Evaluating Eurycomanone as a Potential Antiviral Agent Against SARS-CoV-2 Variants

Aims: The present study aimed to analyse the molecular interactions of the phytoconstituents known for their antiviral activity with the SARS-CoV-2 nonstructural proteins such as main protease (6LU7), Nsp12 polymerase (6M71), and Nsp13 helicase (6JYT). The applied in silico methodologies were molecular docking and pharmacophore modeling using Schrodinger software. Methods: The phytoconstituents were taken from PubChem, and SARS-CoV-2 proteins were downloaded from the protein data bank. The molecular interactions, binding energy, ADMET properties, and pharmacophoric features were analysed by glide XP, prime MM-GBSA, qikprop, and phase application of Schrodinger, respectively. The antiviral activity of the selected phytoconstituents was carried out by PASS predictor online tools. Results: The docking score analysis showed that quercetin 3-rhamnoside (-8.77 kcal/mol) and quercetin 3-rhamnoside (-7.89 kcal/mol) were excellent products to bind with their respective targets such as 6LU7, 6M71, and 6JYT. The generated pharmacophore hypothesis model validated the docking results, confirming the hydrogen bonding interactions of the amino acids. The PASS online tool predicted constituent's antiviral potentials. Conclusion: The docked phytoconstituents showed excellent interactions with the SARS-CoV-2 proteins, and on the outset, quercetin 3-rhamnoside and quercetin 7-rhamnoside interacted well with all the three proteins; these belong to the plant Houttuynia cordata. The pharmacophore hypothesis has revealed the characteristic features responsible for their interactions, and PASS prediction data has supported their antiviral activities. Thus, these natural compounds could be developed as lead molecules for antiviral treatment against SARS-CoV-2. Further in-vitro and invivo studies could be carried out to provide better drug therapy.

To identify and develop effective antiviral agents against SARS-CoV-2, research is ongoing in the field of drug discovery. Heterocyclic compounds such as Chalcone, Chromene, and Dihydropyrimidinone (DHPM) derivatives are of particular interest because of their structural diversity, easily synthesized and broad pharmacological activities, including antiviral effects. Therefore, we investigated the potential of these derivatives against SARS-CoV-2 using cell-based assays, supported by in silico studies. Ten synthetic compounds, consist of 4 DHPMs, 2 chromenes, and 4 chalcones were tested for cytotoxicity and antiviral activity in Vero cells infected with a locally isolated SARS-CoV-2 strain (Clade GH, GISAID: EPI_ISL_529965), using a phenotypic screening approach. Moreover, in silico analyses were performed to predict their drug-likeness, including absorption, distribution, metabolism, and excretion properties, using SwissADME. Molecular docking was conducted to evaluate the binding affinity and interactions of compounds with the SARS-CoV-2 main protease (Mpro). Among the tested compounds, S-10 (chromene derivative) and S-12 (DHPM derivative) demonstrated exhibited significant antiviral activity compared to the other tested derivatives (p < 0.05), with IC₅₀ values of 8.52 ± 0.28 µM and 6.19 ± 0.41 µM, and selectivity index (SI) of 158.8 and 309.7, respectively, indicating strong efficacy and high safety margins. In silico ADME suggested favorable drug-likeness profiles without major toxicity alerts. Molecular docking further revealed that both compounds established stable interactions with the SARS-CoV-2 main protease (Mpro), particularly at the catalytic residues His-41 and Cys-145, supporting their in vitro activity. These results suggest their potential as lead compounds for further drug development, supporting the use of integrated phenotypic and computational approaches in the discovery of region-specific antiviral agents. HIGHLIGHTS Two novel compounds (S-10 and S-12) were identified with strong anti-SARS-CoV-2 activity and high selectivity index (SI > 100), compared to the other 8 compounds tested, out of 10 Dihydropyrimidinone, Chromene, and Chalcone derivative candidates, suggesting high efficacy and low cytotoxicity. Phenotypic screening was performed against a locally isolated SARS-CoV-2 strain (Clade GH, Indonesia) provided, direct biological relevance rather than relying solely on predictive models and supporting region-specific therapeutic development. Supplementary in silico analysis (ADME profiling, toxicity prediction, and molecular docking to Mpro) offers, a comprehensive assessment of efficacy, safety, and mechanism of action. GRAPHICAL ABSTRACT

