Bacterial Shikimate Network Offers Dual Targets for Antibiotic and Antivirulence Drugs

A newly published review argues that the bacterial shikimate pathway, long studied as a route to aromatic amino acids, should be treated as a single interconnected shikimate–chorismate metabolic network whose upstream enzymes and downstream virulence products can be attacked together. The review, published as an open-access article in the journal Discover Bacteria on 14 June 2026, synthesizes decades of biochemical work on the pathway’s seven canonical enzymatic steps and links them to the chorismate-derived siderophore systems that many pathogens rely on to seize iron from their hosts. Its central proposal is a dual-targeting strategy: combine inhibitors that suppress bacterial growth with agents that blunt pathogenic traits such as iron acquisition, potentially reducing the selective pressure that drives resistance.

The shikimate pathway culminates in chorismate, a central metabolic intermediate that connects primary carbon metabolism to the biosynthesis of the aromatic amino acids phenylalanine, tyrosine and tryptophan, as well as folate precursors via para-aminobenzoate, quinones and aromatic cofactors. The route is conserved across bacteria, archaea, fungi, algae, plants and certain apicomplexan parasites, but it is absent in metazoans, including humans. That absence is the foundation of the pathway’s appeal as a drug target, because inhibitors can in principle attack microbial enzymes without touching human counterparts. Yet despite extensive biochemical and structural characterization, the review notes, translation of shikimate-pathway inhibition into clinically useful antibiotics has remained limited, reflecting challenges of cellular permeability, metabolic redundancy, pathway plasticity and context-dependent essentiality rather than any lack of intrinsic target validity.

The pathway’s organization differs substantially between prokaryotes and eukaryotes, with direct consequences for drug design. In fungi, particularly ascomycetes, multiple steps can be encoded within a single multifunctional polypeptide, the AROM protein, enabling coordinated catalysis of consecutive reactions. In apicomplexan parasites such as Plasmodium, evidence suggests the pathway may be incomplete or supplemented by alternative metabolic routes, complicating its exploitation and underscoring the need for organism-specific validation. Bacteria, by contrast, typically encode the seven canonical steps as discrete genes scattered across the genome or organized in small operons, often accompanied by isozyme diversification and regulatory variation. In some archaea, alternative routes to aromatic amino acid biosynthesis bypass the classical DAHP synthase entry point entirely. This genomic and biochemical heterogeneity shapes pathway regulation, metabolic buffering and conditional essentiality, all of which determine how susceptible a given organism is to enzymatic inhibition.

From an infection and antimicrobial resistance standpoint, the review emphasizes that the pathway’s significance extends beyond its absence in humans. Chorismate functions as a key branch point connecting primary metabolism to downstream pathways underpinning bacterial fitness and pathogenicity. Chorismate-derived metabolites feed siderophore biosynthesis systems such as enterobactin, yersiniabactin and mycobactin, which facilitate iron acquisition and promote host colonization in diverse pathogens, including members of the ESKAPE group. Disrupting these routes can attenuate virulence without necessarily exerting strong bactericidal pressure, a rationale for antivirulence strategies that may complement conventional antibiotics and potentially reduce selection for resistance. The review also notes that the pathway is critical for survival and virulence in Enterobacteriaceae such as E. coli and Salmonella, in Mycobacteria, and even for UV adaptation in Burkholderia species.

At the top of the pathway sits the first committed step: a Claisen-like condensation of phosphoenolpyruvate from glycolysis with erythrose-4-phosphate from the non-oxidative pentose phosphate pathway, catalyzed by DAHP synthase to form 3-deoxy-D-arabino-heptulosonate-7-phosphate. The catalytic role of DAHP synthase is critical in determining how much carbon flux enters the entire pathway, and in many microorganisms the enzyme undergoes feedback inhibition by the final products, the aromatic amino acids. In the E. coli model, three isozymes—AroF, AroG and AroH—are targeted by feedback regulation from tyrosine, phenylalanine and tryptophan respectively. Structurally, the E. coli enzyme is a homotetramer whose subunits form a (β/α)8 TIM barrel fold, with the active site at the C-terminal end of the barrel interacting with substrate, metal cofactor and competitive inhibitors. The core barrel is largely conserved across bacterial species even as regulatory segments vary, which the review suggests makes it an attractive scaffold for optimized broad-spectrum antibiotics.

Several concrete inhibitor leads illustrate the enzyme-level opportunities. Using a CRISPR interference system, researchers demonstrated that DAHP synthase is a vulnerable target in Mycobacterium tuberculosis. DAHP oxime, a phosphate mimic, binds residues including R165 and K181 in the DAHP synthase active site and potently inhibits its catalytic function, supporting the idea that phosphate-carrying mimetic small molecules hold a competitive advantage. On the allosteric side, quinic acid was recently shown to allosterically inhibit DAHP synthase from Providencia alcalifaciens through a mechanism comparable to feedback inhibition by phenylalanine, suggesting that naturally occurring phenylalanine derivatives could be mined for allosteric-site inhibitors. The best-characterized inhibitor of the pathway overall remains glyphosate, a phosphoenolpyruvate analog that competitively blocks EPSP synthase, while aromatic amino acid antimetabolites, including fluorinated and chlorinated analogues, interfere with downstream processes. More recently, the antimetabolite 7-deoxy-sedoheptulose has been shown to inhibit upstream steps including DAHP synthase, disrupting aromatic amino acid biosynthesis across diverse bacterial species.

