Identification of two natural compound inhibitors of Leishmania donovani Spermidine Synthase (SpdS) through molecular docking and dynamic studies

References

• Adebayo, O. L., Suleman, D., & Samson, A. A. (2013). Natural products in antileishmanial drug discovery: A review. Journal of Asian Scientific Research, 3, 157–173.
   Google Scholar
• Arnold, K., Bordoli, L., Kopp, J., & Schwede, T. (2006). The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling. Bioinformatics, 22, 195–201.10.1093/bioinformatics/bti770
   PubMed Web of Science ®Google Scholar
• Carnesecchi, S., Schneider, Y., Ceraline, J., Duranton, B., Gosse, F., Seiler, N., & Oncology, M. (2001). Geraniol, a component of plant essential oils, inhibits growth and polyamine biosynthesis in human colon cancer cells. Journal of Pharmacology and Experimental Therapeutics, 298, 197–200.
   PubMed Web of Science ®Google Scholar
• Dufe, V. T., Qiu, W., Müller, I. B., Hui, R., Walter, R. D., & Al-Karadaghi, S. (2007). Crystal Structure of Plasmodium falciparum Spermidine Synthase in complex with the substrate decarboxylated S-adenosylmethionine and the potent inhibitors 4MCHA and AdoDATO. Journal of Molecular Biology, 373, 167–177.10.1016/j.jmb.2007.07.053
   PubMed Web of Science ®Google Scholar
• Gilroy, C., Olenyik, T., Roberts, S. C., & Ullman, B. (2011). Spermidine Synthase is required for virulence of Leishmania donovani. Infection and Immunity, 79, 2764–2769.10.1128/IAI.00073-11
   PubMed Web of Science ®Google Scholar
• Grover, A., Katiyar, S. P., Singh, S. K., Dubey, V. K., & Sundar, D. (2012). A leishmaniasis study: Structure-based screening and molecular dynamics mechanistic analysis for discovering potent inhibitors of Spermidine Synthase. BBA – Proteins and Proteomics, 1824, 1476–1483.10.1016/j.bbapap.2012.05.016
   PubMed Web of Science ®Google Scholar
• Haider, N., Eschbach, M., Dias, S. D. S., Gilberger, T., Walter, R. D., & Kai, L. (2005). The Spermidine Synthase of the malaria parasite Plasmodium falciparum: Molecular and biochemical characterisation of the polyamine synthesis enzyme. Molecular & Biochemical Parasitology, 142, 224–236.10.1016/j.molbiopara.2005.04.004
   PubMed Web of Science ®Google Scholar
• Hamaguchi, K., Iwakiri, T., Imamura, K., Furihata, K., Seto, H., & Otake, N. (1987). Juglorin, a new Spermidine Synthase inhibitor. The Journal of Antibiotics, 40, 717–719.10.7164/antibiotics.40.717
   PubMed Web of Science ®Google Scholar
• Heby, O., Roberts, S. C., & Ullman, B. (2003). Polyamine biosynthetic enzymes as drug targets in parasitic protozoa. Biochemical Society Transactions, 31, 415–419.10.1042/bst0310415
   PubMed Web of Science ®Google Scholar
• Hibasami, H., Tanaka, M., Nagai, J., & Ikeda, T. (1980). Dicyclohexylamine, a potent inhibitor of Spermidine Synthase in mammalian cells. FEBS Letters, 116, 99–101.10.1016/0014-5793(80)80537-0
   PubMed Web of Science ®Google Scholar
• Hiroshige, H., Borchardt, R. T., Chen, S. Y., Coward, J. K., & Pegg, A. E. (1980). Studies of inhibition of rat Spermidine Synthase and spermine synthase. Biochemical Journal, 187, 419–428.
   PubMed Web of Science ®Google Scholar
• Induced Fit Docking [Small-molecule drug discovery suite 2014-4]. (2014). New York, NY: Schrödinger, LLC.
   Google Scholar
• Jo, S., Cheng, X., Islam, S. M., Huang, L., Rui, H., Zhu, A., … Im, W. (2014). CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues. Advances in Protein Chemistry and Structural Biology, 96, 235–265.10.1016/bs.apcsb.2014.06.002
   PubMed Web of Science ®Google Scholar
• Jo, S., Kim, T., Iyer, V. G., & Im, W. (2008). CHARMM-GUI: A web-based graphical user interface for CHARMM. Journal of Computational Chemistry, 29, 1859–1865.10.1002/jcc.20945
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., & Tirado-Rives, J. (1988). The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. Journal of the American Chemical Society, 110, 1657–1666.10.1021/ja00214a001
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Source, Open Source Drug Discovery Consortium, & Lynn, A. (2014). g_mmpbsa – a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54, 1951–1962.10.1021/ci500020 m
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26, 283–291.10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., … Im, W. (2016). CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. Journal of Chemical Theory and Computation, 12, 405–413.10.1021/acs.jctc.5b00935
   PubMed Web of Science ®Google Scholar
• LigPrep [Small-molecule drug discovery suite 2014-4]. (2014). New York, NY: Schrödinger, LLC.
   Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 46, 3–26.10.1016/S0169-409X(00)00129-0
   PubMed Web of Science ®Google Scholar
• Mandal, S., Mandal, A., Johansson, H. E., Orjalo, A. V., & Park, M. H. (2013). Depletion of cellular polyamines, spermidine and spermine, causes a total arrest in translation and growth in mammalian cells. Proceedings of National Academy of Sciences USA, 110, 2169–2174.10.1073/pnas.1219002110
   PubMed Web of Science ®Google Scholar
• Melo, F., Sánchez, R., & Sali, A. (2002). Statistical potentials for fold assessment. Protein Science, 11, 430–448.
   PubMed Web of Science ®Google Scholar
• Pegg, A. E., Bitonti, A. J., McCann, P. P., & Coward, J. K. (1983). Inhibition of bacterial aminopropyltransferases by S-adenosyl-1,8-diamino-3-thiooctane and by dicyclohexylamine. FEBS Letters, 155, 192–196.10.1016/0014-5793(82)80600-5
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF chimera – a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25, 1605–1612.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Pieper, U., Webb, B. M., Barkan, D. T., Schneidman-Duhovny, D., Schlessinger, A., Braberg, H., … Sali, A. (2011). ModBase, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Research, 39, 465–474.10.1093/nar/gkq1091
   PubMed Web of Science ®Google Scholar
• Protein Preparation Wizard [Small-molecule drug discovery suite 2014-4]. (2014). New York, NY: Schrödinger, LLC.
   Google Scholar
• QikProp [Schrödinger Suite 2014-4]. (2014). New York, NY: Schrödinger, LLC.
   Google Scholar
• Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42, 320–324.10.1093/nar/gku316
   PubMed Web of Science ®Google Scholar
• Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27, 221–234.10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Sherman, M. L., Shafman, T. D., Coward, J. K., & Kufe, D. W. (1986). Selective inhibition of spermidine biosynthesis and differentiation by S-adenosyl-1,8-diamino-3-thiooctane in murine erythroleukemia cells. Biochemical Pharmacology, 35, 2633–2636.10.1016/0006-2952(86)90066-3
   PubMed Web of Science ®Google Scholar
• Sherman, W., Beard, H. S., & Farid, R. (2006). Use of an induced fit receptor structure in virtual screening. Chemical Biology & Drug Design, 67, 83–84.10.1111/jpp.2006.67.issue-1
   PubMed Web of Science ®Google Scholar
• Shirahata, A., Morohoshi, T., & Samejima, K. (1988). Trans-4-methylcyclohexylamine, a potent new inhibitor of Spermidine Synthase. Chemical & Pharmaceutical Bulletin, 36, 3220–3222.10.1248/cpb.36.3220
   PubMed Web of Science ®Google Scholar
• Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., … So, J. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7, 1–6.
   Web of Science ®Google Scholar
• Singh, N., Kumar, M., & Singh, R. K. (2012). Leishmaniasis : Current status of available drugs and new potential drug targets. Asian Pacific Journal of Tropical Medicine, 5, 485–497.10.1016/S1995-7645(12)60084-4
   PubMed Web of Science ®Google Scholar
• Singh, S., Sarma, S., Katiyar, S. P., Das, M., Bhardwaj, R., Sundar, D., & Dubey, V. K. (2015). Probing the molecular mechanism of hypericin-induced parasite death provides insight into the role of spermidine beyond redox metabolism in Leishmania donovani. Antimicrobial Agents and Chemotherapy, 59, 15–24.10.1128/AAC.04169-14
   PubMed Web of Science ®Google Scholar
• Tovar, J., Wilkinson, S., Mottram, J. C., & Fairlamb, A. H. (1998). Evidence that trypanothione reductase is an essential enzyme in Leishmania by targeted replacement of the tryA gene locus. Molecular Microbiology, 29, 653–660.10.1046/j.1365-2958.1998.00968.x
   PubMed Web of Science ®Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26, 1701–1718.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Vujcic, S., Liang, P., Diegelman, P., Kramer, D. L., & Porter, C. W. (2003). Genomic identification and biochemical characterization of the mammalian polyamine oxidase involved in polyamine back-conversion. Biochemical Journal, 370, 19–28.10.1042/bj20021779
   PubMed Web of Science ®Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web : Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35, 407–410.10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Yang, J., Roy, A., & Zhang, Y. (2013). Protein – ligand binding site recognition using complementary binding-specific substructure comparison and sequence profile alignment. Structural Bioinformatics, 29, 2588–2595.10.1093/bioinformatics/btt447
   PubMed Web of Science ®Google Scholar
• Yang, Z., Lasker, K., Schneidman-Duhovny, D., Webb, B., Huang, C. C., Pettersen, E. F., … Ferrin, T. E. (2012). UCSF Chimera, MODELLER, and IMP : An integrated modeling system. Journal of Structural Biology, 179, 269–278.10.1016/j.jsb.2011.09.006
   PubMed Web of Science ®Google Scholar