Validation of computational approach to study monomer selectivity toward the template Gallic acid for rational molecularly imprinted polymer design

Gallic acid (GA) is important for pharmaceutical industries as an antioxidant. It also finds use in tanning, ink dyes and manufacturing of paper. Molecularly imprinted polymers (MIP), which are tailor made materials, can play an excellent role in separation of GA from complex matrices. Molecular recognition being the most important property of MIP, the present work proposes a methodology based on density functional theory (DFT) calculations for selection of suitable functional monomer for a rational design of MIP with a high binding capacity for GA. A virtual library of 18 functional monomers was created and screened for the template GA. The prepolymerization template-monomer complexes were optimized at B3LYP/6-31G(d) model chemistry and the changes in the Gibbs free energy (ΔG) due to complex formation were determined on the optimized structures. The monomer with the highest Gibbs free energy gain forms most stable complex with the template resulting in formation of more selective binding sites in the polymeric matrix in MIPs. This can lead to high binding capacity of MIP for GA. Amongst the 18 monomers, acrylic acid (AA) and acrylamide (AAm) gave the highest value of ΔG due to complex formation with GA. 4-vinyl pyridine (4-Vp) had intermediate value of ΔG while, methyl methacrylate (MMA) gave least value of ΔG due to complex formation with GA. Based on this study, the MIPs were synthesized and rebinding performance was evaluated using Langmuir-Freundlich model. The imprinting factor for AA and AAm based MIPs were 5.28 and 4.80 respectively, 4-Vp based MIP had imprinting factor of 2.59 while MMA based MIP exhibited an imprinting factor of 1.95. The experimental results were in good agreement with the computational predictions. The experimental data validated the DFT based computational approach.     

A brief review of coarse-grained and other computational studies of molecularly imprinted polymers

Molecular imprinting is an established method for the creation of artificial recognition sites in synthetic materials through polymerization and cross-linking in the presence of template molecules. Removal of the templates leaves cavities that are complementary to the template molecules in size, shape, and functionality. In recent years, various theoretical and computational models have been developed as tools to aid in the design of molecularly imprinted polymers (MIPs) or to provide insight into the features that determine MIP performance. These studies can be grouped into two general approaches-screening for possible functional monomers for particular templates and macromolecular models focusing on the structural characterization of the imprinted material. In this review, we pay special attention to coarse-grained models that characterize the functional heterogeneity in imprinted pores, but also cover recent advances in atomistic and first principle studies. We offer a critical assessment of the potential impact of the various models towards improving the state-of-the-art of molecular imprinting.     

Molecularly imprinted polymer anchored on the surface of denatured bovine serum albumin modified CdTe quantum dots as fluorescent artificial receptor for recognition of target protein

A new type of molecularly imprinted polymer (MIP)-based fluorescent artificial receptor was developed by anchoring MIP on the surface of denatured bovine serum albumin (dBSA) modified CdTe quantum dots (QDs) using the surface molecular imprinting process. The approach combined the merits of molecular imprinting technology and the fluorescent property of the CdTe QDs. The dBSA was used not only to modify the surface defects of the CdTe QDs, but also as assistant monomer to create effective recognition sites. Three different proteins, namely lysozyme (Lyz), cytochrome c (Cyt) and methylated bovine serum albumin (mBSA), were tested as the template molecules and then the receptors were synthesized by sol-gel reaction (imprinting process). The results of fluorescence and binding experiments demonstrated the recognition performance of the receptors toward the corresponding template. Under optimum conditions, the linear range for Lyz was from 1.4×10(-8) to 8.5×10(-6) M, and the detection limit was 6.8 nM. Moreover, the new artificial receptors were applied to separate and detect Lyz in real samples. This fluorescent artificial receptor may serve as a starting point in the design of highly effective synthetic fluorescent receptor for recognition of target protein.     

