Acetyl-CoA-Mediated Post-Biosynthetic Modification of Desferrioxamine B Generates N- and N-O-Acetylated Isomers Controlled by a pH Switch

An elastic siderophore synthetase and rubbery substrates assemble multimeric linear and macrocyclic hydroxamic acid metal chelators

The trihydroxamic acid bacterial siderophore desferrioxamine B (DFOB, 1) produced by the DesABCD biosynthetic cluster coordinates metals beyond Fe(iii), which identifies potential to modify this chelator type to broaden metal sequestration and/or delivery applications. Rather than producing discrete chelators by total chemical synthesis from native monomers including N-hydroxy-N-succinyl-cadaverine (HSC, 2), the recombinant siderophore synthetase from Salinispora tropica CNB-440 (StDesD) was used with different substrate combinations to produce biocombinatorial mixtures of hydroxamic acid chelators. The mixtures were screened with Ga(iii) or Zr(iv) as surrogates of immunological positron emission tomography (PET) imaging radiometals 68Ga(iii) or 89Zr(iv) to inform known or new coordination chemistry. The last-in-line enzyme DesD forms amide bonds between two equivalents of 2 and N-hydroxy-N-acetyl-cadaverine to produce trimeric 1. Although hexadentate 1 is the terminal product evolved for Fe(iii) complexation, it was conceived amine-containing 1 might remain a viable DesD substrate for further iteration with 2 to generate higher-order hydroxamic acid multimers. Incubation of StDesD, cofactors ATP and Mg(ii), and 1 and 2, generated the octadentate hydroxamic acid DFOB-HSC (3) (previously characterised and named DFO*), decadentate DFOB-(HSC)2 (4), dodecadentate DFOB-(HSC)3 (5) and tetradecadentate DFOB-(HSC)4 (6). The system with StDesD and 2 alone generated a set of linear multimers containing flanking amine and carboxylic acid groups (HSC) x -L (x = 2 (7), x = 3 (8), x = 4 (9), x = 5 (10)) and a subset of the cognate ring-closed macrocycles (HSC) x -MC (x = 3 (12), x = 4 (13), x = 5 (14), with x = 2 (11) not detected). Liquid chromatography-mass spectrometry metal screening experiments detected 1 : 1 complexes of Ga(iii) or Zr(iv) and 1, 3-5, 8-10, and 12-14. Complexes of 2 : 1 stoichiometry were formed between Ga(iii) and the high-denticity, high-cavity-volume chelators 4-6, and 14. A processive intra-cavity assembly mechanism has been posited for this flexible siderophore synthetase in delivering a large set of multimeric chelators.

A Mild and Modular Approach to the Total Synthesis of Desferrioxamine B

A mild and modular approach to the total synthesis of the WHO-listed essential medicine desferrioxamine B is described. Hydroxamic acid fragments were installed under mild conditions, a generalized divergent acylation procedure used to access two monomer precursors, and a transfer hydrogenation reaction used to unmask the hydroxamic acid moieties. Desferrioxamine B was generated over ten linear steps as the formate salt in 17% overall yield using standard amide coupling conditions or in 13% overall yield using microwave-assisted amide coupling conditions.

Siderophore Synthetase DesD Catalyzes N-to-C Condensation in Desferrioxamine Biosynthesis

Desferrioxamine siderophores are assembled by the nonribosomal-peptide-synthetase-independent siderophore (NIS) synthetase enzyme DesD via ATP-dependent iterative condensation of three N1-hydroxy-N1-succinyl-cadaverine (HSC) units. Current knowledge of NIS enzymology and the desferrioxamine biosynthetic pathway does not account for the existence of most known members of this natural product family, which differ in substitution patterns of the N- and C-termini. The directionality of desferrioxamine biosynthetic assembly, N-to-C versus C-to-N, is a longstanding knowledge gap that is limiting further progress in understanding the origins of natural products in this structural family. Here, we establish the directionality of desferrioxamine biosynthesis using a chemoenzymatic approach with stable isotope incorporation and dimeric substrates. We propose a mechanism where DesD catalyzes the N-to-C condensation of HSC units to establish a unifying biosynthetic paradigm for desferrioxamine natural products in Streptomyces.

On the origin of amphi-enterobactin fragments produced by Vibrio campbellii species

Amphi-enterobactin is an amphiphilic siderophore isolated from a variety of microbial Vibrio species. Like enterobactin, amphi-enterobactin is a triscatecholate siderophore; however, it is framed on an expanded tetralactone core comprised of four l-Ser residues, of which one l-Ser is appended by a fatty acid and the remaining l-Ser residues are appended by 2,3-dihydroxybenzoate (DHB). Fragments of amphi-enterobactin composed of 2-Ser-1-DHB-FA and 3-Ser-2-DHB-FA have been identified in the supernatant of Vibrio campbellii species. The origin of these fragments has not been determined, although two distinct isomers could exist for 2-Ser-1-DHB-FA and three distinct isomers could exist for 3-Ser-2-DHB-FA. The fragments of amphi-enterobactin could originate from hydrolysis of the amphi-enterobactin macrolactone, or from premature release due to an inefficient biosynthetic pathway. Unique masses in the tandem MS analysis establish that certain fragments isolated from the culture supernatant must originate from hydrolysis of the amphi-enterobactin macrolactone, while others cannot be distinguished from premature release during biosynthesis or hydrolysis of amphi-enterobactin.

An acyl-adenylate mimic reveals the structural basis for substrate recognition by the iterative siderophore synthetase DesD

Siderophores are conditionally essential metabolites used by microbes for environmental iron sequestration. Most Streptomyces strains produce hydroxamate-based desferrioxamine (DFO) siderophores composed of repeating units of N¹-hydroxy-cadaverine (or N¹-hydroxy-putrescine) and succinate. The DFO biosynthetic operon, desABCD, is highly conserved in Streptomyces; however, expression of desABCD alone does not account for the vast structural diversity within this natural product class. Here, we report the in vitro reconstitution and biochemical characterization of four DesD orthologs from Streptomyces strains that produce unique DFO siderophores. Under in vitro conditions, all four DesD orthologs displayed similar saturation steady-state kinetics (V_max = 0.9–2.5 μM⋅min⁻¹) and produced the macrocyclic trimer DFOE as the favored product, suggesting a conserved role for DesD in the biosynthesis of DFO siderophores. We further synthesized a structural mimic of N¹-hydroxy-N¹-succinyl-cadaverine (HSC)-acyl-adenylate, the HSC-acyl sulfamoyl adenosine analog (HSC-AMS), and obtained crystal structures of DesD in the ATP-bound, AMP/PP_i-bound, and HSC-AMS/P_i-bound forms. We found HSC-AMS inhibited DesD orthologs (IC₅₀ values = 48–53 μM) leading to accumulation of linear trimeric DFOG and di-HSC at the expense of macrocyclic DFOE. Addition of exogenous PP_i enhanced DesD inhibition by HSC-AMS, presumably via stabilization of the DesD–HSC-AMS complex, similar to the proposed mode of adenylate stabilization where PP_i remains buried in the active site. In conclusion, our data suggest that acyl-AMS derivatives may have utility as chemical probes and bisubstrate inhibitors to reveal valuable mechanistic and structural insight for this unique family of adenylating enzymes.