Molecular dynamics simulations of the active matrix metalloproteinase-2: Positioning of the N-terminal fragment and binding of a small peptide substrate

2008 ◽  
Vol 72 (1) ◽  
pp. 50-61 ◽  
Author(s):  
Natalia Díaz ◽  
Dimas Suárez
Keyword(s):  
Molecular Dynamics ◽  
Matrix Metalloproteinase ◽  
Molecular Dynamics Simulations ◽  
Matrix Metalloproteinase 2 ◽  
Peptide Substrate ◽  
Small Peptide ◽  
Active Matrix ◽  
Terminal Fragment ◽  
Dynamics Simulations

scholarly journals IDENTIFICATION OF POTENTIAL SALMONELLA TYPHI BETA-LACTAMASE TEM 1 INHIBITORS USING PEPTIDOMIMETICS, VIRTUAL SCREENING, AND MOLECULAR DYNAMICS SIMULATIONS

2018 ◽  
Vol 10 (1) ◽  
pp. 91
Author(s):  
Rakesh K. R. Pandit ◽  
Dinesh Gupta ◽  
Tapan K. Mukherjee
Keyword(s):  
Molecular Dynamics ◽  
Antibiotic Resistance ◽  
Virtual Screening ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Beta Lactamase ◽  
Ramachandran Plot ◽  
Small Peptide ◽  
In Silico Docking ◽  
Dynamics Simulations

Objective: The purpose of this study was to identify a potential peptidomimetic S. typhi Beta-lactamase TEM 1 inhibitor to tackle the antibiotic resistance among S. typhi.Methods: The potential peptidomimetic inhibitor was identified by in silico docking of the small peptide WFRKQLKW with S. typhi Beta-lactamase TEM 1. The 3D coordinate geometry of the residues of small peptide interacting with the active site of the receptor was generated and mimics were identified using PEP: MMs: MIMIC server. All the identified mimics were docked at the active site of the receptor using Autodock 4.2 and the best-docked complex was selected on the basis of binding energy and number of H-bonds. The complex was then subjected to molecular dynamics simulations of 30 ns using AMBER 12 software package. The stereochemical stability of the Beta-lactamase TEM 1-WFRKQLKW complex was estimated with the help of Ramachandran plot using PROCHECK tool.Results: In the present study, a new potential peptidomimetic inhibitor (ZINC05839264) of Beta-lactamase TEM 1 has been identified based on antimicrobial peptide WFRKQLKW by virtual screening of the MMsINC database. The docking and molecular simulation studies revealed that the mimic binds more tightly to the active site of the receptor than the peptide. The Ramachandran plot also shows that the Beta-lactamase TEM 1-mimic complex is stereo chemically more stable than Beta-lactamase TEM 1-WFRKQLKW complex as more number of residues (93.6%) are falling under the core region of the plot in case of the former.Conclusion: The study shows that the peptidomimetic compound can act as a potential inhibitor of S. typhi Beta-lactamase TEM 1 and further it can be developed into more effective therapeutic to tackle the problem of antibiotic resistance.

scholarly journals Studi Dinamika Molekul Stabilisasi Metaloproteinase Matriks 9 oleh Asam Kafeat

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Enade Perdana Istyastono
Keyword(s):  
Molecular Dynamics ◽  
Matrix Metalloproteinase ◽  
Molecular Dynamics Simulations ◽  
Caffeic Acid ◽  
Matrix Metalloproteinase 9 ◽  
Atomic Mechanism ◽  
Ic50 Value ◽  
Dynamics Simulations ◽  
20 Nm ◽  
Metalloproteinase 9

Caffeic acid, a cathecol-containing phytochemical found in coffee, has been reported as a potent matrix metalloproteinase 9 (MMP9) inhibitor. The IC50 value of caffeic acid as MMP9 inhibitor could reach below 20 nM. The research presented in this article employed molecular dynamics simulations to unravel the atomic mechanism of the MMP9 inhibition by caffeic acid. Molecular dynamics simulations of MMP9 for 10 ns using YASARA-Structure were performed with and without caffeic acid as the studied ligand. The results showed that caffeic acid stabilized the stucture of the MMP9.

Stereoselectivity by Enantiomeric Inhibitors of Matrix Metalloproteinase-8:  New Insights from Molecular Dynamics Simulations

2007 ◽  
Vol 50 (2) ◽  
pp. 211-218 ◽  
Author(s):  
Massimiliano Aschi ◽  
Neva Besker ◽  
Nazzareno Re ◽  
Giorgio Pochetti ◽  
Cecilia Coletti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Matrix Metalloproteinase ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations

scholarly journals Oligomerization of Huntingtin N-Terminal Fragment on a Phospholipid Bilayer Revealed by Molecular Dynamics Simulations

2014 ◽  
Vol 106 (2) ◽  
pp. 99a-100a ◽  
Author(s):  
Sebastien Cote ◽  
Vincent Binette ◽  
Evgeniy S. Salnikov ◽  
Burkhard Bechinger ◽  
Guanghong Wei ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Phospholipid Bilayer ◽  
Terminal Fragment ◽  
Dynamics Simulations
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