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

Duprez W, Bachu P, Stoermer MJ, Tay S, McMahon RM, Fairlie DP, Martin JL - PLoS ONE (2015)

Bottom Line: By targeting virulence rather than viability, development of resistance and side effects (through killing host native microbiota) might be minimized.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.

View Article: PubMed Central - PubMed

Affiliation: Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

Chemical structures of the 10 peptidomimetic compounds synthesized and tested in this work.Compound 1 is the hit from the virtual screening from which derivatives 2–10 were designed.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4520593&req=5

pone.0133805.g004: Chemical structures of the 10 peptidomimetic compounds synthesized and tested in this work.Compound 1 is the hit from the virtual screening from which derivatives 2–10 were designed.

Mentions: Nine derivatives of 1 were also synthesized (Fig 4) to explore the binding groove and exploit potential optimization possibilities. N-Boc-tryptophan was coupled with a variety of amines using carbonyliimidazole and then deprotected using trifluoroacetic acid and anisole to give free amines at room temperature. This was subjected to treatment with carbonyldiimidazole to afford the activated carbonyl imidazole urea intermediate which reacted smoothly with morpholine or 1-Boc-piperazine at room temperature to afford compounds 1, and 3–10. The N-Boc of compound 3 was removed with trifluoroacetic acid to afford compound 2.


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

Duprez W, Bachu P, Stoermer MJ, Tay S, McMahon RM, Fairlie DP, Martin JL - PLoS ONE (2015)

Chemical structures of the 10 peptidomimetic compounds synthesized and tested in this work.Compound 1 is the hit from the virtual screening from which derivatives 2–10 were designed.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4520593&req=5

pone.0133805.g004: Chemical structures of the 10 peptidomimetic compounds synthesized and tested in this work.Compound 1 is the hit from the virtual screening from which derivatives 2–10 were designed.
Mentions: Nine derivatives of 1 were also synthesized (Fig 4) to explore the binding groove and exploit potential optimization possibilities. N-Boc-tryptophan was coupled with a variety of amines using carbonyliimidazole and then deprotected using trifluoroacetic acid and anisole to give free amines at room temperature. This was subjected to treatment with carbonyldiimidazole to afford the activated carbonyl imidazole urea intermediate which reacted smoothly with morpholine or 1-Boc-piperazine at room temperature to afford compounds 1, and 3–10. The N-Boc of compound 3 was removed with trifluoroacetic acid to afford compound 2.

Bottom Line: By targeting virulence rather than viability, development of resistance and side effects (through killing host native microbiota) might be minimized.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.

View Article: PubMed Central - PubMed

Affiliation: Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus