The Use of Computational Methods for the Development of Molecularly Imprinted Polymers

Modeling of liquid-liquid hollow fiber supported membrane equilibrium including the non-ideality of the aqueous and organic phases in the recovery systems of radionuclides in sulphate-halide/aliquat-336 in O-xylene

Study of modeling of L/LHFSLM equilibrium based on the Non-ideality of the Aqueous and Organic Phases in the Recovery of 152+154Eu in H2SO4-Halides/Aliquat-336 in 20% kerosene as feeding phase at pH 3.78-4.55, by the ratio 89.7%,while separation of 90Sr and 134Cs there was a problem between them by using hollow HFSLM only, the reason for that the organic solvents affect the rate of reaction in the Diamino-1,2-cyclohexane/tetraacetic acid (DCTA) as stripping phase concentration from 0.15 to 0.55 mol/L. The system has been developed; this led to the extraction of elements in the same time. The Matlab software program was introduced to obtain some mathematical parameters like, standard deviation (SD), equilibrium constant Kex and standard deviation coefficient (SDC).

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.

A surface molecularly imprinted microfluidic paper based device with smartphone assisted colorimetric detection for butachlor in mung bean

A microfluidic paper chip colorimetric detection system based on surface molecular imprinting of zinc ferrite nanoparticles was established, and the detection images were obtained by smartphone for gray value analysis and determination of butachlor. The best functional monomers and addition ratio were selected by quantum chemical simulation calculation, the properties of the prepared molecularly imprinted polymers were analyzed, and the detection conditions were optimized. The linear range, sensitivity, and selectivity of the method were evaluated. The results showed that under the optimum conditions, the concentration of 2-80 ng/g had a good linear relationship (R2 is 0.9953), the detection limit was 1.43 ng/g, the specificity was good, and the whole detection process did not exceed 20 min. The microfluidic paper chip was applied to detect butachlor in mung bean samples. The results showed that the recovery was 93.4-106.4 %, and the relative standard deviation was less than 5.6 %.

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.

In Silico Evaluation of Oligomeric Representations for Molecularly Imprinted Polymer Modeling Using a Biological Template

Molecularly imprinted polymers (MIPs) have significant relevance to analytical sensing due to their functionalized and template-specific structurally complementary cavities, providing increased sensibility and specificity for instrumental analyses, thereby enabling a wide variety of applications, especially for biological processes. Designing and developing MIPs entirely by experimental approaches are time-consuming and costly processes; thus, computational tools are used to assess some of the most critical parameters for imprinting, such as ligand screening. A typical practice is to model functional ligands as monomers; however, this representation fails to predict how ligand-template interactions evolve during polymer growth. In this context, this work aims to evaluate whether additional oligomeric representations affect the formation of noncovalent complexes between typical ligands and the P31 Asian lineage Zika virus epitope, using classical molecular dynamics. The ligands 2-vinylpyridine, 4-vinylaniline, acrylic acid, acrylamide, and 2-hidroxyethyl methacrylate were simulated as monomers, trimers, pentamers, and decamers, and their influence on the epitope structural conservation and ligand-template interactions were evaluated. Analyses of root-mean-square deviation, fluctuation, radius of gyration, pair correlation function, and number of hydrogen bonding-type interactions were conducted, showing the ligand chain size had an influence on the complex formation. However, this influence had no discernible pattern, exhibiting better performance in some cases while noninfluential in others. Of particular significance, in terms of epitope structural conservation, distinct oligomeric chains led to the selection of the distinct most interactive ligands. This observation raises important questions regarding the use of oligomeric chains in MIP simulations, thus prompting the need for further investigations of this subject.

Strategy of Choosing Templates in Molecular Imprinting to Expand the Recognition Width for Family-Selectivity

The class-selective molecular-imprinted polymers (MIPs) have shown the recognition ability to multiple targeted molecules through using one or multiple templates. However, choosing the right templates, the core problem, still lacks a systemic guide and decision-making. In this work, we propose a strategy of selecting templates through expanding the recognition width for the improvement of class-selectivity. First, three families of genotoxic impurity (GTI) were selected as model objects, and the spatial size and binding energy of each GTI-monomer complexes were obtained and compared by computational simulation. The two indexes of energy width (W_E) and size width (W_L) were introduced to compare the similarity and differences on the two recognition factors, binding strength and spatial size, among these GTIs in each family. Through shortening the width to increase similarity on binding energy and size, the dual templates in the aromatic amines (AI) family and sulfonic acid esters (SI) family were successfully selected. Correspondingly, the prepared dual-template MIPs in the two GTI families can simultaneously recognize all the GTIs comparing with that of single template MIP, respectively. Meanwhile, through comparing the adsorption capacity of the selected template and its analogues in one GTI family, the recognition efficiency of the dual-template MIPs was higher than that of the single-template MIP. This indicates that though using the selected right templates, the higher class-selectivity and the larger recognition width can be realized. Thus, this work can solve the problem of blind template selection, and provide the useful theoretical guidance for designing family-selective molecular imprinting.

