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

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.

Immunodetection of Poorly Soluble Substances: Limitations and Their Overcoming

Immunoassays based on the specific antigen-antibody interactions are efficient tools to detect various compounds and estimate their content. Usually, these assays are implemented in water-saline media with composition close to physiological conditions. However, many substances are insoluble or cannot be molecularly dispersed in such media, which objectively creates problems when interacting in aquatic environments. Thus, obtaining immunoreactants and implementing immunoassays of these substances need special methodological solutions. Hydrophobicity of antigens as well as their limited ability to functionalization and conjugation are often overlooked when developing immunoassays for these compounds. The main key finding is the possibility to influence the behavior of hydrophobic compounds for immunoassays, which requires specific approaches summarized in the review. Using the examples of two groups of compounds-surfactants (alkyl- and bisphenols) and fullerenes, we systematized the existing knowledge and experience in the development of immunoassays. This review addresses the challenges of immunodetection of poorly soluble substances and proposes solutions such as the use of hydrotropes, other solubilization techniques, and alternative receptors (aptamers and molecularly imprinted polymers).

Molecular Modeling Methods in the Development of Affine and Specific Protein-Binding Agents

High-affinity and specific agents are widely applied in various areas, including diagnostics, scientific research, and disease therapy (as drugs and drug delivery systems). It takes significant time to develop them. For this reason, development of high-affinity agents extensively utilizes computer methods at various stages for the analysis and modeling of these molecules. The review describes the main affinity and specific agents, such as monoclonal antibodies and their fragments, antibody mimetics, aptamers, and molecularly imprinted polymers. The methods of their obtaining as well as their main advantages and disadvantages are briefly described, with special attention focused on the molecular modeling methods used for their analysis and development.

Rational Design and Evaluation of Photoactive Molecularly Imprinted Nanoparticles for Tetracycline Degradation Under Visible Light

This work presents the use of photoactive molecularly imprinted nanoparticles (MINs) to promote antibiotic degradation under visible light irradiation. Prototype MINs for the model antibiotic tetracycline (TC) were developed using molecular dynamics simulations to predict the TC-binding capacity of seven pre-polymerization mixtures. The studied formulations contained varying proportions of functional monomers with diverse physicochemical profiles, namely N-isopropylacrylamide (NIPAM), N-tert-butylacrylamide (TBAM), acrylic acid (AA), and (N-(3-aminopropyl)methacrylamide hydrochloride) (APMA) and a constant ratio of the cross-linker N,N'-methylene-bis-acrylamide (BIS). Two monomer formulations showed markedly higher TC-binding capacities based on template-monomer interaction energies. These mixtures were used to synthesize photoactive MINs by high-dilution radical polymerization, followed by the EDC/NHS conjugation with the organic photosensitizer toluidine blue. MINs showed higher TC-binding capacities than non-imprinted nanoparticles (nINs) of identical composition. MINs and nINs exhibited photodynamic activity under visible light irradiation, as confirmed by singlet oxygen generation experiments. TC degradation was evaluated in 50 μmol L-1 solutions placed in microplate wells containing immobilized nanoparticles and irradiated with white LED light (150 W m-2) for 1 h at room temperature. Degradation followed pseudo-zero-order kinetics with accelerated profiles in MIN-containing wells. Our findings suggest a key role of molecularly imprinted cavities in bringing TC closer to the photosensitizing moieties, minimizing the loss of oxidative potential due to reactive oxygen species diffusion. This degradation strategy can potentially extend to any organic pollutants for which MINs can be synthesized and opens valuable opportunities for exploring novel applications for molecularly imprinted materials.

Rationally designed protein A surface molecularly imprinted magnetic nanoparticles for the capture and detection of Staphylococcus aureus

Staphylococcus aureus (S. aureus), a commensal organism found on the human skin, is commonly associated with nosocomial infections and exhibits virulence mediated by toxins and resistance to antibiotics. The global threat of antibiotic resistance has necessitated antimicrobial stewardship to improve the safe and appropriate use of antimicrobials; hence, there is an urgent demand for the advanced, cost-effective, and rapid detection of specific bacteria. In this regard, we aimed to selectively detect S. aureus using surface molecularly imprinted magnetic nanoparticles templated with a well-known biomarker protein A, specific to S. aureus. Herein, a highly selective surface molecularly imprinted polymeric thin layer was created on ∼250 nm magnetic nanoparticles (MNPs) through the immobilization of protein A to aldehyde functionalized MNPs, followed by monomer polymerization and template washing. This study employs the rational selection of monomers based on their computationally predicted binding affinity to protein A at multiple surface residues. The resulting MIPs from rationally selected monomer combinations demonstrated an imprinting factor as high as ∼5. Selectivity studies revealed MIPs with four-fold higher binding capacity (BC) to protein A than other non-target proteins, such as lysozyme and serum albumin. In addition, it showed significant binding to S. aureus, whereas negligible binding to other non-specific Gram-negative, i.e. Escherichia coli (E. coli), Pseudomonas aeruginosa (P. aeruginosa), and Gram-positive, i.e. Bacillus subtilis (B. subtilis), bacteria. This MIP was employed for the capture and specific detection of fluorescently labeled S. aureus. Quantitative detection was performed using a conventional plate counting technique in a linear detection range of 101-107 bacterial cells. Remarkably, the MIPs also exhibited approximately 100% cell recovery from milk samples spiked with S. aureus (106 CFU mL-1), underscoring its potential as a robust tool for sensitive and accurate bacterial detection in dairy products. The developed MIP exhibiting high affinity and selective binding to protein A finds its potential applications in the magnetic capture and selective detection of protein A as well as S. aureus infections and contaminations.

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.

Design of Molecularly Imprinted Polymers Using Supercritical Carbon Dioxide Technology

The design and development of affinity polymeric materials through the use of green technology, such as supercritical carbon dioxide (scCO2), is a rapidly evolving field of research with vast applications across diverse areas, including analytical chemistry, pharmaceuticals, biomedicine, energy, food, and environmental remediation. These affinity polymeric materials are specifically engineered to interact with target molecules, demonstrating high affinity and selectivity. The unique properties of scCO2, which present both liquid- and gas-like properties and an accessible critical point, offer an environmentally-friendly and highly efficient technology for the synthesis and processing of polymers. The design and the synthesis of affinity polymeric materials in scCO2 involve several strategies. Commonly, the incorporation of functional groups or ligands into the polymer matrix allows for selective interactions with target compounds. The choice of monomer type, ligands, and synthesis conditions are key parameters of material performance in terms of both affinity and selectivity. In addition, molecular imprinting allied with co-polymerization and surface modification are commonly used in these strategies, enhancing the materials' performance and versatility. This review aims to provide an overview of the key strategies and recent advancements in the design of affinity polymeric materials using scCO2.

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.