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Research Articles

Computational identification and antifungal bioassay reveals phytosterols as potential inhibitor of Alternaria arborescens

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Pages 1143-1157 | Received 02 Nov 2018, Accepted 14 Mar 2019, Published online: 09 Apr 2019

References

  • Akhtar, N., Bashir, U., & Mushtaq, S. (2014). First report of leaf spot of rice caused by Alternaria arborescens in Pakistan. Plant Disease, 98(6), 846. doi:10.1094/PDIS-09-13-0969-PDN
  • Akimitsu, K., Peever, T. L., & Timmer, L. W. (2003). Molecular, ecological and evolutionary approaches to understanding Alternaria diseases of citrus. Molecular Plant Pathology, 4(6), 435–46. doi:10.1046/j.1364-3703.2003.00189.x
  • Amineni, U., Pradhan, D., & Marisetty, H. (2010). In silico identification of common putative drug targets in Leptospira interrogans. Journal of Chemical Biology, 3(4), 165–173. doi:10.1007/s12154-010-0039-1.
  • Arcuri, H., & Palma, M. (2011). Understanding the structure, activity and inhibition of chorismate synthase from Mycobacterium tuberculosis. Current Medicinal Chemistry, 18(9), 1311–1317.
  • Armougom, F., Moretti, S., Poirot, O., Audic, S., Dumas, P., Schaeli, B., … Notredame, C. (2006). Expresso: Automatic incorporation of structural information in multiple sequence alignments using 3D-coffee. Nucleic Acids Research, Web Server Issue, 34, W604–W608. doi:10.1093/nar/gkl092
  • Balasubramanian, S., Davies, G. M., Coggins, J. R., & Abell, C. (1991). Inhibition of chorismate synthase by (6R)-and (6S)-6-fluoro-5-enolpyruvylshikimate 3-phosphate. Journal of the American Chemical Society, 113(23), 8945–8946. doi:10.1021/ja00023a051.
  • Bartlewicz, J., Pozo, M. I., Honnay, O., Lievens, B., & Jacquemyn, H. (2016). Effects of agricultural fungicides on microorganisms associated with floral nectar: Susceptibility assays and field experiments. Environmental Science and Pollution Research, 23(19), 19776–19786. doi:10.1007/s11356-016-7181-4
  • Biovia, D. S. (2015). Discovery studio modeling environment. San Diego, CA: Dassault Systemes.
  • Castrignanò, T., De Meo, P. D., Cozzetto, D., Talamo, I. G., & Tramontano, A. (2006). The PMDB Protein Model Database. Nucleic Acids Research (Database Issue), 34, D306–D309. doi:10.1093/nar/gkj105
  • Choi, N. H., Jang, J. Y., Choi, G. J., Choi, Y. H., Jang, K. S., Nguyen, V. T., …., Kim, J.-C. (2016). Antifungal activity of sterols and dipsacus saponins isolated from Dipsacus asper roots against phytopathogenic fungi. Pesticide Biochemistry and Physiology, 141, 103-108. doi: 10.1016/j.pestbp.2016.12.006.
  • Choudhary, P., Kashyap, P. L., Goswami, S. K., Chakdar, H., Srivastava, A. K., & Saxena, A. K. (2018). Genome-wide analysis of microsatellites in Alternaria arborescens and elucidation of the function of polyketide synthase (PksJ). Interdisciplinary Sciences: Computational Life Sciences, 10(4), 813–822. doi:10.1007/s12539-017-0251-6.
  • Coggins, J. R., Abell, C., Evans, L. B., Frederickson, M., Robinson, D. a, Roszak, a W., & Lapthorn, a P. (2003). Experiences with the shikimate-pathway enzymes as targets for rational drug design. Biochemical Society Transactions, 31(Pt 3), 548–552. doi:10.1042/bst0310548.