Study on the recognition of templates and their analogues on molecularly imprinted polymer using computational and conformational analysis approaches

A simplified computational model was proposed to simulate the synthesis of molecularly imprinted polymers (MIP), removal of template and recognition of the template and its analogues by MIP. The MIPs with nicotinamide and iso-nicotinamide as templates were prepared using methacrylic acid as functional monomer. Based on our computational model, the interaction energies between the monomer and the template or its analogues were calculated, which were well correlated with the retention factors and imprinting factors obtained on HPLC columns packed with the corresponding MIP particles. The imprinting effects of the template and its analogues were also investigated from the viewpoint of conformational analysis. The computational data were successfully used to predict the chromatographic behaviour of some chemicals in separation on HPLC columns. We believe that the computational method will find application in designing monomers for MIP synthesis and in studying recognition of templates and their analogues on MIP.     

Molecularly imprinted polymers (MIP) in electroanalysis of proteins

The review summarizes current knowledge on the main approaches used for creation of high affinity polymer analogs of antibodies (known as molecularly imprinted polymers, MIP) applicable for electroanalysis of functionally important proteins such as myoglobin, troponin T, albumin, ferritin, lysozyme, calmodulin. The main types of monomers for MIP preparation as well as methods convenient for analysis of MIP/protein interactions, such as surface plasmon resonance (SPR), nanogravimetry with the use of a quartz crystal resonator (QCM), spectral and electrochemical methods have been considered. Special attention is paid to experimental data on electrochemical registration of myoglobin by means of o-phenylenediaminebased MIP electrodes. It was shown that the imprinting factor calculated as a ratio of the myoglobin signal obtained after myoglobin insertion in MIP to the myoglobin signal obtained after myoglobin insertion in the polymer lacking the molecular template (NIP) is 2–4.     

Investigation of polyacrylamide hydrogel-based molecularly imprinted polymers using protein gel electrophoresis

In conjunction with polyacrylamide gel electrophoresis (PAGE), molecular imprinting methods have been applied to produce a multilayer mini-slab in order to evaluate how selectively and specifically a hydrogel-based molecularly imprinted polymer (MIP) binds bovine haemoglobin (BHb, ~64.5 kDa). A three-layer mini-slab comprising an upper and lower layer and a MIP, or a non-imprinted control polymer dispersion middle layer has been investigated. The discriminating MIP layer, also based on polyacrylamide, was able to specifically bind BHb molecules in preference to a protein similar in molecular weight such as bovine serum albumin (BSA, ~66 kDa). Protein staining allowed us to visualise the protein retention strength of the MIP layer under the influence of an electric field. This method could be applied to other proteins with implications in effective protein capture, disease diagnostics, and protein analysis.     

Investigation of the nature of MIP recognition: the development and characterisation of a MIP for Ibuprofen

This paper describes the rational design, generation and testing of a molecularly imprinted polymer specific for Ibuprofen. Ibuprofen is a member of the class of drugs termed non-steroidal anti-inflammatory drugs (NSAIDS). In the present study, Ibuprofen was used as a template molecule for the preparation of molecularly imprinted polymers. A MIP has been produced which is capable of recognising Ibuprofen in aqueous media. Furthermore, Ibuprofen can be selectively extracted from aqueous conditions by molecularly imprinted solid phase extraction (MISPE). Recoveries were typically high (>80%) and good selectivity for Ibuprofen over structurally related analogues was seen. Moreover, the nature of the recognition between MIP and template has been investigated by NMR and molecular modelling to analyse whether or not it is possible to predict how well a given MIP will perform under set conditions. In addition, the physical characteristics of the MIP have been investigated including the particle size distribution on exposure of the MIP to different solvents. This has been related to the ability of the MIP to rebind Ibuprofen under the same conditions. The data from the characterisation of the MIP has been used to further enhance the understanding of the nature of MIP recognition.     

Molecularly imprinted polymer using-p-hydroxybenzoic acid, p-hydroxyphenylacetic acid and p-hydroxyphenylpropionic acid as templates.

