Computationally designed monomers and polymers for molecular imprinting of theophylline and its derivatives. Part I

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

Recent years have witnessed a dramatic increase in the use of theoretical and computational approaches in the study and development of molecular imprinting systems. These tools are being used to either improve understanding of the mechanisms underlying the function of molecular imprinting systems or for the design of new systems. Here, we present an overview of the literature describing the application of theoretical and computational techniques to the different stages of the molecular imprinting process (pre-polymerization mixture, polymerization process and ligand-molecularly imprinted polymer rebinding), along with an analysis of trends within and the current status of this aspect of the molecular imprinting field.

Imprinting Technology for Effective Sorbent Fabrication: Current State-of-Art and Future Prospects

In the last 10 years, we have witnessed an extensive development of instrumental techniques in analytical methods for determination of various molecules and ions at very low concentrations. Nevertheless, the presence of interfering components of complex samples hampered the applicability of new analytical strategies. Thus, additional sample pre-treatment steps were proposed to overcome the problem. Solid sorbents were used for clean-up samples but insufficient selectivity of commercial materials limited their utility. Here, the application of molecularly imprinted polymers (MIPs) or ion-imprinted polymers (IIPs) in the separation processes have recently attracted attention due to their many advantages, such as high selectivity, robustness, and low costs of the fabrication process. Bulk or monoliths, microspheres and core-shell materials, magnetically susceptible and stir-bar imprinted materials are applicable to different modes of solid-phase extraction to determine target analytes and ions in a very complex environment such as blood, urine, soil, or food. The capability to perform a specific separation of enantiomers is a substantial advantage in clinical analysis. The ion-imprinted sorbents gained interest in trace analysis of pollutants in environmental samples. In this review, the current synthetic approaches for the preparation of MIPs and IIPs are comprehensively discussed together with a detailed characterization of respective materials. Furthermore, the use of sorbents in environmental, food, and biomedical analyses will be emphasized to point out current limits and highlight the future prospects for further development in the field.

Semiconductor nanocrystal-polymer hybrid nanomaterials and their application in molecular imprinting

Quantum dots (QDs) are attractive semiconductor fluorescent nanomaterials with remarkable optical and electrical properties. The broad absorption spectra and high stability of QD transducers are advantageous for sensing and bioimaging. Molecular imprinting is a technique for manufacturing synthetic polymeric materials with a high recognition ability towards a target analyte. The high selectivity of the molecularly imprinted polymers (MIPs) is a result of the fabrication process based on the template-tailored polymerization of functional monomers. The three-dimensional cavities formed in the polymer network can serve as the recognition elements of sensors because of their specificity and stability. Appending specific molecularly imprinted layers to QDs is a promising strategy to enhance the stability, sensitivity, and selective fluorescence response of the resulting sensors. By merging the benefits of MIPs and QDs, inventive optical sensors are constructed. In this review, the recent synthetic strategies used for the fabrication of QD nanocrystals emphasizing various approaches to effective functionalization in aqueous environments are discussed followed by a detailed presentation of current advances in QD conjugated MIPs (MIP-QDs). Frontiers in manufacturing of specific imprinted layers of these nanomaterials are presented and factors affecting the specific behaviour of an MIP shell are identified. Finally, current limitations of MIP-QDs are defined and prospects are outlined to amplify the capability of MIP-QDs in future sensing.

Green Strategies for Molecularly Imprinted Polymer Development

Molecular imprinting is a powerful technology to create artificial receptors within polymeric matrices. Although it was reported for the first time by Polyakov, eighty-four years ago, it remains, nowadays, a very challenging research area. Molecularly imprinted polymers (MIPs) have been successfully used in several applications where selective binding is a requirement, such as immunoassays, affinity separation, sensors, and catalysis. Conventional methods used on MIP production still use large amounts of organic solvents which, allied with stricter legislation on the use and release of chemicals to the environment and the presence of impurities on final materials, will boost, in our opinion, the use of new cleaner synthetic strategies, in particular, with the application of the principles of green chemistry and engineering. Supercritical carbon dioxide, microwave, ionic liquids, and ultrasound technology are some of the green strategies which have already been applied in MIP production. These strategies can improve MIP properties, such as controlled morphology, homogeneity of the binding sites, and the absence of organic solvents. This review intends to give examples reported in literature on green approaches to MIP development, from nano- to micron-scale applications.

