Probing Microbiome Genotoxicity: A Stable Colibactin Provides Insight into Structure-Activity Relationships and Facilitates Mechanism of Action Studies.

Colibactin is a genotoxic metabolite produced by commensal-pathogenic members of the human microbiome that possess the clb (aka pks) biosynthetic gene cluster. clb+ bacteria induce tumorigenesis in models of intestinal inflammation and have been causally linked to oncogenesis in humans. While colibactin is believed underlie these effects, it has not been possible to study the molecule directly due to its instability. Herein, we report the synthesis and biological studies of colibactin 742 (4), a stable colibactin derivative. We show that colibactin 742 (4) induces DNA interstrand-cross-links, activation of the Fanconi Anemia DNA repair pathway, and G2/M arrest in a manner similar to clb+E. coli. The linear precursor 9, which mimics the biosynthetic precursor to colibactin, also recapitulates the bacterial phenotype. In the course of this work, we discovered a novel cyclization pathway that was previously undetected in MS-based studies of colibactin, suggesting a refinement to the natural product structure and its mode of DNA binding. Colibactin 742 (4) and its precursor 9 will allow researchers to study colibactin's genotoxic effects independent of the producing organism for the first time.

On the Stability and Spectroscopic Properties of 5-Hydroxyoxazole-4-carboxylic Acid Derivatives.

5-Hydroxyoxazole-4-carboxylic acid residues were advanced as substructures within the secondary bacterial metabolites precolibactins 969 and 795a. However, oxazoles containing both 5-hydroxy and 4-carboxy substituents are unprecedented. We have found these oxazoles are unstable with respect to hydrolytic ring opening and decarboxylation. Comparison of reported and theoretical 13C NMR chemical shifts between synthetic intermediates and the isolates revealed discrepancies in the oxazole region. These results suggest that precolibactins 969 and 795a may not contain 5-hydroxyoxazole-4-carboxylic acid residues.

Disruption of mitochondrial redox homeostasis by enzymatic activation of a trialkylphosphine probe.

Redox homeostasis is essential for cell function and its disruption is associated with multiple pathologies. Redox balance is largely regulated by the relative concentrations of reduced and oxidized glutathione. In eukaryotic cells, this ratio is different in each cell compartment, and disruption of the mitochondrial redox balance has been specifically linked to metabolic diseases. Here, we report a probe that is selectively activated by endogenous nitroreductases, and releases tributylphosphine to trigger redox stress in mitochondria. Mechanistic studies revealed that, counterintuitively, release of a reducing agent in mitochondria rapidly induced oxidative stress through accumulation of superoxide. This response is mediated by glutathione, suggesting a link between reductive and oxidative stress. Furthermore, mitochondrial redox stress activates a cellular response orchestrated by transcription factor ATF4, which upregulates genes involved in glutathione catabolism.

Employing chemical synthesis to study the structure and function of colibactin, a "dark matter" metabolite.

Covering: 2015 to 2020 The field of natural products is dominated by a discovery paradigm that follows the sequence: isolation, structure elucidation, chemical synthesis, and then elucidation of mechanism of action and structure-activity relationships. Although this discovery paradigm has proven successful in the past, researchers have amassed enough evidence to conclude that the vast majority of nature's secondary metabolites - biosynthetic "dark matter" - cannot be identified and studied by this approach. Many biosynthetic gene clusters (BGCs) are expressed at low levels, or not at all, and in some instances a molecule's instability to fermentation or isolation prevents detection entirely. Here, we discuss an alternative approach to natural product identification that addresses these challenges by enlisting synthetic chemistry to prepare putative natural product fragments and structures as guided by biosynthetic insight. We demonstrate the utility of this approach through our structure elucidation of colibactin, an unisolable genotoxin produced by pathogenic bacteria in the human gut.

Structure and bioactivity of colibactin.

Colibactin is a secondary metabolite produced by certain strains of bacteria found in the human gut. The presence of colibactin-producing bacteria has been correlated to colorectal cancer in humans. Colibactin was first discovered in 2006, but because it is produced in small quantities and is unstable, it has yet to be isolated from bacterial cultures. Here we summarize advances in the field since ~2017 that have led to the identification of the structure of colibactin as a heterodimer containing two DNA-reactive electrophilic cyclopropane residues. Colibactin has been shown to form interstrand cross-links by alkylation of adenine residues on opposing strands of DNA. The structure of colibactin contains two thiazole rings separated by a two-carbon linker that is thought to exist as an α-aminoketone following completion of the biosynthetic pathway. However, synthetic studies have now established that this α-aminoketone is unstable toward aerobic oxidation; the resulting oxidation products are in turn unstable toward nucleophilic cleavage under mild conditions. These data provide a simple molecular-level explanation for colibactin's instability and potentially also explain the observation that cell-to-cell contact is required for genotoxic effects.