In recent years, several viral diseases have emerged suddenly, leading to widespread infection and fatalities. SARS-CoV-2, which appeared in late 2019, mutates frequently, and current vaccines have limited effectiveness in fully preventing SARS-CoV-2 infections. As a result, natural antiviral medicines have gained attention, particularly sulfated polysaccharides from seaweeds, which are promising sources of bioactive compounds for antiviral activity and immune support. This study screened the types of sulfated polysaccharides, such as carrageenan, fucoidan, and ulvan, using computational analysis to evaluate their antiviral potential against SARS-CoV-2. Molecular docking was conducted to examine potential interactions with human ACE2, SARS-CoV-2's RBD, and main protease. The results of molecular docking analysis showed that kappa carrageenan exhibited better docking scores of -9.3 kcal/mol with ACE2 and -8.1 kcal/mol with spike protein-RBD. Meanwhile, carrageenan showed a better docking score of -7.6 kcal/mol with the main protease. The prediction of drug compounds based on RO5 indicates that all bioactive test compounds have the potential to be used as therapeutic agents. It is concluded that the sulfated polysaccharides derived from red seaweed, namely carrageenan and its derivatives, exhibit greater potential in demonstrating antiviral activity against SARS-CoV-2 compared to fucoidan and ulvan.

Docking and quantum-chemical methods have been used for screening of drug-like compounds from the own database of the Voronezh State University to find inhibitors the SARS-CoV-2 main protease, an important enzyme of the coronavirus responsible for the COVID-19 pandemic. Using the SOL program more than 42000 3D molecular structures were docked into the active site of the main protease, and more than 1000 ligands with most negative values of the SOL score were selected for further processing. For all these top ligands, the protein-ligand binding enthalpy has been calculated using the PM7 semiempirical quantum-chemical method with the COSMO implicit solvent model. 20 ligands with the most negative SOL scores and the most negative binding enthalpies have been selected for further experimental testing. The latter has been made by measurements of the inhibitory activity against the main protease and suppression of SARS-CoV-2 replication in a cell culture. The inhibitory activity \of the compounds was determined using a synthetic fluorescently labeled peptide substrate including the proteolysis site of the main protease. The antiviral activity was tested against SARS-CoV-2 virus in the Vero cell culture. Eight compounds showed inhibitory activity against the main protease of SARS-CoV-2 in the submicromolar and micromolar ranges of the IC50 values. Three compounds suppressed coronavirus replication in the cell culture at the micromolar range of EC50 values and had low cytotoxicity. The found chemically diverse inhibitors can be used for optimization in order to obtain a leader compound, the basis of new direct-acting antiviral drugs against the SARS-CoV-2 coronavirus.

Antiviral activity of castor oil plant (Ricinus communis) leaf extracts

Emerging arboviruses such as Zika virus (ZIKV) and Chikungunya virus (CHIKV) remain significant public health threats. This study aimed to evaluate the antiviral potential of six organochalcogen compounds against ZIKV and CHIKV. Compounds were assessed for cytotoxicity and antiviral activity in Vero cells. Antiviral effects were determined using plaque reduction assays, time-of-addition studies, viral adsorption, and virucidal assays. Molecular docking and density functional theory (DFT) calculations were performed to investigate interactions with viral targets and electronic properties. Compounds 4, 7, 8, and 9 exhibited potent antiviral activity with low cytotoxicity, demonstrating effective inhibition of viral replication with half-maximal effective concentration (EC₅₀) values in the micromolar range and favorable selectivity indices. Mechanistic assays revealed that the compounds interfered with viral adsorption, exhibited virucidal effects, and inhibited multiple stages of the replication cycle. Docking studies confirmed strong binding to key viral enzymes, supported by HOMO (half-maximal effective concentration) - LUMO (lowest unoccupied molecular orbital) analysis. These findings highlight organochalcogen compounds as promising dual-action antiviral candidates with broad-spectrum activity against ZIKV and CHIKV. Further preclinical investigations are warranted to explore their therapeutic potential.

