In Vitro Biosynthesis of the Antitumor Agent Azinomycin B

Synthesis of Depsipeptides via Isocyanide-Based Consecutive Bargellini–Passerini Multicomponent Reactions

An efficient and straightforward approach has been established for the preparation of a new class of depsipeptide structures via isocyanide-based consecutive Bargellini–Passerini multicomponent reactions. 3-Carboxamido-isobutyric acids bearing an amide bond were obtained via Bargellini multicomponent reaction from isocyanides, acetone, and chloroform in the presence of sodium hydroxide. Next, via a Passerini multicomponent-reaction strategy, a new class of depsipeptides was synthesized using the Bargellini reaction products, isocyanides, and aldehydes. The depsipeptides thus prepared have more flexible structures than their pseudopeptidic analogues.

Synthesis of d-glycopyranosyl depsipeptides using Passerini reaction

A protocol based on Passerini multi-component reaction has been developed for facile, efficient and atom economical synthesis of a small library of twenty potential bioactive (2R)-2-(d-glycopyranosyl)-2-acyloxyacetamides using perbenzylated d-glycopyranosyl aldehydes, substituted isocyanides and different aliphatic/aromatic carboxylic acids. All twenty synthesized d-glycopyranosyl α-acyloxy amides, commonly known as depsipeptides were unambiguously identified on the basis of their spectral (IR, ¹H, ¹³C NMR, COSY, HSQC, NOESY and HRMS) data analysis.

The Fate of Molecular Oxygen in Azinomycin Biosynthesis

The azinomycins are a family of aziridine-containing antitumor antibiotics and represent a treasure trove of biosynthetic reactions. The formation of the azabicyclo[3.1.0]hexane ring and functionalization of this ring system remain the least understood aspects of the pathway. This study reports the incorporation of ¹⁸O-labeled molecular oxygen in azinomycin biosynthesis including both oxygens of the diol that ultimately adorn the aziridino[1,2- a]pyrrolidine moiety. Likewise, two other sites of heavy atom incorporation are observed.

Priming of Azabicycle Biosynthesis in the Azinomycin Class of Antitumor Agents

The biosynthesis of the azabicyclic ring system of the azinomycin family of antitumor agents represents the "crown jewel" of the pathway and is a complex process involving at least 14 enzymatic steps. This study reports on the first biosynthetic step, the inroads, in the construction of the novel aziridino [1,2-a]pyrrolidine, azabicyclic core, allowing us to support a new mechanism for azabicycle formation.

Biosynthesis and molecular engineering of templated natural products

Bioactive small molecules that are produced by living organisms, often referred to as natural products (NPs), historically play a critical role in the context of both medicinal chemistry and chemical biology. How nature creates these chemical entities with stunning structural complexity and diversity using a limited range of simple substrates has not been fully understood. Focusing on two types of NPs that share a highly evolvable ‘template’-biosynthetic logic, we here provide specific examples to highlight the conceptual and technological leaps in NP biosynthesis and witness the area of progress since the beginning of the twenty-first century. The biosynthesis of polyketides, non-ribosomal peptides and their hybrids that share an assembly-line enzymology of modular multifunctional proteins exemplifies an extended ‘central dogma’ that correlates the genotype of catalysts with the chemotype of products; in parallel, post-translational modifications of ribosomally synthesized peptides involve a number of unusual biochemical mechanisms for molecular maturation. Understanding the biosynthetic processes of these templated NPs would largely facilitate the design, development and utilization of compatible biosynthetic machineries to address the challenge that often arises from structural complexity to the accessibility and efficiency of current chemical synthesis.

Synthetic Biology for Cell-Free Biosynthesis: Fundamentals of Designing Novel In Vitro Multi-Enzyme Reaction Networks

Cell-free biosynthesis in the form of in vitro multi-enzyme reaction networks or enzyme cascade reactions emerges as a promising tool to carry out complex catalysis in one-step, one-vessel settings. It combines the advantages of well-established in vitro biocatalysis with the power of multi-step in vivo pathways. Such cascades have been successfully applied to the synthesis of fine and bulk chemicals, monomers and complex polymers of chemical importance, and energy molecules from renewable resources as well as electricity. The scale of these initial attempts remains small, suggesting that more robust control of such systems and more efficient optimization are currently major bottlenecks. To this end, the very nature of enzyme cascade reactions as multi-membered systems requires novel approaches for implementation and optimization, some of which can be obtained from in vivo disciplines (such as pathway refactoring and DNA assembly), and some of which can be built on the unique, cell-free properties of cascade reactions (such as easy analytical access to all system intermediates to facilitate modeling).

Cell-free metabolic engineering: biomanufacturing beyond the cell

Industrial biotechnology and microbial metabolic engineering are poised to help meet the growing demand for sustainable, low-cost commodity chemicals and natural products, yet the fraction of biochemicals amenable to commercial production remains limited. Common problems afflicting the current state-of-the-art include low volumetric productivities, build-up of toxic intermediates or products, and byproduct losses via competing pathways. To overcome these limitations, cell-free metabolic engineering (CFME) is expanding the scope of the traditional bioengineering model by using in vitro ensembles of catalytic proteins prepared from purified enzymes or crude lysates of cells for the production of target products. In recent years, the unprecedented level of control and freedom of design, relative to in vivo systems, has inspired the development of engineering foundations for cell-free systems. These efforts have led to activation of long enzymatic pathways (>8 enzymes), near theoretical conversion yields, productivities greater than 100 mg L(-1) h(-1) , reaction scales of >100 L, and new directions in protein purification, spatial organization, and enzyme stability. In the coming years, CFME will offer exciting opportunities to: (i) debug and optimize biosynthetic pathways; (ii) carry out design-build-test iterations without re-engineering organisms; and (iii) perform molecular transformations when bioconversion yields, productivities, or cellular toxicity limit commercial feasibility.

