From Peptide Aptamers to Inhibitors of FUR, Bacterial Transcriptional

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From Peptide Aptamers to Inhibitors of FUR, Bacterial Transcriptional Regulator of Iron Homeostasis and Virulence Sophie Mathieu,†,‡,§ Cheickna Cissé,†,‡,§ Sylvia Vitale,†,‡,§ Aynur Ahmadova,†,‡,§ Mélissa Degardin,†,‡,§,∥,⊥ Julien Pérard,†,‡,§ Pierre Colas,# Roger Miras,†,‡,§ Didier Boturyn,∥,⊥ Jacques Covès,∇,○,⧫ Serge Crouzy,*,†,‡,§ and Isabelle Michaud-Soret*,†,‡,§ †

CNRS, Laboratoire de Chimie et Biologie des Métaux (LCBM) UMR 5249 CNRS-CEA-UJF, F-38054 Grenoble, France CEA, LCBM, F-38054 Grenoble, France § Univ. Grenoble Alpes, LCBM, F-38054 Grenoble, France ∥ Univ. Grenoble Alpes, DCM UMR 5250, F-38000 Grenoble, France ⊥ CNRS, DCM UMR 5250, F-38000 Grenoble, France # P2I2 Group, Protein Phosphorylation and Human Disease Unit, CNRS Unité de Service et de Recherche USR3151, Station Biologique de Roscoff, F-29680 Roscoff, France ∇ Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France ○ CNRS, IBS, F-38044 Grenoble, France ⧫ CEA, IBS, F-38044 Grenoble, France ‡

S Supporting Information *

ABSTRACT: FUR (Ferric Uptake Regulator) protein is a global transcriptional regulator that senses iron status and controls the expression of genes involved in iron homeostasis, virulence, and oxidative stress. Ubiquitous in Gram-negative bacteria and absent in eukaryotes, FUR is an attractive antivirulence target since the inactivation of the f ur gene in various pathogens attenuates their virulence. The characterization of 13-aa-long anti-FUR linear peptides derived from the variable part of the anti-FUR peptide aptamers, that were previously shown to decrease pathogenic E. coli strain virulence in a fly infection model, is described herein. Modeling, docking, and experimental approaches in vitro (activity and interaction assays, mutations) and in cells (yeast two-hybrid assays) were combined to characterize the interactions of the peptides with FUR, and to understand their mechanism of inhibition. As a result, reliable structure models of two peptide−FUR complexes are given. Inhibition sites are mapped in the groove between the two FUR subunits where DNA should also bind. Another peptide behaves differently and interferes with the dimerization itself. These results define these novel small peptide inhibitors as lead compounds for inhibition of the FUR transcription factor.

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responsive transcriptional regulator of genes involved in iron homeostasis critical for bacterial survival during infection.9 Extended roles of FUR consist in regulating the transcription of genes involved in virulence and colonization, quorum sensing, type III secretion, resistance to oxidative stress, and pH homeostasis.10−15 Additionally, the inactivation of the f ur gene in various pathogens, such as Pseudomonas aeruginosa,16 Escherichia coli,17 Vibrio cholerae,18 Staphylococcus aureus,19 or Helicobacter pylori,20 leads to a virulence decrease in animal models of infection. Absent in eukaryotic organisms and

he emergence and spread of antibiotic resistance has raised serious public health problems that require the discovery of new therapeutic approaches to control pathogenic bacteria.1 One novel approach to develop therapies for infectious diseases is to target bacterial virulence. This strategy could allow the host immune system to prevent bacterial colonization and/or fight against established infection. Contrary to traditional antibacterial therapy, this strategy presumably applies less pressure for the development of resistance.2 A number of antivirulence strategies have been explored, including inhibiting bacterial adhesion to the host cell, inhibiting toxins or specialized secretion systems, and interfering with gene regulation of virulence traits.3−8 One of the interesting antivirulence targets is the FUR protein (Ferric Uptake Regulator) that was primarily described as an iron© XXXX American Chemical Society

Received: April 25, 2016 Accepted: July 13, 2016

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DOI: 10.1021/acschembio.6b00360 ACS Chem. Biol. XXXX, XXX, XXX−XXX

