Programming inactive RNA-binding small molecules into bioactive degraders

Target occupancy is often insufficient to elicit biological activity, particularly for RNA, compounded by the longstanding challenges surrounding the molecular recognition of RNA structures by small molecules. Here we studied molecular recognition patterns between a natural-product-inspired small-molecule collection and three-dimensionally folded RNA structures. Mapping these interaction landscapes across the human transcriptome defined structure-activity relationships. Although RNA-binding compounds that bind to functional sites were expected to elicit a biological response, most identified interactions were predicted to be biologically inert as they bind elsewhere. We reasoned that, for such cases, an alternative strategy to modulate RNA biology is to cleave the target through a ribonuclease-targeting chimera, where an RNA-binding molecule is appended to a heterocycle that binds to and locally activates RNase L1. Overlay of the substrate specificity for RNase L with the binding landscape of small molecules revealed many favourable candidate binders that might be bioactive when converted into degraders. We provide a proof of concept, designing selective degraders for the precursor to the disease-associated microRNA-155 (pre-miR-155), JUN mRNA and MYC mRNA. Thus, small-molecule RNA-targeted degradation can be leveraged to convert strong, yet inactive, binding interactions into potent and specific modulators of RNA function.

Photocatalytic Isomerization of (E)-Anethole to (Z)-Anethole

Natural product (E)-anethole was isomerized to (Z)-anethole in a photocatalytic reaction. For this purpose, a self-designed cheap photoreactor was constructed. Among 11 photosensitizers (organo and metal complex compounds), Ir(p-tBu-ppy)₃ led to the highest conversion. Triplet energies of (E)- and (Z)-anethole were predicted theoretically by DFT calculations to support the selection of appropriate photosensitizers. A catalyst loading of 0.1 mol% gave up to 90% conversion in gram scale. Further additives were not required and mild irradiation with light of 400 nm overnight was sufficient. As a proof of concept, (E)- and (Z)-anethole were dihydroxylated diastereoselectively to obtain diastereomerically pure like- and unlike-configured diols, respectively.

Intermolecular [2π+2σ]-photocycloaddition enabled by triplet energy transfer

For more than one century, photochemical [2+2]-cycloadditions have been used by synthetic chemists to make cyclobutanes, four-membered carbon-based rings. In this reaction, typically two olefin subunits (two π-electrons per olefin) cyclize to form two new C-C σ-bonds. Although the development of photochemical [2+2]-cycloadditions has made enormous progress within the last century, research has been focused on such [2π+2π]-systems, in which two π-bonds are converted into two new σ-bonds^1,2. Here we report an intermolecular [2+2]-photocycloaddition that uses bicyclo[1.1.0]butanes as 2σ-electron reactants^3-7. This strain-release-driven [2π+2σ]-photocycloaddition reaction was realized by visible-light-mediated triplet energy transfer catalysis^8,9. A simple, modular and diastereoselective synthesis of bicyclo[2.1.1]hexanes from heterocyclic olefin coupling partners, namely coumarins, flavones and indoles, is disclosed. Given the increasing importance of bicyclo[2.1.1]hexanes as bioisosteres-groups that convey similar biological properties to those they replace-in pharmaceutical research and considering their limited access^10,11, there remains a need for new synthetic methodologies. Applying this strategy enabled us to extend the intermolecular [2+2]-photocycloadditions to σ-bonds and provides previously inaccessible structural motifs.

Radical Carbonyl Umpolung Arylation via Dual Nickel Catalysis

The formation of carbon-carbon bonds lies at the heart of synthetic organic chemistry and is widely applied to construct complex drugs, polymers, and materials. Despite its importance, catalytic carbonyl arylation remains comparatively underdeveloped, due to limited scope and functional group tolerance. Herein we disclose an umpolung strategy to achieve radical carbonyl arylation via dual catalysis. This redox-neutral approach provides a complementary method to construct Grignard-type products from (hetero)aryl bromides and aliphatic aldehydes, without the need for pre-functionalization. A sequential activation, hydrogen-atom transfer, and halogen atom transfer process could directly convert aldehydes to the corresponding ketyl-type radicals, which further react with aryl-nickel intermediates in an overall polarity-reversal process. This radical strategy tolerates─among others─acidic functional groups, heteroaryl motifs, and sterically hindered substrates and has been applied in the late-stage modification of drugs and natural products.