  • Copping, L. G., & Duke, S. O. (2007). Natural products that have been used commercially as crop protection agents. Pest Management Science, 63(6), 524–554. doi:10.1002/ps.1378
  • Dang, H. X., Pryor, B., Peever, T., & Lawrence, C. B. (2015). The Alternaria genomes database: A comprehensive resource for a fungal genus comprised of saprophytes, plant pathogens, and allergenic species. BMC Genomics, 16(1), 239. doi:10.1186/s12864-015-1430-7
  • Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., … Richardson, D. C. (2007). MolProbity: All-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Research, 35(Web Server Issue), W375-83. doi:10.1093/nar/gkm216
  • de Castro, E., Sigrist, C. J. A., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P. S., Gasteiger, E., … Hulo, N. (2006). ScanProsite: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Research, 34(Web Server Issue), W362–65. doi:10.1093/nar/gkl124
  • Derrer, B., Macheroux, P., & Kappes, B. (2013). The shikimate pathway in apicomplexan parasites: Implications for drug development. Frontiers in Bioscience (Bioscience), 18, 944–969. doi:10.2741/4155
  • Dunbrack, R. L. (2006). Sequence comparison and protein structure prediction. Current Opinion in Structural Biology, 16(3), 374–384. doi:10.1016/j.sbi.2006.05.006
  • Essabbah, N., Gorsane, I., Youssef, M., Hadhri, R., Aloui, S., Gorcii, M., … Skhiri, H. (2014). Cutaneous alternariosis in a renal transplant recipient. Cutis, 93(5), 237–240. doi:10.1046/j.1365-4362.2003.01673.x
  • Fazil, M. H. U. T., Kumar, S., Rao, N. S., Selvaraj, C., Singh, S. K., Pandey, H. P., & Singh, D. V. (2012). Comparative structural analysis of two proteins belonging to quorum sensing system in Vibrio cholerae. Journal of Biomolecular Structure and Dynamics, 30(5), 574–584. doi:10.1080/07391102.2012.687523
  • Gallelli, B., Viviani, M., Nebuloni, M., Marzano, A. V., Pozzi, C., Messa, P., & Fogazzi, G. B. (2006). Skin infection due to Alternaria species in kidney allograft recipients: Report of a new case and review of the literature. Journal of Nephrology, 19(5), 668–672.
  • Gilchrist, D. G. (1976). Production and nature of a host-specific toxin from Alternaria alternata f. sp. lycopersici. Phytopathology, 66, 165–171. doi:10.1094/Phyto-66-165
  • Gomes, J., Vilarinho, C., Duarte, M. D. L., & Brito, C. (2011). Cutaneous phaeohyphomycosis caused by Alternaria alternata unresponsive to Itraconazole treatment. Case Reports in Dermatological Medicine, 2011, 3.. doi:10.1155/2011/385803. Article ID 385803.
  • Gunasekaran, D., Sridhar, J., Suryanarayanan, V., Manimaran, N. C., & Singh, S. K. (2017). Molecular modeling and structural analysis of nAChR variants uncovers the mechanism of resistance to snake toxins. Journal of Biomolecular Structure and Dynamics, 35(8), 1654–1671. doi:10.1080/07391102.2016.1190791
  • Gupta, S., Yadav, S., Suryanarayanan, V., Singh, S. K., & Saxena, J. K. (2017). Investigating the folding pathway and substrate induced conformational changes in B. malayi Guanylate kinase. International Journal of Biological Macromolecules, 94, 621–633. doi:10.1016/j.ijbiomac.2016.10.008
  • Hossain, M. M., Roy, P. K., Jannatul Mosnaz, A. T. M., Shakil, S. K., Hasan, M. M., & Prodhan, S. H. (2015). Structural analysis and molecular docking of potential ligands with chorismate synthase of Listeria monocytogenes: A novel antibacterial drug target. Indian Journal of Biochemistry and Biophysics, 52(1), 45–59.