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essential for bacterial survival and host infection, FUR can be considered as a potential target for new antibacterials. Peptide aptamers are combinatorial proteins consisting of a variable peptide loop inserted into a constant scaffold protein which constrains their conformation.21 Due to their ability to specifically bind to a given target protein, they provide a powerful experimental strategy for functional protein analyses, both in vitro and in vivo. One of the most often used methods to select peptide aptamers for their ability to recognize a given target protein in living cells is a yeast two-hybrid assay, where the interaction between two studied proteins (one fused to a DNA binding domain and another to a transcriptional activation domain) leads to the reconstitution of the activity of a split transcription factor in genetically modified yeast cells.22,23 In a previous work, a 20-million-peptide aptamer library was screened by a yeast two-hybrid assay to identify potential inhibitors of the FUR protein from E. coli (EcFUR).24 The antiFUR peptide aptamers, denoted F1 to F4 and selected for their interaction with FUR, consist of thioredoxin A from E. coli as a scaffold and a variable loop of 13 amino acids. They were found to strongly interact with EcFUR and to inhibit the function of EcFUR in a transcriptional repression assay.24 Moreover, they were also able to decrease the virulence of pathogenic E. coli strain in a fly infection model.24 F1, F2, and F3 interact with the DNA binding domain and the dimerization domain of EcFUR, whereas F4 can interact with its dimerization domain alone and was shown to inhibit the homodimerization of the protein.24 In order to develop smaller active molecules, also called “second generation” inhibitors, the 13-amino-acid-long linear peptides pF1 to pF4 (see Figure 2D), corresponding to the variable loops of the peptide aptamers F1 to F4 have been studied. In a recent work, both the characterization of the first anti-FUR linear peptides derived from aptamer F1 and their interaction with EcFUR were performed using in silico and in vitro methods.25 A minimal active sequence was determined, and an inhibition pocket in EcFUR was proposed. There is no evident similarity in the sequence of pF1 to pF4 (see Figure 2D): at physiological pH, pF2 possesses a net +1 positive charge, pF1 and pF3 have a +2 charge, and pF4 has a +3 charge. pF2 to pF4 contain two Cys residues against only one for pF1. Consistent with the behavior of F4,24 we confirmed that pF4 inhibits FUR by preventing the protein homodimerization, while the other peptides bind a distinct molecular surface. The inhibitory properties of pF2 and pF3 were further investigated, with a focus on pF2. The overall experimental approach is summarized in Scheme 1. The interaction of peptides with EcFUR was studied by yeast two-hybrid and nuclease protection assays. A submicromolar dissociation constant was measured by microcalorimetry for pF2. The structures of EcFUR/pF2 and EcFUR/pF3 complexes are proposed from molecular modeling and docking experiments. Altogether these results show how the peptides interact with this important bacterial transcription regulator by blocking its access to DNA binding, explaining thus their inhibitory properties.

a

SEC-MALLS-RI: size exclusion chromatography coupled to multiangle laser light scattering and refractive index measurement. Ellman: Ellman’s test performed for the determination of free thiols. Y2H: yeast two-hybrid and ITC for isothermal calorimetry. pF: anti-FUR peptide.

expressed as prey fusion proteins), luciferase signals with moderate to strong intensity are observed (Figure 1, black bars), significantly different from the negative control (F5, noninteracting peptide aptamer). These data confirm previous results.24 When peptides are used as prey (Figure 1, gray bars), the signal intensity is lower than observed for peptide aptamers, but still in a detectable range. However, only the EcFUR/pF2 interaction signal is significantly different (Student’s test) from the negative control (pF5). The interactions of pF1 and pF3 with EcFUR are weaker and at the limit of detection reliability compared to the control; no interaction is detected for pF4. The expression level of peptide fusions was compared by Western blot with anti-HA antibodies (Supporting Information Figure S2). The blot reveals the comparable expression level of prey fusions confirming that the differences in the intensity of luciferase signal observed for the yeast two-hybrid phenotypes EcFUR/pF1 to pF5 are related to the strength of interaction. In order to be in a statistically satisfactory signal-to-noise ratio, we decided to continue the yeast two-hybrid assays with the peptide aptamers and pF2 only as prey. These differences in the strength of EcFUR/aptamers and EcFUR/peptides interactions may be explained by the constraints imposed on the peptides inserted into this scaffold compared to the linear peptides which can adopt many different conformations.33 It could also come from the difference in expression level of prey fusion proteins (peptide aptamers and peptide derivatives), probably from an enhanced aptamer expression, due to the high solubility and easy expression of the “molecular chaperone” thioredoxin.33 In Vitro Inhibitory Activity of pF1 to pF4. The inhibitory potential of peptides was evaluated by determination of IC50 values, corresponding to the concentration of peptide necessary to inhibit 50% of the DNA binding activity of EcFUR (Figure 2) in a nuclease protection assay (principle of the test described in Supporting Information Figure S1). The peptide pF1 was previously shown to interact with dimeric EcFUR and to inhibit its DNA-binding activity with

