Complete Stereoinversion of l-Tryptophan by a Fungal Single-Module Nonribosomal Peptide Synthetase

Visible Light-Promoted Deracemization of α-Amino Aldehyde by Synergistic Chiral Primary Amine and Hypervalent Iodine Catalysis

α-Amino aldehydes, as versatile chiral synthons, are easily racemized under normal acid or base conditions, seriously limiting their synthetic potentials. We report herein an effective deracemization of α-amino aldehydes by a synergistic chiral primary amine and hypervalent iodine catalysis under visible light. The developed catalytic system allows for the on-demand production of α-Boc- or Cbz-protected amino aldehydes with high enantioselectivity. Mechanistic studies verified a photochemical Z-E isomerization mechanism that drives the deracemization process.

Enzymatic ester bond formation strategies in fungal macrolide skeletons

Covering: up to August 2024Macrolides, the core skeletons of numerous marketed drugs and bioactive natural products, have garnered considerable scientific interest owing to their structural diversity and broad spectrum of pharmaceutical activities. The formation of intramolecular ester bonds is a critical biocatalytic step in constructing macrolide skeletons. Here, we summarised enzymatic ester bond formation strategies in fungal polyketide (PK)-type, nonribosomal peptide (NRP)-type, and PK-NRP hybrid-type macrolides. In PK-type macrolides, ester bond formation is commonly catalysed by a trans-acting thioesterase (TE) or a cis-acting TE domain during the product release process. In NRP-type and PK-NRP hybrid-type macrolides, the ester bond is usually introduced through condensation (C) domain-catalysed esterification during the elongation or product release step. Although the TE and C domains share similarities in their catalytic mechanism, using hydroxyl groups as nucleophiles in an intramolecular nucleophilic attack, they differ in terms of the hydroxyl origin, the timing of ester bond formation, and domain location. Furthermore, some TE domains are utilized as chemoenzymatic catalysts to construct macrolides with different ring sizes. A comparison of ester bond formation between fungi and bacteria is also discussed. Exploring the biosynthetic pathways of fungal macrolides, elucidating the diverse strategies employed in the formation of ester bonds, and understanding the application of enzymes/domains in chemoenzymatic synthesis hold promise for the discovery of new bioactive macrolides in the future.

Chemical Logic of Peptide Branching by Iterative Nonlinear Nonribosomal Peptide Synthetases

Branch-point syntheses in nonribosomal peptide assembly are rare but useful strategies to generate tripodal peptides with advantageous hexadentate iron-chelating capabilities, as seen in siderophores. However, the chemical logic underlying the peptide branching by nonribosomal peptide synthetase (NRPS) often remains complex and elusive. Here, we review the common strategies for the biosynthesis of branched nonribosomal peptides (NRPs) and present our biochemical investigation on the NRPS-catalyzed assembly of fimsbactin A, a branched mixed-ligand siderophore produced by the human pathogenic strain Acinetobacter baumannii. We untangled the unusual branching mechanism of fimsbactin A biosynthesis through a combination of bioinformatics, site-directed mutagenesis, in vitro reconstitution, molecular modeling, and molecular dynamics simulation. Our findings clarify the roles of the fimsbactin NRPS enzymes, uncovering catalytically redundant domains and identifying the multifunctional nature of the FbsF cyclization (Cy) domain. We demonstrate the dynamic interplay between l-serine and 2,3-dihydroxybenzoic acid derived dipeptides, partitioning between amide and ester forms via a 1,2-N-to-O-acyl shift orchestrated by the noncanonical, multichannel FbsF Cy domain. The branching event occurs in a secondary condensation event facilitated by this Cy domain with two dipeptidyl intermediates, which generates a branched tetrapeptide thioester. Finally, the terminal condensation domain of FbsG recruits a soluble nucleophile to release the final product. This study advances our understanding of the intricate biosynthetic pathways and chemical logic employed by NRPSs, shedding light on the mechanisms underlying the synthesis of complex branched peptides.