Towards EMIC rational design: setting the molecular simulation toolbox for enantiopure molecularly imprinted catalysts

A critical appraisal of the current strategies for the synthesis of enantiopure drugs is presented, along with a systematic background for the computational design of stereoselective porous polymers. These materials aim to achieve the enantiomeric excess of any chiral drug, avoiding the racemic separation. Particular emphasis is given to link statistical mechanics methods to the description of each one of the experimental stages within the catalyst’s synthesis, setting a framework for the fundamental study of the emerging field of molecularly imprinted catalysts.Graphical abstract

Synthesis, recognition characteristics and properties of l-3-n-butylphthalide molecularly imprinted polymers as sorbent for solid-phase extraction through precipitation polymerization

L-3-n-butylphthalide molecularly imprinted polymers (MIPs) were synthesized using l-3-n-butylphthalide as template molecule, acrylamide as functional monomer, ethylene glycol dimethacrylate as cross-linking agent, and acetone as the porogenic solvent through precipitation polymerization. The non-imprinted polymers (NIPs) were prepared with the same procedure, but with the absence of template molecule. The optimum preparation conditions of the MIPs such as the functional monomer, the porogenic solvent, the molar ratio of the template to the functional monomer and the molar ratio of the template to the cross-linker were investigated in detail. Prior to the polymerization, the molecular simulation with the computer-aided design was used to help choose a suitable polymerization porogen for the molecularly imprinted pre-assembled system and study the interactions between l-NBP and the functional monomers. The synthesized polymers were characterized with FTIR and SEM to observe their structures as well as the morphologies, and their adsorption properties were respectively evaluated by static and dynamic adsorption as well as selectivity experiments. Scatchard analyses revealed that there were high and low affinity sites formed in the MIPs, which elucidated good affinity to l-NBP in the ethanol system. The adsorption capacity of the MIPs for l-NBP was 3.561 mg g(-1), with an imprinting factor (α) of 2.321 when compared with that of the NIPs. Scatchard analysis illustrated that the binding sites with affinity for l-3-n-butylphthalide molecules were formed in the prepared MIPs.

Molecular imprinting science and technology: a survey of the literature for the years 2004-2011

Herein, we present a survey of the literature covering the development of molecular imprinting science and technology over the years 2004-2011. In total, 3779 references to the original papers, reviews, edited volumes and monographs from this period are included, along with recently identified uncited materials from prior to 2004, which were omitted in the first instalment of this series covering the years 1930-2003. In the presentation of the assembled references, a section presenting reviews and monographs covering the area is followed by sections describing fundamental aspects of molecular imprinting including the development of novel polymer formats. Thereafter, literature describing efforts to apply these polymeric materials to a range of application areas is presented. Current trends and areas of rapid development are discussed.

Molecularly Imprinted Hydrogels for Affinity-controlled and Stimuli-responsive Drug Delivery

The performance of smart or intelligent hydrogels as drug-delivery systems (DDSs) can be notably improved if the network is endowed with high-affinity receptors for the therapeutic molecule. Conventional molecular imprinting technology aims to create tailored binding pockets (artificial receptors) in the structure of rigid polymers by means of a template polymerization, in which the target molecules themselves induce a specific arrangement of the functional monomers during polymer synthesis. Adaptation of this technology to hydrogel synthesis implicates the optimization of the imprinting pocket to be able to recover the high-affinity conformation when distorted by swelling or after the action of a stimulus. This chapter analyzes the implementation of the molecular imprinting technology to the synthesis of both non-responsive and responsive loosely cross-linked hydrogels, and provides recent examples of the suitability of the imprinted networks to attain affinity-controlled, activation-controlled or stimuli-triggered drug and protein release.

Conformational studies of common protein templates in macromolecularly imprinted polymers

Unlike the molecular imprinting of small molecule templates, molecularly imprinted polymers specific to large templates (>1,500 Da), have achieved limited success to date. Conformational stability of these labile macromolecules is one of the main factors that prevent the direct extension of successful procedures from the small molecule regime. We continue our systematic investigation of the effect of common components in macromolecular MIPs on the conformation of protein templates. Circular dichroism was used to show that frequently employed monomers and crosslinkers induce significant changes in the secondary structures of lysozyme and bovine hemoglobin. The extent to which this change occurs, at ligand concentrations far below what are typically used reported work, is cause for concern and provides as rational explanation for the lack of success in this arena. This is because a change in the template structure prior to polymerization would lead to the binding sites formed during polymerization to be specific to this alternate conformation. Subsequent studies with the macromolecule in its native state and the crosslinked network would not be successful. Using this information as a guide, we offer suggestions as to where work in macromolecular imprinted polymers should focus going forward in order for these antibody mimics to reach their vast potential as a new class of biomedical diagnostic devices.

