In vitro and computational insights revealing the potential inhibitory effect of Tanshinone IIA against influenza A virus

Elebeedy, Dalia; Badawy, Ingy; Elmaaty, Ayman Abo; Saleh, Moustafa M.; Kandeil, Ahmed; Ghanem, Aml; Kutkat, Omnia; Alnajjar, Radwan; Maksoud, Ahmed I. Abd El; Al‐Karmalawy, Ahmed A.

doi:10.1016/j.compbiomed.2021.105149

Cited by 48 publications

(31 citation statements)

References 62 publications

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“…Two program validation processes were carried out before the docking steps by redocking the co-crystallized inhibitors at their corresponding M pro binding pockets [46][47][48] . The valid performance was confirmed by obtaining low RMSD values (< 2) between the co-crystallized and redocked inhibitor molecules in each case [49][50][51][52][53][54][55] . Moreover, the superimposed docked structure with the crystal structure was presented for each validation process in the supplementary data (Fig.…”

Section: Docking Studiesmentioning

confidence: 95%

Robust antiviral activity of commonly prescribed antidepressants against emerging coronaviruses: in vitro and in silico drug repurposing studies

Kutkat

Moatasim

Al‐Karmalawy

et al. 2022

Sci Rep

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During the current coronavirus disease 2019 (COVID-19) pandemic, symptoms of depression are commonly documented among both symptomatic and asymptomatic quarantined COVID-19 patients. Despite that many of the FDA-approved drugs have been showed anti-SARS-CoV-2 activity in vitro and remarkable efficacy against COVID-19 in clinical trials, no pharmaceutical products have yet been declared to be fully effective for treating COVID-19. Antidepressants comprise five major drug classes for the treatment of depression, neuralgia, migraine prophylaxis, and eating disorders which are frequently reported symptoms in COVID-19 patients. Herein, the efficacy of eight frequently prescribed FDA-approved antidepressants on the inhibition of both SARS-CoV-2 and MERS-CoV was assessed. Additionally, the in vitro anti-SARS-CoV-2 and anti-MERS-CoV activities were evaluated. Furthermore, molecular docking studies have been performed for these drugs against the spike (S) and main protease (Mpro) pockets of both SARS-CoV-2 and MERS-CoV. Results showed that Amitriptyline, Imipramine, Paroxetine, and Sertraline had potential anti-viral activities. Our findings suggested that the aforementioned drugs deserve more in vitro and in vivo studies targeting COVID-19 especially for those patients suffering from depression.

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Section: Docking Studiesmentioning

confidence: 95%

Robust antiviral activity of commonly prescribed antidepressants against emerging coronaviruses: in vitro and in silico drug repurposing studies

Kutkat

Moatasim

Al‐Karmalawy

et al. 2022

Sci Rep

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“…We performed 100 ns MD simulations of the protein-ligand complexes obtained by molecular docking and compared them with the corresponding co-crystal inhibitors in each case [ 43 ]. This study used the GROMACS software (2020.6-MODIFIED version) running on Linux operating system [ 44 ].…”

Section: Methodsmentioning

confidence: 99%

Exploring the potential mechanism of emetine against coronavirus disease 2019 combined with lung adenocarcinoma: bioinformatics and molecular simulation analyses

et al. 2022

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Background Patients with lung adenocarcinoma (LUAD) may be more predisposed to coronavirus disease 2019 (COVID-19) and have a poorer prognosis. Currently, there is still a lack of effective anti-LUAD/COVID-19 drugs. Thus, this study aimed to screen for an effective anti-LUAD/COVID-19 drug and explore the potential mechanisms. Methods Firstly, we performed differentially expressed gene (DEG) analysis on LUAD transcriptome profiling data in The Cancer Genome Atlas (TCGA), where intersections with COVID-19-related genes were screened out. Then, we conducted Cox proportional hazards analyses on these LUAD/COVID-19 DEGs to construct a risk score. Next, LUAD/COVID-19 DEGs were uploaded on Connectivity Map to obtain drugs for anti-LUAD/COVID-19. Finally, we used network pharmacology, molecular docking, and molecular dynamics (MD) simulation to explore the drug’s therapeutic targets and potential mechanisms for anti-LUAD/COVID-19. Results We identified 230 LUAD/COVID-19 DEGs and constructed a risk score containing 7 genes (BTK, CCL20, FURIN, LDHA, TRPA1, ZIC5, and SDK1) that could classify LUAD patients into two risk groups. Then, we screened emetine as an effective drug for anti-LUAD/COVID-19. Network pharmacology analyses identified 6 potential targets (IL6, DPP4, MIF, PRF1, SERPING1, and SLC6A4) for emetine in anti-LUAD/COVID-19. Molecular docking and MD simulation analyses showed that emetine exhibited excellent binding capacities to DDP4 and the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Conclusions This study found that emetine may inhibit the entry and replication of SARS-CoV-2 and enhance tumor immunity by bounding to DDP4 and Mpro.

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“…Three protein–protein docking studies were conducted to describe the possible interactions of three SARS-CoV-2 Egyptian strains, hCoV-19/Egypt/NRC-03/2020 (B.1 lineage), hCoV-19/Egypt/NRC-369/2021 (C.36.3 lineage), and hCoV-19/Egypt/NRC-6071/2021 (C.36 lineage), respectively, with the hACE2 receptor. The MOE 2019.0102 drug design suite [ 20 ] was used to carry out the docking studies to examine the binding affinities and modes for each of the three SARS-CoV-2 Egyptian strains with the hACE2 receptor extracted from the spike receptor-binding domain (PDB ID: 7DDN). We confirmed inhibitory potentials as well.…”

Section: Methodsmentioning

confidence: 99%

Insight into Genetic Characteristics of Identified SARS-CoV-2 Variants in Egypt from March 2020 to May 2021

et al. 2022

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Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first detected in Egypt in February 2020. Data about the prevalence rates of the SARS-CoV-2 lineages are relatively scarce. To understand the genetic characteristics of SARS-CoV-2 in Egypt during several waves of the pandemic, we analyzed sequences of 1256 Egyptian SARS-CoV-2 full genomes from March 2020 to May 2021. From one wave to the next, dominant strains have been observed to be replaced by other dominant strains. We detected an emerging lineage of SARS-CoV-2 in Egypt that shares mutations with the variant of concern (VOC). The neutralizing capacity of sera collected from cases infected with C.36.3 against dominant strains detected in Egypt showed a higher cross reactivity of sera with C.36.3 compared to other strains. Using in silico tools, mutations in the spike of SARS-CoV-2 induced a difference in binding affinity to the viral receptor. The C.36 lineage is the most dominant SARS-CoV-2 lineage in Egypt, and the heterotrophic antigenicity of SARS-CoV-2 variants is asymmetric. These results highlight the value of genetic and antigenic analyses of circulating strains in regions where published sequences are limited.

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In vitro and computational insights revealing the potential inhibitory effect of Tanshinone IIA against influenza A virus

Cited by 48 publications

References 62 publications

Robust antiviral activity of commonly prescribed antidepressants against emerging coronaviruses: in vitro and in silico drug repurposing studies

Robust antiviral activity of commonly prescribed antidepressants against emerging coronaviruses: in vitro and in silico drug repurposing studies

Exploring the potential mechanism of emetine against coronavirus disease 2019 combined with lung adenocarcinoma: bioinformatics and molecular simulation analyses

Insight into Genetic Characteristics of Identified SARS-CoV-2 Variants in Egypt from March 2020 to May 2021

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