Homology modeling, docking and molecular dynamics studies of some secondary metabolites of actinomycetes as biocontrol agents against the 3HNR enzyme of the phytopathogenic fungus Alternaria alternata

References

• Aamir, M., Singh, V. K., Dubey, M. K., Meena, M., Kashyap, S. P., Katari, S. K., Upadhyay, R. S., Umamaheswari, A., & Singh, S. (2018). In silico prediction, characterization, molecular docking, and dynamic studies on fungal SDRs as novel targets for searching potential fungicides against fusarium wilt in tomato. Frontiers in Pharmacology, 9, 1038. https://doi.org/10.3389/fphar.2018.01038
   PubMed Web of Science ®Google Scholar
• Avenot, H. F., & Michailides, T. J. (2007). Resistance to boscalid fungicide in Alternaria alternata isolates from Pistachio in California. Plant Disease, 91 (10), 1345–1350. https://doi.org/10.1094/PDIS-91-10-1345
   PubMed Web of Science ®Google Scholar
• Avenot, H. F., Solorio, C., Morgan, D. P., & Michailides, T. J. (2016). Sensitivity and cross-resistance patterns to demethylation-inhibiting fungicides in California populations of Alternaria alternata pathogenic on pistachio. Crop Protection, 88, 72–78. https://doi.org/10.1016/j.cropro.2016.05.012
   Web of Science ®Google Scholar
• Benkert, P., Biasini, M., & Schwede, T. (2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics (Oxford, England), 27(3), 343–350. https://doi.org/10.1093/bioinformatics/btq662
   PubMed Web of Science ®Google Scholar
• Binkowski, T. A., Naghibzadeh, S., & Liang, J. (2003). CASTp: Computed atlas of surface topography of proteins. Nucleic Acids Research, 31(13), 3352–3355. https://doi.org/10.1093/nar/gkg512
   PubMed Web of Science ®Google Scholar
• Colovos, C., & Yeates, T. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science: A Publication of the Protein Society, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• Cordero, R. J. B., & Casadevall, A. (2017). Functions of fungal melanin beyond virulence. Fungal Biology Reviews, 31(2), 99–e112. https://doi.org/10.1016/j.fbr.2016.12.003
   PubMed Web of Science ®Google Scholar
• Eisenberg, D., Lüthy, R., & Bowie, J. U. (1997). VERIFY3D: Assessment of protein models with three-dimensional profiles. Methods in Enzymology, 277, 396–404. Available: http://www.ncbi.nlm.nih.gov/pubmed/9379925 https://doi.org/10.1016/s0076-6879(97)77022-8
   PubMed Web of Science ®Google Scholar
• Eisenman, H. C., & Casadevall, A. (2012). Synthesis and assembly of fungal melanin. Applied Microbiology and Biotechnology, 93(3), 931–940. https://doi.org/10.1007/s00253-011-3777-2
   PubMed Web of Science ®Google Scholar
• Geourjon, C., & Deléage, G. (1995). SOPMA: Significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Computer Applications in the Biosciences: CABIOS, 11(6), 681–684. https://doi.org/10.1093/bioinformatics/11.6.681
   PubMedGoogle Scholar
• Gundliffe, E. (2006). Antibiotic production by actinomycetes: The Janus faces of regulation. Indian Journal of Microbiology Biotechnology, 33, 500–506.
   PubMed Web of Science ®Google Scholar
• Intra, B., Mungsuntisuk, I., Nihira, T., Igarashi, Y., & Panbangred, W. (2011). Identification of actinomycetes from plant rhizospheric soils with inhibitory activity against Colletotrichum spp., the causative agent of anthracnose disease. BMC Research Notes, 4, 98. https://doi.org/10.1186/1756-0500-4-98
   PubMedGoogle Scholar
• John, B., & Sali, A. (2003). Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic Acids Research, 31(14), 3982–3992. https://doi.org/10.1093/nar/gkg460
   PubMed Web of Science ®Google Scholar
• Khamna, S., Yokota, A., & Lumyong, S. (2009). Actinomycetes isolated from medicinal plant rhizosphere soils: Diversity and screening of antifungal compounds, indole-3-acetic acid and siderophore production. World Journal of Microbiology and Biotechnology, 25(4), 649–655. https://doi.org/10.1007/s11274-008-9933-x
   Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A, Open Source Drug Discovery Consortium (2014). g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Langfelder, K., Streibel, M., Jahn, B., Haase, G., & Brakhage, A. A. (2003). Brakhage AA Biosynthesis of fungal melanins and their importance for human pathogenic fungi. Fungal Genetics and Biology: FG & B, 38(2), 143–158. Mar; https://doi.org/10.1016/s1087-1845(02)00526-1
   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(2), 283–291. https://doi.org/10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Liao, D.-L., Basarab, G. S., Gatenby, A. A., Valent, B., & Jordan, D. B. (2001). Structures of trihydroxynaphthalene reductase-fungicide complexes: Implications for structure-based design and catalysis. Structure (London, England: 1993), 9(1), 19–27. https://doi.org/10.1016/S0969-2126(00)00548-7
   PubMed Web of Science ®Google Scholar
• Merzaeva, O. V., & Shirokikh, I. G. (2006). Colonization of plant rhizosphere by actinomycetes of different genera. Mikrobiologiia, 75(2), 271–276.
