Predicting retrosynthetic pathways using transformer-based models and a hyper-graph exploration strategy

We present an extension of our Molecular Transformer model combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention. The single-step retrosynthetic model sets a new state of the art for predicting reactants as well as reagents, solvents and catalysts for each retrosynthetic step. We introduce four metrics (coverage, class diversity, round-trip accuracy and Jensen–Shannon divergence) to evaluate the single-step retrosynthetic models, using the forward prediction and a reaction classification model always based on the transformer architecture. The hypergraph is constructed on the fly, and the nodes are filtered and further expanded based on a Bayesian-like probability. We critically assessed the end-to-end framework with several retrosynthesis examples from literature and academic exams. Overall, the frameworks have an excellent performance with few weaknesses related to the training data. The use of the introduced metrics opens up the possibility to optimize entire retrosynthetic frameworks by focusing on the performance of the single-step model only.

We present an extension of our Molecular Transformer model combined with a hyper-graph exploration strategy for automatic retrosynthesis route planning without human intervention.     

Exploring the self-assembly of dumbbell-shaped polyoxometalate hybrids,from molecular building units to nanostructured soft materials

The formation of hierarchical nanostructures using preformed dumbbell-like species made of covalent organic–inorganic polyoxometalate (POM)-based hybrids is herein described. In this system, the presence of charged subunits (POM, metal linkers, and counter ions) in the complex molecular architecture can drive their aggregation, which results from a competition between the solvation energy of the discrete species and intermolecular electrostatic interactions. We show that the nature of the POM and the charge of the metal linker are key parameters for the hierarchical nanoorganization. The experimental findings were corroborated with a computational investigation combining DFT and molecular dynamics simulation methods, which outlines the importance of solvation of the counter ion and POM/counter ion association in the aggregation process. The dumbbell-like species can also form gels, in the presence of a poorer solvent, displaying similar nanoorganization of the aggregates. We show that starting from the designed molecular building units whose internal charges can be controlled by redox trigger we can achieve their implementation into soft nanostructured materials through the control of their supramolecular organization.

The formation of hierarchical nanostructures using supramolecular dumbbell-like species made of organic–inorganic polyoxometalate-based hybrids is investigated by combination of SAXS and computational methods.     

Combining alkali metals and zinc to harness heterometallic cooperativity in cyclic ester ring-opening polymerisation

Heterometallic cooperativity is an emerging strategy to elevate polymerisation catalyst performance. Here, we report the first heterotrimetallic Na/Zn₂ and K/Zn₂ complexes supported by a ProPhenol ligand, which deliver “best of both” in cyclic ester ring-opening polymerisation, combining the outstanding activity (Na/K) and good control (Zn₂) of homometallic analogues. Detailed NMR studies and density-functional theory calculations suggest that the Na/Zn₂ and K/Zn₂ complexes retain their heterometallic structures in the solution-state. To the best of our knowledge, the K/Zn₂ analogue is the most active heterometallic catalyst reported for rac-lactide polymerisation (k_obs = 1.7 × 10⁻² s⁻¹), giving activities five times faster than the Na/Zn₂ complex. These versatile catalysts also display outstanding performance in ε-caprolatone and δ-valerolactone ring-opening polymerisation. These studies provide underpinning methodologies for future heterometallic polymerisation catalyst design, both in cyclic ester polymerisation and other ring-opening (co)polymerisation reactions.

Cooperative heterotrimetallic Na/Zn₂ and K/Zn₂ complexes combine the excellent activities and control of the homometallic analogues, giving “best of both” in cyclic ester ring-opening polymerisation.     

Structures and Stability of Complexes of E(C6F5)3 (E = B,Al, Ga,In) with Acetonitrile

Complexes formed by interaction of E(C₆F₅)₃ (E = B, Al, Ga, In) with excess of acetonitrile (AN) were structurally characterized. Quantum chemical computations indicate that for Al(C₆F₅)₃ and In(C₆F₅)₃ the formation of a complex of 1:2 composition is more advantageous than for B(C₆F₅)₃ and Ga(C₆F₅)₃, in line with experimental observations. Formation of the solvate [Al(C₆F₅)₃ · 2AN] · AN is in agreement with predicted thermodynamic instability of [Al(C₆F₅)₃ · 3AN]. Tensimetry study of B(C₆F₅)₃ · CH₃CN reveals its stability in the solid state up to 197 °C. With the temperature increase, the complex undergoes irreversible thermal decomposition with pentafluorobenzene formation.     

Effects of Grape Polyphenols on the Life Span and Neuroinflammatory Alterations Related to Neurodegenerative Parkinson Disease-Like Disturbances in Mice

Functional nutrition is a valuable supplementation to dietary therapy. Functional foods are enriched with biologically active substances. Plant polyphenols attract particular attention due to multiple beneficial properties attributed to their high antioxidant and other biological activities. We assessed the effect of grape polyphenols on the life span of C57BL/6 mice and on behavioral and neuroinflammatory alterations in a transgenic mouse model of Parkinson disease (PD) with overexpression of the A53T-mutant human α-synuclein. C57BL/6 mice were given a dietary supplement containing grape polyphenol concentrate (GPC—1.5 mL/kg/day) with drinking water from the age of 6–8 weeks for life. Transgenic PD mice received GPC beginning at the age of 10 weeks for four months. GPC significantly influenced the cumulative proportion of surviving and substantially augmented the average life span in mice. In the transgenic PD model, the grape polyphenol (GP) diet enhanced memory reconsolidation and diminished memory extinction in a passive avoidance test. Behavioral effects of GP treatment were accompanied by a decrease in α-synuclein accumulation in the frontal cortex and a reduction in the expression of neuroinflammatory markers (IBA1 and CD54) in the frontal cortex and hippocampus. Thus, a GP-rich diet is recommended as promising functional nutrition for aging people and patients with neurodegenerative disorders.     

