Engineering Amino Acid and Peptide Supramolecular Architectures through Fluorination.

Fluorinated non-natural amino acids are attracting considerable research interest, especially in the biomedical field and in materials science, thanks to their ability to self-assemble into peculiar supramolecular structures. The conformational changes induced by the presence of fluorine atoms obviously affect their functions, as well as the biological activity of the deriving peptides and proteins. Here, we will briefly describe the main effects of fluorination on the aggregation behavior of such building blocks, focusing in particular on their improved tendency to form fibrils, and gels therefrom. Our aim is to underline the promising potential of fluorination as a tool to affect the self-assembly features of amino acids, both when used alone and when inserted into polypeptide sequences. The ability of fluorine to influence physical, chemical, and structural properties of these substrates offers the possibility to engineer bioinspired materials with specific and tunable functions.

Structural Insights on the Role of Halogen Bonding in Protein MEK Kinase-Inhibitor Complexes.

Kinases are enzymes that play a critical role in governing essential biological processes. Due to their pivotal involvement in cancer cell signaling, they have become key targets in the development of anti-cancer drugs. Among these drugs, those containing the 2,4-dihalophenyl moiety demonstrated significant potential. Here we show how this moiety, particularly the 2-fluoro-4-iodophenyl one, is crucial for the structural stability of the formed drug-enzyme complexes. Crystallographic analysis of reported kinase-inhibitor complex structures highlights the role of the halogen bonding that this moiety forms with specific residues of the kinase binding site. This interaction is not limited to FDA-approved MEK inhibitors, but it is also relevant for other kinase inhibitors, indicating its broad relevance in the design of this class of drugs.

Superfluorinated Extracellular Vesicles for In Vivo Imaging by 19F-MRI.

Extracellular vesicles (EVs) play a crucial role in cell-to-cell communication and have great potential as efficient delivery vectors. However, a better understanding of EV in vivo behavior is hampered by the limitations of current imaging tools. In addition, chemical labels present the risk of altering the EV membrane features and, thus, in vivo behavior. 19F-MRI is a safe bioimaging technique providing selective images of exogenous probes. Here, we present the first example of fluorinated EVs containing PERFECTA, a branched molecule with 36 magnetically equivalent 19F atoms. A PERFECTA emulsion is given to the cells, and PERFECTA-containing EVs are naturally produced. PERFECTA-EVs maintain the physicochemical features, morphology, and biological fingerprint as native EVs but exhibit an intense 19F-NMR signal and excellent 19F relaxation times. In vivo 19F-MRI and tumor-targeting capabilities of stem cell-derived PERFECTA-EVs are also proved. We propose PERFECTA-EVs as promising biohybrids for imaging biodistribution and delivery of EVs throughout the body.

Emergence of Elastic Properties in a Minimalist Resilin-Derived Heptapeptide upon Bromination.

Bromination is herein exploited to promote the emergence of elastic behavior in a short peptide-SDSYGAP-derived from resilin, a rubber-like protein exerting its role in the jumping and flight systems of insects. Elastic and resilient hydrogels are obtained, which also show self-healing behavior, thanks to the promoted non-covalent interactions that limit deformations and contribute to the structural recovery of the peptide-based hydrogel. In particular, halogen bonds may stabilize the ß-sheet organization working as non-covalent cross-links between nearby peptide strands. Importantly, the unmodified peptide (i.e., wild type) does not show such properties. Thus, SDSY(3,5-Br)GAP is a novel minimalist peptide elastomer.

Composite Peptide-Agarose Hydrogels for Robust and High-Sensitivity 3D Immunoassays.

