Selected peptide-based fluorescent probes for biological applications

Peptide Multifunctionalization via Modular Construction of Trans-AB2C Porphyrin on Resin

Peptide multifunctionalization is a crucial technique to develop peptide-based agents for various purposes. Porphyrin-peptide conjugates are a class of popular multifunctional peptides renowned for their multifunctional and multimodal properties. However, the tedious synthetic works for porphyrin building blocks are involved in most previous studies. In this work, a modular solid-phase synthetic approach is reported to construct trans-AB2C porphyrin on peptide chains without presynthesized porphyrin building blocks. The products from this approach, which inherit both functionalities from the porphyrins and the modules employed for constructing porphyrins, show potential in biomedical and biomaterial applications. Furthermore, by extending this synthetic approach, the first example of "resin-to-resin" reaction is reported to link two peptides together along the construction of porphyrin motifs to give porphyrin-peptide conjugates with two different peptide chains.

A peptide-based fluorescent bioprobe for EphA2-overexpressing tumor targeting and image-guided surgical resection

Fluorescence-guided surgery (FGS) is an emerging and highly promising surgical technique in clinic. Owing to its real-time and visual characteristics, it assists in achieving clear pictures on lesion site, tumor boundary and degree of metastasis, which will definitely improve surgery accuracy and minimize cancer recurrence as much as possible. Herein, we report a near-infrared fluorescent bioprobe, YK80, which utilizes a modified heptamethine cyanine dye as the fluorophore and a self-assembling peptide targeting Ephrin receptor A2 (EphA2) proteins as the ligand. The design strategy and the synthetic route to YK80 are described, and then optical properties, pharmacokinetics, binding affinity between YK80 and the protein are further investigated. YK80 shows high affinity (KD ≈ 100 nM) with EphA2-expressing cancer cells and excellent targeting ability in mouse models bearing colorectal tumors. Meanwhile, indocyanine green (ICG), the commonly used non-targeted fluorescent contrast agent is employed as the comparison for in vivo experiments. However, ICG owns no such capability towards cancer cells or solid tumors. Thus, YK80 could potentially serve as a targeted contrast agent for image-guided surgery and this successful example will boost the development of medical imaging, surgical methods as well as translational medicine.

Peptide-based therapeutics targeting genetic disorders

Genetic disorders (GDs) are challenging to treat owing to a lack of optimal treatment regimens and intricate and often difficult-to-understand underlying biological processes. Limited therapeutic approaches, which mostly provide symptomatic relief, are available. To date, a limited number of peptide-based drugs for the treatment of GDs are available, and several candidates are under clinical study. This review provides mechanistic insights into GDs and potential target areas where peptide-based drugs are beneficial. In addition, it emphasizes the usefulness of peptides as carriers for gene delivery, biomarkers for mutation detection and peptide-based vaccines for treating GDs.

Design of C2-symmetric pseudopeptides for in vivo detection of Cu(II) through controlled supramolecular nano-assembly

Pseudopeptides are emerging next-generation soft bioinspired materials for biological applications. Therefore, a new class of C2-symmetric L-valine-derived pseudopeptides has been designed and developed. The newly developed pseudopeptides exhibit intracellular Cu(II) ion detection in live-cell fluorescence studies on RAW264.7 cells. We find that the changes in the amino acid side chain in desired pseudopeptidic moieties lead to a drastic change in their selectivity towards different metal ions. The L-valine-derived pseudopeptides exhibit selectivity towards Cu(II) ions through turn-off fluorescence, and the L-phenylalanine-derived pseudopeptides exhibit selectivity towards Zn(II) ions through turn-on fluorescence. In addition, the L-valine-derived pseudopeptides show an increase in spherical-shaped structures upon incubation with Cu(II) ions during supramolecular nano-assembly formation. In contrast, the L-phenylalanine-derived pseudopeptides show a decrease in spherical-shaped structures upon adding Zn(II) ions. The judiciously designed L-valine-derived and L-phenylalanine-derived bioinspired pseudopeptides are promising for exploring similar effects in various peptidomimetics in advanced biological applications.

