Synthetic Biology-Based Discovery of Diterpenoid Pyrones from the Genome of Eupenicillium shearii

Genome mining of labdane-related diterpenoids: Discovery of the two-enzyme pathway leading to (-)-sandaracopimaradiene in the fungus Arthrinium sacchari

Labdane-related diterpenoids (LRDs) in fungi are a pharmaceutically important, but underexplored family of natural products. In the biosynthesis of fungal LRDs, bifunctional terpene cyclases (TCs) consisting of αβγ domains are generally used to synthesize the polycyclic skeletones of LRDs. Herein, we conducted genome mining of LRDs in our fungal genome database and identified a unique pair of TCs, AsPS and AsCPS, in the fungus Arthrinium sacchari. AsPS consists of catalytically active α and inactive β domains, whereas AsCPS contains βγ domains and a truncated α domain. Heterologous expression in Aspergillus oryzae and biochemical characterization of recombinant proteins demonstrated that AsCPS synthesized copalyl diphosphate and that AsPS then converted it to (-)-sandaracopimaradiene. Since AsPS and AsCPS have distinct domain organizations from those of known fungal TCs and are likely generated through fusion or loss of catalytic domains, our findings provide insight into the evolution of TCs in fungi.

Recent developments in the engineered biosynthesis of fungal meroterpenoids

Meroterpenoids are hybrid compounds that are partially derived from terpenoids. This group of natural products displays large structural diversity, and many members exhibit beneficial biological activities. This mini-review highlights recent advances in the engineered biosynthesis of meroterpenoid compounds with C15 and C20 terpenoid moieties, with the reconstruction of fungal meroterpenoid biosynthetic pathways in heterologous expression hosts and the mutagenesis of key enzymes, including terpene cyclases and α-ketoglutarate (αKG)-dependent dioxygenases, that contribute to the structural diversity. Notable progress in genome sequencing has led to the discovery of many novel genes encoding these enzymes, while continued efforts in X-ray crystallographic analyses of these enzymes and the invention of AlphaFold2 have facilitated access to their structures. Structure-based mutagenesis combined with applications of unnatural substrates has further diversified the catalytic repertoire of these enzymes. The information in this review provides useful knowledge for the design of biosynthetic machineries to produce a variety of bioactive meroterpenoids.

Iridium-Catalyzed Asymmetric Allylic Substitution Reaction of 4-Hydroxypyran-2-one

Pyranones have raised great concerns owing to their considerable applications in a variety of sectors. However, the development of direct asymmetric allylation of 4-hydroxypyran-2-ones is still restricted. Herein, we present an effective iridium-catalyzed asymmetric functionalization technique for the synthesis of 4-hydroxypyran-2-one derivatives over direct and efficient catalytic asymmetric Friedel-Crafts-type allylation by using allyl alcohols. The allylation products could be obtained with good to high yields (up to 96%) and excellent enantioselectivities (>99% ee). Therefore, the disclosed technique provides a new asymmetric synthetic strategy to explore pyranone derivatives in depth, thus providing an interesting approach for global application and further utilization in organic synthesis and pharmaceutical chemistry.

Structure-based engineering of α-ketoglutarate dependent oxygenases in fungal meroterpenoid biosynthesis

Non-heme iron- and α-ketoglutarate-dependent oxygenases (αKG OXs) are key enzymes that play a major role in diversifying the structure of fungal meroterpenoids. They activate a specific C-H bond of the substrate to first generate radical species, which is usually followed by oxygen rebound to produce cannonical hydroxylated products. However, in some cases remarkable chemistry induces dramatic structural changes in the molecular scaffolds, depending on the stereoelectronic characters of the substrate/intermediates and the resulting conformational changes/movements of the active site of the enzyme. Their molecular bases have been extensively investigated by crystallographic structural analyses and structure-based mutagenesis, which revealed intimate structural details of the enzyme reactions. This information facilitates the manipulation of the enzyme reactions to create unnatural, novel molecules for drug discovery. This review summarizes recent progress in the structure-based engineering of αKG OX enzymes, involved in the biosynthesis of polyketide-derived fungal meroterpenoids. The literature published from 2016 through February 2022 is reviewed.

Lysine-targeting inhibition of amyloid β oligomerization by a green perilla-derived metastable chalcone in vitro and in vivo

Oligomers of amyloid β (Aβ) represent an early aggregative form that causes neurotoxicity in the pathogenesis of Alzheimer's disease (AD). Thus, preventing Aβ aggregation is important for preventing AD. Despite intensive studies on dietary compounds with anti-aggregation properties, some identified compounds are susceptible to autoxidation and/or hydration upon incubation in water, leaving unanswered issues regarding which active structures in metastable compounds are actually responsible for the inhibition of Aβ aggregation. In this study, we observed the site-specific inhibition of 42-mer Aβ (Aβ42) oligomerization by the green perilla-derived chalcone 2',3'-dihydroxy-4',6'-dimethoxychalcone (DDC), which was converted to its decomposed flavonoids (dDDC, 1-3) via nucleophilic aromatic substitution with water molecules. DDC suppressed Aβ42 fibrillization and slowed the transformation of the β-sheet structure, which is rich in Aβ42 aggregates. To validate the contribution of dDDC to the inhibitory effects of DDC on Aβ42 aggregation, we synthesized 1-3 and identified 3, a catechol-type flavonoid, as one of the active forms of DDC. ¹H-¹⁵N SOFAST-HMQC NMR revealed that 1-3 as well as DDC could interact with residues between His13 and Leu17, which were near the intermolecular β-sheet (Gln15-Ala21). The nucleation in Aβ42 aggregates involves the rate-limiting formation of low-molecular-weight oligomers. The formation of a Schiff base with dDDC at Lys16 and Lys28 in the dimer through autoxidation of dDDC was associated with the suppression of Aβ42 nucleation. Of note, in two AD mouse models using immunoaffinity purification-mass spectrometry, adduct formation between dDDC and brain Aβ was observed in a similar manner as reported in vitro. The present findings unraveled the lysine-targeting inhibitory mechanism of metastable dietary ingredients regarding Aβ oligomerization.

Discovery of a Cyclic Depsipeptide from Chaetomium mollipilium by the Genome Mining Approach

Genome mining and bioinformatics analyses allowed us to rationally find a candidate biosynthetic gene cluster for a new cyclic depsipeptide of Chaetomium mollipilium. A heterologous reconstitution of the identified biosynthetic pathway predictably afforded a new cyclic depsipeptide composed of l-leucine, l-tryptophan, and a polyketide moiety. Interestingly, the 10-membered macrocycle structure generated equilibrium to an unprecedented cyclol structure. This study demonstrates the advantage of a synthetic biology method in achieving rational access to new natural products.