In Silico Drug Designing of Protease Inhibitors to Find the Potential Drug Candidate for HIV1

Alka Dwivedi; Vijay Laxmi Saxena

doi:doi:10.11648/j.cbb.20130103.11

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In Silico Drug Designing of Protease Inhibitors to Find the Potential Drug Candidate for HIV1

Alka Dwivedi, Vijay Laxmi Saxena

Published in Computational Biology and Bioinformatics (Volume 1, Issue 3)

Received: 15 June 2013 Published: 20 July 2013

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Abstract

Acquired immunodeficiency syndrome (AIDS)was first reported by the us centre of disease (CDC),a few years later it was found that’s a retrovirus called human immune deficiency virus (HIV) and this causative agent in AIDS, the study of HIV protease is one of the most important approaches for the therapeutic intervention in HIV infection and their development is regarded as major success of design, HIV attacks on the CD4+ (T helper cells in human ) lymphocyte and these are key component of the body’s immune system. The present anti retroviral HIV drugs targets based on three protein reverse transcriptase, protease, integrase in this project work on protease enzyme for block the protein malfunction who is responsible for this activity with the help of computer aided drug designing and the best dynamical and statical parameters like homology modeling ,model verification , binding site identification, docking , according there procedure active and effective site of the protease is determined and dock with suitable ligand with receptor and calculate the statical values , NVP is the most suitable ligand and can be use as a inhibit the activity of protease enzyme NVP molecule with a drug likeness property can be considered for in vitro and finally it can acts as a potential lead inhibitor for HIV1.

Published in	Computational Biology and Bioinformatics (Volume 1, Issue 3)
DOI	10.11648/j.cbb.20130103.11
Page(s)	10-14
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2013. Published by Science Publishing Group

Keywords

Protease, T-Helper Cells, CO-Receptor, Reverse Transcriptase, Integrase, AIDS, HIV1

References

[1]	Kohl N.E. Emini E.A. Schleif W.A. Davis L.J. Heimbach J.C. Dixon R.A. Scolnick E.M.Sigal I.S, "Active human immunodeficiency virus protease is required for viral infectivity" Proc.Natl Acad. Sci. U S A , 8: 4686-4690,1988.
[2]	Winters M.A and Merigan T, "Insertions in the human immunodeficiency virus type 1 proteaseand reverse transcriptase genes:clinical impact and molecular mechanisms" Antimicrob Agents Chemother, 49:2575-2582,2005.
[3]	Kozisek M. Saskova K.G. Rezacova P. Brynda J. van Maarseveen. N.M. de Jong. D Boucher. C.A. Kagan. R.M Nijhuis. M Konvalinka, "Ninety-nine is not enough: molecular characterization of inhibitor-resistant human immunodeficiency virus type 1 protease mutants with insertions in the flap region" J. Virol, 82:5869-5878,2008.
[4]	Doyon L. Croteau G. Thibeault D. Poulin F. Pilote Lamarre, "Second locus involved inhuman immunodeficiency virus type 1 resistance to protease inhibitors" J. Virol, 70:3763-3769, 1996.
[5]	Mammano F. Petit C. Clavel F, "Resistance-associated loss of viral fitness in human immunodeficiency virus type 1: phenotypic analysis of protease and gag coevolution in protease inhibitor-treated patients" J. Virol, 72:7632-7637, 1998.
[6]	Navia MA. Fitzgerald PM. McKeever BM. Leu CT. Heimbach JC, "Three-dimensional structure of a spartyl protease from human immune deﬁciency virus HIV-1" Nature, 337:615–20, 1989.
[7]	Pearl LH and Taylor WR, "A structural model for the retroviral proteases"Nature.329:351–54, 1987.
[8]	Olson M. Hood L. Cantor C. Botstein D, "A common language for physical mapping of the human genome" Science, 245(4925):1434–1435, 1989.
[9]	Berman H, "The Protein Data Bank: a historical perspective". ActaCrystallographica Section A: Foundations of Crystallography" A64, (1): 88–95, 2008.
[10]	Meyer EF, "The first years of the Protein Data Bank. Protein Science" Cambridge University Press) 6 (7): 1591–1597, 1997.
[11]	Berman HM. Westbrook J. Feng Z. Gilliland G. Bhat TN. Weissig H. Shindyalov IN. Bourne PE, "The Protein Data Bank" Nucleic Acids Res, 28 (1): 235–242,2000.
[12]	Knox C. Law V. Jewison T. Liu P. Ly S. Frolkis A. Pon A. Banco K. Mak C. Neveu V. Djoumbou Y. Eisner R. Guo AC. Wishart DS, "DrugBank 3.0: a comprehensive resource for 'omics' research on drugs" Nucleic Acids Res, 39:D1035-41,2011.
[13]	Wishart DS. Knox C. Guo AC. Cheng D. Shrivastava S. Tzur D. Gautam B. Hassanali M, "DrugBank: a knowledgebase for drugs, drug actions and drug targets" Nucleic Acids Res, 36:D901-6,2008
[14]	Wishart DS. Knox C. Guo AC. Shrivastava S. Hassanali M. Stothard P, Chang Z. Woolsey J, "DrugBank: a comprehensive resource for in silico drug discovery and exploration" Nucleic Acids Res, Jan 1; 34:D668-72, 2006.
[15]	Altschul, S Gish, W Miller, W Myers, E Lipman, D (1990). "Basic local alignment search tool". Journal of Molecular Biology 215 (3): 403–410, 1990.
[16]	Brady G, Stouten P,(2000) Fast prediction and visualization of protein binding pockets with PASS. J Comput Aided MolDes 14:383-401, 2000.
[17]	Laurie A, Jackson R: Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005, 21:1908-1916, 2005.
[18]	Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery. (2009).Fpocket: An open source platform for ligand pocket detection", BMC Bioinformatics. 10:168, 2009.
[19]	Kawabata T, "Detection of multi-scale pockets on protein surfaces using mathematical morphology" Proteins, 78: 1195-1121, 2010.
[20]	Capra JA. Laskowski RA. Thornton JM. Singh M. Funkhouser TA, "Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure"PLoSComputBiol, 5:(12),2009.
[21]	D.W. Ritchie and V. Venkatraman, "Ultra-Fast FFT Protein Docking On Graphics Processors" Bioinformatics, 26: 2398-2405, 2010.
[22]	Moore M. S.,"The GTP-binding protein Ran/TC4 is required for protein import into the nucleus" Nature, 365:661–663,1993.

