Selective virus capture via hexon imprinting

Rational design based on multi-monomer simultaneous docking for epitope imprinting of SARS-CoV-2 spike protein

Among biomimetic strategies shaping engineering designs, molecularly imprinted polymer (MIP) technology stands out, involving chemically synthesised receptors emulating natural antigen-antibody interactions. These versatile 'designer polymers' with remarkable stability and low cost, are pivotal for in vitro diagnostics. Amid the recent global health crisis, we probed MIPs' potential to capture SARS-CoV-2 virions. Large biotemplates complicate MIP design, influencing generated binding site specificity. To precisely structure recognition sites within polymers, we innovated an epitope imprinting method supplemented by in silico polymerization component screening. A viral surface Spike protein informed epitope selection was targeted for MIP development. A novel multi-monomer docking approach (MMSD) was employed to simulate classical receptor-ligand interactions, mimicking binding reinforcement across multiple amino acids. Around 40 monomer combinations were docked to the epitope sequence and top performers experimentally validated via rapid fluorescence binding assays. Notably, high imprinting factor polymers correlated with MMSD predictions, promising rational MIP design applicable to diverse viral pathologies.

Advances and opportunities in process analytical technologies for viral vector manufacturing

Viral vectors are an emerging, exciting class of biologics whose application in vaccines, oncology, and gene therapy has grown exponentially in recent years. Following first regulatory approval, this class of therapeutics has been vigorously pursued to treat monogenic disorders including orphan diseases, entering hundreds of new products into pipelines. Viral vector manufacturing supporting clinical efforts has spurred the introduction of a broad swath of analytical techniques dedicated to assessing the diverse and evolving panel of Critical Quality Attributes (CQAs) of these products. Herein, we provide an overview of the current state of analytics enabling measurement of CQAs such as capsid and vector identities, product titer, transduction efficiency, impurity clearance etc. We highlight orthogonal methods and discuss the advantages and limitations of these techniques while evaluating their adaptation as process analytical technologies. Finally, we identify gaps and propose opportunities in enabling existing technologies for real-time monitoring from hardware, software, and data analysis viewpoints for technology development within viral vector biomanufacturing.

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.

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 In Silico Design of Molecularly Imprinted Polymers: Current Challenges and Future Potential

The rational design of molecularly imprinted polymers has evolved along with state-of-the-art experimental imprinting strategies taking advantage of sophisticated computational tools. In silico methods enable the screening and simulation of innovative polymerization components and conditions superseding conventional formulations. The combined use of quantum mechanics, molecular mechanics, and molecular dynamics strategies allows for macromolecular modelling to study the systematic translation from the pre- to the post-polymerization stage. However, predictive design and high-performance computing to advance MIP development are neither fully explored nor practiced comprehensively on a routine basis to date. In this review, we focus on different steps along the molecular imprinting process and discuss appropriate computational methods that may assist in optimizing the associated experimental strategies. We discuss the potential, challenges, and limitations of computational approaches including ML/AI and present perspectives that may guide next-generation rational MIP design for accelerating the discovery of innovative molecularly templated materials.

Icosahedral gold nanoparticles decorated with hexon protein: a surrogate for adenovirus serotype 5

Abstract

The development of synthetic particles that emulate real viruses in size, shape, and chemical composition is vital to the development of imprinted polymer-based sorbent materials (molecularly imprinted polymers, MIPs). In this study, we address surrogates for adenovirus type 5 (Adv 5) via the synthesis and subsequent modification of icosahedral gold nanoparticles (iAuNPs) decorated with the most abundant protein of the Adv 5 (i.e., hexon protein) at the surface. CTAB-capped iAuNPs with dimensions in the range of 40–90 nm were synthesized, and then CTAB was replaced by a variety of polyethylene glycols (PEGs) in order to introduce suitable functionalities serving as anchoring points for the attachment of the hexon protein. The latter was achieved by non-covalent linking of the protein to the iAuNP surface using a PEG without reactive termination (i.e., methoxy PEG thiol, mPEG-SH, Mn=800). Alternatively, covalent anchoring points were generated by modifying the iAuNPs with a bifunctional PEG (i.e., thiol PEG amine, SH-PEG-NH₂) followed by the addition of glutaraldehyde. X-ray photoelectron spectroscopy (XPS) confirmed the formation of the anchoring points at the iAuNP surface. Next, the amino groups present in the amino acids of the hexon protein interacted with the glutaraldehyde. iAuNPs before and after PEGylation were characterized using dynamic light scattering (DLS), XPS, transmission electron microscopy (TEM), scanning electron microscopy (SEM), and UV–Vis spectroscopy, confirming the CTAB–PEG exchange. Finally, the distinct red shift obtained in the UV–Vis spectra of the pegylated iAuNPs in the presence of the hexon protein, the increase in the hydrodynamic diameter, the change in the zeta potential, and the selective binding of the hexon-modified iAuNPs towards a hexon-imprinted polymer (HIP) confirmed success in both the covalent and non-covalent attachment at the iAuNP surface.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s00216-022-04368-x.