Canonical immunoassays rely on highly sensitive and specific capturing of circulating biomarkers by interacting biomolecular baits. In this frame, bioprobe immobilization in spatially discrete three-dimensional (3D) spots onto analytical surfaces by hydrogel encapsulation was shown to provide relevant advantages over conventional two-dimensional (2D) platforms. Yet, the broad application of 3D systems is still hampered by hurdles in matching their straightforward fabrication with optimal functional properties. Herein, we report on a composite hydrogel obtained by combining a self-assembling peptide (namely, Q3 peptide) with low-temperature gelling agarose that is proved to have simple and robust application in the fabrication of microdroplet arrays, overcoming hurdles and limitations commonly associated with 3D hydrogel assays. We demonstrate the real-case scenario feasibility of our 3D system in the profiling of Covid-19 patients' serum IgG immunoreactivity, which showed remarkably improved signal-to-noise ratio over canonical assays in the 2D format and exquisite specificity. Overall, the new two-component hydrogel widens the perspectives of hydrogel-based arrays and represents a step forward towards their routine use in analytical practices.

Fibril Structure Demonstrates the Role of Iodine Labelling on a Pentapeptide Self-Assembly.

Iodination has long been employed as a successful labelling strategy to gain structural insights into proteins and other biomolecules via several techniques, including Small Angle X-ray Scattering, Inductively Coupled Plasma Mass Spectrometer (ICP-MS), and single-crystal crystallography. However, when dealing with smaller biomolecular systems, interactions driven by iodine may significantly alter their self-assembly behaviour. The engineering of amyloidogenic peptides for the development of ordered nanomaterials has greatly benefitted from this possibility. Still, to date, iodination has exclusively been applied to aromatic residues. In this work, an aliphatic bis-iodinated amino acid was synthesized and included into a custom pentapeptide, which showed enhanced fibrillogenic behaviour. Peptide single crystal X-ray structure and powder X-ray diffraction on its dried water solution demonstrated the key role of iodine atoms in promoting intermolecular interactions that drive the peptide self-assembly into amyloid fibrils. These findings enlarge the library of halogenated moieties available for directing and engineering the self-assembly of amyloidogenic peptides.

Graphene and its derivatives: understanding the main chemical and medicinal chemistry roles for biomedical applications.

Over the past few years, there has been a growing potential use of graphene and its derivatives in several biomedical areas, such as drug delivery systems, biosensors, and imaging systems, especially for having excellent optical, electronic, thermal, and mechanical properties. Therefore, nanomaterials in the graphene family have shown promising results in several areas of science. The different physicochemical properties of graphene and its derivatives guide its biocompatibility and toxicity. Hence, further studies to explain the interactions of these nanomaterials with biological systems are fundamental. This review has shown the applicability of the graphene family in several biomedical modalities, with particular attention for cancer therapy and diagnosis, as a potent theranostic. This ability is derivative from the considerable number of forms that the graphene family can assume. The graphene-based materials biodistribution profile, clearance, toxicity, and cytotoxicity, interacting with biological systems, are discussed here, focusing on its synthesis methodology, physicochemical properties, and production quality. Despite the growing increase in the bioavailability and toxicity studies of graphene and its derivatives, there is still much to be unveiled to develop safe and effective formulations.

Halogenation of the N-Terminus Tyrosine 10 Promotes Supramolecular Stabilization of the Amyloid-ß Sequence 7-12.

Here, we demonstrate that introduction of halogen atoms at the tyrosine 10 phenol ring of the DSGYEV sequence derived from the flexible amyloid-ß N-terminus, promotes its self-assembly in the solid state. In particular, we report the crystal structures of two halogen-modified sequences, which we found to be stabilized in the solid state by halogen-mediated interactions. The structural study is corroborated by Non-Covalent Interaction (NCI) analysis. Our results prove that selective halogenation of an amino acid enhances the supramolecular organization of otherwise unstructured biologically-relevant sequences. This method may develop as a general strategy for stabilizing highly polymorphic peptide regions.

The Impact of Halogenated Phenylalanine Derivatives on NFGAIL Amyloid Formation.

