Discovery of direct-acting antiviral agents with a graphene-based fluorescent nanosensor

Antiviral Activity of an Indole-Type Compound Derived from Natural Products, Identified by Virtual Screening by Interaction on Dengue Virus NS5 Protein

Dengue is an acute febrile illness caused by the Dengue virus (DENV), with a high number of cases worldwide. There is no available treatment that directly affects the virus or the viral cycle. The objective of this study was to identify a compound derived from natural products that interacts with the NS5 protein of the dengue virus through virtual screening and evaluate its in vitro antiviral effect on DENV-2. Molecular docking was performed on NS5 using AutoDock Vina software, and compounds with physicochemical and pharmacological properties of interest were selected. The preliminary antiviral effect was evaluated by the expression of the NS1 protein. The effect on viral genome replication and/or translation was determined by NS5 production using DENV-2 Huh-7 replicon through ELISA and viral RNA quantification using RT-qPCR. The in silico strategy proved effective in finding a compound (M78) with an indole-like structure and with an effect on the replication cycle of DENV-2. Treatment at 50 µM reduced the expression of the NS5 protein by 70% and decreased viral RNA by 1.7 times. M78 is involved in the replication and/or translation of the viral genome.

Graphene oxide for photonics, electronics and optoelectronics

Graphene oxide (GO) was initially developed to emulate graphene, but it was soon recognized as a functional material in its own right, addressing an application space that is not accessible to graphene and other carbon materials. Over the past decade, research on GO has made tremendous advances in material synthesis and property tailoring. These, in turn, have led to rapid progress in GO-based photonics, electronics and optoelectronics, paving the way for technological breakthroughs with exceptional performance. In this Review, we provide an overview of the optical, electrical and optoelectronic properties of GO and reduced GO on the basis of their chemical structures and fabrication approaches, together with their applications in key technologies such as solar energy harvesting, energy storage, medical diagnosis, image display and optical communications. We also discuss the challenges of this field, together with exciting opportunities for future technological advances.

Examples of Structural Motifs in Viral Genomes and Approaches for RNA Structure Characterization

The relationship between conserved structural motifs and their biological function in the virus replication cycle is the interest of many researchers around the world. RNA structure is closely related to RNA function. Therefore, technological progress in high-throughput approaches for RNA structure analysis and the development of new ones are very important. In this mini review, we discuss a few perspectives on the structural elements of viral genomes and some methods used for RNA structure prediction and characterization. Based on the recent literature, we describe several examples of studies concerning the viral genomes, especially severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus (IAV). Herein, we emphasize that a better understanding of viral genome architecture allows for the discovery of the structure-function relationship, and as a result, the discovery of new potential antiviral therapeutics.

Combining printing and nanoparticle assembly: Methodology and application of nanoparticle patterning

Functional nanoparticles (NPs) with unique photoelectric, mechanical, magnetic, and chemical properties have attracted considerable attention. Aggregated NPs rather than individual NPs are generally required for sensing, electronics, and catalysis. However, the transformation of functional NP aggregates into scalable, controllable, and affordable functional devices remains challenging. Printing is a promising additive manufacturing technology for fabricating devices from NP building blocks because of its capabilities for rapid prototyping and versatile multifunctional manufacturing. This paper reviews recent advances in NP patterning based on the combination of self-assembly and printing technologies (including two-, three-, and four-dimensional printing), introduces the basic characteristics of these methods, and discusses various fields of NP patterning applications.

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Nanoparticles (NPs) printing assembly is a good solution for patterned devices

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NPs assembly can be combined with 2D, 3D, and 4D printing technologies

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A variety of ink-dispersed NPs are available for printing assembly

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NPs printing assembly technology is applied for nanosensing, energy storage, photodetector

Inhibitory effect and mechanism of gelatin stabilized ferrous sulfide nanoparticles on porcine reproductive and respiratory syndrome virus

Background

The infection and spread of porcine reproductive and respiratory syndrome virus (PRRSV) pose a serious threat to the global pig industry, and inhibiting the viral infection process is a promising treatment strategy. Nanomaterials can interact with viruses and have attracted much attention due to their large specific surface area and unique physicochemical properties. Ferrous sulfide nanoparticles (FeS NPs) with the characteristics of high reactivity, large specific surface area, and low cost are widely applied to environmental remediation, catalysis, energy storage and medicine. However, there is no report on the application of FeS NPs in the antiviral field. In this study, gelatin stabilized FeS nanoparticles (Gel-FeS NPs) were large-scale synthesized rapidly by the one-pot method of co-precipitation of Fe²⁺ and S^2‒.

