Peptide-Based Flavivirus Biosensors: From Cell Structure to Virological and Serological Detection Methods.

In tropical and developing countries, mosquito-borne diseases by flaviviruses pose a serious threat to public health. Early detection is critical for preventing their spread, but conventional methods are time-consuming and require skilled technicians. Biosensors have been developed to address this issue, but cross-reactivity with other flaviviruses remains a challenge. Peptides are essentially biomaterials used in diagnostics that allow virological and serological techniques to identify flavivirus selectively. This biomaterial originated as a small protein consisting of two to 50 amino acid chains. They offer flexibility in chemical modification and can be easily synthesized and applied to living cells in the engineering process. Peptides could potentially be developed as robust, low-cost, sensitive, and selective receptors for detecting flaviviruses. However, modification and selection of the receptor agents are crucial to determine the effectiveness of binding between the targets and the receptors. This paper addresses two potential peptide nucleic acids (PNAs) and affinity peptides that can detect flavivirus from another target-based biosensor as well as the potential peptide behaviors of flaviviruses. The PNAs detect flaviviruses based on the nucleotide base sequence of the target's virological profile via Watson-Crick base pairing, while the affinity peptides sense the epitope or immunological profile of the targets. Recent developments in the functionalization of peptides for flavivirus biosensors are explored in this Review by division into electrochemical, optical, and other detection methods.

Enhancing Urine Glucose Sensing Performance through the Introduction of Two Dimensional-Transition Metal Dichalcogenides and Gold Nanoparticles into Silver/UiO-66 Chip of Surface Plasmon Resonance.

This work presents a high-performance surface plasmon resonance (SPR)-based biosensor for glucose detection. While adding a metal-organic framework (MOF) layer, UiO-66, to the biosensor improves selectivity and enables direct detection without additional receptors, it does not significantly enhance sensitivity. A SPR-based biosensor is proposed to overcome this limitation by introducing a layer of 2D-transition metal dichalcogenides (2D-TMD) and decorating the UiO-66 structure with gold nanoparticles (UiO-66AuNP). The optical properties of the biosensor for glucose detection in urine are investigated by employing the finite difference time domain (FDTD) method with Kretschmann configuration at a wavelength of 633 nm, and its performance is effectively improved by incorporating 2D-TMD and AuNP layers into the biosensor structure. Notably, the SPR-based biosensor with the decorated UiO-66 layer exhibits a further change in the SPR angle in the presence of glucose-containing urine. Using computational studies, various performance parameters, such as the biosensors' signal-to-noise ratio (SNR) and quality factor (QF), are evaluated in addition to sensitivity. The maximum sensitivity achieved is 309.3°/RIU for the BK7/Ag/PtSe2/WSe2/MoS2/UiO-66AuNP/sensing medium structure. The exceptional performance of the proposed biosensor structure demonstrates its suitability for precise glucose detection in urine while also opening new avenues for developing bioreceptor-free SPR-based sensors.

Surface plasmon resonance biosensor chips integrated with MoS2-MoO3 hybrid microflowers for rapid CFP-10 tuberculosis detection.

This study reports on the modification of surface plasmon resonance (SPR) chips with molybdenum disulfide-molybdenum trioxide (MoS2-MoO3) microflowers to detect the tuberculosis (TB) markers of CFP-10. The MoS2-MoO3 microflowers were prepared by hydrothermal methods with variations in the pH and amount of trisodium citrate (Na3Ct), which were projected to influence the shape and size of microflower particles. The analysis shows that optimum MoS2-MoO3 hybrid microflowers were obtained at neutral pH using 0.5 g Na3Ct. The modified SPR biosensor exhibits a ten times higher response than the bare Au. Moreover, increasing MoS2-MoO3 thickness results in a higher detection response, sensitivity, and a smaller limit of detection (LOD). Using the optimized material composition, the Au/MoS2-MoO3-integrated SPR sensor can demonstrate sensitivity and LOD of 1.005 and 3.45 ng mL-1, respectively. This biosensor also has good selectivity, stability, and reproducibility based on cross-sensitivity characterization with other analytes and repeated measurements on several chips with different storing times and fabrication batch. Therefore, this proposed SPR biosensor possesses high potential to be further developed and applied as a detection technology for CFP-10 in monitoring and diagnosing TB.

