Open Access Article
S.
Pellegrino
*a,
N.
Tonali
b,
E.
Erba
a,
J.
Kaffy
b,
M.
Taverna
c,
A.
Contini
a,
M.
Taylor
d,
D.
Allsop
d,
M. L.
Gelmi
a and
S.
Ongeri
*b
aDISFARM-Sez. Chimica Generale e Organica “A. Marchesini”, Universitá degli Studi di Milano, via Venezian 21, 20133 Milano, Italy. E-mail: sara.pellegrino@unimi.it
bMolécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France. E-mail: Sandrine.ongeri@u-psud.fr
cProtéines et Nanotechnologies en Sciences Séparatives, Institut Galien Paris-Sud, Univ. Paris-Sud, CNRS, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
dLancaster University, Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster LA1 4YQ, UK
First published on 7th October 2016
Alzheimer's disease is a neurodegenerative disorder linked to oligomerization and fibrillization of amyloid β peptides, with Aβ1–42 being the most aggregative and neurotoxic one. We report herein the synthesis and conformational analysis of Aβ1–42-amyloid related β-hairpin peptidomimetics, built on a piperidine–pyrrolidine semi rigid β-turn inducer and bearing two small recognition peptide sequences, designed on oligomeric and fibril structures of Aβ1–42. According to these peptide sequences, a stable β-hairpin or a dynamic equilibrium between two possible architectures was observed. These original constructs are able to greatly delay the kinetics of Aβ1–42 aggregation process as demonstrated by thioflavin-T fluorescence, and transmission electron microscopy. Capillary electrophoresis indicates their ability to preserve the monomer species, inhibiting the formation of toxic oligomers. Furthermore, compounds protect against toxic effects of Aβ on neuroblastoma cells even at substoichiometric concentrations. This study is the first example of acyclic small β-hairpin mimics possessing such a highly efficient anti-aggregation activity. The protective effect is more pronounced than that observed with molecules which have undergone clinical trials. The structural elements made in this study provide valuable insights in the understanding of the aggregation process and insights to explore the design of novel acyclic β-hairpin targeting other types of amyloid-forming proteins.
Peptides are today reasonable alternatives to small molecule pharmaceuticals. They often offer greater efficacy, selectivity, specificity and a reduced risk of unforeseen side-reactions compared to small organic molecules, while some of their pharmacodynamic weaknesses can be circumvented by innovative formulations.6 A variety of small peptides that inhibit aggregation of Aβ and reduce its toxic effects have been already described.7 In particular, inhibition of Aβ-aggregation has been targeted using self-recognition elements (SREs). Indeed, molecules based on fragments of the Aβ-peptide, essentially on the nucleation sequence Aβ16–20 (KLVFF), were found promising as SREs.8 The design of macrocycles β-sheet mimics containing an unnatural tripeptide unit (Nowick's Hao) and SREs, has been a valid strategy.9 To our knowledge, the use of small acyclic β-hairpins has been very rarely explored as β-sheet binders and inhibitors of aggregation.10
Interestingly, compounds possessing several kinetically and thermodynamically accessible local minima representing conformations might be much more powerful inhibitors with respect to rigid ones in modulating protein–protein interactions.11 As Aβ-aggregation is a dynamic and complex process, we hypothesized that flexible β-hairpins could adapt themselves in the interaction with the different Aβ1–42 conformations present during the aggregation process, and in particular in the early stages of oligomerization. For that purpose, we designed two acyclic, β-hairpin mimics G1 and G2 based on the piperidine–pyrrolidine semi-rigid scaffold S1,12 developed recently as a flexible β-turn inducer (Fig. 1), and on different SREs of Aβ1–42. The nucleation sequence Aβ16–20 (KLVFF) has been introduced in the C-terminal sequence of both G1 and G2. However, the choice of the N-terminal sequence was driven by the strategy to develop both a flexible and a more structured β-hairpin. The hydrophobic sequence G33LMVG37, facing K16LVFF20 in the more flexible oligomeric structures13 has been introduced