Sophisticated natural products as antibiotics

Abstract

In this Review, we explore natural product antibiotics that do more than simply inhibit an active site of an essential enzyme. We review these compounds to provide inspiration for the design of much-needed new antibacterial agents, and examine the complex mechanisms that have evolved to effectively target bacteria, including covalent binders, inhibitors of resistance, compounds that utilize self-promoted entry, those that evade resistance, prodrugs, target corrupters, inhibitors of 'undruggable' targets, compounds that form supramolecular complexes, and selective membrane-acting agents. These are exemplified by β-lactams that bind covalently to inhibit transpeptidases and β-lactamases, siderophore chimeras that hijack import mechanisms to smuggle antibiotics into the cell, compounds that are activated by bacterial enzymes to produce reactive molecules, and antibiotics such as aminoglycosides that corrupt, rather than merely inhibit, their targets. Some of these mechanisms are highly sophisticated, such as the preformed β-strands of darobactins that target the undruggable β-barrel chaperone BamA, or teixobactin, which binds to a precursor of peptidoglycan and then forms a supramolecular structure that damages the membrane, impeding the emergence of resistance. Many of the compounds exhibit more than one notable feature, such as resistance evasion and target corruption. Understanding the surprising complexity of the best antimicrobial compounds provides a roadmap for developing novel compounds to address the antimicrobial resistance crisis by mining for new natural products and inspiring us to design similarly sophisticated antibiotics.

Fig. 1.. Beta lactams are molecular mimics of the D-Ala D-Ala terminal peptidoglycan motif

a, Penicillin binding proteins normally recognize the terminal D-Ala D-Ala motif and form an acyl-enzyme intermediate by insertion into D-Ala D-Ala bond eliminating the terminal D-Ala. The acyl-enzyme intermediate subsequently reacts with a second strand of peptidoglycan to form a cross link completing the catalytic cycle. b, Penicillin binding proteins mistake penicillin for their natural substrate D-Ala D-Ala due to molecular mimicry reacting with the lactam ring and are then unable to eliminate the terminal D-Ala (thiazole) motif, irreversibly blocking subsequent deacylation and catalytic turnover.

Fig. 2.. Resistance-evasive compounds.

a, Lipid II/antibiotic interaction sites (pink). Vancomycin interacts with the C-terminus of the pentapeptide, teixobactin with the PPi-group and the MurNAc sugar, and Clovibactin with the PPi-group. b, Vancomycin binds the D-Ala-D-Ala C-terminus of the Lipid II-pentapeptide with five hydrogen bonds. c, Teixobactin – Lipid II complex interface. The backbone amino-protons of the depsi-cycle of teixobactin, the End10 sidechain and the N terminus of an adjacent teixobactin coordinate the lipid II PPi group. In addition, End10 interacts with the MurNAc sugar via hydrogen bonds. Blue spheres represent backbone nitrogens; numbers indicate the residue numbers. d, Clovibactin – Lipid II complex interface. The backbone amino-protons of the depsi-cycle of clovibactin tightly bind the PPi-group, while hydrophobic sidechains (Ala6, Leu7, Leu8) seamlessly wrap around PPi, but do not specifically interact with the sugars. e, Model of the mode of action of teixobactin. Teixobactin first forms small β-sheets upon binding of lipid II, then elongates into fibrils that eventually associate into lateral fibrillar sheets, obstructing biosynthesis of peptidoglycan and causing membrane defects. f, Model of the mode of action of clovibactin. At the membrane surface, clovibactin binds lipid II and forms small oligomers that serve as nuclei for the formation of fibrils. Fibril formation enables a stable binding of lipid II and other cell wall precursors, blocking cell wall biosynthesis Panels c, e reproduced from Shukla et al.

Figure 3.. Acyldepsipeptide (ADEP) as an anti-persister compound.

a, The S. aureus ClpP protease is a tetradecamer of stacked heptameric rings (closed conformation, PDB 6TTY). The individual protomers are rendered as protein surfaces and colored in shades of pink. b, The chemical structure of ADEP4 and its respective binding pose on S. aureus ClpP (open conformation, PDB 6PMD). ADEP4 is shown in blue, and ClpP is rendered as pink surfaces with cartoon ribbons in the binding site. c, The molecular mechanism of bacterial ClpP proteases. For regulated degradation in the presence of ATP, Clp chaperones bind specific protein substrates and bring them to ClpP for complex formation. Protein substrates unfold and translocate into the proteolytic chamber for controlled proteolysis. For dysregulated degradation, ADEPs bind to ClpP and compete out the chaperones for an unregulated, activated proteolytic state, leading to the proteolysis of essential proteins and causing cell death.

Figure 4.. Darobactin and Dynobactin.

a, Chemical structure of darobactin A. b, Close-up of the darobactin A binding site at the BamA lateral gate. c, Cryo-EM structure of BAM complex with bound darobactin A. d, Scheme of daro/dynobactin evolution. e, Chemical structure of dynobactin A. f, Comparison of darobactin A and dynobactin A binding to BamA. Panels b, c reproduced from Kaur et al. Panels d, f reproduced from ref..