Combining Different Docking Engines and Consensus Strategies to Design and Validate Optimized Virtual Screening Protocols for the SARS-CoV-2 3CL Protease

The 3CL-Protease appears to be a very promising medicinal target to develop anti-SARS-CoV-2 agents. The availability of resolved structures allows structure-based computational approaches to be carried out even though the lack of known inhibitors prevents a proper validation of the performed simulations. The innovative idea of the study is to exploit known inhibitors of SARS-CoV 3CL-Pro as a training set to perform and validate multiple virtual screening campaigns. Docking simulations using four different programs (Fred, Glide, LiGen, and PLANTS) were performed investigating the role of both multiple binding modes (by binding space) and multiple isomers/states (by developing the corresponding isomeric space). The computed docking scores were used to develop consensus models, which allow an in-depth comparison of the resulting performances. On average, the reached performances revealed the different sensitivity to isomeric differences and multiple binding modes between the four docking engines. In detail, Glide and LiGen are the tools that best benefit from isomeric and binding space, respectively, while Fred is the most insensitive program. The obtained results emphasize the fruitful role of combining various docking tools to optimize the predictive performances. Taken together, the performed simulations allowed the rational development of highly performing virtual screening workflows, which could be further optimized by considering different 3CL-Pro structures and, more importantly, by including true SARS-CoV-2 3CL-Pro inhibitors (as learning set) when available.     

Impact of Matrix Metalloproteinase-9 during Periodontitis and Cardiovascular Diseases

Matrix metalloproteinase-9 (MMP-9) has been shown to play a key role in endothelial function and perhaps pivotal in the correlation between periodontal disease and cardiovascular disease (CVD). For the study, the impact of MMP-9 of periodontitis and CVD on serum and saliva concentrations was analyzed. For the study patients with periodontitis (n = 31), CVD (n = 31), periodontitis + CVD (n = 31), and healthy patients (n = 31) were enrolled. Clinical and demographic characteristics as well as serum and salivary MMP-9 were evaluated. MMP-9 concentrations in serum and saliva were statistically elevated in patients with CVD (p < 0.01) and in patients with periodontitis plus CVD (p < 0.001) compared to patients with periodontitis and healthy subjects. Multivariate regression analysis showed that c-reactive protein (hs-CRP) was the only significant predictor for MMP-9 serum (p < 0.001), whereas hs-CRP (p < 0.001) and total cholesterol (p = 0.029) were the statistically significant salivary MMP-9 predictors. This study evidenced that patients with CVD and periodontitis + CVD presented elevated MMP-9 concentrations in serum and saliva compared to patients with periodontitis and healthy subjects. Furthermore, hs-CRP was a negative predictor of serum and salivary MMP-9.     

Vegetable Extracts and Nutrients Useful in the Recovery from Helicobacter pylori Infection: A Systematic Review on Clinical Trials

Helicobacter pylori (H. pylori) infections affect almost half of the world’s population, with gradually increasing incidence in developed countries. Eradication of H. pylori may provide significant benefits to the affected individual by healing a number of gastrointestinal and extra-digestive disorders. But due to increased microbial resistance and lack of patient adherence to the therapy, the eradication rate of H. pylori is below 80% with current pharmacological therapies. The usage of botanicals for their therapeutic purposes and medicinal properties have been increased in last decades. They can be use as alternative H. pylori treatments, especially against drug-resistant strains. Epidemiological studies have revealed that people with lower vegetable and micronutrient intake may be at increased risk of H. pylori infection. We have undertaken a review of clinical trials to evaluate the efficacy of vegetable extracts and micronutrients in patients with H. pylori. Various databases, such as Google Scholar, PubMed, Scopus, Web of Science, and the Cochrane Library, were searched for the articles published in English. A total of 24 clinical studies (15 for vegetable extracts and 9 for micronutrients) were selected to be reviewed and summarized in this article. Vegetable extracts (Broccoli sprouts, curcumin, Burdock complex, and Nigella sativa) and micronutrients (vitamin C and E) were not found to be as effective as single agents in H. pylori eradication, rather their efficacy synergized with conventional pharmacological therapies. Conversely, GutGard was found to be significantly effective as a single agent when compared to placebo control.     

