Multi-target potential of Indian phytochemicals against SARS-CoV-2: A docking, molecular dynamics and MM-GBSA approach extended to Omicron B.1.1.529.

Roshni, Jency; Vaishali, R; Ganesh, KS; Dharani, N; Alzahrani, Khalid J.; Banjer, Hamsa Jameel; Al-Ghamdi, Ali; Theyab, Abdulrahman; Ahmed, Shiek S. S. J.; Patil, Shankargouda

doi:10.1016/j.jiph.2022.05.002

Cited by 18 publications

(19 citation statements)

References 40 publications

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“…A recent study based on computational biology analysis reported that plant-based medicines like Calanolides A, Holy Basil, Kuwanon-L, and Patentiflorin A could be regarded as potential anti-HIV viral medicines which can also be administered against SARS-CoV-2. Some studies highlighted that inhibitory machinery blocking the binding of host cell receptors to viruses and inhibiting the cellular entry of viral protein could be an effective therapeutic target [147,148]. However, experimental results are yet to be done to validate the above-mentioned therapeutic options.…”

Section: Discussionmentioning

confidence: 99%

Epigenetic perspectives associated with COVID-19 infection and related cytokine storm: an updated review

et al. 2023

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Purpose The COVID-19 pandemic caused by the novel Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) has put the world in a medical crisis for the past three years; nearly 6.3 million lives have been diminished due to the virus outbreak. This review aims to update the recent findings on COVID-19 infections from an epigenetic scenario and develop future perspectives of epi-drugs to treat the disease. Methods Original research articles and review studies related to COVID-19 were searched and analyzed from the Google Scholar/PubMed/Medline databases mainly between 2019 and 2022 to brief the recent work. Results Numerous in-depth studies of the mechanisms used by SARS-CoV-2 have been going on to minimize the consequences of the viral outburst. Angiotensin-Converting Enzyme 2 receptors and Transmembrane serine protease 2 facilitate viral entry to the host cells. Upon internalization, it uses the host machinery to replicate viral copies and alter the downstream regulation of the normal cells, causing infection-related morbidities and mortalities. In addition, several epigenetic regulations such as DNA methylation, acetylation, histone modifications, microRNA, and other factors (age, sex, etc.) are responsible for the regulations of viral entry, its immune evasion, and cytokine responses also play a major modulatory role in COVID-19 severity, which has been discussed in detail in this review. Conclusion Findings of epigenetic regulation of viral pathogenicity open a new window for epi-drugs as a possible therapeutical approach against COVID-19.

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Section: Discussionmentioning

confidence: 99%

Epigenetic perspectives associated with COVID-19 infection and related cytokine storm: an updated review

et al. 2023

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“…Some molecular docking studies showed a high affinity of favipiravir to the main Mpro protease of SARS-CoV-2. 74,75…”

Section: Promising Targets For Pharmacological Action On Sars-cov-2mentioning

confidence: 99%

Main and papain-like proteases as prospective targets for pharmacological treatment of coronavirus SARS-CoV-2

Yevsieieva,

Lohachova,

Kyrychenko

et al. 2023

RSC Adv.

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“…Taking curcumin as a reference, a novel cyclohexanone compound (ZINC07333416) was recently proposed as a potential agent against the SARS‐CoV‐2 main protease based on computational studies 17 . The phytocompounds 4,8‐dihydroxysesamin and arboreal from Gmelina arborea can be used against Omicron and WT SGp 18 . Polyphenols such as quercetin and luteolin restrict SARS‐CoV entry into Vero E6 cells with a higher efficacy, with EC 50 values of 10 μM and 83 μM, respectively 19 .…”

Section: Introductionmentioning

confidence: 99%

“…17 The phytocompounds 4,8-dihydroxysesamin and arboreal from Gmelina arborea can be used against Omicron and WT SGp. 18 Polyphenols such as quercetin and luteolin restrict SARS-CoV entry into Vero E6 cells with a higher efficacy, with EC 50 values of 10 μM and 83 μM, respectively. 19 Similarly, emodin found in rhubarb roots (Rheum officinale)…”

mentioning

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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Multi-target potential of Indian phytochemicals against SARS-CoV-2: A docking, molecular dynamics and MM-GBSA approach extended to Omicron B.1.1.529.

Cited by 18 publications

References 40 publications

Epigenetic perspectives associated with COVID-19 infection and related cytokine storm: an updated review

Epigenetic perspectives associated with COVID-19 infection and related cytokine storm: an updated review

Main and papain-like proteases as prospective targets for pharmacological treatment of coronavirus SARS-CoV-2

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

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