Retention and molecular-recognition mechanisms of molecularly imprinted polymers for promazine derivatives

Recent developments in molecular modeling tools and applications related to pharmaceutical and biomedical research

In modern pharmaceutical and biomedical research, molecular modeling represents a useful tool to explore processes and their mechanistic bases at the molecular level. Integrating experimental and virtual analysis is a fruitful approach to study ligand-receptor interaction in chemical, biochemical and biological environments. In these fields, molecular docking and molecular dynamics are considered privileged techniques for modeling (bio)macromolecules and related complexes. This review aims to present the current landscape of molecular modeling in pharmaceutical and biomedical research by examining selected representative applications published in the last years and highlighting current topics and trends of this field. Thus, a systematic compilation of all published literature has not been attempted herein. After a brief overview of the main theoretical and computational tools used to investigate mechanisms at molecular level, recent applications of molecular modeling in drug discovery, ligand binding and for studying protein conformation and function will be discussed. Furthermore, specific sections will be devoted to the application of molecular modeling for unravelling enantioselective mechanisms underlying the enantioseparation of chiral compounds of pharmaceutical and biomedical interest as well as for studying new forms of noncovalent interactivity identified in biochemical and biological environments. The general aim of this review is to provide the reader with a modern overview of the topic, highlighting advancements and outlooks as well as drawbacks and pitfalls still affecting the applicability of theoretical and computational methods in the field of pharmaceutical and biomedical research.

Fabrication of a Lactate-Specific Molecularly Imprinted Polymer toward Disease Detection

The development of sensitive and selective robust sensor materials for targeted biomarker detection aims to contribute to self-health monitoring and management. Molecularly imprinted polymeric (MIP) materials can perform as biomimetic recognition elements via tailored routes of synthesis for specific target analyte extraction and/or detection. In this work, a sensitive- and selective-lactate MIP has been developed utilizing methacrylic acid and ethylene glycol dimethacrylate as the functional monomer and cross-linker, respectively. The sensitivity of the as-synthesized imprinted species was evaluated by determining the target analyte retention, imprinting factor, and selectivity adsorption of up to 63.5%, 6.86, and 0.82, respectively. MIP selectivity elucidated the imprinting mechanism between the functional monomers and target analyte lactate, further experimentally evidenced by using structurally competitive analytes malic acid and sodium 2-hydroxybutyrate, where retentions of 22.6 and 25.2%, respectively, were observed. Understanding the specific intermolecular mechanisms of both the template analyte and structural interferents with the MIP enables experimentalists to make informed decisions regarding monomer-target and porogen selections and possible sites of interaction for improved molecular imprinting. This imprinting system highlights the potential to be further developed into artificial receptor sensor materials for the detection of disease.

Experimental spectra, electronic properties (liquid and gaseous phases) and activity against SARS-CoV-2 main protease of Fluphenazine dihydrochloride: DFT and MD simulations

The Gaussian 09 DFT tool is used to investigate the formational electronic behaviour, reactivity analysis and biological properties of fluphenazine dihydrochloride (FDD). The quantum computation is used to determine the spectroscopic and vibrational assignments of FDD. The NBO method explains charge transfer and molecular interactions. Energy gap values are determined using FMO analysis in different solvents and toluene is a better solvent due to higher value of solvation energy. The UV-visible spectra are investigated in various solvents using the TD-DFT method. Electrostatic potential, the wave function related properties such as LOL, NCI and RDG are determined in gaseous phase. Furthermore, the drug likeness is analyzed. At last, a docking study with MD simulation is used to investigate FDD's antiviral activity against SARS-CoV-2 main protease.

Molecularly Imprinted Polymers in Diagnostics: Accessing Analytes in Biofluids

Bio-applied molecularly imprinted polymers (MIPs) are biomimetic materials with tailor-made synthetic recognition sites, mimicking biological counterparts known for their sensitive and selective analyte detection. MIPs, specifically designed for biomarker analysis...

