Propolis,Bee Honey,and Their Components Protect against Coronavirus Disease 2019 (COVID-19): A Review of In Silico,In Vitro,and Clinical Studies

Despite the virulence and high fatality of coronavirus disease 2019 (COVID-19), no specific antiviral treatment exists until the current moment. Natural agents with immune-promoting potentials such as bee products are being explored as possible treatments. Bee honey and propolis are rich in bioactive compounds that express strong antimicrobial, bactericidal, antiviral, anti-inflammatory, immunomodulatory, and antioxidant activities. This review examined the literature for the anti-COVID-19 effects of bee honey and propolis, with the aim of optimizing the use of these handy products as prophylactic or adjuvant treatments for people infected with severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). Molecular simulations show that flavonoids in propolis and honey (e.g., rutin, naringin, caffeic acid phenyl ester, luteolin, and artepillin C) may inhibit viral spike fusion in host cells, viral-host interactions that trigger the cytokine storm, and viral replication. Similar to the potent antiviral drug remdesivir, rutin, propolis ethanolic extract, and propolis liposomes inhibited non-structural proteins of SARS-CoV-2 in vitro, and these compounds along with naringin inhibited SARS-CoV-2 infection in Vero E6 cells. Propolis extracts delivered by nanocarriers exhibit better antiviral effects against SARS-CoV-2 than ethanolic extracts. In line, hospitalized COVID-19 patients receiving green Brazilian propolis or a combination of honey and Nigella sativa exhibited earlier viral clearance, symptom recovery, discharge from the hospital as well as less mortality than counterparts receiving standard care alone. Thus, the use of bee products as an adjuvant treatment for COVID-19 may produce beneficial effects. Implications for treatment outcomes and issues to be considered in future studies are discussed.     

Quantum dots as a promising agent to combat COVID-19

Approximately every 100 years, as witnessed in the last two centuries, we are facing an influenza pandemic, necessitating the need to combat a novel virus strain. As a result of the new coronavirus (severe acute respiratory syndrome coronavirus type 2 [SARS-CoV-2] outbreak in January 2020, many clinical studies are being carried out with the aim of combating or eradicating the disease altogether. However, so far, developing coronavirus disease 2019 (COVID-19) detection kits or vaccines has remained elusive. In this regard, the development of antiviral nanomaterials by surface engineering with enhanced specificity might prove valuable to combat this novel virus. Quantum dots (QDs) are multifaceted agents with the ability to fight against/inhibit the activity of COVID-19 virus. This article exclusively discusses the potential role of QDs as biosensors and antiviral agents for attenuation of viral infection.     

Curcumin Inhibits In Vitro SARS-CoV-2 Infection In Vero E6 Cells through Multiple Antiviral Mechanisms

Due to the scarcity of therapeutic approaches for COVID-19, we investigated the antiviral and anti-inflammatory properties of curcumin against SARS-CoV-2 using in vitro models. The cytotoxicity of curcumin was evaluated using MTT assay in Vero E6 cells. The antiviral activity of this compound against SARS-CoV-2 was evaluated using four treatment strategies (i. pre–post infection treatment, ii. co-treatment, iii. pre-infection, and iv. post-infection). The D614G strain and Delta variant of SARS-CoV-2 were used, and the viral titer was quantified by plaque assay. The anti-inflammatory effect was evaluated in peripheral blood mononuclear cells (PBMCs) using qPCR and ELISA. By pre–post infection treatment, Curcumin (10 µg/mL) exhibited antiviral effect of 99% and 99.8% against DG614 strain and Delta variant, respectively. Curcumin also inhibited D614G strain by pre-infection and post-infection treatment. In addition, curcumin showed a virucidal effect against D614G strain and Delta variant. Finally, the pro-inflammatory cytokines (IL-1β, IL-6, and IL-8) released by PBMCs triggered by SARS-CoV-2 were decreased after treatment with curcumin. Our results suggest that curcumin affects the SARS-CoV-2 replicative cycle and exhibits virucidal effect with a variant/strain independent antiviral effect and immune-modulatory properties. This is the first study that showed a combined (antiviral/anti-inflammatory) effect of curcumin during SARS-CoV-2 infection. However, additional studies are required to define its use as a treatment for the COVID-19.     

