Exploring the Esterase Catalytic Activity of Minimalist Heptapeptide Amyloid Fibers.

This paper investigates the esterase activity of minimalist amyloid fibers composed of short seven-residue peptides, IHIHIHI (IH7) and IHIHIQI (IH7Q), with a particular focus on the role of the sixth residue position within the peptide sequence. Through computational simulations and analyses, we explore the molecular mechanisms underlying catalysis in these amyloid-based enzymes. Contrary to initial hypotheses, our study reveals that the twist angle of the fiber, and thus the catalytic site's environment, is not notably affected by the sixth residue. Instead, the sixth residue interacts with the p-nitrophenylacetate (pNPA) substrate, particularly through its -NO2 group, potentially enhancing catalysis. Quantum mechanics/molecular mechanics (QM/MM) simulations of the reaction mechanism suggest that the polarizing effect of glutamine enhances catalytic activity by forming a stabilizing network of hydrogen bonds with pNPA, leading to lower energy barriers and a more exergonic reaction. Our findings provide valuable insights into the intricate interplay between peptide sequence, structural arrangement, and catalytic function in amyloid-based enzymes, offering potentially valuable information for the design and optimization of biomimetic catalysts.

Tripodal BODIPY-Tagged and Functional Molecular Probes: Synthesis, Computational Investigations and Explorations by Multiphoton Fluorescence Lifetime Imaging Microscopy.

A range of novel BODIPY derivatives with a tripodal aromatic core was synthesized and characterized spectroscopically. These new fluorophores showed promising features as probes for in vitro assays in live cells and offer strategic routes for further functionalization towards hybrid nanomaterials. Incorporation of biotin tags facilitated proof-of-concept access to targeted bioconjugates as molecular probes. Computational explorations using DFT and TD-DFT calculations identified the most stable tripodal linker conformations and predicted their absorption and emission behavior. The uptake and speciation of these molecules in living prostate cancer cells was imaged by single- and two-photon excitation techniques coupled with two-photon fluorescence lifetime imaging (2P FLIM).

Computational Study of Amyloidß42 Familial Mutations and Metal Interaction: Impact on Monomers and Aggregates Dynamical Behaviors.

One of the main hallmarks of Alzheimer's Disease is the formation of ß-amyloid plaques, whose formation may be enhanced by metal binding or the appearance of familial mutations. In the present study, the simultaneous effect of familial mutations (E22Q, E22G, E22K, and D23N) and binding to metal ions (Cu(II) or Al(III)) is studied at the Aß42 monomeric and fibrillar levels. With the application of GaMD and MD simulations, it is observed that the effects of metal binding and mutations differ in the monomeric and fibrillar forms. In the monomeric structures, without metal binding, all mutations reduce the amount of α-helix and increase, in some cases, the ß-sheet content. In the presence of Cu(II) and Al(III) metal ions, the peptide becomes less flexible, and the ß-sheet content decreases in favor of forming α-helix motifs that stabilize the system through interhelical contacts. Regarding the fibrillar structures, mutations decrease the opening of the fiber in the vertical axis, thereby stabilizing the S-shaped structure of the fiber. This effect is, in general, enhanced upon metal binding. These results may explain the different Aß42 aggregation patterns observed in familial mutations.

Conformationally Restricted ß-Sheet Breaker Peptides Incorporating Cyclic α-Methylisoserine Sulfamidates.

Peptides containing variations of the ß-amyloid hydrophobic core and five-membered sulfamidates derived from ß-amino acid α-methylisoserine have been synthesized and fully characterized in the gas phase, solid state and in aqueous solution by a combination of experimental and computational techniques. The cyclic sulfamidate group effectively locks the secondary structure at the N-terminus of such hybrid peptides imposing a conformational restriction and stabilizing non-extended structures. This conformational bias, which is maintained in the gas phase, solid state and aqueous solution, is shown to be resistant to structure templating through assays of in vitro ß-amyloid aggregation, acting as ß-sheet breaker peptides with moderate activity.

On the stability of peptide secondary structures on the TiO2 (101) anatase surface: a computational insight.

