Computational approach and electrochemical measurements for protein detection with MIP-based sensor

Rethinking the use of redox probes for the detection of electroactive proteins with electrochemical sensors modified with molecularly imprinted polymers

This study aims to demonstrate that redox couples, regardless of their electrical charges, are unnecessary for detecting and quantifying electroactive proteins using an electrochemical sensor functionalized with a molecularly imprinted polymer. Our approach involved designing a polydopamine imprinted biosensor for detecting bovine serum albumin as the model protein. Electrochemical measurements were conducted in a phosphate-buffered solution (PBS) and solutions containing the negatively charged hexacyanoferrate, the neutral ferrocene, or the positively charged hexaammineruthenium (III) probes. The dissociation constants Kd (in mg.mL-1), estimated from an extended Langmuir/one-site model, were of order of (1.0 ± 0.5)×10-8, (4.4 ± 2.1)×10-2, (7.6 ± 5.1)×10-4 and in the presence of [Fe(CN)6]-3/-4, Fe(C5H5)2, [RuN6H18]+3 respectively, and (8.7 ± 5.9)×10-11 in PBS. The non-use of probes, therefore, enhances the interaction between the analytes and the imprints. To understand the origin of this finding, we investigated ultraviolet and Fourier-transform infrared spectroscopies. Results indicated that redox probes could alter the proteins' intrinsic properties and adsorb to the polydopamine polymeric matrix, thus reducing the specific interactions between the protein and the imprints. To confirm the feasibility of electrochemical quantification of electroactive proteins in PBS, we designed three polydopamine-imprinted biosensors for detecting human serum albumin, prostate-specific antigen, and immunoglobulin G. Results validated the potential for quantifying electroactive proteins in PBS without adding any probe. This pioneering study was carried out with dopamine, which is taken here as a typical example of a functional monomer. It paves the way towards the detection of electroactive proteins without adding any redox couple of any nature.

Formation of molecularly imprinted polymers: Strategies applied for the removal of protein template (review)

The key step in the entire molecularly imprinted polymer (MIP) preparation process is the formation of the complementary cavities in the polymer matrix through the template removal process. The template is removed using chemical treatments, leaving behind selective binding sites for target molecules within the polymer matrix. Other MIP preparation steps include mixing monomers and template molecules in the appropriate solvent(s), monomer-template complex equilibration, and polymerisation of the monomers around the template. However, template removal is the most important among all the preparation steps because the final structure, which can be accepted and recognised as the MIP, is obtained only after the template removal. A thorough analysis of the studies dedicated to MIP applications demonstrates that this MIP preparation step, namely the template removal, is relatively understudied. MIP template removal is especially challenging in the synthesis, where the molecular template is a macromolecule such as a protein. This review aims to provide a deliberate, systematic, and consistent overview of protein removal as the MIP template molecules. The most prevalent template removal methods are outlined for removing protein templates from electrochemically synthesised MIPs, particularly thin layers on electrodes used in electrochemical sensors. Five protein template removal approaches involving chemical treatment are highlighted, which include the utilisation of (i) chaotropic agents, (ii) salt, (iii) acidic cleavage, (iv) alkaline, and finally, (v) proteolytic treatment focusing on studies conducted over the past decade. In addition, we discuss the interactions driving the removal of protein templates in each approach and associated challenges. This review provides insights into MIPs protein template removal strategies while highlighting the prevalent issue of this understudied step of template removal.

Dynamic simulation and experimental studies of molecularly imprinted label-free sensor for determination of milk quality marker

Bovine serum albumin (BSA) has emerged as a biomarker for mammary gland health and cow quality, being recognized as a significant allergenic protein. In this study, a novel flexible molecular imprinted electrochemical sensor by surface electropolymerization using pyrrole (Py) as functional monomer, which can be better applied to the detection of milk quality marker BSA. Based on computational results, with regard to all polypyrrole (PPy) conformations and amino-acid positions within the protein, the BSA molecule remained firmly embedded into PPy polymers with no biological changes. The molecular imprinted electrochemical sensor displayed a broad linear detection range from 1.0 × 10-4 to 50 ng·mL-1 (R2 = 0.995) with a low detection limit (LOD) of 4.5 × 10-2 pg·mL-1. Additionally, the sensor was highly selective, reproducible, stable and recoverable, suggesting that it might be utilized for the evaluation of milk quality.

