251
Views
14
CrossRef citations to date
0
Altmetric
Articles

Pharmacoinformatics analysis to identify inhibitors of Mtb-ASADH

, &
Pages 1-14 | Received 11 Aug 2014, Accepted 05 Jan 2015, Published online: 11 Feb 2015

References

  • Arachea, B. T., Liu, X., Pavlovsky, A. G., & Viola, R. E. (2010). Expansion of the aspartate-semialdehyde dehydrogenase family: The first structure of a fungal ortholog. Acta Crystallographica Section D: Biological Crystallography, 66, 205–212.10.1107/S0907444909052834
  • Azevedo, R. A., Lancien, M., & Lea, P. J. (2006). The aspartic acid metabolic pathway, an exciting and essential pathway in plants. Amino Acids, 30, 143–162.10.1007/s00726-005-0245-2
  • Bharatam, P. V., Khanna, S., & Francis, S. M. (2008). Modeling and informatics in drug design. Pharmaceutical Sciences Encyclopedia: Drug Discovery, Development, and Manufacturing, 31, 1–46.
  • Blanco, J., Moore, R. A., Faehnle, C. R., Coe, D. M., & Viola, R. E. (2004). The role of substrate-binding groups in the mechanism of aspartate-beta-semialdehyde dehydrogenase. Acta Crystallographica Section D: Biological Crystallography, 60, 1388–1395.10.1107/S0907444904012971
  • Blanco, J., Moore, R. A., Faehnle, C. R., & Viola, R. E. (2004). Critical catalytic functional groups in the mechanism of aspartate-beta-semialdehyde dehydrogenase. Acta Crystallographica Section D: Biological Crystallography, 60, 1808–1815.10.1107/S0907444904020104
  • Blanco, J., Moore, R. A., Kabaleeswaran, V., & Viola, R. E. (2003). A structural basis for the mechanism of aspartate semialdehyde dehydrogenase from Vibrio cholerae. Protein Science, 12, 27–33.10.1110/ps.0230803
  • Blanco, J., Moore, R. A., & Viola, R. E. (2003). Capture of an intermediate in the catalytic cycle of L-aspartate-beta-semialdehyde dehydrogenase. Proceedings of the National Academy of Sciences of the United States of America, 100, 12613–12617.10.1073/pnas.1634958100
  • Cardineau, G. A., & Curtiss, R. (1987). Nucleotide sequence of the asd gene of Streptococcus mutans. Identification of the promoter region and evidence for attenuator-like sequences preceding the structural gene. Journal of Biological Chemistry, 262, 3344–3353.
  • Case, D. A., Cheatham, T. E., Darden, T., Gohlke, H., Luo, R., Merz, K. M., … Woods, R. J. (2005). The Amber biomolecular simulation programs. Journal of Computational Chemistry, 26, 1668–1688.10.1002/(ISSN)1096-987X
  • Chen, X., Schauder, S., Potier, N., Van Dorsselaer, A., Pelczer, I., Bassler, B. L., & Hughson, F. M. (2002). Structural identification of a bacterial quorum-sensing signal containing boron. Nature, 415, 545–549.10.1038/415545a
  • Cox, R. J., Gibson, J. S., & Hadfield, A. T. (2005). Design, synthesis and analysis of inhibitors of bacterial aspartate semialdehyde dehydrogenase. ChemBioChem, 6, 2255–2260.10.1002/cbic.v6:12
  • Cox, R. J., Gibson, J. S., & Mayo Martin, M. B. (2002). Aspartyl phosphonates and phosphoramidates: The first synthetic inhibitors of bacterial aspartate-semialdehyde dehydrogenase. ChemBioChem, 3, 874–886.10.1002/1439-7633(20020902)3:9<874::AID-CBIC874>3.0.CO;2-V
  • Cox, R. J., Hadfield, A. T., & Mayo-Martin, M. B. (2001). Difluoromethylene analogues of aspartyl phosphate: The first synthetic inhibitors of aspartate semi-aldehyde dehydrogenase. Chemical Communications, 18, 1710–1711.10.1039/b103988c
  • Faehnle, C. R., Le Coq, J., Liu, X., & Viola, R. E. (2006). Examination of key intermediates in the catalytic cycle of aspartate-beta-semialdehyde dehydrogenase from a gram-positive infectious bacteria. Journal of Biological Chemistry, 281, 31031–31040.10.1074/jbc.M605926200
  • Faehnle, C. R., Ohren, J. F., & Viola, R. E. (2005). A new branch in the family: Structure of aspartate-beta-semialdehyde dehydrogenase from Methanococcus jannaschii. Journal of Molecular Biology, 353, 1055–1068.10.1016/j.jmb.2005.09.027
  • Galan, J. E., Nakayama, K., & Curtiss, 3rd, R. (1990). Cloning and characterization of the asd gene of Salmonella typhimurium: Use in stable maintenance of recombinant plasmids in Salmonella vaccine strains. Gene, 94, 29–35.10.1016/0378-1119(90)90464-3
  • Gao, G., Liu, X., Pavlovsky, A., & Viola, R. E. (2010). Identification of selective enzyme inhibitors by fragment library screening. Journal of Biomolecular Screening, 15, 1042–1050.10.1177/1087057110381383
