A unique peptide deformylase platform to rationally design and challenge novel active compounds

Abstract

Peptide deformylase (PDF) is considered an excellent target to develop antibiotics. We have performed an extensive characterization of a new PDF from the pathogen Streptococcus agalactiae, showing properties similar to other known PDFs. S. agalactiae PDF could be used as PDF prototype as it allowed to get complete sets of 3-dimensional, biophysical and kinetic data with virtually any inhibitor compound. Structure-activity relationship analysis with this single reference system allowed us to reveal distinct binding modes for different PDF inhibitors and the key role of a hydrogen bond in potentiating the interaction between ligand and target. We propose this protein as an irreplaceable tool, allowing easy and relevant fine comparisons between series, to design, challenge and validate novel series of inhibitors. As proof-of-concept, we report here the design and synthesis of effective specific bacterial PDF inhibitors of an oxadiazole series with potent antimicrobial activity against a multidrug resistant clinical isolate.

Figure 1. Chemical structures of PDF inhibitors.

(a) compounds synthesized in previous studies. (b,c) new compounds of the oxadiazole series with either an n-butyl (b) or a cyclopentyl (c) at P1’. (d) new compounds of the oxazole series.

Figure 2. SaPDF substrate binding site.

(a) Tripeptide Met-Ala-Ser bound to SaPDF between N- and C-terminal sub-domains is shown in sticks format and colored in yellow, with O in red, N in blue, and S in yellow. α and 3₁₀ helices of protein are in pink, β strands in green and insertions in light blue. The three consensus motifs I, II and III are colored in light orange. (b) The network of interactions of the ligand binding site of Met-Ala-Ser in SaPDF is represented: the free amine group coordinates the catalytic metal (Me) and is hydrogen bonded to Glu175; the side chain of Met fits into a hydrophobic pocket called S1’, made of residues Val71, Leu125, Glu129, Tyr167, Val171, His174; the backbone of peptide is hydrogen bonded to Val71, Gly69 and Gly130 of SaPDF. Dotted lines represent the hydrogen bonds. (c) The solvent-accessible surface of S1’ pocket is represented, in apo SaPDF (top) and in the complex with Met-Ala-Ser (bottom). (d) Close-up view of hydrogen bonds that link the backbone of Met-Ala-Ser with residues Val71, Gly69 and Gly130 of SaPDF, linking strands β1 and β4. The color code of panel a is used.

Figure 3. Binding mode of various PDFIs, with various scaffolds.

Binding mode of PDFIs in SaPDF is represented. From the left to the right: close-up view of each PDFI within the ligand binding site, with the color code used in Fig.1a for protein; network of interactions of each PDFI; solvent-accessible surface of S1’ pocket in presence of each PDFI; volume occupied by each PDFI in the vicinity of some key residues coming from S1’ pocket. (a) actinonin. (b) AB47. (c) SMP289. (d) RAS358. (e,f) AT002 and AT019; P3’ group of oxadiazoles being flexible, only P1’ and P2’ are visible (see Supplementary Fig. 2c). Consequently, modeled part of AT002 and AT018 on the one hand and AT019 and AT020 on the other hand are identical (see Fig. 2e,f) and were found fully superimposable in both structures (see Supplementary Fig. 2c). Only AT002 and AT019 are represented here.

Figure 4. 3D comparison of the binding between various PDFIs and actinonin.

(a) Overall superimposition of actinonin, AT002, AT019, AT020, AB47, SMP289 and RAS358. The color code used is that of Fig. 1a for SaPDF and Fig. 3 for PDFIs. Two distinct orientations are displayed. (b) Comparison of the Tyr167 side chain position of SaPDF in complex with AB47 (pink) or SMP289 (orange).