Medicinal Plants,Phytochemicals, and Herbs to Combat Viral Pathogens Including SARS-CoV-2

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome corona virus-2 (SARS-CoV-2), is the most important health issue, internationally. With no specific and effective antiviral therapy for COVID-19, new or repurposed antiviral are urgently needed. Phytochemicals pose a ray of hope for human health during this pandemic, and a great deal of research is concentrated on it. Phytochemicals have been used as antiviral agents against several viruses since they could inhibit several viruses via different mechanisms of direct inhibition either at the viral entry point or the replication stages and via immunomodulation potentials. Recent evidence also suggests that some plants and its components have shown promising antiviral properties against SARS-CoV-2. This review summarizes certain phytochemical agents along with their mode of actions and potential antiviral activities against important viral pathogens. A special focus has been given on medicinal plants and their extracts as well as herbs which have shown promising results to combat SARS-CoV-2 infection and can be useful in treating patients with COVID-19 as alternatives for treatment under phytotherapy approaches during this devastating pandemic situation.     

In Silico Mining of Terpenes from Red-Sea Invertebrates for SARS-CoV-2 Main Protease (Mpro) Inhibitors

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent for the COVID-19 pandemic, which generated more than 1.82 million deaths in 2020 alone, in addition to 83.8 million infections. Currently, there is no antiviral medication to treat COVID-19. In the search for drug leads, marine-derived metabolites are reported here as prospective SARS-CoV-2 inhibitors. Two hundred and twenty-seven terpene natural products isolated from the biodiverse Red-Sea ecosystem were screened for inhibitor activity against the SARS-CoV-2 main protease (M^pro) using molecular docking and molecular dynamics (MD) simulations combined with molecular mechanics/generalized Born surface area binding energy calculations. On the basis of in silico analyses, six terpenes demonstrated high potency as M^pro inhibitors with ΔG_binding ≤ −40.0 kcal/mol. The stability and binding affinity of the most potent metabolite, erylosides B, were compared to the human immunodeficiency virus protease inhibitor, lopinavir. Erylosides B showed greater binding affinity towards SARS-CoV-2 M^pro than lopinavir over 100 ns with ΔG_binding values of −51.9 vs. −33.6 kcal/mol, respectively. Protein–protein interactions indicate that erylosides B biochemical signaling shares gene components that mediate severe acute respiratory syndrome diseases, including the cytokine- and immune-signaling components BCL2L1, IL2, and PRKC. Pathway enrichment analysis and Boolean network modeling were performed towards a deep dissection and mining of the erylosides B target–function interactions. The current study identifies erylosides B as a promising anti-COVID-19 drug lead that warrants further in vitro and in vivo testing.     

Type I and III interferon responses in SARS-CoV-2 infection

Coronavirus disease 2019 (COVID-19), the current pandemic disease, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Type I and III interferons (IFNs) are innate cytokines that are important in the first-line defense against viruses. Similar to many other viruses, SARS-CoV-2 has evolved mechanisms for evading the antiviral effects of type I and III IFNs at multiple levels, including the induction of IFN expression and cellular responses to IFNs. In this review, we describe the innate sensing mechanisms of SARS-CoV-2 and the mechanisms used by SARS-CoV-2 to evade type I and III IFN responses. We also discuss contradictory reports regarding impaired and robust type I IFN responses in patients with severe COVID-19. Finally, we discuss how delayed but exaggerated type I IFN responses can exacerbate inflammation and contribute to the severe progression of COVID-19.Subject terms: Infectious diseases, Infection     

Identification of SARS-CoV-2 Receptor Binding Inhibitors by In Vitro Screening of Drug Libraries

