Location, Location, Location: Establishing Design Principles for New Antibacterials from Ferric Siderophore Transport Systems

Abstract

This review strives to assemble a set of molecular design principles that enables the delivery of antibiotic warheads to Gram-negative bacterial targets (ESKAPE pathogens) using iron-chelating siderophores, known as the Trojan Horse strategy for antibiotic development. Principles are derived along two main lines. First, archetypical siderophores and their conjugates are used as case studies for native iron transport. They enable the consideration of the correspondence of iron transport and antibacterial target location. The second line of study charts the rationale behind the clinical antibiotic cefiderocol. It illustrates the potential versatility for the design of new Trojan Horse-based antibiotics. Themes such as matching the warhead to a location where the siderophore delivers its cargo (i.e., periplasm vs. cytoplasm), whether or not a cleavable linker is required, and the relevance of cheaters to the effectiveness and selectivity of new conjugates will be explored. The effort to articulate rules has identified gaps in the current understanding of iron transport pathways and suggests directions for new investigations.

Keywords: Trojan Horse; antibiotics; cefiderocol; iron transport; siderophore.

Figure 1

Generalized process of siderophore-mediated microbial iron uptake in Gram-negative bacteria.

Figure 2

Examples of siderophores containing various iron-chelating units (red: catecholate, green: α-hydroxycarboxylate, blue: hydroxamate, and orange: other iron-chelating moieties).

Figure 3

Structural comparison of ferrichrome and albomycins (blue: hydroxamate, grey: linker, pink: warhead).

Figure 4

Selected siderophore uptake systems in (A) A. baumannii, (B) E. coli, and (C) P. aeruginosa.

Figure 5

(A) Isomerization of preacinetobactin to acinetobactin. (B) Fe(III)–(PreAcb)₂ and Fe(III)–(Acb)₂ complexes. (C) Mixed Fe(III)–(PreAcb)(Acb) complex.

Figure 6

Structures of fimsbactin A–F (red: catecholate, blue: hydroxamate, and orange: other iron-chelating moieties).

Figure 7

Hydroxamate (blue) siderophores that utilize the Fhu pathway in E. coli.

Figure 8

Structures of salmochelin S4, agrobactin, and vibriobactin (red: catecholate).

Figure 9

The 1:1 and 2:1 Fe(III)–Pch complexes (orange: other iron-chelating moieties).

Figure 10

Structures of azotochelin and protochelin catecholate siderophores produced by A. vinelandii (red: catecholate).

Figure 11

Structure of a mycobactin–artemisinin conjugate (blue: hydroxamate, orange: other iron-chelating moieties, pink: warhead).

Figure 12

Warheads employed in Trojan Horse siderophore conjugates (blue: core motif).

Figure 13

Site of cleavage of albomycin liberation of nucleoside antibiotic (blue: hydroxamate, grey: linker, pink: warhead).

Figure 14

Hydroxamate and fimsbactin conjugates used in antibiotic studies (red: catecholate, blue: hydroxamate, grey: linker, pink: warhead).

Figure 15

Conjugates of enterobactin and related derivatives used in antibiotic studies (red: catecholate, grey: linker, pink: warhead).

Figure 16

Catecholate conjugates used in antibiotic studies (red: catecholate, grey: linker, pink: warhead).

Figure 17

A β-lactamase activated Trojan Horse antibiotic (red: catecholate, grey: linker, pink: warhead).

Figure 18

Pyochelin conjugates used in antibiotic studies (orange: other iron chelating moiety, grey: linker, pink: warhead).

Figure 19

Evolution of cefiderocol via E-0702 and S-9096 (red: catecholate, blue: β-lactams).