A single-residue substitution inhibits fibrillization of Ala-based pentapeptides. A spectroscopic and molecular dynamics investigation

Assessment of the MARTINI 3 Performance for Short Peptide Self-Assembly

The coarse-grained MARTINI force field, initially developed for membranes, has proven to be an exceptional tool for investigating supramolecular peptide assemblies. Over the years, the force field underwent refinements to enhance accuracy, enabling, for example, the reproduction of protein-ligand interactions and constant pH behavior. However, these protein-focused improvements seem to have compromised its ability to model short peptide self-assembly. In this study, we assess the performance of MARTINI 3 in reproducing peptide self-assembly using the well-established diphenylalanine (FF) as our test case. Unlike its success in version 2.1, FF does not even exhibit aggregation in version 3. By systematically exploring parameters for the aromatic side chains and charged backbone beads, we established a parameter set that effectively reproduces tube formation. Remarkably, these parameter adjustments also replicate the self-assembly of other di- and tripeptides and coassemblies. Furthermore, our analysis uncovers pivotal insights for enhancing the performance of MARTINI in modeling short peptide self-assembly. Specifically, we identify issues stemming from overestimated hydrophilicity arising from charged termini and disruptions in π-stacking interactions due to insufficient planarity in aromatic groups and a discrepancy in intermolecular distances between this and backbone-backbone interactions. This investigation demonstrates that strategic modifications can harness the advancements offered by MARTINI 3 for the realm of short peptide self-assembly.

Fundamental advances in hydrogels for the development of the next generation of smart delivery systems as biopharmaceuticals

Recent advances in developing and applying therapeutic peptides for anticancer, antimicrobial and immunomodulatory remedies have opened a new era in therapeutics. This development has resulted in the engineering of new biologics as part of a concerted effort by the pharmaceutical industry. Many alternative routes of administration and delivery vehicles, targeting better patient compliance and optimal therapeutic bioavailability, have emerged. However, the design of drug delivery systems to protect a range of unstable macromolecules, including peptides and proteins, from high temperatures, acidic environments, and enzymatic degradation remains a priority. Herein, we give chronological insights in the development of controlled-release drug delivery systems that occurred in the last 70 years or so. Subsequently, we summarise the key physicochemical characteristics of hydrogels contributing to the development of protective delivery systems concerning drug-targeted delivery in the chronospatial domain for biopharmaceuticals. Furthermore, we shed some light on promising hydrogels that can be utilised for systemic bioactive administration.

Non-Conventional Peptide Self-Assembly into a Conductive Supramolecular Rope

Structures composed of alternating α and β amino acids can give rise to peculiar secondary structural motifs, which could self-assemble into complex structures of controlled geometries. This work describes the self-assembly properties of an α,β-peptide, containing three units of syn H2-(2-F-Phe)-h-PheGly-OH, able to self-organize on surfaces into a fascinating supramolecular rope. This material was characterized by AFM, electronic conduction and fluorescence measurements. Molecular dynamics simulations showed that this hexapeptide can self-assemble into an antiparallel β-sheet layer, stabilized by intermolecular H-bonds, which, in turn, can self-assemble into many side-by-side layers, due to π-π interactions. As a matter of fact, we demonstrated that in this system, the presence of aromatic residues at the intramolecular interface promoted by the alternation of α,β-amino-acids in the primary sequence, endorses the formation of a super-secondary structure where the aromatic groups are close to each other, conferring to the system good electron conduction properties. This work demonstrates the capability and future potential of designing and fabricating distinctive nanostructures and efficient bioelectronic interfaces based on an α,β-peptide, by controlling structure and interaction processes beyond those obtained with α- or β-peptides alone.

Peptide Self-Assembled Nanostructures: From Models to Therapeutic Peptides

Self-assembly is the most suitable approach to obtaining peptide-based materials on the nano- and mesoscopic scales. Applications span from peptide drugs for personalized therapy to light harvesting and electron conductive media for solar energy production and bioelectronics, respectively. In this study, we will discuss the self-assembly of selected model and bioactive peptides, in particular reviewing our recent work on the formation of peptide architectures of nano- and mesoscopic size in solution and on solid substrates. The hierarchical and cooperative characters of peptide self-assembly will be highlighted, focusing on the structural and dynamical properties of the peptide building blocks and on the nature of the intermolecular interactions driving the aggregation phenomena in a given environment. These results will pave the way for the understanding of the still-debated mechanism of action of an antimicrobial peptide (trichogin GA IV) and the pharmacokinetic properties of a peptide drug (semaglutide) currently in use for the therapy of type-II diabetes.