Molecular Modeling Methods in the Development of Affine and Specific Protein-Binding Agents

High-affinity and specific agents are widely applied in various areas, including diagnostics, scientific research, and disease therapy (as drugs and drug delivery systems). It takes significant time to develop them. For this reason, development of high-affinity agents extensively utilizes computer methods at various stages for the analysis and modeling of these molecules. The review describes the main affinity and specific agents, such as monoclonal antibodies and their fragments, antibody mimetics, aptamers, and molecularly imprinted polymers. The methods of their obtaining as well as their main advantages and disadvantages are briefly described, with special attention focused on the molecular modeling methods used for their analysis and development.

Selective determination of an ovarian cancer biomarker at low concentrations with surface imprinted nanotube based chemosensor

In this study, an electrochemical chemosensor that utilizes a conductive polymer-based molecularly imprinted polymer (MIP) surface for rapid and reliable determination of CA125 was devised. A novel method has been applied to fabricate CA125 imprinted polypyrrole nanotubes (MI-PPy NT) via vapor deposition polymerization (VDP) as a recognition element for highly selective and sensitive determination of CA125. The chemosensor was prepared by immobilizing MI-PPy NT onto screen-printed gold electrodes (Au-SPE) and the performance of the sensor was evaluated by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) in terms of selectivity, sensitivity, linear dynamic concentration range (LDR) and limit of detection (LOD). The MI-PPy NT@Au-SPE sensor exhibited high sensitivity (68.57 μA per decade) to the CA125 concentration ranging from 0.1 U mL-1 to 100 U mL-1 at an LOD of 0.4 U mL-1 with a correlation coefficient of 0.9922. The developed chemosensors with their novel design combined with a facile fabrication method, prove to be promising as future state-of-the-art biosensors.

Designing a Simple Electrochemical Genosensor for the Detection of Urinary PCA3, a Prostate Cancer Biomarker

This study investigates the feasibility of a simple electrochemical detection of Prostate Cancer Antigen 3 (PCA3) fragments extracted from patients' urine, using a thiolated single-strand DNA probe immobilized on a gold surface without using a redox probe. To enhance the PCA3 recognition process, we conducted a comparative analysis of the hybridization location using two thiolated DNA probes: Probe 1 targets the first 40 bases, while Probe 2 targets the fragment from bases 47 to 86. Hybridization with PCA3 followed, using square wave voltammetry. The limit of detection of the designed genosenors were of the order of (2.2 ng/mL), and (1.6 ng/mL) for Probes 1 and 2, respectively, and the subsequent sensitivities were of the order of (0.09 ± 0.01) µA-1 · µg-1 · mL and (0.10 ± 0.01) µA-1 · µg-1 · mL. Specificity tests were then conducted with the sensor functionalized with Probe 2, as it presents better analytical performances. The electrochemical results indicate that the designed sensor can clearly discriminate a complementary target from a non-complementary one. A further modeling of the calibration curves with the Power Law/Hill model indicates that the dissociation constant increases by one order of magnitude, confirming the ability of the designed sensor to perfectly discriminate complementary targets from non-complementary ones.

An advanced ratiometric molecularly imprinted sensor based on metal ion reoxidation for indirect and ultrasensitive glyphosate detection in fruit

An indirect and ultrasensitive ratiometric molecularly imprinted (MIP) sensor, based on metal ion reoxidation, is introduced for glyphosate (GLY) determination in fruit. As high-performance signal amplification substrates, carbon nanotubes (MWCNTs) and gold nanoparticles (AuNPs) are conveniently modified on GCE. The artificial antibody-MIP membrane, presents typical three-dimensional structure to GLY template. Built-in reference methylene blue (MB) is directly electropolymerized on MWCNTs-Au/GCE. Particularly, Cu2+ and GLY interestingly form chelate complex, and the Cu2+ (ICu) in Cu(Ⅱ)-GLY-complex can be reoxidized, and indirectly quantizes GLY. The reference signal (IMB) presents noteworthy stability with different GLY levels, and the ratiometric readout (ICu/IMB) is recognized as a more trustworthy indicator to quantize GLY. Proposed sensor presents broad range as 1.73 ∼ 400 ng/mL, and limit of detection is well found as 0.24 ng/mL (S/N = 3). Finally, as-fabricated method is verified with standard HPLC in real-fruit-sample, and the errors and recovery rates are calculated as 3.4% ∼ 6.7% and 94.4% ∼ 104.6%, respectively.