Optimization of Cortisol-Selective Molecularly Imprinted Polymers Enabled by Molecular Dynamics Simulations

Today, we heavily rely on technology and increasingly utilize it to monitor our own health. The identification of sensitive, accurate biosensors that are capable of real-time cortisol analysis is one important potential feature for these technologies to aid us in the maintenance of our physical and mental wellbeing. Detection and quantification of cortisol, a well-known stress biomarker present in sweat, offers a noninvasive and potentially real-time method for monitoring anxiety. Molecularly imprinted polymers are attractive candidates for cortisol recognition elements in such devices as they can selectively rebind a targeted template molecule. However, mechanisms of imprinting and subsequent rebinding depend on the choice and composition of the prepolymerization mixture where the molecular interactions between the template, functional monomer, cross-linker, and solvent molecules are not fully understood. Here, we report the synthesis and evaluation of a molecularly imprinted polymer selective for cortisol detection. Molecular dynamics simulations were used to investigate the interactions between all components in the prepolymerization mixture of the as-synthesized molecularly imprinted polymer. Varying the component ratio of the prepolymerization mixture indicates that the number of cross-linker molecules relative to the template impacts the quality of imprinting. It was determined that a component ratio of 1:6:30 of cortisol, methacrylic acid, and ethylene glycol dimethacrylate, respectively, yields the optimal theoretical complexation of cortisol for the polymeric systems investigated. Experimental synthesis and rebinding results demonstrate an imprinting factor of up to 6.45. The trends in cortisol affinity predicted by molecular dynamics simulations of the prepolymerization mixture were also corroborated through experimental analysis of those modeled molecularly imprinted compositions, demonstrating the predictive capabilities of these simulations.

Retention and molecular-recognition mechanisms of molecularly imprinted polymers for warfarin derivatives and their application for the determination of warfarin in human serum

Monodisperse molecularly imprinted polymers (MIPs) for warfarin (WF), 4'-chlorowarfarin (CWF), 4'-bromowarfarin (BWF), 4'-nitrowarfarin (NWF) and 4'-methylwarfarin (MWF) (MIP_WF, MIP_CWF, MIP_BWF, MIP_NWF and MIP_MWF, respectively) were prepared using 4-vinylpyridine (4-VPY) and ethylene glycol dimethacrylate as a functional monomer and crosslinker, respectively, by multi-step swelling and polymerization. The retention and molecular-recognition properties of those MIPs were evaluated in HILIC, and reversed- and normal-phase modes. According to ¹H NMR studies, one-to-three complex formation of one WF or CWF molecule with three 4-VPY molecules occurred. Via computational approaches, the intermolecular interaction modes and energies between WF derivatives and 4-VPYs were evaluated by semi-empirical quantum chemistry methods and density functional theory calculations. Three major possible hydrogen bonding interaction modes were identified: the interactions between the 4-hydroxy group, α-proton (methylene C-H) and α-proton (methyl C-H) of the WF derivative and the nitrogen atoms of 4-VPYs. In HILIC and normal-phase modes, the interaction energies showed satisfactory correlations with the retention factors of the WF derivatives. In reversed-phase mode, the retention factors of the WF derivatives were described by the hydrophobicity and the acidity of the 4-hydroxy groups of the WF derivatives. These results demonstrate that three hydrogen bonding interactions in HILIC and normal-phase modes, and hydrogen bonding or ionic interactions and hydrophobic interactions in reversed-phase mode play important roles in the retention and molecular-recognition of the WF derivatives on MIPs. Furthermore, MIP_BWF was successfully applied to the determination of WF in human serum by column-switching LC with high accuracy, precision and selectivity and without template-leakage problems.