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APA Style

Alka Dwivedi, Vijay Laxmi Saxena. (2013). In Silico Drug Designing of Protease Inhibitors to Find the Potential Drug Candidate for HIV1. Computational Biology and Bioinformatics, 1(3), 10-14. https://doi.org/10.11648/j.cbb.20130103.11

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ACS Style

Alka Dwivedi; Vijay Laxmi Saxena. In Silico Drug Designing of Protease Inhibitors to Find the Potential Drug Candidate for HIV1. Comput. Biol. Bioinform. 2013, 1(3), 10-14. doi: 10.11648/j.cbb.20130103.11

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AMA Style

Alka Dwivedi, Vijay Laxmi Saxena. In Silico Drug Designing of Protease Inhibitors to Find the Potential Drug Candidate for HIV1. Comput Biol Bioinform. 2013;1(3):10-14. doi: 10.11648/j.cbb.20130103.11

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@article{10.11648/j.cbb.20130103.11,
  author = {Alka Dwivedi and Vijay Laxmi Saxena},
  title = {In Silico Drug Designing of Protease Inhibitors to Find the Potential Drug Candidate for HIV1},
  journal = {Computational Biology and Bioinformatics},
  volume = {1},
  number = {3},
  pages = {10-14},
  doi = {10.11648/j.cbb.20130103.11},
  url = {https://doi.org/10.11648/j.cbb.20130103.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20130103.11},
  abstract = {Acquired immunodeficiency syndrome (AIDS)was first reported by the us centre of disease (CDC),a few years later it was found that’s a retrovirus called human immune deficiency virus (HIV) and this causative agent in AIDS, the study of HIV protease is one of the most important approaches for the therapeutic intervention in HIV infection and their development is regarded as  major success of design, HIV attacks on the CD4+ (T helper cells in human ) lymphocyte and these are key component of the body’s immune system. The present anti retroviral HIV drugs targets based on three protein reverse transcriptase, protease, integrase in this project work on protease enzyme for block the protein malfunction who is responsible for this activity with the help of computer aided drug designing and the best dynamical and statical parameters like homology modeling ,model verification , binding site identification, docking , according there procedure active  and effective site of the protease is determined and dock with suitable ligand with receptor and calculate the statical values , NVP is the most suitable ligand  and can be use as a inhibit the activity of protease enzyme NVP molecule with a drug likeness property can be considered for in vitro and finally it can acts as a potential lead inhibitor for HIV1.},
 year = {2013}
}

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TY  - JOUR
T1  - In Silico Drug Designing of Protease Inhibitors to Find the Potential Drug Candidate for HIV1
AU  - Alka Dwivedi
AU  - Vijay Laxmi Saxena
Y1  - 2013/07/20
PY  - 2013
N1  - https://doi.org/10.11648/j.cbb.20130103.11
DO  - 10.11648/j.cbb.20130103.11
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 10
EP  - 14
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20130103.11
AB  - Acquired immunodeficiency syndrome (AIDS)was first reported by the us centre of disease (CDC),a few years later it was found that’s a retrovirus called human immune deficiency virus (HIV) and this causative agent in AIDS, the study of HIV protease is one of the most important approaches for the therapeutic intervention in HIV infection and their development is regarded as  major success of design, HIV attacks on the CD4+ (T helper cells in human ) lymphocyte and these are key component of the body’s immune system. The present anti retroviral HIV drugs targets based on three protein reverse transcriptase, protease, integrase in this project work on protease enzyme for block the protein malfunction who is responsible for this activity with the help of computer aided drug designing and the best dynamical and statical parameters like homology modeling ,model verification , binding site identification, docking , according there procedure active  and effective site of the protease is determined and dock with suitable ligand with receptor and calculate the statical values , NVP is the most suitable ligand  and can be use as a inhibit the activity of protease enzyme NVP molecule with a drug likeness property can be considered for in vitro and finally it can acts as a potential lead inhibitor for HIV1.
VL  - 1
IS  - 3
ER  -