Investigating the potential antiviral activity drugs against SARS-CoV-2 by molecular docking simulation

Background: p97 (also known as valosin-containing protein, VCP) is a member of the AAA+ ATPase family and is intimately associated with protein quality control and homeostasis regulation. Therefore, pharmaceutical inhibition of p97 has been actively pursued as an anticancer strategy. Recently, p97 has emerged as an important pro-viral host factor and p97 inhibitors are being evaluated as potential antiviral agents. Methods: We designed and synthesized novel p97 inhibitors based on the rearrangement of the central fused ring of our previously reported p97 inhibitors. These compounds were tested for inhibition of p97, cytotoxicity, and antiviral activity against SARS-CoV-2. Molecular docking was also performed on selected inhibitors to shed light on their binding modes. Results: Among these new p97 inhibitors, two compounds possess enhanced anti-p97 activity over their parent compounds. More significantly, these two inhibitors exhibit strong antiviral activity against SARS-CoV-2 at doses with no significant cytotoxicity. Molecular docking reveals no major change of the binding mode relative to that of their parent compounds, further supporting our design strategy. Conclusions: These compounds are structurally novel p97 inhibitors that display low toxicity and possess promising antiviral activity against SARS-CoV-2 and potentially other viruses. Further structural exploration is therefore justified and improved analogs will serve as useful tools for studying p97 as a promising host antiviral target.

Coronavirus infection (COVID-19), designated a global health emergency by the World Health Organization in 2020, continues to spur the search for effective therapeutics. The causative agent, SARS-CoV-2, depends on viral proteins and host metabolic reprogramming for replication. This study explores the potential of glycolytic inhibitors as dual-action agents against SARS-CoV-2, explicitly targeting the main protease and the spike protein due to their critical roles in viral replication and cellular entry. These inhibitors disrupt the activity of viral proteins and host cell glycolysis, thereby preventing viral propagation. Through a combination of virtual screening, molecular docking, and molecular dynamics simulations, fluoro-deoxy-glucose folate (FDGF) and N-(2-fluoro-3-(6-O-glucosylpropyl-azomycin)) were identified as potent candidates. The docking results showed strong binding affinities, with scores of -8.6 and -7.1kcal/mol for main protease and -9.9 and - 7.5kcal/mol for spike receptor-binding domain bound to ACE2. Further molecular dynamic simulations confirmed the stability of the FDGF complexes, with RMSD fluctuations consistently remained within 1.6-2.9 Å over a 100 ns trajectory. Additionally, MM-GBSA binding free energy calculations revealed favorable binding energies, underscoring the stability and potential efficacy of these compounds. Overall, the findings suggest that FDGF and N-(2-fluoro-3-(6-O-glucosylpropyl-azomycin)) show promise as SARS-CoV-2 therapeutics, warranting further in vitro and in vivo validation to confirm their antiviral potential. The online version contains supplementary material available at 10.1007/s40203-025-00336-2.

Anisodamine potently inhibits SARS-CoV-2 infection in vitro and targets its main protease

Potent and biostable inhibitors of the main protease of SARS-CoV-2

The search for natural resources with antiviral potential, as an alternative to synthetic drugs, has been growing and, in this sense, oregano presents itself as a potential candidate. However, the antiviral studies with oregano are still poorly explored. BoHV-1 stands out among veterinary pathogens, for its economic impact on cattle production. In this study, the antiviral and virucidal activity of polar extracts of Origanum vulgare was evaluated against BoHV-1. Infusion (INF10), decoction (DEC), and hydroalcoholic (HAE) extracts were tested to cytotoxic and antiviral assays on MDBK cells. Cytotoxic effects were analyzed through MTT assay and the antiviral activity was expressed as a percentage of inhibition (PI). BoHV-1 was incubated with O. vulgare extracts as virucidal assay. Concentrations ≤3.12 mg/ml (INF10) and ≤1.56 mg/ml (DEC/HAE) preserved the cell viability above 60%, and all extracts were safe (>96%) between 0.78 and 0.39 mg/ml. Regarding the antiviral activity, pre-treatment of all extracts highlighted in comparison to the post-treatment. The pre-treatment of infusion at 2 mg/ml highlighted due to the high cell viability (84.69%) and the elimination of the viral load. All extracts inactivated BoHV-1 from 2 hours of incubation (20 mg/ml), showing virucidal activity. These findings may be related to 4-hydroxybenzoic acid as prevalent in all extracts. These findings showed the in vitro antiviral and virucidal activity of oregano polar extracts against BoHV-1 and may be promising for the therapeutic use against herpesviruses infections.

