Triterpene Derivatives as Potential Inhibitors of the RBD Spike Protein from SARS-CoV-2: An In Silico Approach.

The appearance of a new coronavirus, SARS-CoV-2, in 2019 kicked off an international public health emergency. Although rapid progress in vaccination has reduced the number of deaths, the development of alternative treatments to overcome the disease is still necessary. It is known that the infection begins with the interaction of the spike glycoprotein (at the virus surface) and the angiotensin-converting enzyme 2 cell receptor (ACE2). Therefore, a straightforward solution for promoting virus inhibition seems to be the search for molecules capable of abolishing such attachment. In this work, we tested 18 triterpene derivatives as potential inhibitors of SARS-CoV-2 against the receptor-binding domain (RBD) of the spike protein by means of molecular docking and molecular dynamics simulations, modeling the RBD S1 subunit from the X-ray structure of the RBD-ACE2 complex (PDB ID: 6M0J). Molecular docking revealed that at least three triterpene derivatives of each type (i.e., oleanolic, moronic and ursolic) present similar interaction energies as the reference molecule, i.e., glycyrrhizic acid. Molecular dynamics suggest that two compounds from oleanolic and ursolic acid, OA5 and UA2, can induce conformational changes capable of disrupting the RBD-ACE2 interaction. Finally, physicochemical and pharmacokinetic properties simulations revealed favorable biological activity as antivirals.

Electronic structure and interfacial features of triphenylamine- and phenothiazine-based hole transport materials for methylammonium lead iodide perovskite solar cells.

Recently, great research efforts have been devoted to perovskite solar cells (PSCs) leading to sunlight-to-power conversion efficiencies above 25%. However, several barriers still hinder the full deployment of these devices. Critical issues are related to PCE stability and device lifetimes, which could be improved by targeted engineering of the hole transport material (HTM). Indeed, the HTM is not only responsible for transporting holes and preventing direct contact between the photo-active perovskite and the charge collector layer, but it plays important structural and protective roles too. As alternatives to the widely used yet expensive and unstable Spiro-OMeTAD, organic HTMs based on triphenylamine (TPA) and phenothiazine (PTZ) moieties have been proposed. However, their performances in PSC devices, and in particular their interfacial properties with the most popular methylammonium lead iodide perovskite (MAPI) still need investigations to be fully determined. In this framework, here we report a first-principles study on the structural and the electronic properties of a recently designed TPA and PTZ-based HTM (HTM1) and its interface with the MAPI (001) surface, considering both the PbI2- and the MAI-terminations. We also addressed already known HTM molecular systems to allow for a direct comparison with the recently proposed HTM1: we characterized the molecular parameters and the MAPI/HTM interfacial properties for Spiro-OMeTAD, PTZ1, and PTZ2. Our results suggest that good adhesion properties do not ensure effective and efficient MAPI-HTM hole injection. Despite the theoretical good alignment between HTM1 HOMO and MAPI valence band edge, our results for the mutually polarized interface point out the lack of a sufficient driving force for hole transport. While the hole mobility of HTM1 outperforms those of the other HTM molecules, for this HTM molecule, our findings suggest the application of lead halide perovskite compositions other than MAPI, with substituents that lower its valence band maximum potential value.

Synthesis and Characterization of New Organic Dyes Containing the Indigo Core.

A new series of symmetrical organic dyes containing an indigo central core decorated with different electron donor groups have been prepared, starting from Tyrian Purple and using the Pd-catalyzed Stille-Migita coupling process. The effect of substituents on the spectroscopic properties of the dyes has been investigated theoretically and experimentally. In general, all dyes presented intense light absorption bands, both in the blue and red regions of the visible spectrum, conferring them a bright green color in solution. Using the same approach, an asymmetrically substituted D-A-π-A green dye, bearing a triarylamine electron donor and the cyanoacrylate acceptor/anchoring group, has been synthesized for the first time and fully characterized, confirming that spectroscopic and electrochemical properties are consistent with a possible application in dye-sensitized solar cells (DSSC).