Enhanced NIR-II Fluorescent Lateral Flow Biosensing Platform Based on Supramolecular Host-Guest Self-Assembly for Point-of-Care Testing of Tumor Biomarkers

Point-of-care detection of tumor biomarkers with high sensitivity remains an enormous challenge in the early diagnosis and mass screening of cancer. Fluorescent lateral flow immunoassay (LFA) is an attractive platform for point-of-care testing due to its inherent advantages. Particularly, a fluorescent probe is crucial to improving the analytical performance of the LFA platform. Herein, we developed an enhanced second near-infrared (NIR-II) LFA (ENIR-II LFA) platform based on supramolecular host-guest self-assembly for detection of the prostate-specific antigen (PSA) as a model analyte. In this platform, depending on the effective supramolecular surface modification strategy, cucurbit[7]uril (CB[7])-covered rare-earth nanoparticles (RENPs) emitting in the NIR-II (1000-1700 nm) window were prepared and employed as an efficient fluorescent probe (RENPs-CB[7]). Benefiting from its superior optical properties, such as low autofluorescence, excellent photostability, enhanced fluorescence intensity, and increased antibody-conjugation efficiency, the ENIR-II LFA platform displayed a wide linear detection range from 0.65 to 120 ng mL-1, and the limit of detection was down to 0.22 ng mL-1 for PSA, which was 18.2 times lower than the clinical cutoff value. Moreover, the testing time was also shortened to 6 min. Compared with the commercial visible fluorescence LFA kit (VIS LFA) and the previously reported NIR-II LFA based on a RENPs-PAA probe, this ENIR-II LFA demonstrated more competitive advantages in analytical sensitivity, detection range, testing time, and production cost. Overall, the ENIR-II LFA platform offers great potential for the highly sensitive, rapid, and convenient detection of tumor biomarkers and is expected to serve as a useful technique in the general population screening of the high-incidence cancer region.

Molecularly imprinted polymers: A closer look at the template removal and analyte binding

Molecularly imprinted polymers (MIPs), which first appeared over half a century ago, are now attracting considerable attention as artificial receptors, particularly for sensing. MIPs, especially applied to biomedical analysis in biofluids, contribute significantly to patient diagnosis at the point of care, thereby allowing health monitoring. Despite the importance given to MIPs, removal of templates and binding of analytes have received little attention and are currently the least focused steps in MIP development. This critical review is dedicated to a comprehensive analysis and discussion of cutting-edge concepts and methodologies in the removal and binding steps pertaining to various types of analytes, including ions, molecules, epitopes, proteins, viruses, and bacteria. The central objective of this review is to comprehensively examine and discuss a range of removal methods, including soxhlet extraction, immersion, microwave-assisted technique, ultrasonication, electrochemical approach, and proteolytic digestion, among others. Additionally, we will explore various binding methods, such as soaking, drop-casting, and batch sorption, to provide a comprehensive overview of the subject. Furthermore, the current challenges and perspectives in removal and binding are highlighted. Our review, at the interface of chemistry and sensors, will offer a wide range of opportunities for researchers whose interests include MIPs, (bio)sensors, analytical chemistry, and diagnostics.

A novel molecularly imprinting polypyrrole electrochemiluminescence sensor based on MIL-101-g-C3N4 for supersensitive determination of ciprofloxacin

Ciprofloxacin (CIP), a quinolone antibiotic, was rapidly and sensitively detected by integrating the molecularly imprinted polymer (MIP) with an ultra-sensitive electrochemiluminescence (ECL) method. g-C3N4, a typical polymer semiconductor, exhibited outstanding ECL efficiency and excellent ECL stability after combining with an iron-based metal-organic framework (MIL-101). Subsequently, the molecularly imprinted polypyrrole was electropolymerized on the composites of MIL-101-g-C3N4 modified glassy carbon electrode (GCE). The specific sites that could target rebinding the CIP molecules were formed on the surface of MIP after extracting the CIP templates. The determination of specific concentrations of CIP could be realized according to the difference in ECL intensity (△ECL) between the eluting and rebinding of the CIP. Under optimal conditions, a good linear response of △ECL and the logarithm of CIP concentrations was obtained in the range 1.0 × 10-9 ~ 1.0 × 10-5 mol/L, with a detection limit of 4.5 × 10-10 mol/L (S/N = 3) (the working potential was -1.8 ~ 0 V). The RSD of all points in the calibration plot was less than 5.0% and the real samples recovery was between 98.0 and 104%. This paper displays satisfactory selectivity and sensitivity, providing a rapid, convenient, and cheap method for the determination of CIP in real samples.

DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion

The elucidation of structural interfaces between proteins and inorganic surfaces is a crucial aspect of bionanotechnology development. Despite its significance, the interfacial structures between proteins and metallic surfaces are yet to be fully understood, and the lack of experimental investigation has impeded the development of many devices. To overcome this limitation, we suggest considering the generation of protein/surface structures as a molecular docking problem with a homogenous plan as the target. To this extent, we propose a new software, DockSurf, which aims to quickly propose reliable protein/surface structures. Our approach considers the conformational exploration with Euler's angles, which provide a cartography instead of a unique structure. Interaction energies were derived from quantum mechanics computations for a set of small molecules that describe protein atom types and implemented in a Derjaguin, Landau, Verwey, and Overbeek potential for the consideration of large systems such as proteins. The validation of DockSurf software was conducted with molecular dynamics for corona proteins with gold surfaces and provided enthusiastic results. This software is implemented in the RPBS platform to facilitate widespread access to the scientific community.

Comparative study of electrochemical-based sensors and immunosensors in terms of advantageous features for detection of cancer biomarkers

Cancer, becoming increasingly common globally, has a high mortality rate. Despite the much research on diagnosis and treatment methods, the benefits of technological developments, and newly developed sensor devices, cancer is still one of the leading causes of death worldwide. Early detection using powerful and noninvasive tools could be a future focus for prognosis and treatment follow-up. Therefore, electrochemical biosensors can be a strong choice for the detection of cancer biomarkers (such as alpha-fetoprotein, cytochrome c, prostate-specific antigen, myoglobin, carcinoembryonic antigen, alpha-fetoprotein, a cancer antigen, epidermal growth factor receptor, vascular endothelial growth factor, circulating tumor cell, and breast cancer antigen 1/2) due to their advantages such as high sensitivity, excellent selectivity, low cost, short analysis time, and simplicity. Furthermore, electrochemical biosensors are better suited for point-of-care applications due to their mass production and miniaturization ease. This review provides an overview of different electrochemical measurement techniques, bioreceptor surfaces, signal production and amplification, and the integration of electrochemical-modified sensors. Cancer biomarkers based on electrochemical biosensors were given in detail. In addition, studies with MIP-based sensors and immunosensors have been extensively discussed. Integrating electrochemical biosensors with cancer biomarkers was also emphasized as a new research trend. Finally, we provide an overview of current advances in measuring and analyzing cancer biomarkers using electrochemical biosensors and detail current challenges and future perspectives.

Evaluation of the interaction between SARS-CoV-2 spike glycoproteins and the molecularly imprinted polypyrrole

The SARS-CoV-2 spike glycoprotein (SARS-CoV-2-S) was used as a template molecule and polypyrrole (Ppy) was applied as an electro-generated conducting polymer, which was acting as a matrix for the formation of molecular imprints. Two types of Ppy-layers: molecularly imprinted polypyrrole (MIP-Ppy) and non-imprinted polypyrrole (NIP-Ppy) were electrochemically deposited on the working platinum electrode. The performance of electrodes modified by MIP-Ppy and NIP-Ppy layers was evaluated by pulsed amperometric detection (PAD). During the assessment of measurement results registered by PAD, the integrated Cottrell equation (Anson plot) was used to calculate the amount of charge passed through the MIP-Ppy and NIP-Ppy layers. The interaction between SARS-CoV-2 spike glycoproteins and molecularly imprinted polypyrrole (MIP-Ppy) was assessed by the Anson plot based calculations. This assessment reveals that SARS-CoV-2-S glycoproteins are interacting with MIP-Ppy more strongly than with NIP-Ppy.

