The E. coli Siderophores Enterobactin and Salmochelin Form Six-Coordinate Silicon Complexes at Physiological pH

DFT-based analysis of siderophore-metal ion interaction for efficient heavy metal remediation

Siderophores have great application potential in metal pollutant remediation because of their effective cost and friendly impact on the environment. However, the practical use of siderophores in the remediation of specific metals is rather limited because of the weak nonspecific interactions between the siderophores and different metals. Thus, screening for a siderophore with optimal interaction with a specific metal would be necessary. In this study, the interaction between metal ions and moieties that donate the oxygen ligands for the coordination of four types of siderophore (hydroxamates, catecholates, phenolates, and carboxylates) was modeled and analyzed. As revealed by DFT-based analysis, the four types of siderophore generally exhibited selection preference for different metal ions in the order Ga3+  > Al3+  > Fe3+  > Cr3+  > Ni2+  > Cu2+  > Zn2+  > Co2+  > Mn2+  > Hg2+  > Pb2+  > Cd2+, which was determined mainly by the electronegativity of the siderophore functional groups, the electronegativity of the metals, and the ionic radius of the metals, as well as the interaction between the siderophores and the metals. Moreover, the effect of linear or nonlinear (cyclic) structure on the affinity of each siderophore for different metal ions was evaluated. In most situations, metal-bound cyclic siderophores were found to be more stable than their linear counterparts. Thus, proper siderophores for the remediation of metal pollution may be rapidly screened using this model.

Advances in the Synthesis of Enterobactin, Artificial Analogues, and Enterobactin-Derived Antimicrobial Drug Conjugates and Imaging Tools for Infection Diagnosis

Iron is an essential growth factor for bacteria, but although highly abundant in nature, its bioavailability during infection in the human host or the environment is limited. Therefore, bacteria produce and secrete siderophores to ensure their supply of iron. The triscatecholate siderophore enterobactin and its glycosylated derivatives, the salmochelins, play a crucial role for iron acquisition in several bacteria. As these compounds can serve as carrier molecules for the design of antimicrobial siderophore drug conjugates as well as siderophore-derived tool compounds for the detection of infections with bacteria, their synthesis and the design of artificial analogues is of interest. In this review, we give an overview on the synthesis of enterobactin, biomimetic as well as totally artificial analogues, and related drug-conjugates covering up to 12/2021.

1 Introduction

2 Antibiotic Crisis and Sideromycins as Natural Templates for New Antimicrobial Drugs

3 Biosynthesis of Enterobactin, Salmochelins, and Microcins

4 Total Synthesis of Enterobactin and Salmochelins

5 Chemoenzymatic Semi-synthesis of Salmochelins and Microcin E492m Derivatives

6 Synthesis of Biomimetic Enterobactin Derivatives with Natural Tris-lactone Backbone

7 Synthesis of Artificial Enterobactin Derivatives without Tris-lactone Backbone

8 Conclusions

Silicon Forms a Rich Diversity of Aliphatic Polyol Complexes in Aqueous Solution

A detailed examination of aqueous Si complexation by alditols and aldonic acids was conducted using high-sensitivity ²⁹Si NMR spectroscopy of isotopically enriched solutions combined with theoretical modeling. Contrary to previous thinking, we have established that aliphatic polyols do not require a threo pair of hydroxy groups to form hypercoordinated Si complexes, although formation constants may be orders of magnitude higher if they are present. Thirteen distinctly different molecular assemblages containing 4-, 5-, or 6-coordinate Si centers have been identified, with significant concentrations of 5-coordinate Si bis-ligand complex being detected even under biologically relevant solution conditions.

Metal binding ability of microbial natural metal chelators and potential applications

Metallophores can chelate many different metal and metalloid ions next to iron, make them valuable for many applications.

The kinetics of siderophore-mediated olivine dissolution

Silicate minerals represent an important reservoir of nutrients at Earth's surface and a source of alkalinity that modulates long-term geochemical cycles. Due to the slow kinetics of primary silicate mineral dissolution and the potential for nutrient immobilization by secondary mineral precipitation, the bioavailability of many silicate-bound nutrients may be limited by the ability of micro-organisms to actively scavenge these nutrients via redox alteration and/or organic ligand production. In this study, we use targeted laboratory experiments with olivine and the siderophore deferoxamine B to explore how microbial ligands affect nutrient (Fe) release and the overall rate of mineral dissolution. Our results show that olivine dissolution rates are accelerated in the presence of micromolar concentrations of deferoxamine B. Based on the non-linear decrease in rates with time and formation of a Fe³⁺ -ligand complex, we attribute this acceleration in dissolution rates to the removal of an oxidized surface coating that forms during the dissolution of olivine at circum-neutral pH in the presence of O₂ and the absence of organic ligands. While increases in dissolution rates are observed with micromolar concentrations of siderophores, it remains unclear whether such conditions could be realized in natural environments due to the strong physiological control on microbial siderophore production. So, to contextualize our experimental results, we also developed a feedback model, which considers how microbial physiology and ligand-promoted mineral dissolution kinetics interact to control the extent of biotic enhancement of dissolution rates expected for different environments. The model predicts that physiological feedbacks severely limit the extent to which dissolution rates may be enhanced by microbial activity, though the rate of physical transport modulates this limitation.

How Many O-Donor Groups in Enterobactin Does It Take to Bind a Metal Cation?