Fibrils of α-Synuclein Abolish the Affinity of Cu2+-Binding Site to His50 and Induce Hopping of Cu2+ Ions in the Termini.

The effect of Cu2+ on α-synuclein (AS) aggregation is important because clinical studies of patients with Parkinson's disease have shown elevated levels of Cu2+ in the cerebrospinal fluid. So far, the molecular architectures of Cu2+-AS fibril complexes at atomic resolution are unknown. The current work identifies for the first time that His50 cannot bind Cu2+ ions in mature fibrils. Moreover, it shows hopping of Cu2+ ions between residues in AS fibrils and changes in the Cu2+ coordination mode in Cu2+ ions that bind in the termini of AS. The current study combines extensive experimental techniques, density functional theory calculations, and computational modeling tools to provide a complete description of the Cu2+ binding site in AS fibrils. Our findings illustrate for the first time the specific interactions between Cu2+ ions and AS fibrils, suggesting a new mechanistic perspective on the effect of Cu2+ ions on AS aggregation.

Photoinduced excitation and charge transfer processes of organic dyes with siloxane anchoring groups: a combined spectroscopic and computational study.

Dye-sensitized solar cells (DSSCs) have attracted significant interest in the last few years as effective low-cost devices for solar energy conversion. We have analyzed the excited state dynamics of several organic dyes bearing both cyanoacrylic acid and siloxane anchoring groups. The spectroscopic properties of the dyes have been studied both in solution and when adsorbed on a TiO2 film using stationary and time-resolved techniques, probing the sub-picosecond to nanosecond time interval. The comparison between the spectra registered in solution and on the solid substrate evidences different pathways for energy and electron relaxation. The transient spectra of the TiO2-adsorbed dyes show the appearance of a long wavelength excited state absorption band, attributed to the cationic dye species, which is absent in the spectra measured in solution. Furthermore, the kinetic traces of the samples adsorbed on the TiO2 film show a long decay component not present in solution which constitutes indirect evidence of electron transfer between the dye and the semiconductor. The interpretation of the experimental results has been supported by theoretical DFT calculations of the excited state energies and by the analysis of molecular orbitals of the analyzed dye molecules.

Tyrosine or Tryptophan? Modifying a Metalloradical Catalytic Site by Removal of the Cys-Tyr Cross-Link in the Galactose 6-Oxidase Homologue GlxA.

The concerted redox action of a metal ion and an organic cofactor is a unique way to maximize the catalytic power of an enzyme. An example of such synergy is the fungal galactose 6-oxidase, which has inspired the creation of biomimetic copper oxidation catalysts. Galactose 6-oxidase and its bacterial homologue, GlxA, possess a metalloradical catalytic site that contains a free radical on a covalently linked Cys-Tyr and a copper atom. Such a catalytic site enables for the two-electron oxidation of alcohols to aldehydes. When the ability to form the Cys-Tyr in GlxA is disrupted, a radical can still be formed. Surprisingly, the radical species is not the Tyr residue but rather a copper second-coordination sphere Trp residue. This is demonstrated through the introduction of a new algorithm for Trp-radical EPR spectra simulation. Our findings suggest a new mechanism of free-radical transfer between aromatic residues and that the Cys-Tyr cross-link prevents radical migration away from the catalytic site.

Spectroscopic and computational characterization of laccases and their substrate radical intermediates.

Laccases are multicopper oxidases which oxidize a wide variety of aromatic compounds with the concomitant reduction of oxygen to water as by-product. Due to their high stability and biochemical versatility, laccases are key enzymes to be used as eco-friendly biocatalyst in biotechnological applications. The presence of copper paramagnetic species in the catalytic site paired with the substrate radical species produced in the catalytic cycle makes laccases particularly attractive to be studied by spectroscopic approaches. In this review, the potentiality of a combined multifrequency electron paramagnetic spectroscopy /computational approach to gain information on the nature of the catalytic site and radical species is presented. The knowledge at molecular level of the enzyme oxidative process can be of great help to model new enzymes with increased efficiency and robustness.

