Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries.

In vitro screening of large compound libraries with automated high-throughput screening is expensive and time-consuming and requires dedicated infrastructures. Conversely, the selection of DNA-encoded chemical libraries (DECLs) can be rapidly performed with routine equipment available in most laboratories. In this study, we identified novel inhibitors of SARS-CoV-2 main protease (Mpro) through the affinity-based selection of the DELopen library (open access for academics), containing 4.2 billion compounds. The identified inhibitors were peptide-like compounds containing an N-terminal electrophilic group able to form a covalent bond with the nucleophilic Cys145 of Mpro, as confirmed by x-ray crystallography. This DECL selection campaign enabled the discovery of the unoptimized compound SLL11 (IC50 = 30 nM), proving that the rapid exploration of large chemical spaces enabled by DECL technology allows for the direct identification of potent inhibitors avoiding several rounds of iterative medicinal chemistry. As demonstrated further by x-ray crystallography, SLL11 was found to adopt a highly unique U-shaped binding conformation, which allows the N-terminal electrophilic group to loop back to the S1' subsite while the C-terminal amino acid sits in the S1 subsite. MP1, a close analog of SLL11, showed antiviral activity against SARS-CoV-2 in the low micromolar range when tested in Caco-2 and Calu-3 (EC50 = 2.3 µM) cell lines. As peptide-like compounds can suffer from low cell permeability and metabolic stability, the cyclization of the compounds will be explored in the future to improve their antiviral activity.

Electrochemical Palladium-Catalyzed Oxidative Carbonylation-Cyclization of Enallenols.

Herein, we report an electrochemical oxidative palladium-catalyzed carbonylation-carbocyclization of enallenols to afford γ-lactones and spirolactones, which proceeds with excellent chemoselectivity. Interestingly, electrocatalysis was found to have an accelerating effect on the rate of the tandem process, leading to a more efficient reaction than that under chemical redox conditions.

Ruthenium containing molecular electrocatalyst on glassy carbon for electrochemical water splitting.

Electrochemical water splitting constitutes one of the most promising strategies for converting water into hydrogen-based fuels, and this technology is predicted to play a key role in the transition towards a carbon-neutral energy economy. To enable the design of cost-effective electrolysis cells based on this technology, new and more efficient anodes with augmented water splitting activity and stability will be required. Herein, we report an active molecular Ru-based catalyst for electrochemically-driven water oxidation (overpotential of ∼395 mV at pH 7 phosphate buffer) and two simple methods for preparing anodes by attaching this catalyst onto glassy carbon through multi-walled carbon nanotubes to improve stability as well as reactivity. The anodes modified with the molecular catalyst were characterized by a broad toolbox of microscopy and spectroscopy techniques, and interestingly no RuO2 formation was detected during electrocatalysis over 4 h. These results demonstrate that the herein presented strategy can be used to prepare anodes that rival the performance of state-of-the-art metal oxide anodes.

The Impact of Ligand Carboxylates on Electrocatalyzed Water Oxidation.

Fossil fuel shortage and severe climate changes due to global warming have prompted extensive research on carbon-neutral and renewable energy resources. Hydrogen gas (H2), a clean and high energy density fuel, has emerged as a potential solution for both fulfilling energy demands and diminishing the emission of greenhouse gases. Currently, water oxidation (WO) constitutes the bottleneck in the overall process of producing H2 from water. As a result, the design of efficient catalysts for WO has become an intensively pursued area of research in recent years. Among all the molecular catalysts reported to date, ruthenium-based catalysts have attracted particular attention due to their robust nature and higher activity compared to catalysts based on other transition metals.Over the past two decades, we and others have studied a wide range of ruthenium complexes displaying impressive catalytic performance for WO in terms of turnover number (TON) and turnover frequency (TOF). However, to produce practically applicable electrochemical, photochemical, or photo-electrochemical WO reactors, further improvement of the catalysts' structure to decrease the overpotential and increase the WO rate is of utmost importance. WO reaction, that is, the production of molecular oxygen and protons from water, requires the formation of an O-O bond through the orchestration of multiple proton and electron transfers. Promotion of these processes using redox noninnocent ligand frameworks that can accept and transfer electrons has therefore attracted substantial attention. The strategic modifications of the ligand structure in ruthenium complexes to enable proton-coupled electron transfer (PCET) and atom proton transfer (APT; in the context of WO, it is the oxygen atom (metal oxo) transfer to the oxygen atom of a water molecule in concert with proton transfer to another water molecule) to facilitate the O-O bond formation have played a central role in these efforts.In particular, promising results have been obtained with ligand frameworks containing carboxylic acid groups that either are directly bonded to the metal center or reside in the close vicinity. The improvement of redox and chemical properties of the catalysts by introduction of carboxylate groups in the ligands has proven to be quite general as demonstrated for a range of mono- and dinuclear ruthenium complexes featuring ligand scaffolds based on pyridine, imidazole, and pyridazine cores. In the first coordination sphere, the carboxylate groups are firmly coordinated to the metal center as negatively charged ligands, improving the stability of the complexes and preventing metal leaching during catalysis. Another important phenomenon is the reduction of the potentials required for the formation of higher valent intermediates, especially metal-oxo species, which take active part in the key O-O bond formation step. Furthermore, the free carboxylic acid/carboxylate units in the proximity to the active center have shown exciting proton donor/acceptor properties (through PCET or APT, chemically noninnocent) that can dramatically improve the rate as well as the overpotential of the WO reaction.