  • Hadfield, A., Kryger, G., Ouyang, J., Petsko, G. A., Ringe, D., & Viola, R. (1999). Structure of aspartate-[beta]-semialdehyde dehydrogenase from Escherichia coli, a key enzyme in the aspartate family of amino acid biosynthesis. Journal of Molecular Biology, 289, 991–1002.10.1006/jmbi.1999.2828
  • Hadfield, A., Shammas, C., Kryger, G., Ringe, D., Petsko, G. A., Ouyang, J., & Viola, R. E. (2001). Active site analysis of the potential antimicrobial target aspartate semialdehyde dehydrogenase. Biochemistry, 40, 14475–14483.10.1021/bi015713o
  • Han, S., Moore, R. A. & Viola, R. E. (2003). A facile synthesis of a difluoromethylene analog of beta-aspartyl phosphate as an inhibitor of L-aspartate-beta-semialdehyde dehydrogenase. Synlett, 6, 845–846.
  • Harb, O. S., & Kwaik, Y. A. (1998). Identification of the aspartate-β-semialdehyde dehydrogenase gene of Legionella pneumophila and characterization of a null mutant. Infection and Immunity, 66, 1898–1903.
  • van Heijenoort, J. (2001). Recent advances in the formation of the bacterial peptidoglycan monomer unit. Natural Product Reports, 18, 503–519.10.1039/a804532a
  • Karsten, W. E. & Viola, R. E. (1991). Chemical and kinetic mechanisms of aspartate-[beta]-semialdehyde dehydrogenase from Escherichia coli. Biochimica et Biophysica Acta (BBA)–Protein Structure and Molecular Enzymology, 1077, 209–219.10.1016/0167-4838(91)90060-D
  • Karsten, W. E. & Viola, R. E. (1992). Identification of an essential cysteine in the reaction catalyzed by aspartate-[beta]-semialdehyde dehydrogenase from Escherichia coli. Biochimica et Biophysica Acta (BBA)–Protein Structure and Molecular Enzymology, 1121, 234–238.10.1016/0167-4838(92)90360-P
  • Kumar, R., & Garg, P. (2013). Molecular modeling and active site binding mode characterization of aspartate β-semialdehyde dehydrogenase family. Molecular Informatics, 32, 377–383.10.1002/minf.201200128
  • Kumar, R., Garg, P., & Bharatam, P. (2014). Shape-based virtual screening, docking and molecular dynamics simulations to identify Mtb-ASADH inhibitors. Journal of Biomolecular Structure and Dynamics. doi:10.1080/07391102.2015.1005137
  • Luniwal, A., Wang, L., Pavlovsky, A., Erhardt, P. W., & Viola, R. E. (2012). Molecular docking and enzymatic evaluation to identify selective inhibitors of aspartate semialdehyde dehydrogenase. Bioorganic and Medicinal Chemistry, 20, 2950–2956.
  • Lyon, G. J., & Novick, R. P. (2004). Peptide signaling in Staphylococcus aureus and other Gram-positive bacteria. Peptides, 25, 1389–1403.10.1016/j.peptides.2003.11.026
  • Morris, G. M., Goodsell, D. S., Halliday, R. S., Huey, R., Hart, W. E., Belew, R. K., & Olson, A. J. (1998). Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. Journal of Computational Chemistry, 19, 1639–1662.10.1002/(ISSN)1096-987X
  • Ouyang, J., & Viola, R. E. (1995). Use of structural comparisons to select mutagenic targets in aspartate-.beta.-semialdehyde dehydrogenase. Biochemistry, 34, 6394–6399.10.1021/bi00019a019
  • Ragkousi, K., Eichenberger, P., van Ooij, C., & Setlow, P. (2003). Identification of a new gene essential for germination of Bacillus subtilis spores with Ca2+-dipicolinate. Journal of Bacteriology, 185, 2315–2329.10.1128/JB.185.7.2315-2329.2003
  • SYBYL7.1. St. Louis, MO: Tripos.
  • Viola, R. E. (2001). The central enzymes of the aspartate family of amino acid biosynthesis. Accounts of Chemical Research, 34, 339–349.10.1021/ar000057q
  • Viola, R. E., Faehnle, C. R., Blanco, J., Moore, R. A., Liu, X., Arachea, B. T., & Pavlovsky, A. G. (2011). The catalytic machinery of a key enzyme in amino acid biosynthesis. Journal of Amino Acids 2011. Article ID: 352538. doi: 10.4061/2011/352538
  • Vyas, R., Tewari, R., Weiss, M. S., & Karthikeyan, S. (2012). Structures of ternary complexes of aspartate-semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis H37Rv. Acta Crystallographica Section D: Biological Crystallography, 68, 671–679.10.1107/S0907444912007330
  • Wickstrom, L., Okur, A., & Simmerling, C. (2009). Evaluating the performance of the ff99SB force field based on NMR scalar coupling data. Biophysical Journal, 97, 853–856.10.1016/j.bpj.2009.04.063
  • Wolber, G., & Langer, T. (2005). LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. Journal of Chemical Information and Modeling, 45, 160–169.10.1021/ci049885e

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.