Catalytic surface radical in dye-decolorizing peroxidase: a computational, spectroscopic and site-directed mutagenesis study.

Dye-decolorizing peroxidase (DyP) of Auricularia auricula-judae has been expressed in Escherichia coli as a representative of a new DyP family, and subjected to mutagenic, spectroscopic, crystallographic and computational studies. The crystal structure of DyP shows a buried haem cofactor, and surface tryptophan and tyrosine residues potentially involved in long-range electron transfer from bulky dyes. Simulations using PELE (Protein Energy Landscape Exploration) software provided several binding-energy optima for the anthraquinone-type RB19 (Reactive Blue 19) near the above aromatic residues and the haem access-channel. Subsequent QM/MM (quantum mechanics/molecular mechanics) calculations showed a higher tendency of Trp-377 than other exposed haem-neighbouring residues to harbour a catalytic protein radical, and identified the electron-transfer pathway. The existence of such a radical in H2O2-activated DyP was shown by low-temperature EPR, being identified as a mixed tryptophanyl/tyrosyl radical in multifrequency experiments. The signal was dominated by the Trp-377 neutral radical contribution, which disappeared in the W377S variant, and included a tyrosyl contribution assigned to Tyr-337 after analysing the W377S spectra. Kinetics of substrate oxidation by DyP suggests the existence of high- and low-turnover sites. The high-turnover site for oxidation of RB19 (k(cat) > 200 s⁻¹) and other DyP substrates was assigned to Trp-377 since it was absent from the W377S variant. The low-turnover site/s (RB19 k(cat) ~20 s⁻¹) could correspond to the haem access-channel, since activity was decreased when the haem channel was occluded by the G169L mutation. If a tyrosine residue is also involved, it will be different from Tyr-337 since all activities are largely unaffected in the Y337S variant.

Copper-induced structural propensities of the amyloidogenic region of human prion protein.

Transmissible spongiform encephalopathies are associated with the misfolding of the cellular Prion Protein (PrP(C)) to an abnormal protein isoform, called scrapie prion protein (PrP(Sc)). The structural rearrangement of the fragment of N-terminal domain of the protein spanning residues 91-127 is critical for the observed structural transition. The amyloidogenic domain of the protein encloses two copper-binding sites corresponding to His-96 and His-111 residues that act as anchors for metal ion binding. Previous studies have shown that Cu(II) sequestration by both sites may modulate the peptide's tendency to aggregation as it inflicts the hairpin-like structure that stabilizes the transition states leading to ß-sheet formation. On the other hand, since both His sites differ in their ability to Cu(II) sequestration, with His-111 as a preferred binding site, we found it interesting to test the role of Cu(II) coordination to this single site on the structural properties of amyloidogenic domain. The obtained results reveal that copper binding to His-111 site imposes precise backbone bending and weakens the natural tendency of apo peptide to ß-sheet formation.

Formation of a tyrosine adduct involved in lignin degradation by Trametopsis cervina lignin peroxidase: a novel peroxidase activation mechanism.

LiP (lignin peroxidase) from Trametopsis cervina has an exposed catalytic tyrosine residue (Tyr181) instead of the tryptophan conserved in other lignin-degrading peroxidases. Pristine LiP showed a lag period in VA (veratryl alcohol) oxidation. However, VA-LiP (LiP after treatment with H2O2 and VA) lacked this lag, and H2O2-LiP (H2O2-treated LiP) was inactive. MS analyses revealed that VA-LiP includes one VA molecule covalently bound to the side chain of Tyr181, whereas H2O2-LiP contains a hydroxylated Tyr181. No adduct is formed in the Y171N variant. Molecular docking showed that VA binding is favoured by sandwich π stacking with Tyr181 and Phe89. EPR spectroscopy after peroxide activation of the pre-treated LiPs showed protein radicals other than the tyrosine radical found in pristine LiP, which were assigned to a tyrosine-VA adduct radical in VA-LiP and a dihydroxyphenyalanine radical in H2O2-LiP. Both radicals are able to oxidize large low-redox-potential substrates, but H2O2-LiP is unable to oxidize high-redox-potential substrates. Transient-state kinetics showed that the tyrosine-VA adduct strongly promotes (>100-fold) substrate oxidation by compound II, the rate-limiting step in catalysis. The novel activation mechanism is involved in ligninolysis, as demonstrated using lignin model substrates. The present paper is the first report on autocatalytic modification, resulting in functional alteration, among class II peroxidases.