A Study of an 8-Aminoquinoline-Directed C(sp2)-H Arylation Reaction on the Route to Chiral Cyclobutane Keto Acids from Myrtenal.

This work outlines a synthetic route that can be used to access chiral cyclobutane keto acids with two stereocenters in five steps from the inexpensive terpene myrtenal. Furthermore, the developed route includes an 8-aminoquinoline-directed C(sp2)-H arylation as one of its key steps, which allows a wide range of aryl and heteroaryl groups to be incorporated into the bicyclic myrtenal scaffold prior to the ozonolysis-based ring-opening step that furnishes the target cyclobutane keto acids. This synthetic route is expected to find many applications connected to the synthesis of natural product-like compounds and small molecule libraries.

Investigation of the Deactivation and Reactivation Mechanism of a Heterogeneous Palladium(II) Catalyst in the Cycloisomerization of Acetylenic Acids by In Situ XAS .

A well-studied heterogeneous palladium(II) catalyst used for the cycloisomerization of acetylenic acids is known to be susceptible to deactivation through reduction. To gain a deeper understanding of this deactivation process and to enable the design of a reactivation strategy, in situ X-ray absorption spectroscopy (XAS) was used. With this technique, changes in the palladium oxidation state and coordination environment could be studied in close detail, which provided experimental evidence that the deactivation was primarily caused by triethylamine-promoted reduction of palladium(II) to metallic palladium nanoparticles. Furthermore, it was observed that the choice of the acetylenic acid substrate influenced the distribution between palladium(II) and palladium(0) species in the heterogeneous catalyst after the reaction. From the mechanistic insight gained through XAS, an improved catalytic protocol was developed that did not suffer from deactivation and allowed for more efficient recycling of the catalyst.

Synthesis of Elaborate Benzofuran-2-carboxamide Derivatives through a Combination of 8-Aminoquinoline Directed C-H Arylation and Transamidation Chemistry.

Herein, we present a short and highly modular synthetic route that involves 8-aminoquinoline directed C-H arylation and transamidation chemistry, and which enables access to a wide range of elaborate benzofuran-2-carboxamides. For the directed C-H arylation reactions, Pd catalysis was used to install a wide range of aryl and heteroaryl substituents at the C3 position of the benzofuran scaffold in high efficiency. Directing group cleavage and further diversification of the C3-arylated benzofuran products were then achieved in a single synthetic operation through the utilization of a one-pot, two-step transamidation procedure, which proceeded via the intermediate N-acyl-Boc-carbamates. Given the high efficiency and modularity of this synthetic strategy, it constitutes a very attractive method for generating structurally diverse collections of benzofuran derivatives for small molecule screening campaigns.

Efficient 1,3-Oxazolidin-2-one Synthesis through Heterogeneous PdII -Catalyzed Intramolecular Hydroamination of Propargylic Carbamates.

Herein, we present an operationally simple protocol for the cycloisomerization of propargylic carbamates in which a heterogeneous catalyst consisting of Pd species immobilized on amino-functionalized siliceous mesocellular foam (PdII -AmP-MCF) is used. This Pd nanocatalyst displayed high efficiency at low catalyst loading and reaction temperatures, which allowed for the efficient and mild synthesis of a wide range of 1,3-oxazolidin-2-one derivatives and related compounds. Moreover, it proved possible to re-use the Pd nanocatalyst for several reactions, although a gradual decrease in activity was observed in the subsequent cycles.

Convenient Access to Chiral Cyclobutanes with Three Contiguous Stereocenters from Verbenone by Directed C(sp3 )-H arylation.

This work demonstrates how a series of complex, chiral cyclobutane derivatives can be accessed in four steps from the terpene verbenone through the application of a directed C-H functionalization approach. The developed synthetic route involved an 8-aminoquinoline-directed C(sp3 )-H arylation as the key step, and this reaction could be carried out with a wide range of aryl and heteroaryl iodides to furnish a variety of cyclobutane products with three contiguous stereocenters. Moreover, it was shown that the 8-aminoquinoline auxiliary could be effectively removed from the cyclobutane derivatives using an ozonolysis-based cleavage method.

