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.     

Breakdown of a topological phase: quantum phase transition in a loop gas model with tension

We study the stability of topological order against local perturbations by considering the effect of a magnetic field on a spin model--the toric code--which is in a topological phase. The model can be mapped onto a quantum loop gas where the perturbation introduces a bare loop tension. When the loop tension is small, the topological order survives. When it is large, it drives a continuous quantum phase transition into a magnetic state. The transition can be understood as the condensation of "magnetic" vortices, leading to confinement of the elementary "charge" excitations. We also show how the topological order breaks down when the system is coupled to an Ohmic heat bath and relate our results to error rates for topological quantum computations.     

Rb[Li5Si2O7] – A Latecomer in the Family of Alkali Lithosilicates Hiding a Green-Emitting Lithosilicate

In order to expand the field of alkali lithosilicates, a new representative of the substance class with a previously unknown structure type was found based on solid-state synthesis. The novel compound with the sum formula Rb[Li₅Si₂O₇] crystallizes in the orthorhombic space group Pbcm (no. 57) with a=7.6269(3), b=9.5415(4), and c=9.4095(3) Å by means of single-crystal X-ray diffraction. The structure consists of a highly condensed lithosilicate framework, built up of corner- and edge-linked [LiO₄]-tetrahedra and [Si₂O₇]-units, and the rubidium ions aligned in channels. Suitable crystals of the material were obtained using sealed tantalum ampoules as reaction tube at a temperature of 750 °C. The new compound was further characterized via powder diffraction, Rietveld analysis, and EDX measurements. At first glance, Eu²⁺-doped Rb[Li₅Si₂O₇] reveals an intense green luminescence. In-depth crystal analysis shows that a core-shell formation is present even for apparently high quality single-crystals. As a minority phase, the known green phosphor RbLi[Li₃SiO₄]₂:Eu²⁺ is the origin of the luminescence, representing a tiny core inside of the particles surrounded by a large matrix of transparent Rb[Li₅Si₂O₇] dominating the single-crystal diffraction pattern.     

An Enantioselective Inverse‐Electron‐Demand Imino Diels–Alder Reaction

The imino Diels–Alder reaction is an efficient method for the synthesis of aza‐heterocycles. While different stereo‐ and enantioselective inverse‐electron‐demand imino Diels–Alder (IEDIDA) reactions have been reported before, IEDIDA reactions including electron‐deficient dienes are unprecedented. The first enantioselective IEDIDA reaction between electron‐poor chromone dienes and cyclic imines, catalyzed by zinc/binol complexes is described. The novel reaction provides a facile entry to a natural product inspired collection of ring‐fused quinolizines including a potent modulator of mitosis.     

Enzymatic Conversion of Flavonoids using Bacterial Chalcone Isomerase and Enoate Reductase

Flavonoids are a large group of plant secondary metabolites with a variety of biological properties and are therefore of interest to many scientists, as they can lead to industrially interesting intermediates. The anaerobic gut bacterium Eubacterium ramulus can catabolize flavonoids, but until now, the pathway has not been experimentally confirmed. In the present work, a chalcone isomerase (CHI) and an enoate reductase (ERED) could be identified through whole genome sequencing and gene motif search. These two enzymes were successfully cloned and expressed in Escherichia coli in their active form, even under aerobic conditions. The catabolic pathway of E. ramulus was confirmed by biotransformations of flavanones into dihydrochalcones. The engineered E. coli strain that expresses both enzymes was used for the conversion of several flavanones, underlining the applicability of this biocatalytic cascade reaction.     

