Computer-aided molecular modeling study on antibody recognition of small molecules: an immunoassay for triazine herbicides

A novel electrochemical aptasensor for ultrasensitive detection of herbicide prometryn based on its highly specific aptamer and Ag@Au nanoflowers

Herbicide prometryn has become a common pollutant in aquatic environments and caused adverse impacts on ecosystems. This study developed an ultrasensitive electrochemical aptasensor for prometryn based on its highly affinitive and specific aptamer and Ag@Au nanoflowers (Ag@AuNFs) for signal amplification. Firstly, this study improved the Capture-SELEX strategy to screen aptamers and obtained aptamer P60-1, which had a high affinity (Kd: 23 nM) and could distinguish prometryn from its structural analogues. Moreover, the typical stem-loop structure in aptamer P60-1 was found to be the binding pocket for prometryn. Subsequently, an electrochemical aptasensor for prometryn was established using multiwalled carbon nanotubes and reduced graphene oxide as electrode substrate, Ag@Au NFs as signal amplification element, and aptamer P60-1 as recognition element. The aptasensor had a detection range of 0.16-500 ng/mL and a detection limit of 60 pg/mL, which was much lower than those of existing detection methods. The aptasensor had high stability and good repeatability, and could specifically detecting prometryn. Furthermore, the utility of the aptasensor was validated by measuring prometryn in environmental and biological components. Therefore, this study provides a robust and ultrasensitive aptasensor for accurate detection for prometryn pollution.

Monovalent Antigen-Induced Aggregation (MAA) Biosensors Using Immunomagnetic Beads in Both Sample Separation and Signal Generation for Label-Free Detection of Enrofloxacin

Exploring new functions of nanomaterials can help facilitate the development of biosensors for the detection of antibiotics. Herein, a new detection modality based on monovalent antigen-induced aggregation (MAA) of immunomagnetic beads (IMBs) was proposed for rapid and label-free detection of enrofloxacin (ENR), which endowed IMBs with the abilities of both sample separation and signal generation. In the presence of ENR, the initially well-dispersed IMBs were aggregated and the degree of aggregation was in a concentration-dependent manner. After exploring the mechanism underlying IMB aggregation and investigating the key parameters affecting it, a label-free biosensing platform was developed for rapid and sensitive detection of ENR. Based on the significant differences in the magnetic separation speed and size between the aggregated and well-dispersed IMBs, two methods were proposed for quantitatively determining ENR, i.e., measuring the turbidity of the IMB supernatant after magnetic separation for a given time and visualizing and calculating the grayscale value of the aggregated IMBs trapped on the surface of a nitrocellulose membrane. A three-dimensional (3D)-printed syringe was designed and fabricated for automatic filtration of IMBs. This immunosensor allowed for sensitive detection of ENR in less than 15 min without any labels. It exhibited a satisfactory limit of detection of 0.79 ng mL^-1 and showed the feasibility for ENR detection of spiked chicken meat with recovery rates ranging from 74.8 to 98.3%. The MAA immunosensor can act as a promising tool to detect trace levels of ENR and has the potential to be applied to complex food samples.

Improved molecular softness of tadalafil hapten enhancing antibody performance in immunoassay: Evidence from computational chemistry

The tadalafil-like compounds have appeared recently as adulterants in drinks and healthcare dietary supplements sourced from medicinal and edible food, which may cause illness and even death. In this work, the rationality of haptens was explored by computational chemistry and molecular simulation theories such as frontier molecular orbital (FMO)-based softness (S), three-dimensional (3D) structure, surface electrostatic potential (ESP), and lipophilic potential (LP). An antiserum from hapten H5 with the highest softness and maintaining the appropriate three-dimensional (3D) structure showed the optimal immunoassay performance, indicating an increasing softness was a critical factor for effective hapten. Based on the antibody induced by hapten H5, an indirect competitive enzyme-linked immunosorbent assay (icELISA) method for detecting multiple tadalafil-like adulterants was established. The icELISA showed a limit of detection (LOD), 50% inhibition concentration (IC₅₀ ), and a working range of 0.004-0.396, 0.89-4.27, and 0.094-16.71 ng/ml for tadalafil, amino tadalafil, acetamino tadalafil, nortadalafil, and N-desmethyl ent-tadalafil, respectively. The spiked recoveries of tadalafil-like adulterants in samples ranged from 84.9% to 116.2%. The results of the icELISA and HPLC-MS/MS methods had a good correlation for real samples with the R² of 0.9955. Specially, this work not only provided a convenient immunoassay method for measuring tadalafil-like adulterants in spirit drinks and dietary supplements in group-screening manner, but also suggested that softness was likely to be a general theory for rational hapten design. PRACTICAL APPLICATION: Rapid monitoring of tadalafil-like adulterants in food samples is very necessary and important for consumers, regulatory agencies, and the food industry.

