scholarly journals Identification of potential plant-based inhibitor against viral proteases of SARS-CoV-2 through molecular docking, MM-PBSA binding energy calculations and molecular dynamics simulation

2021 ◽  
Author(s):  
Bhaskarjyoti Gogoi ◽  
Purvita Chowdhury ◽  
Nabajyoti Goswami ◽  
Neelutpal Gogoi ◽  
Tufan Naiya ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Binding Energy ◽  
Dynamics Simulation ◽  
Energy Calculations ◽  
Viral Proteases ◽  
Binding Energy Calculations

scholarly journals Qualitative and quantitative analysis of anti-viral compounds against SARS-CoV-2 protease enzyme by molecular dynamics simulation and MM/PBSA method

2021 ◽  
Author(s):  
Saghi Sepehri ◽  
Niloufar Hashemidanesh ◽  
Karim Mahnam ◽  
Hila Asham
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Quantitative Analysis ◽  
Molecular Dynamics Simulation ◽  
Binding Energy ◽  
Active Site ◽  
Dynamics Simulation ◽  
Qualitative And Quantitative Analysis ◽  
Qualitative And Quantitative ◽  
In Silico Studies

Background: A significant worry for global public health is the international spread of the coronavirus disease-19 triggered through the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Herein, an attempt was performed to qualitative and quantitative analysis of a series of compounds against SARS-CoV-2 main protease (M<[pro]) by in silico studies. Methods: About one hundred anti-viral compounds were collected from DrugBank database. In the second stage, molecular docking simulation was carried out to identify interactions of the molecules with the key residues in the M<[pro] active site. Finally, the molecular dynamics simulation of four top-ranked compounds and X77 as Co-crystal ligand were investigated. Results:Based on molecular docking studies, four compounds DB00224, DB00220, DB01232 and DB08873 exhibited the best results among compounds against M<[pro] enzyme. Additionally, molecular dynamic simulation and free binding energy were accomplished to compute the interaction energies and stability of the top-ranked compounds at the active site. The binding energy portions of the compounds into the enzyme active site exposed that Van der Waals and non-polar interactions were fundamental factors in the molecule binding. The ligand connections were steadied via hydrophobic interactions and several key hydrogen bonds especially with Glu166 and His41 residues into the active site. Conclusion: According to calculations of docking and MD, it was observed that the active site is mostly hydrophobic, where the value of the ∆Evdw is higher than that of the ∆Eele. Additionally, the results showed the steady of selected ligands binding with SARS-CoV-2 M<[pro] active site.

Exploring the effect of inhibitor AKB‐9778 on VE‐PTP by molecular docking and molecular dynamics simulation

2019 ◽  
Vol 120 (10) ◽  
pp. 17015-17029 ◽  
Author(s):  
Wen‐Shan Liu ◽  
Rui‐Rui Wang ◽  
Ying‐Zhan Sun ◽  
Wei‐Ya Li ◽  
Hong‐Lian Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation

scholarly journals Computational Study on Selective PDE9 Inhibitors on PDE9-Mg/Mg, PDE9-Zn/Mg, and PDE9-Zn/Zn Systems

Biomolecules ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 709
Author(s):  
Dakshinamurthy Sivakumar ◽  
Sathish-Kumar Mudedla ◽  
Seonghun Jang ◽  
Hyunjun Kim ◽  
Hyunjin Park ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Erectile Dysfunction ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Cardiovascular Diseases ◽  
Neurodegenerative Disorders ◽  
Computational Study ◽  
Dynamics Simulation ◽  
Interaction Patterns

PDE9 inhibitors have been studied to validate their potential to treat diabetes, neurodegenerative disorders, cardiovascular diseases, and erectile dysfunction. In this report, we have selected highly potent previously reported selective PDE9 inhibitors BAY73-6691R, BAY73-6691S, 28r, 28s, 3r, 3s, PF-0447943, PF-4181366, and 4r to elucidate the differences in their interaction patterns in the presence of different metal systems such as Zn/Mg, Mg/Mg, and Zn/Zn. The initial complexes were generated by molecular docking followed by molecular dynamics simulation for 100 ns in triplicate for each system to understand the interactions’ stability. The results were carefully analyzed, focusing on the ligands’ non-bonded interactions with PDE9 in different metal systems.

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