Computational design and synthesis of molecularly imprinted polymers with high binding capacity for pharmaceutical applications-model case: Adsorbent for abacavir

Design and Optimization of Molecularly Imprinted Polymer Targeting Epinephrine Molecule: A Theoretical Approach

Molecularly imprinted polymers (MIPs) are a growing highlight in polymer chemistry. They are chemically and thermally stable, may be used in a variety of environments, and fulfill a wide range of applications. Computer-aided studies of MIPs often involve the use of computational techniques to design, analyze, and optimize the production of MIPs. Limited information is available on the computational study of interactions between the epinephrine (EPI) MIP and its target molecule. A rational design for EPI-MIP preparation was performed in this study. First, density functional theory (DFT) and molecular dynamic (MD) simulation were used for the screening of functional monomers suitable for the design of MIPs of EPI in the presence of a crosslinker and a solvent environment. Among the tested functional monomers, acrylic acid (AA) was the most appropriate monomer for EPI-MIP formulation. The trends observed for five out of six DFT functionals assessed confirmed AA as the suitable monomer. The theoretical optimal molar ratio was 1:4 EPI:AA in the presence of ethylene glycol dimethacrylate (EGDMA) and acetonitrile. The effect of temperature was analyzed at this ratio of EPI:AA on mean square displacement, X-ray diffraction, density distribution, specific volume, radius of gyration, and equilibrium energies. The stability observed for all these parameters is much better, ranging from 338 to 353 K. This temperature may determine the processing and operating temperature range of EPI-MIP development using AA as a functional monomer. For cost-effectiveness and to reduce time used to prepare MIPs in the laboratory, these results could serve as a useful template for designing and developing EPI-MIPs.

Integrating DFT and machine learning for the design and optimization of sodium alginate-based hydrogel adsorbents: Efficient removal of pollutants from wastewater

This study presents a novel approach to design and optimize a sodium alginate-based hydrogel (SAH) for efficient adsorption of the model water pollutant methylene blue (MB) dye. Utilizing density functional theory (DFT) calculations, sodium alginate-g-poly (acrylamide-co-itaconic acid) was identified with the lowest adsorption energy (Eads) for MB dye among 14 different clusters. SAHs were prepared using selected monomers and sodium alginate combinations through graft co-polymerization, and swelling studies were conducted to optimize grafting conditions. Advanced characterization techniques, including FTIR, XRD, XPS, SEM, EDS, and TGA, were employed, and the process was optimized using statistical and machine learning tools. Screening tests demonstrated that Eads serves as an effective predicting indicator for adsorption capacity (qe) and MB removal efficiency (RRMB,%), with reasonable agreement between Eads and both responses under given conditions. Process modeling and optimization revealed that 5 mg of selected SAH achieves a maximum qe of 3244 mg g-1 at 84.4% RRMB under pH 8.05, 98.8 min, and MB concentration of 383.3 mg L-1, as identified by the desirability function approach. Moreover, SAH effectively eliminated various contaminants from aqueous solutions, including sulfasalazine (SFZ) and dibenzothiophene (DBT). MB adsorption onto selected SAH was exothermic, spontaneous, and followed the pseudo-first-order and Langmuir-Freundlich isotherm models. The remarkable ability of SAH to adsorb MB is attributed to its well-designed structure predicted through DFT and optimal operational conditions achieved by AI-based parametric optimization. By integrating DFT-based computations and machine-learning tools, this study contributes to the efficient design of adsorbent materials and optimization of adsorption processes, also showcasing the potential of SAH as an efficient adsorbent for the abatement of aqueous pollution.