The E. coli siderophore enterobactin, the strongest Fe^III chelator known to date, forms hexacoordinate complexes with Si^IV , Ge^IV , and Ti^IV . Synthetic protocols have been developed to prepare non-symmetric enterobactin analogues with varying denticities. Various benzoic acid residues were coupled to the macrocyclic lactone to afford a diverse library of ligands. These enterobactin analogues were bound to Si^IV , Ge^IV , and Ti^IV , and the complexes were investigated through experimental and computational techniques. The binding behavior of the synthesized chelators enabled assessment of the contribution of each of the phenolic hydroxy groups in enterobactin to metal-ion complexation. It was found that at least four O-donors are needed for enterobactin derivatives to act as metal binders. Density functional theory calculations indicate that the strong binding behavior of enterobactin can be ascribed to a diminished translational entropy penalty, a common feature of the chelate effect, coupled with the structural arrangement of the three catechol moieties, which allows the triseryl base to be installed without distorting the preferred local metal-binding geometry of the catecholate ligands.

Determination of the Molecular Structures of Ferric Enterobactin and Ferric Enantioenterobactin Using Racemic Crystallography

Enterobactin is a secondary metabolite produced by Enterobacteriaceae for acquiring iron, an essential metal nutrient. The biosynthesis and utilization of enterobactin permits many Gram-negative bacteria to thrive in environments where low soluble iron concentrations would otherwise preclude survival. Despite extensive work carried out on this celebrated molecule since its discovery over 40 years ago, the ferric enterobactin complex has eluded crystallographic structural characterization. We report the successful growth of single crystals containing ferric enterobactin using racemic crystallization, a method that involves cocrystallization of a chiral molecule with its mirror image. The structures of ferric enterobactin and ferric enantioenterobactin obtained in this work provide a definitive assignment of the stereochemistry at the metal center and reveal secondary coordination sphere interactions. The structures were employed in computational investigations of the interactions of these complexes with two enterobactin-binding proteins, which illuminate the influence of metal-centered chirality on these interactions. This work highlights the utility of small-molecule racemic crystallography for obtaining elusive structures of coordination complexes.

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.

Beyond iron: non-classical biological functions of bacterial siderophores

Bacteria secrete small molecules known as siderophores to acquire iron from their surroundings. For over 60 years, investigations into the bioinorganic chemistry of these molecules, including fundamental coordination chemistry studies, have provided insight into the crucial role that siderophores play in bacterial iron homeostasis. The importance of understanding the fundamental chemistry underlying bacterial life has been highlighted evermore in recent years because of the emergence of antibiotic-resistant bacteria and the need to prevent the global rise of these superbugs. Increasing reports of siderophores functioning in capacities other than iron transport have appeared recently, but reports of "non-classical" siderophore functions have long paralleled those of iron transport. One particular non-classical function of these iron chelators, namely antibiotic activity, was documented before the role of siderophores in iron transport was established. In this Perspective, we present an exposition of past and current work into non-classical functions of siderophores and highlight the directions in which we anticipate that this research is headed. Examples include the ability of siderophores to function as zincophores, chalkophores, and metallophores for a variety of other metals, sequester heavy metal toxins, transport boron, act as signalling molecules, regulate oxidative stress, and provide antibacterial activity.

Si-enterobactin from the endophytic Streptomyces sp. KT-S1-B5--a potential silicon transporter in Nature?

Si-enterobactin (2a), a hexacoordinated complex of the siderophore enterobactin (2b) with silicon as the central atom, was isolated from an endophytic Streptomyces sp. occurring in Piper guinensis roots. The structure and absolute configuration were determined from NMR and MS data, and by X-ray diffraction. The orientation of the molecule along the pseudo-3-fold axis shows that the coordination environment of the silicon atom complexed with three bidentate ligands is Δ. We assume that 2a or related complexes may be involved in the transport of silicon in plants, diatoms, or other silicon-dependent organisms.

Synthesis and structural characterization of hexacoordinate silicon, germanium, and titanium complexes of the E. coli siderophore enterobactin

The E. coli siderophore enterobactin, one of the strongest Fe(III) chelators known to date, is also capable of binding Si(IV) under physiological conditions. We report on the synthesis and structural characterization of the tris(catecholate) Si(IV) -enterobactin complex and its Ge(IV) and Ti(IV) analogues. Comparative structural analysis, supported by quantum-chemical calculations, reveals the correlation between the ionic radius and the structural changes in enterobactin upon complexation.

Towards establishing broad-spectrum disease resistance in plants: silicon leads the way

Plants are constantly threatened by a wide array of microbial pathogens. Pathogen invasion can lead to vast yield losses and the demand for sustainable plant-protection strategies has never been greater. Chemical plant activators and selected strains of rhizobacteria can increase resistance against specific types of pathogens but these treatments are often ineffective or even cause susceptibility against others. Silicon application is one of the scarce examples of a treatment that effectively induces broad-spectrum disease resistance. The prophylactic effect of silicon is considered to be the result of both passive and active defences. Although the phenomenon has been known for decades, very little is known about the molecular basis of silicon-afforded disease control. By combining knowledge on how silicon interacts with cell metabolism in diatoms and plants, this review describes silicon-induced regulatory mechanisms that might account for broad-spectrum plant disease resistance. Priming of plant immune responses, alterations in phytohormone homeostasis, regulation of iron homeostasis, silicon-driven photorespiration and interaction with defence signalling components all are potential mechanisms involved in regulating silicon-triggered resistance responses. Further elucidating how silicon exerts its beneficial properties may create new avenues for developing plants that are better able to withstand multiple attackers.