Deciphering antiviral efficacy of malaria box compounds against malaria exacerbating viral pathogens- Epstein Barr virus and SARS-CoV-2, an in silico study

Indari, Omkar; Singh, Ajit; Tiwari, Deeksha; Jha, Hem Chandra; Jha, Anupam Nath

doi:10.1016/j.medidd.2022.100146

Cited by 17 publications

(14 citation statements)

References 63 publications

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“…Nowadays, targeted drug repurposing represents a very useful strategy to identify libraries of pre-existing molecules or approved drugs that could prevent COVID-19 [ 60 , 61 ].…”

Section: Discussionmentioning

confidence: 99%

In Silico Screening of Drugs That Target Different Forms of E Protein for Potential Treatment of COVID-19

et al. 2023

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Recently the E protein of SARS-CoV-2 has become a very important target in the potential treatment of COVID-19 since it is known to regulate different stages of the viral cycle. There is biochemical evidence that E protein exists in two forms, as monomer and homopentamer. An in silico screening analysis was carried out employing 5852 ligands (from Zinc databases), and performing an ADMET analysis, remaining a set of 2155 compounds. Furthermore, docking analysis was performed on specific sites and different forms of the E protein. From this study we could identify that the following ligands showed the highest binding affinity: nilotinib, dutasteride, irinotecan, saquinavir and alectinib. We carried out some molecular dynamics simulations and free energy MM–PBSA calculations of the protein–ligand complexes (with the mentioned ligands). Of worthy interest is that saquinavir, nilotinib and alectinib are also considered as a promising multitarget ligand because it seems to inhibit three targets, which play an important role in the viral cycle. On the other side, saquinavir was shown to be able to bind to E protein both in its monomeric as well as pentameric forms. Finally, further experimental assays are needed to probe our hypothesis derived from in silico studies.

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“…Nowadays, targeted drug repurposing represents a very useful strategy to identify libraries of pre-existing molecules or approved drugs that could prevent COVID-19 [ 60 , 61 ].…”

Section: Discussionmentioning

confidence: 99%

In Silico Screening of Drugs That Target Different Forms of E Protein for Potential Treatment of COVID-19

et al. 2023

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“…3.13.3 Molecular dynamics simulation. Recent years have seen a significant increase in the application of molecular dynamic (MD) simulation for a better understanding of the structure, mutation, dynamic behavior of protein 92 and protein-ligand interaction. 93 The time-dependent behavior of a system is precisely recorded by this simulation analysis.…”

Section: Inhibition Properties Of Coumarin Derivatives On the Fibrill...mentioning

confidence: 99%

In vitro interactions of esculin and esculetin with bovine hemoglobin alter its structure and inhibit aggregation: insights from spectroscopic and computational studies

et al. 2023

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“…32 Recent computational studies were conducted to decipher the antiviral properties of malaria box compounds against SARS-CoV-2 and Epstein-Barr virus. 33 Molecular dynamics (MD) simulations supported the notion that phytochemicals such as 26-deoxyactein, 25-O-anhydrocimigenol 3-O-β-D-xylopyranoside, tomentosolic acid, timosaponin A-I, shizukaol A, limonin, 25-O-anhydrocimigenol 3-Oα-l-arabinopyranoside, and asperagenin potentially target the catalytic sites of the nsp13, nsp14, and nsp15 proteins. 34 In silico methods are very useful in modeling epidemiology-based data, identifying targeted therapies for novel drug design, repurposing drugs, predicting vaccine epitopes, and formulating diagnostic models for COVID-19.…”

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confidence: 94%

“…Compounds derived from Curcuma longa exhibited more effective binding to the spike protein's S1 domain than the compound VE607 and to the RNA‐dependent RNA polymerase (RdRp) protein than ribavirin and remdesivir 32 . Recent computational studies were conducted to decipher the antiviral properties of malaria box compounds against SARS‐CoV‐2 and Epstein–Barr virus 33 . Molecular dynamics (MD) simulations supported the notion that phytochemicals such as 26‐deoxyactein, 25‐ O ‐anhydrocimigenol 3‐ O ‐β‐ d ‐xylopyranoside, tomentosolic acid, timosaponin A–I, shizukaol A, limonin, 25‐ O ‐anhydrocimigenol 3‐ O ‐α‐l‐arabinopyranoside, and asperagenin potentially target the catalytic sites of the nsp13, nsp14, and nsp15 proteins 34 .…”

Section: Introductionmentioning

confidence: 99%

Computational studies on the interaction of Omicron subvariants (BA.1, BA.2, and BA.3) with ACE2 and polyphenols

Vardhan

Sahoo

2023

Phytochemical Analysis

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IntroductionThe SARS‐CoV‐2 Omicron variant BA.2 is spreading widely across the globe. The World Health Organization (WHO) designated BA.2 as a variant of concern due to its high transmission rate and pathogenicity. To elucidate the structural changes caused by mutations, we conducted a comparative analysis of BA.2 with variants BA.1 and BA.3.ObjectiveIn the present study, we aimed to investigate the interactions of the spike glycoprotein receptor‐binding domain (SGp RBD) of Omicron variants BA.1, BA.2, and BA.3 with the human receptor hACE2. Further, a library of 233 polyphenols was screened by molecular docking with the SGp RBDs of Omicron variants BA.1, BA.2, and BA.3.MethodsProtein–protein and protein–ligand molecular docking simulations were performed with AutoDock Vina and the ClusPro 2.0 server, respectively. The protein–ligand interactions were evaluated by BIOVIA Discovery Studio and ChimeraX 1.4. The molecular dynamics simulations for 100 ns were performed using GROMACS 2021.ResultsCompared to other variants of concern, the structural changes in Omicron caused by mutations at key positions improved its ability to cause infection. Despite multiple mutations, many important polyphenols bind effectively at the RBDs of Omicron variants, with the required pharmacokinetic and ADME features and obeying the Lipinski rule.ConclusionEven though Omicron variants have multiple mutations and their transmission rate is relatively high, the computed binding affinities of lead polyphenols like epigallocatechin‐3‐O‐gallate (EGCG) and luteolin‐7‐O‐glucuronide (L7G) indicate that traditional medicines and proper immunity booster diets may be useful in the long‐term fight against SARS‐CoV‐2.

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Deciphering antiviral efficacy of malaria box compounds against malaria exacerbating viral pathogens- Epstein Barr virus and SARS-CoV-2, an in silico study

Cited by 17 publications

References 63 publications

In Silico Screening of Drugs That Target Different Forms of E Protein for Potential Treatment of COVID-19

In Silico Screening of Drugs That Target Different Forms of E Protein for Potential Treatment of COVID-19

In vitro interactions of esculin and esculetin with bovine hemoglobin alter its structure and inhibit aggregation: insights from spectroscopic and computational studies

Computational studies on the interaction of Omicron subvariants (BA.1, BA.2, and BA.3) with ACE2 and polyphenols

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