Deep insight into selective adsorption behavior and mechanism of novel deep eutectic solvent functionalized bio-sorbent towards methcathinone: Experiments and DFT calculation

This work designed and synthesized novelly selective, highly efficient and friendly environmental biochar nanomaterial (ZMBC@ChCl-EG) by screening suitable deep eutectic solvent (DES) as the functional monomer via Density Functional Theory (DFT). The prepared ZMBC@ChCl-EG achieved the highly efficient adsorption of methcathinone (MC) and exhibited excellent selectivity as well as good reusability. Selectivity analysis concluded that the distribution coefficient value (K_D) of ZMBC@ChCl-EG towards MC was 3.247 L/g, which was about 3 times higher than that of ZMBC, corresponding to stronger selective adsorption capacity. The studies of isothermal and kinetics indicated that ZMBC@ChCl-EG had an excellent adsorption capacity towards MC and the adsorption was mainly chemically controlled. In addition, DFT was used to calculate the binding energies between MC and each component. The binding energies were -10.57 kcal/mol for ChCl-EG/MC, -3.15∼-9.51 kcal/mol for BCs/MC, -2.33 kcal/mol for ZIF-8/MC, respectively, suggesting that DES played a major role in enhancing methcathinone adsorption. Lastly, the adsorption mechanisms were revealed by variables experiment combined with characterizations and DFT calculation. The main mechanisms were hydrogen bonding and π-π interaction.

Biodegradable and Sustainable Synthetic Antibodies-A Perspective

Molecular imprinting technology has been around for almost a century, and we have witnessed dramatic advancements in the overall design and production of molecularly imprinted polymers (MIPs), particularly in terms of possible formats of the final products when it comes to truly resembling antibody substitutes, i.e., MIP nanoparticles (MIP NPs). Nonetheless, the overall technology appears to struggle to keep up with the current global sustainability efforts, as recently elucidated in the latest comprehensive reviews, which introduced the "GREENIFICATION" concept. In this review, we will try to elucidate if these advancements in MIP nanotechnology have indeed resulted in a sustainability amelioration. We will do so by discussing the general production and purification strategies for MIP NPs, specifically from a sustainability and biodegradation perspective, also considering the final intended application and ultimate waste management.

Rationally designed molecularly imprinted polymer membranes as antibody and enzyme mimics in analytical biotechnology

The paper is a self-review of works on development of new approaches to formation of mimics of receptor and catalytic sites of biological macromolecules in the structure of highly cross-linked polymer membranes and thin films. The general strategy for formation of the binding sites in molecularly imprinted polymer (MIP) membranes and thin films was described. A selective recognition of a number of food toxins, endocrine disruptors and metabolites is based on the results of computational modeling data for the prediction and optimization of their structure. A strategy proposed for the design of the artificial binding sites in MIP membranes was supported by the research performed by the authors on development of a number of the MIP membrane-based affinity and catalytic biosensors for selective and sensitive measurement (detection limits 0.3-100 nM) of the target analytes. Novel versatile approaches aimed at improving sensitivity of the developed biosensor systems were discussed.

Green molecularly imprinted polymers for sustainable sample preparation

The use of molecularly imprinted polymers in sample preparation as selective sorbent materials has received great attention during the last years leading to analytical methods with unprecedented selectivity. However, with the progressive implementation of Green Analytical Chemistry principles, it is necessary to critically review the greenness of synthesis and further use of molecularly imprinted polymers in sample preparation. Accordingly, in the present review, the different steps and strategies for the preparation of molecularly imprinted polymers, the used reagents, as well as their incorporation to microextraction techniques are reviewed from a green perspective and recent alternatives to make the use of molecularly imprinted polymers more sustainable are provided.

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.

Effect of the Molecularly Imprinted Polymer Component Ratio on Analytical Performance

Molecular imprinting technology is a new analytical method that is highly selective and specific for certain analytes in artificial receptor design. The renewal possibilities of this technology make it an ideal material for sundry application fields. Molecularly imprinted polymers (MIPs) are polymeric matrices that have molecules printed on their surfaces; these surfaces can chemically interact with molecules or follow the pattern of the available template cavities obtained using imprinting technology. A MIP is useful for separating and analysing complex samples, such as biological fluids and environmental samples, because it is a strong analytical recognition element that can mimick natural recognition entities like biological receptors and antibodies. The MIP components consist of the target template, functional monomer, crosslinker, polymerisation initiator, and porogen. The effectiveness and selectivity of a MIP are greatly influenced by variations in the components. This review will provide an overview of the effect of MIP component ratio on analytical performance to each target analyte; it will also provide a strategy to obtain the best MIP performance. For every MIP, each template : monomer : crosslinker ratio shows a distinct performance for a specific analyte. The effects of the template : monomer : crosslinker ratio on a MIP's analytical performances-measured by the imprinting factor, sorbent binding capacity, and sorbent selectivity-are briefly outlined.