Exploring the Antioxidant and Anti-Inflammatory Potential of Saffron (Crocus sativus) Tepals Extract within the Circular Bioeconomy.

Repurposing saffron (Crocus sativus) waste presents a sustainable strategy for generating high-value products within the bioeconomy framework. Typically, flower components are discarded after stigma harvest, resulting in significant waste-350 kg of tepals per kilogram of stigmas. This research employed a comprehensive approach, integrating bioactivity studies (in vitro and in silico) with Life Cycle Assessment (LCA) evaluations, to extract and assess bioactive compounds from C. sativus tepals sourced in Tuscany, Italy. Phytochemical characterization using UPLC-MS/MS revealed a high abundance and variety of flavonoids in the hydro-ethanolic extract (CST). The antioxidant capacity was validated through various assays, and the ability to mitigate H2O2-induced oxidative stress and enhance fermentation was demonstrated in Saccharomyces cerevisiae. This study reports that C. sativus tepals extract reduces oxidative stress and boosts ethanol fermentation in yeast, paving the way for applications in the food and biofuels sectors. Further validation in RAW 264.7 macrophages confirmed CST's significant anti-inflammatory effects, indicating its potential for pharmaceutical, cosmeceutical, and nutraceutical applications. In silico studies identified potential targets involved in antioxidant and anti-inflammatory processes, shedding light on possible interaction mechanisms with Kaempferol 3-O-sophoroside (KOS-3), the predominant compound in the extract. The integration of LCA studies highlighted the environmental benefits of this approach. Overall, this research underscores the value of using waste-derived extracts through "green" methodologies, offering a model that may provide significant advantages for further evaluations compared to traditional methodologies and supporting the circular bioeconomy.

Effects of the protein environment on the spectral properties of tryptophan radicals in Pseudomonas aeruginosa azurin.

Many biological electron-transfer reactions involve short-lived tryptophan radicals as key reactive intermediates. While these species are difficult to investigate, the recent photogeneration of a long-lived neutral tryptophan radical in two Pseudomonas aeruginosa azurin mutants (Az48W and ReAz108W) made it possible to characterize the electronic, vibrational, and magnetic properties of such species and their sensitivity to the molecular environment. Indeed, in Az48W the radical is embedded in the hydrophobic core while, in ReAz108W it is solvent-exposed. Here we use density functional theory and multiconfigurational perturbation theory to construct quantum-mechanics/molecular-mechanics models of Az48W(•) and ReAz108W(•) capable of reproducing specific features of their observed UV-vis, resonance Raman, and electron paramagnetic resonance spectra. The results show that the models can correctly replicate the spectral changes imposed by the two contrasting hydrophobic and hydrophilic environments. Most importantly, the same models can be employed to disentangle the molecular-level interactions responsible for such changes. It is found that the control of the hydrogen bonding between the tryptophan radical and a single specific surface water molecule in ReAz108W(•) represents an effective means of spectral modulation. Similarly, a specific electrostatic interaction between the radical moiety and a Val residue is found to control the Az48W(•) excitation energy. These modulations appear to be mediated by the increase in nitrogen negative charge (and consequent increase in hydrogen bonding) of the spectroscopic D2 state with respect to the D0 state of the chromophore. Finally, the same protein models are used to predict the relaxed Az48W(•) and ReAz108W(•) D2 structures, showing that the effect of the environment on the corresponding fluorescence maxima must parallel that of D0 absorption spectra.

