Anti-COVID-19 terpenoid from marine sources: A docking, admet and molecular dynamics study

Sepay, Nayim; Sekar, Aishwarya; Halder, Umesh Chandra; Alarifi, Abdullah; Afzal, Mohd

doi:10.1016/j.molstruc.2020.129433

Cited by 57 publications

(46 citation statements)

References 38 publications

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“…Similarly, a previously established binding mode for Lopinavir and Ritonavir against 3CL pro was obtained during our analysis which provides support for the binding mode of identified Hit compounds (Bolcato et al, 2020;. Recently, a terpenoid (T3) from marine sponge Cacospongia mycofijiensis was also identified through in silico studies against SARS CoV-2 3CL pro showing similar binding interactions like our hit molecules (Sepay et al, 2021). A recent pharmacophore-based study was published where authors screened the same MNP library against SARS-CoV-2 3CL pro (Gentile et al, 2020) and identified 17 different hits with different scaffolds.…”

Section: Discussionsupporting

confidence: 84%

Computational Simulations Identified Marine-Derived Natural Bioactive Compounds as Replication Inhibitors of SARS-CoV-2

et al. 2021

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The rapid spread of COVID-19, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a worldwide health emergency. Unfortunately, to date, a very small number of remedies have been to be found effective against SARS-CoV-2 infection. Therefore, further research is required to achieve a lasting solution against this deadly disease. Repurposing available drugs and evaluating natural product inhibitors against target proteins of SARS-CoV-2 could be an effective approach to accelerate drug discovery and development. With this strategy in mind, we derived Marine Natural Products (MNP)-based drug-like small molecules and evaluated them against three major target proteins of the SARS-CoV-2 virus replication cycle. A drug-like database from MNP library was generated using Lipinski’s rule of five and ADMET descriptors. A total of 2,033 compounds were obtained and were subsequently subjected to molecular docking with 3CLpro, PLpro, and RdRp. The docking analyses revealed that a total of 14 compounds displayed better docking scores than the reference compounds and have significant molecular interactions with the active site residues of SARS-CoV-2 virus targeted proteins. Furthermore, the stability of docking-derived complexes was analyzed using molecular dynamics simulations and binding free energy calculations. The analyses revealed two hit compounds against each targeted protein displaying stable behavior, binding affinity, and molecular interactions. Our investigation identified two hit compounds against each targeted proteins displaying stable behavior, higher binding affinity and key residual molecular interactions, with good in silico pharmacokinetic properties, therefore can be considered for further in vitro studies.

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Section: Discussionsupporting

confidence: 84%

Computational Simulations Identified Marine-Derived Natural Bioactive Compounds as Replication Inhibitors of SARS-CoV-2

et al. 2021

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“…The top three phytoligands from each medicinal plants showing good binding affinity and interaction with the M pro and ACE2 were subjected to 25ns of MD simulation analysis using Gromacs 5.1.4 simulation package ( Sepay et al, 2020 ). The topology parameter files of the proteins were generated with GROMOS96 all force filed and the ligand topology file was generated using PRODRG2 web server.…”

Section: Methodsmentioning

confidence: 99%

Promising phytochemicals of traditional Indian herbal steam inhalation therapy to combat COVID-19 – An in silico study

Gowrishankar

Muthumanickam

Kamaladevi

et al. 2021

Food and Chemical Toxicology

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“…Sulphated polysaccharides from marine microorganisms like sea cucumber Stichopus japonicus and Fucoidan from brown algae can have an excellent inhibitory effect on SARS-CoV-2 [184]. Recent reports revealed a T3 terpenoid isolated from marine sponge Cacospongia mycofinensis inhibits the action of Mpro via hydrogen bond interactions [185].…”

Section: Microbial Metabolites and Compounds From Marine Microorganisms Targeted Against Sars-cov-2mentioning

confidence: 99%

Factors for COVID-19 Infection that Govern the Severity of Illness

Ghosh¹,

Sarkar

Sepay³

et al. 2021

SciMed. J.

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Coronaviruses have been posing a serious threat to mammals and birds and a new class of SARS-CoV is creating havoc to the world after its first incidence in Wuhan City in China in December 2019. These viruses are mainly responsible for causing serious respiratory tract infections which generally appear initially as the common cold and can be lethal just like SARS-CoV. The problems seem to vary and worsen from one person to another depending on age, gender, ethnicity, blood groups, host genetics, and associated comorbidities. Complications should also arise as this virus keeps mutating and evolving. This review points out the various underlying causes behind the severity of the illness and the mechanisms associated with it. This review will help society to understand the risks and severities associated with COVID-19. Individuals with health complexities and predispositions listed in this review are the most vulnerable in terms of severity and should take every possible measure to protect themselves from getting infected. As a consequence, this will lead to a decrease in mortality rates arising from COVID-19. Doi: 10.28991/SciMedJ-2021-0302-9 Full Text: PDF

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Anti-COVID-19 terpenoid from marine sources: A docking, admet and molecular dynamics study

Cited by 57 publications

References 38 publications

Computational Simulations Identified Marine-Derived Natural Bioactive Compounds as Replication Inhibitors of SARS-CoV-2

Computational Simulations Identified Marine-Derived Natural Bioactive Compounds as Replication Inhibitors of SARS-CoV-2

Promising phytochemicals of traditional Indian herbal steam inhalation therapy to combat COVID-19 – An in silico study

Factors for COVID-19 Infection that Govern the Severity of Illness

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