   PubMedGoogle Scholar
• Najibi, S. M., Maadooliat, M., Zhou, L., Huang, J. Z., & Gao, X. (2017). Protein structure classification and loop modeling using multiple Ramachandran distributions. Computational and Structural Biotechnology Journal, 15, 243–254. https://doi.org/10.1016/j.csbj.2017.01.011
   PubMed Web of Science ®Google Scholar
• Nassar, A. H., El-Tarabily, K. A., & Sivasithamparam, K. (2003). Growth promotion of bean (Phaseolus vulgaris L.) by a polyamine-producing isolate of Streptomyces griseoluteus. Plant Growth Regulation, 40(2), 97–106. https://doi.org/10.1023/A:1024233303526
   Web of Science ®Google Scholar
• Nosanchuk, J. D., & Casadevall, A. (2003). The contribution of melanin to microbial pathogenesis. Cellular Microbiology, 5(4), 203–223. https://doi.org/10.1046/j.1462-5814.2003.00268.x
   PubMed Web of Science ®Google Scholar
• Nosanchuk, J. D., Stark, R. E., & Casadevall, A. (2015). Fungal melanin: What do we know about structure? Frontiers in Microbiology, 6, 1463. https://doi.org/10.3389/fmicb.2015.01463.
   PubMed Web of Science ®Google Scholar
• Pryor, B. M., & Michailides, T. J. (2002). Morphological, pathogenic, and molecular characterization of alternaria isolates associated with alternaria late blight of pistachio. Phytopathology, 92(4), 406–416. https://doi.org/10.1094/PHYTO.2002.92.4.406
   PubMed Web of Science ®Google Scholar
• Rahman, M. A., Islam, M. Z., & Islam, M. A. (2011). Antibacterial activities of actinomycete isolates collected from soils of Rajshahi, Bangladesh. Biotechnology Research International, 2011, 857925–857926. https://doi.org/10.4061/2011/857925
   PubMedGoogle Scholar
• Rakotoarimanga, N., Zananirina, J., Ramamonjisoa, D., & Ramanankierana, H. (2014). Lutte biologique antifongique: Actinomycètes du sol rhizosphérique antagonistes de Fusarium isolé du fruit de tomate (Solanumlycopersicum L., 1753) pourrie. Afrique Science, 10(3), 243–255.
   Google Scholar
• Reis, R. F., de Goes, A., Mondal, S. N., Shilts, T., Brentu, F. C., & Timmer, L. W. (2006). Effect of lesion age, humidity, and fungicide application on sporulation of Alternaria alternata, the cause of brown spot of tangerine. Plant Disease, 90(8), 1051–1054. https://doi.org/10.1094/PD-90-1051
   PubMed Web of Science ®Google Scholar
• Shen, M. Y., & Sali, A. (2006). Statistical potential for assessment and prediction of protein structures. Protein Science: A Publication of the Protein Society, 15(11), 2507–2524. https://doi.org/10.1110/ps.062416606
   PubMed Web of Science ®Google Scholar
• Solfrizzo, M., Girolamo, A. D., Vitti, C., Tylkowska, K., Grabarkiewicz-Szczęsna, J., Szopińska, D., & Dorna, H. (2005). Toxigenic profile of Alternaria alternata and Alternaria radicina occurring on umbelliferous plants. Food Additives and Contaminants, 22(4), 302–308. https://doi.org/10.1080/02652030500058379
   PubMed Web of Science ®Google Scholar
• Stammler, G., Böhme, F., Philippi, J., Miessner, S., & Tegge, V. (2014). Pathogenicity of alternaria species on potatoes and tomatoes. Proceedings of the Fourteenth EuroBlight Workshop, Limassol, Cyprus, 16, 85–96.
   Google Scholar
• Thompson, J. E., Fahnestock, S., Farrall, L., Liao, D.-I., Valent, B., & Jordan, D. B. (2000). The second naphthol reductase of fungal melanin biosynthesis in Magnaporthe grisea: Tetrahydroxynaphthalene reductase. The Journal of Biological Chemistry, 275(45), 34867–33487. https://doi.org/10.1074/jbc.M006659200
   PubMed Web of Science ®Google Scholar
• Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., & Shim, J. (2009). CHARMM general force field: A force field for druglike molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry, 31(4), 671–690.
   Web of Science ®Google Scholar
• Wang, H., Huang, Y., Wang, J., Chen, X., Wei, K., Wang, M., & Shang, S. (2016). Activities of azoxystrobin and difenoconazole against Alternaria alternata and their control efficacy. Crop Protection, 90, 54–58. https://doi.org/10.1016/j.cropro.2016.08.022
   Web of Science ®Google Scholar
• Weir, T. L., Huff, D. R., Christ, B. J., & Romaine, C. P. (1998). RAPD-PCR analysis of genetic variation among isolates of Alternaria solani and Alternaria alternata from potato and tomato. Mycologia, 90(5), 813–821. https://doi.org/10.1080/00275514.1998.12026975
   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(Web Server issue), W407–W410. https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Xu, D., & Zhang, Y. (2011). Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical Journal, 101(10), 2525–2534. https://doi.org/10.1016/j.bpj.2011.10.024
   PubMed Web of Science ®Google Scholar
• Zheng, H. H., Zhao, J., Wang, T. Y., & Wu, X. H. (2015). Characterization of Alternaria species associated with potato foliar diseases in China. Plant Pathology, 64(2), 425–433. https://doi.org/10.1111/ppa.12274
   Web of Science ®Google Scholar