Peptide epitope-imprinted polymer microarrays for selective protein recognition. Application for SARS-CoV-2 RBD protein

Rational design of MIPs for the detection of Myxovirus resistance protein A (MxA), a biomarker for viral infection

Accurate diagnosis is crucial for effective patient care and the containment of antimicrobial resistance outbreaks. The intricate challenge of distinguishing bacterial from viral infections, coupled with limited diagnostic tools and overlapping symptoms has driven the utilization of molecular imprinting techniques. This study focuses on developing cost-effective, chemically stable antibody analogs for the interferon-induced protein myxovirus resistance protein A (MxA). MxA is an intracellular, cytoplasmic GTPase having activity against a wide range of viruses and serves as a distinctive biomarker for viral infections. We utilized computational design to guide the polymer assembly, centering on epitope imprinting to target MxA-specific regions crucial for interaction. Molecular docking calculations, alongside a pioneering multi-monomer simultaneous docking (MMSD) protocol, efficiently elucidate cooperativity during pre-polymerization. Monomer binding affinity scores, such as for APTMS, exhibited notable increase, ranging from -3.11 to -13.03 kcal/mol across various MMSD combinations compared to a maximum of -2.78 kcal/mol in single monomer docking, highlighting the capacity of MMSD in elucidating crucial monomer-monomer interactions. This computational approach provides a theoretical alternative to labor-intensive experimental optimization, streamlining the development process for synthetic receptors. Simulations reveal unique interactions enhancing MIP-peptide complementarity, yielding optimized receptors selectively binding to MxA epitopes. The obtained MIPs demonstrated a maximum adsorption capacity of approximately 12 mg/g and captured 1.6 times more epitope and 2.6 times more epitope containing MxA protein than corresponding NIPs. A proof-of-concept study demonstrates MxA protein binding to synthetic receptors, highlighting the potential of MIPs, analogous to antibodies, in overcoming current diagnostic challenges for precise detection of viral infection.

Computationally Designed Epitope-Mediated Imprinted Polymers versus Conventional Epitope Imprints for the Detection of Human Adenovirus in Water and Human Serum Samples

Detection of pathogenic viruses for point-of-care applications has attracted great attention since the COVID-19 pandemic. Current virus diagnostic tools are laborious and expensive, while requiring medically trained staff. Although user-friendly and cost-effective biosensors are utilized for virus detection, many of them rely on recognition elements that suffer major drawbacks. Herein, computationally designed epitope-imprinted polymers (eIPs) are conjugated with a portable piezoelectric sensing platform to establish a sensitive and robust biosensor for the human pathogenic adenovirus (HAdV). The template epitope is selected from the knob part of the HAdV capsid, ensuring surface accessibility. Computational simulations are performed to evaluate the conformational stability of the selected epitope. Further, molecular dynamics simulations are executed to investigate the interactions between the epitope and the different functional monomers for the smart design of eIPs. The HAdV epitope is imprinted via the solid-phase synthesis method to produce eIPs using in silico-selected ingredients. The synthetic receptors show a remarkable detection sensitivity (LOD: 102 pfu mL-1) and affinity (dissociation constant (Kd): 6.48 × 10-12 M) for HAdV. Moreover, the computational eIPs lead to around twofold improved binding behavior than the eIPs synthesized with a well-established conventional recipe. The proposed computational strategy holds enormous potential for the intelligent design of ultrasensitive imprinted polymer binders.

Specific features of epitope-MIPs and whole-protein MIPs as illustrated for AFP and RBD of SARS-CoV-2

Molecularly imprinted polymer (MIP) nanofilms for alpha-fetoprotein (AFP) and the receptor binding domain (RBD) of the spike protein of SARS-CoV-2 using either a peptide (epitope-MIP) or the whole protein (protein-MIP) as the template were prepared by electropolymerization of scopoletin. Conducting atomic force microscopy revealed after template removal and electrochemical deposition of gold a larger surface density of imprinted cavities for the epitope-imprinted polymers than when using the whole protein as template. However, comparable affinities towards the respective target protein (AFP and RBD) were obtained for both types of MIPs as expressed by the KD values in the lower nanomolar range. On the other hand, while the cross reactivity of both protein-MIPs towards human serum albumin (HSA) amounts to around 50% in the saturation region, the nonspecific binding to the respective epitope-MIPs is as low as that for the non-imprinted polymer (NIP). This effect might be caused by the different sizes of the imprinted cavities. Thus, in addition to the lower costs the reduced nonspecific binding is an advantage of epitope-imprinted polymers for the recognition of proteins.

