An Evolutionary Conservation and Druggability Analysis of Enzymes Belonging to the Bacterial Shikimate Pathway

Abstract

Enzymes belonging to the shikimate pathway have long been considered promising targets for antibacterial drugs because they have no counterpart in mammals and are essential for bacterial growth and virulence. However, despite decades of research, there are currently no clinically relevant antibacterial drugs targeting any of these enzymes, and there are legitimate concerns about whether they are sufficiently druggable, i.e., whether they can be adequately modulated by small and potent drug-like molecules. In the present work, in silico analyses combining evolutionary conservation and druggability are performed to determine whether these enzymes are candidates for broad-spectrum antibacterial therapy. The results presented here indicate that the substrate-binding sites of most enzymes in this pathway are suitable drug targets because of their reasonable conservation and druggability scores. An exception was the substrate-binding site of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase, which was found to be undruggable because of its high content of charged residues and extremely high overall polarity. Although the presented study was designed from the perspective of broad-spectrum antibacterial drug development, this workflow can be readily applied to any antimicrobial target analysis, whether narrow- or broad-spectrum. Moreover, this research also contributes to a deeper understanding of these enzymes and provides valuable insights into their properties.

Design and Preparation of Antimicrobial Agents

“…Frlan evaluated the importance of enzymes belonging to the shikimate pathway as promising targets for antibacterial drugs [ 6 ]. In silico analyses combining evolutionary conservation and druggability were performed to determine whether these enzymes are candidates for broad-spectrum antibacterial therapy.…”

Genome-wide CRISPRi screens reveal the essentialome and determinants for susceptibility to dalbavancin inStaphylococcus aureus

“…6 ). The Shikimate pathway has been considered a promising target for antibacterial drugs, because it has no counterpart in mammals and is essential for bacterial growth and virulence in many contexts (62). However, the results shown here argue against Shikimate pathway genes as therapeutic targets, as their depletion may also reduce antibiotic susceptibility.…”

The low mutational flexibility of the EPSP synthase in Bacillus subtilis is due to a higher demand for shikimate pathway intermediates

“…MurA is an essential enzyme that is inhibited by the epoxid antibiotic fosfomycin and catalyzes the first committed step in peptidoglycan biosynthesis in Gram‐negative and Gram‐positive bacteria (Kahan et al, 1974). Thus, MurA and to some extent also the EPSP synthase are highly attractive antibiotic targets (Frlan, 2022; Dewachter et al, 2023). However, in the case of B. subtilis and closely related species only antibiotics that are not taken up via GltT are suitable because the bacteria rapidly accumulate loss‐of‐function mutations in the gltT glutamate transporter gene.…”

“…Given the importance of the shikimate pathway in the generation of the precursor chorismate, it is not surprising that the GS‐dependent inhibition of the EPSP synthase severely impairs cell viability. In fact, the enzymes of the shikimate, quinone and folate biosynthesis pathways are attractive targets for novel antibiotics (Brilisauer et al, 2019; Frlan, 2022).…”