A Scaffold-Diversity Synthesis of Biologically Intriguing Cyclic Sulfonamides

Substrate-Regulated Divergent Addition of N-Sulfonyl Ketimines to Bicyclo[1.1.0]butanes Enabled by Photoinduced Energy Transfer

A substrate-regulated divergent addition of N-sulfonyl ketimines to bicyclo[1.1.0]butanes (BCBs) was developed using a photoinduced energy transfer strategy. The [2π+2σ] cycloaddition of BCBs with saccharin-derived cyclic ketimines yields benzosultam-fused aza-BCHs with good yields and excellent diastereoselectivity. In contrast, reactions of chain N-sulfonyl ketimines with BCBs produce 1,3-fully substituted cyclobutanes via energy-transfer-induced N-S bond homolysis. The ease of large-scale synthesis and derivatizations of products highlight their application potentials.

Base-Controlled Synthesis of Heteroatom-Embedded 9-Membered Cycloalkynes and 6-Membered Sultams through Copper-Catalyzed Cyclization

A facile copper-catalyzed, base-controlled cyclization reaction has been developed for the synthesis of 9-membered cycloalkyne and 6-membered heterocycle sultams under mild conditions. This protocol utilizes a copper-catalyzed intramolecular A3 (alkyne-aldehyde-amine) coupling reaction to efficiently synthesize 9-membered cycloalkyne sultams in yields up to 90%. Alternatively, by substituting NaHCO3 with DBU, the protocol achieves selective deprotection of the N-propargyl group, thereby facilitating the formation of 6-membered heterocyclic sultams, also in high yields.

Acid-Mediated Intramolecular Cyclizations of (N-Aryl)-acetylenic Sulfonamides: Synthesis of Fused and Spirocyclic Sultams

Herein, we report acid-mediated divergent annulations of (N-aryl)-alkynyl sulfonamides. The substituent at the para position of the N-aryl group determines two diverse reaction paths, leading to the selective assembly of benzo-fused sultams and spirocyclic sultams. This strategy provides a series of benzo/spiro-sultams with wide functional group compatibility and good to excellent yields under mild reaction conditions. Additionally, scale-up reaction and further transformations of the products were also carried out to demonstrate the utility of the protocol.

Identification of lysosomotropism using explainable machine learning and morphological profiling cell painting data

Lysosomotropism is a phenomenon of diverse pharmaceutical interests because it is a property of compounds with diverse chemical structures and primary targets. While it is primarily reported to be caused by compounds having suitable lipophilicity and basicity values, not all compounds that fulfill such criteria are in fact lysosomotropic. Here, we use morphological profiling by means of the cell painting assay (CPA) as a reliable surrogate to identify lysosomotropism. We noticed that only 35% of the compound subset with matching physicochemical properties show the lysosomotropic phenotype. Based on a matched molecular pair analysis (MMPA), no key substructures driving lysosomotropism could be identified. However, using explainable machine learning (XML), we were able to highlight that higher lipophilicity, basicity, molecular weight, and lower topological polar surface area are among the important properties that induce lysosomotropism in the compounds of this subset.

Synthesis of Polycyclic Imidazolidinones via Cascade [3 + 2]-Annulation of β-Oxo-acrylamides with Cyclic N-Sulfonyl Imines

An Et3N-catalyzed cascade [3 + 2]-annulation of β-oxo-acrylamides with cyclic N-sulfonyl ketimines or sulfamate-derived imines is developed under mild reaction conditions, which provides a concise and efficient route to access valuable sultam- or sulfamidate-fused imidazolidinone derivatives in good to excellent yields (80-95% yields) with excellent diastereoselectivities (>20:1 drs). The current protocol features atom economy, a transition-metal-free process, and broad functional group tolerance. Moreover, the asymmetric variant of the [3 + 2]-cycloaddition reaction was achieved in the presence of diphenylethanediamine or quinine-based bifunctional squaramide organocatalysts C-1 and C-11, giving the corresponding chiral polycyclic imidazolidinones in 68-90% yields with 25-94% ees and >20:1 drs in all cases.