Molecularly imprinted polymers (MIPs) using p-hydroxybenzoic acid (p-HB), p-hydroxyphenylacetic acid (p-HPA) and p-hydroxyphenylpropionic acid (p-HPPA) as templates were synthesized. The performance of the templates and their analogues on polymer-based high performance liquid chromatography (HPLC) columns was studied. The imprinting effect of the MIP using p-HB as template is more obvious than that of MIP using either p-HPA or p-HPPA as template, and the mixture of p-HB and p-HPA can be well separated on the MIP using p-HB as template, but not on the blank. Interestingly, the recognition of MIP (p-HB as the template) to p-HB showed a synergistic effect. The retention factor of p-HB is not the sum of those of phenol and benzoic acid. We also found that the imprinting effect decreased when increasing the concentration of acetic acid in mobile phase. The possible reason is that acetic acid molecules occupied the binding sites of the polymer, thereby decreasing the concentration of binding sites. Furthermore, polymers, which showed specificity to 3,4-dihydroxybenzoic acid, can be prepared with p-HB as template. It is thus possible to synthesize a specific polymer for a compound that is either expensive or unstable by using a structurally similar compound as template.     

Size-selective recognition of catecholamines by molecular imprinting on silica-alumina gel

The preparation of a catecholamine receptor was carried out using a molecular imprinting method with silica-alumina gel to form complementary structures for template recognition. The molecularly imprinted polymer (MIP) was synthesized by the condensation of silicate from tetraethyl orthosilictate (TEOS) under hydrothermal conditions at 60 degrees C. Aluminum chloride was added as a functional monomer to increase the material's rebinding ability. The selectivity of the MIP receptor prepared with different ratios of template to Si and Al, was examined with seven analytes including: dopamine, epinephrine, norepinephrine, ascorbic acid, homovanillic acid, uric acid, and l-tyrosine. The results showed a size selective effect for the receptors with respect to the recognition of the catecholamines. Some factors affecting the recognition ability were investigated including: the solution pH of analytes, surface capping on the MIP, and the imprinting pH of the silica-alumina solution. Also, the catecholamine MIP films on quartz crystal microbalance (QCM) electrodes were fabricated as sensors for in situ monitoring of the analytes in a 2-propanol solution.     

Molecularly imprinted polymers—A closer look at the control polymer used in determining the imprinting effect: A mini review

Molecular recognition displayed by naturally occurring receptors has continued to inspire new innovations aimed at developing systems that can mimic this natural phenomenon. Since 1930s, a technology called molecular imprinting for producing biomimetic receptors has been in place. In this technology, tailor made binding sites that selectively bind a given target analyte (also called template) are incorporated in a polymer matrix by polymerizing functional monomers and cross‐linking monomers around a target analyte followed by removal of the analyte to leave behind cavities specific to the analyte. The success of the imprinting process is defined by two main figures of merit, that is, the imprinting factor, and selectivity, which are determined by comparing the amount of target analyte or structural analogue bound by the molecularly imprinted polymer (MIP) and the nonimprinted polymer (NIP). NIP is a control synthesized alongside the MIP but in the absence of the template. However, questions arise on whether these figures of merit are reliable measures of the imprinting effect because of the significant differences between the MIP and the NIP in terms of their physical and chemical characteristics. Therefore, this review critically looks into this subject, with a view of defining the best approaches for determining the imprinting effect.     

Towards water compatible MIPs for sensing in aqueous media

When synthesizing molecularly imprinted polymers (MIPs), a few fundamental principles should be kept in mind. There is a strong correlation between porogen polarity, MIP microenvironment polarity and the imprinting effect itself. The combination of these parameters eventually determines the overall binding behavior of a MIP in a given solvent. In addition, it is shown that MIP binding is strongly influenced by the polarity of the rebinding solvent. Because the use of MIPs in biomedical environments is of considerable interest, it is important that these MIPs perform well in aqueous media. In this article, various approaches are explored towards a water compatible MIP for the target molecule l-nicotine. To this end, the imprinting effect together with the MIP matrix polarity is fine-tuned during MIP synthesis. The binding behavior of the resulting MIPs is evaluated by performing batch rebinding experiments that makes it possible to select the most suitable MIP/non-imprinted polymer couple for future application in aqueous environments. One method to achieve improved compatibility with water is referred to as porogen tuning, in which porogens of varying polarities are used. It is demonstrated that, especially when multiple porogens are mixed, this approach can lead to superior performance in aqueous environments. Another method involves the incorporation of polar or non-polar comonomers in the MIP matrix. It is shown that by carefully selecting these monomers, it is also possible to obtain MIPs, which can selectively bind their target in water.     

