Isozyme-Specific Ligands for O-acetylserine sulfhydrylase, a Novel Antibiotic Target

Conceived and designed the experiments: FS PC BC ES AM. Performed the experiments: FS RS ES PF SR. Analyzed the data: FS BC ES PF GEK PFC AM. Contributed reagents/materials/analysis tools: PC PB GC. Wrote the paper: FS GEK BC AM.The last step of cysteine biosynthesis in bacteria and plants is catalyzed by O-acetylserine sulfhydrylase. In bacteria, two isozymes, O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, have been identified that share similar binding sites, although the respective specific functions are still debated. O-acetylserine sulfhydrylase plays a key role in the adaptation of bacteria to the host environment, in the defense mechanisms to oxidative stress and in antibiotic resistance. Because mammals synthesize cysteine from methionine and lack O-acetylserine sulfhydrylase, the enzyme is a potential target for antimicrobials. With this aim, we first identified potential inhibitors of the two isozymes via a ligand- and structure-based in silico screening of a subset of the ZINC library using FLAP. The binding affinities of the most promising candidates were measured in vitro on purified O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B from Salmonella typhimurium by a direct method that exploits the change in the cofactor fluorescence. Two molecules were identified with dissociation constants of 3.7 and 33 µM for O-acetylserine sulfhydrylase-A and O-acetylserine sulfhydrylase-B, respectively. Because GRID analysis of the two isoenzymes indicates the presence of a few common pharmacophoric features, cross binding titrations were carried out. It was found that the best binder for O-acetylserine sulfhydrylase-B exhibits a dissociation constant of 29 µM for O-acetylserine sulfhydrylase-A, thus displaying a limited selectivity, whereas the best binder for O-acetylserine sulfhydrylase-A exhibits a dissociation constant of 50 µM for O-acetylserine sulfhydrylase-B and is thus 8-fold selective towards the former isozyme. Therefore, isoform-specific and isoform-independent ligands allow to either selectively target the isozyme that predominantly supports bacteria during infection and long-term survival or to completely block bacterial cysteine biosynthesis.Yeshttp://www.plosone.org/static/editorial#pee

LigPlot of the wild type tetrapeptide ligand in the active site of <i>Haemophilus influenzae</i> OASS.

<p>The interactions between the Asn-Leu-Asn-Ile tetrapeptide and the active site residues of <i>H. influenzae</i> OASS-A (PDB code: 1Y7L) are reported. The figure was drawn with LigPlot program version 4.5.3 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077558#pone.0077558-Laskowski1" target="_blank">[124]</a>.</p

GRID MIFs calculated for OASS-A and OASS-B.

<p>Red, blue and green contours identify the hydrogen bond acceptor, hydrogen bond donor and hydrophobic MIFs, respectively, calculated for OASS-A (pink cartoons) towards OASS-B (cyan cartoons). In <b>Panel B</b> compounds <b>1</b> and <b>13</b> are shown in ball and stick.</p

List of compounds tested against both OASS-A and OASS-B.

<p>List of compounds tested against both OASS-A and OASS-B.</p

List of compounds selected from virtual screening and tested against OASS-B.

*<p>due to the strong emission at 500 nm for excitation at 412 nm, this compound was assayed at concentrations lower than 100 µM and no binding was observed.</p

Best HINT scored conformations of the compounds selected by the LBVS/docking procedures for OASS-B.

<p>The images were prepared with PyMOL (The PyMOL Molecular Graphics System, Version 1.5.0.4 Schrödinger, LLC.)</p

Structural comparison of OASS-A and OASS-B.

<p><b>Panel A</b>: Structure-based amino acid sequence alignment of OASS-A and OASS-B from <i>Salmonella typhimurium</i>. The alignment, carried out on the PDB entries 1OAS and 2JC3 using the Flexible structure AlignmenT (FATCAT) method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077558#pone.0077558-Ye1" target="_blank">[122]</a>, gave an overall identity of 40.32% and a similarity of 56.51%. Identical residues have a red background and residues with similar physicochemical properties are shown in red. Similarity scores were calculated by the ESPript program <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0077558#pone.0077558-Gouet1" target="_blank">[123]</a> using the Blosum62 matrix set at global score of 0.2. Residues of the first active site shell are indicated by dark circles below the alignment. <b>Panel B</b>: Active site of OASS-A. Residues of the first active site shell and PLP are shown in ball and stick style, colored pink and yellow, respectively. <b>Panel C</b>: Active site of OASS-B. Residues of the first active site shell and PLP are shown in ball and stick style, colored cyan and yellow, respectively.</p

Compounds selected by SBVS/LBVS-docking procedures for OASS-A and OASS-B.

<p>Compounds selected by SBVS/LBVS-docking procedures for OASS-A and OASS-B.</p