Synergistic Effects of Stereochemistry and Appendages on the Performance Diversity of a Collection of Synthetic Compounds.

Target- and phenotype-agnostic assessments of biological activity have emerged as viable strategies for prioritizing scaffolds, structural features, and synthetic pathways in screening sets, with the goal of increasing performance diversity. Here, we describe the synthesis of a small library of functionalized stereoisomeric azetidines and its biological annotation by "cell painting," a multiplexed, high-content imaging assay capable of measuring many hundreds of compound-induced changes in cell morphology in a quantitative and unbiased fashion. Using this approach, we systematically compare the degrees to which a core scaffold's biological activity, inferred from its effects on cell morphology, is affected by variations in stereochemistry and appendages. We show that stereoisomerism and appendage diversification can produce effects of similar magnitude, and that the concurrent use of these strategies results in a broader sampling of biological activity.

A Two-Step Procedure for the Overall Transamidation of 8-Aminoquinoline Amides Proceeding via the Intermediate N-Acyl-Boc-Carbamates.

Herein a two-step strategy for achieving overall transamidation of 8-aminoquinoline amides has been explored. In this protocol, the 8-aminoquinoline amides were first treated with Boc2O and DMAP to form the corresponding N-acyl-Boc-carbamates, which were found to be sufficiently reactive to undergo subsequent aminolysis with different amines in the absence of any additional reagents or catalysts. To demonstrate the utility of this approach, it was applied on a number of 8-aminoquinoline amides from the recent C-H functionalization literature, enabling access to a range of elaborate amide derivatives in good to high yields.

Stereospecific Palladium-Catalyzed C-H Arylation of Pyroglutamic Acid Derivatives at the C3 Position Enabled by 8-Aminoquinoline as a Directing Group.

An efficient and stereospecific Pd-catalyzed protocol for the C-H arylation of pyroglutamic acid derivatives that uses 8-aminoquinoline as a directing group is described. The reaction was shown to proceed efficiently with a variety of aryl and heteroaryl iodides bearing different functional groups, giving C3-arylated cis products in good to high yields. Removal of the 8-aminoquinoline unit from these C-H arylation products enables access to synthetically useful cis and trans pyroglutamic acid-based building blocks.

Synthesis of a Bicyclic Azetidine with In Vivo Antimalarial Activity Enabled by Stereospecific, Directed C(sp3)-H Arylation.

The development of new antimalarial therapeutics is necessary to address the increasing resistance to current drugs. Bicyclic azetidines targeting Plasmodium falciparum phenylalanyl-tRNA synthetase comprise one promising new class of antimalarials, especially due to their activities against three stages of the parasite's life cycle, but a lengthy synthetic route to these compounds may affect the feasibility of delivering new therapeutic agents within the cost constraints of antimalarial drugs. Here, we report an efficient synthesis of antimalarial compound BRD3914 (EC50 = 15 nM) that hinges on a Pd-catalyzed, directed C(sp3)-H arylation of azetidines at the C3 position. This newly developed protocol exhibits a broad substrate scope and provides access to valuable, stereochemically defined building blocks. BRD3914 was evaluated in P. falciparum-infected mice, providing a cure after four oral doses.

Discovery of 8-Membered Ring Sulfonamides as Inhibitors of Oncogenic Mutant Isocitrate Dehydrogenase 1.

Evidence suggests that specific mutations of isocitrate dehydrogenases 1 and 2 (IDH1/2) are critical for the initiation and maintenance of certain tumor types and that inhibiting these mutant enzymes with small molecules may be therapeutically beneficial. In order to discover mutant allele-selective IDH1 inhibitors with chemical features distinct from existing probes, we screened a collection of small molecules derived from diversity-oriented synthesis. The assay identified compounds that inhibit the IDH1-R132H mutant allele commonly found in glioma. Here, we report the discovery of a potent (IC50 = 50 nM) series of IDH1-R132H inhibitors having 8-membered ring sulfonamides as exemplified by the compound BRD2879. The inhibitors suppress (R)-2-hydroxyglutarate production in cells without apparent toxicity. Although the solubility and pharmacokinetic properties of the specific inhibitor BRD2879 prevent its use in vivo, the scaffold presents a validated starting point for the synthesis of future IDH1-R132H inhibitors having improved pharmacological properties.

Real-Time Biological Annotation of Synthetic Compounds.