Coarse-grained molecular dynamics-guided immunoinformatics to explain the binder and non-binder classification of Cytotoxic T-cell epitope for SARS-CoV-2 peptide-based vaccine discovery.

Epitope-based peptide vaccine can elicit T-cell immunity against SARS-CoV-2 to clear the infection. However, finding the best epitope from the whole antigen is challenging. A peptide screening using immunoinformatics usually starts from MHC-binding peptide, immunogenicity, cross-reactivity with the human proteome, to toxicity analysis. This pipeline classified the peptides into three categories, i.e., strong-, weak-, and non-binder, without incorporating the structural aspect. For this reason, the molecular detail that discriminates the binders from non-binder is interesting to be investigated. In this study, five CTL epitopes against HLA-A*02:01 were identified from the coarse-grained molecular dynamics-guided immunoinformatics screening. The strong binder showed distinctive activities from the non-binder in terms of structural and energetic properties. Furthermore, the second residue from the nonameric peptide was most important in the interaction with HLA-A*02:01. By understanding the nature of MHC-peptide interaction, we hoped to improve the chance of finding the best epitope for a peptide vaccine candidate.

The revelation of glucose adsorption mechanisms on hierarchical metal-organic frameworks using a surface plasmon resonance sensor.

The gold layer on the surface plasmon resonance (SPR) sensor chip cannot detect small molecules, such as glucose without the use of specific receptors. Metal-organic frameworks (MOFs) are useful in biosensing technologies for capturing and co-localizing enzymes and receptors with the target biomolecule. In many previous studies, the properties of the MOFs were often ignored, with these studies focusing on the selection of appropriate receptors. To take advantage of the unique properties of MOFs in biosensors, one must also consider the technique and transducer used because these aspects will strongly influence the detection mechanism. In this work, we have investigated for the first time, the applications of hierarchical metal-BDC (M-BDC) MOFs for glucose detection using the SPR technique without the use of specific receptors. The underlying interactions and adsorption mechanisms were analyzed using adsorption isotherm and kinetic models. The sensing measurements show that the SPR chips functionalized with M-BDC MOFs exhibit higher sensitivity and lower limit of detection (LOD). Specifically, the sensitivity follows the order of Zr-BDC > Cu-BDC > Mn-BDC > Ni-BDC > bare Au SPR chips with the LOD in the order of Zr-BDC < Mn-BDC < Ni-BDC < Cu-BDC < bare Au SPR chips. The selectivity test results reveal that Zr-BDC exhibits a decent selectivity to glucose in the presence of other interfering compounds, such as ascorbic acid, uric acid, maltose, and urea. These results demonstrate the promising potential of MOFs for SPR biosensing.

The nanomolar affinity of C-phycocyanin from virtual screening of microalgal bioactive as potential ACE2 inhibitor for COVID-19 therapy.

The global pandemic of COVID-19 caused by SARS-CoV-2 has caused more than 400 million infections with more than 5.7 million deaths worldwide, and the number of validated therapies from natural products for treating coronavirus infections needs to be increased. Therefore, the virtual screening of bioactive compounds from natural products based on computational methods could be an interesting strategy. Among many sources of bioactive natural products, compounds from marine organisms, particularly microalgae and cyanobacteria, can be potential antiviral agents. The present study investigates bioactive antiviral compounds from microalgae and cyanobacteria as a potential inhibitor of SARS-CoV-2 by targeting Angiotensin-Converting Enzyme II (ACE2) using integrated in silico and in vitro approaches. Our in silico analysis demonstrates that C-Phycocyanin (CPC) can potentially inhibit the binding of ACE2 receptor and SARS-CoV-2 with the docking score of -9.7 kcal mol-1. This score is relatively more favorable than the native ligand on ACE2 receptor. Molecular dynamics simulation also reveals the stability interaction between both CPC and ACE2 receptor with a root mean square deviation (RMSD) value of 1.5 Å. Additionally, our in vitro analysis using the surface plasmon resonance (SPR) method shows that CPC has a high affinity for ACE2 with a binding affinity range from 5 to 125 µM, with KD 3.37 nM. This study could serve as a reference to design microalgae- or cyanobacteria-based antiviral drugs for prophylaxis in SARS-CoV-2 infections.