The biological activity of proteins is partly due to their secondary structures and conformational states. Peptide chains are rather flexible so that finding ways inducing protein folding in a well-defined state is of great importance. Among the different constraint techniques, the interaction of proteins with inorganic surfaces is a fruitful strategy to stabilize selected folded states. Surface-induced peptide folding can have potential applications in different biomedicine areas, but it can also be of fundamental interest in prebiotic chemistry since the biological activity of a peptide can turn-on when folded in a given state. In this work, periodic quantum mechanical simulations (including implicit solvation effects) at the PBE-D2* level have been carried out to study the adsorption and the stability of the secondary structures (α-helix and ß-sheet) of polypeptides with different chemical composition (i.e., polyglycine, polyalanine, polyglutamic acid, polylysine, and polyarginine) on the TiO2 (101) anatase surface. The computational cost is reduced by applying periodic boundary conditions to both the surface and the peptides, thus obtaining full periodic polypeptide/TiO2 surface systems. At variance with polyglycine, the interaction of the other polypeptides with the surface takes place with the lateral chain functionalities, leaving the secondary structures almost undistorted. Results indicate that the preferred conformation upon adsorption is the α-helix over the ß-sheet, with the exception of the polyglutamic acid. According to the calculated adsorption energies, the affinity trend of the polypeptides with the (101) anatase surface is: polyarginine ≈ polylysine > polyglutamic acid > polyglycine ≈ polyalanine, both when adsorbed in gas phase and in presence of the implicit water solvent, which is very similar to the trend for the single amino acids. A set of implications related to the areas of surface-induced peptide folding, biomedicine and prebiotic chemistry are finally discussed.

First-Principles Modeling of Protein/Surface Interactions. Polyglycine Secondary Structure Adsorption on the TiO2 (101) Anatase Surface Adopting a Full Periodic Approach.

Computational modeling of protein/surface systems is challenging since the conformational variations of the protein and its interactions with the surface need to be considered at once. Adoption of first-principles methods to this purpose is overwhelming and computationally extremely expensive so that, in many cases, dramatically simplified systems (e.g., small peptides or amino acids) are used at the expenses of modeling nonrealistic systems. In this work, we propose a cost-effective strategy for the modeling of peptide/surface interactions at a full quantum mechanical level, taking the adsorption of polyglycine on the TiO2 (101) anatase surface as a test case. Our approach is based on applying the periodic boundary conditions for both the surface model and the polyglycine peptide, giving rise to full periodic polyglycine/TiO2 surface systems. By proceeding this way, the considered complexes are modeled with a drastically reduced number of atoms compared with the finite-analogous systems, modeling the polypeptide structures at the same time in a realistic way. Within our modeling approach, full periodic density functional theory calculations (including implicit solvation effects) and ab initio molecular dynamics (AIMD) simulations at the PBE-D2* theory level have been carried out to investigate the adsorption and relative stability of the different polyglycine structures (i.e., extended primary, ß-sheet, and α-helix) on the TiO2 surface. It has been found that, upon adsorption, secondary structures become partially denatured because the peptide C═O groups form Ti-O═C dative bonds. AIMD simulations have been fundamental to identify these phenomena because thermal and entropic effects are of paramount importance. Irrespective of the simulated environments (gas phase and implicit solvent), adsorption of the α-helix is more favorable than that of the ß-sheet because in the former, more Ti-O═C bonds are formed and the adsorbed secondary structure results less distorted with respect to the isolated state. Under the implicit water solvent, additionally, adsorbed ß-sheet structures weaken with respect to their isolated states as the H-bonds between the strands are longer due to solvation effects. Accordingly, the results indicate that the preferred conformation upon adsorption is the α-helix over the ß-sheet.

Impact of Cu(II) and Al(III) on the conformational landscape of amyloidß1-42.