Advances in Electrochemical Nano-Biosensors for Biomedical and Environmental Applications: From Current Work to Future Perspectives

Modern life quality is strongly supported by the advances made in biosensors, which has been attributed to their crucial and viable contribution in point-of-care (POC) technology developments. POC devices are exploited for the fast tracing of disease progression, rapid analysis of water, and food quality assessment. Blood glucose meters, home pregnancy strips, and COVID-19 rapid tests all represent common examples of successful biosensors. Biosensors can provide great specificity due to the incorporation of selective bio-recognition elements and portability at significantly reduced costs. Electrochemical biosensor platforms are one of the most advantageous of these platforms because they offer many merits, such as being cheap, selective, specific, rapid, and portable. Furthermore, they can be incorporated into smartphones and various analytical approaches in order to increase their sensitivity and many other properties. As a very broad and interdisciplinary area of research and development, biosensors include all disciplines and backgrounds from materials science, chemistry, physics, medicine, microbiology/biology, and engineering. Accordingly, in this state-of-the-art article, historical background alongside the long journey of biosensing construction and development, starting from the Clark oxygen electrode until reaching highly advanced wearable stretchable biosensing devices, are discussed. Consequently, selected examples among the miscellaneous applications of nanobiosensors (such as microbial detection, cancer diagnosis, toxicity analysis, food quality-control assurance, point of care, and health prognosis) are described. Eventually, future perspectives for intelligent biosensor commercialization and exploitation in real-life that is going to be supported by machine learning and artificial intelligence (AI) are stated.

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 in silico predictive method to select multi-monomer combinations for peptide imprinting

In silico methods enable optimizing artificial receptors such that constructive mimics of natural antibodies can be envisaged. The introduction of combinatorial synthesis strategies via multi-monomer combinations has improved the performance of molecularly imprinted polymers (MIP) significantly. However, it remains experimentally challenging to screen thousands of combinations resulting from a large library of monomers. The present study introduces a molecular mechanics based multi-monomer simultaneous docking approach (MMSD) to computationally screen monomer combinations according to their potential, facilitating selective molecular imprints. Thereby, the diversity of multipoint interactions realizable with a peptide surface is efficiently explored yielding how individual monomer binding capacities constructively or adversely add up when docked together. Additionally, spatially distributed molecular models were mapped for analyzing intermolecular H-bonding and hydrophobic interactions resulting from single monomer docking, as well as bi- and tri-monomer simultaneous docking. A direct impact of complex formation on the binding capacity of the resulting MIPs has been observed. In a first small-scale study, the predictive potential of the MMSD approach was validated via experimentally applied polymer combinations for peptide imprinting via the scoring functions established during the screening process. MMSD clearly enables rational design of MIPs for synthesizing more sensitive and selective artificial receptor materials especially for peptide and protein-epitope templates.

Molecularly imprinted polymers by epitope imprinting: a journey from molecular interactions to the available bioinformatics resources to scout for epitope templates

The molecular imprinting of proteins is the process of forming biomimetics with entailed protein-recognition by means of a template-assisted synthesis. Protein-imprinted polymers (pMIPs) have been successfully employed in separations, assays, sensors, and imaging. From a technical point of view, imprinting a protein is both costly, for protein expression and purification, and challenging, for the preservation of the protein's structural properties. In fact, the imprinting process needs to guarantee the preservation of the same protein three-dimensional conformation that later would be recognized. So far, the captivating idea to imprint just a portion of the protein, i.e., an epitope, instead of the whole, proved successful, offering reduced costs, compatibility with many synthetic conditions (solvents, pH, temperatures), and fine-tuning of the peptide sequence so to target specific physiological and functional conditions of the protein, such as post-translational modifications. Here, protein-protein interactions and the biochemical features of the epitopes are inspected, deriving lessons to prepare more effective pMIPs. Epitopes are categorized in linear or structured, immunogenic or not, located at the protein's surface or buried in its core and the imprinting strategies are discussed. Moreover, attention is given to freely available online bioinformatics resources that might offer key tools to gain further rationale amid the selection process of suitable epitopes templates.

An Overview of Bio-Inspired Intelligent Imprinted Polymers for Virus Determination

The molecular imprinting polymers (MIPs) have shown their potential in various applications including pharmaceuticals, chemical sensing and biosensing, medical diagnosis, and environmental related issues, owing to their artificial selective biomimetic recognition ability. Despite the challenges posed in the imprinting and recognition of biomacromolecules, the use of MIP for the imprinting of large biomolecular oragnism such as viruses is of huge interest because of the necessity of early diagnosis of virus-induced diseases for clinical and point-of-care (POC) purposes. Thus, many fascinating works have been documented in which such synthetic systems undoubtedly explore a variety of potential implementations, from virus elimination, purification, and diagnosis to virus and bacteria-borne disease therapy. This study is focused comprehensively on the fabrication strategies and their usage in many virus-imprinted works that have appeared in the literature. The drawbacks, challenges, and perspectives are also highlighted.

COVID-19: A challenge for electrochemical biosensors

Coronavirus disease (COVID-19) caused by SARS-CoV-2 has spread since the end of 2019 and has resulted in a pandemic with unprecedented socioeconomic consequences. This situation has created enormous demand for the improvement of current diagnostic methods and the development of new diagnostic methods for fast, low-cost and user-friendly confirmation of SARS-CoV-2 infection. This critical review focuses on viral electrochemical biosensors that are promising for the development of rapid medical COVID-19 diagnostic tools. The molecular biological properties of SARS-CoV-2 as well as currently known biochemical attributes of infection necessary for biosensor development are outlined. The advantages and drawbacks of conventional diagnostic methods, such as quantitative reverse-transcription polymerase chain reaction (qRT-PCR), are critically discussed. Electrochemical biosensors focusing on viral nucleic acid and whole viral particle detection are highlighted and discussed in detail. Finally, future perspectives on viral electrochemical biosensor development are briefly mentioned.