Exploring the Potential of Endophytes and Fungi as Sources of Antimicrobial Compounds

Abstract

Microbes are leading producers of numerous active natural products, many of which have been developed as antibiotics, anticancer agents, and immunosuppressants. The importance and significance of microbial natural products was recognized by the Nobel Prizes in Physiology or Medicine awarded for discovery of penicillin, streptomycin, and avermectin in 1945, 1952 and 2015, respectively. The high occurrence of drug resistance and the high rate of re-isolation represent new challenges. In order to respond to the current challenges and meet the urgently clinical need, new approaches are required to exploit new sources from under-explored habitats and their biosynthetic potentials. This thesis presents efforts to investigate antimicrobial natural products from fungi and endophytes with the combination of genome mining, NMR fingerprint HRMS, and HRMS/MS.\nThe thesis begins with a review on recent advances on anti-TB natural products (NPs) and their potential molecular targets (Chapter 1). 53 natural products showing antimycobacterial activity with defined molecular targets were summarized. Compounds with activity against drug-resistant TB (thiolactomycin, pyridomycin, novobiocin, lipiarmycin A3, gladiolin, kanglemycin A, (S)-(−)-acidomycin, ecumicin, lassomycin, and cyclomarin A) and novel targets (Mtb biotin synthase, ATP synthase, 1,4-dihydroxy-2-naphthoate prenyltransferase, biofilm) were highlighted.\nChapter 2 reports on genome- and MS-based investigation of chlorinated compounds from the phytopathogenic fungus Bipolaris sorokiniana 11134 (BS11134). MS- and UV-guided isolation and purification led to the identification of six new compounds together with seven known xanthones. The biosynthetic gene cluster and putative biosynthetic pathway of isolated compounds were proposed. New chlorinated compound methyl 4-chloro-3,8-dihydroxy-6-methyl-9-oxo-9H-xanthene-1-carboxylate showed activity against Staphylococcus aureus, methicillin-resistant S. aureus, and three clinical-resistant S. aureus strains with a shared minimum inhibitory concentration (MIC) of 12.5 μg/mL.\nIn chapter 3, MS- and UV-guided isolations led to the isolation of ten meroterpenoids from BS11134, including two new compounds 19-dehydroxyl-3-epiarthripenoid A and 12-keto-cochlioquinone A. The stereochemistry difference of aliphatic side chain C-1–C-5 in isocochlioquinone F was proposed to result from stereospecificity of enoyl reductase (ER) of highly reducing polyketide synthase CcqF. Four compounds showed activity against S. aureus and methicillin-resistant S. aureus, with MIC values of 12.5–100 μg/mL. Cochlioquinone B exhibited activity against four clinical resistant S. aureus strains and synergistic antifungal activity against Candida albicans with MIC values of 12.5–25 μg/mL.\nChapter 4 describes the genome-inspired chemical exploration of the marinederived fungus Aspergillus fumigatus MF071. Two new compounds 19S,20-epoxy-18-oxotryprostatin A and 20-hydroxy-18-oxotryprostatin A, in addition to 28 known compounds, were isolated from MF071. NMR data of monomethylsulochrin-4-sulphate and pseurotin H as naturally occurring compounds were firstly reported. The antibacterial activities of these compounds were evaluated. Helvolinic acid and helvolic acid exhibited strong activity against S. aureus (MIC: 6.25 and 3.13 μg/mL, respectively) and E. coli (MIC: 6.25 and 3.13 μg/mL, respectively). Genomic data analyses revealed the putative biosynthetic gene clusters ftm for fumitremorgins, pso for pseurotins, fga for fumigaclavines, and hel for helvolinic acid.\nFinally, chapter 5 describes the analytical method using 1H NMR and HR-LCMS to investigate the chemical profile of microbial co-cultures. A microbial single culture extract and co-culture extract library was constructed and subjected to antimycobacterial activity screening. The chemical investigation of Talaromyces sp. MF059 and Bacillus sp. LF017 co-culture led to the discovery of bacillibactin, one siderophore with catecholic trilactone structure.\nIn summary, this thesis reports on the isolation and characterization of 67 secondary metabolites from fungi and endophytes, including 10 new compounds. 20 out of 67 showed antimicrobial activities against different bacteria. The structures of isolated compounds were elucidated based on NMR, HRESIMS, density functional theory (DFT) calculation, and DP4 probability analysis. The results show the great biosynthetic capacity of fungi and endophytes to produce diverse active metabolites. This thesis also demonstrates that the unexplored “biosynthetic dark matter” can be discovered using genome mining, HRMS, NMR, HRMS/MS, and co-culture.