Organic chemists are able to synthesize molecules in greater number and chemical complexity than ever before. Yet, a majority of these compounds go untested in biological systems, and those that do are often tested long after the chemist can incorporate the results into synthetic planning. We propose the use of high-dimensional "multiplex" assays, which are capable of measuring thousands of cellular features in one experiment, to annotate rapidly and inexpensively the biological activities of newly synthesized compounds. This readily accessible and inexpensive "real-time" profiling method can be used in a prospective manner to facilitate, for example, the efficient construction of performance-diverse small-molecule libraries that are enriched in bioactives. Here, we demonstrate this concept by synthesizing ten triads of constitutionally isomeric compounds via complexity-generating photochemical and thermal rearrangements and measuring compound-induced changes in cellular morphology via an imaging-based "cell painting" assay. Our results indicate that real-time biological annotation can inform optimization efforts and library syntheses by illuminating trends relating to biological activity that would be difficult to predict if only chemical structure were considered. We anticipate that probe and drug discovery will benefit from the use of optimization efforts and libraries that implement this approach.

Evaluation of Fe and Ru Pincer-Type Complexes as Catalysts for the Racemization of Secondary Benzylic Alcohols.

Fe and Ru pincer-type catalysts are used for the racemization of benzylic alcohols. Racemization with the Fe catalyst was achieved within 30 minutes under mild reaction conditions, with a catalyst loading as low as 2 mol %. This reaction constitutes the first example of an iron-catalyzed racemization of an alcohol. The efficiency for racemization of the Fe catalyst and its Ru analogue was evaluated for a wide range of sec-benzylic alcohols. The commercially available Ru complex proved to be highly robust and even tolerated the presence of water in the reaction mixture.

Mild and Selective Catalytic Hydrogenation of the C=C Bond in α,ß-Unsaturated Carbonyl Compounds Using Supported Palladium Nanoparticles.

Chemoselective reduction of the C=C bond in a variety of α,ß-unsaturated carbonyl compounds using supported palladium nanoparticles is reported. Three different heterogeneous catalysts were compared using 1 atm of H2 : 1) nano-Pd on a metal-organic framework (MOF: Pd(0) -MIL-101-NH2 (Cr)), 2) nano-Pd on a siliceous mesocellular foam (MCF: Pd(0) -AmP-MCF), and 3) commercially available palladium on carbon (Pd/C). Initial studies showed that the Pd@MOF and Pd@MCF nanocatalysts were superior in activity and selectivity compared to commercial Pd/C. Both Pd(0) -MIL-101-NH2 (Cr) and Pd(0) -AmP-MCF were capable of delivering the desired products in very short reaction times (10-90 min) with low loadings of Pd (0.5-1 mol %). Additionally, the two catalytic systems exhibited high recyclability and very low levels of metal leaching.

Chemoenzymatic dynamic kinetic resolution: a powerful tool for the preparation of enantiomerically pure alcohols and amines.

Chemoenzymatic dynamic kinetic resolution (DKR) constitutes a convenient and efficient method to access enantiomerically pure alcohol and amine derivatives. This Perspective highlights the work carried out within this field during the past two decades and pinpoints important avenues for future research. First, the Perspective will summarize the more developed area of alcohol DKR, by delineating the way from the earliest proof-of-concept protocols to the current state-of-the-art systems that allows for the highly efficient and selective preparation of a wide range of enantiomerically pure alcohol derivatives. Thereafter, the Perspective will focus on the more challenging DKR of amines, by presenting the currently available homogeneous and heterogeneous methods and their respective limitations. In these two parts, significant attention will be dedicated to the design of efficient racemization methods as an important means of developing milder DKR protocols. In the final part of the Perspective, a brief overview of the research that has been devoted toward improving enzymes as biocatalysts is presented.

Well-defined palladium nanoparticles supported on siliceous mesocellular foam as heterogeneous catalysts for the oxidation of water.

Herein, we describe the use of Pd nanoparticles immobilized on an amino-functionalized siliceous mesocellular foam for the catalytic oxidation of H2O. The Pd nanocatalyst proved to be capable of mediating the four-electron oxidation of H2O to O2, both chemically and photochemically. The Pd nanocatalyst is easy to prepare and shows high chemical stability, low leaching, and recyclability. Together with its promising catalytic activity, these features make the Pd nanocatalyst of potential interest for future sustainable solar-fuel production.

Mild deoxygenation of aromatic ketones and aldehydes over Pd/C using polymethylhydrosiloxane as the reducing agent.

Herein, a practical and mild method for the deoxygenation of a wide range of benzylic aldehydes and ketones is described, which utilizes heterogeneous Pd/C as the catalyst together with the green hydride source, polymethylhydrosiloxane. The developed catalytic protocol is scalable and robust, as exemplified by the deoxygenation of ethyl vanillin, which was performed on a 30 mmol scale in an open-to-air setup using only 0.085 mol % Pd/C catalyst to furnish the corresponding deoxygenated product in 93 % yield within 3 hours at room temperature. Furthermore, the Pd/C catalyst was shown to be recyclable up to 6 times without any observable decrease in efficiency and it exhibited low metal leaching under the reaction conditions.