Dynamic Kinetic Sensitization of β-Dicarbonyl Compounds-Access to Medium-Sized Rings by De Mayo-Type Ring Expansion

Herein, we present a photocatalyzed two-carbon ring expansion of β-dicarbonyl compounds with unactivated olefins that provides facile access to medium-sized rings. Selective sensitization of the substoichiometric enol tautomer enables reactivity of substrates incompatible with the classical De Mayo reaction conditions. Key to success is the identification of the metal-based sensitizer fac-[Ir(CF₃ -pmb)₃ ], which can be excited using common near-visible LEDs, and possesses a high triplet excited state energy of 73.3 kcal mol^-1 . This exactly falls in the range between the triplet energies of the enol and keto tautomer, thereby enabling a dynamic kinetic sensitization. Demonstrating the applicability of fac-[Ir(CF₃ -pmb)₃ ] as a photocatalyst in organic synthesis for the first time, we describe a two-step photocycloaddition-ring-opening cascade with β-ketoesters, -diketones, and -ketoamides. The mechanism has been corroborated by time-resolved spectroscopy, as well as further experimental and computational studies.

Bipolar Imidazolium-Based Lipid Analogues for Artificial Archaeosomes

Archaeal lipids have harvested biomedical and biotechnological interest because of their ability to form membranes with low permeability and enhanced temperature and pressure stability. Because of problems in isolating archaeal lipids, chemical synthesis appears to be a suitable means of producing model lipids that mimic the biological counterparts. Here, we introduce a new concept: we synthesized bipolar alkylated imidazolium salts of different chain lengths (BIm10-32) and studied their structure and lyotropic phase behavior. Furthermore, mixtures of the bolalipid analogues with phospholipid model biomembranes of diverse complexity were studied. DSC, fluorescence and FTIR spectroscopy, confocal fluorescence microscopy, DLS, SAXS, and TEM were used to reveal changes in lipid phase behavior, fluidity, the lipid's conformational order, and membrane morphology over a wide range of temperatures and for selected pressures. It could be shown that the long-chain BImN32 can form monolayer sheets. Integrated in phospholipid membranes, it reveals a fluidizing effect. Here, the two polar head groups, connected by a long alkyl chain, enable the integration into the bilayer. Interestingly, addition of BImN32 to fluid DPPC liposomes increased the lipid packing markedly, rendering the membrane system more stable at higher temperatures. The membrane system is also stable against compression as indicated by the high-pressure stability of the system, mimicking an archaeal lipid-like behavior. BImN32 incorporation into raft-like anionic model biomembranes led to marked changes in lateral membrane organization, topology, and fusogenicity of the membrane. Overall, it was found that long-chain imidazolium-based bolalipid analogues can help adjust membrane's biophysical properties, while the imidazolium headgroup provides the ability for crucial electrostatic interaction for vesicle fusion or selective interaction with membrane-related signaling molecules and polypeptides in a synthetically tractable manner. The results obtained may help to develop new approaches for rational design of extremophilic bolalipid-based liposomes for various applications, including delivery of drugs and vaccines.

Visible-Light-Induced Cycloaddition of α-Ketoacylsilanes with Imines: Facile Access to β-Lactams

We report the synthesis of β-lactams from α-ketoacylsilanes and imines, which proceeds via a formal [2+2] photochemical cycloaddition with in situ generation of siloxyketene. This mild and operationally simple reaction proceeds in an atom-economic fashion with broad substrate scope, including aldimines, ketimines, hydrazones, and fused nitrogen heterocycles, affording a variety of important β-lactams with satisfactory diastereoselectivities in most cases. This reaction also features good functional-group tolerance, facile scalability and product diversification. Experimental and computational studies suggest that α-ketoacylsilanes can serve as photochemical precursors by engaging in a 1,3 silicon shift to the distal carbonyl group.