An Update on Molecularly Imprinted Polymer Design through a Computational Approach to Produce Molecular Recognition Material with Enhanced Analytical Performance

Molecularly imprinted polymer (MIP) computational design is expected to become a routine technique prior to synthesis to produce polymers with high affinity and selectivity towards target molecules. Furthermore, using these simulations reduces the cost of optimizing polymerization composition. There are several computational methods used in MIP fabrication and each requires a comprehensive study in order to select a process with results that are most similar to properties exhibited by polymers synthesized through laboratory experiments. Until now, no review has linked computational strategies with experimental results, which are needed to determine the method that is most appropriate for use in designing MIP with high molecular recognition. This review will present an update of the computational approaches started from 2016 until now on quantum mechanics, molecular mechanics and molecular dynamics that have been widely used. It will also discuss the linear correlation between computational results and the polymer performance tests through laboratory experiments to examine to what extent these methods can be relied upon to obtain polymers with high molecular recognition. Based on the literature search, density functional theory (DFT) with various hybrid functions and basis sets is most often used as a theoretical method to provide a shorter MIP manufacturing process as well as good analytical performance as recognition material.

DFT computational study towards investigating psychotropic drugs, promazine and trifluoperazine adsorption on graphene, fullerene and carbon cyclic ring nanoclusters

Detection and qualification process related to impurities assume importance in pharmacological drug development programmes and the present article gives the structural and spectral characterisation of phenothiazine derivatives, promazine (PME) and trifluoperazine (TPE) and their self-assembly with graphene/fullerene/carbon ring (CG/CF/CR) systems theoretically. The investigation of adsorption behaviour of these compounds can provide valuable information about its reactivity, electronic and structural properties. Three-dimensional electrostatic potential diagrams were mapped. The frontier orbital energies and energy band gaps of the molecules were computed. Delocalization of charge density between the bonding or lone pair and antibonding orbitals is calculated by NBO analysis. Docking was executed to investigate binding areas of chemical compounds. Bioactivity scores show that the pharmacokinetic and pharmacological properties of the ligands are appropriate leading to be considered potential drug agents. The obtained theoretical wavenumber results of the present study were fully compatible with the experimental results.

A novel magnetic fluorescent molecularly imprinted sensor for highly selective and sensitive detection of 4-nitrophenol in food samples through a dual-recognition mechanism

In this study, surface imprinting, magnetic separation, and fluorescent detection were integrated to develop a dual-recognition sensor (MF-MIPs), which was used for highly selective and sensitive detection of 4-nitrophenol (4-NP) in food samples. Silane-functionalized carbon dots (Si-CDs) participated in the imprinting process and were uniformly distributed into the MIPs layers. MF-MIPs sensor exhibited a high fluorescence response and selectivity based on the dual-recognition mechanism of imprinting recognition and fluorescence identification. The relative fluorescence intensity of MF-MIPs sensor presented a good linear relationship in the range of 0.08-10 μmol·L^-1 with a low limit of detection (23.45 nmol·L¹) for 4NP. MF-MIPs sensor showed high anti-interference, as well as excellent stability and reusability. The 4-NP recovery from spiked food samples ranged from 93.20 to 102.15%, and the relative standard deviation was lower than 5.0%. Therefore, MF-MIPs sensor may be a promising method for 4-NP detection in food samples.

A new approach for microextraction of trace albendazole sulfoxide drug from the samples of human plasma and urine, and water by the molecularly imprinted polymer nanoparticles combined with HPLC

In this research study, a method of dispersive-micro-solid phase extraction (D-µ-SPE) combined with molecularly imprinted polymer nanoparticles (MIP-NPs) with HPLC-UV was developed for the fast and selective detection of the trace amount of albendazole sulfoxide (ABZSO) in the biological samples. To investigate the effective factors on ABZSO microextraction by the method, central composite design (CCD) was utilized, and the optimum conditions for ABZSO microextraction were sample pH of 8.0, MIP-mass of 15 mg, sonication time of 12 min, and eluent (methanol) volume of 0.25 mL. Under the obtained optimal extraction conditions, the value for the limit of detection (LOD) and limit of quantification (LOQ) was respectively showed to be 0.074 and 0.246 ng mL^-1. In addition, the calculated peak areas exhibited a linear relationship with the ABZSO concentration ranging from 0.4 to 4200 ng mL^-1. The analyses of the samples including human plasma and urine, and water were successfully performed by the usage of the D-µ-SPE method, which was a simple and sensitive technique and a suitable alternative for the analysis of ABZSO. In the analysis of ABZSO in various samples, the recoveries at various levels of ABZSO concentrations (50, 300, and 500 ng mL^-1) were in the range of 95.7-103.0 %, and the relative standard deviations (RSDs; n = 3) varied from 2.2 to 4.4%.

