Biosensors in Drug Discovery and Drug Analysis

C. difficile biomarkers, pathogenicity and detection

BACKGROUND

Clostridioides difficile infection (CDI) is the main etiologic agent of antibiotic-associated diarrhea. CDI contributes to gut inflammation and can lead to disruption of the intestinal epithelial barrier. Recently, the rate of CDI cases has been increased. Thus, early diagnosis of C. difficile is critical for controlling the infection and guiding efficacious therapy.

APPROACH

A search strategy was set up using the terms C. difficile biomarkers and diagnosis. The found references were classified into two general categories; conventional and advanced methods.

RESULTS

The pathogenicity and biomarkers of C. difficile, and the collection manners for CDI-suspected specimens were briefly explained. Then, the conventional CDI diagnostic methods were subtly compared in terms of duration, level of difficulty, sensitivity, advantages, and disadvantages. Thereafter, an extensive review of the various newly proposed techniques available for CDI detection was conducted including nucleic acid isothermal amplification-based methods, biosensors, and gene/single-molecule microarrays. Also, the detection mechanisms, pros and cons of these methods were highlighted and compared with each other. In addition, approximately complete information on FDA-approved platforms for CDI diagnosis was collected.

CONCLUSION

To overcome the deficiencies of conventional methods, the potential of advanced methods for C. difficile diagnosis, their direction, perspective, and challenges ahead were discussed.

State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering

Genetically encoded biosensors are crucial for enhancing our understanding of how molecules regulate biological systems. Small molecule biosensors, in particular, help us understand the interaction between chemicals and biological processes. They also accelerate metabolic engineering by increasing screening throughput and eliminating the need for sample preparation through traditional chemical analysis. Additionally, they offer significantly higher spatial and temporal resolution in cellular analyte measurements. In this review, we discuss recent progress in in vivo biosensors and control systems-biosensor-based controllers-for metabolic engineering. We also specifically explore protein-based biosensors that utilize less commonly exploited signaling mechanisms, such as protein stability and induced degradation, compared to more prevalent transcription factor and allosteric regulation mechanism. We propose that these lesser-used mechanisms will be significant for engineering eukaryotic systems and slower-growing prokaryotic systems where protein turnover may facilitate more rapid and reliable measurement and regulation of the current cellular state. Lastly, we emphasize the utilization of cutting-edge and state-of-the-art techniques in the development of protein-based biosensors, achieved through rational design, directed evolution, and collaborative approaches.

A comparison of the detection and quantification of praziquantel via electrochemical and gas chromatography methods in freshwater and saltwater samples

Two new techniques for analyzing praziquantel (PZQ), an effective antiparasitic drug used in fresh and saltwater aquariums, were optimized and compared. One method was based on voltammetry and the other method used gas chromatography combined with mass spectrometry (GC-MS), although both procedures utilized the same sample pretreatment strategy which involved the PZQ being quantitatively transferred into acetonitrile using solid phase extraction. GC-MS analysis led to lower limits of detection (0.32 μM, 0.10 ppm) and quantification (0.72 μM, 0.22 ppm) compared to voltammetry, although both methods gave acceptable quantification for levels of PZQ > 25 μM (7.8 ppm). GC-MS is preferred for the most accurate determination, but voltammetry may provide a cost-effective alternative for detecting PZQ where on site testing is required.

Selective Aptamer Modification of Au Surfaces in a Microelectrode Sensor Array for Simultaneous Detection of Multiple Analytes

Aptamers have been employed as the biorecognition element in electrochemical aptamer-based (E-AB) biosensors, for the detection of a diverse range of analyte molecules, on electrodes with sizescales ranging from a few microns to several millimeters. Simultaneous detection of multiple different analytes requires the selective modification of multiple electrode surfaces with different aptamers. This process is typically achieved by incubating separate macroscale electrodes in a solution with the desired aptamer, which is unsuitable for microelectrode arrays in which the electrodes are closely spaced. In this work, we selectively modified electrode surfaces with thiolated aptamers of different single-stranded DNA sequences, by successive removal and addition of thiol monolayers. This was achieved by electrodesorption of thiol monolayers using controlled potential, to expose unmodified gold electrodes to be modified with a different thiolated aptamer, thus enabling multiple different aptamers to be used on the surfaces of closely spaced microelectrodes. All aptamers were methylene blue terminated, allowing redox currents to be measured and used to monitor aptamer probe packing density on the electrode surface and the selectivity of the sensors. Here, we demonstrate the microscale E-AB sensor multianalyte detection method using aptamers for target analytes, adenosine triphosphate, dopamine, and serotonin, which can ultimately be applied to perform localized simultaneous detection using electrode arrays.