Optimization of adsorption configuration by DFT calculation for design of adsorbent: A case study of palladium ion-imprinted polymers

Trial-and-error method is widely used to seek an efficient adsorbent, although it is time- and money-consuming. Rationally design of functional materials via theoretical calculation is an emerging and appealing strategy in material science. However, exploiting of theoretical calculation for assistance of adsorbent design is rarely to be attempted despite it is usually utilized to explore the adsorption mechanism. In this work, density functional theory (DFT) calculation is exploited to design an adsorbent with high adsorption capacity and selectivity. The well-known palladium ion-imprinted polymer (IIP) was used as a model adsorbent. Then, three types of given adsorption configurations (a-Pd-IIP, b-Pd-IIP and c-Pd-IIP) were optimized. Further, their adsorption energies were calculated by DFT, which were -13.978 eV for b-Pd-IIP, -8.764 eV for a-Pd-IIP and -3.587 eV for c-Pd-IIP, respectively. The correlation coefficient (R²) between the theoretical adsorption energy and the experimental adsorption capacity reached to as high as 0.985. In addition, the dynamics and selectivity experimental results further consolidated the tendency of the calculation result. All these results demonstrate that the adsorption energy derived from DFT calculations is an important factor in guiding the design of IIPs.

Rational design and tailoring of imprinted polymeric enantioselective sensor layered on multiwalled carbon nanotubes for the chiral recognition of d-mandelic acid

Attempts have been made to investigate the feasibility of fabricating an enantiomeric sensor for the specific detection of d-mandelic acid layered on vinyl-MWCNT using molecular imprinting technology.

Environmental fate and ecotoxicological effects of antiretrovirals: A current global status and future perspectives

The therapeutic efficacy of antiretroviral drugs as well as challenges and side effects against the human immunodeficiency virus is well documented and reviewed. Evidence is available in literature indication that antiretrovirals are only partially transformed and become completely excreted from the human body in their original form and/or as metabolites in urine and feces. The possibility of massive release of antiretrovirals through human excreta that enters surface water through surface runoff and wastewater treatment plant effluents is now of environmental concern because the public might be experiencing chronic exposure to antiretrovirals. The primary concern of this review is limited data concerning environmental fate and ecotoxicity of antiretrovirals and their metabolites. The review aims to provide a comprehensive insight into the evaluation of antiretrovirals in environmental samples. The objective is therefore to assess the extent of analysis of antiretrovirals in environmental samples and also look at strategies including instrumentation and predictive models that have been reported in literature on the fate and ecotoxicological effects due to presence of antiretrovirals in different environmental compartments. The review also looks at current challenges and offers possible areas of exploration that could help minimize the presence of antiretrovirals in the environment.

The molecularly imprinted polymer essentials: curation of anticancer, ophthalmic, and projected gene therapy drug delivery systems

The development of polymeric materials as drug delivery systems has advanced from systems that rely on classical passive targeting to carriers that can sustain the precisely controlled release of payloads upon physicochemical triggers in desired microenvironment. Molecularly imprinted polymers (MIP), materials designed to capture specific molecules based on their molecular shape and charge distribution, are attractive candidates for fulfilling these purposes. In particular, drug-imprinted polymers coupled with active targeting mechanisms have been explored as potential drug delivery systems. In this review, we have curated important recent efforts in the development of drug-imprinted polymers in a variety of clinical applications, especially oncology and ophthalmology. MIP possesses properties that may complement the traditional delivery systems of these two disciplines, such as passive enhanced permeability and retention effect (EPR) in cancer tumors, and passive drug diffusion in delivering ophthalmic therapeutics. Furthermore, the prospects of MIP integration with the emerging gene therapies will be discussed.