The Bioorthogonal Isonitrile-Chlorooxime Ligation.

Bioorthogonal reactions are valuable tools for the selective labeling and imaging of natural products and proteins. Here, we present the reaction between isonitriles and chlorooximes as a ligation that proceeds quickly (k ≈ 1 M-1 s-1) and with high chemoselectivity in an aqueous environment. Imaging of metabolically labeled cell surface glycans underlined the tolerance of the ligation to common functional groups in cellular systems. Live-cell dual-labeling experiments revealed that the isonitrile-chlorooxime ligation is orthogonal to the strain-promoted azide-alkyne cycloaddition.

Peptide Targeting of an Intracellular Receptor of the Secretory Pathway.

Numerous peptides serve as natural ligands of intra- and extracellular receptors. The presence of charged amino acids, however, often hinders the membrane-crossing ability of some of these peptides and renders them unsuitable as chemical probes for perturbing or imaging intracellular targets. In this report, we show that addition of a few natural and unnatural amino acids enhances the cellular uptake and intracellular localization of a highly charged Lys-Asp-Glu-Leu (KDEL) peptide to target the corresponding receptor of the secretory pathway. Live-cell imaging experiments revealed that, through interaction with the KDEL receptor, the peptide is delivered to the endoplasmic reticulum (ER), where it accumulates preferentially. The enhanced uptake and selectivity of this peptide make it a good probe for monitoring disruptions in retrograde transport and ER stress in living cells without any genetic modifications.

Catalytic Isohypsic-Redox Sequences for the Rapid Generation of Csp3 -Containing Heterocycles.

Cross-coupling reactions catalyzed by transition metals are among the most influential in modern synthetic chemistry. The vast majority of transition-metal-catalyzed cross-couplings rely on a catalytic cycle involving alternating oxidation and reduction of the metal center and are generally limited to forging just one type of new bond per reaction (e.g., the biaryl linkage formed during a Suzuki cross-coupling). This work presents an Isohypsic-Redox Sequence (IRS) that uses one metal to effect two catalytic cycles, thereby generating multiple new types of bonds from a single catalyst source. We show that the IRS strategy is amenable to several widely used transformations including the Suzuki-Miyaura coupling, Buchwald-Hartwig amination, and Wacker oxidation. Furthermore, each of these reactions generates value-added heterocycles with significant sp3 -C (3-dimensional) content. Our results provide a general framework for generating complex products by using a single metal to fulfill multiple roles. By uniting different combinations of reactions in the isohypsic and redox phases of the process, this type of catalytic multiple bond-forming platform has the potential for wide applicability in the efficient synthesis of functional organic molecules.

Induction of Intracellular Reductive Stress with a Photoactivatable Phosphine Probe.

Reductive stress is a condition present in cells that have an increased concentration of reducing species, and it has been associated with a number of pathologies, such as neurodegenerative diseases and cancer. The tools available to study reductive stress lack both in selectivity and specific targeting and some of these shortcomings can be addressed by using photoactivatable compounds. We developed a photoactivatable phosphonium probe, which upon irradiation releases a fluorescent molecule and a trialkyphosphine. The probes can permeate through the plasma membrane and the photoreleased phosphine can induce intracellular reductive stress as proven by the detection of protein aggregates.

Development of a Photoactivatable Phosphine Probe for Induction of Intracellular Reductive Stress with Single-Cell Precision.

Photoactivatable phosphines that induce intracellular reductive stress are reported. The design of these probes takes advantage of the conjugate addition of trialkylphosphines to carbocyanine dyes, which can be reverted photochemically to produce the trialkylphosphine and a fluorescent reporter. The photochemical release depends on the efficiency of photoinduced electron transfer from the indolenine arm of the probe to the coumarin acceptor. These probes readily permeate the mammalian plasma membrane and can be photoactivated in live cells. Upon irradiation of the probe, the released trialkylphosphine induces intracellular reductive stress, which ultimately leads to formation of thioflavin-positive intracellular protein aggregates. These effects could be induced in individual cells within a monolayer, with minimal disturbance of neighboring cells.