Multiple detection of 15 triazine herbicides by gold nanoparticle based-paper sensor

Triazine herbicides have been widely used in agriculture, but their residues can harm the environment and human health. To help monitor these, we have developed an effective immunochromatographic strip test that can simultaneously detect 15 different triazines in grain samples (including ametryn, cyprazine, atraton, prometon, prometryn, atrazine, propazine, terbuthylazine, simetryn, trietazine, secbumeton, simazine, desmetryn, terbumeton and simetone). Based on our optimization procedure, the visual limit of detection (vLOD) for these triazines was found to be 2-10 ng/mL in assay buffer, and 0.02-0.1 mg/kg in grain samples. Four different grain matrices including corn, brown rice, wheat, and sorghum were studied and the test results showed no significant differences between the 15 triazines analyzed using this method. This test is simple, convenient, rapid, and low-cost, and could be an effective tool for primary screening of triazine residues in grain samples.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material (UV-vis spectra of 15 nm-GNP; K₂CO₃ usage; cross reactivity; strip images for spiked rice, wheat and sorghum samples, UPLC-MS/MS parameters; gray values for strip optimization) is available in the online version of this article at 10.1007/s12274-022-4164-2.

Epitopes prediction for microcystin-LR by molecular docking

Microcystin-LR (MC-LR) is one of the most worldwide harmful cyanobacterial toxins. A lots of antibodies against MC-LR have been generated and characterized. However, the knowledge about the epitopes of MC-LR was still limited. The objective of this study was to analyze the epitopes of MC-LR and demonstrate the binding mode of MC-LR with its antibody. The variable genes of a mouse hybridoma cell line (Mab5H1-3B3) raised against MC-LR have been cloned and assembled in a single chain variable fragment (scFv), and then soluble expressed in E.coli BL21. Based on the scFv, the IC₅₀ and IC₁₀ for MC-LR were determined to be 7.45 nM and 0.30 nM by competitive ELISA. And the scFv also showed 115% and 112% cross-reactivities to MC-RR and MC-YR, and 59% to MC-LA. By molecular docking, the binding mode between MC-LR and its scFv was demonstrated. A hydrogen bond interaction was observed between the carbonyl group of Adda⁵ residue of MC-LR and its scFv, and the guanidyl group of Arg⁴ residue and phenyl group of Adda⁵ residue of MC-LR were also involved in the interaction. These predicted epitopes were supported by antibody cross-reactivity data. By comparing the antibody informatics of MC-LR scFv with its predicted paratopes, VH-CDR1 was crucial for MC-LR binding, and its specificity could be tuned by engineering in Vκ-CDR1 and Vκ-CDR3. These information would be useful for the hapten design for microcystins or improving the properties of MC-LR scFv in vitro.

Real-time forecasting of pesticide concentrations in soil

Forecasting pesticide residues in soils in real time is essential for agronomic purposes, to manage phytotoxic effects, and in catchments to manage surface and ground water quality. This has not been possible in the past due to both modelling and measurement constraints. Here, the analytical transient probability distribution (pdf) of pesticide concentrations is derived. The pdf results from the random ways in which rain events occur after pesticide application. First-order degradation kinetics and linear equilibrium sorption are assumed. The analytical pdfs allow understanding of the relative contributions that climate (mean storm depth and mean rainfall event frequency) and chemical (sorption and degradation) properties have on the variability of soil concentrations into the future. We demonstrated the two uncertain reaction parameters can be constrained using Bayesian methods. An approach to a Bayesian informed forecast is then presented. With the use of new rapid tests capable of providing quantitative measurements of soil concentrations in the field, real-time forecasting of future pesticide concentrations now looks possible for the first time. Such an approach offers new means to manage crops, soils and water quality, and may be extended to other classes of pesticides for ecological risk assessment purposes.

QSAR analysis of immune recognition for triazine herbicides based on immunoassay data for polyclonal and monoclonal antibodies

A common task in the immunodetection of structurally close compounds is to analyze the selectivity of immune recognition; it is required to understand the regularities of immune recognition and to elucidate the basic structural elements which provide it. Triazines are compounds of particular interest for such research due to their high variability and the necessity of their monitoring to provide safety for agricultural products and foodstuffs. We evaluated the binding of 20 triazines with polyclonal (pAb) and monoclonal (mAb) antibodies obtained using atrazine as the immunogenic hapten. A total of over 3000 descriptors were used in the quantitative structure-activity relationship (QSAR) analysis of binding activities (pIC₅₀). A comparison of the two enzyme immunoassay systems showed that the system with pAb is much easier to describe using 2D QSAR methodology, while the system with mAb can be described using the 3D QSAR CoMFA. Thus, for the 3D QSAR model of the polyclonal antibodies, the main statistical parameter q² (‘leave-many-out’) is equal to 0.498, and for monoclonal antibodies, q² is equal to 0.566. Obviously, in the case of pAb, we deal with several targets, while in the case of mAb the target is one, and therefore it is easier to describe it using specific fields of molecular interactions distributed in space.