Recent molecularly imprinted polymers applications in bioanalysis

Molecular imprinted polymers (MIPs) as extraordinary compounds with unique features have presented a wide range of applications and benefits to researchers. In particular when used as a sorbent in sample preparation methods for the analysis of biological samples and complex matrices. Its application in the extraction of medicinal species has attracted much attention and a growing interest. This review focus on articles and research that deals with the application of MIPs in the analysis of components such as biomarkers, drugs, hormones, blockers and inhibitors, especially in biological matrices. The studies based on MIP applications in bioanalysis and the deployment of MIPs in high-throughput settings and optimization of extraction methods are presented. A review of more than 200 articles and research works clearly shows that the superiority of MIP techniques lies in high accuracy, reproducibility, sensitivity, speed and cost effectiveness which make them suitable for clinical usage. Furthermore, this review present MIP-based extraction techniques and MIP-biosensors which are categorized on their classes based on common properties of target components. Extraction methods, studied sample matrices, target analytes, analytical techniques and their results for each study are described. Investigations indicate satisfactory results using MIP-based bioanalysis. According to the increasing number of studies on method development over the last decade, the use of MIPs in bioanalysis is growing and will further expand the scope of MIP applications for less studied samples and analytes.

Molecularly imprinted polymers as effective capturing receptors in a pseudo-ELISA immunoassay for procalcitonin detection in veterinary species

In this study, a new sandwich-type immunoenzymatic assay, based on a molecularly imprinted polymer (MIP) as an artificial antibody (pseudo-ELISA), was developed for the determination of procalcitonin (PCT) in veterinary species. The quantification of PCT in human medicine represents the state of the art for the diagnosis of sepsis; instead the clinical studies on the relevance of PCT as a sepsis predictor in veterinary patients are few, likely due to the total absence of validated assays. MIPs have been widely used as antibody mimics for important applications, and MIP-based sandwich assays have emerged as promising analytical tools for the detection of disease biomarkers. Herein, a polynorepinephrine (PNE)-based imprinted film was directly synthesized on the well surface of a 96-well plate. Subsequently, based on a commercial ELISA kit, the PCT quantification was accomplished via a colorimetric sandwich assay by replacing the capture antibody of the kit with the PNE-based MIP. This method was performed to detect canine and equine PCT in buffer and in plasma samples. Under optimal conditions, the results obtained in plasma samples showed a limit of detection (LOD) of 5.87 ng mL^-1 and a reproducibility (CV_av%) of 10.0% for canine samples, while a LOD = 4.46 ng mL^-1 and CV_av% = 7.61% were obtained for equine samples.

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

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

Molecularly Imprinted Solid Phase Extraction Strategy for Quinic Acid

Quinic acid (QA) and its ester conjugates have been subjected to in-depth scientific investigations for their antioxidant properties. In this study, molecularly imprinted polymers (MIPs) were used for selective extraction of quinic acid (QA) from coffee bean extract. Computational modelling was performed to optimize the process of MIP preparation. Three different functional monomers (allylamine, methacrylic acid (MAA) and 4-vinylpyridine (4-VP)) were tested for imprinting. The ratio of each monomer to template chosen was based on the optimum ratio obtained from computational studies. Equilibrium rebinding studies were conducted and MIP C, which was prepared using 4-VP as functional monomer with template to monomer ratio of 1:5, showed better binding performance than the other prepared MIPs. Accordingly, MIP C was chosen to be applied for selective separation of QA using solid-phase extraction. The selectivity of MIP C towards QA was tested versus its analogues found in coffee (caffeic acid and chlorogenic acid). Molecularly imprinted solid-phase extraction (MISPE) using MIP C as sorbent was then applied for selective extraction of QA from aqueous coffee extract. The applied MISPE was able to retrieve 81.918 ± 3.027% of QA with a significant reduction in the amount of other components in the extract.

Recent Advances of Point-of-Care Devices Integrated with Molecularly Imprinted Polymers-Based Biosensors: From Biomolecule Sensing Design to Intraoral Fluid Testing

Recent developments of point-of-care testing (POCT) and in vitro diagnostic medical devices have provided analytical capabilities and reliable diagnostic results for rapid access at or near the patient's location. Nevertheless, the challenges of reliable diagnosis still remain an important factor in actual clinical trials before on-site medical treatment and making clinical decisions. New classes of POCT devices depict precise diagnostic technologies that can detect biomarkers in biofluids such as sweat, tears, saliva or urine. The introduction of a novel molecularly imprinted polymer (MIP) system as an artificial bioreceptor for the POCT devices could be one of the emerging candidates to improve the analytical performance along with physicochemical stability when used in harsh environments. Here, we review the potential availability of MIP-based biorecognition systems as custom artificial receptors with high selectivity and chemical affinity for specific molecules. Further developments to the progress of advanced MIP technology for biomolecule recognition are introduced. Finally, to improve the POCT-based diagnostic system, we summarized the perspectives for high expandability to MIP-based periodontal diagnosis and the future directions of MIP-based biosensors as a wearable format.