Electrochemically Synthesized MIP Sensors: Applications in Healthcare Diagnostics

Early-stage detection and diagnosis of diseases is essential to the prompt commencement of treatment regimens, curbing the spread of the disease, and improving human health. Thus, the accurate detection of disease biomarkers through the development of robust, sensitive, and selective diagnostic tools has remained cutting-edge scientific research for decades. Due to their merits of being selective, stable, simple, and having a low preparation cost, molecularly imprinted polymers (MIPs) are increasingly becoming artificial substitutes for natural receptors in the design of state-of-the-art sensing devices. While there are different MIP preparation approaches, electrochemical synthesis presents a unique and outstanding method for chemical sensing applications, allowing the direct formation of the polymer on the transducer as well as simplicity in tuning the film properties, thus accelerating the trend in the design of commercial MIP-based sensors. This review evaluates recent achievements in the applications of electrosynthesized MIP sensors for clinical analysis of disease biomarkers, identifying major trends and highlighting interesting perspectives on the realization of commercial MIP-endowed testing devices for rapid determination of prevailing diseases.

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.

Sequentially Controlled Recognition of Different Proteins Using Programmable Protein Imprinted Nanospheres

Although protein imprinted materials with multiple templates are developed to selectively separate different proteins, it is difficult to achieve the programmed adsorption and separation of different proteins using one material, because the available protein imprinted materials are constructed through irreversible crosslinking and their structures are unprogrammable and non-reconstructive. Herein, a novel nanosphere (MS@PTL-g-PNIPAM) is designed, which not only is temperature and pH responsive but also can dynamically reversibly crosslink/de-crosslink under ultraviolet light of different wavelengths. With the help of the dynamically reversible photo-crosslinking, the nanospheres can be repeatedly programmed into protein imprinted nanospheres toward different target proteins. Moreover, the prepared imprinted nanospheres can easily achieve the controlled rebinding and release of target proteins, benefiting from the introduced temperature- and pH-responsive moieties. As a consequence, this study realizes the specific separation of different target proteins from protein mixture and the real bovine blood sequentially by programming one material. It is resource saving, time saving, recyclable, and it will provide convenience for protein imprinted materials to use in the blood purification, drug delivery, and virus detection.

Rapid sub-nanomolar protein determination in serum using electropolymerized molecularly imprinted polymers (E-MIPs)

Rapid detection of biologicals is important for a range of applications such as medical screening and diagnostics. Antibodies are typically employed for biosensing with high sensitivity and selectivity but can take months to prepare. Here, we investigate electropolymerized molecularly imprinted polymers (E-MIPs), which are produced in minutes as alternative-antibody rapid biosensors for the selective recognition of model proteins bovine haemoglobin (BHb) and bovine serum albumin (BSA). We evaluated two disposable screen-printed electrodes (SPE) designated AT-Au and BT-Au based on their different annealing temperatures. E-MIPs for BHb demonstrated an imprinting factor of 146 : 1 at 1 nM and 12 : 1 at 0.1 nM, showing high effectiveness of E-MIPs compared to their control non-imprinted polymers. The BHb imprinted E-MIP, when tested against BSA as a non-target protein, gave a selectivity factor of 6 : 1 for BHb. Sensor sensitivity directly depended on the nature of the SPE, with AT-Au SPE demonstrating limits of detection in the sub-micromolar range typically achieved for MIPs, while BT-Au SPE exhibited sensitivity in the sub-nanomolar range for target protein. We attribute this to differences in electrode surface area between AT-Au and BT-Au SPEs. The E-MIPs were also tested in calf serum as a model biological medium. The BT-Au SPE MIPs detected the presence of target protein in <10 min with an LOD of 50 pM and LOQ of 100 pM, suggesting their suitability for protein determination in serum with minimal sample preparation. Using electrochemical impedance spectroscopy, we determine equilibrium dissociation constants (KD) for E-MIPs using the Hill-Langmuir adsorption model. KD of BHb E-MIP was determined to be 0.86 ± 0.11 nM.

