scholarly journals Tapping the Unexplored Potential of Marine Fungi and Edible Mushrooms for in Silico Screening of Anti-Viral Bioactive Compounds Against SARS-CoV-2 for Rapid Development of Nutraceuticals

2020 ◽  
Author(s):  
Amit Kumar Srivastav ◽  
Jyoti Jaiswal ◽  
Umesh Kumar
Keyword(s):  
Natural Resources ◽  
Bioactive Compounds ◽  
In Silico ◽  
Marine Fungi ◽  
Edible Mushroom ◽  
Edible Mushrooms ◽  
Strong Potential ◽  
Medicinal Compounds ◽  
Main Protease ◽  
In Silico Studies

<p>Severe Acute Respiratory Syndrome Coronavirus 2 (SARS- CoV-2) affects human respiratory function that causes COVID-19 disease. COVID-19 has spread rapidly all over the world and became a pandemic within no time. Therefore, it is the need of hour to screen potential lead candidates from natural resources like edible mushrooms and marine fungi. These natural resources are very less explored till now and known to be the source for many medicinal compounds with several health benefits. These medicinal compounds can be easily exploited for the faster development of nutraceuticals for controlling SARS-CoV-2 infections. Our in-silico research suggests that bioactive compounds originating from mushroom and marine fungi shows strong potential to interact with ACE2 receptor or main protease of SARS-CoV-2, showing the inhibition activity towards the enzymatic protease. We performed a series of in silico studies for the validation of our results, which includes Molecular docking, drug likeness property investigation by Swiss ADME tools, MD simulation, and thermodynamically stable free binding energy calculation. Overall, these results suggest that Ganodermadiol and Heliantriol F bioactive compounds originating from edible mushroom has strong potential to be developed as low-cost nutraceutical against SARS-CoV-2 viral infection. The drug candidate isolated from marine fungi and edible mushroom are highly unexplored for the development of potential alternative drug against SARS-CoV-2 virus with minimum side effects. That is why we decided to screen some active metabolites from the marine fungi and mushrooms, which offer some encouraging results. Though our in-silico studies of these compounds are showing a promising result against SARS-CoV-2 main protease and ACE2 receptor binding domain, the effectiveness of these bioactive compounds should be further validated by proper clinical trials.</p>

scholarly journals Tapping the Unexplored Potential of Marine Fungi and Edible Mushrooms for in Silico Screening of Anti-Viral Bioactive Compounds Against SARS-CoV-2 for Rapid Development of Nutraceuticals

2020 ◽  
Author(s):  
Amit Kumar Srivastav ◽  
Jyoti Jaiswal ◽  
Umesh Kumar
Keyword(s):  
Natural Resources ◽  
Bioactive Compounds ◽  
In Silico ◽  
Marine Fungi ◽  
Edible Mushroom ◽  
Edible Mushrooms ◽  
Strong Potential ◽  
Medicinal Compounds ◽  
Main Protease ◽  
In Silico Studies

<p>Severe Acute Respiratory Syndrome Coronavirus 2 (SARS- CoV-2) affects human respiratory function that causes COVID-19 disease. COVID-19 has spread rapidly all over the world and became a pandemic within no time. Therefore, it is the need of hour to screen potential lead candidates from natural resources like edible mushrooms and marine fungi. These natural resources are very less explored till now and known to be the source for many medicinal compounds with several health benefits. These medicinal compounds can be easily exploited for the faster development of nutraceuticals for controlling SARS-CoV-2 infections. Our in-silico research suggests that bioactive compounds originating from mushroom and marine fungi shows strong potential to interact with ACE2 receptor or main protease of SARS-CoV-2, showing the inhibition activity towards the enzymatic protease. We performed a series of in silico studies for the validation of our results, which includes Molecular docking, drug likeness property investigation by Swiss ADME tools, MD simulation, and thermodynamically stable free binding energy calculation. Overall, these results suggest that Ganodermadiol and Heliantriol F bioactive compounds originating from edible mushroom has strong potential to be developed as low-cost nutraceutical against SARS-CoV-2 viral infection. The drug candidate isolated from marine fungi and edible mushroom are highly unexplored for the development of potential alternative drug against SARS-CoV-2 virus with minimum side effects. That is why we decided to screen some active metabolites from the marine fungi and mushrooms, which offer some encouraging results. Though our in-silico studies of these compounds are showing a promising result against SARS-CoV-2 main protease and ACE2 receptor binding domain, the effectiveness of these bioactive compounds should be further validated by proper clinical trials.</p>

scholarly journals Computational Studies to Identify Potential Main Protease Inhibitors for SARS-CoV-2