  • Hu, J., Chen, C., Peever, T., Dang, H., Lawrence, C., & Mitchell, T. (2012). Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer. BMC Genomics, 13(1), 171. doi:10.1186/1471-2164-13-171
  • Hu, W., Ran, Y., Zhuang, K., Lama, J., & Zhang, C. (2015). Alternaria arborescens infection in a healthy individual and literature review of cutaneous alternariosis. Mycopathologia, 179(1-2), 147–152. doi:10.1007/s11046-014-9822-9
  • Hunter, S., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., … Yeats, C. (2009). InterPro: The integrative protein signature database. Nucleic Acids Research, 37(Database issue), D211–5. doi:10.1093/nar/gkn785
  • Ioannidou, D., Maraki, S., Krüger Krasagakis, S., Stefanidou, M., Krasagakis, K., Alexandrakis, M., & Tosca, A. (2004). Cutaneous alternariosis revealing acute myeloid leukaemia in an adult patient. Mycoses, 47(5-6), 227–230. doi:10.1111/j.1439-0507.2004.00954.x
  • Jayaram, B., Singh, T., Mukherjee, G., Mathur, A., Shekhar, S., & Shekhar, V. (2012). Sanjeevini: A freely accessible web-server for target directed lead molecule discovery. BMC Bioinformatics, 13 (Suppl 17: S7). doi:10.1186/1471-2105-13-S17-S7
  • Kaltdorf, M., Srivastava, M., Gupta, S. K., Liang, C., Binder, J., Dietl, A.-M., … Dandekar, T. (2016). Systematic identification of anti-fungal drug targets by a metabolic network approach. Frontiers in Molecular Biosciences, 3(22). doi:10.3389/fmolb.2016.00022
  • Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. E. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols, 10(6), 845–858. doi:10.1038/nprot.2015.053
  • Kim, M., Choi, G., & Lee, H. (2003). Fungicidal property of Curcuma longa L. rhizome-derived curcumin against phytopathogenic fungi in a greenhouse. Journal of Agricultural and Food Chemistry, 51(6), 1578–1581. doi:10.1021/jf0210369
  • Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., … Bryant, S. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44( D1), D1202–D1213. doi:10.1093/nar/gkv951
  • Kitzing, K., Auweter, S., Amrhein, N., & Macheroux, P. (2004). Mechanism of chorismate synthase: Role of the two invariant histidine residues in the active site. Journal of Biological Chemistry, 279(10), 9451–9461. doi:10.1074/jbc.M312471200
  • Kitzing, K., Macheroux, P., & Amrhein, N. (2001). Spectroscopic and kinetic characterization of the bifunctional chorismate synthase from Neurospora crassa: Evidence for a common binding site for 5-enolpyruvylshikimate 3-phosphate and NADPH. Journal of Biological Chemistry, 276(46), 42658–42666. doi:10.1074/jbc.M107249200
  • Lall, N., Weiganand, O., Hussein, A. A., & Meyer, J. J. M. (2006). Antifungal activity of naphthoquinones and triterpenes isolated from the root bark of Euclea natalensis. South African Journal of Botany, 72(4), 579–583. doi:10.1016/j.sajb.2006.03.005
  • Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development setting. Advanced Drug Delivery Reviews, 23(1-3), 3–25. doi:10.1016/S0169-409X(96)00423-1
  • Macheroux, P., Bornemann, S., Ghisla, S., & Thorneley, R. N. F. (1996). Studies with flavin analogs provide evidence that a protonated reduced FMN is the substrate-induced transient intermediate in the reaction of Escherichia coli chorismate synthase. Journal of Biological Chemistry, 271(42), 25850–25858. doi:10.1074/jbc.271.42.25850.