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.

Biomolecular Fishing: Design, Green Synthesis, and Performance of l-Leucine-Molecularly Imprinted Polymers

Biopurification is a challenging and growing market. Despite great efforts in the past years, current purification strategies still lack specificity, efficiency, and cost-effectiveness. The development of more sustainable functional materials and processes needs to address pressing environmental goals, efficiency, scale-up, and cost. Herein, l-leucine (LEU)-molecularly imprinted polymers (MIPs), LEU-MIPs, are presented as novel biomolecular fishing polymers for affinity sustainable biopurification. Rational design was performed using quantum mechanics calculations and molecular modeling for selecting the most appropriate monomers. LEU-MIPs were synthesized for the first time by two different green approaches, supercritical carbon dioxide (scCO₂) technology and mechanochemistry. A significant imprinting factor of 12 and a binding capacity of 27 mg LEU/g polymer were obtained for the LEU-MIP synthesized in scCO₂ using 2-vinylpyridine as a functional monomer, while the LEU-MIP using acrylamide as a functional monomer synthesized by mechanochemistry showed an imprinting factor of 1.4 and a binding capacity of 18 mg LEU/g polymer, both systems operating at a low binding concentration (0.5 mg LEU/mL) under physiological conditions. As expected, at a higher concentration (1.5 mg LEU/mL), the binding capacity was considerably increased. Both green technologies show high potential in obtaining ready-to-use, stable, and low-cost polymers with a molecular recognition ability for target biomolecules, being promising materials for biopurification processes.

Inspirations of Biomimetic Affinity Ligands: A Review

Affinity chromatography is a well-known method dependent on molecular recognition and is used to purify biomolecules by mimicking the specific interactions between the biomolecules and their substrates. Enzyme substrates, cofactors, antigens, and inhibitors are generally utilized as bioligands in affinity chromatography. However, their cost, instability, and leakage problems are the main drawbacks of these bioligands. Biomimetic affinity ligands can recognize their target molecules with high selectivity. Their cost-effectiveness and chemical and biological stabilities make these antibody analogs favorable candidates for affinity chromatography applications. Biomimetics applies to nature and aims to develop nanodevices, processes, and nanomaterials. Today, biomimetics provides a design approach to the biomimetic affinity ligands with the aid of computational methods, rational design, and other approaches to meet the requirements of the bioligands and improve the downstream process. This review highlighted the recent trends in designing biomimetic affinity ligands and summarized their binding interactions with the target molecules with computational approaches.

Advances in fabrication of molecularly imprinted electrochemical sensors for detection of contaminants and toxicants

Worldwide growing concerns about water contamination and pollution have increased significant interest in trace level sensing of variety of contaminants. Thus, there is demand for fabrication of low cost, miniaturized sensing device for in-situ detection of contaminants from the complex environmental matrices capable of providing selective and sensitive detection. Molecularly imprinted polymers (MIPs) has portrayed a substantial potential for selective recognition of various toxicants from a variety of environmental matrices, thus widely used as artificial recognition element in the electrochemical sensors (ECS) owing to their chemical stability, easy and low cost synthesis. The combination of nanomaterials modifiers with MIPs has endowed MIP-ECS with significantly improved sensing performance in the recent years, as the nanomaterial provide properties such as increased surface area, increased conductivity and electrocatalytic activity with enhanced electron transport phenomena, whereas MIPs provide selective recognition effect. In the present review, we have summarized the advances of MIP-ECS electrochemical sensors reported in last six years (2017-2022) for sensing of variety of contaminates including drugs, metal ions, hormones and emerging contaminates. Scope of computational modelling in design of sensitive and selective MIP-ECS is reviewed. We have focused particularly on the synthetic protocols for MIPs preparation including bulk, precipitation, electropolymerization, sol-gel and magnetic MIPs. Moreover, use of various nanomaterial as modifiers and sensitizers and their effects on the sensing performance of resulting MIP-ECS is described. Finally, the potential challenges and future prospects in the research area of MIP-ECS have been discussed.