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RESULTS AND DISCUSSION pF2 Interacts with EcFUR in Two-Hybrid Assay. An optimized yeast two-hybrid assay was performed to evaluate the interaction of anti-FUR peptide aptamers or peptide derivatives with EcFUR. Upon interaction of EcFUR (expressed as a bait fusion protein) with peptide aptamers F1−F4 (conditionally B


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Figure 1. Interactions of EcFUR with peptide aptamers (F1 to F5) and peptides (pF1 to pF5) by yeast two-hybrid assay. Experiments were performed using luciferase as a reporter gene and fusions of EcFUR as bait and inhibitors as prey. Quantification of luminescence signals was performed after 24 h galactose induction at 30 °C. All data are corrected with the empty prey vector as a negative control. Stars represent the reliability of the results between signals obtained for interactions EcFUR/F5 and EcFUR/pF5, for aptamers and peptides, respectively, by Student’s test (*p value < 5%, **p value < 1%, ***p value < 0.1%).

Figure 2. Interaction of EcFUR with pF2 to pF5 peptides tested in the nuclease protection assay. (A) Four- and three-band profile patterns for inactive and active protein, respectively. (B and C) The dimeric and monomeric forms of the protein, respectively. EcFUR at 1 μM concentration was metaled by two equivalents of Mn2+. The indicated concentrations of peptides (μM) and 10 nM of pDT10 were added. The Hinf I digestion pattern was analyzed on 0.8% agarose gel. For each peptide, at least three biological replicates were performed. (D) IC50 values for pF1 to pF5 peptides determined from EcFUR inhibition by nuclease protection assay. The values in parentheses indicate the number of assays performed. ND for “not determined” and NI for “no inhibition.” *Data already presented25 and given for comparison.

IC50 values of 53 ± 6 μM.25 Peptides pF2 and pF3 show better inhibitory activities than pF1 with lower IC50 values, 12.5 ± 5 and 30 ± 17 μM, respectively (Figure 2D). The profile pattern for pF4 is similar to that of the negative control (pF5), indicating the absence of inhibitory effect on the DNA binding activity of the EcFUR dimer (Figure 2B). However, it was previously shown in vivo that peptide aptamer F4 inhibits EcFUR by interacting with the dimerization domain located at the C-terminus of the protein.24 Thus, we can suggest that pF4 only interacts with the monomeric form of EcFUR, preventing its dimerization. To confirm this hypothesis, the peptide was first incubated with the EcFUR monomer in reductive conditions, and then stoichiometric zinc ions followed by manganese were added to allow dimerization and activation of the protein,26 respectively. The steps of nuclease protection assay were performed as described before. This experiment revealed the inhibitory activity of pF4 on EcFUR monomer with IC50 of 37.5 ± 12.5 μM (Figure 2C). Redox Stability of Peptides. The large variation in IC50 values (Figure 2D) observed in nuclease protection assay, especially for pF3, may be related to the redox instability of peptides that contain cysteine residues, susceptible to oxidation. To verify this hypothesis, the oligomeric state and oxidation degree of peptides pF1 to pF3 were evaluated by SEC and Ellman’s test (Supporting Information Figure S3 and details of the results in the Supporting Information text).

The results are in agreement with 1% of pF1 and 15% of pF2 being oxidized after 3 h of incubation at RT. Intramolecular oxidation of pF2 (disulfide bridge) occurs more rapidly than intermolecular pF1 oxidative dimerization, probably because of the close proximity of cysteine thiols located in the same molecule for pF2. For pF3, partial intramolecular oxidation seems to occur. It is noteworthy that the oxidized forms of pF2 and pF3 were not active on EcFUR in the nuclease protection assay. However, the inhibitory activity of oxidized peptides was restored after reductive treatment with TCEP (see Supporting Information Figure S4). In Vitro Inhibitory Activity. The inhibitory activities of shorter and mutated peptides derived from pF2 and pF3, as well as peptides mutated on the residues proposed by the docking experiments (see below) were measured by nuclease protection assays. All the corresponding representative gels are presented in Supporting Information Figure S4. Concerning pF2 derivatives, the pF2(3−13) is inactive, suggesting that the N-terminal residues are essential for inhibitory activity in contrast with the last two residues on the C-terminus. Actually, pF2(1−11) and pF2(1−10) are even stronger inhibitors than pF2(1−13) with IC50’s of 7 μM (9 samples) and 6.25 μM (11 samples), respectively. The shortest active peptide is pF2(2− 10) with an IC50 of 56.3 ± 12.5 μM (4 samples), but the loss of the arginine in position one triggers a 9-fold increase of the IC50. Concerning the pF3 derivatives, pF3(1−11) and pF3(3− C


