The total synthesis of nannochelin: a novel cinnamoyl hydroxamate-containing siderophore

Design and Syntheses of New Antibiotics Inspired by Nature's Quest for Iron in an Oxidative Climate

This Account describes fundamental chemistry that promoted the discovery of new antibiotics. Specifically, the NH acidity of simple hydroxamic acid derivatives facilitated the syntheses of novel β-lactams (oxamazins and monobactams), siderophore mimics that limit bacterial iron uptake and bacterially targeted sideromycins (siderophore-antibiotic conjugates). The development of resistance to our current limited set of antibiotic scaffolds has created a dire medical situation. As recently stated, "if you weren't taking antibiotic resistance seriously before, now would be a good time to start." A project commissioned by the British government (https://amr-review.org/) has released estimates of the near-future global toll of antibiotic resistance that are jaw-dropping in their seriousness and scale: 10 million deaths per year and at least $100 trillion in sacrificed gross national product. The 2020 COVID pandemic confirmed that infectious disease problems are no longer localized but worldwide. Many classical antibiotics, especially β-lactams, previously provided economical cures, but the evolution of antibiotic destructive enzymes (i.e., β-lactamases), efflux pumps, and bacterial cell wall permeability barriers has made many types of bacteria, especially Gram-negative strains, resistant. Still, and in contrast to other therapies, the public expectation is that any new antibiotic must be inexpensive. This creates market limitations that have caused most major pharmaceutical companies to abandon antibiotic research. Much needs to be done to address this significant problem.The critical need for bacteria to sequester essential iron provides an Achilles' heel for new antibiotic development. Although ferric iron is extremely insoluble, bacteria need micromolar intracellular concentrations for growth and virulence. To this end, they biosynthesize siderophores (Gr. iron bearer) and excrete them into their environment, where they bind iron with high affinity. The iron complexes are recognized by specific outer-membrane transporters, and once actively internalized, the iron is released for essential processes. To conserve biosynthetic energy, some bacteria recognize and utilize siderophores made by competing strains. As a counter-revolution in the never-ending fight for survival, bacteria have also evolved sideromycins, which are siderophores conjugated to warheads that are lethal to rogue bacteria. While none are now used therapeutically, natural sideromycins called albomycins have been used clinically, and others have been shown to be well tolerated and active in animal infection models. Herein we describe practical methods to synthesize new antibiotics and artificial sideromycins with the generalized structure shown above (siderophore-linker drug). Utilizing the molecular-recognition-based siderophore/sideromycin bacterial assimilation processes, it is possible to design both broad spectrum and exquisitely narrow spectrum (targeted) sideromycins and even repurpose older or more classical antibiotics. Relevant microbiological assays, in vivo animal infection studies, and the recent FDA approval of cefiderocol demonstrate their effectiveness.

Synthetic strategies in construction of organic low molecular-weight carrier-drug conjugates

Inefficient transportation of polar metabolic inhibitors through cell membranes of eukaryotic and prokaryotic cells precludes their direct use as drug candidates in chemotherapy. One of the possible solutions to this problem is application of the 'Trojan horse' strategy, i.e. conjugation of an active substance with a molecular carrier of organic or inorganic nature, facilitating membrane penetration. In this work, the synthetic strategies used in rational design and preparation of conjugates of bioactive agents with three types of organic low molecular-weight carriers have been reviewed. These include iron-chelating agents, siderophores and cell-penetrating peptides. Moreover, a less known but very promising "molecular umbrella" conjugation strategy has been presented. Special attention has been paid on appropriate linking strategies, especially these allowing intracellular drug release after internalisation of a conjugate.

Total synthesis and antimicrobial evaluation of natural albomycins against clinical pathogens

Development of effective antimicrobial agents continues to be a great challenge, particularly due to the increasing resistance of superbugs and frequent hospital breakouts. There is an urgent need for more potent and safer antibiotics with novel scaffolds. As historically many commercial drugs were derived from natural products, discovery of antimicrobial agents from complex natural product structures still holds a great promise. Herein, we report the total synthesis of natural albomycins δ₁ (1a), δ₂ (1b), and ε (1c), which validates the structures of these peptidylnucleoside compounds and allows for synthetic access to bioactive albomycin analogs. The efficient synthesis of albomycins enables extensive evaluations of these natural products against model bacteria and clinical pathogens. Albomycin δ₂ has the potential to be developed into an antibacterial drug to treat Streptococcus pneumoniae and Staphylococcus aureus infections.