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) global pandemic. The first step of viral infection is cell attachment, which is mediated by the binding of the SARS-CoV-2 receptor binding domain (RBD), part of the virus spike protein, to human angiotensin-converting enzyme 2 (ACE2). Therefore, drug repurposing to discover RBD-ACE2 binding inhibitors may provide a rapid and safe approach for COVID-19 therapy. Here, we describe the development of an in vitro RBD-ACE2 binding assay and its application to identify inhibitors of the interaction of the SARS-CoV-2 RBD to ACE2 by the high-throughput screening of two compound libraries (LOPAC^®1280 and DiscoveryProbeTM). Three compounds, heparin sodium, aurintricarboxylic acid (ATA), and ellagic acid, were found to exert an effective binding inhibition, with IC50 values ranging from 0.6 to 5.5 µg/mL. A plaque reduction assay in Vero E6 cells infected with a SARS-CoV-2 surrogate virus confirmed the inhibition efficacy of heparin sodium and ATA. Molecular docking analysis located potential binding sites of these compounds in the RBD. In light of these findings, the screening system described herein can be applied to other drug libraries to discover potent SARS-CoV-2 inhibitors.     

核磁共振方法研究瓜环[n](n=7,8)与枸橼酸西地那非的相互作用

利用1H NMR技术、电喷雾质谱、红外光谱以及紫外吸收光谱法等手段研究了瓜环[n](n=7,8)与枸橼酸西地那非的相互作用。结果表明:枸橼酸西地那非与两种瓜环都形成了1∶1的包结配合物,但是其配合物的作用模式随瓜环的大小而不同。通过计算得出瓜环[n](n=7,8)与枸橼酸西地那非的包结常数分别为958和1530 L/mol,说明瓜环对枸橼酸西地那非具有潜在的缓释作用。     

Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay

Caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the COVID-19 pandemic is ongoing, with no proven safe and effective vaccine to date. Further, effective therapeutic agents for COVID-19 are limited, and as a result, the identification of potential small molecule antiviral drugs is of particular importance. A critical antiviral target is the SARS-CoV-2 main protease (M^pro), and our aim was to identify lead compounds with potential inhibitory effects. We performed an initial molecular docking screen of 300 small molecules, which included phenolic compounds and fatty acids from our OliveNet™ library (224), and an additional group of curated pharmacological and dietary compounds. The prototypical α-ketoamide 13b inhibitor was used as a control to guide selection of the top 30 compounds with respect to binding affinity to the M^pro active site. Further studies and analyses including blind docking were performed to identify hypericin, cyanidin-3-O-glucoside and SRT2104 as potential leads. Molecular dynamics simulations demonstrated that hypericin (ΔG = -18.6 and -19.3 kcal/mol), cyanidin-3-O-glucoside (ΔG = -50.8 and -42.1 kcal/mol), and SRT2104 (ΔG = -8.7 and -20.6 kcal/mol), formed stable interactions with the M^pro active site. An enzyme-linked immunosorbent assay indicated that, albeit, not as potent as the covalent positive control (GC376), our leads inhibited the M^pro with activity in the micromolar range, and an order of effectiveness of hypericin and cyanidin-3-O-glucoside > SRT2104 > SRT1720. Overall, our findings, and those highlighted by others indicate that hypericin and cyanidin-3-O-glucoside are suitable candidates for progress to in vitro and in vivo antiviral studies.     

Potential of graphene-based materials to combat COVID-19: properties,perspectives, and prospects

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a new virus in the coronavirus family that causes coronavirus disease (COVID-19), emerges as a big threat to the human race. To date, there is no medicine and vaccine available for COVID-19 treatment. While the development of medicines and vaccines are essentially and urgently required, what is also extremely important is the repurposing of smart materials to design effective systems for combating COVID-19. Graphene and graphene-related materials (GRMs) exhibit extraordinary physicochemical, electrical, optical, antiviral, antimicrobial, and other fascinating properties that warrant them as potential candidates for designing and development of high-performance components and devices required for COVID-19 pandemic and other futuristic calamities. In this article, we discuss the potential of graphene and GRMs for healthcare applications and how they may contribute to fighting against COVID-19.     