Morphological Profiling Identifies the Motor Protein Eg5 as Cellular Target of Spirooxindoles

Oxindoles and iso-oxindoles are natural product-derived scaffolds that provide inspiration for the design and synthesis of novel biologically relevant compound classes. Notably, the spirocyclic connection of oxindoles with iso-oxindoles has not been explored by nature but promises to provide structurally related compounds endowed with novel bioactivity. Therefore, methods for their efficient synthesis and the conclusive discovery of their cellular targets are highly desirable. We describe a selective RhIII -catalyzed scaffold-divergent synthesis of spirooxindole-isooxindoles and spirooxindole-oxindoles from differently protected diazooxindoles and N-pivaloyloxy aryl amides which includes a functional group-controlled Lossen rearrangement as key step. Unbiased morphological profiling of a corresponding compound collection in the Cell Painting assay efficiently identified the mitotic kinesin Eg5 as the cellular target of the spirooxindoles, defining a unique Eg5 inhibitor chemotype.

Ring Expansion Strategies for the Synthesis of Medium Sized Ring and Macrocyclic Sulfonamides

Two new ring expansion strategies are reported for the synthesis of medium sized ring and macrocyclic sulfonamides. Both methods can be performed without using classical protecting groups, with the key ring expansion step initiated by nitro reduction and amine conjugate addition respectively. Each method can be used to make diversely functionalised cyclic sulfonamides in good to excellent yields, in a range of ring sizes. The ring size dependency of the synthetic reactions is in good agreement with the outcomes modelled by Density Functional Theory calculations.

Swapping Copper-Catalytic Process: Selective Access to Pyrazoles and Conjugated Ketimines from Oxime Acetates and Cyclic Sulfamidate Imines

A powerful CuCl-catalyzed sequential one-pot reaction of aryl methyl ketoxime acetates with cyclic N-sulfonyl imines followed by elimination in the presence of base is reported. This hydrazine-free method conveniently makes C-C and N-N bonds via a radical cleavage of the N-O bond, delivering a special class of C3-hydroxyarylated pyrazoles in good yields. Surprisingly, while employing CuI as a catalyst instead of CuCl, the reaction proceeds through a non-radical pathway which embodies a new tactic for the high-yielding access to value-added conjugated N-unsubstituted ketimines. Moreover, additive-free approach to sulfamidate-fused-pyrazoles was achieved by successfully catalyzing addition and oxidative N-N bond-making reactions by CuI and CuCl, respectively. Significantly, our novel technique could convert the prepared ketimines into the pharmacologically recognized 6H-benzo[c]chromene frameworks.

[3 + 2] cycloaddition of nonstabilized azomethine ylides and 2-benzothiazolamines to access imidazolidine derivatives

A simple and practical method for the construction of 1,3,5-trisubstituted imidazolidine derivatives via [3 + 2] cycloaddition reaction has been developed. This reaction could smoothly proceed between nonstabilized azomethine ylides generated in situ and 2-benzothiazolamines to deliver a wide scope of differently substituted imidazolidines in high yields (up to 98%). The structure of one example was confirmed by X-ray single-crystal structure analysis.

Leveraging the Domino Skeletal Expansion of Thia-/Selenazolidinones via Nitrogen-Atom Transfer in Hexafluoroisopropanol: Room Temperature Access to Six-Membered S/Se,N-Heterocycles

Herein, a highly regioselective domino skeletal-expansion process that transforms 2-aminothiazolidinone into six-membered S,N-heterocycle is developed with the aid of TMS-azide in hexafluoroisopropanol (HFIP) at ambient temperature. Functioning of the C2 tertiary amine as latent reactive group on thiazolidinone moiety was the key to this development, which allowed relay substitution with azide and imparted subsequent ring-expansion under metal/acid free-conditions. The reaction also underscored an intermolecular nitrogen-atom transfer process from TMS-azide leading to final products, where any intermediary azidothiazolidinone was absent. The strategy was extendable to analogous synthesis of Se,N-heterocycles, and furthermore, late-stage drug-modification and follow-up transformations were also performed. Density functional theory calculations and control experiments provided important mechanistic insights and highlighted potential roles of HFIP in the transformation.

