Honey Bee Dry Venom Reduces Hepatitis B Virus Surface Antigen Secretion in PLC/PRF/5 Cell Line

Khani, Hussein; Ghorbani, Mahdi; Nojoomi, Farshad; Mohebbi, Alireza

doi:10.18502/ijml.v6i4.2013

Cited by 5 publications

(5 citation statements)

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“…There is an excellent opportunity to use natural products and plant-derived small antiviral molecules to deal with challenging viral diseases [33][34][35]. In this regard, in silico approaches have the advantage of using different chemical libraries for drug discovery against SARS-CoV-2 with fewer resources.…”

Section: Discussionmentioning

confidence: 99%

Digging for the Discovery of SARS-CoV-2 nsp12 Inhibitors: A Pharmacophore-Based and Molecular Dynamics Simulation Study

Askari¹,

Ebrahimi

Parhiz

et al. 2022

Future Virol.

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Aim: COVID-19 is a global health threat. Therapeutics are urgently needed to cure patients severely infected with COVID-19. Objective: to investigate potential candidates of nsp12 inhibitors by searching for druggable cavity pockets within the viral protein and drug discovery. Methods: A virtual screening of ZINC natural products on SARS-CoV-2 nsp12's druggable cavity was performed. A lead compound with the highest affinity to nsp12 was simulated dynamically for 10 ns. Results: ZINC03977803 was nominated as the lead compound. The results showed stable interaction between ZINC03977803 and nsp12 during 10 ns. Discussion: ZINC03977803 showed stable interaction with the catalytic subunit of SARS-CoV-2, nsp12. It could inhibit the SARS-CoV-2 life cycle by direct interaction with nsp12 and inhibit RdRp complex formation.

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Section: Discussionmentioning

confidence: 99%

Digging for the Discovery of SARS-CoV-2 nsp12 Inhibitors: A Pharmacophore-Based and Molecular Dynamics Simulation Study

Askari¹,

Ebrahimi

Parhiz

et al. 2022

Future Virol.

Self Cite

View full text Add to dashboard Cite

show abstract

Section: Discussionmentioning

confidence: 99%

Digging for the Discovery of SARS-CoV-2 nsp12 Inhibitors: A Pharmacophore-Based and Molecular Dynamics Simulation Study

Askari¹,

Ebrahimi

Parhiz

et al. 2021

Preprint

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Background: The severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is a grave global threat causing Coronavirus Disease 2019 (COVID-19). The therapeutics are urgently needed to cure patients severely infected with COVID-19. The aim of the study was to investigate for potential candidates of nsp12 inhibitors by searching for druggable cavity pockets within the viral protein and drug discovery.Methods: The crystallographic structure of SARS-CoV-2 nsp12 was searched for strong druggable cavity pockets and pharmacophore features by the CavityPlus server. The features were selected for high-throughput screening (HTS) of a chemical library of ZINC natural products and hit identification database by ZINCPharmer. Autodock Vina was furthered utilized for estimation of hits' affinities to nsp12. A lead compound with the highest affinity to nsp12 was simulated dynamically by GROMACS for 10 nanoseconds (ns) to measure the hit stability in complex with nsp12 and conformational changes.Results: 1 of 6 cavities with the highest score was selected for extraction of pharmacophore features and hit-identification. 9 pharmacophores were screened, and a total of unique 1274 hits were identified. One compound, ZINV03977803, with an -11.0 Kcal.mol-1 affinity was selected as the lead compound for molecular dynamic simulation (MDS). The results showed stable interaction between ZINV03977803 and nsp12 during 10 ns of simulation. The room-mean-square of deviation (RMSD) measure showed dramatically high conformational changes in the complex of ZINV03977803 and nsp12 compare two the viral proteins alone.Conclusions: The lead compound ZINV03977803 showed stable interaction with higher potential and hydrogen bonding with the catalytic subunit of SARS-CoV-2, nsp12. It could also inhibit the SARS-CoV-2 life cycle by direct interaction with nsp12 and inhibits RdRp complex formation.

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“…Hepatitis B virus (HBV) is a significant worldwide health problem because it can lead to acute and chronic liver infections [1,2]. HBV is a DNA virus with partial double-stranded characteristics, and a member of the Hepadnaviridae family.…”

Section: Introductionmentioning

confidence: 99%

Ligand-based pharmacophore modeling, virtual screening, and 2D quantitative structure-activity relationship performance on anti-Hepatitis B virus flavonols

Mohebbi,

Askari,

Askari

et al. 2024

Preprint

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Background: Targeting Hepatitis B virus (HBV) infection in human is crucial due to its adverse. Herbal medicine has long been significant in this regard, with flavonoids demonstrating promising results. Hence, establishing a way of identifying flavonoids with anti-HBV activities is the aim of the present study. Methods: Flavonoid structures with anti-HBV activities were retrieved. A flavonol-based pharmacophore model was established using LigandScout v4.4. Screening was performed using the PharmIt server. A QSAR equation was developed and validated with independent sets of compounds. Applicability domain (AD) was defined using Euclidean distance calculations for model validation. Results: The best model, consisting of 57 features was generated. HTS using the flavonol-based model resulted in 509 unique hits. The model's sensitivity and specificity were 71% and 100%, respectively. The QSAR model with two predictors, x4a and qed, exhibited strong predictive performance with an adjusted-R² value of 0.85 and 0.90 of Q2. Conclusion: The QSAR model has been validated with two separate chemical sets, guaranteeing the model's reproducibility and usefulness for other flavonols by utilizing the predictive characteristics of X4A and qed. These results provide new possibilities for discovering future anti-HBV drugs by integrating modeling and experimental research.

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Honey Bee Dry Venom Reduces Hepatitis B Virus Surface Antigen Secretion in PLC/PRF/5 Cell Line

Cited by 5 publications

References 0 publications

Digging for the Discovery of SARS-CoV-2 nsp12 Inhibitors: A Pharmacophore-Based and Molecular Dynamics Simulation Study

Digging for the Discovery of SARS-CoV-2 nsp12 Inhibitors: A Pharmacophore-Based and Molecular Dynamics Simulation Study

Digging for the Discovery of SARS-CoV-2 nsp12 Inhibitors: A Pharmacophore-Based and Molecular Dynamics Simulation Study

Ligand-based pharmacophore modeling, virtual screening, and 2D quantitative structure-activity relationship performance on anti-Hepatitis B virus flavonols

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