Synthesis and molecular docking study of novel COVID-19 inhibitors

In 2020, the world tried to combat the corona virus (COVID-19) pandemic. A proven treatment method specific to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is still not found. In this study, seven new antiviral compounds were designed for COVID-19 treatment. The ability of these compounds to inhibit COVID-19’s RNA processing was calculated by the molecular docking study. It has been observed that the compounds can have high binding affinities especially against NSP12 (between -9.06 and -8.00 kcal/mol). The molecular dynamics simulation of NSP12-ZG 7 complex proved the stability of interaction. The synthesis of two most active molecules was performed by one-pot reaction and characterized by FT-IR, ¹H-NMR, ¹³C-NMR, and mass spectroscopy. The compounds presented with their synthesis are inhibitory core structures against SARS-CoV-2 infection.     

快速高分离度液相色谱/质谱方法筛选组织蛋白酶B的抑制剂

1引言组织蛋白酶B(CB)是溶酶体内半胱氨酸蛋白水解酶,属于木瓜蛋白酶家族,其特异性底物为Z-Arg-Arg-7-氨基-4-甲基香豆素[1],CB催化底物肽键断裂生成7-氨基-4-甲基香豆素。近年来的研究表明,CB在肿瘤的发展中起作用的一类关键酶[2],CB通过多种机制促进血管形成,从而促进肿瘤生长,同时降解基底膜主要成分以及激活胶原酶、尿激酶等其它蛋白酶发生协同作用,使肿瘤易侵袭、转移和扩散。在肿瘤组织中还发现CB与CB抑制剂平衡作用也参与肿瘤的发     

Structure-based virtual screening and molecular dynamics of phytochemicals derived from Saudi medicinal plants to identify potential COVID-19 therapeutics

Coronavirus disease 2019 (COVID-19) has affected almost every country in the world by causing a global pandemic with a high mortality rate. Lack of an effective vaccine and/or antiviral drugs against SARS-CoV-2, the causative agent, has severely hampered the response to this novel coronavirus. Natural products have long been used in traditional medicines to treat various diseases, and purified phytochemicals from medicinal plants provide a valuable scaffold for the discovery of new drug leads. In the present study, we performed a computational screening of an in-house database composed of ~1000 phytochemicals derived from traditional Saudi medicinal plants with recognised antiviral activity. Structure-based virtual screening was carried out against three druggable SARS-CoV-2 targets, viral RNA-dependent RNA polymerase (RdRp), 3-chymotrypsin-like cysteine protease (3CL^pro) and papain like protease (PL^pro) to identify putative inhibitors that could facilitate the development of potential anti-COVID-19 drug candidates. Computational analyses identified three compounds inhibiting each target, with binding affinity scores ranging from −9.9 to −6.5 kcal/mol. Among these, luteolin 7-rutinoside, chrysophanol 8-(6-galloylglucoside) and kaempferol 7-(6″-galloylglucoside) bound efficiently to RdRp, while chrysophanol 8-(6-galloylglucoside), 3,4,5-tri-O-galloylquinic acid and mulberrofuran G interacted strongly with 3CL^pro, and withanolide A, isocodonocarpine and calonysterone bound tightly to PL^pro. These potential drug candidates will be subjected to further in vitro and in vivo studies and may assist the development of effective anti-COVID-19 drugs.     

Cucurbit[6]uril functionalized gold nanoparticles and electrode for the detection of metformin drug