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Figure 3. Isothermal titration calorimetry data. The ITC plots were obtained from the titration of Mn-activated EcFUR with pF1(1−13) (A) and pF2(1−13) (B), and of apo-EcFUR dimer with pF2(1−13) (C). The plots in the lower panel show the total heat released as a function of total ligand concentration for the titration shown in the upper panels. The solid line represents the best least-squares fit to the experimental data using a one site model. (D) Thermodynamic data for the binding of pF1(1−13), pF2(1−13), and pF2(1−11) peptides to Mn-activated EcFUR. n represents the peptide stoichiometry by EcFUR subunit. All measured values are averaged over two experiments. Standard deviations are indicated in parentheses. ITC data for the shortest active peptide, pF2(1−10), are not given due to the difficulty in accurately quantifying peptide concentration in the absence of aromatic amino acids.

110 ± 30 μM (Figure 3D). This value is in the same range as determined previously using fluorescence spectroscopy.25 The 3-fold difference could be explained by the fact that the protein is titrated by the peptide in the microcalorimetry experiment, and inversely in the fluorescence assay. The interaction of pF2 with Mn-activated EcFUR is driven by a strong enthalpy counterbalanced by unfavorable entropy. The negative ΔH reflects the strength of the protein/peptide interaction relative to solvent, likely due to hydrogen bond formation and van der Waals interactions. The unfavorable entropy, lower for the shorter pF2(1−11) peptide, probably results from a loss of peptide flexibility upon binding to EcFUR. The dissociation constant is ≤0.49 ± 0.10 μM, confirming that pF2 has a stronger inhibitory potential compared to pF1 (Figure 3D). Note that lower Kd and thus better binding does not necessarily mean better inhibition: to inhibit the protein activity, the peptide must not only bind to FUR but also prevent its further binding to DNA and the IC50’s from the nuclease protection assays varying from 6 to 56 μM (Table 2) may be more informative in this respect. In the case of pF2, a stoichiometry of 1.16 ± 0.18 peptide by EcFUR subunit was determined, resulting in the fixation of two pF2’s by EcFUR dimer. This value, slightly larger than 1.0, can result from a minor overestimation of the active peptide concentration, or can be the consequence of the partial oxidation of pF2, becoming inactive as demonstrated above. Similarly to pF1, pF2 does not bind apo-EcFUR (Figure 3C). The binding of the pF2(1−11) derivative, lacking the two C-terminal residues, is in accordance with its IC50 and gives similar stoichiometry and

13) are inactive showing that both the N-ter and the C-ter residues are essential for inhibitory activity. In order to confirm the role of peptide residues Q8 and R11, suggested to be important for the interaction with EcFUR from the docking experiments, the inhibitory ability of the mutated peptides pF3(1−13)Q8A and pF3(1−13)R11A was analyzed by nuclease protection assays. pF3(1−13)Q8A is inactive, and pF3(1−13)R11A is still able to inhibit EcFUR but after the addition of a large amount of peptide (200 equiv). The easy oxidation of pF3 in solution could explain the large variability of the results obtained in the nuclease protection assay for pF3(1−13). Additionally, it makes it difficult to further characterize its EcFUR inhibitory activity. Determination of Dissociation Constants. The interaction of pF1 and pF2 with apo- and activated-EcFUR was studied by isothermal titration calorimetry. Aliquots of peptide solutions were injected into the calorimeter cell containing the protein. The affinity, stoichiometry, and thermodynamic parameters of the protein/peptides interaction were obtained by fitting the thermograms (Figure 3) with a one site model (no fit found with a two site model). The binding isotherms for pF1 and pF2 were exothermic. Because of the relatively low affinity of pF1 for Mn-activated EcFUR (30 μM; no binding to apo),25 the experiment was performed with ligand excess,34 fixing the stoichiometry to 0.5 peptide by EcFUR subunit (i.e., one peptide by EcFUR dimer) as previously demonstrated by molecular modeling and docking studies.25 These conditions allowed the determination of affinity parameters only. For pF1, the dissociation constant is D