Hollow mesoporous structured molecularly imprinted polymer as adsorbent in pipette-tip solid-phase extraction for the determination of antiretrovirals from plasma of HIV-infected patients

In this work a hollow mesoporous structured molecularly imprinted polymer was synthetized and used as adsorbent in pipette-tip solid-phase extraction for the determination of lamivudine (3TC), zidovudine (AZT) and efavirenz (EFZ) from plasma of human immunodeficiency virus (HIV) infected patients by high-performance liquid chromatography (HPLC). All parameters that influence the recovery of the pipette tip based on hollow mesoporous molecularly imprinted polymer solid-phase extraction (PT-HM-MIP-SPE) method were systematically studied and discussed in detail. The adsorbent material was prepared using methacrylic acid and 4-vinylpyridine as functional monomers, ethylene glycol dimethacrylate as crosslinker, acetonitrile as solvent, 4,4'-azobis(4-cyanovaleric acid) as radical initiator, benzalkonium chloride as surfactant, 3TC, and AZT as templates. The simultaneous separation of 3TC, AZT and EFZ by HPLC-UV was performed using a Gemini C18 Phenomenex® column (250 mm × 4.6 mm, 5 μm) and mobile phase consisting of acetonitrile: water pH 3.2 (68:32, v/v), flow rate of 1.0 mL/min and λ = 260 nm. The method was linear over the concentration range from 0.25 to 10 μg/mL for 3TC and EFZ, and 0.05 to 2.0 μg mL^-1 for AZT, with correlation coefficients larger than 0.99 for all analytes. Recovery ± relative standard deviations (RSDs %) were 41.99 ± 2.38%, 82.29 ± 1.63%, and 83.72 ± 7.52% for 3TC, AZT, and EFZ, respectively. The RSDs and relative errors (REs) were lower than 15% for intra and interday assays. The method has been successfully applied for monitoring HIV-infected patients outside the therapeutic dosage.

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

Integrating sampling techniques and inverse virtual screening: toward the discovery of artificial peptide-based receptors for ligands

A novel heuristic using an iterative select-and-purge strategy is proposed. It combines statistical techniques for sampling and classification by rigid molecular docking through an inverse virtual screening scheme. This approach aims to the de novo discovery of short peptides that may act as docking receptors for small target molecules when there are no data available about known association complexes between them. The algorithm performs an unbiased stochastic exploration of the sample space, acting as a binary classifier when analyzing the entire peptides population. It uses a novel and effective criterion for weighting the likelihood of a given peptide to form an association complex with a particular ligand molecule based on amino acid sequences. The exploratory analysis relies on chemical information of peptides composition, sequence patterns, and association free energies (docking scores) in order to converge to those peptides forming the association complexes with higher affinities. Statistical estimations support these results providing an association probability by improving predictions accuracy even in cases where only a fraction of all possible combinations are sampled. False positives/false negatives ratio was also improved with this method. A simple rigid-body docking approach together with the proper information about amino acid sequences was used. The methodology was applied in a retrospective docking study to all 8000 possible tripeptide combinations using the 20 natural amino acids, screened against a training set of 77 different ligands with diverse functional groups. Afterward, all tripeptides were screened against a test set of 82 ligands, also containing different functional groups. Results show that our integrated methodology is capable of finding a representative group of the top-scoring tripeptides. The associated probability of identifying the best receptor or a group of the top-ranked receptors is more than double and about 10 times higher, respectively, when compared to classical random sampling methods.