Ultrasensitive electrochemical biosensors based on zinc sulfide/graphene hybrid for rapid detection of SARS-CoV-2

The coronavirus disease 2019 (COVID-19) is a highly contagious and fatal disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In general, the diagnostic tests for COVID-19 are based on the detection of nucleic acid, antibodies, and protein. Among different analytes, the gold standard of the COVID-19 test is the viral nucleic acid detection performed by the quantitative reverse transcription polymerase chain reaction (qRT-PCR) method. However, the gold standard test is time-consuming and requires expensive instrumentation, as well as trained personnel. Herein, we report an ultrasensitive electrochemical biosensor based on zinc sulfide/graphene (ZnS/graphene) nanocomposite for rapid and direct nucleic acid detection of SARS-CoV-2. We demonstrated a simple one-step route for manufacturing ZnS/graphene by employing an ultrafast (90 s) microwave-based non-equilibrium heating approach. The biosensor assay involves the hybridization of target DNA or RNA samples with probes that are immersed into a redox active electrolyte, which are detectable by electrochemical measurements. In this study, we have performed the tests for synthetic DNA samples and, SARS-CoV-2 standard samples. Experimental results revealed that the proposed biosensor could detect low concentrations of all different SARS-CoV-2 samples, using such as S, ORF 1a, and ORF 1b gene sequences as targets. This microwave-synthesized ZnS/graphene-based biosensor could be reliably used as an on-site, real-time, and rapid diagnostic test for COVID-19.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s42114-023-00630-7.

A Dual-Sensor-Based Screening System for In Vitro Selection of TDP1 Inhibitors

DNA sensors can be used as robust tools for high-throughput drug screening of small molecules with the potential to inhibit specific enzymes. As enzymes work in complex biological pathways, it is important to screen for both desired and undesired inhibitory effects. We here report a screening system utilizing specific sensors for tyrosyl-DNA phosphodiesterase 1 (TDP1) and topoisomerase 1 (TOP1) activity to screen in vitro for drugs inhibiting TDP1 without affecting TOP1. As the main function of TDP1 is repair of TOP1 cleavage-induced DNA damage, inhibition of TOP1 cleavage could thus reduce the biological effect of the TDP1 drugs. We identified three new drug candidates of the 1,5-naphthyridine and 1,2,3,4-tetrahydroquinolinylphosphine sulfide families. All three TDP1 inhibitors had no effect on TOP1 activity and acted synergistically with the TOP1 poison SN-38 to increase the amount of TOP1 cleavage-induced DNA damage. Further, they promoted cell death even with low dose SN-38, thereby establishing two new classes of TDP1 inhibitors with clinical potential. Thus, we here report a dual-sensor screening approach for in vitro selection of TDP1 drugs and three new TDP1 drug candidates that act synergistically with TOP1 poisons.

Advances in Electrochemical Aptasensors Based on Carbon Nanomaterials

Carbon nanomaterials offer unique opportunities for the assembling of electrochemical aptasensors due to their high electroconductivity, redox activity, compatibility with biochemical receptors and broad possibilities of functionalization and combination with other auxiliary reagents. In this review, the progress in the development of electrochemical aptasensors based on carbon nanomaterials in 2016–2020 is considered with particular emphasis on the role of carbon materials in aptamer immobilization and signal generation. The synthesis and properties of carbon nanotubes, graphene materials, carbon nitride, carbon black particles and fullerene are described and their implementation in the electrochemical biosensors are summarized. Examples of electrochemical aptasensors are classified in accordance with the content of the surface layer and signal measurement mode. In conclusion, the drawbacks and future prospects of carbon nanomaterials’ application in electrochemical aptasensors are briefly discussed.