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domain,24 does not interact with S126 or Y128 when bound to EcFUR. The same luminescence intensity signals obtained for homodimerization (EcFUR WT or EcFUR S126A/Y128A in bait and prey) and heterodimerization (EcFUR WT in bait and EcFUR S126A/Y128A in prey and vice versa) conditions confirm that these two different protein subunits are interchangeable and are used as a positive control (two last couples of bars in the bar chart of Figure 4A). After control of the formation of a dimeric mutated protein by size exclusion chromatography, ITC experiments were performed under the same conditions as presented in Figure 3 and show that the interaction between EcFUR S126A/Y128A and pF1 and pF2 is no longer observed (Supporting Information Figure S5), thus confirming that S126 and Y128 are key actors of the interaction. Docking Experiments. Use of EcFUR-ΔCter15. In a previous work, models of full-length EcFUR were used.25 These models were built by homology with the structure of FUR from Vibrio cholerae (VcFUR). However, the structure of the C-terminus of EcFUR cannot be confidently modeled because the sequence of EcFUR does not align with that of VcFUR after residue 133. In addition, the 15-aa-long Cterminus extension (134-AEGDCREDEHAHEGK-148) was shown to form adventitious complexes in silico with peptides that do not bind Ec-FUR in vitro, such as pF5, for instance. For these reasons, we have constructed a new EcFUR model that excludes the last 15 amino acids, named EcFUR-ΔCter15. pF1 was docked to EcFUR-ΔCter15, and a binding free energy of −18.6 kcal mol−1 was calculated, a value comparable to the −17.8 kcal mol−1 obtained after binding of pF1 to the previously used model of full-length EcFUR.25 The residues involved in interaction did not significantly change regardless of the model used. Similarly, the binding free energy of pF1(1− 13) to the EcFUR-ΔCter15 S126A/Y128A double mutant is now −15.3 kcal mol−1 close to the previously reported value of −15.9 kcal mol−1. The inactive pF5 control peptide was docked to EcFUR-ΔCter15 (see Supporting Information) with a poor binding energy of −10.5 kcal mol−1 in good agreement with experiments. Altogether, these results validate EcFUR-ΔCter15 as a reliable new model for further binding experiments. To support this reliability, we produced experimentally EcFUR-ΔCter8, the shortest C-ter-truncated version of EcFUR still able to form dimers in vitro. Nuclease activity assays of the EcFUR-ΔCter8 inhibition by all peptides showed almost no difference compared to the wild type 148-aa-long protein (See Supporting Information Figure S6).

dissociation constant values, indicating that this C-terminal part is not essential for the interaction with EcFUR and that this short peptide is also a good EcFUR inhibitor. These aspects of stoichiometry will be further discussed in the molecular modeling paragraph. The submicromolar dissociation constant for a nonmodified peptide demonstrates that pF2 could be a good lead inhibitor compound for the development of new antibacterial molecules. Validation of the Peptide Binding Site. pF1 was previously shown to interact with residues S126 and Y128 of the protein.25 These residues were changed for alanine and the interaction between peptide aptamers or peptide derivatives, and mutated FUR was studied by yeast two-hybrid and ITC. The interaction of the peptide aptamer F2 with EcFUR S126A/ Y128A is 2-fold lower than with the WT (Figure 4A), and a

Figure 4. Interaction of peptide-aptamers F1 to F5 (A) and pF2 (B) with EcFUR WT and EcFUR S126A/Y128A in yeast two-hybrid assay. Experiments were performed with proteins as bait and inhibitors as prey with induction at 30 °C over 24 h. All data are corrected with prey empty vector as a negative control. Stars represent the reliability of the difference between signals obtained with EcFUR WT (black box) and EcFUR S126A/Y128A (hatched) by Student’s test (*p value < 5%, **p value < 1%, ***p value < 0.1%). The right side of the left panel shows the interaction of the WT and mutant FUR by homodimerization and heterodimerization as a confirmation of the validity of the assay.

similar result is obtained with pF2 (Figure 4B). The interaction of F1 and F3 with the double FUR mutant is severely affected. This experiment also shows that the signal obtained for the interaction of F4 with FUR WT or S126A/Y128A is identical, which means that F4, shown to interfere with the dimerization

Table 1. Docking Free Energies and Interaction Energies between pF2 and EcFUR-ΔCter15a peptide pF2A(1−13) pF2A(1−11) pF2A(1−13)

protein EcFUR-ΔCter15 EcFUR-ΔCter15 EcFURΔCter15S126A/ Y128A

free energy (kcal mol−1)

cluster average energy (kcal mol−1)

number in cluster

CHARMM total energy (kcal mol−1)

CHARMM interaction energy (kcal mol−1)

−21.0 (+2.7) −23.1 (−2.0) −20.0 (+0.5)

−20.4 −20.9 −18.7

62 63 47

−6907(42) −6775(41) −6843(42)

−121.2(11.2), pF2B −120.0(9.0) −110.2(8.5), pF2B −101.9(8.2) −127.0(7.4), pF2B −117.9(8.6)

a These simulations involve two pF2 peptides and the EcFUR-ΔCter15 dimer. Issues concerning the symmetry of the docking of pF2 are discussed in the Supporting Information. The Autodock binding free energy, minimum energy cluster and number of poses in this cluster (out of 256 total) are indicated (free energy of the second cluster in parentheses). Finally, the total CHARMM potential energy of the system and average interaction energies between the selected peptide and the protein averaged over a 5 ns MD simulation are shown in columns 6 and 7 (standard deviation in parentheses).

