scholarly journals A double-edged sword: supramolecular complexes of triazavirine display multicenter binding effects which influence aggregate formation

2018 ◽  
Author(s):  
Yana A Zabrodskaya ◽  
Alexey V Shvetsov ◽  
Vladimir B Tsvetkov ◽  
Vladimir V Egorov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Weight ◽  
Molecular Docking ◽  
Molecular Dynamics Simulation ◽  
Antiviral Activity ◽  
Small Molecule ◽  
Broad Spectrum ◽  
Dynamics Simulation ◽  
Supramolecular Complexes ◽  
Aggregate Formation

Triazavirine (TZV), a small molecule with a broad spectrum of antiviral activity, shows a tendency to induce the aggregation of melittin (MLT), a cationic membrane-disrupting peptide from the poison of the European bee. In MLT:TZV mixtures, high molecular weight precipitates form once a critical MLT:TZV ratio has been exceeded. Molecular dynamics simulation of MLT-TZV interactions, followed by molecular docking, led us to the hypothesis of multicenter binding of TZV supramolecular complexes to MLT.

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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