Tailoring Chirality and Optimizing Enantioselective Recognition in Strategic Defect Engineering of Chiral Metal-Organic Frameworks

Introducing chiral molecules into metal-organic frameworks (MOFs) to obtain chiral MOFs (CMOFs), the tunability of their structures makes them a highly anticipated class of chiral materials for electrochemical sensing. However, the structure of CMOFs is often limited by synthesis challenges, and introducing chiral molecules into MOFs often leads to a decrease in their internal space. This study introduces a defect engineering strategy into the synthesis of CMOFs to obtain CMOFs with defects, which is an efficient synthesis method. The two CMOFs constructed with different structures not only have more chiral recognition sites but also greatly increase the substrate capacity due to the defects, making them have a wide range of substrates and enhancing the enantioselective recognition effect of the two defective CMOFs. In addition, using MOF as a chiral carrier greatly overcomes the problem of low conductivity of chiral molecules. Based on the advantages of defective CMOFs, we have designed a novel chiral electrochemical sensor with an excellent enantiomer recognition performance. This study provides a simple and scalable synthetic method for constructing CMOFs with defects and high stability.

Structure, Function and Engineering of the Nonribosomal Peptide Synthetase Condensation Domain

The nonribosomal peptide synthetase (NRPS) is a highly precise molecular assembly machinery for synthesizing structurally diverse peptides, which have broad medicinal applications. Withinthe NRPS, the condensation (C) domain is a core catalytic domain responsible for the formation of amide bonds between individual monomer residues during peptide elongation. This review summarizes various aspects of the C domain, including its structural characteristics, catalytic mechanisms, substrate specificity, substrate gating function, and auxiliary functions. Moreover, through case analyses of the NRPS engineering targeting the C domains, the vast potential of the C domain in the combinatorial biosynthesis of peptide natural product derivatives is demonstrated.

The sugar cube: Network control and emergence in stereoediting reactions

Stereochemical editing strategies have recently enabled the transformation of readily accessible substrates into rare and valuable products. Typically, site selectivity is achieved by minimizing kinetic complexity by using protecting groups to suppress reactivity at undesired sites (substrate control) or by using catalysts with tailored shapes to drive reactivity at the desired site (catalyst control). We propose "network control," a contrasting paradigm that exploits hidden interactions between rate constants to greatly amplify modest intrinsic biases and enable precise multisite editing. When network control is applied to the photochemical isomerization of hexoses, six of the eight possible diastereomers can be selectively obtained. The amplification effect can be viewed as a mesoscale phenomenon between the limiting regimes of kinetic control in simple chemical systems and metabolic regulation in complex biological systems.

Metabolomics-Guided Discovery, Isolation, Structure Elucidation, and Bioactivity of Myropeptins C-E from Myrothecium inundatum

The saprotrophic filamentous fungus Myrothecium inundatum represents a chemically underexplored ascomycete with a high number of putative biosynthetic gene clusters in its genome. Here, we present new linear lipopeptides from nongenetic gene activation experiments using nutrient and salt variations. Metabolomics studies revealed four myropeptins, and structural analyses by NMR, HRMS, Marfey's analysis, and ECD assessment for their helical properties established their absolute configuration. A myropeptin biosynthetic gene cluster in the genome was identified. The myropeptins exhibit general nonspecific toxicity against all cancer cell lines in the NCI-60 panel, larval zebrafish with EC50 concentrations of 5-30 μM, and pathogenic bacteria and fungi (MICs of 4-32 μg/mL against multidrug-resistant S. aureus and C. auris). In vitro hemolysis, cell viability, and ionophore assays indicate that the myropeptins target mitochondrial and cellular membranes, inducing cell depolarization and cell death. The toxic activity is modulated by the length of the lipid side chain, which provides valuable insight into their structure-activity relationships.

