Neurotrophic Activity and Its Modulation by Zinc Ion of a Dimeric Peptide Mimicking the Brain-Derived Neurotrophic Factor N-Terminal Region

Brain-derived neurotrophic factor (BDNF) is a neurotrophin (NT) essential for neuronal development and synaptic plasticity. Dysregulation of BDNF signaling is implicated in different neurological disorders. The direct NT administration as therapeutics has revealed to be challenging. This has prompted the design of peptides mimicking different regions of the BDNF structure. Although loops 2 and 4 have been thoroughly investigated, less is known regarding the BDNF N-terminal region, which is involved in the selective recognition of the TrkB receptor. Herein, a dimeric form of the linear peptide encompassing the 1-12 residues of the BDNF N-terminal (d-bdnf) was synthesized. It demonstrated to act as an agonist promoting specific phosphorylation of TrkB and downstream ERK and AKT effectors. The ability to promote TrkB dimerization was investigated by advanced fluorescence microscopy and molecular dynamics (MD) simulations, finding activation modes shared with BDNF. Furthermore, d-bdnf was able to sustain neurite outgrowth and increase the expression of differentiation (NEFM, LAMC1) and polarization markers (MAP2, MAPT) demonstrating its neurotrophic activity. As TrkB activity is affected by zinc ions in the synaptic cleft, we first verified the ability of d-bdnf to coordinate zinc and then the effect of such complexation on its activity. The d-bdnf neurotrophic activity was reduced by zinc complexation, demonstrating the role of the latter in tuning the activity of the new peptido-mimetic. Taken together our data uncover the neurotrophic properties of a novel BDNF mimetic peptide and pave the way for future studies to understand the pharmacological basis of d-bdnf action and develop novel BDNF-based therapeutic strategies

Theoretical investigation of bioinorganic compounds: biomimetic catalysts and metal-mediated mismatched DNA base-Pairs

Dottorato Scienza e Tecnica "Bernardino Telesio", Metodologie Inorganiche, Ciclo XXVIII, a.a. 2015-2016Una delle principali sfide nel mondo scientifico è superare la linea di confine tra la natura e il mondo inanimato. La Chimica Biomimetica e la Biologia Sintetica collaborano al raggiungimento di questo obiettivo. Lo sviluppo della Chimica Biomimetica è stato ispirato dall’elevata efficacia catalitica degli enzimi naturali, che giocano un ruolo chiave nella maggior parte delle reazioni chimiche che avvengono nell’organismo. Essa può essere definita come una branca della chimica che cerca di imitare le reazioni naturali e i processi enzimatici allo scopo di accrescere il potere della chimica stessa. La Biologia Sintetica, invece, è una nuova area di ricerca che rappresenta la convergenza di nuovi sviluppi in chimica, in biologia e in scienza computazionale al fine di progettare e creare nuovi sistemi biologici, partendo da materiale biologico già esistente e modificato mediante l’applicazione di processi chimici, da utilizzare in ambito industriale, energetico, medico e ambientale. La presente tesi pone l’attenzione sul meccanismo di azione seguito da alcuni catalizzatori biomimetici, per i quali sono state investigate sia la regioselettività, sia l’attività riscontrata sperimentalmente, e sullo studio delle proprietà energetiche e strutturali relative a nuovi sistemi bio-ispirati. I catalizzatori biomimetici e i nuovi sistemi biologici il cui comportamento è stato studiato e razionalizzato come scopo di questo lavoro di tesi possono essere suddivisi in tre categorie: i- Alcuni composti del naftalene caratterizzati dalla presenza di atomi di selenio, zolfo o tellurio, come mimici degli enzimi iodotironine deiodinase (ID), coinvolti nell’attivazione e inattivazione degli ormoni tiroidei. ii- Una serie di complessi di monooxomolibdeno(IV) come biomimetici dell’enzima trimetilammina-N-ossidoreduttase (TMAOR). iii- Alcuni modelli di DNA duplex, contenenti coppie di nucleobasi non complementari mediate da metalli di transizione. Lo studio teorico dei sistemi sopra elencati è stato effettuato utilizzando l’approccio quantomeccanici (QM) basato sulla teoria del funzionale della densità (DFT).Università della Calabri

Multi-replica biased sampling for photoswitchable π-conjugated polymers

International audienceIn recent years, conjugated polymers are attracting considerable interest in view of their lightdependent torsional reorganization around the p-conjugated backbone, which determines peculiar light-emitting properties. Motivated by the interest in designing conjugated polymers with tunable photoisomerization pathways, we devised a computational framework to enhance the sampling of the polymer conformational space and at the same time estimate ground to excited-state free-energy differences. This scheme is based on a combination of Hamiltonian Replica Exchange (REM), Parallel Bias metadynamics, and free-energy perturbation theory. In our scheme, each REM replica samples different intermediate states connecting the ground to the first two excited states, which are characterized by TD-DFT simulations at the B3LYP/6-31G* level of theory. We applied the method on a 5-mer of poly(9,9-dioctylfluoren-2,7-diyl) and compared the results with the emission energies measured experimentally, showing a quantitative agreement with the prediction provided by our simulation framework