Highly Selective Aptamer-Molecularly Imprinted Polymer Hybrids for Recognition of SARS-CoV-2 Spike Protein Variants

Virus recognition has been driven to the forefront of molecular recognition research due to the COVID-19 pandemic. Development of highly sensitive recognition elements, both natural and synthetic is critical to facing such a global issue. However, as viruses mutate, it is possible for their recognition to wane through changes in the target substrate, which can lead to detection avoidance and increased false negatives. Likewise, the ability to detect specific variants is of great interest for clinical analysis of all viruses. Here, a hybrid aptamer-molecularly imprinted polymer (aptaMIP), that maintains selective recognition for the spike protein template across various mutations, while improving performance over individual aptamer or MIP components (which themselves demonstrate excellent performance). The aptaMIP exhibits an equilibrium dissociation constant of 1.61 nM toward its template which matches or exceeds published examples of imprinting of the spike protein. The work here demonstrates that "fixing" the aptamer within a polymeric scaffold increases its capability to selectivity recognize its original target and points toward a methodology that will allow variant selective molecular recognition with exceptional affinity.

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.

Past and present of electrochemical science in Hungary

The electrochemistry-related scientific activities in Hungary over the past 3 decades are reviewed. In the first section, we summarize those research areas that are already ceased; in the next section, the ongoing research is discussed; finally, the trends and outlook are highlighted. A special emphasis is put on new experimental methods elaborated in the country.

Evaluation of the interaction between SARS-CoV-2 spike glycoproteins and the molecularly imprinted polypyrrole

The SARS-CoV-2 spike glycoprotein (SARS-CoV-2-S) was used as a template molecule and polypyrrole (Ppy) was applied as an electro-generated conducting polymer, which was acting as a matrix for the formation of molecular imprints. Two types of Ppy-layers: molecularly imprinted polypyrrole (MIP-Ppy) and non-imprinted polypyrrole (NIP-Ppy) were electrochemically deposited on the working platinum electrode. The performance of electrodes modified by MIP-Ppy and NIP-Ppy layers was evaluated by pulsed amperometric detection (PAD). During the assessment of measurement results registered by PAD, the integrated Cottrell equation (Anson plot) was used to calculate the amount of charge passed through the MIP-Ppy and NIP-Ppy layers. The interaction between SARS-CoV-2 spike glycoproteins and molecularly imprinted polypyrrole (MIP-Ppy) was assessed by the Anson plot based calculations. This assessment reveals that SARS-CoV-2-S glycoproteins are interacting with MIP-Ppy more strongly than with NIP-Ppy.

How an ACE2 mimicking epitope-MIP nanofilm recognizes template-related peptides and the receptor binding domain of SARS-CoV-2

Here we aim to gain a mechanistic understanding of the formation of epitope-imprinted polymer nanofilms using a non-terminal peptide sequence, i.e. the peptide GFNCYFP (G485 to P491) of the SARS-CoV-2 receptor binding domain (RBD). This epitope is chemisorbed on the gold surface through the central cysteine 488 followed by the electrosynthesis of a ∼5 nm thick polyscopoletin film around the surface confined templates. The interaction of peptides and the parent RBD and spike protein with the imprinted polyscopoletin nanofilm was followed by electrochemical redox marker gating, surface enhanced infrared absorption spectroscopy and conductive AFM. Because the use of non-terminal epitopes is especially intricate, here we characterize the binding pockets through their interaction with 5 peptides rationally derived from the template sequence, i.e. implementing central single amino acid mismatch as well as elongations and truncations at its C- and N- termini. Already a single amino acid mismatch, i.e. the central Cys488 substituted by a serine, results in ca. 15-fold lower affinity. Further truncation of the peptides to tetrapeptide (EGFN) and hexapeptide (YFPLQS) results also in a significantly lower affinity. We concluded that the affinity towards the different peptides is mainly determined by the four amino acid motif CYFP present in the sequence of the template peptide. A higher affinity than that for the peptides is found for the parent proteins RBD and spike protein, which seems to be due to out of cavity effects caused by their larger footprint on the nanofilm surface.