Catalytic Deracemization Reactions

Deracemization, which converts a racemate into its single enantiomer without separation of the intermediate, has gained renewed interest in asymmetric synthesis with its inherent atomic economy and high efficiency. However, this ideal process requires selective energy input and delicate reaction design to surmount the thermodynamical and kinetical constraints. With the rapid development of asymmetric catalysis, many catalytic strategies in concert with exogenous energy input have been exploited to facilitate this nonspontaneous enantioenrichment. In this perspective, we will discuss the basic ideas to accomplish catalytic deracemization, categorized by the three major exogenous energy sources including chemical (redox)-, photo- and mechanical energy from attrition. Emphasis will be given to the catalytic features and the underlying deracemization mechanism together with perspectives on future development.

Characterization and catalytic investigation of fungal single-module nonribosomal peptide synthetase in terpene-amino acid meroterpenoid biosynthesis

Hybrid natural products are compounds that originate from diverse biosynthetic pathways and undergo a conjugation process, which enables them to expand their chemical diversity and biological functionality. Terpene-amino acid meroterpenoids have garnered increasing attention in recent years, driven by the discovery of noteworthy examples such as the anthelmintic CJ-12662, the insecticidal paeciloxazine, and aculene A (1). In the biosynthesis of terpene-amino acid natural products, single-module nonribosomal peptide synthetases (NRPSs) have been identified to be involved in the esterification step, catalyzing the fusion of modified terpene and amino acid components. Despite prior investigations into these NRPSs through gene deletion or in vivo experiments, the enzymatic basis and mechanistic insights underlying this family of single-module NRPSs remain unclear. In this study, we performed biochemical characterization of AneB by in vitro characterization, molecular docking, and site-directed mutagenesis. The enzyme reaction analyses, performed with L-proline and daucane/nordaucane sesquiterpene substrates, revealed that AneB specifically esterifies the C10-OH of aculenes with L-proline. Notably, in contrast to ThmA in CJ-12662 biosynthesis, which exclusively recognizes oxygenated amorpha-4,11-diene sesquiterpenes for L-tryptophan transfer, AneB demonstrates broad substrate selectivity, including oxygenated amorpha-4,11-diene and 2-phenylethanol, resulting in the production of diverse unnatural prolyl compounds. Furthermore, site-directed mutagenesis experiments indicated the involvement of H794 and D798 in the esterification catalyzed by AneB. Lastly, domain swapping between AneB and ThmA unveiled that the A‒T domains of ThmA can be effectively harnessed by the C domain of AneB for L-tryptophan transfer, thus highlighting the potential of the C domain of AneB for generating various terpene-amino acid meroterpenoid derivatives.

ONE-SENTENCE SUMMARY

The enzymatic basis and mechanistic insights into AneB, a single-module NRPS, highlight its capacity to generate various terpene-amino acid meroterpenoid derivatives.

Engineering the biosynthesis of fungal nonribosomal peptides

Covering: 2011 up to the end of 2021.Fungal nonribosomal peptides (NRPs) and the related polyketide-nonribosomal peptide hybrid products (PK-NRPs) are a prolific source of bioactive compounds, some of which have been developed into essential drugs. The synthesis of these complex natural products (NPs) utilizes nonribosomal peptide synthetases (NRPSs), multidomain megaenzymes that assemble specific peptide products by sequential condensation of amino acids and amino acid-like substances, independent of the ribosome. NRPSs, collaborating polyketide synthase modules, and their associated tailoring enzymes involved in product maturation represent promising targets for NP structure diversification and the generation of small molecule unnatural products (uNPs) with improved or novel bioactivities. Indeed, reprogramming of NRPSs and recruiting of novel tailoring enzymes is the strategy by which nature evolves NRP products. The recent years have witnessed a rapid development in the discovery and identification of novel NRPs and PK-NRPs, and significant advances have also been made towards the engineering of fungal NRP assembly lines to generate uNP peptides. However, the intrinsic complexities of fungal NRP and PK-NRP biosynthesis, and the large size of the NRPSs still present formidable conceptual and technical challenges for the rational and efficient reprogramming of these pathways. This review examines key examples for the successful (and for some less-successful) re-engineering of fungal NRPS assembly lines to inform future efforts towards generating novel, biologically active peptides and PK-NRPs.

