Identification of novel selective MMP-9 inhibitors as potential anti-metastatic lead using structure-based hierarchical virtual screening and molecular dynamics simulation

2016 ◽  
Vol 12 (8) ◽  
pp. 2519-2531 ◽  
Author(s):  
Sukesh Kalva ◽  
Nikhil Agrawal ◽  
Adam A. Skelton ◽  
Lilly M. Saleena
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Virtual Screening ◽  
Binding Free Energy ◽  
Pharmacophore Modeling ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Cross Docking

In this study, a novel MMP-9 inhibitor was identified using structure-based pharmacophore modeling, cross docking, binding free energy and molecular dynamics simulation studies.

scholarly journals Identification of Novel Inhibitors of Type-I Mycobacterium Tuberculosis Fatty Acid Synthase Using Docking-Based Virtual Screening and Molecular Dynamics Simulation

2021 ◽  
Vol 11 (15) ◽  
pp. 6977
Author(s):  
Nidhi Singh ◽  
Shi-Qing Mao ◽  
Wenjin Li
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Mycobacterium Tuberculosis ◽  
Fatty Acid ◽  
Molecular Dynamics Simulation ◽  
Virtual Screening ◽  
Fatty Acid Synthase ◽  
Binding Free Energy ◽  
Dynamics Simulation ◽  
Type I

Mycobacterial fatty acid synthase type-I (FAS-I) has an important role in the de novo synthesis of fatty acids, which constitute a major component of the cell wall. The essentiality of FAS-I in the survival and growth of mycobacterium makes it an attractive drug target. However, targeted inhibitors against Mycobacterial FAS-I have not been reported yet. Recently, the structure of FAS-I from Mycobacterium tuberculosis was solved. Therefore, in a quest to find potential inhibitors against FAS-I, molecular docking-based virtual screening and molecular dynamics simulation were done. Subsequently, molecular dynamic simulations based on binding free energy calculations were done to gain insight into the predicted binding mode of putative hits. The detailed analysis resulted in the selection of four putative inhibitors. For compounds BTB14738, RH00608, SPB02705, and CD01000, binding free energy was calculated as −72.27 ± 12.63, −68.06 ± 11.80, −63.57 ± 12.22, and −51.28 ± 13.74 KJ/mol, respectively. These compounds are proposed to be promising pioneer hits.

Insight into the adsorption profiles of the Saprolegnia monoica chitin synthase MIT domain on POPA and POPC membranes by molecular dynamics simulation studies

2016 ◽  
Vol 18 (7) ◽  
pp. 5281-5290 ◽  
Author(s):  
Guanglin Kuang ◽  
Lijun Liang ◽  
Christian Brown ◽  
Qi Wang ◽  
Vincent Bulone ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Molecular Dynamics Simulation ◽  
Binding Free Energy ◽  
Binding Mode ◽  
Chitin Synthase ◽  
Dynamics Simulation ◽  
Simulation Methods ◽  
Simulation Studies ◽  
Insight Into

The binding mode and binding free energy of the Saprolegnia monoica chitin synthase MIT domain with the POPA membrane have been studied by molecular simulation methods.

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