Atomistic Simulations of Functionalized Nano-Materials for Biosensors Applications

Nanoscale biosensors, a highly promising technique in clinical analysis, can provide sensitive yet label-free detection of biomolecules. The spatial and chemical specificity of the surface coverage, the proper immobilization of the bioreceptor as well as the underlying interfacial phenomena are crucial elements for optimizing the performance of a biosensor. Due to experimental limitations at the microscopic level, integrated cross-disciplinary approaches that combine in silico design with experimental measurements have the potential to present a powerful new paradigm that tackles the issue of developing novel biosensors. In some cases, computational studies can be seen as alternative approaches to assess the microscopic working mechanisms of biosensors. Nonetheless, the complex architecture of a biosensor, associated with the collective contribution from "substrate-receptor-analyte" conjugate in a solvent, often requires extensive atomistic simulations and systems of prohibitive size which need to be addressed. In silico studies of functionalized surfaces also require ad hoc force field parameterization, as existing force fields for biomolecules are usually unable to correctly describe the biomolecule/surface interface. Thus, the computational studies in this field are limited to date. In this review, we aim to introduce fundamental principles that govern the absorption of biomolecules onto functionalized nanomaterials and to report state-of-the-art computational strategies to rationally design nanoscale biosensors. A detailed account of available in silico strategies used to drive and/or optimize the synthesis of functionalized nanomaterials for biosensing will be presented. The insights will not only stimulate the field to rationally design functionalized nanomaterials with improved biosensing performance but also foster research on the required functionalization to improve biomolecule-surface complex formation as a whole.

Molecularly imprinted polypyrrole based sensor for the detection of SARS-CoV-2 spike glycoprotein

This study describes the application of a polypyrrole-based sensor for the determination of SARS-CoV-2-S spike glycoprotein. The SARS-CoV-2-S spike glycoprotein is a spike protein of the coronavirus SARS-CoV-2 that recently caused the worldwide spread of COVID-19 disease. This study is dedicated to the development of an electrochemical determination method based on the application of molecularly imprinted polymer technology. The electrochemical sensor was designed by molecular imprinting of polypyrrole (Ppy) with SARS-CoV-2-S spike glycoprotein (MIP-Ppy). The electrochemical sensors with MIP-Ppy and with polypyrrole without imprints (NIP-Ppy) layers were electrochemically deposited on a platinum electrode surface by a sequence of potential pulses. The performance of polymer layers was evaluated by pulsed amperometric detection. According to the obtained results, a sensor based on MIP-Ppy is more sensitive to the SARS-CoV-2-S spike glycoprotein than a sensor based on NIP-Ppy. Also, the results demonstrate that the MIP-Ppy layer is more selectively interacting with SARS-CoV-2-S glycoprotein than with bovine serum albumin. This proves that molecularly imprinted MIP-Ppy-based sensors can be applied for the detection of SARS-CoV-2 virus proteins.

Sensitive and selective "signal-off" electrochemiluminescence sensing of prostate-specific antigen based on an aptamer and molecularly imprinted polymer

Specific and sensitive determination of prostate-specific antigen (PSA) in complex real samples holds significant importance as it is an effective molecular biomarker for the clinical diagnosis of prostate cancer. Herein, we constructed a dual-recognition electrochemiluminescence (ECL) sensor based on both the recognition elements of an aptamer and molecularly imprinted polymers (MIP) for the selective and ultrasensitive determination of PSA. The aptamer was self-assembled on gold nanoparticle (AuNP) modified electrodes through Au-S bonds. Subsequently, a layer of MIP membrane was synthesized by electropolymerization of dopamine (DA) to fabricate an aptamer-MIP sensor. After the rebinding of PSA onto imprinted cavities, the ECL response of luminol in the solution decreased. This "signal-off" strategy was employed for PSA detection with a wide linear range and a low limit of detection of 5 pg mL^-1-50 ng mL^-1 and 3.0 pg mL^-1, respectively. Compared with individual aptamer sensors, the dual-recognition sensor showed higher specific recognition ability for the determination of PSA. Meanwhile, the good stability, reproducibility, and regenerability endowed the dual recognition sensor with favorable application value in early clinical diagnosis.