Discovery of a σ1 receptor antagonist by combination of unbiased cell painting and thermal proteome profiling

Phenotypic screening for bioactive small molecules is typically combined with affinity-based chemical proteomics to uncover the respective molecular targets. However, such assays and the explored bioactivity are biased toward the monitored phenotype, and target identification often requires chemical derivatization of the hit compound. In contrast, unbiased cellular profiling approaches record hundreds of parameters upon compound perturbation to map bioactivity in a broader biological context and may link a profile to the molecular target or mode of action. Herein we report the discovery of the diaminopyrimidine DP68 as a Sigma 1 (σ1) receptor antagonist by combining morphological profiling using the Cell Painting assay and thermal proteome profiling. Our results highlight that integration of complementary profiling approaches may enable both detection of bioactivity and target identification for small molecules.

Merging Imidazolidines with a Trifluoromethylated Tetrasubstituted Carbon through Tungsten Catalyzed 1,3-Dipolar Cycloaddition

An unprecedented 1,3-dipole cycloaddition between acyclic CF₃-ketimines and N-benzyl azomethine ylide has been allowed by tungsten catalysis, furnishing a range of novel imidazolidines bearing a trifluoromethylated tetrasubstituted carbon center. This reaction appears as one of rare examples that challenging acyclic CF₃-ketimines have been engaged in 1,3-cycloaddition reactions. The capability for gram-scale synthesis and variant derivatizations of cycloaddition adducts illustrates the synthetic potential of this approach. This protocol provides a facile access to a rapidly enlarging pool of motifs with a trifluoromethylated fully substituted carbon.

Morphological profiling of small molecules

Profiling approaches such as gene expression or proteome profiling generate small-molecule bioactivity profiles that describe a perturbed cellular state in a rather unbiased manner and have become indispensable tools in the evaluation of bioactive small molecules. Automated imaging and image analysis can record morphological alterations that are induced by small molecules through the detection of hundreds of morphological features in high-throughput experiments. Thus, morphological profiling has gained growing attention in academia and the pharmaceutical industry as it enables detection of bioactivity in compound collections in a broader biological context in the early stages of compound development and the drug-discovery process. Profiling may be used successfully to predict mode of action or targets of unexplored compounds and to uncover unanticipated activity for already characterized small molecules. Here, we review the reported approaches to morphological profiling and the kind of bioactivity that can be detected so far and, thus, predicted.

Contrasting Carboannulation Involving δ-Acetoxy Allenoate as a Four-Carbon Synthon Using DABCO and DMAP: Access to Spiro-carbocyclic and m-Teraryl Scaffolds

Spiro-annulation involving δ-acetoxy allenoate and alkyl benzoisothiazole dioxide (N-sulfonyl ketimine) triggered by DABCO/MeCO₂H combination leads to an essentially single diastereomer via chemo- and regiospecific [4 + 2]-carboannulation and a new hydroxyl group is introduced. In contrast, DMAP-catalyzed benzannulation using the same reactants affords unsymmetrical m-teraryls via Mannich coupling, sequential proton transfers, and C-N bond cleavage. Here, δ-acetoxy allenoate serves as a 4C-synthon and the carboannulation is completely base dependent and mutually exclusive.

Image-based profiling for drug discovery: due for a machine-learning upgrade?

Image-based profiling is a maturing strategy by which the rich information present in biological images is reduced to a multidimensional profile, a collection of extracted image-based features. These profiles can be mined for relevant patterns, revealing unexpected biological activity that is useful for many steps in the drug discovery process. Such applications include identifying disease-associated screenable phenotypes, understanding disease mechanisms and predicting a drug's activity, toxicity or mechanism of action. Several of these applications have been recently validated and have moved into production mode within academia and the pharmaceutical industry. Some of these have yielded disappointing results in practice but are now of renewed interest due to improved machine-learning strategies that better leverage image-based information. Although challenges remain, novel computational technologies such as deep learning and single-cell methods that better capture the biological information in images hold promise for accelerating drug discovery.

A Scaffold-Diversity Synthesis of Biologically Intriguing Cyclic Sulfonamides

A "branching-folding" synthetic strategy that affords a range of diverse cyclic benzo-sulfonamide scaffolds is presented. Whereas different annulation reactions on common ketimine substrates build the branching phase of the scaffold synthesis, a common hydrogenative ring-expansion method, facilitated by an increase of the ring-strain during the branching phase, led to sulfonamides bearing medium-sized rings in a folding pathway. Cell painting assay was successfully employed to identify tubulin targeting sulfonamides as novel mitotic inhibitors.