Orange/Red Benzo[1,2-b:4,5-b']dithiophene 1,1,5,5-Tetraoxide-Based Emitters for Luminescent Solar Concentrators: Effect of Structures on Fluorescence Properties and Device Performances.

Luminescent solar concentrators (LSCs) are a class of optical devices able to harvest, downshift, and concentrate sunlight, thanks to the presence of emitting materials embedded in a polymer matrix. Use of LSCs in combination with silicon-based photovoltaic (PV) devices has been proposed as a viable strategy to enhance their ability to harvest diffuse light and facilitate their integration in the built environment. LSC performances can be improved by employing organic fluorophores with strong light absorption in the center of the solar spectrum and intense, red-shifted emission. In this work, we present the design, synthesis, characterization, and application in LSCs of a series of orange/red organic emitters featuring a benzo[1,2-b:4,5-b']dithiophene 1,1,5,5-tetraoxide central core as an acceptor (A) unit. The latter was connected to different donor (D) and acceptor (A') moieties by means of Pd-catalyzed direct arylation reactions, yielding compounds with either symmetric (D-A-D) or non-symmetric (D-A-A') structures. We found that upon light absorption, the compounds attained excited states with a strong intramolecular charge-transfer character, whose evolution was greatly influenced by the nature of the substituents. In general, symmetric structures showed better photophysical properties for the application in LSCs than their non-symmetric counterparts, and using a donor group of moderate strength such as triphenylamine was found preferable. The best LSC built with these compounds presented photonic (external quantum efficiency of 8.4 ± 0.1%) and PV (device efficiency of 0.94 ± 0.06%) performances close to the state-of-the-art, coupled with a sufficient stability in accelerated aging tests.

The nature of tryptophan radicals involved in the long-range electron transfer of lignin peroxidase and lignin peroxidase-like systems: Insights from quantum mechanical/molecular mechanics simulations.

A catalytically active tryptophan radical has been demonstrated to be involved in the long-range electron transfer to the heme cofactor of lignin peroxidase (LiP) from Phanerochaete chrysosporium although no direct detection by EPR spectroscopy of the tryptophan radical intermediate has been reported to date. An engineering-based approach has been used to manipulate the microenvironment of the redox-active tryptophan site in LiP and Coprinus cinereus Peroxidase (CiP), allowing the direct evidence of the tryptophan radical species. In light of the newly available EPR experimental data, we performed a quantum mechanical/molecular mechanics computational study to characterize the tryptophan radicals in the above protein matrices as well as in pristine LiP. The nature of the tryptophan radicals is discussed together with the analysis of their environment with the aim of understanding the different behavior of pristine LiP in comparison with that of LiP and CiP variants.

EPR parameters of amino acid radicals in P. eryngii versatile peroxidase and its W164Y variant computed at the QM/MM level.

Quantum mechanics/molecular mechanics (QM/MM) methods, employing density functional theory (DFT), have been used to compute the electron paramagnetic resonance (EPR) parameters of tryptophan and tyrosyl radical intermediates involved in the catalytic cycle of Pleurotus eryngii versatile peroxidase (VP) and its W164Y variant, respectively. These radicals have been previously experimentally detected and characterized both in the two-electron and one-electron activated forms of the enzymes. In this work, the well-studied W164 radical in VP has been chosen for calibration purposes because its spectroscopic properties have been extensively studied by multifrequency EPR and ENDOR spectroscopies. Using a B3LYP/CHARMM procedure, appropriately accounting for electrostatic, such as hydrogen bonding, and steric environmental interactions, a good agreement between the calculated and measured EPR parameters for both radicals has been achieved; g-tensors, hyperfine coupling constants (hfcc) and Mulliken spin densities have been correlated to changes in geometries, hydrogen bond networks and electrostatic environment, with the aim of understanding the influence of the protein surroundings on EPR properties. In addition, the present calculations demonstrate, for VP, the formation of a neutral tryptophan radical, hydrogen bonded to the nearby E243, via a stepwise electron and proton transfer with earlier involvement of a short-lived tryptophan cationic species. Instead, for W164Y, the QM/MM dynamics simulation shows that the tyrosine oxidation proceeds via a concerted electron and proton transfer and is accompanied by a significant reorganization of residues and water molecules surrounding the tyrosyl radical.