2020 ◽  
Author(s):  
M. Elizabeth Sobhia ◽  
Ketan Ghosh ◽  
Srikanth Sivangula ◽  
Harmanpreet Singh ◽  
Siva Kumar
Keyword(s):  
In Silico ◽  
Experimental Studies ◽  
Binding Pocket ◽  
Vital Role ◽  
Active Site Residues ◽  
X Ray Diffraction ◽  
Main Protease ◽  
Docking Protocol ◽  
In Silico Studies

The Coronavirus pandemic has put the entire humanity in total shock and has forced the world to go under total lockdown. It is time for the entire scientific community across the globe to find a solution for this deadly and unseen enemy. In silico studies play a vital role in situations like this, as experimental studies are not feasible by all researchers particularly with relevance to BSL4 procedures. In this study, using the high resolution crystal structure of SARS-CoV-2 main protease (PDB: 5R82), we have identified molecules which can potentially inhibit the main protease (Mpro). We used a three-tier docking protocol making use of three different databases. We analysed the residues which are lying near the ligand binding pocket of the main protease structure and it shows a wide cavity, which can accommodate chemically diverse ligands, occupying different sub-pockets. Using the small fragment bound in the 5R82, we have identified several larger molecules whose functional groups make interactions with the active site residues covering. This study also presumably steers the structure determination of many ligand-main protease complexes using x- ray diffraction methods. These molecules can be used as ‘in silico leads’ and further be explored in the development of SARS-CoV-2 drugs.

scholarly journals Computational Studies to Identify Potential Main Protease Inhibitors for SARS-CoV-2

2020 ◽  
Author(s):  
M. Elizabeth Sobhia ◽  
Ketan Ghosh ◽  
Srikanth Sivangula ◽  
Harmanpreet Singh ◽  
Siva Kumar
Keyword(s):  
In Silico ◽  
Experimental Studies ◽  
Binding Pocket ◽  
Vital Role ◽  
Active Site Residues ◽  
X Ray Diffraction ◽  
Main Protease ◽  
Docking Protocol ◽  
In Silico Studies

The Coronavirus pandemic has put the entire humanity in total shock and has forced the world to go under total lockdown. It is time for the entire scientific community across the globe to find a solution for this deadly and unseen enemy. In silico studies play a vital role in situations like this, as experimental studies are not feasible by all researchers particularly with relevance to BSL4 procedures. In this study, using the high resolution crystal structure of SARS-CoV-2 main protease (PDB: 5R82), we have identified molecules which can potentially inhibit the main protease (Mpro). We used a three-tier docking protocol making use of three different databases. We analysed the residues which are lying near the ligand binding pocket of the main protease structure and it shows a wide cavity, which can accommodate chemically diverse ligands, occupying different sub-pockets. Using the small fragment bound in the 5R82, we have identified several larger molecules whose functional groups make interactions with the active site residues covering. This study also presumably steers the structure determination of many ligand-main protease complexes using x- ray diffraction methods. These molecules can be used as ‘in silico leads’ and further be explored in the development of SARS-CoV-2 drugs.

Activity of Thiazine substituted 9-anilinoacridines against Corona virus (COVID19): An In-silico approach

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 482-490
Author(s):  
Kalirajan Rajagopal ◽  
Potlapati Varakumar ◽  
Baliwada Aparna ◽  
Vulsi Bodhya Sri ◽  
Gowramma Byran ◽  
...  
Keyword(s):  
In Silico ◽  
Binding Free Energy ◽  
Viral Disease ◽  
Docking Studies ◽  
Binding Modes ◽  
Main Protease ◽  
In Silico Admet ◽  
In Silico Studies ◽  
Life Threatening ◽  
Similar Mode

