Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory

2008 ◽  
Vol 128 (18) ◽  
pp. 185102 ◽  
Author(s):  
Yoshiteru Yonetani ◽  
Yutaka Maruyama ◽  
Fumio Hirata ◽  
Hidetoshi Kono
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Computational Methods ◽  
Model Theory ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Interaction Site ◽  
Site Model ◽  
Dna Hydration ◽  
Reference Interaction Site

Role of Mg2+Ions in DNA Hydrolysis byEcoRV, Studied by the 3D-Reference Interaction Site Model and Molecular Dynamics

2018 ◽  
Vol 122 (39) ◽  
pp. 9061-9075 ◽  
Author(s):  
Itaru Onishi ◽  
Shunya Sunaba ◽  
Norio Yoshida ◽  
Fumio Hirata ◽  
Masayuki Irisa
Keyword(s):  
Molecular Dynamics ◽  
Dna Hydrolysis ◽  
Interaction Site ◽  
Site Model ◽  
Reference Interaction Site

scholarly journals An Analysis Based on Molecular Docking and Molecular Dynamics Simulation Study of Bromelain as Anti-SARS-CoV-2 Variants

2021 ◽  
Vol 12 ◽  
Author(s):  
Trina Ekawati Tallei ◽  
Fatimawali ◽  
Afriza Yelnetty ◽  
Rinaldi Idroes ◽  
Diah Kusumawaty ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Three Dimensional ◽  
Md Simulations ◽  
Inhibitory Effect ◽  
Dynamics Simulation ◽  
Novel Coronavirus

The rapid spread of a novel coronavirus known as SARS-CoV-2 has compelled the entire world to seek ways to weaken this virus, prevent its spread and also eliminate it. However, no drug has been approved to treat COVID-19. Furthermore, the receptor-binding domain (RBD) on this viral spike protein, as well as several other important parts of this virus, have recently undergone mutations, resulting in new virus variants. While no treatment is currently available, a naturally derived molecule with known antiviral properties could be used as a potential treatment. Bromelain is an enzyme found in the fruit and stem of pineapples. This substance has been shown to have a broad antiviral activity. In this article, we analyse the ability of bromelain to counteract various variants of the SARS-CoV-2 by targeting bromelain binding on the side of this viral interaction with human angiotensin-converting enzyme 2 (hACE2) using molecular docking and molecular dynamics simulation approaches. We have succeeded in making three-dimensional configurations of various RBD variants using protein modelling. Bromelain exhibited good binding affinity toward various variants of RBDs and binds right at the binding site between RBDs and hACE2. This result is also presented in the modelling between Bromelain, RBD, and hACE2. The molecular dynamics (MD) simulations study revealed significant stability of the bromelain and RBD proteins separately up to 100 ns with an RMSD value of 2 Å. Furthermore, despite increases in RMSD and changes in Rog values of complexes, which are likely due to some destabilized interactions between bromelain and RBD proteins, two proteins in each complex remained bonded, and the site where the two proteins bind remained unchanged. This finding indicated that bromelain could have an inhibitory effect on different SARS-CoV-2 variants, paving the way for a new SARS-CoV-2 inhibitor drug. However, more in vitro and in vivo research on this potential mechanism of action is required.

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