Metal ions have been found to play an important role in the formation of extracellular ß-amyloid plaques, a major hallmark of Alzheimer's disease. In the present study, the conformational landscape of Aß42 with Al(iii) and Cu(ii) has been explored using Gaussian accelerated molecular dynamics. Both metals reduce the flexibility of the peptide and entail a higher structural organization, although to different degrees. As a general trend, Cu(ii) binding leads to an increased α-helix content and to the formation of two α-helices that tend to organize in a U-shape. By contrast, most Al(iii) complexes induce a decrease in helical content, leading to more extended structures that favor the appearance of transitory ß-strands.

Atomistic insights into the structure of heptapeptide nanofibers.

Artificial amyloid-like nanofibers formed from short peptides are emerging as new supramolecular structures for catalysis and advanced materials. In this work, we analyze, by means of computational approaches, the preferred atomistic fibrillar architectures that result from the self-assembly of polar NY7, NF7, SY7, SF7, and GY7 peptides into steric zippers formed by two ß-sheets (describing an individual steric zipper) and by four ß-sheets. For all heptapeptides, except GY7, parallel ß-sheet organizations with polar residues packed at the steric zipper appear to be the preferred assemblies for the two ß-sheets system due to the formation of a strong network of hydrogen bonds. For GY7, however, an antiparallel organization with glycine at the steric zipper is the most stable one. The preferred architecture is mostly conserved when enlarging our model from two to four ß-sheets. The present work shows that the relative stability of different architectures results from a delicate balance between peptide composition, side chain hydrophobicity, and non-covalent interactions at the interface and provides the basis for a rational design of new improved artificial prion-inspired materials.

Small molecule inhibits α-synuclein aggregation, disrupts amyloid fibrils, and prevents degeneration of dopaminergic neurons.

Parkinson's disease (PD) is characterized by a progressive loss of dopaminergic neurons, a process that current therapeutic approaches cannot prevent. In PD, the typical pathological hallmark is the accumulation of intracellular protein inclusions, known as Lewy bodies and Lewy neurites, which are mainly composed of α-synuclein. Here, we exploited a high-throughput screening methodology to identify a small molecule (SynuClean-D) able to inhibit α-synuclein aggregation. SynuClean-D significantly reduces the in vitro aggregation of wild-type α-synuclein and the familiar A30P and H50Q variants in a substoichiometric molar ratio. This compound prevents fibril propagation in protein-misfolding cyclic amplification assays and decreases the number of α-synuclein inclusions in human neuroglioma cells. Computational analysis suggests that SynuClean-D can bind to cavities in mature α-synuclein fibrils and, indeed, it displays a strong fibril disaggregation activity. The treatment with SynuClean-D of two PD Caenorhabditis elegans models, expressing α-synuclein either in muscle or in dopaminergic neurons, significantly reduces the toxicity exerted by α-synuclein. SynuClean-D-treated worms show decreased α-synuclein aggregation in muscle and a concomitant motility recovery. More importantly, this compound is able to rescue dopaminergic neurons from α-synuclein-induced degeneration. Overall, SynuClean-D appears to be a promising molecule for therapeutic intervention in Parkinson's disease.

Enhanced Metallophilicity in Metal-Carbene Systems: Stronger Character of Aurophilic Interactions in Solution.

Metallophilicity is an essential concept that builds upon the attraction between closed shell metal ions. We report on the [M2 (bisNHC)2 ]2+ (M=AuI , AgI ; NHC=N-heterocyclic carbene) systems, which display almost identical features in the solid state. However, in solution the Au2 cation exhibits a significantly higher degree of rigidity owed to the stronger character of the aurophilic interactions. Both Au2 and Ag2 cationic constructs are able to accommodate Ag+ ions via M-M interactions, despite their inherent Coulombic repulsion. When electrostatic repulsion between host and guest is partially diminished, M-M distances are substantially shortened. Quantum chemical calculations estimate intermetallic bond orders up to 0.2. Although at the limit of (or beyond) the van der Waals radii, metallophilic interactions are responsible for their behavior in solution.

Activating a Peroxo Ligand for C-O Bond Formation.

