of polymerization can also provide new applications for these materials. This paper provides a comprehensive comparison of the new challenges in molecular imprinting as materials of the future in Spain.

Controlled synthesis of open-mouthed epitope-imprinted polymer nanocapsules with a PEGylated nanocore and their application for fluorescence detection of target protein

Epitope imprinting is an effective way to create artificial receptors for protein recognition. Surface imprinting with immobilized templates and sacrificial supports can generate high-quality imprinted cavities of homogeneous orientation and good accessibility, but it is still challenging to fabricate nanoscale imprinted materials by this approach. Herein, we propose a method for the controlled synthesis of open-mouthed epitope-imprinted polymer nanocapsules (OM-MIP NCs) by limiting the imprinting polymerization on the template-bearing side of the Janus nanoparticles (JNPs). Concurrent bromoacetyl (Ac–Br) and 2-bromoisobutyryl (iB–Br) functionalization of the major portion of SiO₂ nanoparticles is achieved via the molten-wax-in-water Pickering emulsion approach. The cysteinyl-derived epitope templates are immobilized through the Ac–Br groups, and then surface imprinting is fulfilled via ATRP initiated by the iB–Br groups. The SiO₂ supports are partially etched and then PEGlated, affording OM-MIP NCs with a PEGylated nanocore. The inside nanocore can facilitate collection of the NCs by centrifugation, and its PEGylation can inhibit non-specific binding. The surface imprinting can be optimized through the ATRP time, and the etching can be tailored via the concentration of NH₄HF₂ employed. For proof-of-concept, with a C-terminus nonapeptide of bovine serum albumin (BSA) chosen as a model epitope and polymerizable carbon dots added to the pre-polymerization solution, fluorescent OM-MIP NCs were fabricated for BSA sensing. The as-synthesized NCs exhibited satisfactory detection performance, with an imprinting factor of 6.1, a limit of detection of 38.1 nM, a linear range of 0.25–6 μM, and recoveries of 98.0 to 104.0% in bovine serum samples.

Surface epitope imprinting over the one side of Janus SiO₂ NPs via ATRP affords open-mouthed epitope-imprinted nanocapsules with imprinted cavities of homogeneous orientation and good accessibility for fluorescence detection of target protein.

Recent Advances in Quartz Crystal Microbalance Biosensors Based on the Molecular Imprinting Technique for Disease-Related Biomarkers

The molecular imprinting technique is a quickly developing field of interest regarding the synthesis of artificial recognition elements that enable the specific determination of target molecule/analyte from a matrix. Recently, these smart materials can be successfully applied to biomolecule detection in biomimetic biosensors. These biosensors contain a biorecognition element (a bioreceptor) and a transducer, like their biosensor analogs. Here, the basic difference is that molecular imprinting-based biosensors use a synthetic recognition element. Molecular imprinting polymers used as the artificial recognition elements in biosensor platforms are complementary in shape, size, specific binding sites, and functionality to their template analytes. Recent progress in biomolecular recognition has supplied extra diagnostic and treatment methods for various diseases. Cost-effective, more robust, and high-throughput assays are needed for monitoring biomarkers in clinical settings. Quartz crystal microbalance (QCM) biosensors are promising tools for the real-time and quick detection of biomolecules in the past two decades A quick, simple-to-use, and cheap biomarkers detection technology based on biosensors has been developed. This critical review presents current applications in molecular imprinting-based quartz crystal microbalance biosensors for the quantification of biomarkers for disease monitoring and diagnostic results.

Tag-mediated single-step purification and immobilization of recombinant proteins toward protein-engineered advanced materials

Background

The potential applications of protein-engineered functional materials are so wide and exciting that the interest in these eco-friendly advanced materials will further expand in the future. Tag-mediated protein purification/immobilization technologies have emerged as green and cost-effective approaches for the fabrication of such materials. Strategies that combine the purification and immobilization of recombinant proteins/peptides onto/into natural, synthetic or hybrid materials in a single-step are arising and attracting increasing interest.

Aim of Review

This review highlights the most significant advances of the last 5 years within the scope of tag-mediated protein purification/immobilization and elucidates their contributions for the development of efficient single-step purification and immobilization strategies. Recent progresses in the field of protein-engineered materials created using innovative protein-tag combinations and future opportunities created by these new technologies are also summarized and identified herein.

Key Scientific Concepts of Review

Protein purification/immobilization tags present a remarkable ability to establish specific non-covalent/covalent interactions between solid materials and biological elements, which prompted the creation of tailor-made and advanced functional materials, and of next-generation hybrid materials. Affinity tags can bind to a wide range of materials (of synthetic, natural or hybrid nature), being most suitable for protein purification. Covalently binding tags are most suitable for long-term protein immobilization, but can only bind naturally to protein-based materials. Hybrid affinity-covalently binding tags have allowed efficient one-step purification and immobilization of proteins onto different materials, as well as the development of innovative protein-engineered materials. Self-aggregating tags have been particularly useful in combination with other tags for generating protein-engineered materials with self-assembling, flexible and/or responsive properties. While these tags have been mainly explored for independent protein purification, immobilization or functionalization purposes, efficient strategies that combine tag-mediated purification and immobilization/functionalization in a single-step will be essential to guarantee the sustainable manufacturing of advanced protein-engineered materials.

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.

Detection of Dengue Fever Nonstructural Protein 1 Antigen by Proteolytic Peptide Imprinting Technology and UHPLC-MS/MS

Dengue fever is caused by mosquito-transmitted dengue virus infection and continues to increase worldwide, threatening public health in tropical and subtropical regions. The primary difficulties in preventing a reduction of the medical burden of dengue fever lies in the lack of effective mosquito control, preventive dengue vaccines, and clinically effective antiviral drugs to treat dengue infections. Rapid and accurate diagnosis is crucial for proper patient care and effective control of epidemics. The present work proposes an alternative strategy for detecting the dengue virus nonstructural protein 1 (NS1) antigen in clinical serum samples by using ultrahigh-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) in combination with the molecularly imprinted polymers. Rather than the whole protein, the NS1 signature peptide is selected as a template for molecular imprinting and quantified as a stoichiometric readout of NS1. Three functional monomers with hydrophobic, positively charged, and negatively charged groups were synthesized by click reactions in terms of the signature peptide. These three functional monomers provide abundant recognition sites for the peptide, allowing the peptide template to be effectively imprinted during polymerization. The imprinting conditions were optimized, and the molecularly imprinted polymers were characterized and used for enriching the signature peptide from digested serum samples by solid-phase extraction and then detected by UHPLC-MS/MS. The proposed method is used to detect the dengue virus NS1 in clinical samples and holds significant promise for early confirmation of dengue virus infection.

Dummy Molecularly Imprinted Polymers Using DNP as a Template Molecule for Explosive Sensing and Nitroaromatic Compound Discrimination

This work reports a rapid, simple and low-cost voltammetric sensor based on a dummy molecularly imprinted polymer (MIP) that uses 2,4-dinitrophenol (DNP) as a template for the quantification of 2,4,6-trinitrotoluene (TNT) and DNP, and the identification of related substances. Once the polymer was synthesised by thermal precipitation polymerisation, it was integrated onto a graphite epoxy composite (GEC) electrode via sol–gel immobilisation. Scanning electron microscopy (SEM) was performed in order to characterise the polymer and the sensor surface. Responses towards DNP and TNT were evaluated, displaying a linear response range of 1.5 to 8.0 µmol L−1 for DNP and 1.3 to 6.5 µmol L−1 for TNT; the estimated limits of detection were 0.59 µmol L−1 and 0.29 µmol L−1, for DNP and TNT, respectively. Chemometric tools, in particular principal component analysis (PCA), demonstrated the possibilities of the MIP-modified electrodes in nitroaromatic and potential interfering species discrimination with multiple potential applications in the environmental field.

A sandwich sensor based on imprinted polymers and aptamers for highly specific double recognition of viruses

Highly selective and highly efficient identification of large viruses has been a major obstacle in the field of virus detection. In this work, a novel sandwich resonance light scattering sensor was designed based on molecularly imprinted polymers (MIPs) and aptamers for the first time. One of the recognition probes was obtained by molecular imprinting using environmentally friendly carbon spheres as carriers and the other by modification of the aptamer that can specifically recognize hepatitis B virus (HBV) on the surface of silicon spheres. In the presence of both probes, an MIP-HBV-aptamer sandwich structure was formed continuously in the system with the increase in HBV concentration, resulting in a strong resonance light scattering response. Finally, satisfactory selectivity and sensitivity were obtained, and the imprinting factor was as high as 7.56, which was higher than that reported in previous works of viral molecular imprinting sensor. In addition, it is of great significance to solve the problem of insufficient selectivity of traditional detection methods for macromolecular targets.

Ultra-durable, multi-template molecularly imprinted polymers for ultrasensitive monitoring and multicomponent quantification of trace sulfa antibiotics

Traditional analysis methods are susceptible to interference caused by the complexity of sample matrices, and detector surface fouling arising from nonspecific adsorption of microorganisms (in biological samples) which leads in particular to a gradual loss of sensitivity. Imprinted materials can be used to effectively reduce interference originating in the matrices. However, the poor reproducibility and multicomponent quantification of trace antibiotics represent significant challenges to the detection process. Meanwhile, the high biological risk presented by bacterial antibiotic immunity and the persistence of antibiotics in foodstuffs, especially meat, both caused by the overuse of sulfonamide antibiotics, remain urgent issues. Here, we present the first example of a method for the accurate quantification of trace sulfa antibiotics (SAs) based on multi-template imprinted polymers (MMIPs). Levels of multiple SAs have been simultaneously successfully quantified by applying MMIP extraction coupled with UPLC-MS/MS analysis. This method shows excellent linearity of detection in the range of 0.1-500 μg L^-1, and ultrasensitivity with low limits of detection of 0.03 μg L^-1. The maximum SA residue recovered from sample tissues by using MMIPs was 5.48 μg g^-1. MMIP-coupled UPLC-MS/MS quantification of SAs is an accurate and repeatable method for the monitoring of SA accumulation in mouse tissue samples. It also provides an effective strategy for the tracking and quantification of drugs in other biological samples.

Construction of a microfluidic platform integrating online protein fractionation, denaturation, digestion, and peptide enrichment

Microfluidic system with multi-functional integration of high-throughput protein/peptide separation ability has great potential for improving the identification capacity of biological samples in proteomics. In this paper, a sample treatment platform was constructed by integrating reversed phase chromatography, immobilized enzyme reactor (IMER) and imprinted monolith through a microfluidic chip to achieve the online proteins fractionation, denaturation, digestion and peptides enrichment. We firstly synthesized a poly-allyl phenoxyacetate (AP) monolith and a lysine-glycine-glycine (KGG) imprinted monolith separately, and investigated in detail their performance in fractionating proteins and extracting KGG from the protein digests of MCF-7 cell. The removal percentage of 94.6% for MCF-7 cell protein and the recovery of 90.8% for KGG were obtained. The number of proteins and peptides identified on this microfluidic platform was 2,004 and 8,797, respectively, which was 2.8-fold and 3.0-fold higher than that of untreatment sample. The time consumed by this platform for a sample treatment was about 9.6 h, less than that of conventional method (approximate 13.3 h). In addition, this platform can enrich some peptide fragments containing KGG based on imprinted monolith, which can be served for the identification of ubiquitin-modified proteomics. The successful construction of this integrated microfluidic platform provides a considerable and efficient technical tool for simultaneous identification of proteomics and post-translational modification proteomics information.

Metal-organic frameworks as advanced materials for sample preparation of bioactive peptides

Development of novel affinity materials and separation techniques is crucial for the progress of modern proteomics and peptidomics. Detection of peptides and proteins from complex matrices still remains a challenging task due to the highly complicated biological composition, low abundance of target molecules, and large dynamic range of proteins. As an emerging area of analytical science, metal-organic framework (MOF)-based separation of proteins and peptides is attracting growing interest. This minireview summarizes the recent advances in MOF-based affinity materials for the sample preparation of proteins and peptides. Some newly emerging MOF nanoreactors for the degradation of peptides and proteins are introduced. An update of MOF-based affinity materials for the isolation of glycopeptides, phosphopeptides and low-abundance endogenous peptides in the last two years is focused on. The separation mechanism is discussed along with the chemical structures of MOFs. Finally, the remaining challenges and future development of MOFs in analyzing peptides and proteins in complicated biological samples are discussed.

Hierarchically Imprinted Polymer for Peptide Tag Recognition Based on an Oriented Surface Epitope Approach

FLAG tag (DYKDDDDK) is a short peptide commonly used for the purification of recombinant proteins. The high price of the affinity columns and their limited reusability are a shortcoming for their widespread use in biotechnology applications. Molecularly imprinted polymers (MIPs) can circumvent some of the limitations of bioaffinity columns for such applications, including long-term stability, reusability, and cost. We report herein the synthesis of MIPs selective to the FLAG tag by hierarchical imprinting. Using the epitope imprinting approach, a 5-amino acid peptide DYKDC was selected as a template and was covalently immobilized on the surface of microporous silica beads, previously functionalized with different aminosilanes, namely, 3-(2-aminoethylamino)propyldimethoxymethylsilane, AEAPMS, and N-(2-aminoethyl)-2,2,4-trimethyl-1-aza-2-silacyclopentane, AETAZS. We investigated the effect of the type of silane on the production of homogeneous silane-grafted layers with the highest extent of silanol condensation as possible using ²⁹Si CP/MAS NMR. We observed that the right orientation of the imprinted cavities can substantially improve analyte recoveries from the MIP. After template and silica removal, the DYKDC-MIPs were used as sorbents for solid-phase extraction (molecularly imprinted solid-phase extraction) of the FLAG peptide, showing that the polymer prepared with AETAZS-bound silica beads contained binding sites more selective to the tag (R_MIP-AZA = 87.4% vs R_NIP-AZA = 4.1%, n = 3, RSD ≤ 4.2%) than those prepared using AEAPMS (R_MIP-DM = 73.4% vs R_NIP-DM = 23.2%, n = 3, RSD ≤ 4.0%) as a functionalization agent. An extensive computational molecular modeling study was also conducted, shedding some light on the interaction mechanism between the FLAG peptide and the imprinted template in the binding cavities.

