- About this Journal ·
- Abstracting and Indexing ·
- Aims and Scope ·
- Annual Issues ·
- Article Processing Charges ·
- Author Guidelines ·
- Bibliographic Information ·
- Citations to this Journal ·
- Contact Information ·
- Editorial Board ·
- Editorial Workflow ·
- Free eTOC Alerts ·
- Publication Ethics ·
- Recently Accepted Articles ·
- Reviewers Acknowledgment ·
- Submit a Manuscript ·
- Subscription Information ·
- Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 609289, 14 pages
Computational Elucidation of Structural Basis for Ligand Binding with Leishmania donovani Adenosine Kinase
1Biomedical Informatics Centre, Rajendra Memorial Research Institute of Medical Science, Patna 800007, India
2Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur 844102, India
Received 30 March 2013; Revised 17 June 2013; Accepted 18 June 2013
Academic Editor: Ali Ouaissi
Copyright © 2013 Rajiv K. Kar et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- The World Health Report on leishmaniasis, http://www.who.int/leishmaniasis/en/.
- P. K. Sinha, S. Bimal, S. K. Singh, K. Pandey, D. N. Gangopadhyay, and S. K. Bhattacharya, “Pre- & post-treatment evaluation of immunological features in Indian visceral leishmaniasis (VL) patients with HIV co-infection,” Indian Journal of Medical Research, vol. 123, no. 3, pp. 197–202, 2006.
- F. Chappuis, S. Sundar, A. Hailu et al., “Visceral leishmaniasis: what are the needs for diagnosis, treatment and control?” Nature Reviews Microbiology, vol. 5, no. 11, pp. 873–882, 2007.
- S. L. Croft, M. P. Barrett, and J. A. Urbina, “Chemotherapy of trypanosomiases and leishmaniasis,” Trends in Parasitology, vol. 21, no. 11, pp. 508–512, 2005.
- S. Singh and R. Sivakumar, “Challenges and new discoveries in the treatment of leishmaniasis,” Journal of Infection and Chemotherapy, vol. 10, no. 6, pp. 307–315, 2004.
- J. Park and R. S. Gupta, “Adenosine kinase and ribokinase—the RK family of proteins,” Cellular and Molecular Life Sciences, vol. 65, no. 18, pp. 2875–2896, 2008.
- J. V. Tuttle and T. A. Krenitsky, “Purine phosphoribosyltransferases from Leishmania donovani,” Journal of Biological Chemistry, vol. 255, no. 3, pp. 909–916, 1980.
- A. K. Datta, R. Datta, and B. Sen, “Antiparasitic chemotherapy: tinkering with the purine salvage pathway,” Advances in Experimental Medicine and Biology, vol. 625, pp. 116–132, 2008.
- D. L. Looker, R. L. Berens, and J. J. Marr, “Purine metabolism in Leishmania donovani amastigotes and promastigotes,” Molecular and Biochemical Parasitology, vol. 9, no. 1, pp. 15–28, 1983.
- A. K. Datta, D. Bhaumik, and R. Chatterjee, “Isolation and characterization of adenosine kinase from Leishmania donovani,” Journal of Biological Chemistry, vol. 262, no. 12, pp. 5515–5521, 1987.
- M. Berg, P. van der Veken, A. Goeminne, A. Haemers, and K. Augustyns, “Inhibitors of the purine salvage pathway: a valuable approach for antiprotozoal chemotherapy?” Current Medicinal Chemistry, vol. 17, no. 23, pp. 2456–2481, 2010.
- M. Vodnala, A. Fijolek, R. Rofougaran, M. Mosimann, P. Mäser, and A. Hofer, “Adenosine kinase mediates high affinity adenosine salvage in Trypanosoma brucei,” Journal of Biological Chemistry, vol. 283, no. 9, pp. 5380–5388, 2008.
- K. M. Sinha, M. Ghosh, I. Das, and A. K. Datta, “Molecular cloning and expression of adenosine kinase from Leishmania donovani: identification of unconventional P-loop motif,” Biochemical Journal, vol. 339, no. 3, pp. 667–673, 1999.
- M. A. Matulenko, E. S. Paight, R. R. Frey et al., “4-Amino-5-aryl-6-arylethynylpyrimidines: structure-activity relationships of non-nucleoside adenosine kinase inhibitors,” Bioorganic and Medicinal Chemistry, vol. 15, no. 4, pp. 1586–1605, 2007.