Photocatalytic Oxidation of HMF under Solar Irradiation: Coupling of Microemulsion and Lyophilization to Obtain Innovative TiO2-Based Materials

The photocatalytic oxidation of biomass-derived building blocks such as 5-hydroxymethylfurfural (HMF) is a promising reaction for obtaining valuable chemicals and the efficient long-term storage of solar radiation. In this work, we developed innovative TiO₂-based materials capable of base-free HMF photo-oxidation in water using simulated solar irradiation. The materials were prepared by combining microemulsion and spray-freeze drying (SFD), resulting in highly porous systems with a large surface area. The effect of titania/silica composition and the presence of gold-copper alloy nanoparticles on the properties of materials as well as photocatalytic performance were evaluated. Among the lab-synthesized photocatalysts, Ti₁₅Si₈₅ SFD and Au₃Cu₁/Ti₁₅Si₈₅ SFD achieved the higher conversions, while the best selectivity was observed for Au₃Cu₁/Ti₁₅Si₈₅ SFD. The tests with radical scavengers for both TiO₂-m and Au₃Cu₁/Ti₁₅Si₈₅ SFD suggested that primary species responsible for the selective photo-oxidation of HMF are photo-generated electrons and/or superoxide radicals.     

Comparative Study of the Chemical Compositions and Antioxidant Activities of Fresh Juices from Romanian Cucurbitaceae Varieties

Cucurbitaceae is a family of health-promoting plants due to their compounds with beneficial effects. The aim of this study was to analyze, for the first time, the chemical composition, the antioxidant activity and the metal chelating properties of fruit juices obtained from four different species of the Cucurbitaceae family cultivated in Romania, namely Momordica charantia, Cucumis metuliferus, Benincasa hispida and Trichosanthes cucumerina. The samples of juice were analyzed by high-performance liquid chromatography (HPLC) and all the four species displayed high levels of the two triterpenes, oleanolic and ursolic acids, and also in phenolic compounds, including catechin, (−)-epicatechin and gallic acid. The juices demonstrated significant antioxidant activity against the free radical 2,2-diphenyl-1-picrylhydrazyl (ranging from 20 to 95%,), a good iron binding ability (ranging from 7.45 ± 0.28% to 86.95 ± 0.97%) and also promising antioxidant potential against the ABTS radical (ranging from 4.97 to 32.60 μETx/mL juice). Our findings raise interesting questions for further research on Cucurbitaceae fruit juices and, consequently, their very good antioxidant potential suggests these fruits should be further explored for their protective effect against oxidative damage. This is the first time the chemical composition and antioxidant activities of fruit juices from these four Romanian Cucurbitaceae varieties have been investigated.     

Proteomic Profiling of the Human Fetal Multipotent Mesenchymal Stromal Cells Secretome

Secretome of multipotent mesenchymal stromal cells (MSCs) is actively used in biomedical applications such as alveolar bone regeneration, treatment of cardiovascular disease, and neurodegenerative disorders. Nevertheless, hMSCs have low proliferative potential and production of the industrial quantity of their secretome might be challenging. Human fetal multipotent mesenchymal stromal cells (FetMSCs) isolated from early human embryo bone marrow are easy to expand and might be a potential source for pharmaceutical substances production based on their secretome. However, the secretome of FetMSCs was not previously analyzed. Here, we describe the secretome of FetMSCs using LC-MALDI shotgun proteomics. We identified 236 proteins. Functional annotation of the identified proteins revealed their involvement in angiogenesis, ossification, regulation of apoptosis, and immune response processes, which made it promising for biomedical applications. The proteins identified in the FetMSCs secretome are involved in the same biological processes as proteins from previously described adult hMSCs secretomes. Nevertheless, many of the common hMSCs secretome components (such as VEGF, FGF, Wnt and TGF-β) have not been identified in the FetMSCs secretome.     

Natural Products Extracted from Fungal Species as New Potential Anti-Cancer Drugs: A Structure-Based Drug Repurposing Approach Targeting HDAC7

Mushrooms can be considered a valuable source of natural bioactive compounds with potential polypharmacological effects due to their proven antimicrobial, antiviral, antitumor, and antioxidant activities. In order to identify new potential anticancer compounds, an in-house chemical database of molecules extracted from both edible and non-edible fungal species was employed in a virtual screening against the isoform 7 of the Histone deacetylase (HDAC). This target is known to be implicated in different cancer processes, and in particular in both breast and ovarian tumors. In this work, we proposed the ibotenic acid as lead compound for the development of novel HDAC7 inhibitors, due to its antiproliferative activity in human breast cancer cells (MCF-7). These promising results represent the starting point for the discovery and the optimization of new HDAC7 inhibitors and highlight the interesting opportunity to apply the “drug repositioning” paradigm also to natural compounds deriving from mushrooms.     

Saffron: Chemical Composition and Neuroprotective Activity

Crocus sativus L. belongs to the Iridaceae family and it is commonly known as saffron. The different cultures together with the geoclimatic characteristics of the territory determine a different chemical composition that characterizes the final product. This is why a complete knowledge of this product is fundamental, from which more than 150 chemical compounds have been extracted from, but only about one third of them have been identified. The chemical composition of saffron has been studied in relation to its efficacy in coping with neurodegenerative retinal diseases. Accordingly, experimental results provide evidence of a strict correlation between chemical composition and neuroprotective capacity. We found that saffron’s ability to cope with retinal neurodegeneration is related to: (1) the presence of specific crocins and (2) the contribution of other saffron components. We summarize previous evidence and provide original data showing that results obtained both “in vivo” and “in vitro” lead to the same conclusion.