Drug discovery using very large numbers of patents. General strategy with extensive use of match and edit operations

A patent data base of 6.7 million compounds generated by a very high performance computer (Blue Gene) requires new techniques for exploitation when extensive use of chemical similarity is involved. Such exploitation includes the taxonomic classification of chemical themes, and data mining to assess mutual information between themes and companies. Importantly, we also launch candidates that evolve by “natural selection” as failure of partial match against the patent data base and their ability to bind to the protein target appropriately, by simulation on Blue Gene. An unusual feature of our method is that algorithms and workflows rely on dynamic interaction between match-and-edit instructions, which in practice are regular expressions. Similarity testing by these uses SMILES strings and, less frequently, graph or connectivity representations. Examining how this performs in high throughput, we note that chemical similarity and novelty are human concepts that largely have meaning by utility in specific contexts. For some purposes, mutual information involving chemical themes might be a better concept.     

Fluorine extraction from organofluorine molecules to make fluorinated clusters in yttrium MOFs

A new rare earth based two-dimensional coordination network and a three-dimensional metal–organic framework (MOF) have been synthesized using bicinchoninic acid (BCA) and yttrium(iii) ions. Yttrium dimer nodes are formed in the absence of a modulator, resulting in a 2D layered coordination network (Y–BCA-2D). The presence of fluorinating agents, e.g., 2-fluorobenzoic acid (2-FBA), 2,6-difluorobenzoic acid (2,6-DFBA), and perfluorohexanoic acid (PFHxA) result in μ₃-F bridged metal hexaclusters (Y₆F₈) that form a three-dimensional MOF (Y–BCA-3D). It was found that Y³⁺ can break highly stable C–F bonds in aromatic and aliphatic fluorinated compounds. Single-crystal X-ray diffraction (SC-XRD) shows the presence of fluorine in the metal cluster which was confirmed by energy dispersive X-ray spectroscopy (EDS). High resolution X-ray photoelectron spectroscopy (XPS) and ¹⁹F Nuclear Magnetic Resonance (NMR) also verify the presence of metal–fluorine bonds in the cluster. The Y–BCA-3D MOF selectively adsorbs CO₂ but not N₂.

The reaction of yttrium(iii) and linker makes a 2D metal–organic framework. The addition of fluorinated modulators result in fluorine extraction from modulators and makes a 3D-MOF.     

Aminoquinolones and Their Benzoquinone Dimer Hybrids as Modulators of Prion Protein Conversion

Prion Diseases or Transmissible Spongiform Encephalopathies are neurodegenerative conditions associated with a long incubation period and progressive clinical evolution, leading to death. Their pathogenesis is characterized by conformational changes of the cellular prion protein—PrP^C—in its infectious isoform—PrP^Sc—which can form polymeric aggregates that precipitate in brain tissues. Currently, there are no effective treatments for these diseases. The 2,5-diamino-1,4-benzoquinone structure is associated with an anti-prion profile and, considering the biodynamic properties associated with 4-quinolones, in this work, 6-amino-4-quinolones derivatives and their respective benzoquinone dimeric hybrids were synthesized and had their bioactive profile evaluated through their ability to prevent prion conversion. Two hybrids, namely, 2,5-dichloro-3,6-bis((3-carboxy-1-pentyl-4-quinolone-6-yl)amino)-1,4-benzoquinone (8e) and 2,5-dichloro-3,6-bis((1-benzyl-3-carboxy-4-quinolone-6-yl)amino)-1,4-benzoquinone (8f), stood out for their prion conversion inhibition ability, affecting the fibrillation process in both the kinetics—with a shortening of the lag phase—and thermodynamics and their ability to inhibit the formation of protein aggregates without significant cytotoxicity at ten micromolar.     

Electron Spin Resonance Dosimetry Studies of Irradiated Sulfite Salts

The study of new materials for radiation dosimetry is important to improve the present state of the art and to help in cases of accidents for retrospective dosimetry. Sulfites are compounds that contain a sulfur ion, widely used in the food industry. Due to the significant application of these compounds, sulfites are interesting candidates for accidental dosimetry, as fortuitous radiation detectors. The presence of the SO₃⁻ anion enables its detection by electron spin resonance (ESR) spectroscopy. The Dose–Response behavior, signal stability and other spectral features were investigated for sodium sulfite, sodium bisulfite, sodium metabisulfite and potassium metabisulfite, all in crystalline forms. The ESR spectrum of salts presented stability and proportional response with dose, presenting potential for dosimetry applications.     

Evidence of the Beneficial Effects of Ursolic Acid against Lung Cancer

Lung cancer is the leading cause of cancer-related deaths globally. Despite current treatment approaches that include surgery, chemotherapy, radiation and immunotherapies, lung cancer accounted for 1.79 million deaths worldwide in 2020, emphasizing the urgent need to find novel agents and approaches for more effective treatment. Traditionally, chemicals derived from plants, such as paclitaxel and docetaxel, have been used in cancer treatment, and in recent years, research has focused on finding other plant-derived chemicals that can be used in the fight against lung cancer. Ursolic acid is a polyphenol found in high concentrations in cranberries and other fruits and has been demonstrated to have anti-inflammatory, antioxidant and anticancer properties. In this review, we summarize recent research examining the effects of ursolic acid and its derivatives on lung cancer. Data from in vitro cell culture and in vivo animal studies show potent anticancer effects of ursolic acid and indicate the need for clinical studies.     

Creating permanent 3D arrangements of isolated cells using holographic optical tweezers

We report the creation of permanent 3D configurations of cells, at predefined positions, within a gelatin matrix. The technique used holographic optical tweezers to manipulate individual E. coli within a solution comprising monomer precursors. The matrix was then set and after the laser beam was removed, we were able to demonstrate that the structures remained intact for many days. We were also able to demonstrate that, in the presence of appropriate nutrients, the E. coli survived within the gelatin matrix for several days. The technique could have a number of potential future applications, including the arrangement of a variety of different cell types in complex architectures, as motifs for promoting tissue differentiation and growth within the field of cell engineering.     

Three‐Dimensional Branched and Faceted Gold–Ruthenium Nanoparticles: Using Nanostructure to Improve Stability in Oxygen Evolution Electrocatalysis

Achieving stability with highly active Ru nanoparticles for electrocatalysis is a major challenge for the oxygen evolution reaction. As improved stability of Ru catalysts has been shown for bulk surfaces with low‐index facets, there is an opportunity to incorporate these stable facets into Ru nanoparticles. Now, a new solution synthesis is presented in which hexagonal close‐packed structured Ru is grown on Au to form nanoparticles with 3D branches. Exposing low‐index facets on these 3D branches creates stable reaction kinetics to achieve high activity and the highest stability observed for Ru nanoparticle oxygen evolution reaction catalysts. These design principles provide a synthetic strategy to achieve stable and active electrocatalysts.     

Vicinal functionalization of propiolate esters via a tandem catalytic carbocupration-Mukaiyama aldol reaction sequence

The vicinal functionalization of propiolate esters via a tandem catalytic carbocupration-Mukaiyama aldol reaction sequence has been investigated. It has been shown that catalyst loadings as low as 8 mol % readily allow for good yields and excellent diastereoselectivities (>20:1) for a series of Grignard reagents and aldehydes.     

Cross-conjugated poly(p-phenylene) aided supramolecular self-organization of fullerene nanocrystallites

Formation and characterization of nanocrystallite spheres from a hybrid of functionalized cross-conjugated poly(p-phenylene) and C(60) are reported.