Systematic Comparison of Peptidic Proteasome Inhibitors Highlights the α‐Ketoamide Electrophile as an Auspicious Reversible Lead Motif

The ubiquitin–proteasome system (UPS) has been successfully targeted by both academia and the pharmaceutical industry for oncological and immunological applications. Typical proteasome inhibitors are based on a peptidic backbone endowed with an electrophilic C‐terminus by which they react with the active proteolytic sites. Although the peptide moiety has attracted much attention in terms of subunit selectivity, the target specificity and biological stability of the compounds are largely determined by the reactive warheads. In this study, we have carried out a systematic investigation of described electrophiles by a combination of in vitro, in vivo, and structural methods in order to disclose the implications of altered functionality and chemical reactivity. Thereby, we were able to introduce and characterize the class of α‐ketoamides as the most potent reversible inhibitors with possible applications for the therapy of solid tumors as well as autoimmune disorders.     

A Rechargeable Hydrogen Battery Based on Ru Catalysis

Apart from energy generation, the storage and liberation of energy are among the major problems in establishing a sustainable energy supply chain. Herein we report the development of a rechargeable H₂ battery which is based on the principle of the Ru‐catalyzed hydrogenation of CO₂ to formic acid (charging process) and the Ru‐catalyzed decomposition of formic acid to CO₂ and H₂ (discharging process). Both processes are driven by the same catalyst at elevated temperature either under pressure (charging process) or pressure‐free conditions (discharging process). Up to five charging–discharging cycles were performed without decrease of storage capacity. The resulting CO₂/H₂ mixture is free of CO and can be employed directly in fuel‐cell technology.     

Mechanism of Host–Guest Complex Formation and Identification of Intermediates through NMR Titration and Diffusion NMR Spectroscopy

The formation of host–guest (H‐G) complexes between 1,8‐bis[(diethylgallanyl)ethynyl]anthracene (H) and the N‐heterocycles pyridine and pyrimidine (G) was studied in solution using a combination of NMR titration and diffusion NMR experiments. For the latter, diffusion coefficients of potential host–guest structures in solution were compared with those of tailor‐made reference compounds of similar shape (synthesized and characterized by NMR, HRMS, and in part XRD). Highly dynamic behavior was observed in both cases, but with different host–guest species and equilibria. With increasing concentrations of the pyridine guest, the equilibrium H₂?H₂κ¹‐G₁?HG₂ is observed (in the second step a host dimer coordinates one guest molecule); for pyrimidine the equilibrium H₂→H₁κ²‐G₁?HG₂ is observed (the formation of a 1:1 aggregate is the second step).     

The Synthesis of α‐Azidoesters and Geminal Triazides

Three simple methods for the synthesis of geminal triazides are described: Starting from 1) 3‐oxocarboxylic acids, 2) iodomethyl ketones, or 3) terminal olefins, a range of triazidomethyl ketones can be constructed under mild oxidative reaction conditions by the use of IBX‐SO₃K, a sulfonylated derivative of 2‐iodoxybenzoic acid (IBX), and NaN₃ as an azide source. This is the first report of representatives of this novel class of triazide compounds: Despite their high nitrogen content, the geminal triazides are easy to handle, even when preparative‐scale syntheses are performed. (Caution: These procedures still require protective measures!) The triazides are now broadly available for further studies regarding their properties and reactivity. Furthermore, we show how the method can be used to provide α‐azidoesters, which are potential building blocks for amino acids.     

Isolation of a Neutral Boron‐Containing Radical Stabilized by a Cyclic (Alkyl)(Amino)Carbene

Utilizing a cyclic (alkyl)(amino)carbene (CAAC) as a ligand, neutral CAAC‐stabilized radicals containing a boryl functionality could be prepared by reduction of the corresponding haloborane adducts. The radical species with a duryl substituent was fully characterized by single‐crystal X‐ray structural analysis, EPR spectroscopy, and DFT calculations. Compared to known neutral boryl radicals, the isolated radical species showed larger spin density on the boron atom. Furthermore, the compound that was isolated is extraordinarily stable to high temperatures under inert conditions, both in solution and in the solid state. Electrochemical investigations of the radical suggest the possibility to generate a stable formal boryl anion species.