- B. G. Ugarkar, J. M. DaRe, J. J. Kopcho et al., “Adenosine kinase inhibitors. 1. Synthesis, enzyme inhibition, and antiseizure activity of 5-iodotubercidin analogues,” Journal of Medicinal Chemistry, vol. 43, no. 15, pp. 2883–2893, 2000.
- M. A. Matulenko, C.-H. Lee, M. Jiang et al., “5-(3-Bromophenyl)-7-(6-morpholin-4-ylpyridin-3-yl)pyrido[2,3-d] pyrimidin-4-ylamine: structure-activity relationships of 7-substituted heteroaryl analogs as non-nucleoside adenosine kinase inhibitors,” Bioorganic and Medicinal Chemistry, vol. 13, no. 11, pp. 3705–3720, 2005.
- J. Caballero, M. Fernández, and F. D. González-Nilo, “A CoMSIA study on the adenosine kinase inhibition of pyrrolo[2,3-d]pyrimidine nucleoside analogues,” Bioorganic and Medicinal Chemistry, vol. 16, no. 9, pp. 5103–5108, 2008.
- E. F. F. da Cunha, D. T. Mancini, and T. C. Ramalho, “Molecular modeling of the Toxoplasma gondii adenosine kinase inhibitors,” Medicinal Chemistry Research, vol. 21, no. 5, pp. 590–600, 2011.
- S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997.
- S. Kuettel, J. Greenwald, D. Kostrewa, S. Ahmed, L. Scapozza, and R. Perozzo, “Crystal structures of T. b. rhodesiense adenosine kinase complexed with inhibitor and activator: implications for catalysis and hyperactivation,” PLoS Neglected Tropical Diseases, vol. 5, no. 5, Article ID e1164, 2011.
- K. Arnold, L. Bordoli, J. Kopp, and T. Schwede, “The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling,” Bioinformatics, vol. 22, no. 2, pp. 195–201, 2006.
- J. Peng and J. Xu, “Raptorx: exploiting structure information for protein alignment by statistical inference,” Proteins, vol. 79, no. 10, pp. 161–171, 2011.
- M. Nielsen, C. Lundegaard, O. Lund, and T. N. Petersen, “CPHmodels-3.0-remote homology modeling using structure-guided sequence profiles,” Nucleic Acids Research, vol. 38, no. 2, pp. W576–W581, 2010.
- J. Söding, A. Biegert, and A. N. Lupas, “The HHpred interactive server for protein homology detection and structure prediction,” Nucleic Acids Research, vol. 33, no. 2, pp. W244–W248, 2005.
- N. Eswar, B. Webb, M. A. Marti-Renom et al., “Comparative protein structure modeling using MODELLER,” Current Protocols in Protein Science, chapter 2, unit 2.9, 2007.
- R. Luthy, J. U. Bowie, and D. Eisenberg, “Assesment of protein models with three-dimensional profiles,” Nature, vol. 356, no. 6364, pp. 83–85, 1992.
- R. A. Laskowski, M. W. MacArthur, D. S. Moss, and J. M. Thornton, “PROCHECK: a program to check the stereochemical quality of protein structures,” Journal of Applied Crystallography, vol. 26, pp. 283–291, 1993.
- V. Z. Spassov, P. K. Flook, and L. Yan, “LOOPER: a molecular mechanics-based algorithm for protein loop prediction,” Protein Engineering, Design and Selection, vol. 21, no. 2, pp. 91–100, 2008.
- C. Colovos and T. O. Yeates, “Verification of protein structures: patterns of nonbonded atomic interactions,” Protein Science, vol. 2, no. 9, pp. 1511–1519, 1993.
- M. Wiederstein and M. J. Sippl, “ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins,” Nucleic Acids Research, vol. 35, pp. W407–W410, 2007.
- R. Maiti, G. H. Van Domselaar, H. Zhang, and D. S. Wishart, “SuperPose: a simple server for sophisticated structural superposition,” Nucleic Acids Research, vol. 32, pp. W590–W594, 2004.
- W. N. Setzer and I. V. Ogungbe, “In-silico investigation of antitrypanosomal Phytochemicals from Nigerian medicinal plants,” Plos Neglected Tropical Diseases, vol. 6, no. 7, Article ID e1727, 2012.