Coronavirus Disease 2019 (COVID-19), a life-threatening viral disease affected first in Wuhan, China, and quickly spread to more than 200 countries in the world in the year 2020. So many scientists are trying to discover novel drugs and vaccines for coronavirus and treatment for COVID-19. In the present article, in-silico studies have been performed to explore the binding modes of Thiazine substituted 9-anilinoacridines (1a-z) against SARS CoV 2 main protease (PDB id - 5R82) targeting the coronavirus using Schrodinger suit 2019-4. The molecular docking studies are performed by Glide module, in-silico ADMET screening was performed by Qik prop module, and the binding free energy of ligands was calculated using PRIME MM-GB/SA module of Schrodinger suite 2019-4, Maestro 21.2 version. From the in-silico results, Thiazine substituted 9-anilinoacridines like 1m, 1j, 1s and 1b are significantly active against SARS CoV 2 main protease with Glide score more than -5.4 when compared with the currently recommended drug for COVID19, Hydroxychloroquine (G score -5.47). The docking results of the Thiazine substituted 9-anilinoacridines exhibited similar mode of interactions with COVID19 and the residues GLN19, THR24, THR25, THR26, LEU27, HIE41, SER46, MET49, ASN142, GLN143, HIE164, MET165, ASP187, ARG188 and GLN189, play a crucial role in binding with ligands.

Antidiabetic bioactive compounds from Tetrastigma angustifolia (Roxb.) Deb and Oxalis debilis Kunth.: Validation of ethnomedicinal claim by in vitro and in silico studies

2021 ◽  
Vol 143 ◽  
pp. 164-175
Author(s):  
Julfikar Ali Junejo ◽  
Kamaruz Zaman ◽  
Mithun Rudrapal ◽  
Ismail Celik ◽  
Emmanuel Ifeanyi Attah
Keyword(s):  
Bioactive Compounds ◽  
In Silico ◽  
In Silico Studies

scholarly journals In silico studies of bioactive compounds from selected African plants with inhibitory activity against nitric oxide synthase and arginase implicated in asthma

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Haruna Isiyaku Umar ◽  
Tolulope Peter Saliu ◽  
Sunday Solomon Josiah ◽  
Adeola Ajayi ◽  
Jamilu Bala Danjuma
Keyword(s):  
Nitric Oxide ◽  
Nitric Oxide Synthase ◽  
Bioactive Compounds ◽  
In Silico ◽  
Active Sites ◽  
Binding Energies ◽  
Protein Database ◽  
In Silico Studies ◽  
Nos Inhibitors ◽  
Oxide Synthase

Abstract Background It is a known fact that arginine is a common substrate for arginase and nitric oxide synthase (NOS). However, an imbalance between both enzymes could lead to a change in airway responses. Reports suggest that increased activities of both enzymes could lead to airway hyper-responsiveness. Thus, the requests for NOS inhibitors that can also inhibit arginase as the elevated activities of both enzymes have detrimental consequence on airways in asthma. Bioactive compounds from Azadirachta indica, Crinum glaucum, and Mangifera indica are documented for anti-inflammatory, immunomodulatory, anti-histaminic, smooth-muscle relaxants, and anti-allergic potentials. However, the mechanisms of action of these bioactive compounds in conferring the aforementioned protections are not well characterized. The objective of this present study is to assess in silico inhibitory potentials of these bioactive compounds against NOS and arginase via binding at their active sites. The crystal structures of NOS and arginase were retrieved from the protein database, while the bioactive compounds were retrieved from PubChem. Drug-likeness of the selected bioactive compounds was assessed using DruLiTo software. The successful compounds were docked with active sites of enzymes using AutoDock Vina docking software, and the docked complexes were analyzed using LigPlot and protein-ligand profiler web server. Results The findings of the study revealed that the bioactive compounds from A. indica, C. glaucum, and M. indica were able to interact with the active sites of NOS and arginase with the exception of gallic acid (from M. indica) and nimbandiol (from A. indica); these compounds showed differential binding energies (kcal/mol) and a number of them had higher binding energies than l-arginine when docked with NOS. Conclusion Conclusively, the in silico analysis proposes that these compounds could prove to be probable anti-asthmatic drugs.