Based on the host-guest molecular recognition capability of cucurbit[6]uril (CB[6]) modified on the gold surface, sensitive spectrophotometric and electrochemical methods for the detection of metformin (MET) have been developed. The molecular recognition between cucurbit[7]uril (CB[7]) or CB[6] and MET is initially demonstrated and the related recognition mechanism is further deliberated. First, CB[6]-modified gold nanoparticles (AuNPs/CB[6]) were synthesized and then characterized by ultraviolet visible light spectrum (UV–vis) and transmission electron microscopy (TEM). The aggregation of AuNPs/CB[6] prompted by MET triggered changes of color and the absorption spectrum, that explored for the visual identification and spectrophotometric determination of MET. Under the optimized detection conditions, the UV–vis spectrometry had a good linear relationship in the range of 6–700 µmol/L, and the detection limit was 2 µmol/L. In addition, a single-layer CB[6]-modified gold electrode (GE-CB[6]) detection system for MET was constructed. As the concentration of MET in the solution continues to increase, the charge transfer resistance (Rct) in the Nyquist diagram of the electrochemical impedance method (EIS) continues to increase. In the concentration range from 10 pmol/L to 20 nmol/L, the logarithm of the MET concentration has a good linear relationship with Rct, and the detection limit of this method is 1.35 pmol/L. Both methods have good concentration sensitivity to MET in different concentration ranges, providing a powerful tool for the detection of MET.     

In-silico investigation of phenolic compounds from leaves of Phillyrea angustifolia L. as a potential inhibitor against the SARS-CoV-2 main protease (Mpro PDB ID:5R83) using a virtual screening method

There is currently a global COVID-19 pandemic caused by the severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and its variants. This highly contagious viral disease continues to pose a major health threat global. The discovery of vaccinations is not enough to prevent their spread and dire consequences. To take advantage of the current drugs and isolated compounds, and immediately qualifying approach is required. The aim of our research is evaluation the potency for natural antiviral compounds against the SARS CoV-2 M^pro. Molecular docking of four phenolic compounds from Phillyrea angustifolia leaves with SARS-CoV-2 M^pro has been conducted. Similarly, the stability of selected ligand–protein interactions has been determined using MD simulations. Moreover, the quantitative structure–activity relationship (QSAR), MMGBSA binding energies, pharmacokinetics, and drug-likeness predictions for selected phenolic have been reported. The selected phenolic compounds (Luteolin-7-O-glucoside, Apigenin-7-O-glucoside, Demethyl-oleuropein, and Oleuropein aglycone) revealed strong binding contacts in the two active pockets of a target protein of SARS-CoV-2 M^pro with the docking scores and highest binding energies with a binding energy of ?8.2 kcal/mol; ?7.8 kcal/mol; ?7.2 kcal/mol and ?7.0 kcal/mol respectively. Both Demethyloleoeuropein and Oleuropein aglycone can interact with residues His41 and Cys145 (catalytic dyad) and other amino acids of the binding pocket of M^pro. According to QSAR, studies on pharmacokinetics and drug-like properties suggested that oleuropein aglycone could be the best inhibitor of SARS-CoV-2 for new drug design and development. Further in vivo, in vitro, and clinical studies are highly needed to examine the potential of these phenolic compounds in the fight against COVID-19.     

In silico study of remdesivir with and without ionic liquids having different cations using DFT calculations and molecular docking

The new coronavirus is trying best to kill the humanity with its highly infectious nature and its first infection was reported in 2019; later this infection was named as COVID-19. Health-care systems are still the using repurposing drugs to cure the patients from this infection. Remdesivir is found to have good potential to cure the patients from this infection and is being extensively used during the 1^st and 2^nd wave of COVID-19. Therefore, in the present work, authors have studied the interaction of remdesivir with different ionic liquids with change in cations using density functional theory calculation in gaseous and water. Based on the DFT calculations, it was found that remdesivir interacts effectively with different ionic liquids based on the energy; further, the change in free energy for Remdesivir-[Bet-ester][Lev] (1) was found to be ?3223.5758 and ?3223.6533 hartree per particle in gaseous and water respectively and most stable; further, 2 and 3 have the comparable free energies. Further, the potential of remdesivir with and without ionic liquids against the main protease of SARS-CoV-2 was investigated using molecular docking. Results revealed that Remdesivir-[Chol][Lev] (2) and Remdesivir-[Chol-ether][Lev] (3) have shown promising results with binding energy of ?129.64 ?kcal/mol and ?125.44 ?kcal/mol respectively while Remdesivir [Bet-ester][Lev] (1) have a binding energy of -123.86 kcal/mol. It is important to mention that changing the cations in ionic liquid play an important role in the docking. It is also observed that the ionic liquid having sodium as cation, then the binding energy against Mpro of CoV is poor and even less than the remdesivir alone.     