BackgroundIn recent years, an increase in the occurrence of illnesses caused by two clinically- important arboviruses has been reported: Zika virus (ZIKV) and Chikungunya virus (CHIKV). There is no licensed antiviral treatment for either of the two abovementioned viruses. Bearing in mind that the antiviral effect of indole alkaloids has been reported for other arboviral models, the present study proposed to evaluate the antiviral in vitro and in silico effects of four indole alkaloids on infections by these two viruses in different cell lines.MethodsThe antiviral effects of voacangine (VOAC), voacangine-7-hydroxyindolenine (VOAC-OH), rupicoline and 3-oxo voacangine (OXO-VOAC) were evaluated in Vero, U937 and A549 cells using different experimental strategies (Pre, Trans, Post and combined treatment). Viral infection was quantified by different methodologies, including infectious viral particles by plating, viral genome by RT-qPCR, and viral protein by cell ELISA. Moreover, molecular docking was used to evaluate the possible interactions between structural and nonstructural viral proteins and the compounds. The results obtained from the antiviral strategies for each experimental condition were compared in all cases with the untreated controls. Statistically significant differences were identified using a parametric Student’s t-test. In all cases, p values below 0.05 (p < 0.05) were considered statistically significant.ResultsIn the pre-treatment strategy in Vero cells, VOAC and VOAC-OH inhibited both viral models and OXO-VOAC inhibited only ZIKV; in U937 cells infected with CHIKV/Col, only VOAC-OH inhibited infection, but none of the compounds had activity in A549 cells; in U937 cells and A549 cells infected with ZIKV/Col, the three compounds that were effective in Vero cells also had antiviral activity. In the trans-treatment strategy, only VOAC-OH was virucidal against ZIKV/Col. In the post-treatment strategy, only rupicoline was effective in the CHIKV/Col model in Vero and A549 cells, whereas VOAC and VOAC-OH inhibited ZIKV infection in all three cell lines. In the combined strategy, VOAC, VOAC-OH and rupicoline inhibited CHIKV/Col and ZIKV/Col, but only rupicoline improved the antiviral effect of ZIKV/Col-infected cultures with respect to the individual strategies. Molecular docking showed that all the compounds had favorable binding energies with the structural proteins E2 and NSP2 (CHIKV) and E and NS5 (ZIKV).ConclusionsThe present study demonstrates that indole alkaloids are promising antiviral drugs in the process of ZIKV and CHIKV infection; however, the mechanisms of action evaluated in this study would indicate that the effect is different in each viral model and, in turn, dependent on the cell line.

BackgroundSince effective antiviral drugs for COVID-19 are still limited in number, the exploration of compounds that have antiviral activity against SARS-CoV-2 is in high demand. Porphyrin is potentially developed as a COVID-19 antiviral drug. However, its low solubility in water restricts its clinical application. Reconstruction of porphyrin into carbon dots is expected to possess better solubility and bioavailability as well as lower biotoxicity. Methods and resultsIn this study, we investigated the antiviral activity of porphyrin and porphyrin-derived carbon dots against SARS-CoV-2. Through the in silico analysis and assessment using a novel drug screening platform, namely dimer-based screening system, we demonstrated the capability of the antivirus candidates in inhibiting the dimerization of the C-terminal domain of SARS-CoV-2 Nucleocapsid. It was shown that porphyrin-derived carbon dots possessed lower cytotoxicity on Vero E6 cells than porphyrin. Furthermore, we also assessed their antiviral activity on the SARS-CoV-2-infected Vero E6 cells. The transformation of porphyrin into carbon dots substantially augmented its performance in disrupting SARS-CoV-2 propagation in vitro. ConclusionsTherefore, this study comprehensively demonstrated the potential of porphyrin-derived carbon dots to be developed further as a promisingly safe and effective COVID-19 antiviral drug.

Evaluation of inhibition effect and interaction mechanism of antiviral drugs on main protease of novel coronavirus: Molecular docking and molecular dynamics studies