scholarly journals Activity of phytochemical constituents of Curcuma longa (turmeric) and Andrographis paniculata against coronavirus (COVID-19): an in silico approach

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Kalirajan Rajagopal ◽  
Potlapati Varakumar ◽  
Aparma Baliwada ◽  
Gowramma Byran
Keyword(s):  
Active Site ◽  
In Silico ◽  
Chemical Constituents ◽  
Curcuma Longa ◽  
Andrographis Paniculata ◽  
Significant Activity ◽  
Binding Modes ◽  
Main Protease ◽  
In Silico Admet ◽  
In Silico Studies

Abstract Background In early 2020, many scientists are rushing to discover novel drugs and vaccines against the coronavirus, and treatments for COVID-19, because coronavirus disease 2019 (COVID-19), a life-threatening viral disease, affected first in China and quickly spread throughout the world. In this article, in silico studies have been performed to explore the binding modes of chemical constituents for natural remedies like Curcuma longa (turmeric) and Andrographis paniculata against COVID-19 (PDB ID 5R82) targeting coronavirus using Schrodinger suit 2019-4. The molecular docking studies are performed by the Glide module, in silico ADMET screening was performed by the QikProp module, and binding energy of ligands was calculated using the Prime MM-GB/SA module. Results The chemical constituents from turmeric like cyclocurcumin and curcumin and from Andrographis paniculata like andrographolide and dihydroxy dimethoxy flavone are significantly binding with the active site of SARS CoV-2 main protease with Glide score more than − 6 when compared to the currently used drugs hydroxychloroquine (− 5.47) and nelfinavir (− 5.93). When compared to remdesivir (− 6.38), cyclocurcumin from turmeric is significantly more active. The docking results of the compounds exhibited similar mode of interactions with SARS CoV-2. Main protease and the residues THR24, THR25, THR26, LEU27, SER46, MET49, HIE41, GLN189, ARG188, ASP187, MET165, HIE164, PHE181, and THR54 play a crucial role in binding with ligands. Conclusion Based on in silico investigations, the chemical constituents from turmeric like cyclocurcumin and curcumin and from Andrographis paniculata like andrographolide and dihydroxy dimethoxy flavone, significantly binding with the active site of SARS CoV-2 main protease, may produce significant activity and be useful for further development.

scholarly journals Evaluation of Phytochemicals of Cassia occidentalis L. for their Binding Affinities to SARS-CoV-2 3C-Like Protease: An in Silico Approach

2020 ◽  
pp. 8-14
Author(s):  
Tohmina Afroze Bondhon ◽  
Md. Aynal Haque Rana ◽  
Anamul Hasan ◽  
Rownak Jahan ◽  
Khoshnur Jannat ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Virtual Screening ◽  
In Silico ◽  
Binding Affinities ◽  
Autodock Vina ◽  
Cassia Occidentalis ◽  
Main Protease ◽  
In Silico Studies ◽  
The World ◽  
Docking Approach

Aims: Corona virus SARS-CoV-2, otherwise known as COVID-19 has created a pandemic resulting in social and financial crisis throughout the world. The virus has no known drugs or vaccines for preventive or therapeutic purposes. The objective of the present study was to screen phytochemicals from Cassia occidentalis L. in virtual screening (in silico) studies to evaluate their potential of binding to the main 3C-like protease of the virus and so stop its replication. Study Design: Molecular docking approach was used for virtual screening studies. Place and Duration of Study: University of Development Alternative between April and July 2020. Methodology: Molecular docking (blind) were done with the help of Autodock Vina. We have used the pdb file (6LU7) of the main protease of SARS-CoV-2 3C-like protease or SARS-CoV-2 3CLpro (monomeric form) to study binding of the phytochemicals. Results: Of the nine phytochemicals studied, the C-glycosidic flavonoids, cassiaoccidentalins A-C demonstrated excellent binding affinities to the protease. The compounds bound to the active site of the protease with binding energy values of -8.2 to-8.4 kcal/mol. Conclusion: The in silico studies suggest that the compounds merit actual COVID-19 inhibitory tests and have potential for anti-COVID-19 use.

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