Computational Modeling and Theoretical Calculations on the Interactions between Spermidine and Functional Monomer (Methacrylic Acid) in a Molecularly Imprinted Polymer

This paper theoretically investigates interactions between a template and functional monomer required for synthesizing an efficient molecularly imprinted polymer (MIP). We employed density functional theory (DFT) to compute geometry, single-point energy, and binding energy (ΔE) of an MIP system, where spermidine (SPD) and methacrylic acid (MAA) were selected as template and functional monomer, respectively. The geometry was calculated by using B3LYP method with 6-31+(d) basis set. Furthermore, 6-311++(d, p) basis set was used to compute the single-point energy of the above geometry. The optimized geometries at different template to functional monomer molar ratios, mode of bonding between template and functional monomer, changes in charge on natural bond orbital (NBO), and binding energy were analyzed. The simulation results show that SPD and MAA form a stable complex via hydrogen bonding. At 1 : 5 SPD to MAA ratio, the binding energy is minimum, while the amount of transferred charge between the molecules is maximum; SPD and MAA form a stable complex at 1 : 5 molar ratio through six hydrogen bonds. Optimizing structure of template-functional monomer complex, through computational modeling prior synthesis, significantly contributes towards choosing a suitable pair of template-functional monomer that yields an efficient MIP with high specificity and selectivity.

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.

On the influence of crosslinker on template complexation in molecularly imprinted polymers: a computational study of prepolymerization mixture events with correlations to template-polymer recognition behavior and NMR spectroscopic studies

Aspects of the molecular-level basis for the function of ethylene glycol dimethacrylate and trimethylolproprane trimethacrylate crosslinked methacrylic acid copolymers molecularly imprinted with (S)-propranolol have been studied using a series of all-component and all-atom molecular dynamics studies of the corresponding prepolymerization systems. The crosslinking agents were observed to contribute to template complexation, and the results were contrasted with previously reported template-recognition behavior of the corresponding polymers. Differences in the extent to which the two crosslinkers interacted with the functional monomer were identified, and correlations were made to polymer-ligand recognition behavior and the results of nuclear magnetic resonance spectroscopic studies studies. This study demonstrates the importance of considering the functional monomer–crosslinker interaction when designing molecularly imprinted polymers, and highlights the often neglected general contribution of crosslinker to determining the nature of molecularly imprinted polymer-template selectivity.

Study on monomer suitability toward the template in molecularly imprinted polymer: an ab initio approach

Study of monomer-template interactions in molecularly imprinted polymer (MIP) is inevitable to comprehend best selectivity at the molecular level in pre-polymer solution. In the present work, binding energies of tryptophan, an amino acid template, complexed with different monomers were computed using second order Moller Plesset theory (MP2) at 6-311++g** level in gas phase. This helped in recommending a generic MIP, suitable for the selective and sensitive diagnosis of tryptophan, in clinical setting as disease biomarker, at primitive level. The tryptophan is an important biomarker owing to its highly regulated physiological process in the treatment of premenstrual dysphoric disorder and pellagra like diseases. Frequency calculations were performed using Density Functional Theory (DFT) at B3LYP employing 6-31+g (2d, 2p) level including thermal and entropy corrections. The monomer, p-nitrophenyl acrylate (2 mol), was adjudged having giving best binding score for the complexation at ground state with tryptophan (1 mol) for MIP development.

Application of a molecularly imprinted polymer for the extraction of kukoamine a from potato peels

A molecularly imprinted polymer (MIP) for the purification of N(1),N(12)-bis(dihydrocaffeoyl)spermine (kukoamine A) was computationally designed and tested. The properties of the polymer were characterized. The protocol of the solid phase extraction (SPE) of kukoamine A from potato peels was optimized. A HPLC-MS method for the quantification of kukoamine A was developed and used for all optimization studies. The capacity of the MIP in relation to kukoamine A from the potato peels extract was estimated at 54 mg/g of the polymer. The kukoamine A purified from potato extract using MIP was exceptionally pure (≈ 90%). Although the corresponding blank polymer was less selective than the MIP for the extraction of kukoamine A from the potato extract, it was shown that the blank polymer could be effectively used for the purification of the crude synthetic kukoamine (polymer capacity = 80 mg of kukoamine A/g of the adsorbent, kukoamine A purity ≈ 86%). Therefore, selective adsorbents could be computationally designed for other plant products, allowing their purification in quantities that would be sufficient for more detailed studies and potential practical applications.