Identification of Scytalone Dehydratase Inhibitors Effective against Melanin Biosynthesis Dehydratase Inhibitor-Resistant Pyricularia oryzae

Chemical biology research in RIKEN NPDepo aimed at agricultural applications

This review outlines research on chemical biology using mainly microbial metabolites for agricultural applications. We established the RIKEN Natural Products Depository (NPDepo), housing many microbial metabolites, to support academic researchers who focus on drug discovery. We studied methods to stimulate secondary metabolism in microorganisms to collect various microbial products. The switch of secondary metabolism in microorganisms changes depending on the culture conditions. We discovered compounds that activate biosynthetic gene clusters in actinomycetes and filamentous fungi. Using these compounds, we succeeded in inducing the production of active compounds. Two approaches for screening bioactive compounds are described. One is phenotypic screening to explore antifungal compounds assisted by artificial intelligence (AI). AI can distinguish the morphological changes induced by antifungal compounds in filamentous fungi. The other is the chemical array method for detecting interactions between compounds and target proteins. Our chemical biology approach yielded many new compounds as fungicide candidates.

Various amino acid substitutions in succinate dehydrogenase complex regulating differential resistance to pydiflumetofen in Magnaporthe oryzae

Rice blast, caused by Magnaporthe oryzae, is a devastating fungal disease worldwide. Pydiflumetofen (Pyd) is a new succinate dehydrogenase inhibitor (SDHI) that exhibited anti-fungal activity against M. oryzae. However, control of rice blast by Pyd and risk of resistance to Pyd are not well studied in this pathogen. The baseline sensitivity of 109 M. oryzae strains to Pyd was determined using mycelial growth rate assay, with EC50 values ranging from 0.291 to 2.1313 μg/mL, and an average EC50 value of 1.1005 ± 0.3727 μg/mL. Totally 28 Pyd-resistant (PydR) mutants with 15 genotypes of point mutations in succinate dehydrogenase (SDH) complex were obtained, and the resistance level could be divided into three categories of very high resistance (VHR), high resistance (HR) and moderate resistance (MR) with the resistance factors (RFs) of >1000, 105.74-986.13 and 81.92-99.48, respectively. Molecular docking revealed that all 15 mutations decreased the binding-force score for the affinity between Pyd and target subunits, which further confirmed that these 15 genotypes of point mutations were responsible for the resistance to Pyd in M. oryzae. There was positive cross resistance between Pyd and other SDHIs, such as fluxapyroxad, penflufen or carboxin, while there was no cross-resistance between Pyd and carbendazim, prochloraz or azoxystrobin in M. oryzae, however, PydR mutants with SdhBP198Q, SdhCL66F or SdhCL66R genotype were still sensitive to the other 3 SDHIs, indicating lack of cross resistance. The results of fitness study revealed that the point mutations in MoSdhB/C/D genes might reduce the hyphae growth and sporulation, but could improve the pathogenicity in M. oryzae. Taken together, the risk of resistance to Pyd might be moderate to high, and it should be used as tank-mixtures with other classes of fungicides to delay resistance development when it is used for the control of rice blast in the field.

In-silico bioprospecting of secondary metabolites from endophytic Streptomyces spp. against Magnaporthe oryzae, a cereal killer fungus

Rice blast disease, caused by Magnaporthe oryzae, is the most devastating cereal killer worldwide. Note that melanin pigment is an essential factor of M. oryzae virulence, thus fungicides interfering with melanin biosynthesizing enzymes would reduce the pathogenicity. Scytalone dehydratase (SDH) is the key target for commercial fungicides, like carpropamid, due to its role in the dehydration reaction of the fungal melanin pathway. However, a single-point mutation (V75M) in SDH elicits resistance to carpropamid. A lack of effective fungicides against this resistant strain expedited the quest for novel bioactive inhibitors. Currently, bacterial endophytes like Streptomyces have been heralded for synthesizing bioactive metabolites to protect plants from phytopathogens. The literature search led to the identification of 21 Streptomyces spp. symbionts of paddy that can suppress M. oryzae growth. An antiSMASH server was used to explore Streptomyces spp. gene clusters and found 4463 putative metabolites. Besides, 745 unique metabolites were subjected to a series of virtual screening techniques. Ideally, this process identified five potential SDH inhibitors. The docking result highlights that the metabolite pseudopyronine A interacted hydrophobically with both Val75 of SDHWT and Met75 of SDHV75M targets. Moreover, pseudopyronine A has a higher binding free energy with SDHWT (- 89.94 kcal/mol) and SDHV75M (- 71.95 kcal/mol). Interestingly, the pyranones scaffold of pseudopyronine A was reported for antifungal activity against phytopathogens. Dynamic behavior confirms that pseudopyronine A has excellent conformational states with both SDHWT and SDHV75M. Altogether, we hope that this study creates a new avenue for the discovery of novel phytopathogen inhibitors from endophytes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03859-7.

Light regulation of secondary metabolism in fungi

Fungi have evolved unique metabolic regulation mechanisms for adapting to the changing environments. One of the key features of fungal adaptation is the production of secondary metabolites (SMs), which are essential for survival and beneficial to the organism. Many of these SMs are produced in response to the environmental cues, such as light. In all fungal species studied, the Velvet complex transcription factor VeA is a central player of the light regulatory network. In addition to growth and development, the intensity and wavelength of light affects the formation of a broad range of secondary metabolites. Recent studies, mainly on species of the genus Aspergillus, revealed that the dimer of VeA-VelB and LaeA does not only regulate gene expression in response to light, but can also be involved in regulating production of SMs. Furthermore, the complexes have a wide regulatory effect on different types of secondary metabolites. In this review, we discussed the role of light in the regulation of fungal secondary metabolism. In addition, we reviewed the photoreceptors, transcription factors, and signaling pathways that are involved in light-dependent regulation of secondary metabolism. The effects of transcription factors on the production of secondary metabolites, as well as the potential applications of light regulation for the production of pharmaceuticals and other products were discussed. Finally, we provided an overview of the current research in this field and suggested potential areas for future research.