Molecular Docking Interaction of Mycobacterium Tuberculosis LipB Enzyme with Isoniazid, Pyrazinamide and a Structurally Altered Drug 2, 6 Dimethoxyisonicotinohydrazide
Computational Biology and Bioinformatics
Volume 3, Issue 4, August 2015, Pages: 45-51
Received: Jul. 8, 2015; Accepted: Jul. 18, 2015; Published: Jul. 28, 2015
Views 4977      Downloads 213
Authors
Muthuraman Namasivayam, Center of Advance Study in Crystallography and Biophysics, University of Madras, Chennai, India
Suresh Ramraj Subashchandrabose, Global Centre for Environmental Risk Assessment and Remediation Faculty of Science and Information Technology, The University of New Castle, Newcastle, Australia
Article Tools
Follow on us
Abstract
Tuberculosis is an infectious airborne disease caused by a bacterial infection that affects the lungs and other parts of the body. Vaccination against tuberculosis is available but proved to be unsuccessful against emerging multi drug and extensive drug resistant bacterial strains. This in turn raises the pressure to speed up the research on developing new and more efficient anti-tuberculosis drugs. Lipoate biosynthesis protein B (LipB) is found to play vital role in the lipoylation process in Mycobacterium tuberculosis and thus making it a very promising drug target. The existing first line drugs such as Isoniazid, Pyrazinamide and Rifampicin etc shows only profound binding affinity with this target protein. Therefore, new or modified drugs with better docking approach that exhibit a closer and stronger binding affinity is essential. This current study opens up a novel approach towards anti-tuberculosis agents by determining drugs that share similar structures with some of the best available first line drug and also happen to possess better binding affinity. In this article, a computational method by which, pristine as well certain first line and structurally modified drugs were docked with the LipB protein target; where, structurally modified 2, 6 Dimethoxyisonicotinohydrazide show superior target docking.
Keywords
Mycobacterium Tuberculosis, Multi-drug Resistant Tuberculosis, Anti-tuberculosis Drugs, LipB, Isoniazid, Lipoylation, Molecular Docking, Drug Design, 2,6 Dimethoxyisonicotinohydrazide
To cite this article
Muthuraman Namasivayam, Suresh Ramraj Subashchandrabose, Molecular Docking Interaction of Mycobacterium Tuberculosis LipB Enzyme with Isoniazid, Pyrazinamide and a Structurally Altered Drug 2, 6 Dimethoxyisonicotinohydrazide, Computational Biology and Bioinformatics. Vol. 3, No. 4, 2015, pp. 45-51. doi: 10.11648/j.cbb.20150304.11
References
[1]
Abad-Zapatero C. and Metz J.T. (2005) “Ligand efficiency indices as guideposts for drug discovery” Drug Discov. Today, 10:464-9.
[2]
Altschul, S. F, Madden T.L, Schäffer A.A, Zhang J, Zhang Z, Miller W, and Lipman DJ. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res 25(17): 3389-402.
[3]
Arnold, K., Bordoli L, Kopp J, and Schwede T (2006) "The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling." Bioinformatics 22(2): 195-201.
[4]
Brooijmans, N, Kuntz, I.D. (2003) “Molecular recognition and docking algorithms” Annu. Rev. Biophys.Biomol. Struct., 32, 335–373.
[5]
C. B. Bhagat, S. K. Tank, P. R. Dudhagara N. D. Trivedi and U. N. Trivedi (2014) “In silico Study of Target Proteins for Mycobacterium tuberculosis” American Journal of Phytomedicine and Clinical Therapeutics 2, 3, 455-462.
[6]
Cade C.E, Dlouhy A.C, Medzihradszky K.F, Salas-Castillo S.P, and Ghiladi R.A (2010) “Isoniazid-resistance conferring mutations in Mycobacterium tuberculosis KatG: catalase, peroxidase, and INH-NADH adduct formation activities.” Protein Sci.; 19(3): 458-74.
[7]
Cheng T, Li Q, Zhou Z, Wang Y, and Bryant, S.H (2012) “Structure-based virtual screening for drug discovery: A problem-centric review.” AAPS J. 14, 133–141.
