Identification of a Direct-Acting Antiviral Agent Targeting RNA Helicase via a Graphene Oxide Nanobiosensor

Molecular interactions of the Omicron, Kappa, and Delta SARS-CoV-2 spike proteins with quantum dots of graphene oxide

CONTEXT

The Omicron, Kappa, and Delta variants are different strains of the SARS-CoV-2 virus. Graphene oxide quantum dots (GOQDs) represent a burgeoning class of oxygen-enriched, zero-dimensional materials characterized by their sub-20-nm dimensions. Exhibiting pronounced quantum confinement and edge effects, GOQDs manifest exceptional physical-chemical attributes. This study delves into the potential of graphene oxide quantum dots, elucidating their inherent properties pertinent to the surface structures of SARS-CoV-2, employing an integrated computational approach for the repositioning of inhibitory agents.

METHODS

Following rigorous adjustment tests, a spectrum of divergent bonding conformations emerged, with particular emphasis placed on identifying the conformation exhibiting optimal adjustment scores and interactions. The investigation employed molecular docking simulations integrating affinity energy evaluations, electrostatic potential clouds, molecular dynamics encompassing average square root calculations, and the computation of Gibbs-free energy. These values quantify the strength of interaction between GOQDs and SARS-CoV-2 spike protein variants. The receptor structures were optimized using the CHARM-GUI server employing force field AMBERFF14SB. The algorithm embedded in CHARMM offers an efficient interpolation scheme and automatic step size selection, enhancing the efficiency of the optimization process. The 3D structures of the ligands are constructed and optimized with density functional theory (DFT) method based on the most stable conformer of each binder. Autodock Vina Software (ADV) was utilized, where essential parameters were specified. Electrostatic potential maps (MEPs) provide a visual depiction of molecules' charge distributions and related properties. After this, molecular dynamics simulations employing the CHARM36 force field in Gromacs 2022.2 were conducted to investigate GOs' interactions with surface macromolecules of SARS-CoV-2 in an explicit aqueous environment. Furthermore, our investigation suggests that lower values indicate stronger binding. Notably, GO-E consistently showed the most negative values across interactions with different variants, suggesting a higher affinity compared to other GOQDs (GO-A to GO-D).

Exploring the Targets of Dengue Virus and Designs of Potential Inhibitors

BACKGROUND

Dengue, a mosquito-borne viral disease spread by the dengue virus (DENV), has become one of the most alarming health issues in the global scenario in recent days. The risk of infection by DENV is mostly high in tropical and subtropical areas of the world. The mortality rate of patients affected with DENV is ever-increasing, mainly due to a lack of anti-dengue viral-specific synthetic drug components.

INTRODUCTION

Repurposing synthetic drugs has been an effective tool in combating several pathogens, including DENV. However, only the Dengvaxia vaccine has been developed so far to fight against the deadly disease despite the grave situation, mainly because of the limitations of understanding the actual pathogenicity of the disease.

METHODS

To address this particular issue and explore the actual disease pathobiology, several potential targets, like three structural proteins and seven non-structural (NS) proteins, along with their inhibitors of synthetic and natural origin, have been screened using docking simulation.

RESULTS

Exploration of these targets, along with their inhibitors, has been extensively studied in culmination with molecular docking-based screening to potentiate the treatment.

CONCLUSION

These screened inhibitors could possibly be helpful for the designing of new congeneric potential compounds to combat dengue fever and its complications.

Coronaviruses SARS-CoV, MERS-CoV, and SARS-CoV-2 helicase inhibitors: A systematic review of in vitro studies

Introduction

The recent outbreak of SARS-CoV-2 significantly increased the need to find inhibitors that target the essential enzymes for virus replication in the host cells. This systematic review was conducted to identify potential inhibitors of SARS-CoV, MERS-CoV, and SARS-CoV-2 helicases that have been tested by in vitro methods. The inhibition mechanisms of these compounds were discussed in this review, in addition to their cytotoxic and viral infection protection properties.

Methods

The databases PUBMED/MEDLINE, EMBASE, SCOPUS, and Web of Science were searched using different combinations of the keywords "helicase", "nsp13", "inhibitors", "coronaviridae", "coronaviruses", "virus replication", "replication", and "antagonists and inhibitors".

Results

By the end of this search, a total of 6854 articles had been identified. Thirty-one articles were included in this review. These studies reported the inhibitory effects of 309 compounds on SARS-CoV, MERS-CoV, and SARS-CoV-2 helicase activities measured by in vitro methods. Helicase inhibitors were categorized according to the type of coronavirus and the type of tested enzymatic activity, nature, approval, inhibition level, cytotoxicity, and viral infection protection effects. These inhibitors are classified according to the site of their interaction with the coronavirus helicases into four types: zinc-binding site inhibitors, nucleic acid binding site inhibitors, nucleotide-binding site inhibitors, and inhibitors with no clear interaction site.