Molecularly Imprinted Nanoparticles towards MMP9 for Controlling Cardiac ECM after Myocardial Infarction: A Predictive Experimental-Computational Chemistry Investigation

The recent advances in nanotechnology are revolutionizing preventive and therapeutic approaches to treating cardiovascular diseases. Controlling the extracellular matrix metalloproteinase (MMP) activation and expression in the failing human left ventricular myocardium represents a significant therapeutic target for heart disease. In this study, we used molecularly imprinting polymers (MIPs) to restore the correct balance between MMPs and their tissue inhibitors (TIMPs), and explored the potential of this technique exhaustively through chemical synthesis, physicochemical and biological characterizations, and computational chemistry methods. By molecular dynamics simulations based on classical force fields, we simulated the early stages of the imprinting process in solution disclosing the pivotal interaction established between the monomers and the MMP9 protein template. The average interaction energies of methacrylic acid (MAA) and poly (ethylene glycol) ethyl ether methacrylate (PEG) units were in the ranges 17–22 and 30–37 kcal/mol, respectively. At low coverage, the PEG monomers seemed firmly anchored to the protein surface and were not displaced by water, while only about 20% of MAA was replaced by water. The synthesis of MIPs was successfully with a monomer conversion higher than 99% and the production of spherical particles with average diameter of 344 ± 33 nm. HPLC analysis showed a specific recognition factor of MMP9 on MIPs of about 1.3. FT-IR Chemical Imaging confirmed the mechanisms necessary to generate a “selective memory” of the MIPs towards the enzyme. HPLC results indicated that the rebound amount of both TIMP1 and MMP2 to MIPs is lower than that of the template, showing a selectivity factor of 2.1 and 2.3, respectively. Preliminary tests on the effect of MIPs on H9C2 cells revealed that this treatment has no cytotoxic effects.

Advances in Detection of Antibiotic Pollutants in Aqueous Media Using Molecular Imprinting Technique-A Review

Antibiotics constitute one of the emerging categories of persistent organic pollutants, characterised by their expansion of resistant pathogens. Antibiotic pollutants create a major public health challenge, with already identifiable detrimental effects on human and animal health. A fundamental aspect of controlling and preventing the spread of pollutants is the continuous screening and monitoring of environmental samples. Molecular imprinting is a state-of-the-art technique for designing robust biomimetic receptors called molecularly imprinted polymers (MIPs), which mimic natural biomolecules in target-selective recognition. When integrated with an appropriate sensor transducer, MIP demonstrates a potential for the needed environmental monitoring, thus justifying the observed rise in interest in this field of research. This review examines scientific interventions within the last decade on the determination of antibiotic water pollutants using MIP receptors interfaced with label-free sensing platforms, with an expanded focus on optical, piezoelectric, and electrochemical systems. Following these, the review evaluates the analytical performance of outstanding MIP-based sensors for environmentally significant antibiotics, while highlighting the importance of computational chemistry in functional monomer selection and the strategies for signal amplification and performance improvement. Lastly, the review points out the future trends in antibiotic MIP research, as it transits from a proof of concept to the much demanded commercially available entity.

Computational Modelling and Sustainable Synthesis of a Highly Selective Electrochemical MIP-Based Sensor for Citalopram Detection

A novel molecularly imprinted polymer (MIP) has been developed based on a simple and sustainable strategy for the selective determination of citalopram (CTL) using screen-printed carbon electrodes (SPCEs). The MIP layer was prepared by electrochemical in situ polymerization of the 3-amino-4 hydroxybenzoic acid (AHBA) functional monomer and CTL as a template molecule. To simulate the polymerization mixture and predict the most suitable ratio between the template and functional monomer, computational studies, namely molecular dynamics (MD) simulations, were carried out. During the experimental preparation process, essential parameters controlling the performance of the MIP sensor, including CTL:AHBA concentration, number of polymerization cycles, and square wave voltammetry (SWV) frequency were investigated and optimized. The electrochemical characteristics of the prepared MIP sensor were evaluated by both cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) techniques. Based on the optimal conditions, a linear electrochemical response of the sensor was obtained by SWV measurements from 0.1 to 1.25 µmol L-1 with a limit of detection (LOD) of 0.162 µmol L-1 (S/N = 3). Moreover, the MIP sensor revealed excellent CTL selectivity against very close analogues, as well as high imprinting factor of 22. Its applicability in spiked river water samples demonstrated its potential for adequate monitoring of CTL. This sensor offers a facile strategy to achieve portability while expressing a willingness to care for the environment.