Sensing HIV Protease and Its Inhibitor Using "Helical Epitope"-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.

Preparation and Application Progress of Imprinted Polymers

Due to the specific recognition performance, imprinted polymers have been widely investigated and applied in the field of separation and detection. Based on the introduction of the imprinting principles, the classification of imprinted polymers (bulk imprinting, surface imprinting, and epitope imprinting) are summarized according to their structure first. Secondly, the preparation methods of imprinted polymers are summarized in detail, including traditional thermal polymerization, novel radiation polymerization, and green polymerization. Then, the practical applications of imprinted polymers for the selective recognition of different substrates, such as metal ions, organic molecules, and biological macromolecules, are systematically summarized. Finally, the existing problems in its preparation and application are summarized, and its prospects have been prospected.

Molecularly imprinted nanoparticles with recognition properties towards diphtheria toxin for ELISA applications

Plastic antibodies can be used for in vitro neutralization of biomacromolecules with different fragments due to their potential in separation, purification, chemical sensor, catalysis and drug production studies. These polymer nanoparticles with binding affinity and selectivity comparable to natural antibodies were prepared using functional monomer synthesis and copolymerization of acrylic monomers via miniemulsion polymerization. As a result, the in vitro cytotoxic effect from diphtheria toxin was reduced by MIPs. In vitro imaging experiments of polymer nanoparticles (plastic antibodies) were performed to examine the interaction of diphtheria toxin with actin filaments, and MIPs inhibited diphtheria toxin damage on actin filaments. The enzyme-linked immunosorbent assay (ELISA) was performed with plastic antibodies labeled with biotin, and it was determined that plastic antibodies could also be used for diagnostic purposes. We report that molecularly imprinted polymers (MIPs), which are biocompatible polymer nanoparticles, can capture and reduce the effect of diphtheria toxic and its fragment A.

Peptide conformational imprints enhanced the catalytic activity of papain for esterification

Peptide conformational imprints (PCIs) offer a promising perspective to directly generate binding sites for preserving enzymes with high catalytic activity and stability. In this study, we synthesized a new chiral cross-linker cost-effectively for controlling the matrix morphology of PCIs on magnetic particles (PCIMPs) to stabilize their recognition capability. Meanwhile, based on the flank part of the sequences on papain (PAP), three epitope peptides were selected and synthesized. Molecularly imprinted polymers (MIPs) were then fabricated in the presence of the epitope peptide using our new cross-linker on magnetic particles (MPs) to generate PCIMPs. PCIMPs were formed with helical cavities that complement the PAP structure to adsorb specifically at the targeted position of PAP. PCIMPs^65–79 were found to have the best binding parameters to the PAP with K_d = 0.087 μM and B_max = 4.56 μM. Upon esterification of N-Boc-His-OH, proton nuclear magnetic resonance (¹H-NMR) was used to monitor the yield of the reaction and evaluate the activity of PAP/PCIMPs. The kinetic parameters of PAP/PCIMPs^65–79 were calculated as V_max = 3.0 μM s⁻¹, K_m = 5 × 10⁻² M, k_cat = 1.1 × 10^–1 s⁻¹, and k_cat/K_m = 2.2 M⁻¹ s⁻¹. In addition, PAP is bound tightly to PCIMPs to sustain its activity after four consecutive cycles.

Integration of Adenylate Kinase 1 with Its Peptide Conformational Imprint

In the present study, molecularly imprinted polymers (MIPs) were used as a tool to grasp a targeted α-helix or β-sheet of protein. During the fabrication of the hinge-mediated MIPs, elegant cavities took shape in a special solvent on quartz crystal microbalance (QCM) chips. The cavities, which were complementary to the protein secondary structure, acted as a peptide conformational imprint (PCI) for adenylate kinase 1 (AK1). We established a promising strategy to examine the binding affinities of human AK1 in conformational dynamics using the peptide-imprinting method. Moreover, when bound to AK1, PCIs are able to gain stability and tend to maintain higher catalytic activities than free AK1. Such designed fixations not only act on hinges as accelerators; some are also inhibitors. One example of PCI inhibition of AK1 catalytic activity takes place when PCI integrates with an AK1_9-23 β-sheet. In addition, conformation ties, a general MIP method derived from random-coil AK1_133-144 in buffer/acetonitrile, are also inhibitors. The inhibition may be due to the need for this peptide to execute conformational transition during catalysis.

Plastic Antibodies Mimicking the ACE2 Receptor for Selective Binding of SARS-CoV-2 Spike

Molecular imprinting has proven to be a versatile and simple strategy to obtain selective materials also termed "plastic antibodies" for a wide variety of species, i.e., from ions to macromolecules and viruses. However, to the best of the authors' knowledge, the development of epitope-imprinted polymers for selective binding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not reported to date. An epitope from the SARS-CoV-2 spike protein comprising 17 amino acids is used as a template during the imprinting process. The interactions between the epitope template and organosilane monomers used for the polymer synthesis are predicted via molecular docking simulations. The molecularly imprinted polymer presents a 1.8-fold higher selectivity against the target epitope compared to non-imprinted control polymers. Rebinding studies with pseudoviruses containing SARS-CoV-2 spike protein demonstrate the superior selectivity of the molecularly imprinted matrices, which mimic the interactions of angiotensin-converting enzyme 2 receptors from human cells. The obtained results highlight the potential of SARS-CoV-2 molecularly imprinted polymers for a variety of applications including chem/biosensing and antiviral delivery.

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.