E


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Figure 5. (A) Model of [pF2(1−11)]2-EcFUR-ΔCter15 complex obtained by docking. Peptide pF2A(1−11) was docked to EcFUR-ΔCter15 in the presence of a second peptide (pF2B) with a binding free energy ΔG = −23.1 kcal mol−1. Cartoon representations are used for the secondary structures of FUR monomers A (yellow) and B (green), pF2A (magenta) and pF2B (violet). Important residues of pF2A and the protein dimer are highlighted in magenta and black, respectively. This figure corresponds to Table 1, Line 2. (B) Interacting residues in the docking of pF2 to EcFURΔCter15. Protein and peptide residues with more than 5 kcal mol−1 interaction energy (more than 10 in bold) after docking and energy minimization are listed ranked in decreasing order of their interaction energy.

Docking of Two pF2 Peptides to EcFUR-ΔCter15. Two pF2 peptides are able to bind simultaneously to two separate, almost symmetrical, binding sites on the EcFUR dimer. A first peptide (pF2A) was docked to the dimer in the presence of the second symmetrical peptide (pF2B). A very good docking of pF2 is obtained with a large binding free energy of −21.0 kcal mol−1 with good confidence (one cluster of 62/256 poses; Table 1). Similarly to the binding of pF1, some FUR residues such as R70, N72, G75, and Y128 seem crucial for a good binding of the peptides (Figure 5). A large stabilizing interaction energy comes from hydrogen bonds between the peptide S9 and L10 oxygens and the ammonium group of K77 (−18 kcal mol−1) of the protein. The shorter peptide pF2(1−11) shows an even better binding energy of −23.1 kcal mol−1. This gain in binding energy between pF2(1−13) and pF2(1−11) agrees with the experimental decrease of the IC50 values from 12 to 7 μM. pF2 amino acid R1 presents a high interaction energy of −35 kcal mol−1 with the protein and especially with amino acids N124, S126, and Y128 in monomer B and E74 in monomer A (Figure 5). Using ITC, a binding free energy of pF2(1−11) to EcFUR was evaluated to −8.9 kcal mol−1 with ΔH = −17.7 and ΔS = −8.8 kcal mol−1 (Figure 3 after division by 4.18 to transform J into cal). In Autodock, the conformational entropy term is directly proportional to the number of rotatable dihedral angles in the peptides (ΔS = −12.5 kcal mol−1 for pF2(1−11) with 42

degrees of freedom) and cannot be compared to the measured ΔS term. In our systems, the calculated ΔG is always largely lower (more stabilizing) than the value given by microcalorimetry. In general, only the differences between calculated ΔG’s of equivalent systems should be compared to the experimental data: between pF2(1−11) and pF2(1−13) the binding free energy differences are +0.2 kcal mol−1 and +2.1 kcal mol−1 from experiment and docking, respectively, two values which can be considered as almost identical given the precision of the results. Another view of the complex between pF2 and EcFURΔCter15 is shown in Supporting Information Figure S7. The symmetry of the docking of pF2A and pF2B is clear and agrees with the detection of one single binding site per subunit using ITC. The docking of pF2 to the EcFUR-ΔCter15 S126A/Y128A double mutant results in a moderate decrease of the free energy of binding down to −20.0 kcal mol−1, also in good agreement with experiments (Table 1 and Figure 5). Cysteine residues C3 and C6 of pF2 both show a more than 5 kcal mol−1 interaction energy (in bold in Figure 5B) with the protein dimer in agreement with the fact that the pF2(1− 10)C3S and pF2(1−10)C3S C6S mutants are inactive experimentally and that oxidized pF2 is inactive too (see Supporting Information Figure S4). F


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Figure 6. Model of pF3-EcFUR-ΔCter15 complex obtained by docking. (A) Cartoon representations are used for the secondary structures of FUR monomers A (yellow) and B (green) and pF3 (magenta). Important residues of pF3 and the protein dimer are highlighted in magenta and black, respectively. (B) Interacting residues in the docking of pF3 to EcFUR-ΔCter15. Protein and peptide residues with more than 5 kcal mol−1 interaction energy (more than 10 in bold) after docking and energy minimization are listed ranked in decreasing order of their interaction energy.