A Molecularly Imprinted Polymer-based Dye Displacement Assay for the Rapid Visual Detection of Amphetamine in Urine

The rapid sensing of drug compounds has traditionally relied on antibodies, enzymes and electrochemical reactions. These technologies can frequently produce false positives/negatives and require specific conditions to operate. Akin to antibodies, molecularly imprinted polymers (MIPs) are a more robust synthetic alternative with the ability to bind a target molecule with an affinity comparable to that of its natural counterparts. With this in mind, the research presented in this article introduces a facile MIP-based dye displacement assay for the detection of (±) amphetamine in urine. The selective nature of MIPs coupled with a displaceable dye enables the resulting low-cost assay to rapidly produce a clear visual confirmation of a target's presence, offering huge commercial potential. The following manuscript characterizes the proposed assay, drawing attention to various facets of the sensor design and optimization. To this end, synthesis of a MIP tailored towards amphetamine is described, scrutinizing the composition and selectivity (ibuprofen, naproxen, 2-methoxphenidine, quetiapine) of the reported synthetic receptor. Dye selection for the development of the displacement assay follows, proceeded by optimization of the displacement process by investigating the time taken and the amount of MIP powder required for optimum displacement. An optimized dose-response curve is then presented, introducing (±) amphetamine hydrochloride (0.01-1 mg mL^-1) to the engineered sensor and determining the limit of detection (LoD). The research culminates in the assay being used for the analysis of spiked urine samples (amphetamine, ibuprofen, naproxen, 2-methoxphenidine, quetiapine, bupropion, pheniramine, bromopheniramine) and evaluating its potential as a low-cost, rapid and selective method of analysis.

Molecularly imprinted polymers in biological applications

Molecularly imprinted polymers (MIPs) are currently widely used and further developed for biological applications. The MIP synthesis procedure is a key process, and a wide variety of protocols exist. The templates that are used for imprinting vary from the smallest glycosylated glycan structures or even amino acids to whole proteins or bacteria. The low cost, quick preparation, stability and reproducibility have been highlighted as advantages of MIPs. The biological applications utilizing MIPs discussed here include enzyme-linked assays, sensors, in vivo applications, drug delivery, cancer diagnostics and more. Indeed, there are numerous examples of how MIPs can be used as recognition elements similar to natural antibodies.

Selective Adsorption and Purification of the Acteoside in Cistanche tubulosa by Molecularly Imprinted Polymers

Acteoside (ACT) is the main component of phenylethanoid glycosides in Cistanche tubulosa, and it is extremely desirable for obtaining high purification of ACT by molecularly imprinted polymers (MIPs) from their extracts. In this study, MIPs were designed and synthetized to adsorb selectively the ACT in C. tubulosa. The effects of different functional monomers, cross-linkers, and solvents of MIPs were investigated. MIPs were studied in terms of static adsorption experiments, dynamic adsorption experiments, and selectivity experiments. The optimal functional monomer, cross-linking agent, and solvent are 4-vinylpyridine, ethylene glycol dimethylacrylate, and the mixed solvent (acetonitrile and N,N-dimethylformamide, 1:1.5, v/v), respectively. Under the optimal conditions, the synthesized MIP1 has a high adsorption performance for ACT. The adsorption capacity of MIP1 to ACT reached 112.60 mg/g, and the separation factor of ACT/echinacoside was 4.68. Because the molecularly imprinted cavities of MIP1 resulted from template molecules of ACT, it enables MIP1 to recognize selectively ACT. Moreover, the N–H groups on MIP1 can form hydrogen bonds with the hydroxyl groups on the ACT; this improves the separation factor of MIP1. The dynamic adsorption of ACT accorded with the quasi-second-order kinetics; it indicated that the adsorption process of MIP1 is the process of chemical adsorption to ACT. MIPs can be applied as a potential adsorption material to purify the active ingredients of herbal medicines.