Photoresponsive Surface Molecularly Imprinted Polymers for the Detection of Profenofos in Tomato and Mangosteen

As a moderately toxic organophosphorus pesticide, profenofos (PFF) is widely used in agricultural practice, resulting in the accumulation of a high amount of PFF in agricultural products and the environment. This will inevitably damage our health. Therefore, it is important to establish a convenient and sensitive method for the detection of PFF. This paper reports a photoresponsive surface-imprinted polymer based on poly(styrene-co-methyl acrylic acid) (PS-co-PMAA@PSMIPs) for the detection of PFF by using carboxyl-capped polystyrene microspheres (PS-co-PMAA), PFF, 4-((4-(methacryloyloxy)phenyl)diazenyl) benzoic acid, and triethanolamine trimethacrylate as the substrate, template, functional monomer, and cross-linker, respectively. PS-co-PMAA@PSMIP shows good photoresponsive properties in DMSO/H2O (3:1, v/v). Its photoisomerization rate constant exhibits a good linear relationship with PFF concentration in the range of 0~15 μmol/L. PS-co-PMAA@PSMIP was applied for the determination of PFF in spiked tomato and mangosteen with good recoveries ranging in 94.4-102.4%.

Carbon dots-embedded epitope imprinted polymer for targeted fluorescence imaging of cervical cancer via recognition of epidermal growth factor receptor

A carbon dots-embedded epitope imprinted polymer (C-MIP) was fabricated for targeted fluorescence imaging of cervical cancer by specifically recognizing the epidermal growth factor receptor (EGFR). The core-shell C-MIP was prepared by a reverse microemulsion polymerization method. This method used silica nanoparticles embedded with carbon dots as carriers, acrylamide as the main functional monomer, and N-terminal nonapeptides of EGFR modified by palmitic acid as templates. A series of characterizations (transmission electron microscope, dynamic light scattering, X-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, zeta potential, and energy dispersive X-ray spectroscopy) prove the successful synthesis of C-MIP. The fluorescence of C-MIP is quenched by the epitopes of EGFR due to the specific recognition of epitopes of EGFR through their imprinted cavities (analytical excitation/emission wavelengths, 540 nm/610 nm). The linear range of fluorescence quenching is 2.0 to 15.0 μg mL^-1 and the determination limit is 0.73 μg mL^-1. The targeted imaging capabilities of C-MIP are demonstrated through in vitro and in vivo experiments. The laser confocal imaging results indicate that HeLa cells (over-expression EGFR) incubated with C-MIP show stronger fluorescence than that of MCF-7 cells (low-expression EGFR), revealing that C-MIP can target tumor cells overexpressing EGFR. The results of imaging experiments in tumor-bearing mice exhibit that C-MIP has a better imaging effect than C-NIP, which further proves the targeted imaging ability of C-MIP in vivo. Graphical abstract An oriented epitope imprinted polymer embedded with carbon dots was prepared for the determination of the epitopes of epidermal growth factor receptor and targeted fluorescence imaging of cervical cancer.

Combinatorial screening of polymer nanoparticles for their ability to recognize epitopes of AAV-neutralizing antibodies

A library of 17 nanoparticles made of acrylate and methacrylate copolymers is prepared, characterized, and screened against six epitopes of adeno-associated viruses (AAV)-neutralizing antibodies to assess their affinity and specificity. Peptide epitopes are immobilized onto the surface of glass beads, packed in filtration microplates, and incubated with fluorescein-labelled nanoparticles. Following intense washing, the affinity of nanoparticles to immobilized epitopes is assessed by measuring the fluorescence of captured nanoparticles. The results show that polar monomers, acrylic acid in particular, have a positive impact on polymer affinity towards all peptides used in this study. The presence of hydrophobic monomers, on other hand, has a negative impact on polymer binding. The composition of peptides used in this study has no noticeable impact on the affinity of synthesized nanoparticles. The affinity of nanoparticles with the highest affinity to peptide targets does not exceed millimolar level. Overall, it is found that the synthesized library showed modest affinity but lacked specificity, which should be further "tuned," for example, by using molecular imprinting to achieve an acceptable level of affinity and specificity for practical application.

New protocol for optimisation of polymer composition for imprinting of peptides and proteins

A novel screening tool for high-throughput optimisation of monomer composition for imprinting of peptides and proteins.