Molecular docking simulations for macromolecularly imprinted polymers

Molecularly imprinted polymers are fully synthetic antibody mimics prepared via the crosslinking of organic monomers in the presence of an analyte. This general procedure is now well developed for small molecule templates; however, attempts to extend the same techniques to the macromolecular regime have achieved limited success to date. We employ molecular docking simulations to investigate the interactions between albumin, a common protein template, and frequently employed ligands used in the literature at the molecular level. Specifically, we determine the most favorable binding sites for these ligands on albumin and determine the types of non-covalent interactions taking place based on the amino acids present nearby this binding pocket. Our results show that hydrogen bonding, electrostatic interactions, and hydrophobic interactions occur between amino acids side chains and ligands. Several interactions are also taking place with the polypeptide backbone, potentially disrupting the protein's secondary structure. We show that several of the ligands preferentially bind to the same sites on the protein, which indicates that if multiple monomers are used during synthesis then competition for the same amino acids could lead to non-specific recognition. Both of these results provide rational explanations for the lack of success to date in the field.

New method for affinity adsorbent screening using gold colloids

A rapid, effective method for the screening of adsorbent ligands based on the unique optical properties of gold colloid has been developed. Different interactions between adsorbate and ligands induce different states of aggregation of the gold colloid, and the associated distinct color changes of the colloid have been utilized to estimate the affinity of the ligands toward the adsorbate. In this work, phosphorylated peptide CGGFGGpSG was appended to a gold colloid to obtain the adsorbate-modified gold colloid (CG8-AuNPs). Candidate ligands Dpa-Zn(2+), DMAPAA, and AAn were copolymerized with acrylamide to form linear polymers and cross-linked CG8-AuNPs to induce aggregation. Screening of the candidate ligands revealed that Dpa-Zn(2+) showed the highest affinity among those tested, inducing a color change of the gold colloid at a concentration of 10 μM, which is much lower than those of ligands DMAPAA (40 μM) and AAn (almost no color change could be observed). Subsequent statistical adsorption experiments confirmed these screening results, with the adsorbent A-AAm-Dpa-Zn(2+) showing the highest adsorption capacity (426 mg/g) for CG-8, almost twice that of adsorbent A-AAm-DMAPAA. This reported method has low sample consumption, and the screening may be simply monitored by the naked eye.

Molecularly imprinted polymers for ochratoxin a extraction and analysis

Molecularly imprinted polymers (MIPs) are considered as polymeric materials that mimic the functionality of antibodies. MIPs have been utilized for a wide variety of applications in chromatography, solid phase extraction, immunoassays, and sensor recognition. In this article, recent advances of MIPs for the extraction and analysis of ochratoxins are discussed. Selection of functional monomers to bind ochratoxin A (OTA) with high affinities, optimization of extraction procedures, and limitations of MIPs are compared from different reports. The most relevant examples in the literature are described to clearly show how useful these materials are. Strategies on MIP preparation and schemes of analytical methods are also reviewed in order to suggest the next step that would make better use of MIPs in the field of ochratoxin research. The review ends by outlining the remaining issues and impediments.

Development of a model for the rational design of molecular imprinted polymer: computational approach for combined molecular dynamics/quantum mechanics calculations

A new rational approach for the preparation of molecularly imprinted polymer (MIP) based on the combination of molecular dynamics (MD) simulations and quantum mechanics (QM) calculations is described in this work. Before performing molecular modeling, a virtual library of functional monomers was created containing forty frequently used monomers. The MD simulations were first conducted to screen the top three monomers from virtual library in each porogen-acetonitrile, chloroform and carbon tetrachloride. QM simulations were then performed with an aim to select the optimum monomer and progen solvent in which the QM simulations were carried out; the monomers giving the highest binding energies were chosen as the candidate to prepare MIP in its corresponding solvent. The acetochlor, a widely used herbicide, was chosen as the target analyte. According to the theoretical calculation results, the MIP with acetochlor as template was prepared by emulsion polymerization method using N,N-methylene bisacrylamide (MBAAM) as functional monomer and divinylbenzene (DVB) as cross-linker in chloroform. The synthesized MIP was then tested by equilibrium-adsorption method, and the MIP demonstrated high removal efficiency to the acetochlor. Mulliken charge distribution and 1H NMR spectroscopy of the synthesized MIP provided insight on the nature of recognition during the imprinting process probing the governing interactions for selective binding site formation at a molecular level. We think the computer simulation method first proposed in this paper is a novel and reliable method for the design and synthesis of MIP.