Results

The prepared Gel-FeS NPs exhibited good stability and dispersibility with an average diameter of 47.3 nm. Additionally, they were characterized with good biocompatibility and high antiviral activity against PRRSV proliferation in the stages of adsorption, invasion, and replication.

Conclusions

We reported for the first time the virucidal and antiviral activity of Gel-FeS NPs. The synthesized Gel-FeS NPs exhibited good dispersibility and biocompatibility as well as effective inhibition on PRRSV proliferation. Moreover, the Fe²⁺ released from degraded Gel-FeS NPs still displayed an antiviral effect, demonstrating the advantage of Gel-FeS NPs as an antiviral nanomaterial compared to other nanomaterials. This work highlighted the antiviral effect of Gel-FeS NPs and provided a new strategy for ferrous-based nanoparticles against PRRSV.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-022-01281-4.

Development of MIF/IL-1β biosensors for discovery of critical quality attributes and potential allergic rhinitis targets from clinical real-world data by intelligent algorithm coupled with in vitro and vivo mechanism validation

There are still huge challenges from clinical real-world data to accurate targets and critical quality attributes (CQAs) for effective treatment of allergic rhinitis (AR). Here, we present a novel integrated strategy that biosensors and intelligent algorithms were used to angle AR targets and CQAs from clinical real world. Firstly, bagging and boosting partial least squares discrimination analysis (PLS-DA) and Monte-Carlo sampling were proposed to screen accurate AR targets. Macrophage migration inhibitory factor (MIF) and Interleukin-1beta (IL-1β) potential targets were obtained based on large-scale analysis of one thousand proteins and in-depth precise screening of seventy proteins. Furthermore, high electron mobility transistor (HEMT) biosensors were fabricated and successfully modified by MIF and IL-1β potential targets with a low detection concentration as 1 pM and quantitative range from 1 pM to 10 nM. Surprisingly, through MIF/IL-1β biosensors, we angled 5-O-methylvisammioside, amygdalin, and cimicifugoside three CQAs. The strong interaction was discovered among three CQAs and MIF/IL-1β biosensors with almost all KD up to 10-11 M. Finally, interaction among three CQAs and MIF/IL-1β biosensors were evaluated by in vitro and vivo experiments. In this paper, two critical potential targets and three effective CQAs for AR treatment were discovered and validated by biosensor and advanced algorithms. It provides a superior integrated idea for angling critical targets and CQAs from clinical real-world data by biosensors and informatics.

Graphene oxide-based fluorescent biosensors and their biomedical applications in diagnosis and drug discovery

Graphene oxide (GO), an oxidized derivative of graphene, has received much attention for developing novel fluorescent bioanalytic platforms due to its remarkable optical properties and biocompatibility. The reliable performance and robustness of GO-based biosensors have enabled various applications in the biomedical field including diagnosis and drug discovery. Here, recent advances in the development of GO-based fluorescent biosensors are overviewed, particularly nucleic acid detection and enzyme activity assay. In addition, practical applications in biomarker detection and high-throughput screening are also examined. Lastly, basic design principles and remaining challenges of these types of biosensors are discussed for further progress.