Ring -opening of polythiolactones to construct protein-imprinted nanospheres with high recognition and regulation capabilities

Developing and preparing novel protein-imprinted nanomaterials with high recognition ability remains challenging because it is difficult to controllably and orderly design and arrange functional groups on the imprinted polymer layers of protein-imprinted nanomaterials to improve their protein identification. Herein, we present a new technology using rationally designed polythiolactone-decorated magnetic nanospheres as the precursor of multifunctionalized imprinted materials. Moreover, the strategy of ring-opening the polythiolactione layers using primary amines with terminal alcohols, acids and pyrrolidines introduces abundant recognition sites, which enhance the recognition for template proteins through multiple hydrogen-bonding and hydrophobic interactions. Thiols generated in situ by the ring-opening reaction provide sufficient crosslinking sites proximate to each recognition site for the formation of imprinting cavities, endowing the imprinted nanospheres with promising regulation capabilities. Based on the rational design, the imprinted nanospheres can be prepared conveniently and present tunable rebinding capacity and specificity for bovine serum albumin (BSA). The maximum saturated rebinding capacity of imprinted materials for BSA is up to 285 ± 15 mg g^-1 and the highest imprinting factor reaches 5.79. The simple and versatile strategy demonstrated in this study shows promise for the design of other protein-imprinted materials with high recognition ability.

An advantageous application of molecularly imprinted polymers in food processing and quality control

In the global market era, food product control is very challenging. It is impossible to track and control all production and delivery chains not only for regular customers but also for the State Sanitary Inspections. Certified laboratories currently use accurate food safety and quality inspection methods. However, these methods are very laborious and costly. The present review highlights the need to develop fast, robust, and cost-effective analytical assays to determine food contamination. Application of the molecularly imprinted polymers (MIPs) as selective recognition units for chemosensors' fabrication was herein explored. MIPs enable fast and inexpensive electrochemical and optical transduction, significantly improving detectability, sensitivity, and selectivity. MIPs compromise durability of synthetic materials with a high affinity to target analytes and selectivity of molecular recognition. Imprinted molecular cavities, present in MIPs structure, are complementary to the target analyte molecules in terms of size, shape, and location of recognizing sites. They perfectly mimic natural molecular recognition. The present review article critically covers MIPs' applications in selective assays for a wide range of food products. Moreover, numerous potential applications of MIPs in the food industry, including sample pretreatment before analysis, removal of contaminants, or extraction of high-value ingredients, are discussed.

The critical experimental aspects for developing pathogen electrochemical biosensors: A lesson during the COVID-19 pandemic

Though the bitter global pandemic posed a severe public health threat, it set an unprecedented stage for different research teams to present various technologies for detecting SARS-CoV-2, providing a rare and hard-won lesson for one to comprehensively survey the core experimental aspects in developing pathogens electrochemical biosensors. Apart from collecting all the published biosensor studies, we focused on the effects and consequences of using different receptors, such as antibodies, aptamers, ACE 2, and MIPs, which are one of the core topics of developing a pathogen biosensor. In addition, we tried to find an appropriate and distinctive application scenario (e.g., wastewater-based epidemiology) to maximize the advantages of using electrochemical biosensors to detect pathogens. Based on the enormous amount of information from those published studies, features that fit and favor wastewater pathogen detection can be picked up and integrated into a specific strategy to perform quantitative measurements in wastewater samples.