- D. Van Der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, “GROMACS: fast, flexible, and free,” Journal of Computational Chemistry, vol. 26, no. 16, pp. 1701–1718, 2005.
- H. J. C. Berendsen, J. R. Grigera, and T. P. Straatsma, “The missing term in effective pair potentials,” Journal of Physical Chemistry, vol. 91, no. 24, pp. 6269–6271, 1987.
- H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Dinola, and J. R. Haak, “Molecular dynamics with coupling to an external bath,” The Journal of Chemical Physics, vol. 81, no. 8, pp. 3684–3690, 1984.
- R. Martoňák, A. Laio, and M. Parrinello, “Predicting crystal structures: the Parrinello-Rahman method revisited,” Physical Review Letters, vol. 90, no. 7, Article ID 75503, 4 pages, 2003.
- J.-P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, “Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes,” Journal of Computational Physics, vol. 23, no. 3, pp. 327–341, 1977.
- P. P. Ewald, “Die Berechnung optischer und elektrostatischer Gitterpotentiale,” Annals of Physics, vol. 369, pp. 253–287, 1921.
- A. T. R. Laurie and R. M. Jackson, “Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites,” Bioinformatics, vol. 21, no. 9, pp. 1908–1916, 2005.
- Schrödinger Suite 2012 Schrِdinger Suite, Epik Version 2.2, Schrِdinger, LLC, New York, NY, USA, 2012.
- Schrödinger Suite 2012 Schrِdinger Suite, Impact Version 5.7, Schrِdinger, LLC, New York, NY, USA, 2012.
- Schrödinger Suite 2012 Schrِdinger Suite, Prime Version 2.3, Schrِdinger, LLC, New York, NY, USA, 2012.
- R. K. Kar, P. Suryadevara, B. R. Sahoo, G. C. Sahoo, M. R. Dikhit, and P. Das, “Exploring novel KDR inhibitors based on pharmaco-informatics methodology,” SAR and QSAR in Environmental Research, vol. 24, no. 3, pp. 215–234, 2013.
- R. A. Friesner, R. B. Murphy, M. P. Repasky et al., “Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes,” Journal of Medicinal Chemistry, vol. 49, no. 21, pp. 6177–6196, 2006.
- M. P. Repasky, M. Shelley, and R. A. Friesner, “Flexible ligand docking with Glide,” Current Protocols in Bioinformatics, chapter 8, unit 8, 2007.
- M. A. Miteva, W. H. Lee, M. O. Montes, and B. O. Villoutreix, “Fast structure-based virtual ligand screening combining FRED, DOCK, and surflex,” Journal of Medicinal Chemistry, vol. 48, no. 19, pp. 6012–6022, 2005.
- B. Kramer, M. Rarey, and T. Lengauer, “Evaluation of the FLEXX incremental construction algorithm for protein-ligand docking,” Proteins-Structure Function and Genetics, vol. 37, pp. 228–241, 1999.
- G. Jones, P. Willett, R. C. Glen, A. R. Leach, and R. Taylor, “Development and validation of a genetic algorithm for flexible docking,” Journal of Molecular Biology, vol. 267, no. 3, pp. 727–748, 1997.
- A. W. Schüttelkopf and D. M. F. Van Aalten, “PRODRG: a tool for high-throughput crystallography of protein-ligand complexes,” Acta Crystallographica D, vol. 60, no. 8, pp. 1355–1363, 2004.
- M. Ghosh and A. K. Datta, “Probing the function(s) of active-site arginine residue in Leishmania donovani adenosine kinase,” Biochemical Journal, vol. 298, no. 2, pp. 295–301, 1994.
- M. C. A. Costa, L. E. S. Barata, and Y. Takahata, “Conformation of neolignans that bind to the arginine residue in adenosine-kinase from Leishmania donovani,” Journal of Molecular Structure, vol. 464, no. 1–3, pp. 281–287, 1999.
- R. Datta, I. Das, B. Sen et al., “Mutational analysis of the active-site residues crucial for catalytic activity of adenosine kinase from Leishmania donovani,” Biochemical Journal, vol. 387, no. 3, pp. 591–600, 2005.
- R. Datta, I. Das, B. Sen et al., “Homology-model-guided site-specific mutagenesis reveals the mechanisms of substrate binding and product-regulation of adenosine kinase from Leishmania donovani,” Biochemical Journal, vol. 394, no. 1, pp. 35–42, 2006.