scholarly journals Interactive Molecular Dynamics in Virtual Reality Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease

2020 ◽  
Vol 60 (12) ◽  
pp. 5803-5814 ◽  
Author(s):  
Helen M. Deeks ◽  
Rebecca K. Walters ◽  
Jonathan Barnoud ◽  
David R. Glowacki ◽  
Adrian J. Mulholland
Keyword(s):  
Molecular Dynamics ◽  
Virtual Reality ◽  
Flexible Substrate ◽  
Main Protease

scholarly journals Interactive Molecular Dynamics in Virtual Reality (iMD-VR) Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease

2020 ◽  
Author(s):  
Helen Deeks ◽  
Rebecca Walters ◽  
Jonathan Barnoud ◽  
David Glowacki ◽  
Adrian Mulholland
Keyword(s):  
Molecular Dynamics ◽  
Virtual Reality ◽  
Drug Development ◽  
Flexible Substrate ◽  
Main Protease

The main protease (Mpro) of the SARS-CoV-2 virus is one focus of drug development efforts for antivirals to combat COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) is a useful and effective tool for predicting structures of Mpro-ligand complexes.

scholarly journals Interactive Molecular Dynamics in Virtual Reality (iMD-VR) Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease

2020 ◽  
Author(s):  
Helen Deeks ◽  
Rebecca Walters ◽  
Jonathan Barnoud ◽  
David Glowacki ◽  
Adrian Mulholland
Keyword(s):  
Molecular Dynamics ◽  
Virtual Reality ◽  
Drug Development ◽  
Flexible Substrate ◽  
Main Protease

The main protease (Mpro) of the SARS-CoV-2 virus is one focus of drug development efforts for antivirals to combat COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) is a useful and effective tool for predicting structures of Mpro-ligand complexes.

scholarly journals Interactive Molecular Dynamics in Virtual Reality (iMD-VR) Is an Effective Tool for Flexible Substrate and Inhibitor Docking to the SARS-CoV-2 Main Protease

2020 ◽  
Author(s):  
Helen Deeks ◽  
Rebecca Walters ◽  
Jonathan Barnoud ◽  
David Glowacki ◽  
Adrian Mulholland
Keyword(s):  
Molecular Dynamics ◽  
Virtual Reality ◽  
Drug Development ◽  
Flexible Substrate ◽  
Main Protease

The main protease (Mpro) of the SARS-CoV-2 virus is one focus of drug development efforts for antivirals to combat COVID-19. Here, we show that interactive molecular dynamics in virtual reality (iMD-VR) is a useful and effective tool for predicting structures of Mpro-ligand complexes.

scholarly journals Visual Continuity of Protein Secondary Structure Rendering: Application to SARS-CoV-2 Mpro in Virtual Reality

2021 ◽  
Vol 3 ◽  
Author(s):  
Alexander D. Jamieson-Binnie ◽  
David R. Glowacki
Keyword(s):  
Molecular Dynamics ◽  
Virtual Reality ◽  
Secondary Structure ◽  
Cross Sections ◽  
Protein Secondary Structure ◽  
New Method ◽  
Dynamic Simulations ◽  
Potential Target ◽  
Main Protease ◽  
Visual Continuity

Ribbon diagrams are important for protein visualization, used to convey the secondary structure in a clear and concise manner. However, most algorithms used to generate these diagrams do not maintain visual continuity when viewing a molecular trajectory, with certain sections of ribbons flipping between clockwise and counterclockwise twists. Here we outline a new method which prevents this artifact by morphing between consecutive cross sections instead of rotating. This yields diagrams which are well suited for viewing dynamic simulations, such as those used for interactive molecular dynamics. We illustrate the utility of this algorithm by using it to visualize iMD-VR (interactive molecular dynamics in virtual reality) simulations of the secondary structure of the SARS-CoV-2 main protease (Mpro), which is being investigated as a potential target for COVID drug therapies.

scholarly journals From genomes to molecular dynamics – A bottom up approach in extrication of SARS CoV-2 main protease inhibitors

2021 ◽  
Vol 18 ◽  
pp. 100156
Author(s):  
S. Aishwarya ◽  
K. Gunasekaran ◽  
R. Sagaya Jansi ◽  
G. Sangeetha
Keyword(s):  
Molecular Dynamics ◽  
Protease Inhibitors ◽  
Bottom Up ◽  
Main Protease

scholarly journals Identification of Anti-SARS-CoV-2 Compounds from Food Using QSAR-Based Virtual Screening, Molecular Docking, and Molecular Dynamics Simulation Analysis

2021 ◽  
Vol 14 (4) ◽  
pp. 357
Author(s):  
Magdi E. A. Zaki ◽  
Sami A. Al-Hussain ◽  
Vijay H. Masand ◽  
Siddhartha Akasapu ◽  
Sumit O. Bajaj ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Virtual Screening ◽  
Simulation Analysis ◽  
Qsar Model ◽  
Quantitative Structure Activity Relationship ◽  
Dynamics Simulation ◽  
Multilinear Regression ◽  
Qsar Analysis ◽  
Main Protease

Due to the genetic similarity between SARS-CoV-2 and SARS-CoV, the present work endeavored to derive a balanced Quantitative Structure−Activity Relationship (QSAR) model, molecular docking, and molecular dynamics (MD) simulation studies to identify novel molecules having inhibitory potential against the main protease (Mpro) of SARS-CoV-2. The QSAR analysis developed on multivariate GA–MLR (Genetic Algorithm–Multilinear Regression) model with acceptable statistical performance (R2 = 0.898, Q2loo = 0.859, etc.). QSAR analysis attributed the good correlation with different types of atoms like non-ring Carbons and Nitrogens, amide Nitrogen, sp2-hybridized Carbons, etc. Thus, the QSAR model has a good balance of qualitative and quantitative requirements (balanced QSAR model) and satisfies the Organisation for Economic Co-operation and Development (OECD) guidelines. After that, a QSAR-based virtual screening of 26,467 food compounds and 360 heterocyclic variants of molecule 1 (benzotriazole–indole hybrid molecule) helped to identify promising hits. Furthermore, the molecular docking and molecular dynamics (MD) simulations of Mpro with molecule 1 recognized the structural motifs with significant stability. Molecular docking and QSAR provided consensus and complementary results. The validated analyses are capable of optimizing a drug/lead candidate for better inhibitory activity against the main protease of SARS-CoV-2.

scholarly journals High-resolution mining of the SARS-CoV-2 main protease conformational space: supercomputer-driven unsupervised adaptive sampling

2021 ◽  
Author(s):  
Théo Jaffrelot Inizan ◽  
Frédéric Célerse ◽  
Olivier Adjoua ◽  
Dina El Ahdab ◽  
Luc-Henri Jolly ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
High Resolution ◽  
Adaptive Sampling ◽  
Force Fields ◽  
Sampling Strategy ◽  
Md Simulations ◽  
Conformational Space ◽  
Many Body ◽  
Polarizable Force Fields ◽  
Main Protease

We provide an unsupervised adaptive sampling strategy capable of producing μs-timescale molecular dynamics (MD) simulations of large biosystems using many-body polarizable force fields (PFFs).

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