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

Dengue virus (DENV), an arbovirus transmitted by mosquitoes, causes infectious diseases such as dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. Despite the dangers posed by DENV, there are no approved antiviral drugs for treatment of DENV infection. Considering the potential for a global dengue outbreak, rapid development of antiviral agents against DENV infections is crucial as a preemptive measure; thus, the selection of apparent drug targets, such as the viral enzymes involved in the viral life cycle, is recommended. Helicase, a potential drug target in DENV, is a crucial viral enzyme that unwinds double-stranded viral RNA, releasing single-stranded RNA genomes during viral replication. Therefore, an inhibitor of helicase activity could serve as a direct-acting antiviral agent. Here, we introduce an RNA helicase assay based on graphene oxide, which enables fluorescence-based analysis of RNA substrate-specific helicase enzyme activity. This assay demonstrated high reliability and ability for high-throughput screening, identifying a new helicase inhibitor candidate, micafungin (MCFG), from an FDA-approved drug library. As a direct-acting antiviral agent targeting RNA helicase, MCFG inhibits DENV proliferation in cells and an animal model. Notably, in vivo, MCFG treatment reduced viremia, inflammatory cytokine levels, and viral loads in several tissues and improved survival rates by up to 40% in a lethal mouse model. Therefore, we suggest MCFG as a potential direct-acting antiviral drug candidate.

Screening of drug databank against WT and mutant main protease of SARS-CoV-2: Towards finding potential compound for repurposing against COVID-19

Although several pharmacological agents are under investigation to be repurposed as therapeutic against COVID-19, not much success has been achieved yet. So, the search for an effective and active option for the treatment of COVID-19 is still a big challenge. The Spike protein (S), RNA-dependent RNA polymerase (RdRp), and Main protease (Mpro) are considered to be the primary therapeutic drug target for COVID-19. In this study we have screened the drugbank compound library against the Main Protease. But our search was not limited to just Mpro. Like other viruses, SARS-CoV-2, have also acquired unique mutations. These mutations within the active site of these target proteins may be an important factor hindering effective drug candidate development. In the present study we identified important active site mutations within the SARS-CoV-2 Mpro (Y54C, N142S, T190I and A191V). Further the drugbank database was computationally screened against Mpro and the selected mutants. Finally, we came up with the common molecules effective against the wild type (WT) and all the selected Mpro. The study found Imiglitazar, was found to be the most active compound against the wild type of Mpro. While PF-03715455 (Y54C), Salvianolic acid A (N142S and T190I), and Montelukast (A191V) were found to be most active against the other selected mutants. It was also found that some other compounds such as Acteoside, 4-Amino-N- {4-[2-(2,6-Dimethyl-Phenoxy)-Acetylamino]-3-Hydroxy-1-Isobutyl-5-Phenyl-Pentyl}-Benzamide, PF-00610355, 4-Amino-N-4-[2-(2,6-Dimethyl-Phenoxy)-Acetylamino]-3-Hydroxy-1-Isobutyl-5-Phenyl-Pentyl}-Benzamide and Atorvastatin were showing high efficacy against the WT as well as other selected mutants. We believe that these molecules will provide a better and effective option for the treatment of COVID-19 clinical manifestations.

A graphene oxide-based fluorescent nanosensor to identify antiviral agents via a drug repurposing screen

Currently, there are no approved therapeutics for Dengue virus (DENV) infection, even though it can cause fatal complications. Understanding DENV infection and its propagation process in host cells is necessary to develop specific antiviral therapeutics. Here, we developed a graphene oxide-based fluorescent system (Graphene Oxide-based Viral RNA Analysis system, GOViRA) that enables sensitive and quantitative real-time monitoring of the intracellular viral RNA level in living cells. The GOViRA system consists of a fluorescent dye-labeled peptide nucleic acid (PNA) with a complementary sequence to the DENV genome and a dextran-coated reduced graphene oxide nanocolloid (DRGON). When the dye labeled PNA is adsorbed onto DRGON, the fluorescence of the dye is effectively quenched. The quenched fluorescence signal is recovered when the dye labeled PNA forms interaction with intracellular viral RNA in DENV infected host cells. We demonstrated the successful use of the GOViRA platform for high-throughput screening to discover novel antiviral compounds. Through a cell-based high-throughput screening of FDA-approved small-molecule drugs, we identified ulipristal, a selective progesterone receptor modulator (SPRM), as a potent inhibitor against DENV infection. The anti-DENV activity of ulipristal was confirmed both in vitro and in vivo. Moreover, we suggest that the mode of action of ulipristal is mediated by inhibiting viral entry into the host cells.