Antiviral Properties of the NSAID Drug Naproxen Targeting the Nucleoprotein of SARS-CoV-2 Coronavirus

There is an urgent need for specific antiviral treatments directed against SARS-CoV-2 to prevent the most severe forms of COVID-19. By drug repurposing, affordable therapeutics could be supplied worldwide in the present pandemic context. Targeting the nucleoprotein N of the SARS-CoV-2 coronavirus could be a strategy to impede viral replication and possibly other essential functions associated with viral N. The antiviral properties of naproxen, a non-steroidal anti-inflammatory drug (NSAID) that was previously demonstrated to be active against Influenza A virus, were evaluated against SARS-CoV-2. Intrinsic fluorescence spectroscopy, fluorescence anisotropy, and dynamic light scattering assays demonstrated naproxen binding to the nucleoprotein of SARS-Cov-2 as predicted by molecular modeling. Naproxen impeded recombinant N oligomerization and inhibited viral replication in infected cells. In VeroE6 cells and reconstituted human primary respiratory epithelium models of SARS-CoV-2 infection, naproxen specifically inhibited viral replication and protected the bronchial epithelia against SARS-CoV-2-induced damage. No inhibition of viral replication was observed with paracetamol or the COX-2 inhibitor celecoxib. Thus, among the NSAID tested, only naproxen combined antiviral and anti-inflammatory properties. Naproxen addition to the standard of care could be beneficial in a clinical setting, as tested in an ongoing clinical study.     

Structure-based linker optimization of 6-(2-cyclohexyl-1-alkyl)-2-(2-oxo-2-phenylethylsulfanyl)pyrimidin-4(3H)-ones as potent non-nucleoside HIV-1 reverse transcriptase inhibitors

In continuation of our efforts toward the discovery of potent HIV-1 NNRTIs with diverse structures,a series of novel S-DACO analogues of 6-(2-cyclohexyl-1-allkyl)-2-(2-oxo-2-phenyl-ethylsulfanyl)pyrimidin-4(3 H)-ones were designed,synthesized and evaluated for their antiviral activities in MT-4 cells.Most of these new compounds showed moderate to good activities against wild type HIV-1 with IC_(50) values ranging from 7.55 μmol/L to 0.018 μmol/L.Among them,compound 5 c was identified as the most promising inhibitor against HIV-1 replication with an IC_(50)=0.018 μmol/L,CC_(50)=194 μmol/L,and SI=12791,which was much more potent than the reference drugs NVP and DLV and comparable to AZT and EFV.In addition,5 c also exhibited improved activity against double mutant HIV-1 strain RES056 compared to that of the reference drugs NVP/DLV and DB02.The preliminary structure-activity relationship(SAR) and molecular modeling studies were also discussed,which provides some useful indications for guiding the further rational design of new S-DACO analogues.     

Trends in biosensing platforms for SARS-CoV-2 detection: A critical appraisal against standard detection tools

In this ongoing theme of coronavirus disease 2019 (COVID-19) pandemic, highly sensitive analytical testing platforms are extremely necessary to detect SARS-CoV-2 RNA and antiviral antibodies. To limit the viral spread, prompt and precise diagnosis is crucial to facilitate treatment and ensure effective isolation. Accurate detection of antibodies (IgG and IgM) is imperative to understand the prevalence of SARS-CoV-2 in public and to inspect the proportion of immune individuals. In this review, we demonstrate and evaluate some tests that have been used commonly to detect SARS-CoV-2. These include nucleic acid and serological tests for the detection of SARS-CoV-2 RNA and specific antibodies in infected people. Moreover, the vitality of biosensing technologies emphasizing on optical and electrochemical biosensors toward the detection of SARS-CoV-2 has also been discussed here. The early diagnosis of COVID-19 based on detection of reactive oxygen species overproduction because of virus-induced dysfunctioning of lung cells has also been highlighted.