Computer simulation of volatile organic compound adsorption in atomistic models of molecularly imprinted polymers

Molecularly imprinted polymers (MIPs) offer a unique opportunity to significantly advance volatile organic compound (VOC) sensing technologies and a number of other applications. However, the development of these applications using MIPs has been hindered by poor understanding of the microstructure of MIPs, geometry of binding sites, and the details of molecular recognition processes in these materials. This is further complicated by the vast number of optimization parameters such as building components and processing conditions. Computer simulations and molecular modeling can help us understand adsorption and binding phenomena in MIPs on the molecular level and thus provide a route to more efficient MIP design strategies. So far, molecular models have been either oversimplified or severely limited in length scale, essentially focusing on a single binding site. Here, we propose a more general, atomistically detailed model that describes the microstructure of MIPs. We apply this model to investigate adsorption of pyridine, benzene, and toluene in MIPs and demonstrate that it is able to capture a number of essential experimental features. Therefore, this model can serve as a starting point in computational design and optimization of MIPs.

Selective recognition of veterinary drugs residues by artificial antibodies designed using a computational approach

In this work we introduce a simple and inexpensive veterinary drugs residues detection method. Molecular dynamics simulations and computational screening were used to identify functional monomers capable of interacting with sulfadimidine (SM2). A library of 15 kinds of common functional monomers for preparing molecular imprinted polymer (MIP) was built and their interactions with SM2 in acetonitrile were calculated using the molecular dynamics software (GROMACS 3.3). According to the theoretical calculation results, the surface molecularly imprinted silica (MIP-silica) with SM2 as template was prepared by surface-imprinting technique using methacrylic acid (MAA) as functional monomer and divinylbenzene as cross-linker in acetonitrile. The surface composition of the MIP-silica was determined by Fourier transform infrared spectrometer (FT-IR) and energy dispersive X-ray spectrometer (EDS). Scanning electron microscopy (SEM) was used to characterize the morphological properties of the MIP-silica. The synthesized MIP-silica was then tested by equilibrium-adsorption method, and the MIP-silica demonstrated high binding specificity to the SM2. The molecular recognition of SM2 was analyzed in detail by using molecular modeling software (Gaussian 03).

Theoretical and computational strategies for rational molecularly imprinted polymer design

The further evolution of molecularly imprinted polymer science and technology necessitates the development of robust predictive tools capable of handling the complexity of molecular imprinting systems. A combination of the rapid growth in computer power over the past decade and significant software developments have opened new possibilities for simulating aspects of the complex molecular imprinting process. We present here a survey of the current status of the use of in silico-based approaches to aspects of molecular imprinting. Finally, we highlight areas where ongoing and future efforts should yield information critical to our understanding of the underlying mechanisms sufficient to permit the rational design of molecularly imprinted polymers.

Computational design and synthesis of molecular imprinted polymers with high selectivity for removal of aniline from contaminated water

A computational approach was developed to screening functional monomers and polymerization solvents for rational design of molecularly imprinted polymer (MIP). It was based on the comparison of the binding energy of the complexes between the template and different functional monomers. The effect of the polymerization solvent was included using the polarizable continuum model. According to the theoretical calculation results, the MIP with aniline as template was prepared by emulsion polymerization method using acrylamide (AAM) as functional monomer and divinylbenzene as cross-linker in carbon tetrachloride. The synthesized MIP was then tested by equilibrium-adsorption method, and the MIP demonstrated high removal efficiency to the aniline. The results of this study have indicated the possibility of using computer aided design for rational selection of functional monomers and solvents capable of removal of aniline from contaminated water.

Predicting the Solubility of the Anti-Cancer Agent Docetaxel in Small Molecule Excipients using Computational Methods

PURPOSE

To develop an in silico model that provides an accurate prediction of the relative solubility of the lipophilic anticancer agent docetaxel in various excipients.

MATERIALS AND METHODS

The in silico solubility of docetaxel in the excipients was estimated by means of the solubility (delta) and Flory-Huggins interaction (chi (FH)) parameters. The delta values of docetaxel and excipients were calculated using semi-empirical methods and molecular dynamics (MD) simulations. Cerius(2) software and COMPASS force-field were employed for the MD simulations. The chi (FH) values for the binary mixtures of docetaxel and excipient were also estimated by MD simulations.