A computational approach to study functional monomer‐protein molecular interactions to optimize protein molecular imprinting

Molecular imprinting has become a promising approach for synthesis of polymeric materials having binding sites with a predetermined selectivity for a given analyte, the so‐called molecularly imprinted polymers (MIPs), which can be used as artificial receptors in various application fields. Realization of binding sites in a MIP involves the formation of prepolymerization complexes between a template molecule and monomers, their subsequent polymerization, and the removal of the template. It is believed that the strength of the monomer‐template interactions in the prepolymerization mixture influences directly on the quality of the binding sites in a MIP and consequently on its performance. In this study, a computational approach allowing the rational selection of an appropriate monomer for building a MIP capable of selectively rebinding macromolecular analytes has been developed. Molecular docking combined with quantum chemical calculations was used for modeling and comparing molecular interactions among a model macromolecular template, immunoglobulin G (IgG), and 1 of 3 electropolymerizable functional monomers: m‐phenylenediamine (mPD), dopamine, and 3,4‐ethylenedioxythiophene, as well as to predict the probable arrangement of multiple monomers around the protein. It was revealed that mPD was arranged more uniformly around IgG participating in multiple H‐bond interactions with its polar residues and, therefore, could be considered as more advantageous for synthesis of a MIP for IgG recognition (IgG‐MIP). These theoretical predictions were verified by the experimental results and found to be in good agreement showing higher binding affinity of the mPD‐based IgG‐MIP toward IgG as compared with the IgG‐MIPs generated from the other 2 monomers.     

Gene expression profiling: opening the black box of plant ecosystem responses to global change

The use of genomic techniques to address ecological questions is emerging as the field of genomic ecology. Experimentation under environmentally realistic conditions to investigate the molecular response of plants to meaningful changes in growth conditions and ecological interactions is the defining feature of genomic ecology. Because the impact of global change factors on plant performance are mediated by direct effects at the molecular, biochemical, and physiological scales, gene expression analysis promises important advances in understanding factors that have previously been consigned to the 'black box' of unknown mechanism. Various tools and approaches are available for assessing gene expression in model and nonmodel species as part of global change biology studies. Each approach has its own unique advantages and constraints. A first generation of genomic ecology studies in managed ecosystems and mesocosms have provided a testbed for the approach and have begun to reveal how the experimental design and data analysis of gene expression studies can be tailored for use in an ecological context.     

Host defenses to transposable elements and the evolution of genomic imprinting

Genomic imprinting is the differential expression of maternally and paternally inherited alleles of specific genes. Several organismic level hypotheses have been offered to explain the evolution of genomic imprinting. We argue that evolutionary explanations of the origin of imprinting that focus exclusively on the organismic level are incomplete. We propose that the complex molecular mechanisms that underlie genomic imprinting originally evolved as an adaptive response to the mutagenic potential of transposable elements (TEs). We also present a model of how these mechanisms may have been co-opted by natural selection to evolve molecular features characteristic of genomic imprinting.     