Development of a Single-Chain Variable Fragment of CR3022 for a Plasmonic-Based Biosensor Targeting the SARS-CoV-2 Spike Protein.

Two years after SARS-CoV-2 caused the first case of COVID-19, we are now in the "new normal" period, where people's activity has bounced back, followed by the easing of travel policy restrictions. The lesson learned is that the wide availability of accurate and rapid testing procedures is crucial to overcome possible outbreaks in the future. Therefore, many laboratories worldwide have been racing to develop a new point-of-care diagnostic test. To aid continuous innovation, we developed a plasmonic-based biosensor designed explicitly for portable Surface Plasmon Resonance (SPR). In this study, we designed a single chain variable fragment (scFv) from the CR3022 antibody with a particular linker that inserted a cysteine residue at the second position. It caused the linker to have a strong affinity to the gold surface through thiol-coupling and possibly become a ready-to-use bioreceptor toward a portable SPR gold chip without purification steps. The theoretical affinity of this scFv on spike protein was -64.7 kcal/mol, computed using the Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method from the 100 ns molecular dynamics trajectory. Furthermore, the scFv was produced in Escherichia coli BL21 (DE3) as a soluble protein. The binding activity toward Spike Receptor Binding Domain (RBD) SARS-CoV-2 was confirmed with a spot-test, and the experimental binding free energy of -10.82 kcal/mol was determined using portable SPR spectroscopy. We hope this study will be useful in designing specific and low-cost bioreceptors, particularly early in an outbreak when the information on antibody capture is still limited.

Facile and controllable synthesis of monodisperse gold nanoparticle bipyramid for electrochemical dopamine sensor.

We demonstrated potential features of gold nanoparticle bipyramid (AuNB) for an electrochemical biosensor. The facile synthesis method and controllable shape and size of the AuNB are achieved through the optimization of cetyltrimethylammonium chloride (CTAC) surfactant over citric acid (CA) ratio determining the control of typically spherical Au seed size and its transition into a penta-twinned crystal structure. We observe that the optimized ratio of CTAC and CA facilitates flocculation control in which Au seeds with size as tiny as ∼14.8 nm could be attained and finally transformed into AuNB structures with an average length of ∼55 nm with high reproducibility. To improve the electrochemical sensing performance of a screen-printed carbon electrode, surface modification with AuNB via distinctive linking procedures effectively enhanced the electroactive surface area by 40%. Carried out for the detection of dopamine, a neurotransmitter frequently linked to the risk of Parkinson's, Alzheimer's, and Huntington's diseases, the AuNB decorated-carbon electrode shows outstanding electrocatalytic activity that improves sensing performance, including high sensitivity, low detection limit, wide dynamic range, high selectivity against different analytes, such as ascorbic acid, uric acid and urea, and excellent reproducibility.

General synthesis of hierarchical sheet/plate-like M-BDC (M = Cu, Mn, Ni, and Zr) metal-organic frameworks for electrochemical non-enzymatic glucose sensing.

Two-dimensional metal-organic frameworks (2D MOFs) are an attractive platform to develop new kinds of catalysts because of their structural tunability and large specific surface area that exposes numerous active sites. In this work, we report a general method to synthesize benzene dicarboxylic acid (BDC)-based MOFs with hierarchical 3D morphologies composed of 2D nanosheets or nanoplates. In our proposed strategy, acetonitrile helps solvate the metal ions in solution and affects the morphology, while polyvinylpyrrolidone (PVP) serves as a shape-control agent to assist in the nucleation and growth of MOF nanosheets. PVP also acts as a depletion agent to drive the assembly of the hierarchical sheet/plate-like M-BDC under solvothermal conditions. Further, we also demonstrate the flexibility of the proposed method using numerous coordinating metal ions (M = Cu, Mn, Ni, and Zr). The potential of these MOFs for electrochemical glucose sensing is examined using the hierarchical sheet-like Ni-BDC MOF as the optimum sample. It drives the electrocatalytic oxidation of glucose over a wide range (0.01 mM to 0.8 mM) with high sensitivity (635.9 µA mM-1 cm-2) in the absence of modification with carbon or the use of conductive substrates. It also demonstrates good selectivity with low limit of detection (LoD = 6.68 µM; signal/noise = 3), and fast response time (<5 s).