COVID-19 Update - This is to inform you that the Government of India has announced a complete lockdown in India 22nd March 2020 to 3rd May 2020. As a result, our offices will now be closed till 3rd May 2020 and all our employees will be working from home. Office telephones will not be answered, and therefore you are requested to direct all your queries related to manuscript submission, review process, publication etc. at below mentioned details. editor@innovativepublication.com, rakesh.its@gmail.com, Mob. 8826373757, 8826859373, 9910947804


Print ISSN:-2394-2789

Online ISSN:-2394-2797

CODEN : IJPCN9

Current Issue

Year 2020

Volume: 7 , Issue: 1

Article Access statistics

Viewed: 717

Emailed: 0

PDF Downloaded: 195

International Journal of Pharmaceutical Chemistry and Analysis


Molecular dynamics simulations: A mechanistic probe for understanding antibacterial activity


Full Text PDF Share on Facebook Share on Twitter


Author Details : Arati Prabhu

Volume : 4, Issue : 3, Year : 2017

Article Page : 66-69


Suggest article by email

Abstract

Introduction: Molecular dynamics, in which molecules are allowed to interact over time at a given temperature following the laws of classical mechanics has been shown to be highly successful in simulating various biological phenomena down to atomic detail. When applied to complexes of protein targets and potential binders, this technique, provides a detailed description of the stability of the protein-ligand complexes, thereby throwing light on the binding potential of the ligands to probable target proteins.
Materials and Method: In the present study we have explored the mechanism of protein synthesis inhibition by the antibiotic thiostrepton with the combination of manual docking followed by molecular dynamics simulations to two molecular targets – the L11/23S-rRNA interface and the elongation factor Ef-Tu. Cross-docking runs on the two native co-crystallised ligands of the target proteins were done as a further probe.
Results: Docking of thiostrepton at the L11/23S-rRNA interface as well as Ef-Tu indicated stable binding during 10-ns molecular dynamics simulations, whereas LFF571 binds stably only to its native protein EF-Tu which is in accordance to literature reports. Thus, molecular dynamics simulation studies indicate that thiostrepton has binding potential to two targets of protein synthesis translation, the elongation factor (Ef-Tu) and L11 protein and 23S-rRNA interface.
Conclusion: This study corroborates that thiostrepton inhibits Ef-Tu in addition to the L11-ribosomal RNA complex. Binding to multiple targets probably enhances its inhibitory effect on protein translation.

Keywords:
Thiazolyl peptide, Macrocyclic, Ef-Tu, Molecular dynamics simulations, Thiostrepton, Ribosome

How to cite : Prabhu A, Molecular dynamics simulations: A mechanistic probe for understanding antibacterial activity. Int J Pharm Chem Anal 2017;4(3):66-69

Copyright © 2017 by author(s) and Int J Pharm Chem Anal. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0) (creativecommons.org)