An Imidazolium-Based Lipid Analogue as a Gene Transfer Agent

A dicationic imidazolium salt is described and investigated towards its application for gene transfer. The polar head group and the long alkyl chains in the backbone contribute to a lipid-like behavior, while an alkyl ammonium group provides the ability for crucial electrostatic interaction for the transfection process. Detailed biophysical studies regarding its impact on biological membrane models and the propensity of vesicle fusion are presented. Fluorescence spectroscopy, atomic force microscopy and confocal fluorescence microscopy show that the imidazolium salt leads to negligible changes in lipid packing, while displaying distinct vesicle fusion properties. Cell culture experiments reveal that mixed liposomes containing the novel imidazolium salt can serve as plasmid DNA delivery vehicles. In contrast, a structurally similar imidazolium salt without a second positive charge showed no ability to support DNA transfection into cultured cells. Thus, we introduce a novel and variable structural motif for cationic lipids, expanding the field of lipofection agents.

Interaction of imidazolium-based lipids with phospholipid bilayer membranes of different complexity

In recent years, alkylated imidazolium salts have been shown to affect lipid membranes and exhibit general cytotoxicity as well as significant anti-tumor activity. Here, we examined the interactions of a sterically demanding, biophysically unexplored imidazolium salt, 1,3-bis(2,6-diisopropylphenyl)-4,5-diundecylimidazolium bromide (C₁₁IPr), on the physico-chemical properties of various model biomembrane systems. The results are compared with those for the smaller headgroup variant 1,3-dimethyl-4,5-diundecylimidazolium iodide (C₁₁IMe). We studied the influence of these two lipid-based imidazolium salts at concentrations from 1 to about 10 mol% on model biomembrane systems of different complexity, including anionic heterogeneous raft membranes which are closer to natural membranes. Fluorescence spectroscopic, DSC, surface potential and FTIR measurements were carried out to reveal changes in membrane thermotropic phase behavior, lipid conformational order, fluidity and headgroup charge. Complementary AFM and confocal fluorescence microscopy measurements allowed us to detect changes in the lateral organization and membrane morphology. Both lipidated imidazolium salts increase the membrane fluidity and lead to a deterioration of the lateral domain structure of the membrane, in particular for C₁₁IPr owing to its bulkier headgroup. Moreover, partitioning of the lipidated imidazolium salts into the lipid vesicles leads to marked changes in lateral organization, curvature and morphology of the lipid vesicles at high concentrations, with C₁₁IPr having a more pronounced effect than C₁₁IMe. Hence, these compounds seem to be vastly suitable for biochemical and biotechnological engineering, with high potentials for antimicrobial activity, drug delivery and gene transfer.

1,2-Amino Alcohols via Cr/Photoredox Dual-Catalyzed Addition of α-Amino Carbanion Equivalents to Carbonyls

Herein, we report the synthesis of protected 1,2-amino alcohols starting from carbonyl compounds and α-silyl amines. The reaction is enabled by a Cr/photoredox dual catalytic system that allows the in situ generation of α-amino carbanion equivalents which act as nucleophiles. The unique nature of this reaction was demonstrated through the aminoalkylation of ketones and an acyl silane, classes of electrophiles that were previously unreactive toward addition of alkyl-Cr reagents. Overall, this reaction broadens the scope of Cr-mediated carbonyl alkylations and discloses an underexplored retrosynthetic strategy for the synthesis of 1,2-amino alcohols.

Chain propagation determines the chemo- and regioselectivity of alkyl radical additions to C-O vs. C-C double bonds

Investigations into the selectivity of intermolecular alkyl radical additions to C-O- vs. C-C-double bonds in α,β-unsaturated carbonyl compounds are described. Therefore, a photoredox-initiated radical chain reaction is explored, where the activation of the carbonyl-group through an in situ generated Lewis acid - originating from the substrate - enables the formation of either C-O or the C-C-addition products. α,β-Unsaturated aldehydes form selectively 1,2-, while esters and ketones form the corresponding 1,4-addition products exclusively. Computational studies lead to reason that this chemo- and regioselectivity is determined by the consecutive step, i.e. an electron transfer, after reversible radical addition, which eventually propagates the radical chain.