The coronavirus disease 2019 (COVID-19) pandemic has gained worldwide attention and has prompted the development of innovative diagnostics, therapeutics, and vaccines to mitigate the pandemic. Diagnostic methods based on reverse transcriptase-polymerase chain reaction (RT-PCR) technology are the gold standard in the fight against COVID-19. However, this test might not be easily accessible in low-resource settings for the early detection and diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The lack of access to well-equipped clinical laboratories, requirement for the high level of technical competence, and the cost of the RT-PCR test are the major limitations. Moreover, RT-PCR is unsuitable for application at the point-of-care testing (PoCT) as it is time-consuming and lab-based. Due to emerging mutations of the virus and the burden it has placed on the health care systems, there is a growing urgency to develop sensitive, selective, and rapid diagnostic devices for COVID-19. Nanotechnology has emerged as a versatile technology in the production of reliable diagnostic tools for various diseases and offers new opportunities for the development of COVID-19 diagnostic systems. This review summarizes some of the nano-enabled diagnostic systems that were explored for the detection of SARS-CoV-2. It highlights how the unique physicochemical properties of nanoparticles were exploited in the development of novel colorimetric assays and biosensors for COVID-19 at the PoCT. The potential to improve the efficiency of the current assays, as well as the challenges associated with the development of these innovative diagnostic tools, are also discussed.

The SARS-CoV-2 main protease (M^pro) is one of the molecular targets for drug design. Effective vaccines have been identified as a long-term solution but the rate at which they are being administered is slow in several countries, and mutations of SARS-CoV-2 could render them less effective. Moreover, remdesivir seems to work only with some types of COVID-19 patients. Hence, the continuous investigation of new treatments for this disease is pivotal. This study investigated the inhibitory role of natural products against SARS-CoV-2 M^pro as repurposable agents in the treatment of coronavirus disease 2019 (COVID-19). Through in silico approach, selected flavonoids were docked into the active site of M^pro. The free energies of the ligands complexed with M^pro were computationally estimated using the molecular mechanics-generalized Born surface area (MM/GBSA) method. In addition, the inhibition process of SARS-CoV-2 Mpro with these ligands was simulated at 100 ns in order to uncover the dynamic behavior and complex stability. The docking results showed that the selected flavonoids exhibited good poses in the binding domain of M^pro. The amino acid residues involved in the binding of the selected ligands correlated well with the residues involved with the mechanism-based inhibitor (N3) and the docking score of Quercetin-3-O-Neohesperidoside (−16.8 Kcal/mol) ranked efficiently with this inhibitor (−16.5 Kcal/mol). In addition, single-structure MM/GBSA rescoring method showed that Quercetin-3-O-Neohesperidoside (−87.60 Kcal/mol) is more energetically favored than N3 (−80.88 Kcal/mol) and other ligands (Myricetin 3-Rutinoside (−87.50 Kcal/mol), Quercetin 3-Rhamnoside (−80.17 Kcal/mol), Rutin (−58.98 Kcal/mol), and Myricitrin (−49.22 Kcal/mol). The molecular dynamics simulation (MDs) pinpointed the stability of these complexes over the course of 100 ns with reduced RMSD and RMSF. Based on the docking results and energy calculation, together with the RMSD of 1.98 ± 0.19 Å and RMSF of 1.00 ± 0.51 Å, Quercetin-3-O-Neohesperidoside is a better inhibitor of M^pro compared to N3 and other selected ligands and can be repurposed as a drug candidate for the treatment of COVID-19. In addition, this study demonstrated that in silico docking, free energy calculations, and MDs, respectively, are applicable to estimating the interaction, energetics, and dynamic behavior of molecular targets by natural products and can be used to direct the development of novel target function modulators.

The transmission of Tuberculosis (TB) is very rapid and the burden it places on health care systems is felt globally. The effective management and prevention of this disease requires that it is detected early. Current TB diagnostic approaches, such as the culture, sputum smear, skin tuberculin, and molecular tests are time-consuming, and some are unaffordable for low-income countries. Rapid tests for disease biomarker detection are mostly based on immunological assays that use antibodies which are costly to produce, have low sensitivity and stability. Aptamers can replace antibodies in these diagnostic tests for the development of new rapid tests that are more cost effective; more stable at high temperatures and therefore have a better shelf life; do not have batch-to-batch variations, and thus more consistently bind to a specific target with similar or higher specificity and selectivity and are therefore more reliable. Advancements in TB research, in particular the application of proteomics to identify TB specific biomarkers, led to the identification of a number of biomarker proteins, that can be used to develop aptamer-based diagnostic assays able to screen individuals at the point-of-care (POC) more efficiently in resource-limited settings.

This study aimed to identify aptamers that bind with high affinity to transgelin-2 (TAGLN2), a potential diagnostic biomarker for a number of diseases, such as cancer and tuberculosis, that is associated with cellular stress. Aptamers targeting recombinant TAGLN2 were selected through magnetic bead-based systematic evolution of ligands by exponential enrichment (SELEX). DNA sequence analysis and Geneious software analysis identified 10 unique aptamer sequences that potentially bind to TAGLN2. A phylogenetic analysis of these sequences shows that these sequences clustered into two clades based on sequence similarity, with the sequences in one of the clades (consisting of 4 unique sequences) showing higher similarity to each other. The secondary structures of aptamer sequences (aptamers 1, 2, 7, and 9) from this highly conserved clade were predicted using the M-fold web server. The binding of two of these aptamer sequences (aptamer 7 and 9) to recombinantly expressed TAGLN2 was verified by microscale thermophoresis (MST). The dissociation constants for aptamers 7 and 9 were determined to be 18 ± 1 and 50 ± 2 nM, respectively. In silico analysis was used to perform molecular docking and molecular dynamics (MD) simulations between TAGLN2 and all 4 aptamers. These in silico analyses support the finding that aptamers 7 and 9 have a high affinity for TAGLN2 and that aptamer 7 has a higher binding affinity than aptamer 9. However, based on the in silico analysis, aptamer 1 may be a stronger binder than aptamer 7. This study demonstrates the advantages of integrating in silico analyses with SELEX to identify high-affinity aptamers. The TAGLN2 targeting aptamers identified in this study can potentially be used for the development of diagnostic tests for the detection of TAGLN2. This presents promising opportunities for early detection and intervention in diseases associated with increased levels of TAGLN2 expression.

HPV16 E6 oncoprotein is a critical driver of cervical cancer, necessitating high-specificity diagnostic and therapeutic agents. This study presents an in silico selection of DNA aptamers targeting the HPV16 E6 oncoprotein through a pipeline of structure-based virtual screening and 250 ns Molecular Dynamics (MD) simulations, performed with GROMACS 2019 and the CHARMM36M. Using AutoDock VinaXB and HADDOCK, eight candidates were evaluated against the F2 RNA benchmark. MM/PBSA calculations identified Apt 9 (−143.76 kcal/mol) as the most potent lead, surpassing the affinity of the F2 control (−142.80 kcal/mol). Apt 8 emerged as a key consensus lead, exhibiting superior structural stability (RMSD 0.23 nm) and the most robust interaction network (11.49 hydrogen bonds). Notably, these leads primarily target critical Histidine residues (His78, His118, and His126) on the E6 protein. These results designate Apt 9 and Apt 8 as high-priority candidates for experimental validation, providing a robust theoretical foundation for novel HPV16-targeted interventions.