Dioxygen activation for effective C-O bond formation in the coordination sphere of a metal is a long-standing challenge in chemistry for which the design of catalysts for oxygenations is slowed down by the complicated, and sometimes poorly understood, mechanistic panorama. In this context, olefin-peroxide complexes could be valuable models for the study of such reactions. Herein, we showcase the isolation of rare "Ir(cod)(peroxide)" complexes (cod=1,5-cyclooctadiene) from reactions with oxygen, and then the activation of the peroxide ligand for O-O bond cleavage and C-O bond formation by transfer of a hydrogen atom through proton transfer/electron transfer reactions to give 2-iradaoxetane complexes and water. 2,4,6-Trimethylphenol, 1,4-hydroquinone, and 1,4-cyclohexadiene were used as hydrogen atom donors. These reactions can be key steps in the oxy-functionalization of olefins with oxygen, and they constitute a novel mechanistic pathway for iridium, whose full reaction profile is supported by DFT calculations.

When the Surface Matters: Prebiotic Peptide-Bond Formation on the TiO2 (101) Anatase Surface through Periodic DFT-D2 Simulations.

The mechanism of the peptide-bond formation between two glycine (Gly) molecules has been investigated by means of PBE-D2* and PBE0-D2* periodic simulations on the TiO2 (101) anatase surface. This is a process of great relevance both in fundamental prebiotic chemistry, as the reaction univocally belongs to one of the different organizational events that ultimately led to the emergence of life on Earth, as well as from an industrial perspective, since formation of amides is a key reaction for pharmaceutical companies. The efficiency of the surface catalytic sites is demonstrated by comparing the reactions in the gas phase and on the surface. At variance with the uncatalyzed gas-phase reaction, which involves a concerted nucleophilic attack and dehydration step, on the surface these two steps occur along a stepwise mechanism. The presence of surface Lewis and Brönsted sites exerts some catalytic effect by lowering the free energy barrier for the peptide-bond formation by about 6 kcal mol-1 compared to the gas-phase reaction. Moreover, the co-presence of molecules acting as proton-transfer assistants (i.e., H2 O and Gly) provide a more significant kinetic energy barrier decrease. The reaction on the surface is also favorable from a thermodynamic standpoint, involving very large and negative reaction energies. This is due to the fact that the anatase surface also acts as a dehydration agent during the condensation reaction, since the outermost coordinatively unsaturated Ti atoms strongly anchor the released water molecules. Our theoretical results provide a comprehensive atomistic interpretation of the experimental results of Martra et al. (Angew. Chem. Int. Ed. 2014, 53, 4671), in which polyglycine formation was obtained by successive feedings of Gly vapor on TiO2 surfaces in dry conditions and are, therefore, relevant in a prebiotic context envisaging dry and wet cycles occurring, at mineral surfaces, in a small pool.

Drastic Effect of the Peptide Sequence on the Copper-Binding Properties of Tripeptides and the Electrochemical Behaviour of Their Copper(II) Complexes.

The binding and electrochemical properties of the complexes CuII -HAH, CuII -HWH, CuII -Ac-HWH, CuII -HHW, and CuII -WHH have been studied by using NMR and UV/Vis spectroscopies, CV, and density functional calculations. The results obtained highlight the importance of the peptidic sequence on the coordination properties and, consequently, on the redox properties of their CuII complexes. For CuII -HAH and CuII -HWH, no cathodic processes are observed up to -1.2 V; that is, the complexes exhibit very high stability towards copper reduction. This behaviour is associated with the formation of very stable square-planar (5,5,6)-membered chelate rings (ATCUN motif), which enclose two deprotonated amides. In contrast, for non-ATCUN CuII -Ac-HWH, CuII -HHW complexes, simulations seem to indicate that only one deprotonated amide is enclosed in the coordination sphere. In these cases, the main electrochemical feature is a reductive irreversible one electron-transfer process from CuII to CuI , accompanied with structural changes of the metal coordination sphere and reprotonation of the amide. Finally, for CuII -WHH, two major species have been detected: one at low pH (<5), with no deprotonated amides, and another one at high pH (>10) with an ATCUN motif, both species coexisting at intermediate pH. The present study shows that the use of CV, using glassy carbon as a working electrode, is an ideal and rapid tool for the determination of the redox properties of CuII metallopeptides.