[Recent advances in applications of fragment/dummy molecularly imprinted polymers]

Molecularly imprinted polymers (MIPs) are designed to mimic the specific binding principle of enzymes to substrates or antigens to antibodies, while holding several advantages such as structure predictability, recognition specificity, easy preparation, low cost, high physical robustness, and thermal stability. Therefore, they have been widely applied in many fields including sample preparation (pretreatment), sensing analysis (chemo/biosensors), biomedicine, and environment/food analysis. To date, several strategies were developed for MIPs preparation, aiming to simplify the preparation process and/or improve the properties of the polymers, greatly broadening its usability. The exploration in various advanced imprinting strategies and their combinational use has become a research hotspot in MIPs preparation, among which the fragment imprinting strategy and the dummy template imprinting strategy are especially favored. Fragment imprinting, also called segment imprinting, uses a partial structure of the target molecule as a pseudo-template to prepare MIPs. This strategy is useful to target molecules that are not easy to obtain or that are too large to be used as templates, providing a feasible method for imprinting target analytes that are easy to inactivate or infect, as well as macromolecules that are difficult to imprint. In turn, dummy template imprinting uses molecules with structure, shape, and size similar to the target analytes as templates for imprinting. Because the target is not directly used as a template, this strategy can overcome problems of template leakage, as well as solve target molecule-related difficulties as they can be expensive, infectious, flammable, explosive, or chemically instable. This mini-review compiles information of several articles published in the last four years across ACS, Elsevier, RSC, and other databases, summarizing the most recent advances in the application of fragment/dummy template MIPs (FMIPs/DMIPs). Herein, the biomedical application of FMIPs is mainly addressed as a strategy for the detection of proteins and microorganisms, and the application of FMIPs in the field of food analysis is also explored. In recent years, the imprinting of mammalian cells has made some progress in the application of FMIPs. Mammalian cells, especially cancer cells, overexpress some proteins and sugars, which are good fragment templates. Consequently, the fragment imprinting strategy is widely used in cancer cell imaging, localization, and treatment. Moreover, due to the complicated structure and easy inactivation of some proteins, their MIPs are often prepared by fragment imprinting (also called epitope imprinting). As some microorganisms are infectious, imprinting microorganisms directly can pose a risk; therefore it is safer to also use the fragment imprinting strategy in such cases. The recent application of fragment imprinting strategy in other areas remains scarce. Nonetheless, three studies in the food analysis have explored this possibility. DMIPs are widely used in sample pretreatment and sensing analysis, and they are mainly used as SPE adsorbents for packed SPE, dispersive SPE (DSPE), magnetic SPE (MSPE), and matrix solid phase dispersion (MSPD) extraction. In addition, DMIPs are employed as molecularly imprinted membrane materials. As a result, by virtue of DMIPs, selective extraction and enrichment of target analytes from complicated samples can be achieved. MIP-based sensors can either recognize or transduce, meaning that they can specifically recognize and bind target analytes as well as generate output signals for detection. Because of the high selectivity of MIPs, the use of a dummy template imprinting strategy solves the problem of template leakage in the process of recognition and adsorption, further improving the detection accuracy and sensitivity of the sensor. These features expand the application range of MIP-based sensors. This review briefly overviews the construction and application of chemiluminescence and fluorescence sensors based on DMIPs. Lastly, the advantages and disadvantages, differences, and relationships among the two strategies are summarized. Despite of their potential, four main challenges still remain as major setbacks for the application of FMIPs and DMIPs: (i) the difficulty to select or prepare appropriate fragment templates and dummy templates; (ii) how to ensure that there is almost no difference in the recognition adsorption selectivity between the fragment/dummy template and the original template, so as to ensure optimal recognition specificity; (iii) the use of, environment-friendly reagents to reduce pollution during FMIPs/DMIPs preparation and use to conform with green chemistry requirements; (iv) how to strengthen the industrial and commercial applications of FMIPs and DMIPs. Therefore, significant efforts should be made to develop new imprinting strategies and techniques, as well as to adopt combinational imprinting approaches for FMIPs/DMIPs preparation to expedite the sustainable development and efficient application of FMIPs and DMIPs.

Deviation of Trypsin Activity Using Peptide Conformational Imprints

In this study, a methodology utilizing peptide conformational imprints (PCIs) as a tool to specifically immobilize porcine pancreatic alpha-trypsin (PPT) at a targeted position is demonstrated. Owing to the fabrication of segment-mediated PCIs on the magnetic particles (PCIMPs), elegant cavities complementary to the PPT structure are constructed. Based on the sequence on targeted PPT, the individual region of the enzyme is trapped with different template-derived PCIMPs to show certain types of inhibition. Upon hydrolysis, N-benzoyl-L-arginine ethyl ester (BAEE) is employed to assess the hydrolytic activity of PCIMPs bound to the trypsin using high-performance liquid chromatography (HPLC) analysis. Further, the kinetic data of four different PCIMPs are compared. As a result, the PCIMPs presented non-competitive inhibition toward trypsin, according to the Lineweaver-Burk plot. Further, the kinetic analysis confirmed that the best parameters of PPT/PCIMPs 233-245+G were Vmax = 1.47 × 10-3 mM s-1, Km = 0.42 mM, kcat = 1.16 s-1, and kcat/Km = 2.79 mM-1 s-1. As PPT is bound tightly to the correct position, its catalytic activities could be sustained. Additionally, our findings stated that the immobilized PPT could maintain stable activity even after four successive cycles.

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.