Development of a broad-specificity antibody-based immunoassay for triazines in ginger and the quantitative structure-activity relationship study of cross-reactive molecules by molecular modeling

In the present study, molecular modeling and principle component analysis (PCA) were used to select appropriate haptens for group detection of triazine herbicides. Four new structures together with three reported triazine derivatives were chosen for the screening of immunizing and coating haptens. A total of 31 triazines coupled with a 3D-QSAR methodology were employed to investigate the relationship between antigen-antibody recognition and molecular structures, the results of which revealed that the antibodies may recognize triazines from the side of molecules with the distinguishing atom and a steric volume matching with the spatial structure of antibodies. Finally, a broad-specificity heterologous immunoassay was developed for determining 10 triazine herbicides in ginger, where the detection limits were 2.5-15.1 μg kg-1 and recoveries were 67.9-102.6%. This study may broaden insight into triazine-antibody interactions and benefit designing novel performance-enhanced antibodies. The developed immunoassay can be further used for triazine detection in other complicated matrices.

Determination of triazine herbicides and their metabolites in multiple medicinal parts of traditional Chinese medicines using streamlined pretreatment and UFLC-ESI-MS/MS

A rapid, sensitive, and reliable ultra-fast liquid chromatography combined with electrospray ionization tandem mass spectrometry (UFLC-ESI-MS/MS) method was established and applied to simultaneous determination of 31 triazine herbicides and their metabolites in multiple medicinal parts of traditional Chinese medicines (TCMs). A streamlined pretreatment approach using one-step extraction and dilution was proposed, which provided high-throughput processing, excellent recovery, and negligible interference. Afterwards, multiple-reaction monitoring (MRM) and information-dependent acquisition (IDA) triggered enhanced product ion spectra (EPI) was adopted to identify and quantify the targets in a single analysis. The optimized method was then validated according to the guidelines of the European Commission for the following parameters: Matrix effects, specificity, accuracy, precision, linearity, range, and stability. The LOD and LOQ for the 31 triazine herbicides were 0.1-10 μg kg^-1 and 0.5-25 μg kg^-1, respectively. Recoveries at three concentration levels were within 67.9-120.3% with an associated precision RSD <20%. Using the proposed approach, trazines herbicides were determined from 44 commercially available TCMs. The detection rate of triazine herbicides residues was 15.9% of the total samples. Among them, atrazine, simeton, and simetryn were found in the radix, herba, and seed TCMs with values far below the referenced maximum residue limits (MRLs), but no residues were detected in either the flos or fructus. Taken together, this method has the potential to provide a means for triazines screening in extensive matrices, thereby laying the foundation for pesticide registration on TCMs. Moreover, it has the potential to guide further triazine residue control in TCMs.

Crystal Structure of the Fab Fragment of an Anti-ofloxacin Antibody and Exploration of Its Specific Binding

The limited knowledge on the mechanism of interactions between small contaminants and the corresponding antibodies greatly inhibits the development of enzyme-linked immunosorbent assay methods. In this study, the crystal structure of a Fab fragment specific for ofloxacin was obtained. On the basis of the crystal characteristics, the modeling of the interactions between ofloxacin and the Fab revealed that TYR31 and HIS99 of the heavy chain and MET20 and GLN79 of the light chain formed a hydrophobic region and that SER52 and ALA97 of the heavy chain and TYR35 of the light chain formed a salt bridge and two hydrogen bonds for specific binding. The key roles of SER52 and ALA97 were further confirmed by site-directed mutation. A specificity analysis using 14 ofloxacin analogues indicates that the length of the bond formed between the piperazine ring and the antibody plays key roles in specific recognition. This work helps to clarify the mechanisms through which antibodies recognize small molecules and improve immune detection methods.

Stereospecific recognition and quantitative structure–activity relationship between antibodies and enantiomers: ofloxacin as a model hapten

In this study, ofloxacin stereoisomers were chosen as a simple model to investigate the stereospecific recognition of chiral haptens and antibodies.

Molecular modeling application on hapten epitope prediction: an enantioselective immunoassay for ofloxacin optical isomers

To deepen our understanding of the physiochemical principles that govern hapten-antibody recognition, ofloxacin enantiomers were chosen as a model for epitope prediction of small molecules. In this study, two monoclonal antibodies (mAbs) mAb-WR1 and mAb-MS1 were raised against R-ofloxacin and S-ofloxacin, respectively. The enantioselective mAbs have a high sensitivity and specificity, and the enantioselectivity is not affected by heterologous coating format reactions. The epitopes of the ofloxacin isomers were predicted using the hologram quantitative structure-activity relationship (HQSAR) and comparative molecular field analysis (CoMFA) approaches. The results consistently show that the epitope of the chiral hapten should be primarily composed of the oxazine ring and the piperazinyl ring and mAbs recognize the hapten from the side of this moiety. The enantioselectivity of mAbs is most likely due to the steric hindrance caused by the stereogenic center of the epitope. Modeling of chiral hapten-protein mimics reveals that ofloxacin isomers remain upright on the surface of the carrier protein. Suggestions to improve the enantioselectivity of antibodies against ofloxacin isomers were also proposed. This study provided a simple, efficient, and general method for predicting the epitopes of small molecules via molecular modeling. The epitope predictions for small molecules may create a theoretical guide for hapten design.