The hexapeptide hIAPP22-27 (NFGAIL) is known as a crucial amyloid core sequence of the human islet amyloid polypeptide (hIAPP) whose aggregates can be used to better understand the wild-type hIAPP's toxicity to ß-cell death. In amyloid research, the role of hydrophobic and aromatic-aromatic interactions as potential driving forces during the aggregation process is controversially discussed not only in case of NFGAIL, but also for amyloidogenic peptides in general. We have used halogenation of the aromatic residue as a strategy to modulate hydrophobic and aromatic-aromatic interactions and prepared a library of NFGAIL variants containing fluorinated and iodinated phenylalanine analogues. We used thioflavin T staining, transmission electron microscopy (TEM) and small-angle X-ray scattering (SAXS) to study the impact of side-chain halogenation on NFGAIL amyloid formation kinetics. Our data revealed a synergy between aggregation behavior and hydrophobicity of the phenylalanine residue. This study introduces systematic fluorination as a toolbox to further investigate the nature of the amyloid self-assembly process.

In Situ Generation of Chiroptically-Active Gold-Peptide Superstructures Promoted by Iodination.

Peptide-mediated routes to the synthesis of plasmonic nanoparticles have been drawing increasing attention for the development of chiroptically active nanoscale architectures. However, designing a multifunctional peptide able to drive the formation of structurally defined nanomaterials endowed with specific functionalities is still challenging. In this work, iodination has been devised as a strategy to strengthen Au-reduction capability of the amyloidogenic peptide DFNKF and combine it with its distinctive self-assembly features. Thanks to the Au-mediated C-I activation on the phenylalanine iodobenzenes, the peptides yield efficient Au-reduction ability promoting the synthesis of Au nanoparticles, and simultaneously working as templates for their spontaneous self-assembly into spherical superstructures endowed with chiroptical activities. The reaction occurs in situ through a one-pot process in aqueous media. The generality of this approach has been demonstrated using an iodinated derivative of the peptide KLVFF, which also showed reducing and templating abilities forming chiroptically active helical superstructures decorated with Au nanoparticles.

Crystallographic insights into the self-assembly of KLVFF amyloid-beta peptides.

Amyloidogenic peptide fragment KLVFF (H2 N-Lys-Leu-Val-Phe-Phe-COOH, Aß16-20 ), the core-sequence of the polypeptide Aß40, is a well-studied model for amyloid formation. However, due to its low crystallinity, detailed atomic information of KLVFF structure is lacking. Here we report the high-resolution single-crystal X-ray structure of two monohalogenated KLVFF derivatives, KLVFF(I) and KLVFF(Br). The obtained results highlight how halogenation is a good strategy to promote crystallization and facilitate the phase determination of KLVFF(I) and KLVFF(Br) fragments. Detailed structural studies on the packing features of both monohalogenated derivatives reveal the role of the halogen atoms showing that when they are positioned on the Phe aromatic moiety at the C-terminus they do not form halogen bonds and thus do not produce any extra stabilization of the ß-sheet in the self-assembly process. The structural evidences gained from these studies corroborate the various polymorphic nanostructures of the halogenated variants of KLVFF and confirm the possibility to use halogenation as innovative strategy to tune the morphology of this pentapeptide.

Bioreducible Hydrophobin-Stabilized Supraparticles for Selective Intracellular Release.

One of the main hurdles in nanomedicine is the low stability of drug-nanocarrier complexes as well as the drug delivery efficiency in the region-of-interest. Here, we describe the use of the film-forming protein hydrophobin HFBII to organize dodecanethiol-protected gold nanoparticles (NPs) into well-defined supraparticles (SPs). The obtained SPs are exceptionally stable in vivo and efficiently encapsulate hydrophobic drug molecules. The HFBII film prevents massive release of the encapsulated drug, which, instead, is activated by selective SP disassembly triggered intracellularly by glutathione reduction of the protein film. As a consequence, the therapeutic efficiency of an encapsulated anticancer drug is highly enhanced (2 orders of magnitude decrease in IC50). Biodistribution and pharmacokinetics studies demonstrate the high stability of the loaded SPs in the bloodstream and the selective release of the payloads once taken up in the tissues. Overall, our results provide a rationale for the development of bioreducible and multifunctional nanomedicines.

Nanostructure and stability of calcitonin amyloids.