RESULTS

The values obtained from the MD simulations for the solubility of docetaxel in the various excipients were in good agreement with the experimentally determined values. The simulated values for solubility of docetaxel in tributyrin, tricaproin and vitamin E were within 2 to 6% of the experimental values. MD simulations predicted docetaxel to be insoluble in beta-caryophyllene and this result correlated well with experimental studies.

CONCLUSIONS

The MD model proved to be a reliable tool for selecting suitable excipients for the solubilization of docetaxel.

Recent advances on noncovalent molecular imprints for affinity separations

Molecularly imprinted polymers (MIPs) are tailor-made synthetic materials capable of selectively rebinding a target analyte, or a group of structurally related compounds based on a combination of recognition mechanisms including size, shape, and functionality. Among the advantageous properties of MIPs are the achievable specific affinity, the relative ease of preparation, and their mechanical and chemical robustness, which renders them ideal materials for applications as stationary phase (e. g., affinity chromatography or SPE), or as antibody mimics (e. g., biomimetic assays). Here, we review recent advancements on the application of MIPs in affinity separations and biomimetic assays, which have focused on the synthesis of size- and shape-uniform particles facilitating reproducibility, improved binding site accessibility, and enhanced affinity. While MIPs certainly offer promising potential as selective separation phase in a variety of applications, deeper understanding of the fundamental interactions governing imprinting, and rational understanding of the imprinting mechanism has yet to be achieved for providing rational guidelines in deliberately designing next-generation MIP materials.

Capturing molecules with templated materials—Analysis and rational design of molecularly imprinted polymers

The creation of synthetic tailor-made receptors capable of recognizing desired molecular targets with high affinity and selectivity is a persistent long-term goal for researchers in the fields of chemical, biological, and pharmaceutical research. Compared to biomacromolecular receptors, these synthetic receptors promise simplified production and processing, less costs, and more robust receptor architectures. During recent decades, molecularly imprinted polymers (MIPs) are widely considered mimics of natural molecular receptors suitable for a diversity of applications ranging from biomimetic sensors, to separations and biocatalysis. A remaining challenge for the next generation of MIPs is the synthesis of deliberately designed and highly efficient receptor architectures suitable for recognizing biologically relevant molecules, for which natural receptors are either not prevalent, or difficult to isolate and utilize. Hence, this review discusses recent advances in synthetic receptor technology for biomolecules (e.g. drugs, amino acids, steroids, proteins, entire cells, etc.) via molecular imprinting techniques. Surface imprinting methods and epitope imprinting approaches have been introduced for protein recognition at imprinted surfaces. Imprinting techniques in aqueous solution or organic-water co-solvents have been introduced avoiding denaturation of biomolecules during MIP synthesis. In addition, improved bioreactivity of entire enzyme or active site mimics generated by molecular imprinting will be highlighted. Finally, the emerging importance of molecular modeling and molecular dynamics studies detailing the intermolecular interactions between the template species, the porogenic solvent molecules, and the involved monomer and cross-linker in the pre-polymerization solution will be addressed yielding a rational approach toward next-generation MIP technology.

Molecularly imprinted materials as advanced excipients for drug delivery systems

The application of the molecular imprinting technology in the design of new drug delivery systems (DDS) and devices useful in closely related fields, such as diagnostic sensors or biological traps, is receiving increasing attention. Molecular imprinting technology can provide polymeric materials with the ability to recognize specific bioactive molecules and with a sorption/release behaviour that can be made sensitive to the properties of the surrounding medium. In this review, an introduction to the imprinting technology presenting the different approaches in preparing selective polymers of different formats is given, and the key factors involved in obtaining of imprinted binding sites in materials useful for pharmaceutical applications are analysed. Examples of DDS based on molecularly imprinted polymers (MIPs) can be found for the three main approaches developed to control the moment at which delivery should begin and/or the drug release rate; i.e., rate-programmed, activation-modulated or feedback-regulated drug delivery. This review seeks to highlight the most remarkable advantages of the imprinting technique in the development of new efficient DDS as well as to point out some possibilities of adapting the synthesis procedures to create systems compatible with both the relative instable drug molecules, especially of peptide nature, and the sensitive physiological tissues with which MIP-based DDS would enter into contact when administered. The prospects for future development are also analysed.