Pomegranate By-Products as Natural Preservative to Prolong the Shelf Life of Breaded Cod Stick

This work evaluated the efficacy of pomegranate byproducts, specifically peel powder, as valid preservatives for food quality. Ready-to-cook cod sticks breaded with pomegranate peel powder were prepared. Shelf-life tests were conducted on breaded cod sticks during refrigerated storage (17 days) at 4 °C, monitoring the pH, microbiological and sensory quality. In addition, the nutritional quality of both the breaded and control samples was assessed. The results highlighted that active samples showed higher phenol and flavonoid content and higher antioxidant activity compared to the control fish, suggesting that pomegranate peel powder was responsible for a significant increase in cod stick nutritional quality. Furthermore, the cod stick active breading led to a delay in microbial growth without affecting the sensory properties; rather, it helped slow down the sensory attribute decline during the refrigerated storage. The data suggest that using pomegranate byproducts in breaded cod stick was effective in prolonging its shelf life, as well as improving its nutritional quality. Therefore, pomegranate peel powder can be considered as a potential resource as natural food preservative.     

Monitoring of the Pre-Equilibrium Step in the Alkyne Hydration Reaction Catalyzed by Au(III) Complexes: A Computational Study Based on Experimental Evidences

The coordination ability of the [(ppy)Au(IPr)]²⁺ fragment [ppy = 2-phenylpyridine, IPr = 1,3-bis(2,6-di-isopropylphenyl)-imidazol-2-ylidene] towards different anionic and neutral X ligands (X = Cl⁻, BF₄⁻, OTf⁻, H₂O, 2-butyne, 3-hexyne) commonly involved in the crucial pre-equilibrium step of the alkyne hydration reaction is computationally investigated to shed light on unexpected experimental observations on its catalytic activity. Experiment reveals that BF₄⁻ and OTf⁻ have very similar coordination ability towards [(ppy)Au(IPr)]²⁺ and slightly less than water, whereas the alkyne complex could not be observed in solution at least at the NMR sensitivity. Due to the steric hindrance/dispersion interaction balance between X and IPr, the [(ppy)Au(IPr)]²⁺ fragment is computationally found to be much less selective than a model [(ppy)Au(NHC)]²⁺ (NHC = 1,3-dimethylimidazol-2-ylidene) fragment towards the different ligands, in particular OTf⁻ and BF₄⁻, in agreement with experiment. Effect of the ancillary ligand substitution demonstrates that the coordination ability of Au(III) is quantitatively strongly affected by the nature of the ligands (even more than the net charge of the complex) and that all the investigated gold fragments coordinate to alkynes more strongly than H₂O. Remarkably, a stabilization of the water-coordinating species with respect to the alkyne-coordinating one can only be achieved within a microsolvation model, which reconciles theory with experiment. All the results reported here suggest that both the Au(III) fragment coordination ability and its proper computational modelling in the experimental conditions are fundamental issues for the design of efficient catalysts.     

Inorganic Elements in Mytilus galloprovincialis Shells: Geographic Traceability by Multivariate Analysis of ICP-MS Data

The international seafood trade is based on food safety, quality, sustainability, and traceability. Mussels are bio-accumulative sessile organisms that need regular control to guarantee their safe consumption. However, no well-established and validated methods exist to trace mussel origin, even if several attempts have been made over the years. Recently, an inorganic multi-elemental fingerprint coupled to multivariate statistics has increasingly been applied in food quality control. The mussel shell can be an excellent reservoir of foreign inorganic chemical species, allowing recording long-term environmental changes. The present work investigates the multi-elemental composition of mussel shells, including Al, Cu, Cr, Zn, Mn, Cd, Co, U, Ba, Ni, Pb, Mg, Sr, and Ca, determined by inductively-coupled plasma mass-spectrometry in Mytilus galloprovincialis collected along the Central Adriatic Coast (Marche Region, Italy) at 25 different sampling sites (18 farms and 7 natural banks) located in seven areas. The experimental data, coupled with chemometric approaches (principal components analysis and linear discriminant analysis), were used to create a statistical model able to discriminate samples as a function of their production site. The LDA model is suitable for achieving a correct assignment of >90% of individuals sampled to their respective harvesting locations and for being applied to counteract fraud.     