Unexpected assembly machinery for 4(3H)-quinazolinone scaffold synthesis

4(3H)-quinazolinone is the core scaffold in more than 200 natural alkaloids and numerous drugs. Many chemosynthetic methodologies have been developed to generate it; however, investigation of its native enzymatic formation mechanism in fungi has been largely limited to fumiquinazolines, where the two nitrogen atoms come from anthranilate (N-1) and the α-NH₂ of amino acids (N-3). Here, via biochemical investigation of the chrysogine pathway, unexpected assembly machinery for 4(3H)-quinazolinone is unveiled, which involves a fungal two-module nonribosomal peptide synthase ftChyA with an unusual terminal condensation domain catalysing tripeptide formation; reveals that N-3 originates from the inorganic ammonium ions or the amide of L-Gln; demonstrates an unusual α-ketoglutarate-dependent dioxygenase ftChyM catalysis of the C-N bond oxidative cleavage of a tripeptide to form a dipeptide. Our study uncovers a unique release and tailoring mechanism for nonribosomal peptides and an alternative route for the synthesis of 4(3H)-quinazolinone scaffolds.

Understanding and Circumventing the Requirement for Native Thioester Substrates for α-Oxoamine Synthase Reactions

Many enzyme classes require thioester electrophiles such as acyl-carrier proteins and acyl-coenzyme A substrates. For in vitro applications, these substrates can render these chemical transformations impractical. To address this challenge, we have investigated the mechanism of coenzyme A in gating catalysis of one α-oxoamine synthase, SxtA AOS. Through investigating the reactivity of SxtA AOS and corresponding enzyme variants against a panel of substrates and coenzyme A mimics, we determined that activity is gated through the binding of the pantetheine arm and a phosphate group that hydrogen bonds to residue Lys154 that is predicted by an AlphaFold2 model to be located in a tunnel leading to the active site. To provide an economical solution for preparative-scale reactions, in situ transthioesterification was used with pantetheine and simple thioester substrate precursors, resulting in productive reactions. These findings outline a strategy for employing ACP- and CoA-dependent enzymes that are inaccessible through other means without the need for cost-prohibitive coenzyme A or carrier protein-activated substrates.

Assessing Microbial Metabolic and Biological Diversity to Inform Natural Product Library Assembly

The pressing need for novel chemical matter to support bioactive compound discovery has led natural product researchers to explore a wide range of source organisms and environments. One of the implicit guiding principles behind those efforts is the notion that sampling different environments is critical to accessing unique natural products. This idea was tested by comparing fungi from disparate biomes: aquatic sediments from Lake Michigan (USA) and terrestrial samples taken from the surrounding soils. Matched sets of Penicillium brevicompactum, Penicillium expansum, and Penicillium oxalicum from the two source environments were compared, revealing modest differences in physiological performance and chemical output. Analysis of LC-MS/MS-derived molecular feature data showed no source-dependent differences in chemical richness. High levels of scaffold homogeneity were also observed with 78-83% of scaffolds shared among the terrestrial and aquatic Penicillium spp. isolates. A comparison of the culturable fungi from the two biomes indicated that certain genera were more strongly associated with aquatic sediments (e.g., Trichoderma, Pseudeurotium, Cladosporium, and Preussia) versus the surrounding terrestrial environment (e.g., Fusarium, Pseudogymnoascus, Humicola, and Acremonium). Taken together, these results suggest that focusing efforts on sampling the microbial resources that are unique to an environment may have a more pronounced effect on enhancing the sought-after natural product diversity needed for chemical discovery and screening collections.

Ribosome-independent peptide biosynthesis: the challenge of a unifying nomenclature

The first machineries for non-ribosomal peptide (NRP) biosynthesis were uncovered over 50 years ago, and the dissection of these megasynthetases set the stage for the nomenclature system that has been used ever since. Although the number of exceptions to the canonical biosynthetic pathways has surged in the intervening years, the NRP synthetase (NRPS) classification system has remained relatively unchanged. This has led to the exclusion of many biosynthetic pathways whose biosynthetic machineries violate the classical rules for NRP assembly, and ultimately to a rupture in the field of NRP biosynthesis. In an attempt to unify the classification of NRP pathways and to facilitate the communication within the research field, we propose a revised framework for grouping ribosome-independent peptide biosynthetic pathways based on recognizable commonalities in their biosynthetic logic. Importantly, the framework can be further refined as needed.