[8]
Cole S.T, Brosch R, Parkhill J, et al. (June 1998) "Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence". Nature 393 (6685): 537–44.
[9]
Davies Peter DO (1999) Multi-Drug Resistant Tuberculosis. Director of the Tuberculosis Research Unit, Cardiothoracic Centre, Thomas Drive, Liverpool.
[10]
Dominguez C, Boelens R, and Bonvin A.M.JJ. Haddock (2003) “A protein-protein docking approach based on biochemical or biophysical information.” J. Am. Chem. Soc.; 125:1731–1737.
[11]
Gyanu Lamichhane. Novel targets in M. tuberculosis: search for new drugs. Trends in Molecular Medicine, Volume 17, Issue 1; 25-33, 2011.
[12]
Ismael Kassim, Ray CG (editors) (2004) Sherris Medical Microbiology (4th Ed.). McGraw Hill.
[13]
Junie B. Billones, Maria Constancia O. Carrillo, Voltaire G. Organi, Stephani Joy Y.Macalino, Inno A. Emnacen and Jamie Bernadette A. Sy. Virtual Screening against Mycobacterium tuberculosis Lipoate Protein Ligase B (MtbLipB) and In Silico ADMET Evaluation of Top Hits. Orient. J. Chem., Vol. 29(4); 1457-1468, 2013.
[14]
Kastritis P.L, Bonvin A. M. (2012). "On the binding affinity of macromolecular interactions: daring to ask why proteins interact." J R Soc Interface 10(79).
[15]
Kitchen D.B, Decornez H, Furr J.R, Bajorath J (2004) "Docking and scoring in virtual screening for drug discovery: methods and applications". Nature reviews. Drug discovery 3 (11): 935–949.
[16]
“Protein Docking Using Spherical Polar Fourier Correlations” Hex 8.0.0 User Manual.
[17]
Ma Q, Zhao X, Nasser Eddine A, Geerlof A, Li X, Cronan JE, Kaufmann S.H, Wilmanns M (2006) “The Mycobacterium tuberculosis LipB enzyme functions as a cysteinelysine dyad acyltransferase” PNAS, vol. 103, no.23, 8662-8667.
[18]
Pereira de Jésus-Tran K, Côté P.L, Cantin L, Blanchet J, Labrie F, Breton R (2006). "Comparison of crystal structures of human androgen receptor ligand-binding domain complexed with various agonists reveals molecular determinants responsible for binding affinity." Protein Science, 15(5): 987-999.
[19]
Quin H. Christensen and John E. Cronan (2010) “Lipoic Acid Synthesis: A New Family of Octanoyltransferases Generally Annotated as Lipoate Protein Ligases” Biochemistry, 49 (46), pp 10024–10036.
[20]
Ritchie, D.W. (2003) Evaluation of protein docking predictions using Hex 3.1 in CAPRI rounds 1 and 2. Proteins, 52:98–106.
[21]
Smith, G.R., Sternberg, M.J. (2002) “Prediction of protein-protein interactions by docking methods.” Curr. Opin. Struct. Biol., 12:28–35.
[22]
Suarez J, Ranguelova K, Jarzecki A.A, Manzerova J, Krymov V, Zhao X, Yu S, Metlitsky L, Gerfen G.J, Magliozzo R.S. (2009). "An oxyferrous heme/protein-based radical intermediate is catalytically competent in the catalase reaction of Mycobacterium tuberculosis catalase-peroxidase (KatG)". The Journal of Biological Chemistry 284 (11): 7017-7029.
[23]
Taylor, J.S. and Burnett, R.M. DARWIN (2000) “A program for docking flexible molecules.” Proteins 41, 173-191.
[24]
World Health Organization (2010) WHO endorses new rapid tuberculosis test.
[25]
Zhao X, Miller J. R, and Cronan, J. E. (2005) “The reaction of LipB, the octanoyl-[acyl carrier protein]: protein N-octanoyltransferase of lipoic acid synthesis, proceeds through an acyl-enzyme intermediate” Biochemistry 44, 16737-46.
ADDRESS
Science Publishing Group
1 Rockefeller Plaza,
10th and 11th Floors,
New York, NY 10020
U.S.A.
Tel: (001)347-983-5186