Rationalizing the design and implementation of chiral hybrid perovskites

Molecular asymmetry occurs at all scales in nature, spanning organic to inorganic frameworks with consequences of high significance. For this reason, asymmetric organic and inorganic materials are incessantly gaining considerable interest owing to the opportunity of reaching tunable chiral signatures. In recent years, the chiral hybrid organic-inorganic perovskites in which the chiral organic ligands usually induce the symmetry breaking are receiving growing attention. Their circularly polarized emissions without the need for expensive ferromagnets or extremely low temperatures are appealing features for the industry. Until now, there has been no clear relationship between the structure of the chiral perovskites and the generated signal. This review aims at focusing on the supramolecular chiral amplification mechanisms in asymmetric perovskites, rationalizing how to enhance their chiral emission signatures. We conclude by broadening our view toward future challenges in exploring modern simulation protocols to optimize the design of chiral hybrid perovskites

The role of the halogen bond in iodothyronine deiodinase: Dependence on chalcogen substitution in naphthyl-based mimetics

The effects on the activity of thyroxine (T4) due to the chalcogen replacement in a series of peri-substituted naphthalenes mimicking the catalytic function of deiodinase enzymes are computationally examined using density functional theory. In particular, T4 inner-ring deiodination pathways assisted by naphthyl-based models bearing two tellurols and a tellurol-thiol pair in peri-position are explored and compared with the analogous energy profiles for the naphthalene mimic having two selenols. The presence of a halogen bond (XB) in the intermediate formed in the first step and involved in the rate-determining step of the reaction is assumed to facilitate the process increasing the rate of the reaction. The rate-determining step calculated energy barrier heights allow rationalizing the experimentally observed superior catalytic activity of tellurium containing mimics. Charge displacement analysis is used to ascertain the presence and the role of the electron density charge transfer occurring in the rate-determining step of the reaction, suggesting the incipient formation or presence of a XB interaction

Multinuclear Metal-Binding Ability of the N-Terminal Region of Human Copper Transporter Ctr1: Dependence Upon pH and Metal Oxidation State

The 14mer peptide corresponding to the N-terminal region of human copper transporter Ctrl was used to investigate the intricate mechanism of metal binding to this plasma membrane permease responsible for copper import in eukaryotic cells. The peptide contains a high-affinity ATCUN Cu(II)/Ni(II)-selective motif, a methionine-only MxMxxM Cu(I)/Ag(I)-selective motif and a double histidine HH(M) motif, which can bind both Cu(II) and Cu(I)/Ag(I) ions. Using a combination of NMR spectroscopy and electrospray mass spectrometry, clear evidence was gained that the Ctr1 peptide, at neutral pH, can bind one or two metal ions in the same or different oxidation states. Addition of ascorbate to a neutral solution containing Ctr1(1-14) and Cu(II) in 1:1 ratio does not cause an appreciable reduction of Cu(II) to Cu(I), which is indicative of a tight binding of Cu(II) to the ATCUN motif. However, by lowering the pH to 3.5, the Cu(II) ion detaches from the peptide and becomes susceptible to reduction to Cu(I) by ascorbate. It is noteworthy that at low pH, unlike Cu(II), Cu(I) stably binds to methionines of the peptide. This redox reaction could take place in the lumen of acidic organelles after Ctr1 internalization. Unlike Ctr1(1-14)-Cu(II) bimetallic Ctr1(1-14)-Cu(II) is susceptible to partial reduction by ascorbate at neutral pH, which is indicative of a lower binding affinity of the second Cu(II) ion. The reduced copper remains bound to the peptide, most likely to the HH(M) motif. By lowering the pH to 3.5, Cu(I) shifts from HH(M) to methionine-only coordination, an indication that only the pH-insensitive methionine motif is competent for metal binding at low pH. The easy interconversion of monovalent cations between different coordination modes was supported by DFT calculations

On the simulation of vibrationally resolved electronic spectra of medium-size molecules: the case of styryl substituted BODIPYs

BODIPY dyes are used in a variety of applications because of their peculiar spectroscopic and photo-physical properties that vary depending on the stereochemistry of the functional groups attached to the boron-dipyrromethene core structure. In this work, we have applied several computational methods, adapted for semi-rigid molecules based on the Franck-Condon principle, for the study of the optical properties of BODIPY systems and for the understanding of the influence of functional groups on their spectroscopic features. We have analyzed the electronic spectra of two styryl substituted BODIPY molecules of technological interest, properly taking into account the vibronic contribution. For comparison with recently recorded experimental data in methanol, the vibrationally resolved electronic spectra of these systems were computed using both Time-Independent (TI) and Time-Dependent (TD) formalisms. The first step toward the analysis of optical properties of the styryl modified BODIPYs was a benchmark of several density functionals, to select the most appropriate one. We have found that all benchmarked functionals provide good results in terms of band shape but some of them show strong discrepancies in terms of band position. Beyond the issue of the electronic structure calculation method, different levels of sophistication can be adopted for the calculation of vibronic transitions. In this study, the effect of mode couplings and the influence of the Herzberg-Teller terms on the theoretical spectra has been investigated. It has been found that all levels of theory considered give reproducible results for the investigated systems: band positions and shapes are similar at all levels and little improvements have been found in terms of band shape with the inclusion of Herzberg-Teller effect. Inclusion of temperature effects proved to be challenging due to the important impact of large amplitude motions. Better agreement can be achieved by adopting a suitable set of coordinates coupled with a reduced-dimensionality scheme