Gene Cluster Analysis of Marine Bacteria Seeking for Natural Anticancer Products

Background: In the past decade, metabolites of marine microorganisms have been increasingly used for their various biological activities. An intense effort has been dedicated to assessing the therapeutic efficacy of the marine natural products and metabolites obtained from marine bacteria in cancer therapy. Fast and reliable analytical bacterial genome sequencing provides specialized bioinformatic tools to identify potential gene clusters in bacteria for obtaining secondary metabolites. Objectives: This study aimed to analyze the genome sequences of marine bacteria to recognize bioactive compounds with anti-cancer properties. Methods: Marine bacteria with the genomic sequences registered in the National Center for Biotechnology Information (NCBI) genome database were used in this study. The genome was analyzed for proteins, tRNAs, and rRNAs from GenBank entries by Feature Extract 1.2L Server. The Anti-SMASH webserver was used for the analysis of unique marine bacterial metabolites of the marine bacterial genome, available from the NCBI database. Results: A number of marine bacterial species, including Salinispora arenicola, Salinispora tropica, Crocosphaera watsonii, and Blastopirellula marina encoded metabolites belonging to the polyketide and nonribosomal peptide (NRP) families, showing anti-cancer properties. Among the marine species described, S. tropica and S. arenicola are richer in the genes encoding polyketide and NRP with potential antitumor activities. Conclusions: Marine bacteria are an excellent and exceptional source of anti-cancer compounds. In silico genome analysis of marine bacteria provided an opportunity to evaluate gene clusters for known natural products. Like this chemical engineering approaches for pharmaceutical application are useful in clinical evaluation of cancer treatment.

Mass Spectrometry Guided Discovery and Design of Novel Asperphenamate Analogs From Penicillium astrolabium Reveals an Extraordinary NRPS Flexibility

Asperphenamate is a small peptide natural product that has gained much interest due to its antitumor activity. In the recent years numerous bioactive synthetic asperphenamate analogs have been reported, whereas only a handful of natural analogs either of microbial or plant origin has been discovered. Herein we describe a UHPLC-HRMS/MS and amino acid supplement approach for discovery and design of novel asperphenamate analogs. Chemical analysis of Penicillium astrolabium, a prolific producer of asperphenamate, revealed three previously described and two novel asperphenamate analogs produced in significant amounts, suggesting a potential for biosynthesis of further asperphenamate analogs by varying the amino acid availability. Subsequent growth on proteogenic and non-proteogenic amino acid enriched media, revealed a series of novel asperphenamate analogs, including single or double amino acid exchange, as well as benzoic acid exchange for nicotinic acid, with the latter observed from a natural source for the first time. In total, 22 new asperphenamate analogs were characterized by HRMS/MS, with one additionally confirmed by isolation and NMR structure elucidation. This study indicates an extraordinary nonribosomal peptide synthetase (NRPS) flexibility based on substrate availability, and therefore the potential for manipulating and designing novel peptide natural products in filamentous fungi.

Bacterial-Like Nonribosomal Peptide Synthetases Produce Cyclopeptides in the Zygomycetous Fungus Mortierella alpina

