Prediction of SARS-CoV-2 main protease inhibitors in medicinal plant-derived compounds by molecular docking approach

2020 ◽  
Vol 3 (4) ◽  
pp. 79
Author(s):  
Sayma Farabi ◽  
Nihar Saha ◽  
Md Hasanuzzaman ◽  
Noushin Khan ◽  
Muhammad Haque
Keyword(s):  
Molecular Docking ◽  
Medicinal Plant ◽  
Protease Inhibitors ◽  
Main Protease ◽  
Docking Approach

scholarly journals Prediction of SARS-CoV-2 Main Protease Inhibitors from Several Medicinal Plant Compounds by Drug Repurposing and Molecular Docking Approach.

2020 ◽  
Author(s):  
Sayma Farabi ◽  
Nihar Ranjan Saha ◽  
Noushin Anika Khan ◽  
Md. Hasanuzzaman
Keyword(s):  
Molecular Docking ◽  
Medicinal Plant ◽  
Drug Repurposing ◽  
Effective Vaccine ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Virulent Strains ◽  
Main Protease ◽  
Docking Approach ◽  
Phytochemical Compounds

<div> <sup>Coronaviruses are endemic in humans and infections normally mild, such as the common cold but cross-species transmission has produced some unusually virulent strains which now causing viral pneumonia and in serious cases even acute respiratory distress syndrome and death. SARS-CoV-2 is the most threatening issue which leads the world to an uncertainty alongside thousands of regular death scenes. For this virus, death toll is increasing in. An effective vaccine to cure this virus is not yet available, thus requires concerted efforts at various scales. The viral Main Protease controls Coronavirus replication and is a proven drug discovery target for SARS-CoV-2. Here, comprehensive computational approaches including drug repurposing and molecular docking were employed to predict the efficacy of medicinal plant-based bioactive compounds against SARS-CoV-2 Mpro. Molecular docking was performed using PyRx-autodock vina to analyze the inhibition probability. MPP (6LU7) was docked with 90 phytochemical compounds and docking was analysed by PyRx-autodock vina, Pymol version 1.7.4.5 Edu, and Biovia Discovery Studio 4.5. Furthermore, ADME analysis along with analysis of toxicity was also investigated to check the pharmacokinetics and drug-likeness properties of the antiviral phytochemicals. Remdesivir and lopinavir were used as standards for comparison. Our analyses revealed that the top ten (Azadirachtin, -12.5kcal/mol; Rutin, -9 kcal/mol; Theaflavin, -9 kcal/mol; Astragalin, -8.8 kcal/mol; Isoquercitrin, -8.7 kcal/mol; Hyperoside, -8.6 kcal/mol; Baicalin, -8.4 kcal/mol; Saponin, -8.3 kcal/mol; Sennoside A, -8.3 kcal/mol; Aloin, -8.2 kcal/mol, while Remdesivir and Lopinavir showed -8.2 and -7.9 kcal/mol) hits might serve as potential anti- SARS-CoV-2 lead molecules for further optimization and drug development process to combat COVID-19. <br></sup></div><div><sup><br></sup></div>

scholarly journals Prediction of SARS-CoV-2 Main Protease Inhibitors from Several Medicinal Plant Compounds by Drug Repurposing and Molecular Docking Approach.

2020 ◽  
Author(s):  
Sayma Farabi ◽  
Nihar Ranjan Saha ◽  
Noushin Anika Khan ◽  
Md. Hasanuzzaman
Keyword(s):  
Molecular Docking ◽  
Medicinal Plant ◽  
Drug Repurposing ◽  
Effective Vaccine ◽  
Autodock Vina ◽  
Discovery Studio ◽  
Virulent Strains ◽  
Main Protease ◽  
Docking Approach ◽  
Phytochemical Compounds

<div> <sup>Coronaviruses are endemic in humans and infections normally mild, such as the common cold but cross-species transmission has produced some unusually virulent strains which now causing viral pneumonia and in serious cases even acute respiratory distress syndrome and death. SARS-CoV-2 is the most threatening issue which leads the world to an uncertainty alongside thousands of regular death scenes. For this virus, death toll is increasing in. An effective vaccine to cure this virus is not yet available, thus requires concerted efforts at various scales. The viral Main Protease controls Coronavirus replication and is a proven drug discovery target for SARS-CoV-2. Here, comprehensive computational approaches including drug repurposing and molecular docking were employed to predict the efficacy of medicinal plant-based bioactive compounds against SARS-CoV-2 Mpro. Molecular docking was performed using PyRx-autodock vina to analyze the inhibition probability. MPP (6LU7) was docked with 90 phytochemical compounds and docking was analysed by PyRx-autodock vina, Pymol version 1.7.4.5 Edu, and Biovia Discovery Studio 4.5. Furthermore, ADME analysis along with analysis of toxicity was also investigated to check the pharmacokinetics and drug-likeness properties of the antiviral phytochemicals. Remdesivir and lopinavir were used as standards for comparison. Our analyses revealed that the top ten (Azadirachtin, -12.5kcal/mol; Rutin, -9 kcal/mol; Theaflavin, -9 kcal/mol; Astragalin, -8.8 kcal/mol; Isoquercitrin, -8.7 kcal/mol; Hyperoside, -8.6 kcal/mol; Baicalin, -8.4 kcal/mol; Saponin, -8.3 kcal/mol; Sennoside A, -8.3 kcal/mol; Aloin, -8.2 kcal/mol, while Remdesivir and Lopinavir showed -8.2 and -7.9 kcal/mol) hits might serve as potential anti- SARS-CoV-2 lead molecules for further optimization and drug development process to combat COVID-19. <br></sup></div><div><sup><br></sup></div>

scholarly journals Main Protease Inhibitors and Drug Surface Hotspots for the Treatment of COVID-19: A Drug Repurposing and Molecular Docking Approach

