How antibiotics kill bacteria: from targets to networks

Abstract

Antibiotic drug-target interactions, and their respective direct effects, are generally well characterized. By contrast, the bacterial responses to antibiotic drug treatments that contribute to cell death are not as well understood and have proven to be complex as they involve many genetic and biochemical pathways. In this Review, we discuss the multilayered effects of drug-target interactions, including the essential cellular processes that are inhibited by bactericidal antibiotics and the associated cellular response mechanisms that contribute to killing. We also discuss new insights into these mechanisms that have been revealed through the study of biological networks, and describe how these insights, together with related developments in synthetic biology, could be exploited to create new antibacterial therapies.

Box 2 inset. Network biology approaches for antibiotic functional analysis and therapeutic development

Introduction of novel connections or alteration of the connectivity among genes in an antibiotic-related network can be used to refine or expand our knowledge of these networks and interrogate drug networks for novel antibiotic targets. Synthetic gene networks, therapeutic proteins or antimicrobial peptides that enhance antibiotic efficacy can also be delivered directly to bacteria through species-specific delivery mechanisms such as bacteriophage.

Figure 1. Drug-target interactions and associated cell death mechanisms

a) Quinolone antibiotics interfere with changes in DNA supercoiling by binding to topoisomerase II or IV. This leads to the formation of double-stranded DNA breaks and cell death in either a protein synthesis dependent or protein synthesis independent fashion. b) β-lactams inhibit transpeptidation by binding to PBPs on maturing peptidoglycan strands. The decrease in peptidoglycan synthesis and increase in autolysins leads to lysis and cell death. c) Aminoglycosides bind to the 30S subunit of the ribosome and cause misincorporation of amino acids into elongating peptides. These mistranslated proteins can misfold, and incorporation of misfolded membrane proteins into the cell envelope leads to increased drug uptake, which together with an increase in ribosome binding has been associated with cell death.

Figure 2. Common mechanism of cell death induced by bactericidal antibiotics

The primary drug-target interactions (aminoglycoside with the ribosome, quinolone with DNA gyrase, and β-lactam with penicillin-binding proteins) stimulate oxidation of NADH through the electron transport chain that is dependent on the TCA cycle. Hyperactivation of the electron transport chain stimulates superoxide formation. Superoxide damages iron-sulfur clusters, making ferrous iron available for oxidation by the Fenton reaction. The Fenton reaction leads to hydroxyl radical formation and the hydroxyl radicals damage DNA, proteins and lipids, which contributes to antibiotic-induced cell death. Quinolones, β-lactams and aminoglycosides also trigger radical formation and cell death through the Cpx and Arc two-component systems. It is also possible that redox-sensitive proteins such as those containing disulfide contribute in an as yet undetermined fashion to the common mechanism (dashed lines). (Modified with permission from ref 8)

Figure 3. Aminoglycoside triggers for radical-mediated cell death

The interaction between the aminglycoside and ribosome causes mistranslation and misfolding of membrane proteins. Incorporation of mistranslated, misfolded proteins into the cell membrane stimulates the envelope (Cpx) and redox-responsive (Arc) two-component systems. Activation of these systems perturbs cellular metabolism and the membrane potential (DY), resulting in the formation of lethal hydroxyl radicals. (Modified with permission from ref 10)