in G1. In G2, GVVIE has been chosen as a mimic of the hydrophobic sequence G38VVIA42, facing K16LVFF20 in the stable fibril structures.14 The alanine residue has been replaced by glutamic acid in order to possibly engage an ionic interaction with the facing lysine residue, thus stabilizing the β-hairpin structure (Fig. 1). The N-terminal amino acid of both G1 and G2 was either acetylated (G1a, G2a) or not (G1b, G2b), in order to evaluate the capacity of the compounds to engage electrostatic interactions with acidic residues of Aβ1–42 and with the view to increase their affinity. Several computational and experimental studies on Aβ1–42 proved in fact that, in addition to the hydrophobic interactions involving in particular the 16–21 sequence (KLVFFA), the formation of a salt-bridge between amino acids Asp23 and Lys28 of amyloid might stabilize a turn motif involving residues 24–28.13 An interaction with Glu22 might be also promoted and beneficial for the activity of the molecules.15
O atoms of residues Ile4/Leu8 and Val2/Phe10, were observed for G2a. On the other hand, the occupancies of intramolecular H-bonds detected for G1a were lower. We observed a minor populated hairpin conformation, characterized by the H-bonds involving Val4/Leu8 and Leu2/Phe10, and a major “mismatched” hairpin involving Val4/Val9 and Leu2/Phe11. The representative structures of the most populated cluster for G1a and G2a (Fig. 2) showed a mismatched β-hairpin for the former peptide, with the N-terminal strand (Gly1–Gly5) that was shifted one residue with respect to the C-terminal strand (Lys7–Phe11). Conversely, for G2a, the two strands were perfectly matched. The higher conformational flexibility of G1a, compared to G2a, was also shown by the root mean square deviation (RMSD) analysis of the corresponding REMD trajectories (Fig. S1, ESI†), confirming the possibility of an equilibrium for the former peptide between multiple β-hairpin like conformations, while a single and fairly rigid β-hairpin conformation was predicted for G2a.
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| Fig. 2 Representative structures of the most populated cluster obtained from cluster analyses of the 302.76 K trajectory of REMD simulations for peptides G1a (left) and G2a (right). | ||
Compounds G1 and G2 were thus prepared by solid phase peptide synthesis, using the Fmoc strategy (see ESI† for details).21 In order to evaluate the efficacy of G1 and G2 molecules with respect to a truncated derivative or the single arms, we also prepared derivative G3 (Fig. 3), containing the scaffold and only the Aβ (16–20) SRE, and compounds SRE1–3 corresponding to the different SREs (Fig. 1, see ESI† for details).
The CD spectra of G1a and G2a were recorded in MeOH at 25 °C (Fig. 4). G1a showed a negative band at 195 nm indicating that in solution this peptidomimetic did not assume a preferred, single conformation. On the other hand, the spectrum of G2a was characterized by a strong positive Cotton effect at around 195 nm (π–π* energetic transition), and a negative band at around 215 nm (n–π* energetic transition), typical of β-sheet structures.
The different behaviour of G1a and G2a was confirmed by 1H-NMR experiments in CD3OH (Tables S6–S8 in ESI†). Compound G1a is present in solution as two different β-hairpin structures (G1a-1/G1a-2, 2
:
1 ratio, Fig. 5), characterized by a different alignment of the two peptide arms. This dynamic equilibrium is proved by the presence of several negative NH/NH ROEs (Fig. S4, ESI†).22 On the other hand, 1H NMR spectrum of G2a showed a good dispersion of the NH chemical shifts indicating the presence of a stable single β-hairpin conformation characterized by a peptide arms alignment similar to G1a-2 (Fig. 5 on the bottom).23
ROESY experiments confirmed the presence of a turn structure in G1a-1, G1a-2, and G2a, as already reported for model sequences (Fig. S5 and S11, ESI†).12a
Several sequential CHα/NH ROEs, indicating β-conformations, were found for both G1a-1 and G1a-2 isomers (Fig. 5 and S6, ESI†). The different alignment of the peptide chains was proven by a ROE between NHPhe11/CHαMet3 in G1a-1, and by another one between NHLeu2/CHαVal9 in G1a-2 (for a complete discussion see ESI†).