Formulation matters! A spectroscopic and molecular dynamics investigation on the peptide CIGB552 as itself and in its therapeutical formulation

Synthetic therapeutic peptides (STP) are intensively studied as new-generation drugs, characterized by high purity, biocompatibility, selectivity and stereochemical control. However, most of the studies are focussed on the bioactivity of STP without considering how the formulation actually used for therapy administration could alter the physico-chemical properties of the active principle. The aggregation properties of a 20-mer STP (Ac-His-Ala-Arg-Ile-Lys-D-Pro-Thr-Phe-Arg-Arg-D-Leu-Lys-Trp-Lys-Tyr-Lys-Gly-Lys-Phe-Trp-NH₂ ), showing antitumor activity, were investigated by optical spectroscopy and atomic force microscopy imaging, as itself (CIGB552) and in its therapeutic formulation (CIGB552TF). It has found that the therapeutic formulation deeply affects the aggregation properties of the investigated peptide and the morphology of the aggregates formed on mica by deposition of CIGB552 and CIGB552TF millimolar solutions. Molecular dynamics simulations studied the first steps of CIGB552 aggregation under physiological ionic strength conditions (NaCl 150 mM), showing that peptide oligomers, from dimers to tetramers, are preferentially formed in this environment. Interestingly, cell viability assays performed on H-460 cell lines indicate a major antiproliferative activity of the peptide in its therapeutic formulation with respect to the peptide aqueous solution.

A spectroscopic and molecular dynamics study on the aggregation process of a long-acting lipidated therapeutic peptide: the case of semaglutide

The aggregation properties of semaglutide, a lipidated peptide drug agonist of the Glucagon-like peptide 1 receptor recently approved for the treatment of type 2 diabetes, have been investigated by spectroscopic techniques (UV-Vis absorption, steady-state and time-resolved fluorescence, and electronic circular dichroism) and molecular dynamics simulations. We show that in the micromolar concentration region, in aqueous solution, semaglutide is present as monomeric and dimeric species, with a characteristic monomer-to-dimer transition occurring at around 20 μM. The lipid chain stabilizes a globular morphology of the monomer and dimer species, giving rise to a locally well-defined polar outer surface where the lipid and peptide portions are packed to each other. At very long times, these peptide clusters nucleate the growth of larger aggregates characterized by blue luminescence and a β-sheet arrangement of the peptide chains. The understanding of the oligomerization and aggregation potential of peptide candidates is key for the development of long acting and stable drugs.

Tryptophan-Based Self-Assembling Peptides with Bacterial Flocculation and Antimicrobial Properties

Tryptophan as an aromatic amino acid with a hydrophobic indole group plays important roles in stabilizing protein structures and enhancing molecular bindings in nature, but was rarely used in the molecular design of self-assembling peptides or gelators. Therefore, we prepared a series of short peptides from Trp amino acids and examined the potential roles of Trp residues for regulating peptide self-assembly and gelation. The introduced Trp amino acids not only diversify the molecular structures of peptide gelators, but also promote aromatic and hydrogen-bonding interactions for supramolecular self-assembling and gelation, which generates self-assembled nanostructures with twisted helical morphologies and supramolecular hydrogels with low minimal gelation concentrations. More importantly, the self-assembling peptides with Trp residues displayed strong preference for interacting with the lipidic membranes of bacteria, which resulted in bacterial flocculation and the death of E. coli and S. aureus.

Controlling the Formation of Peptide Films: Fully Developed Helical Peptides are Required to Obtain a Homogenous Coating over a Large Area

The influence of conformational dynamics on the self-assembly process of a conformationally constrained analogue of the natural antimicrobial peptide Trichogin GA IV was analysed by spectroscopic methods, microscopy imaging at nanometre resolution, and molecular dynamics simulations. The formation of peptide films at the air/water interface and their deposition on a graphite or a mica substrate were investigated. A combination of experimental evidence with molecular dynamics simulation was used to demonstrate that only the fully developed helical structure of the analogue promotes formation of ordered aggregates that nucleate the growth of micrometric rods, which give rise to homogenous coating over wide regions of the hydrophilic mica. This work proves the influence of helix flexibility on peptide self-organization and orientation on surfaces, key steps in the design of bioinspired organic/inorganic hybrid materials.