Scheme 2. Summary of Important Interactions between the Residues of the Peptides (Purple) and the Residues of the Protein (Gray), DD = Dimerization Domain and DBD = DNA Binding Domain

In summary, ITC experiments and calculated interaction energy favor the binding of two pF2’s per EcFUR dimer. Interestingly, the four cysteine residues of the two pF2 peptides are close to each other in the model (see Supporting Information Figure S6), but we did not observe the formation of a disulfide bond between the two pF2 peptides (not shown). Docking of the pF3 Peptide to EcFUR-ΔCter15. Docking of pF3 to EcFUR-ΔCter15 results in a very good binding free energy of −19.6 kcal mol−1 (with good confidence with more than 50 hits in the first cluster). Favorable interactions are found between K4 and E74, N124 and S126, or between Q8 or H12 and Y128 or Y130 (Figure 6). Docking of pF3 to the S126A/Y128A double mutant results in a 2 kcal mol−1 loss in binding energy, again in fair agreement with the experiments. As previously mentioned above, pF3(1−11) and pF3(1− 13)Q8A are inactive, and pF3(1−13)R11A remains able to inhibit FUR only if added in large amounts. Accordingly, compared to pF3(1−13), calculations give a slightly reduced binding energy for pF3(1−13)R11A, more pronounced for pF3(1−11), and large (4.5 kcal/mol) for pF3(1−13)Q8A.

Models of pF2 docked to EcFUR-ΔCter15 are in perfect agreement with the experimental results. Indeed, each residue S126 or Y128 (two pairs of residues per dimer) presents more than 5 kcal mol−1 interaction energies with pF2A or pF2B (Figure 5) (the precise calculation gives a total interaction energy of −27.7 kcal mol−1). Along the same line, the binding free energy of pF2(1−13) to the S126A/Y128A mutant protein is 1 kcal mol−1 lower than to the wild type (Table 1). This slight decrease in binding energy is to be expected from the experiments (Figure 4 and Supporting Information Figure S5). Last but not least, experiments show a better IC50 for pF2(1− 11) compared to pF2(1−13) in perfect agreement with the model (2.1 kcal mol−1 higher binding energy in Table 1). Finally, the CHARMM total energy (including protein− protein, protein−peptide, and peptide−peptide interactions plus the implicit solvation term) seems to be, in this case, a better indicator of the validity of the models than the interaction energy between peptide and protein (columns 6 and 7 in Table 1). G


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Figure 7. (A) Overlap of the model of EcFUR-ΔCter15 dimer complexed to two pF2(1−11) peptides and the EcFUR-ΔCter15 dimer interacting with DNA showing the steric hindrance. Cartoon representations are used for the secondary structures of FUR monomers A (yellow) and B (green). The solvent accessible surfaces of pF2A (violet) and pF2B (dark blue) interpenetrate the accessible surface of the FUR box (gray) showing large steric repulsion. (Zn2+ ions, present in the metal sites during energy minimization, are not represented.) (B) Residues of the FUR and FUR-like proteins interacting with the antiFUR pF2 and pF3 peptides or DNA (deduced from models or X-ray structures). 1Highly conserved and demonstrated to cross-link with thymine doublet;35 2protected by DNA in Lys modification experiment;36 3residues very close to DNA as seen on the PDB files of the structures; 4found in the docking structures; 5model structure37 of the interaction of PaFUR structure38 with DNA; 6deduced from the X-ray structure;39 7deduced from the X-ray structure described.40 Protein interactions with phosphate are marked by “P” signs and with DNA bases highlighted in blue.

pF3 (Q8, R11, H12) binding, and K77 is involved in pF2 binding with residue S9 and Q2, decreasing DNA accessibility to the DNA binding domain. The residues corresponding to Y56, R70, and K77 are highlighted in several FUR−DNA complexes and seem essential for DNA binding and inhibitor efficiency (Figure 7). The very good affinity of some of the antiFUR peptides makes these molecules (especially pF2) good lead inhibitor compounds for the development of new antibacterial molecules directed against FUR, a global transcriptional regulator related to iron homeostasis and virulence. It would be interesting in a future work to check the specificity of these inhibitions by testing these inhibitors against FUR proteins from other pathogens. Another important question will also be to confer to these peptides the ability to reach their cytosolic target through the membranes and to be stabilized by chemical modification in order to resist proteolytic attacks. Another strategy may be the use of these peptidic leads as guides to the discovery of smallmolecule inhibitors.