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Author Information

Alka Dwivedi

National Bioinformatics Infrastructure Facility Center of (DBT), Ministry of Science and Technology (Govt. of India), D.G (PG) College civil lines Kanpur, INDIA
Vijay Laxmi Saxena

Department of Zoology (HOD), (Coordinator) National Bioinformatics Infrastructure Facility Center of (DBT), Ministry of Science and Technology (Govt. of India), D.G (PG) College civil lines Kanpur, INDIA

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Plain Text BibTeX RIS

APA Style

Alka Dwivedi, Vijay Laxmi Saxena. (2013). In Silico Drug Designing of Protease Inhibitors to Find the Potential Drug Candidate for HIV1. Computational Biology and Bioinformatics, 1(3), 10-14. https://doi.org/10.11648/j.cbb.20130103.11

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ACS Style

Alka Dwivedi; Vijay Laxmi Saxena. In Silico Drug Designing of Protease Inhibitors to Find the Potential Drug Candidate for HIV1. Comput. Biol. Bioinform. 2013, 1(3), 10-14. doi: 10.11648/j.cbb.20130103.11

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AMA Style

Alka Dwivedi, Vijay Laxmi Saxena. In Silico Drug Designing of Protease Inhibitors to Find the Potential Drug Candidate for HIV1. Comput Biol Bioinform. 2013;1(3):10-14. doi: 10.11648/j.cbb.20130103.11

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@article{10.11648/j.cbb.20130103.11,
  author = {Alka Dwivedi and Vijay Laxmi Saxena},
  title = {In Silico Drug Designing of Protease Inhibitors to Find the Potential Drug Candidate for HIV1},
  journal = {Computational Biology and Bioinformatics},
  volume = {1},
  number = {3},
  pages = {10-14},
  doi = {10.11648/j.cbb.20130103.11},
  url = {https://doi.org/10.11648/j.cbb.20130103.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20130103.11},
  abstract = {Acquired immunodeficiency syndrome (AIDS)was first reported by the us centre of disease (CDC),a few years later it was found that’s a retrovirus called human immune deficiency virus (HIV) and this causative agent in AIDS, the study of HIV protease is one of the most important approaches for the therapeutic intervention in HIV infection and their development is regarded as  major success of design, HIV attacks on the CD4+ (T helper cells in human ) lymphocyte and these are key component of the body’s immune system. The present anti retroviral HIV drugs targets based on three protein reverse transcriptase, protease, integrase in this project work on protease enzyme for block the protein malfunction who is responsible for this activity with the help of computer aided drug designing and the best dynamical and statical parameters like homology modeling ,model verification , binding site identification, docking , according there procedure active  and effective site of the protease is determined and dock with suitable ligand with receptor and calculate the statical values , NVP is the most suitable ligand  and can be use as a inhibit the activity of protease enzyme NVP molecule with a drug likeness property can be considered for in vitro and finally it can acts as a potential lead inhibitor for HIV1.},
 year = {2013}
}

Copy | Download

TY  - JOUR
T1  - In Silico Drug Designing of Protease Inhibitors to Find the Potential Drug Candidate for HIV1
AU  - Alka Dwivedi
AU  - Vijay Laxmi Saxena
Y1  - 2013/07/20
PY  - 2013
N1  - https://doi.org/10.11648/j.cbb.20130103.11
DO  - 10.11648/j.cbb.20130103.11
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 10
EP  - 14
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20130103.11
AB  - Acquired immunodeficiency syndrome (AIDS)was first reported by the us centre of disease (CDC),a few years later it was found that’s a retrovirus called human immune deficiency virus (HIV) and this causative agent in AIDS, the study of HIV protease is one of the most important approaches for the therapeutic intervention in HIV infection and their development is regarded as  major success of design, HIV attacks on the CD4+ (T helper cells in human ) lymphocyte and these are key component of the body’s immune system. The present anti retroviral HIV drugs targets based on three protein reverse transcriptase, protease, integrase in this project work on protease enzyme for block the protein malfunction who is responsible for this activity with the help of computer aided drug designing and the best dynamical and statical parameters like homology modeling ,model verification , binding site identification, docking , according there procedure active  and effective site of the protease is determined and dock with suitable ligand with receptor and calculate the statical values , NVP is the most suitable ligand  and can be use as a inhibit the activity of protease enzyme NVP molecule with a drug likeness property can be considered for in vitro and finally it can acts as a potential lead inhibitor for HIV1.
VL  - 1
IS  - 3
ER  -

Copy | Download