  • Minagawa, Y., & Konohana, I. (2005). A case of dermal cutaneous alternariosis. Nippon Ishinkin Gakkai Zasshi, 46(3), 183–186. doi:10.3314/jjmm.46.183
  • Mooney, C., Wang, Y. H., & Pollastri, G. (2011). SCLpred: Protein subcellular localization prediction by N-to-1 neural networks. Bioinformatics, 27(20), 2812–2819. doi:10.1093/bioinformatics/btr494
  • Nowicki, M., Nowakowska, M., Niezgoda, A., & Kozik, E. (2012). Alternaria Black spot of crucifers: Symptoms, importance of disease, and perspectives of resistance breeding. Vegetable Crops Research Bulletin, 76(1), 5–19. doi:10.2478/v10032-012-0001-6
  • Schrödinger Release. (2015). Maestro-Desmond Interoperability Tools, Version, 4: Desmond molecular dynamics system, Version 4.4. New York, NY: DE Shaw Research.
  • Osborne, A., Thorneley, R. N. F., Abell, C., & Bornemann, S. (2000). Studies with substrate and cofactor analogues provide evidence for a radical mechanism in the chorismate synthase reaction. Journal of Biological Chemistry, 275(46), 35825–35830. doi:10.1074/jbc.M005796200.
  • Osmond, G. W., Walters, R. W., & Puri, P. K. (2011). Cutaneous alternariosis microscopically mimicking blastomycosis. Journal of Cutaneous Pathology, 38(11), 923–925. doi:10.1111/j.1600-0560.2011.01738.x
  • Peever, T. L. L., Su, G., Carpenter-Boggs, L., & Timmer, L. W. W. (2004). Molecular systematics of citrus-associated Alternaria species. Mycologia, 96(1), 119–134. doi:10.2307/3761993
  • 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(13), 1605–1612. doi:10.1002/jcc.20084
  • Piironen, V., Lindsay, D. G., Miettinen, T. A., Toivo, J., & Lampi, A. (2000). Plant sterols: Biosynthesis, biological function and their importance to human nutrition. Journal of the Science of Food and Agriculture, 80(7), 939–966. doi:10.1002/(SICI)1097-0010(20000515)80:7<939::AID-JSFA644>3.0.CO;2-C
  • Pradiba, D., Aarthy, M., Shunmugapriya, V., Singh, S. K., & Vasanthi, M. (2017). Structural insights into the binding mode of flavonols with the active site of matrix metalloproteinase-9 through molecular docking and molecular dynamic simulations studies. Journal of Biomolecular Structure and Dynamics, 36(14), 3718–3739. doi:10.1080/07391102.2017.1397058.
  • Ratledge, C. (1982). Nutrition, growth and metabolism. In C. Ratledge & J. Stanford (Eds.), The Biology of the Mycobacteria (pp. 186–212). London: Academic Press..
  • Robert, T., Talarmin, J.-P., Leterrier, M., Cassagnau, E., Pape, P. L., Danner-Boucher, I., … Morio, F. (2012). Phaeohyphomycosis due to Alternaria infectoria: A single-center experience with utility of PCR for diagnosis and species identification. Medical Mycology, 50(6), 594–600. doi:10.3109/13693786.2012.663508
  • Robert, X., & Gouet, P. (2014). Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Research, 42(Web Server Issue), W320–4. doi:10.1093/nar/gku316
  • Saegeman, V. S., Dupont, L. J., Verleden, G. M., & Lagrou, K. (2012). Paecilomyces lilacinus and Alternaria infectoria cutaneous infections in a sarcoidosis patient after double-lung transplantation. Acta Clinica Belgica, 67(3), 219–221. doi:10.1179/ACB.67.3.2062660
  • Seyfarth, F., Goetze, S., Gräser, Y., Kaatz, M., Ott, U., Rüster, C., … Hipler, U.-C. (2012). Successful treatment of cutaneous alternariosis with caspofungin in a renal transplant recipient. Mycoses, 55(5), 457–462. doi:10.1111/j.1439-0507.2012.02171.x
  • Sharma, N., Murali, A., Singh, S. K., & Giri, R. (2017). Epigallocatechin gallate, an active green tea compound inhibits the Zika virus entry into host cells via binding the envelope protein. International Journal of Biological Macromolecules, 104, 1046–1054. doi:10.1016/j.ijbiomac.2017.06.105
  • Sillitoe, I., Lewis, T. E., Cuff, A., Das, S., Ashford, P., Dawson, N. L., … Orengo, C. A. (2015). CATH: Comprehensive structural and functional annotations for genome sequences. Nucleic Acids Research, 43(D1), D376–D381. doi:10.1093/nar/gku947
  • Singh, M. K., Khare, G., Iyer, S. K., Sharwan, G., & Tripathi, D. K. (2012). Clerodendrum serratum: A clinical approach. Journal of Applied Pharmaceutical Science, 2(2), 11–15.