Protein-imprinted particles for coronavirus capture from solution

Molecular imprinting is a promising strategy to selectively adsorb viruses, but it requires discerning and validating epitopes that serve as effective imprinting templates. In this work, glycoprotein-imprinted particles were synthesized for coronavirus capture. Adsorption was maximized at pH 6 (the glycoprotein isoelectric point) where the glycoprotein-imprinted particles outperformed non-imprinted particles, adsorbing 4.96 × 10⁶  ± 3.33 × 10³ versus 3.54 × 10⁶  ± 1.39 × 10⁶ median tissue culture infectious dose/mg of the target coronavirus, human coronavirus - organ culture 43, within the first 30 min (p = 0.012). During competitive adsorption, with pH adjustment (pH 6), the glycoprotein-imprinted particles adsorbed more target virus than non-target coronavirus (human coronavirus - Netherland 63) with 2.34 versus 1.94 log removal in 90 min (p < 0.01). In contrast, the non-imprinted particles showed no significant difference in target versus non-target virus removal. Electrostatic potential calculation shows that the human coronavirus - organ culture 43 glycoprotein has positively charged pockets at pH 6, which may facilitate adsorption at lower pH values. Therefore, tuning the target virus glycoprotein charge via pH adjustment enhanced adsorption by minimizing repulsive electrostatic interactions with the particles. Overall, these results highlight the effective use of glycoprotein-imprinted particles for coronavirus capture and discern the merits and limitations of glycoprotein imprinting for the capture of enveloped viruses.

An insight into polyscopoletin electrosynthesis by a quality-by-design approach

Scopoletin (SP) as a functional monomer for electropolymerization has recently been investigated in the context of molecularly imprinted polymers for biosensing applications. Herein we describe an in-depth analysis of the mechanisms involved in the electropolymerization of SP toward the optimization of the experimental conditions for applications in sensor studies. PolySP films have been in situ synthesized on a standard glassy carbon electrodes by varying three independent experimental parameters, and the output of the analysis has been evaluated in terms of the resulting electroactive area and surface coverage. A quality-by-design approach including design-of-experiments principles and response surface methodology produced unbiased observations on the most relevant parameters to be controlled during the electropolymerization of SP. By combining the output of electroactive area and surface overage, we highlighted a strong dependence on the monomer concentration and scan rate. Thus, an appropriate selection of these two parameters should be sought to have an optimal electropolymerization process, leading to uniform films and homogeneous surface behavior. This study shows that the application of multi-factorial analysis in a comprehensive design of experiments allows the systematic study of polymer electrosynthesis. Therefore, this research is expected to guide further efforts in the electropolymerization of several functional monomers.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10853-022-07349-8.

Molecularly Imprinted Polymer-Based Sensors for SARS-CoV-2: Where Are We Now?

Since the first reported case of COVID-19 in 2019 in China and the official declaration from the World Health Organization in March 2021 as a pandemic, fast and accurate diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has played a major role worldwide. For this reason, various methods have been developed, comprising reverse transcriptase-polymerase chain reaction (RT-PCR), immunoassays, clustered regularly interspaced short palindromic repeats (CRISPR), reverse transcription loop-mediated isothermal amplification (RT-LAMP), and bio(mimetic)sensors. Among the developed methods, RT-PCR is so far the gold standard. Herein, we give an overview of the MIP-based sensors utilized since the beginning of the pandemic.

Biosensors for the Determination of SARS-CoV-2 Virus and Diagnosis of COVID-19 Infection

Monitoring and tracking infection is required in order to reduce the spread of the coronavirus disease 2019 (COVID-19), induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To achieve this goal, the development and deployment of quick, accurate, and sensitive diagnostic methods are necessary. The determination of the SARS-CoV-2 virus is performed by biosensing devices, which vary according to detection methods and the biomarkers which are inducing/providing an analytical signal. RNA hybridisation, antigen-antibody affinity interaction, and a variety of other biological reactions are commonly used to generate analytical signals that can be precisely detected using electrochemical, electrochemiluminescence, optical, and other methodologies and transducers. Electrochemical biosensors, in particular, correspond to the current trend of bioanalytical process acceleration and simplification. Immunosensors are based on the determination of antigen-antibody interaction, which on some occasions can be determined in a label-free mode with sufficient sensitivity.