A comparative view of model structures of peptides pF1, pF2, and pF3 docked to the EcFUR-ΔCter15 dimer, in the same orientation, is shown in Supporting Information Figure S8 and important residues in the interaction listed in Supporting Information Table S1. In conclusion, this study and our previous work25 allow us to highlight two important features which should lead to the design of potent inhibitors of the FUR protein (Scheme 2). First, the inhibitor presents at least one residue anchoring it to the binding pocket of EcFUR constituted of residues S126 and Y128, among others: R5 in pF1 interacting with S126, Y128, and Y130; Q2 and R1 in pF2, the first interacting with S126, Y128, Y130, and N72, the second with S126, Y130, and H88; K4, Q8, and H12 in pF3, the first interacting with N124, the second with Y128 and N72, and the third with Y128 and Y130. Second, the inhibitor interacts with Y56 preventing binding of FUR to DNA through residue(s): Y6 and H8 in pF1, C6 in pF2, and R11 in pF3. Figure 7 exhibits the steric hindrance imposed on DNA by the presence of the two pF2 peptides bound to EcFUR-ΔCter15. Moreover, residue R70 is also involved in pF1 (R1, W3, R5), in pF2 (R1, Q2), and in H



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MATERIALS AND METHODS

ACKNOWLEDGMENTS Thanks to A. Imberty, E. Gillon, and P. Catty for their help in the interaction study by ITC and two-hybrid assays, respectively; to S. Galop for inhibition studies; and to M.B. Ould Abeih, E. de Rosny, and G. Mislin for fruitful discussions and the iRTSV SEC-MALLS-RI-QUELS platform.

Most of the techniques have been described in our previous works.24−28 They are shortly mentioned hereafter and detailed in the Supporting Information. Yeast Two-Hybrid Assays and Peptidization. The firefly luciferase reporter strains were constructed using the previously described plasmids and protocols.24 For peptidization experiments (peptides directly used as prey), the peptide coding sequences were cloned into the pWP1C plasmid. Protein Purification. Dimeric, monomeric, and S126A/Y128A mutant EcFUR proteins were overexpressed and purified as previously described.25−27 The EcFUR-ΔCter8 mutant (EcFUR missing the last eight C-terminal amino acids) was constructed in this study and purified as the other FUR proteins. Peptide Preparation. High purity peptides were purchased from Genescript USA Inc. or synthesized manually on a solid phase as described previously.25,28 Activity Assay. EcFUR (dimer or monomer) was activated by the addition of 2 equivalents of Mn2+ before its DNA-binding activity of EcFUR was investigated by the nuclease protection assay25,27 (Supporting Information Figure S1) in the presence or absence of the peptide derivatives. Mn2+ is used in place of Fe2+ because it is more stable than Fe2+ that is easily oxidized. Peptide Characterization. The oligomeric state of the peptides in solution was checked by SEC analysis performed using a Superdex Peptide PC 3.2/30 column. A protocol derived from the standard “Ellman’s Test” for the determination of free thiols29 was used to determine the redox state of the peptide solutions at t = 0 and to follow their oxidability over time. Isothermal Calorimetry (ITC) Measurements. The experiments were performed at 25 °C using an ITC200 calorimeter (Microcal, GE Healthcare). Peptides and EcFUR proteins were dissolved in the same buffer (100 mM BisTrisPropane-HCl, pH 7.5, 100 mM KCl, 5 mM MgCl2). Models of Peptides Docked to EcFUR. In the absence of a full structure for EcFUR, a model (reference structure) was built by homology from the VcFUR dimer structure (PDB entry 2W57) with the program MODELLER30 as previously described.25 Initial models of the peptides pF2, pF3, and pF5 were derived from those of pF1, previously obtained,25 or from preliminary dockings with the PEPSiteFinder program freely available (http://bioserv.rpbs.univ-parisdiderot.fr/PEP-SiteFinder/).31 Several passes of peptide docking to a fixed protein dimer followed by molecular dynamics simulations to account for a slight mobility of the protein were run. Dockings of the peptides to the EcFUR dimer were achieved with the program AutoDock version 4.2.6.32

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REFERENCES

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ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acschembio.6b00360. Supplementary figures and tables, experimental and computational procedures (PDF)

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AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected]. *E-mail: [email protected]. Funding

The authors acknowledge the financial support provided by French national research agency (ANR-11-BS07-0007 PepSiFUR), Region Rhône-Alpes (CIBLE grant), the LabEx Arcane (ANR-11-LABX-0003-01) and CEA. Notes

The authors declare no competing financial interest. I


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From Peptide Aptamers to Inhibitors of FUR, Bacterial Transcriptional

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