The Physico-Chemical Properties of Glipizide: New Findings

The present work is a concrete example of how physico-chemical studies, if performed in depth, are crucial to understand the behavior of pharmaceutical solids and constitute a solid basis for the control of the reproducibility of the industrial batches. In particular, a deep study of the thermal behavior of glipizide, a hypoglycemic drug, was carried out with the aim of clarifying whether the recognition of its polymorphic forms can really be done on the basis of the endothermic peak that the literature studies attribute to the melting of the compound. A number of analytical techniques were used: thermal techniques (DSC, TGA), X-ray powder diffraction (XRPD), FT-IR spectroscopy and scanning electron microscopy (SEM). Great attention was paid to the experimental design and to the interpretation of the combined results obtained by all these techniques. We proved that the attribution of the endothermic peak shown by glipizide to its melting was actually wrong. The DSC peak is no doubt triggered by a decomposition process that involves gas evolution (cyclohexanamine and carbon dioxide) and formation of 5-methyl-N-[2-(4-sulphamoylphenyl) ethyl] pyrazine-2-carboxamide, which remains as decomposition residue. Thermal treatments properly designed and the combined use of DSC with FT-IR and XRPD led to identifying a new polymorphic form of 5-methyl-N-[2-(4-sulphamoylphenyl) ethyl] pyrazine-2-carboxamide, which is obtained by crystallization from the melt. Hence, our results put into evidence that the check of the polymorphic form of glipizide cannot be based on the temperature values of the DSC peak, since such a peak is due to a decomposition process whose Tonset value is strongly affected by the particle size. Kinetic studies of the decomposition process show the high stability of solid glipizide at room temperature.     

Water-Assisted Concerted Proton-Electron Transfer at Co(II)-Aquo Sites in Polyoxotungstates With Photogenerated RuIII(bpy)33+ Oxidant

The cobalt substituted polyoxotungstate [Co₆(H₂O)₂(α-B-PW₉O₃₄)₂(PW₆O₂₆)]¹⁷⁻ ( Co6 ) displays fast electron transfer (ET) kinetics to photogenerated Ru^III(bpy)₃³⁺, 4 to 5 orders of magnitude faster than the corresponding ET observed for cobalt oxide nanoparticles. Mechanistic evidence has been acquired indicating that: (i) the one-electron oxidation of Co6 involves Co(II) aquo or Co(II) hydroxo groups (abbreviated as Co6(II) −OH ₂ and Co6(II) −OH, respectively, whose speciation in aqueous solution is associated to a pK_a of 7.6), and generates a Co(III)−OH moiety ( Co6(III) −OH), as proven by transient absorption spectroscopy; (ii) at pH>pK_a, the Co6(II) −OH→Ru^III(bpy)₃³⁺ ET occurs via bimolecular kinetics, with a rate constant k close to the diffusion limit and dependent on the ionic strength of the medium, consistent with reaction between charged species; (iii) at pH <pK_a, the process involves Co6(II) − OH₂ → Co6(III)−OH transformation and proceeds via a multiple-site, concerted proton electron transfer (CPET) where water assists the transfer of the proton, as proven by the absence of effect of buffer base concentrations on the rate of the ET and by a H/D kinetic isotope in a range of 1.2–1.4. The reactivity of water is ascribed to its organization on the surface of the polyanionic scaffold through hydrogen bond networking involving the Co(II)−OH₂ group.     

Characterizing Pressure‐Induced Uranium CH Agostic Bonds

The diuranium(III) compound [UN′′₂]₂(μ‐η⁶:η⁶‐C₆H₆) (N′′=N(SiMe₃)₂) has been studied using variable, high‐pressure single‐crystal X‐ray crystallography, and density functional theory . In this compound, the low‐coordinate metal cations are coupled through π‐ and δ‐symmetric arene overlap and show close metal? CH contacts with the flexible methyl CH groups of the sterically encumbered amido ligands. The metal–metal separation decreases with increasing pressure, but the most significant structural changes are to the close contacts between ligand CH bonds and the U centers. Although the interatomic distances are suggestive of agostic‐type interactions between the U and ligand peripheral CH groups, QTAIM (quantum theory of atoms‐in‐molecules) computational analysis suggests that there is no such interaction at ambient pressure. However, QTAIM and NBO analyses indicate that the interaction becomes agostic at 3.2 GPa.     

A Family of Molecular Sieves Containing Framework‐Bound Organic Structure‐Directing Agents

Organic structure‐directing agents (OSDAs), such as quaternary ammonium cations and amines, used in the synthesis of zeolites and related crystalline microporous oxides usually end up entrapped inside the void spaces of the crystallized inorganic host lattice. But none of them is known to form direct chemical bonds to the framework of these industrially important catalysts and adsorbents. We demonstrate that ECR‐40, currently regarded as a typical silicoaluminophosphate molecular sieve, constitutes instead a new family of inorganic‐organic hybrid networks in which the OSDAs are covalently bonded to the inorganic framework. ECR‐40 crystallization begins with the formation of an Al–OSDA complex in the liquid phase in which the Al is octahedrally coordinated. This unit is incorporated in the crystallizing ECR‐40. Subsequent removal of framework‐bound OSDAs generates Al‐O‐Al linkages in a fully tetrahedrally coordinated framework.