Conclusion

Evidence from in vitro studies suggests that helicase inhibitors have a high potential as antiviral agents. Several helicase inhibitors tested in vitro showed good antiviral activities while maintaining moderate cytotoxicity. These inhibitors should be clinically investigated to determine their efficiency in treating different coronavirus infections, particularly COVID-19.

Antiviral Activity of Micafungin and Its Derivatives against SARS-CoV-2 RNA Replication

Echinocandin antifungal drugs, including micafungin, anidulafungin, and caspofungin, have been recently reported to exhibit antiviral effects against various viruses such as flavivirus, alphavirus, and coronavirus. In this study, we focused on micafungin and its derivatives and analyzed their antiviral activities against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The micafungin derivatives Mi-2 and Mi-5 showed higher antiviral activity than micafungin, with 50% maximal inhibitory concentration (IC₅₀) of 5.25 and 6.51 µM, respectively (3.8 to 4.7-fold stronger than micafungin) and 50% cytotoxic concentration (CC₅₀) of >64 µM in VeroE6/TMPRSS2 cells. This high anti-SARS-CoV-2 activity was also conserved in human lung epithelial cell-derived Calu-3 cells. Micafungin, Mi-2, and Mi-5 were suggested to inhibit the intracellular virus replication process; additionally, these compounds were active against SARS-CoV-2 variants, including Delta (AY.122, hCoV-19/Japan/TY11-927/2021), Omicron (BA.1.18, hCoV-19/Japan/TY38-873/2021), a variant resistant to remdesivir (R10/E796G C799F), and a variant resistant to casirivimab/imdevimab antibody cocktail (E406W); thus, our results provide basic evidence for the potential use of micafungin derivatives for developing antiviral agents.

A step forward to overcome the cytotoxicity of graphene oxide through decoration with tragacanth gum polysaccharide

Hybridization of nanomaterials (NMs) with natural polymers is one of the best techniques to promote their exciting properties. In this way, the main objective of this work was to investigate the efficiency of decoration of the graphene oxide (GO) nano-sheets with tragacanth gum (TG) polysaccharide. To aim this, different approaches were used (with and without ultrasonic treatment) and various tests (XRD, FTIR, Raman, UV-Vis, DLS, Zeta potential, contact angle, AFM, FE-SEM, TEM, and MTT assay) were conducted. Test results indicated that the nano-hybrids were successfully synthesized. Furthermore, our findings represented that, the TG hybridized GO (TG-GO) appreciably enhanced the biocompatibility of GO. Moreover, it was demonstrated that the ultrasonic treatment of TG solution put a remarkable impact on the microstructure, wettability, and also surface charge characteristic of fabricated nano-hybrids and consequently improved the biocompatibility against L929-fibroblast cells.

Virus-CKB 2.0: Viral-Associated Disease-Specific Chemogenomics Knowledgebase

Transmissible and infectious viruses can cause large-scale epidemics around the world. This is because the virus can constantly mutate and produce different variants and subvariants to counter existing treatments. Therefore, a variety of treatments are urgently needed to keep up with the mutation of the viruses. To facilitate the research of such treatment, we updated our Virus-CKB 1.0 to Virus-CKB 2.0, which contains 10 kinds of viruses, including enterovirus, dengue virus, hepatitis C virus, Zika virus, herpes simplex virus, Andes orthohantavirus, human immunodeficiency virus, Ebola virus, Lassa virus, influenza virus, coronavirus, and norovirus. To date, Virus-CKB 2.0 archived at least 65 antiviral drugs (such as remdesivir, telaprevir, acyclovir, boceprevir, and nelfinavir) in the market, 178 viral-related targets with 292 available 3D crystal or cryo-EM structures, and 3766 chemical agents reported for these target proteins. Virus-CKB 2.0 is integrated with established tools for target prediction and result visualization; these include HTDocking, TargetHunter, blood-brain barrier (BBB) predictor, Spider Plot, etc. The Virus-CKB 2.0 server is accessible at https://www.cbligand.org/g/virus-ckb. By using the established chemogenomic tools and algorithms and newly developed tools, we can screen FDA-approved drugs and chemical compounds that may bind to these proteins involved in viral-associated disease regulation. If the virus strain mutates and the vaccine loses its effect, we can still screen drugs that can be used to treat the mutated virus in a fleeting time. In some cases, we can even repurpose FDA-approved drugs through Virus-CKB 2.0.