Intramolecular Photocycloaddition of 2(5 H)-Furanones to Temporarily Tethered Terminal Alkenes as a Stereoselective Source of Enantiomerically Pure Polyfunctionalyzed Cyclobutanes.

Allyloxymethyloxymethyl and 4-pentenoyloxymethyl substituents have been used as tethering groups to study the intramolecular [2 + 2] photocycloaddition of chiral 5-substituted 2(5 H)-furanones. The photoreactions proceed in good yield and provide the expected regio- and diastereoselective tricyclic compounds with complementary regioselectivity, which depends on whether the vinyl chain is attached to the furanone by an acetal or an ester linkage. Computational simulations agree with experimental observations and indicate that the origin of the different observed regioselectivity in the intramolecular photochemical reaction of lactones 5 and 6 arises from the relative stability of the initial conformers. The synthetic potential of the enantiomerically pure photoadducts is illustrated by preparing an all- cis 1,2,3-trisubstituted cyclobutane bearing fully orthogonally protected hydroxyl groups.

Fluorous l-Carbidopa Precursors: Highly Enantioselective Synthesis and Computational Prediction of Bioactivity.

New fluorous enantiopure (S)-α-aminated ß-keto esters were prepared through a highly enantioselective electrophilic α-amination step in the presence of europium triflate and (R,R)-phenyl-pybox. These compounds are precursors of fluorinated analogues of l-carbidopa, which is known to inhibit DOPA decarboxylase (DDC), a key protein in Parkinson's disease. Fluorination provides better stability for biological applications, which could possibly lead to DDC inhibitors better than l-carbidopa itself. Induced fit docking computational simulations performed on the new structures interacting with DDC highlight that for an efficient binding at the DDC site, at least one hydroxyl substituent must be present at the aromatic ring of the l-carbidopa analogues and show that the presence of fluorine can further fix the position of the ligand in the active site.

Visible-Light Photocatalytic Intramolecular Cyclopropane Ring Expansion.

Described herein is a new visible-light photocatalytic strategy for the synthesis of enantioenriched dihydrofurans and cyclopentenes by an intramolecular nitro cyclopropane ring expansion reaction. Mechanistic studies and DFT calculations are used to elucidate the key factors in this new ring expansion reaction, and the need for the nitro group on the cyclopropane.

Multiple Condensation Reactions Involving Pt(II) /Pd(II) -OH2 , Pt-NH3 , and Cytosine-NH2 Groups: New Twists in Cisplatin-Nucleobase Chemistry.

The coordination chemistry of the antitumor agent cisplatin and related complexes with DNA and its constituents, that is, the nucleobases, appears to be dominated by 1:1 and 1:2 adducts of the types cis-[Pta2 (nucleobase)X] and cis-[Pta2 (nucleobase)2 ] (a=NH3 or amine; a2 =diamine or diimine; X=Cl, OH or OH2 ). Here, we have studied the interactions of the putative 1:1 adducts cis-[Pta2 (1-MeC-N3)(OH2 )](2+) (with a=NH3 , a2 =2,2'-bpy (2,2'-bipyridine), 1-MeC=model nucleobase 1-methylcytosine) with additional cis-[Pt(NH3 )2 (OH2 )2 ](2+) or its kinetically superior analogues [Pd(en)(OH2 )2 ](2+) (en=ethylenediamine) and [Pd(2,2'-bpy)(OH2 )2 ](2+) . Depending upon the conditions applied different compounds of different nuclearity are formed. Without exception they represent condensation products of the components, containing µ-1-MeC-H , µ-OH(-) , as well as µ-NH2 (-) bridges. In the presence of Ag(+) ions, the isolated products in several cases display additionally Pt→Ag dative bonds. On the basis of the cytosine-containing structures established by X-ray crystallography, it is proposed that any of the feasible initial 1:1 nucleobase adducts of cisplatin could form dinuclear Pt complexes upon reaction with additional hydrolyzed cisplatin, thereby generating nucleobase adducts other than the presently established ones. Two findings appear to be of particular significance: First, hydrolyzed cisplatin can have a moderately accelerating effect on the formation of a secondary nucleobase product. Second, NH3 ligands of the cisplatin moiety can be converted into bridging amido ligands following condensation with the diaqua species of cisplatin.