Regarding compound G2a we could detect only one β-hairpin diagnostic ROE between CHαGly1 and the phenyl ring of Phe-10 (Fig. 5 and S12, ESI†). Several CHα signals are indeed overlapped or masked by the solvent. The presence of a β-hairpin structure was confirmed by 3JHN/CHα coupling constants that are higher than 8 Hz (Table S9, ESI†).24,25
Finally, the β-hairpin conformation was definitively confirmed for all compounds by the positive difference between experimental Hα chemical shift values and “random” ones26 (Fig. 6). Only Met-3 of G1a-1 is characterized by a negative ΔδαH value. This is probably due to the anisotropic effect27 of the aromatic ring of Phe-11 that faces Met-3, as evicted from ROESY experiments (Fig. S6A, ESI†).
Taking together both experimental and theoretical results, we can conclude that different hairpin architectures are possible for G1a and G2a, depending on the N-terminus sequence. The GVVIE motif in G2a strongly stabilizes a single “matched” hairpin conformation. On the other hand, the GLMVG motif in G1a gave a dynamic equilibrium between two possible architectures, the “mismatched” hairpin being the more stable.
| Compounds (Compound/Aβ ratio) | t 1/2 extensionb | Change of fluorescence intensity at the plateauc (%) |
|---|---|---|
| a NA = no aggregation, parameters are expressed as mean ± SE, n = 3–6. b See ESI for the calculation of the t1/2 extension. A compound displaying a t1/2 increase >1 is a delayer of aggregation. c See ESI for the calculation of the change of fluorescence intensity at the plateau. d Sat means that a saturation of the fluorescence signal is observed because G2a self-aggregates at 100 μM. | ||
| G1a (10/1) | NA | −97 ± 1% |
| G1a (1/1) | 2.06 ± 0.12 | −71 ± 2% |
| G2a (10/1) | Satd | Satd |
| G2a (1/1) | 1.76 ± 0.11 | −41 ± 7% |
| G1b (10/1) | NA | −97 ± 1% |
| G1b (1/1) | NA | −90 ± 2% |
| G2b (10/1) | NA | −95 ± 1% |
| G2b (1/1) | >3.56 ± 0.12 | −73 ± 3% |
Both G1 and G2 series are able to inhibit Aβ1–42 aggregation. The G1 series, containing the sequence G37VMLG33, and possessing a dynamic equilibrium between two different β-hairpin conformations, exerts a slightly superior inhibitory activity (Fig. 7 and Table 1). Furthermore, the free terminal amine is also important for Aβ1–42 aggregation suppression. Unprotected G1b and G2b were indeed able to totally suppress aggregation at compound/Aβ1–42 ratio of 10/1 and still dramatically delayed Aβ1–42 aggregation at 1/1 ratio (Fig. 7a and Table 1). Acetylated derivatives G1a and G2a retained this activity, but to a lesser extent (Table 1 and Fig. S14†). This result supports our hypothesis on the importance of establishing an ionic interaction between the N-terminal amino group and acidic residues of Aβ1–42.
No activity was observed for the isolated pentapeptides GLMVG (SRE1) and GVVIE (SRE2) (Table S11 and Fig. S14†). KLVFF (SRE3) delayed Aβ1–42 aggregation at compound/Aβ1–42 ratio of 10/1,8a,29 however in a much lesser extent than G1 and G2 series, while exerted no activity at 1/1 ratio (Table S11†). The G3 intermediate containing KLVFF linked to the piperidine–pyrrolidine scaffold S1 is more active than SRE3. These results highlight that the piperidine-pyrrolidine scaffold S1 and the pentapeptide KLVFF are both crucial for the activity, but the whole β-hairpin construct is necessary to strongly delay the Aβ1–42 aggregation kinetics.
In order to assess the selectivity on Aβ1–42 peptide, the ability of compounds G1b and G2b to interact with IAPP (islet amyloid polypeptide), an amyloid protein involved in type 2 diabetes mellitus but having another SRE,30 was also tested by the ThT-fluorescence assay under conditions similar to that described for Aβ1–42 peptide. It is noteworthy that both compounds displayed no activity on IAPP fibrillization process at compound/Aβ1–42 ratio of 1/1 and only slightly delayed it at the higher ratio (10/1) (Fig. S15†). This result suggests that the inhibition of aggregation displayed by compounds G1b and G2b on Aβ1–42 peptide is sequence specific.