An artificial molecular switch that mimics the visual pigment and completes its photocycle in picoseconds.

Single molecules that act as light-energy transducers (e.g., converting the energy of a photon into atomic-level mechanical motion) are examples of minimal molecular devices. Here, we focus on a molecular switch designed by merging a conformationally locked diarylidene skeleton with a retinal-like Schiff base and capable of mimicking, in solution, different aspects of the transduction of the visual pigment Rhodopsin. Complementary ab initio multiconfigurational quantum chemistry-based computations and time-resolved spectroscopy are used to follow the light-induced isomerization of the switch in methanol. The results show that, similar to rhodopsin, the isomerization occurs on a 0.3-ps time scale and is followed by <10-ps cooling and solvation. The entire (2-photon-powered) switch cycle was traced by following the evolution of its infrared spectrum. These measurements indicate that a full cycle can be completed within 20 ps.

The critical issue of using lead for sustainable massive production of perovskite solar cells: a review of relevant literature.

This work aims to review the most significant studies dealing with the environmental issues of the use of lead in perovskite solar cells (PSCs). A careful discussion and rationalization of the environmental and human health toxicity impacts, evaluated by life cycle assessment and risk assessment studies, is presented. The results of this analysis are prospectively related to the possible future massive production of PSC technology.

Modeling, preparation, and characterization of a dipole moment switch driven by Z/E photoisomerization.

We report the results of a multidisciplinary research effort where the methods of computational photochemistry and retrosynthetic analysis/synthesis have contributed to the preparation of a novel N-alkylated indanylidene-pyrroline Schiff base featuring an exocyclic double bond and a permanent zwitterionic head. We show that, due to its large dipole moment and efficient photoisomerization, such a system may constitute the prototype of a novel generation of electrostatic switches achieving a reversible light-induced dipole moment change on the order of 30 D. The modeling of a peptide fragment incorporating the zwitterionic head into a conformationally rigid side chain shows that the switch can effectively modulate the fluorescence of a tryptophan probe.

Environmental and economic optima of solar home systems design: A combined LCA and LCC approach.

This paper compares the economic and environmental optimal design of Solar Home Systems (SHSs) and explores the role of economic incentives (such as tariffs and technology costs) in approximating the two optima. To achieve that, we present a methodology for the environmental and economic evaluation of grid-connected SHSs: user-scale electric systems involving a photovoltaic (PV) power system and a battery energy storage system. The proposed methodology is based on a mixed integer linear programming (MILP) optimization, life cycle assessment and life cycle costing. This methodological framework is applied to a case study involving a typical SHS installation in Italy. The results of the environmental optimal design brought to the evaluation of a 3.25 kW PV assisted by 8.66 kWh of nickel cobalt manganese batteries, whereas the costs of the SHS are minimized by a small PV system (less than 1 kW). Results underline that the environmental optimal configurations rely on battery technologies, which entails a significant cost compared to the grid connection. In contrast, the economic optimal design solutions is less impactful than the grid mix both from an environmental and economic points of view. Thanks to a reduction of batteries and PV costs, the environmental impact of the economic optimal design is expected to decrease in the future.

Life Cycle Inventories datasets for future European electricity mix scenarios.

Datasets concerning the European electricity mix, built employing the Ecoinvent database v.3.3 processes, are reported in this paper. Foreseen future scenarios are modelled based on acknowledged projections for energy market in Europe in 2050. These electricity mix data inventories could be useful for any academic or stakeholder interested in performing long-term prospective assessment of innovative generation technologies in the future European energy market.