Tuning the morphology of mesoscopic structures of porphyrin macrocycles functionalized by an antimicrobial peptide

The aggregation properties of two peptide–porphyrin conjugates were investigated by optical spectroscopy and microscopy imaging with nanometer resolution. Specifically, a tetraphenylporphyrin platform was functionalized by (L)-magainin, a 23-residue long antimicrobial peptide, and by a (L)-magainin analogue differing from the parent peptide by a single residue substitution, [Formula: see text] an Ala vs. Phe replacement in the position 5 of the peptide chain. Spectroscopic and microscopy results show that this single-site substitution has a small effect on the secondary structure attained by the two peptide analogues, but deeply affects the morphology of the mesoscopic structures deposited on hydrophilic mica from methanol/water solutions. In particular, only the Ala-substituted peptide-porphyrin conjugate was shown to be able to form micrometric fibrils, coating homogeneously a hydrophilic mica surface. These results pave the way for potential applications of porphyrin-peptide compounds in localized photodynamic therapy and for designing solid-state stereoselective sensors.

Tuning the Morphology of Nanostructured Peptide Films by the Introduction of a Secondary Structure Conformational Constraint: A Case Study of Hierarchical Self-Assembly

Peptide self-assembly is ubiquitous in nature. It governs the organization of proteins, controlling their folding kinetics and preserving their structural stability and bioactivity. In this connection, model oligopeptides may give important insights into the molecular mechanisms and elementary forces driving the formation of supramolecular structures. In this contribution, we show that a single residue substitution, that is, Aib (α-aminoisobutyric acid) in place of Ala at position 4 of an -(l-Ala)₅-homo-oligomer, strongly alters the aggregation process. In particular, this process is initiated by the formation of small peptide clusters that promote aggregation on the nanometer scale and, through a hierarchical self-assembly, lead to mesoscopic structures of micrometric dimensions. Furthermore, we show that the use of the well-established Langmuir-Blodgett technique represents an effective strategy for coating extended areas of inorganic substrates by densely packed peptide layers, thus paving the way for application of peptide films as templates for biomineralization, biocompatible coating of surfaces, and scaffolds for tissue engineering.

Two-Component Fluorescent-Semiconducting Hydrogel from Naphthalene Diimide-Appended Peptide with Long-Chain Amines: Variation in Thermal and Mechanical Strengths of Gels

Two-component fluorescent hydrogels have been discovered, containing the mixtures of naphthalene diimide (NDI)-conjugated peptide-functionalized bola-amphiphile and primary amines with long alkyl chains at physiological pH 7.46. The aggregation-induced enhanced emission associated with an NDI-appended peptide in aqueous medium is rare, as water is known to be a good quencher of fluorescence. In this study, an NDI-containing gelator peptide forms a highly fluorescent aggregate in aqueous medium. Absorption and emission spectroscopic techniques reveal the formation of J-aggregates among the chromophoric moieties in their aggregated state in aqueous medium. However, this NDI-containing peptide does not form any gel in aqueous medium. In the presence of the primary amines with long alkyl chains in the buffer solution, it forms two-component fluorescent hydrogels exhibiting bright yellow fluorescence under a UV lamp (365 nm). Probably, the acid-amine interaction between the amines and the bola-amphiphile triggers the gel formation, as evident from Fourier transform infrared data, indicating the presence of a carboxylate group (-COO^-) and an ammonium species (NH₃⁺) in the coassembled two-component gel system. Low- and wide-angle powder X-ray diffraction and small-angle X-ray scattering further support the fact that the coassembled state in the gel form is produced by the supramolecular interaction between the NDI-based bola-amphiphile and the long-chain amines. Field-emission scanning electron microscopy and high-resolution transmission electron microscopy images reveal that the π-conjugated coassembled hydrogels exhibit nanofibrillar network morphologies. Interestingly, the coassembled hydrogels exhibit an enhanced fluorescence emission, excited-state lifetime, and quantum yield when compared with those of the NDI-containing amphiphile alone in its self-assembled state in aqueous medium. Moreover, the thermal stability and mechanical strength of these gels have been successfully tuned by varying the alkyl chain length of the corresponding amine. Moreover, these NDI-peptide-conjugated soft materials exhibit semiconducting behavior in their respective coassembled states. This holds future promise to use these peptide-appended NDI-based coassembled soft materials for applications in optoelectronic and other devices.

