Inhibitory effect of anti-HIV compounds extracted from Indian medicinal plants to retard the replication and transcription process of SARS-CoV-2: an insight from molecular docking and MD-simulation studies

HCV is a hepatotropic RNA virus recognized for its frequent virulence and fatality worldwide. Despite many vaccine development programs underway, researchers are on a quest for natural bioactive compounds due to their multivalent efficiencies against viral infections, considering which the current research aimed to figure out the target-specificity and therapeutic potentiality of α, β, and δ subunits of amyrin, as novel bioactive components against the HCV influx mechanism. Initially, the novelty of amyrin subunits was conducted from 203 pharmacophores, comparing their in-silico pharmacokinetic and pharmacodynamic profiles. Besides, the best active site of CD81 was determined following the quantum tunneling algorithm. The molecular dynamic simulation was conducted (100 ns) following the molecular docking steps to reveal the parameters- RMSD (Å); Cα; RMSF (Å); MolSA (Å 2 ); Rg (nm); PSA (Å); SASA (Å 2 ), and the MM-GBSA dG binding scores. Besides, molecular strings of CD81, along with the co-expressed genes, were classified, as responsible for encoding CD81-mediated protein clusters during HCV infection, resulting in the potentiality of amyrins as targeted prophylactics in HCV infection. Finally, in vivo profiling of the oxidative stress marker, liver-specific enzymes, and antioxidant markers was conducted in the DMN-induced mice model, where β -amyrin scored the most significant values in all aspects.

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“…6 D). Similar findings have been reported in several recent pieces of literature (Dutta et al 2021 ).…”

Section: Discussionsupporting

confidence: 92%

Target-specificity of different amyrin subunits in impeding HCV influx mechanism inside the human cells considering the quantum tunnel profiles and molecular strings of the CD81 receptor: a combined in silico and in vivo study

Jabin

Uddin

Azad

et al. 2023

In Silico Pharmacol.

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“…The repurposing potential of 34 bioactive terpenes and their derivatives to Mpro and PLpro was also predicted by docking and MM/PBSA calculations . Other MM/PB(GB)SA-based drug repurposing works considering two or more targets include studies in the literature. − …”

Section: Methods and Approachesmentioning

confidence: 99%

Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

Gao¹,

Wang²,

Chen³

et al. 2022

Chem. Rev.

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Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus–host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein–protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.

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“…GL and 18β-glycyrrhetinic acid induce the expression of nitric oxide synthase in macrophages to enhance the production of nitric oxide. Various studies also described the role of GL in treating HIV-1 patients as it enhances the production of chemokines. , …”

Section: Medicinal Plants Used the Most Traditionally In India And Ch...mentioning

confidence: 99%

A Reappraisal of the Antiviral Properties of and Immune Regulation through Dietary Phytochemicals

Thakur,

Singh,

Kumar

et al. 2023

ACS Pharmacol. Transl. Sci.

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In the present era of the COVID-19 pandemic, viral infections remain a major cause of morbidity and mortality worldwide. In this day and age, viral infections are rampant and spreading rapidly. Among the most aggressive viral infections are ebola, AIDS (acquired immunodeficiency syndrome), influenza, and SARS (severe acute respiratory syndrome). Even though there are few treatment options for viral diseases, most of the antiviral therapies are ineffective owing to frequent mutations, the development of more aggressive strains, drug resistance, and possible side effects. Traditionally, herbal remedies have been used by healers, including for dietary and medicinal purposes. Many clinical and scientific studies have demonstrated the therapeutic potential of plant-derived natural compounds. Because of unsafe practices like blood transfusions and organ transplants from infected patients, medical supply contamination. Our antiviral therapies cannot achieve sterile immunity, and we have yet to find a cure for these pernicious infections. Herbs have been shown to improve therapeutic efficacy against a wide variety of viral diseases because of their high concentration of immunomodulatory phytochemicals (both immunoinhibitory and anti-inflammatory). Combined with biotechnology, this folk medicine system can lead to the development of novel antiviral drugs and therapies. In this Review, we will summarize some selected bioactive compounds with probable mechanisms of their antiviral actions, focusing on the immunological axis of these compounds.

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Inhibitory effect of anti-HIV compounds extracted from Indian medicinal plants to retard the replication and transcription process of SARS-CoV-2: an insight from molecular docking and MD-simulation studies

Cited by 19 publications

References 47 publications

Target-specificity of different amyrin subunits in impeding HCV influx mechanism inside the human cells considering the quantum tunnel profiles and molecular strings of the CD81 receptor: a combined in silico and in vivo study

Target-specificity of different amyrin subunits in impeding HCV influx mechanism inside the human cells considering the quantum tunnel profiles and molecular strings of the CD81 receptor: a combined in silico and in vivo study

Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2

A Reappraisal of the Antiviral Properties of and Immune Regulation through Dietary Phytochemicals

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