Virtual Screening of Peptide and Peptidomimetic Fragments Targeted to Inhibit Bacterial Dithiol Oxidase DsbA.

Publisher: Public Library of Science Country of Publication: United States NLM ID: 101285081 Publication Model: eCollection Cited Medium: Internet ISSN: 1932-6203 (Electronic) Linking ISSN: 19326203 NLM ISO Abbreviation: PLoS One Subsets: MEDLINE

Original Publication: San Francisco, CA : Public Library of Science

Bacterial Proteins/*metabolism ; Oxidoreductases/*metabolism ; Peptides/*pharmacology ; Peptidomimetics/*pharmacology ; Protein Disulfide-Isomerases/*metabolism ; Toluene/*analogs & derivatives; Catalytic Domain/drug effects ; Cysteine/metabolism ; Proteus mirabilis/drug effects ; Proteus mirabilis/metabolism ; Toluene/metabolism ; Virulence/drug effects ; Virulence Factors/metabolism

Antibacterial drugs with novel scaffolds and new mechanisms of action are desperately needed to address the growing problem of antibiotic resistance. The periplasmic oxidative folding system in Gram-negative bacteria represents a possible target for anti-virulence antibacterials. By targeting virulence rather than viability, development of resistance and side effects (through killing host native microbiota) might be minimized. Here, we undertook the design of peptidomimetic inhibitors targeting the interaction between the two key enzymes of oxidative folding, DsbA and DsbB, with the ultimate goal of preventing virulence factor assembly. Structures of DsbB--or peptides--complexed with DsbA revealed key interactions with the DsbA active site cysteine, and with a hydrophobic groove adjacent to the active site. The present work aimed to discover peptidomimetics that target the hydrophobic groove to generate non-covalent DsbA inhibitors. The previously reported structure of a Proteus mirabilis DsbA active site cysteine mutant, in a non-covalent complex with the heptapeptide PWATCDS, was used as an in silico template for virtual screening of a peptidomimetic fragment library. The highest scoring fragment compound and nine derivatives were synthesized and evaluated for DsbA binding and inhibition. These experiments discovered peptidomimetic fragments with inhibitory activity at millimolar concentrations. Although only weakly potent relative to larger covalent peptide inhibitors that interact through the active site cysteine, these fragments offer new opportunities as templates to build non-covalent inhibitors. The results suggest that non-covalent peptidomimetics may need to interact with sites beyond the hydrophobic groove in order to produce potent DsbA inhibitors.

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0 (Bacterial Proteins)
0 (Peptides)
0 (Peptidomimetics)
0 (Virulence Factors)
3FPU23BG52 (Toluene)
EC 1.- (Oxidoreductases)
EC 5.3.4.1 (Protein Disulfide-Isomerases)
K848JZ4886 (Cysteine)
U89B11P7SC (dithiol)

Date Created: 20150731 Date Completed: 20160504 Latest Revision: 20181113

20221213

PMC4520593

10.1371/journal.pone.0133805

26225423