Molecular dynamics simulation study of gold nanosheet as drug delivery vehicles for anti-HIV-1 aptamers

The adsorption process of three aptamers with gold nanosheet (GNS) as a drug carrier has been investigated with the help of molecular dynamics simulations. The sequencing of the considered aptamers are as (CUUCAUUGUAACUUCUCAUAAUUUCCCGAGGCUUUUACUUUCGGGGUCCU) and (CCGGGUCGUCCCCUACGGGGACUAAAGACUGUGUCCAACCGCCCUCGCCU) for AP1 and AP2, respectively. AP3 is a muted version of AP1 in which nucleotide positions 4, 6, 18, 28 and 39 have C4A, U6G, A18G, G28A, and U39C mutations. At positions 24, and 40, a deletion mutation is seen to eliminate U24 and U40 bases. These aptamers are inhibitors for HIV-1 protease and can be candidates as potential pharmaceutics for treatment of AIDS in the future. The interactions between considered aptamers and GNS have been analyzed in detail with help of structural and energetic properties. These analyses showed that all three aptamers could well adsorb on GNS. Overall, the final results show that the adsorption of AP2 on the GNS is more favorable than other considered ones and consequently GNS can be considered as a device in order to immobilize these aptamers.

[Advances in application of molecularly imprinted polymers to the detection of polar pesticide residues]

Polar pesticides can be primarily classified as fungicides, herbicides, and insecticides; their rich variety and low cost have led to their extensive utilization in agriculture. However, the overuse of polar pesticides can lead to environmental contamination, such as water or soil pollution, which can also increase the risk of pesticide exposure among human life directly, or indirectly through contact with animal and plant-derived food. There are considerable differences in the physical and chemical properties of polar pesticides, as well as their trace amounts in complex food and environmental samples, posing immense challenges to their accurate detection. As a kind of artificially prepared selective adsorbent, molecularly imprinted polymers (MIPs) possess specific recognition sites complementary to template molecules in terms of the spatial structure, size, and chemical functional groups. With many advantages such as easy preparation, low cost, as well as good chemical and mechanical stability, MIPs have been widely applied in sample pretreatment and the analysis of polar pesticide residues. MIPs are typically used as adsorption materials in solid phase extraction (SPE) methods, including magnetic solid phase extraction (MSPE), dispersed solid phase extraction (DSPE), and stir bar sorptive extraction (SBSE). To rapidly detect polar pesticide residues with high sensitivity, MIPs are also used in the preparation of fluorescent sensors and electrochemical sensors. Furthermore, MIPs can be employed as the substrate in surface-enhanced Raman spectroscopy and as the substrate for the ion source in mass spectrometry for polar pesticide residue analysis. Thus far, various molecularly imprinted materials have been reported for the efficient separation and analysis of polar pesticide residues in various complex matrices. However, there is no review that summarizes the recent advances in MIPs for the determination of polar pesticides. This review introduces imprinting strategies and polymerization methods for MIPs, and briefly summarizes some new molecular imprinting strategies and preparation technologies. The application of MIPs in recent years (particularly the last five years) to the detection of polar pesticide residues including neonicotinoids, organophosphorus, triazines, azoles, and urea is then systematically summarized. Finally, the future development direction and trends for MIPs are proposed considering existing challenges, with the aim of providing reference to guide future research on MIPs in the field of polar pesticide residue detection.

Liquid crystal-amplified optofluidic biosensor for ultra-highly sensitive and stable protein assay

Protein assays show great importance in medical research and disease diagnoses. Liquid crystals (LCs), as a branch of sensitive materials, offer promising applicability in the field of biosensing. Herein, we developed an ultrasensitive biosensor for the detection of low-concentration protein molecules, employing LC-amplified optofluidic resonators. In this design, the orientation of LCs was disturbed by immobilized protein molecules through the reduction of the vertical anchoring force from the alignment layer. A biosensing platform based on the whispering-gallery mode (WGM) from the LC-amplified optofluidic resonator was developed and explored, in which the spectral wavelength shift was monitored as the sensing parameter. The microbubble structure provided a stable and reliable WGM resonator with a high Q factor for LCs. It is demonstrated that the wall thickness of the microbubble played a key role in enhancing the sensitivity of the LC-amplified WGM microcavity. It is also found that protein molecules coated on the internal surface of microbubble led to their interactions with laser beams and the orientation transition of LCs. Both effects amplified the target information and triggered a sensitive wavelength shift in WGM spectra. A detection limit of 1 fM for bovine serum albumin (BSA) was achieved to demonstrate the high-sensitivity of our sensing platform in protein assays. Compared to the detection using a conventional polarized optical microscope (POM), the sensitivity was improved by seven orders of magnitude. Furthermore, multiple types of proteins and specific biosensing were also investigated to verify the potential of LC-amplified optofluidic resonators in the biomolecular detection. Our studies indicate that LC-amplified optofluidic resonators offer a new solution for the ultrasensitive real-time biosensing and the characterization of biomolecular interactions.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s43074-021-00041-1.