Assessment of interatomic parameters for the reproduction of borosilicate glass structures via DFT‐GIPAW calculations

Borates and borosilicates are potential candidates for the design and development of glass formulations with important industrial and technological applications. A major challenge that retards the pace of development of borate/borosilicate based glasses using predictive modeling is the lack of reliable computational models to predict the structure‐property relationships in these glasses over a wide compositional space. A major hindrance in this pursuit has been the complexity of boron‐oxygen bonding due to which it has been difficult to develop adequate B–O interatomic potentials. In this article, we have evaluated the performance of three B–O interatomic potential models recently developed by Bauchy et al [J. Non‐Cryst. Solids, 2018, 498, 294–304], Du et al [J. Am. Ceram. Soc. https://doi.org/10.1111/jace.16082] and Edèn et al [Phys. Chem. Chem. Phys., 2018, 20, 8192–8209] aiming to reproduce the short‐to‐medium range structures of sodium borosilicate glasses in the system 25 Na2O x B2O3 (75 − x) SiO2 (x = 0‐75 mol%). To evaluate the different force fields, we have computed at the density functional theory level the NMR parameters of 11B, 23Na, and 29Si of the models generated with the three potentials and the simulated MAS NMR spectra compared with the experimental counterparts. It was observed that the rigid ionic models proposed by Bauchy and Du can both reliably reproduce the partitioning between BO3 and BO4 species of the investigated glasses, along with the local environment around sodium in the glass structure. However, they do not accurately reproduce the second coordination sphere of silicon ions and the Si–O–T (T = Si, B) and B‐O‐T distribution angles in the investigated compositional space which strongly affect the NMR parameters and final spectral shape. On the other hand, the core‐shell parameterization model proposed by Edén underestimates the fraction of BO4 species of the glass with composition 25Na2O 18.4B2O3 56.6SiO2 but can accurately reproduce the shape of the 11B and 29Si MAS‐NMR spectra of the glasses investigations due to the narrower B–O–T and Si‐O‐T bond angle distributions. Finally, the effect of the number of boron atoms (also distinguishing the BO3 and BO4 units) in the second coordination sphere of the network former cations on the NMR parameters have been evaluated

Synthesis and characterization of polymethine dyes carrying thiobarbituric and carboxylic acid moieties

International audienceAn efficient synthesis of polymethine dyes carrying thiobarbituric and a carboxylic acid moiety has been developed. Such compounds play a key role in many photometric detections and quantifications of enzyme activities. In such tests, the metabolite of the enzyme activities is transformed into a β-dicarbonyl derivative. In the present study, this compound was prepared from furfural through organic synthesis. Its in situ transformation with thiobarbituric acid derivatives yields the target compounds on a gram-scale (0.4 to 0.6 g). A combined experimental and theoretical study of the photophysical properties of the synthesized compounds was carried out. Absorption and emission spectroscopy measurements highlighted a slight solvatochromism effect. The luminescence was quenched by molecular oxygen, indicating the partial triplet multiplicity character of the lowest excited state. Density Functional Theory (DFT) calculations have been applied for the evaluation of favoured conformations for these new compounds and the study of their optical properties. Within the Franck Condon principle, vibrationally resolved electronic one-photon absorption spectrum has been simulated. This simulation shows the presence of a major band followed by a vibronic sideband, typical of organic chromophores in solution. The performed computational study revealed that the transition from the ground to the first excited electronic state has a π-π* character. Finally, TD-DFT energy level diagram calculations highlighted the presence of triplet states very close to the first singlet excited one, suggesting probable access to the triplet-excited state

Two-Dimensional Electronic Spectroscopy Reveals Dynamics and Mechanisms of Solvent-Driven Inertial Relaxation in Polar BODIPY Dyes

In this work, we demonstrate the use of two-dimensional electronic spectroscopy (2DES) to study the mechanism and time scale of the femtosecond Stokes shift dynamics in molecules characterized by intramolecular charge transfer, such as distyryl-functionalized boron dipyrromethene (BODIPY) molecules. The obtained results demonstrate that 2DES allows clear and direct visualization of the phenomenon. The analysis of the 2D data in terms of 2D frequency-frequency decay associated maps provides indeed not only the time scale of the relaxation process but also the starting and the final point of the energy flow and the associated reorganization energy, identified by looking at the coordinates of a negative signature below the diagonal. The sensitivity of the 2DES technique to vibrational coherence dynamics also allowed the identification of a possible relaxation mechanism involving specific interaction between a vibrational mode of the dye and the solvent