Calcitonin is a 32-amino acid thyroid hormone that can form amyloid fibrils. The structural basis of the fibril formation and stabilization is still debated and poorly understood. The reason is that NMR data strongly suggest antiparallel ß-sheet calcitonin assembly, whereas modeling studies on the short DFNKF peptide (corresponding to the sequence from Asp15 to Phe19 of human calcitonin and reported as the minimal amyloidogenic module) show that it assembles with parallel ß-sheets. In this work, we first predict the structure of human calcitonin through two complementary molecular dynamics (MD) methods, finding that human calcitonin forms an α-helix. We use extensive MD simulations to compare previously proposed calcitonin fibril structures. We find that two conformations, the parallel arrangement and one of the possible antiparallel structures (with Asp15 and Phe19 aligned), are highly stable and ordered. Nonetheless, fibrils with parallel molecules show bulky loops formed by residues 1 to 7 located on the same side, which could limit or prevent the formation of larger amyloids. We investigate fibrils formed by the DFNKF peptide by simulating different arrangements of this amyloidogenic core sequence. We show that DFNKF fibrils are highly stable when assembled in parallel ß-sheets, whereas they quickly unfold in antiparallel conformation. Our results indicate that the DFNKF peptide represents only partially the full-length calcitonin behavior. Contrary to the full-length polypeptide, in fact, the DFNKF sequence is not stable in antiparallel conformation, suggesting that the residue flanking the amyloidogenic peptide contributes to the stabilization of the experimentally observed antiparallel ß-sheet packing.

The 1:1 co-crystal of triphen-yl(2,3,5,6-tetra-fluoro-benz-yl)phospho-nium bromide and 1,1,2,2-tetra-fluoro-1,2-di-iodo-ethane.

The title compound, C25H18F4P(+)·Br(-)·C2F4I2, is a 1:1 co-crystal of triphen-yl(2,3,5,6-tetra-fluoro-benz-yl)phospho-nium (TTPB) bromide and 1,1,2,2-tetra-fluoro-1,2-di-iodo-ethane (TFDIE). The crystal structure consists of a framework of TTPB cations held together by C-H⋯Br inter-actions. In this framework, infinite channels along [100] are filled by TFDIE mol-ecules held together in infinite ribbons by short F⋯F [2.863 (2)-2.901 (2)Å] inter-actions. The structure contains halogen bonds (XB) and hydrogen bonds (HB) in the bromide coordination sphere. TFDIE functions as a monodentate XB donor as only one I atom is linked to the Br(-) anion and forms a short and directional inter-action [I⋯Br(-) 3.1798 (7) Šand C-I⋯Br(-) 177.76 (5)°]. The coordination sphere of the bromide anion is completed by two short HBs of about 2.8 Š(for H⋯Br) with the acidic methyl-ene H atoms and two longer HBs of about 3.0 Šwith H atoms of the phenyl rings. Surprisingly neither the second iodine atom of TFDIE nor the H atom on the tetra-fluoro-phenyl group make any short contacts.

Tetra-phenyl-phospho-nium iodide-1,3,5-tri-fluoro-2,4,6-tri-iodo-benzene-methanol (3/4/1).

The crystallization of a 1:1 molar solution of 1,3,5-tri-fluoro-2,4,6-di-iodo-benzene (TFTIB) and tetra-phenyl-phosponium iodide (TPPI) from methanol produced tetra-gonal needles of pure TPPI and tabular pseudo-hexa-gonal truncated bipyramids of the title compound, 3C24H20P(+)·3I(-)·4C6F3I3·CH4O or (TPPI)3(TFTIB)4·MeOH. The asymmetric unit is composed of six TPPI mol-ecules, eight TFTIB mol-ecules and two methanol mol-ecules, overall 16 constituents. The formation of the architecture is essentially guided by a number of C-I⋯I(-) halogen bonds (XB), whose lengths are in the range 3.276 (1)-3.625 (1) Å. Layers of supra-molecular polyanions are formed parallel to (10-1) wherein iodide anions function as penta-, tetra- or bidentate XB acceptors. The structure is not far from being P21/n, but the centrosymmetry is lost due to a different conformation of a single couple of cations and the small asymmetry in the formed supra-molecular anion. One methanol mol-ecule is hydrogen bonded to an iodide anion, while the second is linked to the first one via an O-H⋯O contact. This second methanol mol-ecule is more loosely pinned in its position than the first and presents very high anisotropic displacement parameters and a seeming shortening of the C-O bond length. The crystal studied was refined as a perfect inversion twin.