Albomycins are promising drug candidates for the treatment of bacterial infections. Here, the authors describe the total syntheses of albomycins δ₁, δ₂, and ε, and evaluate their antimicrobial activity, identifying albomycin δ₂ as a strong agent against S. pneumoniae and S. aureus infections.

Biodegradable siderophores: survey on their production, chelating and complexing properties

The academic and industrial research on the interactions of complexing agents with the environment has received more attention for more than half a century ago and has always been concerned with the applications of chelating agents in the environment. In contrast, in recent years, an increasing scholarly interest has been demonstrated in the chemical and biological degradation of chelating agents. This is reflected by the increasing number of chelating agents-related publications between 1950 and middle of 2016. Consequently, the discovery of new green biodegradable chelating agents is of great importance and has an impact in the non-biodegradable chelating agent’s replacement with their green chemistry analogs. To acquire iron, many bacteria growing aerobically, including marine species, produce siderophores, which are low-molecular-weight compounds produced to facilitate acquisition of iron. To date and to the best of our knowledge, this is a concise and complete review article of the current and previous relevant studies conducted in the field of production, purification of siderophore compounds and their metal complexes, and their roles in biology and medicine.

Desferrithiocin: a search for clinically effective iron chelators

The successful search for orally active iron chelators to treat transfusional iron-overload diseases, e.g., thalassemia, is overviewed. The critical role of iron in nature as a redox engine is first described, as well as how primitive life forms and humans manage the metal. The problems that derive when iron homeostasis in humans is disrupted and the mechanism of the ensuing damage, uncontrolled Fenton chemistry, are discussed. The solution to the problem, chelator-mediated iron removal, is clear. Design options for the assembly of ligands that sequester and decorporate iron are reviewed, along with the shortcomings of the currently available therapeutics. The rationale for choosing desferrithiocin, a natural product iron chelator (a siderophore), as a platform for structure-activity relationship studies in the search for an orally active iron chelator is thoroughly developed. The study provides an excellent example of how to systematically reengineer a pharmacophore in order to overcome toxicological problems while maintaining iron clearing efficacy and has led to three ligands being evaluated in human clinical trials.

Antibiotics from myxobacteria

Covering: up to the end of 2013. Myxobacteria produce a vast range of structurally diverse natural products with prominent biological activities. Here, we provide a detailed description and judge the potential of all antibiotically active myxobacterial compounds as lead structures, pointing out their particularities and, if known, their mode of action. Thus, the review provides an overview of the potential of specific compounds, suitable for future investigations and possible clinical applications.

A suite of citrate-derived siderophores from a marine Vibrio species isolated following the Deepwater Horizon oil spill

Nearly all microbes require iron for growth. The low concentration of iron found in the ocean makes iron acquisition a particularly difficult task. In response to these low iron conditions, many bacteria produce low-molecular-weight iron-binding molecules called siderophores to aid in iron uptake. We report herein the isolation and structural characterization of a suite of amphiphilic siderophores called the ochrobactins-OH, which are produced by a Vibrio species isolated from the Gulf of Mexico after the 2010 Deepwater Horizon oil spill. The citrate-based ochrobactins-OH are derivatives of aerobactin, replacing the acetyl groups with fatty acid appendages ranging in size from C8 to C12, and are distinctly different from the ochrobactins in that the fatty acid appendages are hydroxylated rather than unsaturated. The discovery of the marine amphiphilic ochrobactin-OH suite of siderophores increases the geographic and phylogenetic diversity of siderophore-producing bacteria.