Separation of ursodeoxycholic acid from its isomeric mixture using core–shell molecular imprinting polymer

In order to separate ursodeoxycholic acid (UDCA) from its isomeric mixture, the molecular imprinting polymers (MIPs) were synthesized by using core–shell emulsion polymerization. In the porous imprinting polymer, ursodeoxycholic acid was used as imprinting molecule, acrylamide (AM) and α-methacrylic acid (MAA) were functional monomers, and CaCO₃ was used for the porogen in the polymerization to obtain large pore. Characterization of the MIP structure with IR spectra demonstrated the expected MIPs. Through adsorption and selectivity assays, AM as the functional monomer showed better separation efficiency than MAA, and nonspecific and specific adsorption capacities of MIP with AM were 43.52 and 13.93 mg/g, respectively. The separation factor of MIP with AM for UDCA was 2.20. Furthermore, MIP with AM could be applied to separate UDCA from the isomeric mixture by column chromatography successfully.     

An Ecosystem Health Index for a large and variable river basin: Methodology,challenges and continuous improvement in Queensland’s Fitzroy Basin

Report cards are an increasingly popular method for summarising and communicating relative environmental performance and ecosystem health, including in aquatic environments. They are usually underpinned by an Ecosystem Health Index (EHI) that combines various individual indicators to produce an overall ecosystem health “score”. As a result of public water quality concerns, an integrated means of monitoring and reporting on aquatic ecosystem health was needed for the Fitzroy Basin in central Queensland, Australia. The Fitzroy Partnership for River Health was formed to address this need, and developed an EHI and report card for the Basin using existing monitoring data collected from various third parties including regulated companies operations and government. At 142,000 square kilometres, the Fitzroy Basin is the largest catchment draining to the World Heritage Listed Great Barrier Reef. The Fitzroy Basin provides an example of how to deliver an effective aquatic ecosystem health reporting system in a large and complex river basin. We describe the methodology used to develop an adaptive EHI for the Fitzroy Basin that addresses variability, complexity and scale issues associated with reporting across large areas. As well, we report how to manage the design and reporting stages given limitations in data collection and scientific understanding.     

Measuring the unknown: An estimator and simulation study for assessing case reporting during epidemics

The fraction of cases reported, known as ‘reporting’, is a key performance indicator in an outbreak response, and an essential factor to consider when modelling epidemics and assessing their impact on populations. Unfortunately, its estimation is inherently difficult, as it relates to the part of an epidemic which is, by definition, not observed. We introduce a simple statistical method for estimating reporting, initially developed for the response to Ebola in Eastern Democratic Republic of the Congo (DRC), 2018–2020. This approach uses transmission chain data typically gathered through case investigation and contact tracing, and uses the proportion of investigated cases with a known, reported infector as a proxy for reporting. Using simulated epidemics, we study how this method performs for different outbreak sizes and reporting levels. Results suggest that our method has low bias, reasonable precision, and despite sub-optimal coverage, usually provides estimates within close range (5–10%) of the true value. Being fast and simple, this method could be useful for estimating reporting in real-time in settings where person-to-person transmission is the main driver of the epidemic, and where case investigation is routinely performed as part of surveillance and contact tracing activities.     

‘Bite-and-Switch’ approach using computationally designed molecularly imprinted polymers for sensing of creatinine

A method for the selective detection of creatinine is reported, which is based on the reaction between polymerised hemithioacetal, formed by allyl mercaptan, o-phthalic aldehyde, and primary amine leading to the formation of fluorescent isoindole complex. This method has been demonstrated previously for the detection of creatine using creatine-imprinted molecularly imprinted polymers (MIPs) Since MIPs created using traditional methods were unable to differentiate between creatine and creatinine, a new approach to the rational design of a molecularly imprinted polymer (MIP) selective for creatinine was developed using computer simulation. A virtual library of functional monomers was assigned and screened against the target molecule, creatinine, using molecular modelling software. The monomers giving the highest binding score were further tested using simulated annealing in order to mimic the complexation of the functional monomers with template in the monomer mixture. The result of this simulation gave an optimised MIP composition. The computationally designed polymer demonstrated superior selectivity in comparison to the polymer prepared using traditional approach, a detection limit of 25 μM and good stability. The ‘Bite-and-Switch’ approach combined with molecular imprinting can be used for the design of assays and sensors, selective for amino containing substances.