Fungi are traditionally considered a reservoir of biologically active natural products. However, an active secondary metabolism has long not been attributed to early-diverging fungi such as Mortierella Here, we report on the biosynthesis of two series of cyclic pentapeptides, the malpicyclins and malpibaldins, as products of Mortierella alpina ATCC 32222. The molecular structures of malpicyclins were elucidated by high-resolution tandem mass spectrometry (HR-MS/MS), Marfey's method, and one-dimensional (1D) and 2D nuclear magnetic resonance (NMR) spectroscopy. In addition, malpibaldin biosynthesis was confirmed by HR-MS. Genome mining and comparative quantitative real-time PCR (qRT-PCR) expression analysis pointed at two pentamodular nonribosomal peptide synthetases (NRPSs), malpicyclin synthetase MpcA and malpibaldin synthetase MpbA, as candidate biosynthetic enzymes. Heterologous production of the respective adenylation domains and substrate specificity assays proved promiscuous substrate selection and confirmed their respective biosynthetic roles. In stark contrast to known fungal NRPSs, MpbA and MpcA contain bacterial-like dual epimerase/condensation domains allowing the racemization of enzyme-tethered l-amino acids and the subsequent incorporation of d-amino acids into the metabolites. Phylogenetic analyses of both NRPS genes indicated a bacterial origin and a horizontal gene transfer into the fungal genome. We report on the as-yet-unexplored nonribosomal peptide biosynthesis in basal fungi which highlights this paraphylum as a novel and underrated resource of natural products.IMPORTANCE Fungal natural compounds are industrially produced, with application in antibiotic treatment, cancer medications, and crop plant protection. Traditionally, higher fungi have been intensively investigated concerning their metabolic potential, but reidentification of already known compounds is frequently observed. Hence, alternative strategies to acquire novel bioactive molecules are required. We present the genus Mortierella as representative of the early-diverging fungi as an underestimated resource of natural products. Mortierella alpina produces two families of cyclopeptides, designated malpicyclins and malpibaldins, respectively, via two pentamodular nonribosomal peptide synthetases (NRPSs). These enzymes are much more closely related to bacterial than to other fungal NRPSs, suggesting a bacterial origin of these NRPS genes in Mortierella Both enzymes were biochemically characterized and are involved in as-yet-unknown biosynthetic pathways of natural products in basal fungi. Hence, this report establishes early-diverging fungi as prolific natural compound producers and sheds light on the origin of their biosynthetic capacity.

Fusarochromene, a novel tryptophan-derived metabolite from Fusarium sacchari

Fusarochromene isolated from the plant pathogenic fungus, Fusarium sacchari is closely related to a group of mycotoxins including fusarochromanone previously isolated from various Fusaria spp. Despite their assumed polyketide biogenesis, incorporation studies with 13C-labelled acetate, glycerol and tryptophans show that fusarochromene is unexpectedly derived via oxidative cleavage of the aromatic amino acid tryptophan. A putative biosynthetic gene cluster has been identified.

Beyond peptide bond formation: the versatile role of condensation domains in natural product biosynthesis

Condensation domains perform highly diverse functions during natural product biosynthesis and are capable of generating remarkable chemical diversity.

Fungal siderophore biosynthesis catalysed by an iterative nonribosomal peptide synthetase

Siderophores play a vital role in the viability of fungi and are essential for the virulence of many pathogenic fungal species. Despite their importance in fungal physiology and pathogenesis, the programming rule of siderophore assembly by fungal nonribosomal peptide synthetases (NRPSs) remains unresolved. Here, we report the characterization of the bimodular fungal NRPS, SidD, responsible for construction of the extracellular siderophore fusarinine C. The use of intact protein mass spectrometry, together with in vitro biochemical assays of native and dissected enzymes, provided snapshots of individual biosynthetic steps during NPRS catalysis. The adenylation and condensation domain of SidD can iteratively load and condense the amino acid building block cis-AMHO, respectively, to synthesize fusarinine C. Our study showcases the iterative programming features of fungal siderophore-producing NRPSs.

Biosynthetic Pathways to Nonproteinogenic α-Amino Acids

Natural nonproteinogenic amino acids vastly outnumber the well-known 22 proteinogenic amino acids. Such amino acids are generated in specialized metabolic pathways. In these pathways, diverse biosynthetic transformations, ranging from isomerizations to the stereospecific functionalization of C-H bonds, are employed to generate structural diversity. The resulting nonproteinogenic amino acids can be integrated into more complex natural products. Here we review recently discovered biosynthetic routes to freestanding nonproteinogenic α-amino acids, with an emphasis on work reported between 2013 and mid-2019.