Biosynthetic studies of aziridine formation in azicemicins

The azicemicins, which are angucycline-type antibiotics produced by the actinomycete, Kibdelosporangium sp. MJ126-NF4, contain an aziridine ring attached to the polyketide core. Feeding experiments using [1-(13)C]acetate or [1,2-(13)C(2)]acetate indicated that the angucycline skeleton is biosynthesized by a type II polyketide synthase. Isotope-tracer experiments using deuterium-labeled amino acids revealed that aspartic acid is the precursor of the aziridine moiety. Subsequent cloning and sequencing efforts led to the identification of the azicemicin (azic) gene cluster spanning approximately 50 kbp. The cluster harbors genes typical for type II polyketide synthesis. Also contained in the cluster are genes for two adenylyl transferases, a decarboxylase, an additional acyl carrier protein (ACP), and several oxygenases. On the basis of the assigned functions of these genes, a possible pathway for aziridine ring formation in the azecimicins can now be proposed. To obtain support for the proposed biosynthetic pathway, two genes encoding adenylyltransferases were overexpressed and the resulting proteins were purified. Enzyme assays showed that one of the adenylyltransferases specifically recognizes aspartic acid, providing strong evidence, in addition to the feeding experiments, that aspartate is the precursor of the aziridine moiety. The results reported herein set the stage for future biochemical studies of aziridine biosynthesis and assembly.

Biosynthesis of 3-methoxy-5-methyl naphthoic acid and its incorporation into the antitumor antibiotic azinomycin B

Azinomycin B is a potent antitumor antibiotic that features a set of unusual, densely assembled functionalities. Among them, the 3-methoxy-5-methylnaphthoic acid (NPA) moiety provides an important noncovalent association with DNA, and may, therefore, contribute to the specificity of DNA alkylation for biological activity exhibition. We have previously cloned and sequenced the azinomycin B biosynthetic gene cluster, and proposed that four enzymes: AziB, AziB1, AziB2, and AziA1, are involved in the naphthoate moiety formation and incorporation. In this study, we report in vivo and/or in vitro characterizations of the P450 hydroxylase AziB1, the O-methyltransferase AziB2, and the substrate specificity of the non-ribosomal peptide synthetase (NRPS) AziA1, providing insights into the timing of individual steps in the late-stage modification of 5-methyl-NPA synthesized by the iterative type I polyketide synthase AziB. AziB1 catalyzes a regiospecific hydroxylation at the C3 position of the free naphthoic acid 5-methyl-NPA to produce 3-hydroxy-5-methyl-NPA, and the resulting hydroxyl group is subsequently O-methylated by AziB2 to furnish the methoxy functionality. The di-domain NRPS AziA1 specifically incorporates 3-methoxy-5-methyl-NPA via an unusual A domain to initiate the backbone formation of azinomycin B. AziA1 activates several analogues of the natural starter unit, suggesting a potential for production by metabolic engineering of new azinomycin analogues differing in their NPA moieties.

An improved method for culturing Streptomyces sahachiroi: Biosynthetic origin of the enol fragment of azinomycin B

Azinomycin B is an environmental DNA crosslinking agent produced by the soil microorganism Streptomyces sahachiroi. While the agent displays potent cytotoxic activities against leukemic cell lines and animal mouse models, the lack of a consistent supply of the natural product has hampered detailed biological investigations on the compound, including its mode of action and biosynthesis. We report here a significant methodological improvement in the culturing of the bacterium, which allows reliable and steady production of the natural product in good yields. The key experimental step involves the culturing of the strain on dehydrated plates, followed by the generation of a two-stage starter culture and subsequent fermentation of the strain under nutrient-starved conditions. We illustrate use of this culture system by investigating the formation of the enol fragment of the molecule in isotopic labeling experiments with threonine and several advanced precursors (beta-ketoamino acid 3, beta-hydroxyamino aldehyde 4, and beta-ketoaminoaldehyde 5). The results unequivocally show that threonine is the most advanced precursor accepted by the NRPS (non-ribosomal peptidyl synthetase) machinery for final processing and construction of the enol moiety of the natural product.

Synthesis of Functional “Top-Half” Partial Structures of Azinomycin A and B

The design and synthesis of a detailed series of functional "top-half" substructures of azinomycin A and B is described.

Cellular effects induced by the antitumor agent azinomycin B

Studies on the mechanism of action of the antitumor agent azinomycin B in vitro suggest that the drug elicits its lethal effects by the formation of interstrand crosslinks within the major groove of DNA. Here, we demonstrate the biological effects of the drug in vivo. Fluorescence imaging revealed localization of azinomycin B in the nuclear region of yeast. Moreover, experiments with oligonucleotide microarrays examined the effects of the drug across the yeast transcriptome. The results demonstrated a robust DNA damage response that supports the proposed role of the drug as a covalent DNA modifying agent. RT-PCR analysis validated the gene changes, and flow cytometry of azinomycin-treated yeast cells demonstrated a phenotypic S phase shift consistent with transcriptional effects.