New Noncovalent Inhibitors of Penicillin-Binding Proteins from Penicillin-Resistant Bacteria

BACKGROUND: Penicillin-binding proteins (PBPs) are well known and validated targets for antibacterial therapy. The most important clinically used inhibitors of PBPs beta-lactams inhibit transpeptidase activity of PBPs by forming a covalent penicilloyl-enzyme complex that blocks the normal transpeptidation reaction; this finally results in bacterial death. In some resistant bacteria the resistance is acquired by active-site distortion of PBPs, which lowers their acylation efficiency for beta-lactams. To address this problem we focused our attention to discovery of novel noncovalent inhibitors of PBPs. METHODOLOGY/PRINCIPAL FINDINGS: Our in-house bank of compounds was screened for inhibition of three PBPs from resistant bacteria: PBP2a from Methicillin-resistant Staphylococcus aureus (MRSA), PBP2x from Streptococcus pneumoniae strain 5204, and PBP5fm from Enterococcus faecium strain D63r. Initial hit inhibitor obtained by screening was then used as a starting point for computational similarity searching for structurally related compounds and several new noncovalent inhibitors were discovered. Two compounds had promising inhibitory activities of both PBP2a and PBP2x 5204, and good in-vitro antibacterial activities against a panel of Gram-positive bacterial strains. CONCLUSIONS: We found new noncovalent inhibitors of PBPs which represent important starting points for development of more potent inhibitors of PBPs that can target penicillin-resistant bacteria.Eur-Intafa

Docking of the sulfonamide inhibitor 1.

<p>Inhibitor <b>1</b> (magenta) docked into the active site of PBP2a (pdb code 1vqq). The amino acids that form interactions with inhibitor <b>1</b> are shown as green sticks.</p

Structures of compounds 1–12.

<p>Structures of compounds 1–12.</p

New inhibitors of PBPs from resistant bacteria.^a

a<p>The data represent mean values of three independent experiments. Standard deviations were within ±10% of these mean values. RA = residual activity of the enzyme at 1 mM inhibitor, unless stated otherwise. IC₅₀-values were determined in the presence of 0.01% Triton X-100. ^bResidual activity of the enzyme at 500 µM inhibitor.</p

Synthesis of inhibitor 1.

<p>Synthesis of inhibitor 1.</p

<i>In-vitro</i> antibacterial activities of inhibitors of PBPs from resistant species.

<p><i>In-vitro</i> antibacterial activities of inhibitors of PBPs from resistant species.</p

Sequence identity between PBP2x Sp328 and PBP2x 5204.

<p>PBP2x Sp328 and PBP2x 5204 show high sequence identity with differences in only few places.</p

Query A and query B used for computational similarity search.

<p>Query A and query B used for computational similarity search.</p

Docking of the anthranilic acid derivative inhibitor 9.

<p>Inhibitor <b>9</b> (magenta) docked into the active site of PBP2x 5204. The amino acids that form interactions with inhibitor <b>9</b> are shown as green sticks.</p