Enzymatic tailoring of ornithine in the biosynthesis of the Rhizobium cyclic trihydroxamate siderophore vicibactin

To acquire iron, the N(2)-fixing, symbiotic bacterium Rhizobium sp. produce the cyclic trihydroxamate siderophore vicibactin, containing a 30-membered trilactone scaffold. Herein we report the overproduction and purification of the six proteins VbsACGOLS in the bacterial host Escherichia coli and the reconstitution of the biosynthesis of vicibactin from primary metabolites. The flavoprotein VbsO acts as a pathway-initiating l-ornithine N(5)-hydroxylase, followed by VbsA, which transfers (R)-3-hydroxybutyryl- from the CoA thioester to N(5)-hydroxyornithine to yield N(5)-((R)-3-hydroxybutyryl)-N(5)-hydroxy-l-ornithine. VbsL is a PLP-dependent epimerase acting at C(2) of the 10 atom monomer unit. VbsS, a nonribosomal peptide synthetase free-standing module, then activates N(5)-((R)-3-hydroxybutyryl)-N(5)-hydroxy-d-ornithine as the AMP anhydride on the way to cyclotrimerization to the vicibactin scaffold. The last step, tris-acetylation of the C(2) amino group of desacetyl-d-vicibactin to the mature siderophore vicibactin, is catalyzed distributively by VbsC, using three molecules of acetyl-CoA.

Vibriobactin antibodies: a vaccine strategy

A new target strategy in the development of bacterial vaccines, the induction of antibodies to microbial outer membrane ferrisiderophore complexes, is explored. A vibriobactin (VIB) analogue, with a thiol tether, 1-(2,3-dihydroxybenzoyl)-5,9-bis[[(4S,5R)-2-(2,3-dihydroxyphenyl)-4,5-dihydro-5-methyl-4-oxazolyl]carbonyl]-14-(3-mercaptopropanoyl)-1,5,9,14-tetraazatetradecane, was synthesized and linked to ovalbumin (OVA) and bovine serum albumin (BSA). The antigenicity of the VIB microbial iron chelator conjugates and their iron complexes was evaluated. When mice were immunized with the resulting OVA-VIB conjugate, a selective and unequivocal antigenic response to the VIB hapten was observed; IgG monoclonal antibodies specific to the vibriobactin fragment of the BSA and OVA conjugates were isolated. The results are consistent with the idea that the isolated adducts of siderophores covalently linked to their bacterial outer membrane receptors represent a credible target for vaccine development.

Synthesis and studies of catechol-containing mycobactin S and T analogs

The syntheses of catechol-containing mycobactin S and T analogs are described. These analogs incorporate a catechol-glycine moiety in place of the phenol-oxazoline of the naturally occurring mycobactins S and T. Studies indicated that the new siderophore analogs bind iron, and promote the growth of a number of microbes, especially strains of mycobacteria, as expected.

Structure and membrane affinity of new amphiphilic siderophores produced by Ochrobactrum sp. SP18

The coastal alpha-proteobacterium Ochrobactrum sp. SP18 produces a suite of three citrate-derived, cell-associated amphiphilic siderophores, ochrobactins A-C. The ochrobactins are composed of a citric acid backbone amide-linked to two lysine residues. Each epsilon-amine of lysine is hydroxylated and acylated forming two hydroxamic acid moieties. One of the acylated appendages of each ochrobactin is (E)-2-decenoic acid. The other acylated appendages for ochrobactins A-C are (E)-2-octenoic acid, octanoic acid and (E)-2-decenoic acid, respectively. The ferric ochrobactin complexes are photoreactive in UV light, producing an oxidized ligand with loss of 46 mass units that can still coordinate Fe(III). The relative partitioning of the apo-ochrobactins, Fe(III) ochrobactins and Fe(III) photoproducts into 1,2-dimyristoyl-sn-glycero-3-phosphocholine vesicles is presented. The ochrobactins are the first example of aerobactin-based siderophores with two fatty acid appendages produced in a suite with varying acyl appendage lengths.

Synthesis and structural modeling of the amphiphilic siderophore rhizobactin-1021 and its analogs

We describe two convenient syntheses of rhizobactin-1021 (Rz), a citrate-based siderophore amphiphile produced by the nitrogen-fixing root symbiont Rhizobium meliloti-1021, and several analogs. Our approach features a singly amidated, tert-butyl-protected citrate intermediate that easily affords a variety of Rz analogs in the late stages of the synthesis. Structural modeling and the monolayer behavior of Rz and its metal complexes are consistent with a structural reorganization upon Rz-mediated iron chelation.

Membrane Dynamics of the Amphiphilic Siderophore, Acinetoferrin

Acinetobacter haemolyticus is an antibiotic resistant, pathogenic bacterium responsible for an increasing number of hospital infections. Acinetoferrin (Af), the amphiphilic siderophore isolated from this organism, contains two unusual trans-2-octenoyl hydrocarbon chains reminiscent of a phospholipid structural motif. Here, we have investigated the membrane affinity of Af and its iron complex, Fe-Af, using small and large unilamellar phospholipid vesicles (SUV and LUV) as model membranes. Af shows a high membrane affinity with a partition coefficient, K(x)= 6.8 x 10(5). Membrane partitioning and trans-membrane flip-flop of Fe-Af have also been studied via fluorescence quenching of specifically labeled vesicle leaflets and (1)H NMR line-broadening techniques. Fe-Af is found to rapidly redistribute between lipid and aqueous phases with dissociation/partitioning rates of k(off) = 29 s(-1) and k(on) = 2.4 x 10(4) M(-1) s(-1), respectively. Upon binding iron, the membrane affinity of Af is reduced 30-fold to K'(x) = 2.2 x 10(4) for Fe-Af. In addition, trans-membrane flip-flop of Fe-Af occurs with a rate constant, k(p) = 1.2 x 10(-3) s(-1), with egg-PC LUV and a half-life time around 10 min with DMPC SUV. These properties are due to the phospholipid-like conformation of Af and the more extended conformation of Fe-Af that is enforced by iron binding. Remarkable similarities and differences between Af and another amphiphilic siderophore, marinobactin E, are discussed. The potential biological implications of Af and Fe-Af are also addressed. Our approaches using inner- and outer-leaflet-labeled fluorescent vesicles and (1)H NMR line-broadening techniques to discern Af-mediated membrane partitioning and trans-membrane diffusion are amenable to similar studies for other paramagnetic amphiphiles.

Total synthesis of petrobactin and its homologues as potential growth stimuli for Marinobacter hydrocarbonoclasticus, an oil-degrading bacteria

A modular synthesis was developed to access petrobactin, a catechol-containing siderophore isolated from Marinobacter hydrocarbonoclasticus. A range of petrobactin homologues with differing dihydroxybenzamide motifs and in one case an increased number of carbons in the polyamine backbone were also synthesized. As such, these systems represent new isomeric probes to study iron transport properties in M. hydrocarbonoclasticus. The synthesis of petrobactin and its homologues and the first biological study of how these agents influence the growth of Mycobacterhydrocarbonoclasticus are reported. New synthetic methods were developed to overcome issues (imide formation) encountered in earlier syntheses. Both the (1)H and (13)C NMR of petrobactin were consistent with the recently revised structure showing that petrobactin in fact contains a 3,4-dihydroxybenzene motif rather than a 2,3-dihydroxybenzene motif. The preliminary biological studies suggested that using the native petrobactin 1b for M. hydrocarbonoclasticus-specific growth stimulation may be a poor strategy for oil-spill cleanup.

Synthesis and Biological Evaluation of New Acinetoferrin Homologues for Use as Iron Transport Probes in Mycobacteria

Four new acinetoferrin homologues were synthesized using a modular synthetic approach. Two linear and two cyclic imide derivatives were generated and evaluated for growth stimulating behavior in Mycobacterium avium subsp paratuberculosis. The yield for the tandem coupling of a functionalized aminohydroxamic acid motif (2 equiv) to a tert-butyl citrate derivative was significantly improved using DCC and N-hydroxysuccinimide. (1)H NMR spectroscopy (CD(3)OD) provided a convenient method for monitoring the final imidization step in TFA using the doublet patterns between 2.5 and 3.06 ppm. New protocols demonstrated that only a 20% growth enhancement was observed with M. avium subsp. paratuberculosis using the imide of acinetoferrin. Last, a siderophore from Streptomyces pilosus, deferrioxamine B, was shown to cross-feed M. avium subsp. paratuberculosis with the same efficiency as the more costly, native chelator, mycobactin J.

