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Reseach Article

Molecular Modeling and Docking Analysis of Novel Drug like Compounds for NDM-1

Published on February 2013 by Amrit Jagyasi, Jyotsna Choubey, Ashish Patel, M. K. Verma
National Seminar on Application of Artificial Intelligence in Life Sciences 2013
Foundation of Computer Science USA
NSAAILS - Number 1
February 2013
Authors: Amrit Jagyasi, Jyotsna Choubey, Ashish Patel, M. K. Verma
226d5652-c2d1-41ce-91b0-58ed05f09832

Amrit Jagyasi, Jyotsna Choubey, Ashish Patel, M. K. Verma . Molecular Modeling and Docking Analysis of Novel Drug like Compounds for NDM-1. National Seminar on Application of Artificial Intelligence in Life Sciences 2013. NSAAILS, 1 (February 2013), 47-54.

@article{
author = { Amrit Jagyasi, Jyotsna Choubey, Ashish Patel, M. K. Verma },
title = { Molecular Modeling and Docking Analysis of Novel Drug like Compounds for NDM-1 },
journal = { National Seminar on Application of Artificial Intelligence in Life Sciences 2013 },
issue_date = { February 2013 },
volume = { NSAAILS },
number = { 1 },
month = { February },
year = { 2013 },
issn = 0975-8887,
pages = { 47-54 },
numpages = 8,
url = { /proceedings/nsaails/number1/10385-1011/ },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Proceeding Article
%1 National Seminar on Application of Artificial Intelligence in Life Sciences 2013
%A Amrit Jagyasi
%A Jyotsna Choubey
%A Ashish Patel
%A M. K. Verma
%T Molecular Modeling and Docking Analysis of Novel Drug like Compounds for NDM-1
%J National Seminar on Application of Artificial Intelligence in Life Sciences 2013
%@ 0975-8887
%V NSAAILS
%N 1
%P 47-54
%D 2013
%I International Journal of Computer Applications
Abstract

NDM-1 (New Delhi metallo-?-lactamase 1) is an enzyme that is carried in certain gram negative bacteria like E. coli and Klebsiella, and makes the bacterium resistant to the beta lactam antibiotics, including carbapenems, with the exception of the monobactam agent, aztreonam. Beta-lactamase is also known as carbapenemases, due to its resistance towards carbapenem antibiotics. Resistance to ? –lactam antibiotics mediated by metallo-?-lactamases is an increasingly worrying clinical problem. NDM-1 has been found in several clinically important carbapenem-resistant pathogens, there is a need for inhibitors of this enzyme that could protect broad spectrum antibiotics from hydrolysis and thus extend their utility. In the presented research, the 3D structure of NDM-1 protein was modeled using homology modeling by Modeller9v8. Evaluation of the constructed model is done by PROCHECK, PROSA, ERRAT and Verify3d servers. DEPTH server is used to predict active sites of Protein. Pubchem and ChEMBL, Drug Bank, and SuperNatural databases is used to find novel compounds. These compounds were dokced with the modeled structure, and those showing least Binding Energy were selected. These final compounds were then tested among Online Validation Servers (Molinspiration, and OSIRIS) for Drug Likeness. Also they were validated using ADMET descriptors protocol of Accelrys Discovery Studio.

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Index Terms

Computer Science
Information Sciences

Keywords

Ndm-1 Metallo-?-lactamase Homology Modeling Docking Depth Admet