A combined approach for predicting the cytotoxic effect of drug-nanoaggregates

We present a combined spectroscopic and computational approach aimed to elucidate the mechanism of formation and activity of etoposide nanoaggregates upon release from dextran-etoposide conjugates. Etoposide is an anticancer drug that inhibits cell growth by blocking Topoisomerase II, the key enzyme involved in re-ligation of the DNA chains during the replication process. In silico and spectroscopic analysis indicate that released etoposide nanoaggregates have a different structure, stability, and bioactivity, which depend on the pH experienced during the release. Molecular dynamics simulation and in silico docking of etoposide dimers suggest that the aggregation phenomena inhibit etoposide bioactivity, yet without drastically preventing Topoisomerase II binding. We correlated the diminished cytotoxic activity exerted by dextran-etoposide conjugates on the A549 lung cancer cells, compared to the free drug, to the formation and stability of drug nanoaggregates.

Using experimental and computational energy equilibration to understand hierarchical self-assembly of Fmoc-dipeptide amphiphiles

Despite progress, a fundamental understanding of the relationships between the molecular structure and self-assembly configuration of Fmoc-dipeptides is still in its infancy. In this work, we provide a combined experimental and computational approach that makes use of free energy equilibration of a number of related Fmoc-dipeptides to arrive at an atomistic model of Fmoc-threonine-phenylalanine-amide (Fmoc-TF-NH₂) which forms twisted fibres. By using dynamic peptide libraries where closely related dipeptide sequences are dynamically exchanged to eventually favour the formation of the thermodynamically most stable configuration, the relative importance of C-terminus modifications (amide versus methyl ester) and contributions of aliphatic versus aromatic amino acids (phenylalanine F vs. leucine L) is determined (F > L and NH₂ > OMe). The approach enables a comparative interpretation of spectroscopic data, which can then be used to aid the construction of the atomistic model of the most stable structure (Fmoc-TF-NH₂). The comparison of the relative stabilities of the models using molecular dynamic simulations and the correlation with experimental data using dynamic peptide libraries and a range of spectroscopy methods (FTIR, CD, fluorescence) allow for the determination of the nanostructure with atomistic resolution. The final model obtained through this process is able to reproduce the experimentally observed formation of intertwining fibres for Fmoc-TF-NH₂, providing information of the interactions involved in the hierarchical supramolecular self-assembly. The developed methodology and approach should be of general use for the characterization of supramolecular structures.

CHARMM force field parameterization protocol for self-assembling peptide amphiphiles: the Fmoc moiety

Aromatic peptide amphiphiles are known to self-assemble into nanostructures but the molecular level structure and the mechanism of formation of these nanostructures is not yet understood in detail.

Design of nanostructures based on aromatic peptide amphiphiles

Aromatic peptide amphiphiles are gaining popularity as building blocks for the bottom-up fabrication of nanomaterials, including gels. These materials combine the simplicity of small molecules with the versatility of peptides, with a range of applications proposed in biomedicine, nanotechnology, food science, cosmetics, etc. Despite their simplicity, a wide range of self-assembly behaviours have been described. Due to varying conditions and protocols used, care should be taken when attempting to directly compare results from the literature. In this review, we rationalise the structural features which govern the self-assembly of aromatic peptide amphiphiles by focusing on four segments, (i) the N-terminal aromatic component, (ii) linker segment, (iii) peptide sequence, and (iv) C-terminus. It is clear that the molecular structure of these components significantly influences the self-assembly process and resultant supramolecular architectures. A number of modes of assembly have been proposed, including parallel, antiparallel, and interlocked antiparallel stacking conformations. In addition, the co-assembly arrangements of aromatic peptide amphiphiles are reviewed. Overall, this review elucidates the structural trends and design rules that underpin the field of aromatic peptide amphiphile assembly, paving the way to a more rational design of nanomaterials based on aromatic peptide amphiphiles.