Transmission electron microscopy (TEM) analyses were performed on the most promising G1a, G1b and G2b compounds. Images were recorded at 20 h and 42 h of fibrillization kinetics with samples containing 10 μM of each compound corresponding to the compound/Aβ1–42 ratio of 1/1 (Fig. 7b–d and S16†). Differences were observed in both quantity and morphology of aggregates formed. At 42 h, a very dense network of fibers displaying a typical morphology was observed for Aβ1–42 alone (Fig. 7b). In the samples containing G1a, the network of fibers was significantly less dense than in the control experiment after 20 h and 42 h. However, the fibers displayed the same morphology (Fig. S16, ESI†). In the samples containing G2b, the same trends as with G1a were observed (Fig. 7d and S16†). In samples containing G1b, we mainly observed globular aggregates after 20 h and 42 h (Fig. 7c and S16) indicating that the aggregation pathway could be different from the one observed for Aβ1–42 alone. These results validated the ThT-fluorescence data, indicating that compounds G1a, G1b and G2b dramatically slowed down the aggregation of Aβ1–42 and efficiently reduced the amount of typical amyloid fibrils.
In the presence of G1b, the aggregation kinetics of Aβ1–42 peptide was greatly modified (Fig. 8b and S19†). Noteworthy, the monomeric species (peak ES) was dramatically stabilized. 86% of the monomer remained after 24 h in the presence of G1b, while it was no more detected in the control sample (Fig. 8c). Moreover, the larger aggregated species LS (>dodecamers) were not detected. New aggregated forms of Aβ1–42, between ES′ and LS migration times were observed on each electrophoretic profile. We checked that these new aggregated forms were not due to G1b degradation or self-assemblies (Fig. S17A†). They were probably aggregated forms with a different morphology than both LS and those giving spikes observed in Aβ1–42 control. This observation is in accordance with the TEM images where globular aggregates were observed instead of the classical dense network of fibers (Fig. 7c and S16†). In ThT-assays, no fluorescence was detected, indicating that the globular species were not characterized by highly ordered β-structures (Fig. 7a). Remarkably, the presence of the monomer was maintained even after 4 days (Fig. S19B†). We concluded that G1b is able to prevent the formation of toxic soluble oligomers of Aβ1–42 peptide and to maintain the presence of the non toxic monomer overtime.
G2b also dramatically maintained the presence of the monomer (peak ES, 80% after 24 h, Fig. 8c, S20 and S21†). However, new aggregated forms were only transiently observed but were not anymore detected after 24 h. This result was also in accordance with the TEM images where we observed a much less dense network of fibers, although the typical morphology was retained.
This protective effect is more marked than that observed with molecules which have undergone clinical trials32–34 or other molecules recently described as efficient reducers of Aβ1–42 toxicity.35 In particular, in the literature, resveratrol was reported to protect SH-SY5Y neuroblastoma cells from Aβ1–42 toxicity at 10/1 and 2/1 (resveratrol/Aβ1–42) ratios,32 scyllo-inositol was demonstrated to protect PC-12 cells at 10/1 ratio (scyllo-inositol/Aβ1–42),33 and (−)-epigallocatechin-3-gallate (EGCG) protected murine neuro-2a neuroblastoma cells at 1/1 ratio (−)-epigallocatechin-3-gallate/Aβ1–42.34 In our hands, and comparable to the published data,32 resveratrol efficiently protected SH-SY5Y neuroblastoma cells only at a ratio of 2/1 (resveratrol/Aβ1–42). A stoichiometric ratio 1/1 was less efficient than a substoichiometric ratio of G1b and G2b (0.5/1 compound/Aβ1–42) (Fig. 11). Resveratrol exhibits multi-target activity and thus is not selective for Aβ1–42 aggregation. For example, resveratrol inhibits similarly the aggregation of other amyloid proteins such as IAPP36 (EGCG also inhibits similarly Aβ1–42 and IAPP aggregation in ThT fluorescence assays37,38), which is not the case for G1b and G2b, as mentioned above. By choosing the SREs in our β-hairpin mimics, specifically according to the target amyloid proteins, we can modulate the activity and expect selective activities.
Footnote |
| † Electronic supplementary information (ESI) available: Computational methods and additional figures and tables. NMR additional data. Description of synthetic procedures and characterization of compounds. Experimental procedure for fluorescence-detected ThT binding assay; representative curves of ThT fluorescence assays. Experimental procedure for TEM studies, CE, and cellular evaluation. See DOI: 10.1039/c6sc03176e |
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