Dipeptides Containing Pyrene and Modified Photochemically Reactive Tyrosine: Noncovalent and Covalent Binding to Polynucleotides

Dipeptides 1 and 2 were synthesized from unnatural amino acids containing pyrene as a fluorescent label and polynucleotide binding unit, and modified tyrosine as a photochemically reactive unit. Photophysical properties of the peptides were investigated by steady-state and time-resolved fluorescence. Both peptides are fluorescent (Φf = 0.3-0.4) and do not show a tendency to form pyrene excimers in the concentration range < 10-5 M, which is important for their application in the fluorescent labeling of polynucleotides. Furthermore, both peptides are photochemically reactive and undergo deamination delivering quinone methides (QMs) (ΦR = 0.01-0.02), as indicated from the preparative photomethanolysis study of the corresponding N-Boc protected derivatives 7 and 8. Both peptides form stable complexes with polynucleotides (log Ka > 6) by noncovalent interactions and similar affinities, binding to minor grooves, preferably to the AT reach regions. Peptide 2 with a longer spacer between the fluorophore and the photo-activable unit undergoes a more efficient deamination reaction, based on the comparison with the N-Boc protected derivatives. Upon light excitation of the complex 2·oligoAT10, the photo-generation of QM initiates the alkylation, which results in the fluorescent labeling of the oligonucleotide. This study demonstrated, as a proof of principle, that small molecules can combine dual forms of fluorescent labeling of polynucleotides, whereby initial addition of the dye rapidly forms a reversible high-affinity noncovalent complex with ds-DNA/RNA, which can be, upon irradiation by light, converted to the irreversible (covalent) form. Such a dual labeling ability of a dye could have many applications in biomedicinal sciences.

Recent advances in the modulation of amyloid protein aggregation using the supramolecular host-guest approaches

Misfolding of proteins is associated with many incurable diseases in human beings. Understanding the process of aggregation from monomers to fibrils, the characterization of all intermediate species, and the origin of toxicity is very challenging. Extensive research including computational and experimental shed some light on these tricky phenomena. Non-covalent interactions between amyloidogenic domains of proteins play a major role in their self-assembly which can be disrupted by designed chemical tools. This will lead to the development of inhibitors of detrimental amyloid formations. In supramolecular host-guest chemistry approaches, different macrocycles function as hosts for encapsulating hydrophobic guests, i.e. phenylalanine residues of proteins, in their hydrophobic cavities via non-covalent interactions. In this way, they can disrupt the interactions between adjacent amyloidogenic proteins and prevent their self-aggregation. This supramolecular approach has also emerged as a prospective tool to modify the aggregation of several amyloidogenic proteins. In this review, we discussed recent supramolecular host-guest chemistry-based strategies for the inhibition of amyloid protein aggregation.

Small molecule-based fluorescent probes for the detection of α-Synuclein aggregation states

The formation of aggregates due to protein misfolding is encountered in various neurodegenerative diseases. α-Synuclein (α-Syn) aggregation is linked to Parkinson's disease (PD). It is one of the most prevalent neurodegenerative disorders after Alzheimer's disease. Aggregation of α-Syn is associated with Lewy body formation and degeneration of the dopaminergic neurons in the brain. These are the pathological hallmarks of PD progression. α-Syn aggregates in a multi-step process. The native unstructured α-Syn monomers combine to form oligomers, followed by amyloid fibrils, and finally Lewy bodies. Recent evidence suggests that α-Syn oligomerization and fibrils formation play major roles in PD development. α-Syn oligomeric species is the main contributor to neurotoxicity. Therefore, the detection of α-Syn oligomers and fibrils has drawn significant attention for potential diagnostic and therapeutic development. In this regard, the fluorescence strategy has become the most popular approach for following the protein aggregation process. Thioflavin T (ThT) is the most frequently used probe for monitoring amyloid kinetics. Unfortunately, it suffers from several significant drawbacks including the inability to detect neurotoxic oligomers. Researchers developed several small molecule-based advanced fluorescent probes compared to ThT for the detection/monitoring of α-Syn aggregates states. These are summarized here.

Consideration of a new approach to clarify the mechanism formation of AgNPs, AgNCl and AgNPs@AgNCl synthesized by biological method

The biological methods are considered as environmental-eco-friendly methods for the silver nanocomposites mediation and are widely used in this context. However, the biological methods go along with the relevant limitations, for instance simultaneous synthesis of silver chlorides (AgNCl) type during the AgNPs mediation process. Therefore, the present research is coming to summarize several aspects in this context. Firstly, to present the possible promotion of the sustainable development using bioactive source (e.g. milk) as a source of two different available and new lactobacillus strains (Lactobacillus curvatus and Lactobacillus fermentum). Secondly, to show the ability of the respective isolates to be involved in mediation of various biosilver nanocomposites ((Bio)NCs) synthesis. Moreover, at this stage, for the first time, two (Bio)NCs mediation methods, called "direct method" and "modified method", have been developed, thus three types (AgNPs, AgNCl and AgNP@AgNCl) of nanocomposites mediated by two different Lactobacillus isolates take place. The interdisciplinary approach included using several spectroscopic, microscopic, spectrometric and thermogravimetric methods demonstrated that all six synthesized nanoparticles (three AgNPs, AgNCl and AgNP@AgNCl types from each source) consist of complex structure including both metallic silver core as well as organic surface deposits. The spectrometric technique allowed to identification of the organics branching surface, naturally secreted by the used Lactobacillus isolates during the inoculation step, suggesting the presence of amino-acids sequences which are direct connected with the reduction of silver ion to metal silver, and subsequently with the formation of coated (Bio)NCs and nucleation process. Moreover, based on the obtained results, the mediation mechanism of each (Bio)NCs has been proposed, suggesting that the formation of AgNPs, AgNCl and AgNP@AgNCl types occurs in different manners with faster synthesis firstly of AgNCl, then of the AgNPs type. No differences between the (Bio)NCs synthesized by two different Lactobacillus isolates have been noticed indicating no discrepancies between metabolites secreted by the respective sources.