  • Sirin, S., Pearlman, D. A., & Sherman, W. (2014). Physics‐based enzyme design: Predicting binding affinity and catalytic activity. Proteins: Structure, Function, and Bioinformatics, 82(12), 3397–3409. doi:10.1002/prot.24694
  • Sivashanmugam, M., Sulochana, K., N., & Umashankar, V. (2018). Virtual screening of natural inhibitors targeting ornithine decarboxylase with pharmacophore scaffolding of DFMO and validation by molecular dynamics simulation studies. Journal of Biomolecular Structure and Dynamics, 37(3), 766–780. doi:10.1080/07391102.2018.1439772
  • Sushko, I., Novotarskyi, S., Körner, R., Pandey, A. K., Rupp, M., Teetz, W., … Tetko, I. V. (2011). Online chemical modeling environment (OCHEM): Web platform for data storage, model development and publishing of chemical information. Journal of Computer-Aided Molecular Design, 25(6), 533–554. doi:10.1007/s10822-011-9440-2
  • Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725–2729. doi:10.1093/molbev/mst197
  • Tohge, T., Watanabe, M., Hoefgen, R., & Fernie, A. R. (2013). Shikimate and phenylalanine biosynthesis in the green lineage. Frontiers in Plant Science. 4, 62. doi:10.3389/fpls.2013.00062
  • Ueda, T., Kai, H., & Taniguchi, E. (1990). Growth inhibition of soil-borne pathogenic fungi by typical sterols. Soil Biology and Biochemistry, 22(7), 987–991. doi:10.1016/0038-0717(90)90141-L
  • Wang, C., Wang, F., Zhang, Q., & Liang, W. (2016). Individual and combined effects of tebuconazole and carbendazim on soil microbial activity. European Journal of Soil Biology, 72, 6. doi:10.1016/j.ejsobi.2015.12.005
  • Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2006). Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics and Modelling, 25(2), 247–260. doi:10.1016/j.jmgm.2005.12.005
  • Wang, K., Senthil-Kumar, M., Ryu, C.-M., Kang, L., & Mysore, K. S. (2012). Phytosterols play a key role in plant innate immunity against bacterial pathogens by regulating nutrient efflux into the apoplast. Plant Physiology, 158(4), 1789–1802. doi:10.1104/pp.111.189217
  • Wei, D., Wang, L., Liu, C., & Wang, B. (2010). β-Sitosterol solubility in selected organic solvents. Journal of Chemical and Engineering Data, 55 (8), pp 2917–2919. doi:10.1021/je9009909.
  • 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(Web Server Issue), W407–10. doi:10.1093/nar/gkm290
  • Yoon, M.-Y., Cha, B., & Kim, J.-C. (2013). Recent trends in studies on botanical fungicides in agriculture. The Plant Pathology Journal, 29(1), 1. doi:10.5423/PPJ.RW.05.2012.0072
  • Zhang, M., Wang, W., Zhang, Y., Teng, Y., & Xu, Z. (2017). Effects of fungicide iprodione and nitrification inhibitor 3, 4-dimethylpyrazole phosphate on soil enzyme and bacterial properties. Science of the Total Environment, 599, 254–263.

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