The review devotes substantial attention to noncanonical and context-dependent behavior that can undermine inhibition. Non-orthologous gene displacement replaces canonical pathway enzymes with functionally analogous but structurally unrelated proteins, particularly in archaea, where members of the GHMP kinase family, including homoserine kinases, can substitute for shikimate kinase activity. In bacteria, variability more often takes the form of isozyme diversity, gene loss and pathway modulation: genomic studies indicate that one-third of host-associated bacterial species have lost one or more shikimate-pathway genes, promoting reliance on the host for intermediates or end products such as aromatic amino acids. Some host-associated bacteria therefore become auxotrophic, and exogenous nutrients within the host environment can reduce the apparent essentiality of specific steps. The review also cautions that claims of direct chorismate uptake remain limited and not well established in model bacteria, with evidence for dedicated chorismate import systems currently lacking, meaning the extent of metabolite salvage varies between organisms and requires careful experimental validation.

Downstream of chorismate, the review maps the enterobactin biosynthetic route in detail. Isochorismate synthase (EntC) isomerizes chorismate to isochorismate; the N-terminal domain of isochorismatase (EntB) forms 2,3-dihydro-2,3-dihydroxybenzoate with release of pyruvate; 2,3-DHB dehydrogenase (EntA) oxidizes this to 2,3-dihydroxybenzoate, creating the catechol chelating core. The ligase EntE then adenylates 2,3-DHB and transfers it to the aryl carrier domain of EntB, and the modular nonribosomal peptide synthetase EntF adenylates L-serine residues, condenses them onto the aryl carrier, and finally trimerizes and macrocyclizes the DHB-Ser units into the macrocyclic trilactone enterobactin. Exported by the MFS protein encoded by EntS, enterobactin binds ferric iron with an affinity of roughly Kd ~10⁻⁵² M, sufficient to support bacterial growth. Notably, the same MFS protein acts as a multidrug efflux pump conferring resistance to β-lactams, fluoroquinolones and aminoglycosides, so targeting it could potentially serve as a multidrug resistance breaker. Analogous chorismate-derived siderophores include yersiniabactin in Yersinia, Klebsiella and Pseudomonas, mycobactin in M. tuberculosis, and phenazine and pyocyanin in multiple bacteria.

Genetic and chemical evidence supports the antivirulence value of these downstream targets. Manipulation of genes in the enterobactin, yersiniabactin or mycobactin pathways abrogates virulence, with downstream effects on pathogenicity and immunology, and recent molecular docking findings indicate that the enterobactin intermediate 2,3-dihydroxybenzoic acid can competitively inhibit EntB in E. coli, supporting enterobactin intermediates or analogues as candidate virulence suppressors. In mycobacteria, mycobactin analogues such as a fluorophenyl pyrazolyl phenol compound have been shown to interact with and inhibit siderophore efflux pump proteins, suppressing iron acquisition. The review argues that a dual advantage flows from targeting these reactions: suppressing both growth and virulence, while all the enzymes involved are not encoded by the human genome, promising host safety.

Significant obstacles remain before such strategies reach the clinic. Many inhibitors fail because of poor permeability, active efflux or physiological adaptation before reaching their targets, so successful targeting must integrate enzyme inhibition with uptake, retention and resistance avoidance. Structure-guided approaches are particularly valuable, the review contends, because they can discriminate between homologous enzymes through active-site geometry, allosteric regulation and oligomeric organization. There is also a fundamental paradox in inhibiting central microbial metabolism while avoiding self-toxicity in natural-product producer organisms, which carry resistance mechanisms such as target modification, reduced intracellular accumulation, active efflux, metabolic bypass or regulated biosynthesis. The review concludes that pathway conservation does not preclude selective inhibition; rather, effective targeting depends on exploiting differences in enzyme structure, regulation and physiological context between producers, pathogens and hosts, and that advancing the field will require an integrated framework combining structural biochemistry, chemical biology, genomics and systems-level metabolic analysis.

Subject of Research: Targeting the bacterial shikimate–chorismate metabolic network for antibacterial and antivirulence therapy

Article Title: Targeting upstream and downstream arms of the bacterial shikimate metabolic network as an opportunity for antibacterial and antivirulence therapy

Article References: Maghembe, R. S. (2026). Targeting upstream and downstream arms of the bacterial shikimate metabolic network as an opportunity for antibacterial and antivirulence therapy. Discover Bacteria, 3(1), Article 16. https://doi.org/10.1007/s44351-026-00053-x

Image Credits: AI Generated

DOI: 10.1007/s44351-026-00053-x

Keywords: shikimate pathway, chorismate, DAHP synthase, EPSP synthase, glyphosate, siderophores, enterobactin, yersiniabactin, mycobactin, antimicrobial resistance, antivirulence therapy, drug discovery