Computational study on donor-acceptor optical markers for Alzheimer's disease: a game of charge transfer and electron delocalization.

According to the amyloid cascade hypothesis, amyloid-ß (Aß) deposition is a central event in the Alzheimer's disease and thus, detection of Aß deposits is crucial to monitor the progression of the pathology. Despite its low tissue penetration, fluorescence imaging may become an alternative technique for identifying these deposits because it is less toxic and less costly than positron emission tomography. Suitable dyes, however, should emit in the near infrared (NIR) region, cross the blood-brain barrier and target Aß aggregates. In this work, we use TD-DFT, AIMD simulations and protein energy landscape exploration (PELE) to analyze the photophysical properties of a family of donor-acceptor markers and their binding to amyloid fibrils. These markers are formed by N,N-dimethylaniline donor and propanedinitrile acceptor groups separated by a spacer consisting of one, two or three conjugated double bonds. The smallest compound has a low emission wavelength, can deactivate through a non-radiative process involving a conical intersection and binds weakly to Aß fibrils. In contrast, the largest dye is a suitable compound as it shows an emission wavelength in the NIR region, does not seem to relax through conical intersection processes and binds to Aß fibrils strongly entering hydrophobic voids. Analysis of electronic excitations shows that the transition has an important charge transfer character that increases with the length of the spacer, the π bridge being an active participant in the transition. Therefore, adding double bonds to the dye skeleton has two beneficial effects: (i) it increases the emission wavelength as it enlarges the π system and (ii) it increases the charge transfer character of the transition, which increases the red-shifting of the emission wavelength in polar solvents.

Coordination properties of a metal chelator clioquinol to Zn(2+) studied by static DFT and ab initio molecular dynamics.

Several lines of evidence supporting the role of metal ions in amyloid aggregation, one of the hallmarks of Alzheimer's disease (AD), have turned metal ion chelation into a promising therapeutic treatment. The design of efficient chelating ligands requires proper knowledge of the electronic and molecular structure of the complexes formed, including their hydration properties. Among various potential chelators, clioquinol (5-chloro-7-iodo-8-hydroxyquinoline, CQH) has been evaluated with relative success in in vitro experiments and even in phase 2 clinical trials. Clioquinol interacts with Zn(ii) to lead to a binary metal/ligand 1 : 2 stoichiometric complex in which the phenolic group of CQH is deprotonated, resulting in Zn(CQ)2 neutral complexes, to which additional water molecules may coordinate. In the present work, the coordinative properties of clioquinol in aqueous solution have been analyzed by means of static, minimal cluster based DFT calculations and explicit solvent ab initio molecular dynamics simulations. Results from static calculations accounting for solvent effects by means of polarized continuum models suggest that the preferred metal coordination environment is tetrahedral Zn(CQ)2, whereas ab initio molecular dynamics simulations point to quasi degenerate penta Zn(CQ)2(H2O) and hexa Zn(CQ)2(H2O)2 coordinated complexes. The possible reasons for these discrepant results are discussed.

Dioxygen activation in the Cu-amyloid ß complex.

We investigate, by means of density-functional theory, the binding of dioxygen to Cu(I)-amyloid ß (Aß), one of the first steps in the oxidation of ascorbate by dioxygen. Cu, Aß, ascorbate and dioxygen are all present in the synapse during neurodegeneration, when the above species can trigger an irreversible oxidative stress inducing the eventual death of neurons. The binding of dioxygen to Cu(I) is possible and its role in dioxygen activation of Cu ligands and of residues in the first coordination sphere is described in atomic detail. Dioxygen is activated when a micro-environment suitable for a square-planar Cu(2+) coordination is present and a negatively charged group like Asp 1 carboxylate takes part in the Cu coordination anti to O2.