[5,11,17,23-Tetra-tert-butyl-25,27-(3,6-dioxaoctan-1,8-di-oxy)-26,28-bis-(pyridin-2-ylmeth-oxy)calix[4]arene]sodium iodide-1,2,4,5-tetra-fluoro-3,6-diiodo-benzene-methanol (2/3/4).

The title compound, [Na(C62H76N2O6)]I·1.5C6F4I2·2CH3OH, is composed of five components: a calix[4]arene derivative (hereinafter C4), a sodium cation, an iodide anion, a 1,2,4,5-tetra-fluoro-3,6-diiodo-benzene (tFdIB) mol-ecule and a methanol mol-ecule in a 1:1:1:1.5:2 ratio. The complex shows several inter-esting features: (i) the polyoxygenated loop of C4 effectively chelates a sodium cation in the form of a distorted octahedron and separates it from the iodide counter-ion, the shortest Na(+)⋯I(-) distance being greater than 6.5 Å; (ii) the cavity of C4 is filled by a methanol mol-ecule; (iii) a second methanol mol-ecule is hydrogen-bonded to the N atom of a pyridinyl substituent pendant of C4 and halogen-bonded to the I atom of a tFdIB mol-ecule; (iv) the two I atoms of another tFdIB mol-ecule are halogen-bonded to two iodide anions, which act as monodentate halogen-bond acceptorss; (v) one of the two tFdIB molecules is located about a centre of inversion.

(Tris{2-[2-(2,3,5,6-tetra-fluoro-4-iodo-phen-oxy)eth-oxy]eth-yl}amine)-potassium iodide.

The title adduct, [K(C30H24F12I3NO6)]I, gives an extended tape of cations linked through I⋯I(-) halogen bonds (XBs), two of them being quite short and one quite long. In the structure, the cation is hosted in a cavity formed by the arms of the podand which presents a closed conformation wherein two tetra-fluoro-iodo-benzene rings are near parallel [dihedral angle = 15.8 (4)°; centroid-centroid distance = 3.908 (5) Å] and the third ring is closer to orthogonal [dihedral angles = 66.28 (14) and 75.20 (19)°] to the other two rings. The coordination sphere of the K(+) cation is composed of the six O atoms, the N atom and an F atom in the ortho position of one of the rings.

1,3-Bis(2,3,5,6-tetra-fluoro-4-iodo-phen-oxy)-2,2-bis-[(2,3,5,6-tetra-fluoro-4-iodo-phen-oxy)meth-yl]propane.

In the crystal structure of the title compound, C29H8F16I4O4, short I⋯I and I⋯F contacts, which can be understood as halogen bonds (XBs), represent the strongest inter-molecular inter-actions, consistent with the presence of I and F atoms, and the absence of H atoms, at the periphery of the mol-ecule. In addition, π-π stacking inter-actions between tetra-fluoro-iodo-phenyl (TFIP) groups and five short F⋯F inter-actions are present.

2-Iodo-imidazolium receptor binds oxoanions via charge-assisted halogen bonding.

A detailed (1)H-NMR study of the anion binding properties of the 2-iodo-imidazolium receptor 1 in DMSO allows to fully attribute the observed affinities to strong charge-assisted C-I···X(-) halogen bonding (XB). Stronger binding was observed for oxoanions over halides. Phosphate, in particular, binds to 1 with an association constant of ca. 10(3) M(-1), which is particularly high for a single X-bond. A remarkably short C-I···O(-) contact is observed in the structure of the salt 1·H(2)PO(4)(-).