Synthesis and biological evaluation of new citrate-based siderophores as potential probes for the mechanism of iron uptake in mycobacteria

Several iron chelators containing alpha,beta-unsaturated hydroxamic acid motifs appended to a citric acid platform were synthesized. Mycobacterium paratuberculosis was then challenged to grow in the presence of a panel of siderophores (mycobactin J, deferrioxamine B, acinetoferrin, and nannochelin A) and the new synthetic agents. Of the structures tested, those containing the trans 2-octenoyl motif were preferred over those with trans cinnamoyl groups. In addition, derivatives containing longer tether lengths between the iron binding ligands (C5) were more efficacious and led to higher growth index values. Perhaps most remarkable was the finding that at 2.4 microM a trans 2-octenoylated, citrate-containing imide 6 was nearly 5-fold more effective in stimulating growth than the native chelator, mycobactin J. In this regard, new structural elements were identified (e.g., an imide motif or 2-octenoyl side chain), whose presence stimulated mycobacterial growth.

Synthesis of N-(Hydroxy)amide- and N-(Hydroxy)thioamide-containing peptides

Methods developed with N-(benzoyloxy)amines and hydroxamic acids were used in the synthesis of N-(hydroxy)amide-containing pseudopeptides. Acylation of N-(benzoyloxy)phenethylamine with the acid chloride of N(alpha)-Fmoc-L-leucine provided a N(alpha)-Fmoc-N-(benzoyloxy)-L-leucinamide in 90% yield. Deprotection of the benzoyl group (using 10 vol % NH(4)OH/MeOH) provided the N(alpha)-Fmoc-N-(hydroxy)-L-leucinamide in 87% yield. In general, the appended Fmoc group allowed for further elaboration of the N-hydroxy-N-(alkyl)amides using classic peptide-coupling methods. A practical synthetic strategy was developed, and racemization issues were addressed using diastereomeric Val-Leu derivatives. In addition, N-(hydroxy)thioamides were generated from the corresponding N-(benzoyloxy)thioamides. N-(Benzoyloxy)thioamides were obtained in moderate yields (53-76%) from the reaction of the corresponding N-(benzoyloxy)amides with Lawesson's reagent (i.e., 2, 4-bis(4-methoxyphenyl)-1,3-dithia-2,4-diphosphetane-2,4-disu lfide). In summary, this new technology allows for the introduction of either N-hydroxyamide or N-(hydroxy)thioamide linkages into pseudopeptide chains without racemization.

The origin of the differences in (R)- and (S)-desmethyldesferrithiocin. Iron-clearing properties

The iron clearance properties, toxicity, and pharmacokinetics of (R)- and (S)-desmethyldesferrithiocin (DMDFT) are described. The studies were performed in rodent and primate models. While both enantiomers were found to be effective iron chelators with minimal toxicity in the rodents, only (S)-DMDFT was able to induce the clearance of any iron in the primates. In addition, two out of nine of the monkeys given (R)-DMDFT died within 24 h of drug administration. The reason for the differences in iron clearance properties and the apparent toxicity of the (R)-enantiomer in the primates is likely related to the disparities in the pharmacokinetics of the two analogues. The pharmacokinetic data suggest enantioselectivity in renal clearance of the desferrithiocins and their iron complexes with (S)-DMDFT clearance 3.5 times greater than that of (R)-DMDFT, and FeIII [(S)-DMDFT]2 clearance 6.8 times greater than that of FeIII [R-DMDFT]2. In all primates studied FeIII [(R)-DMDFT]2 in the plasma exceeded 25 mg/L (50 microM) for several hours and remained above 10 mg/L (20 microM) at 8 h while levels of FeIII [(S)-DMDFT]2 never exceeded 50 microM and were at or below the limits of detection 8 h post-injection.

An Improved Synthesis of O-Benzoyl Protected Hydroxamates

Several primary amines (R-NH(2)) were converted to their corresponding O-benzoyl protected hydroxamates under biphasic conditions. The intermediate (benzoyloxy)amines (R-NHOCOPh) were generated using benzoyl peroxide dissolved in CH(2)Cl(2) and an aqueous carbonate buffer (pH 10.5) at room temperature. Subsequent acylation with R'COCl gave the protected hydroxamates (R'CONROCOPh) in good overall yields (56-89%).