Rapid and Highly Selective Fluorescent Labeling of Peptides via a Thia-Diels-Alder Cycloaddition: Application to Apelin

Herein, we describe a catalyst-free thia-Diels-Alder cycloaddition for the chemoselective labeling of fully deprotected phosphonodithioester-peptides in solution with fluorophores functionalized with an exocyclic diene. The reaction was optimized on the model tripeptide 1 containing a lysine residue, which enabled its rapid and straightforward labeling with three different fluorophores (fluorescein, lissamine rhodamine B, and squaraine) in very mild conditions (H₂O/iPrOH, 37 °C, 1 h). The reaction was then successfully applied to the chemoselective labeling of fully deprotected apelin-13 with squaraine dye. The resulting fluorescent ligand 18 exhibited a high affinity (0.17 ± 0.03 nM) for apelinR. It enabled the development of time-resolved FRET-based competition assays for high-throughput screening and drug discovery. Thanks to its fluorogenic properties, ligand 18 was also successfully involved in the live-cell optical imaging of apelinR in no-wash conditions.

Fluorogenic Protein Labeling by Generation of Fluorescent Quinoliziniums Using [Cp*RhCl2]2

Fluorogenic labeling has received considerable attention as a result of the high demand in chemical biology and synthetic biology applications. Herein, we develop a new strategy for fluorescent turn-on ligation targeting alkyne- and quinoline-linked peptides and proteins (λ_em of 515 nm and up to Φ_F of 0.20) using the [Cp*RhCl₂]₂ catalyst. The good conversion, high flexibility, broad utility, ease of use, and mild reaction conditions are great advantages to extend the rhodium-mediated turn-on fluorogenic bioconjugation for further applications.

Non-Covalent Binding of Tripeptides-Containing Tryptophan to Polynucleotides and Photochemical Deamination of Modified Tyrosine to Quinone Methide Leading to Covalent Attachment

A series of tripeptides TrpTrpPhe (1), TrpTrpTyr (2), and TrpTrpTyr[CH₂N(CH₃)₂] (3) were synthesized, and their photophysical properties and non-covalent binding to polynucleotides were investigated. Fluorescent Trp residues (quantum yield in aqueous solvent Φ_F = 0.03–0.06), allowed for the fluorometric study of non-covalent binding to DNA and RNA. Moreover, high and similar affinities of 2×HCl and 3×HCl to all studied double stranded (ds)-polynucleotides were found (logK_a = 6.0–6.8). However, the fluorescence spectral responses were strongly dependent on base pair composition: the GC-containing polynucleotides efficiently quenched Trp emission, at variance to AT- or AU-polynucleotides, which induced bisignate response. Namely, addition of AT(U) polynucleotides at excess over studied peptide induced the quenching (attributed to aggregation in the grooves of polynucleotides), whereas at excess of DNA/RNA over peptide the fluorescence increase of Trp was observed. The thermal denaturation and circular dichroism (CD) experiments supported peptides binding within the grooves of polynucleotides. The photogenerated quinone methide (QM) reacts with nucleophiles giving adducts, as demonstrated by the photomethanolysis (quantum yield Φ_R = 0.11–0.13). Furthermore, we have demonstrated photoalkylation of AT oligonucleotides by QM, at variance to previous reports describing the highest reactivity of QMs with the GC reach regions of polynucleotides. Our investigations show a proof of principle that QM precursor can be imbedded into a peptide and used as a photochemical switch to enable alkylation of polynucleotides, enabling further applications in chemistry and biology.

Self-Assembling Peptides and Carbon Nanomaterials Join Forces for Innovative Biomedical Applications

Self-assembling peptides and carbon nanomaterials have attracted great interest for their respective potential to bring innovation in the biomedical field. Combination of these two types of building blocks is not trivial in light of their very different physico-chemical properties, yet great progress has been made over the years at the interface between these two research areas. This concise review will analyze the latest developments at the forefront of research that combines self-assembling peptides with carbon nanostructures for biological use. Applications span from tissue regeneration, to biosensing and imaging, and bioelectronics.