2021 ◽  
pp. 111742
Author(s):  
Mahmudul Hasan ◽  
Md. Sorwer Alam Parvez ◽  
Kazi Faizul Azim ◽  
Md. Abdus Shukur Imran ◽  
Topu Raihan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Protease Inhibitors ◽  
Drug Repurposing ◽  
Main Protease ◽  
Docking Approach

Computational screening of dual inhibitors from FDA approved antiviral drugs on SARS-CoV-2 spike protein and the main protease using molecular docking approach

2021 ◽  
Vol 65 (02) ◽  
pp. 160-172
Author(s):  
Shanthi Sabarimurugan ◽  
Indu Purushothaman ◽  
Rajarajan Swaminathan ◽  
Arun Dharmarajan ◽  
Sudha Warrier ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Antiviral Drugs ◽  
Spike Protein ◽  
Computational Screening ◽  
Main Protease ◽  
Docking Approach ◽  
Dual Inhibitors

scholarly journals Main Protease Inhibitors and Drug Surface Hotspot for the Treatment of COVID-19: Drug Repurposing and Molecular Docking Approach

2020 ◽  
Author(s):  
Mahmudul Hasan ◽  
Md Sorwer Alam Parvez ◽  
Kazi Faizul Azim ◽  
Abdus Shukur Imran ◽  
Topu Raihan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Drug Repurposing ◽  
Pharmacokinetic Parameters ◽  
The Novel ◽  
Drug Candidates ◽  
Target Drug ◽  
Global Pandemic ◽  
Main Protease ◽  
Docking Approach ◽  
Repurposed Drugs

<div>The world is facing an unprecedented global pandemic caused by the novel SARS-CoV-2. In the absence</div><div>of a specific therapeutic agent to treat COVID-19 patients, the present study aimed to virtually screen out</div><div>the effective drug candidates from the approved main protease protein (MPP) inhibitors and their</div><div>derivatives for the treatment of SARS-CoV-2. Here, drug repurposing and molecular docking were</div><div>employed to screen approved MPP inhibitors and their derivatives. The approved MPP inhibitors against</div><div>HIV and HCV were prioritized, whilst hydroxychloroquine, favipiravir, remdesivir, and alpha-ketoamide</div><div>were studied as control. The target drug surface hotspot was also investigated through the molecular</div><div>docking technique. ADME analysis was conducted to understand the pharmacokinetics and drug-likeness</div><div>of the screened MPP inhibitors. The result of this study revealed that Paritaprevir (-10.9 kcal/mol), and its</div><div>analog (CID 131982844)(-16.3 kcal/mol) showed better binding affinity than the approved MPP inhibitor</div><div>compared in this study including favipiravir, remdesivir, and alpha-ketoamide. A comparative study among</div><div>the screened putative MPP inhibitors revealed that amino acids T25, T26, H41, M49, L141, N142, G143,</div><div>C145, H164, M165, E166, D187, R188, and Q189 are at critical positions for becoming the surface hotspot</div><div>in the MPP of SARS-CoV-2. The study also suggested that paritaprevir and its' analog (CID 131982844),</div><div>may be effective against SARS-CoV-2 as these molecules had the common drug-surface hotspots on the</div><div>main protease protein of SARS-CoV-2. Other pharmacokinetic parameters also indicate that paritaprevir</div><div>and its top analog (CID 131982844) will be either similar or better-repurposed drugs than already approved</div><div>MPP inhibitors. </div><div><br></div>

Pharmacophore feature prediction and molecular docking approach to identify novel anti-HCV protease inhibitors

2017 ◽  
Vol 119 (1) ◽  
pp. 960-966 ◽  
Author(s):  
Arthi Venkatesan ◽  
Majji Rambabu ◽  
Sivaraman Jayanthi ◽  
J Febin Prabhu Dass
Keyword(s):  
Molecular Docking ◽  
Protease Inhibitors ◽  
Pharmacophore Feature ◽  
Docking Approach ◽  
Hcv Protease

Molecular Docking of Novel 5-O-benzoylpinostrobin Derivatives as SARS-CoV-2 Main Protease Inhibitors

2020 ◽  
Vol 26 (Covid-19) ◽  
pp. S63-S77
Author(s):  
Mohammad Rizki Fadhil Pratama ◽  
Hadi Poerwono ◽  
Siswandono Siswodihardjo
Keyword(s):  
Molecular Docking ◽  
Protease Inhibitors ◽  
Main Protease

scholarly journals Interactions of Alkyl Gallates with SARS-CoV-2 Main Protease: A Molecular Docking Approach

2020 ◽  
Vol 3 (1) ◽  
pp. 9
Author(s):  
Amalia Stefaniu ◽  
Lucia Pintilie ◽  
Bujor Albu ◽  
Lucia Pirvu
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Synthetic Compounds ◽  
X Ray ◽  
Lipinski’S Rule ◽  
Alkyl Gallates ◽  
Main Protease ◽  
Docking Approach ◽  
Lipinski’S Rule Of Five ◽  
In Silico Methods

Ten natural and semi-synthetic compounds (gallic acid and alkyl gallates) were investigated by in silico methods in order to evaluate their potential inhibitory activity against SAR-CoV-2 using the X-ray structure of SARS-CoV-2 main protease bound to Boceprevir at 1.45 Å (PDB ID: 6WNP). The evaluation of drug-likeness in terms of Lipinski’s Rule of Five and docking results in terms of docking score and interactions with the amino acids residues from the active binding site of the target protein were reported.

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