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.

Non-enzymatic lactose molecularly imprinted sensor based on disposable graphite paper electrode

Lactose (LAC) is a disaccharide - major sugar, present in milk and dairy products. LAC content is an important indicator of milk quality and abnormalities in food industries, as well as in human and animal health. The present study reports the development of an innovative imprinted voltammetric sensor for sensitive detection of LAC. The sensor was constructed using electropolymerized pyrrole (Py) molecularly imprinted polymer (MIP) on graphite paper electrode (PE). The MIP film was constructed through the electrosynthesis of polypyrrole (PPy) in the presence of LAC (template molecule) on PE (PPy/PE). To optimize the detection conditions, several factors affecting the PPy/PE sensor performance were assessed by multivariate methods (Plackett-Burman design and central composite design). Under optimized conditions, the proposed analytical method was applied for LAC detection in whole and LAC-free milks, where it demonstrated high sensitivity and selectivity, with two dynamic linear ranges of concentration (1.0-10 nmol L^-1 and 25-125 nmol L^-1) and a detection limit of 0.88 nmol L^-1. The MIP sensor showed selective molecular recognition for LAC in the presence of structurally related molecules. The proposed PPy/PE sensor exhibited good stability, as well as excellent reproducibility and repeatability. Based on the results obtained, the PPy/PE is found to be highly promising for sensitive detection of LAC.

Impact of Silane Monolayers on the Adsorption of Streptavidin on Silica and Its Subsequent Interactions with Biotin: Molecular Dynamics and Steered Molecular Dynamics Simulations

Protein adsorption on surfaces is used in analytical tools as an immobilization mean to trap the analyte to be detected. However, protein adsorption can lead to a conformational change in the protein structure, resulting in a loss of bioactivity. Here, we study adsorption of a streptavidin-biotin complex on amorphous SiO₂ surfaces functionalized with five different silane self-assembled monolayers by all-atom molecular dynamics simulations. We find that the streptavidin global conformational change, as well as the nature of residues with high mobility, depends on the alkyl chain length and head-group charge of silane molecules. Effects on interactions with biotin are further investigated by steered molecular dynamics (SMD) simulations, which mimics atomic force microscopy (AFM) with the biotin attached on the tip. We show the combined effects of adsorption-induced global conformational changes and of the position of residues with high mobility on the streptavidin-biotin rupture force. By comparing our results to experimental and SMD rupture forces obtained in water, without any surface, we conclude that silane with uncharged and short alkyl chains allows streptavidin immobilization, while keeping biotin interactions better than silanes with long alkyl chains or charged head groups.

Electrochemical detection of β-lactoglobulin based on a highly selective DNA aptamer and flower-like Au@BiVO4 microspheres

Beta-lactoglobulin is a natural milk protein and the main cause of infant milk allergy. In this work, a sensitive, selective and inexpensive electrochemical biosensor for the detection of β-lactoglobulin was developed. In this sensor, a DNA aptamer was used instead of an expensive antibody as the recognition group highly selective for β-lactoglobulin. The flower-like BiVO₄ microspheres were firstly found to have peroxidase mimic catalytic activity and used to amplify the electrochemical signal. The aptamer can bind β-lactoglobulin and fall off from the working electrode, after which the DNA2/Au/BiVO₄ probe can be fixed to the DNA1/AuNPs/ITO working electrode by the hybridization of DNA2 with DNA1. Therefore, a higher concentration of β-lactoglobulin leads to increased fabrication of the DNA2/Au/BiVO₄ probe on the surface of the working electrode, and thereby increases the electrochemical signal. This electrochemical biosensor exhibited a wide detection range from 0.01 to 1000 ng mL^-1, with a limit of detection (LOD) of 0.007 ng mL^-1, which indicates a good potential application in the field of food analysis.