SNAr Chemistry Research Articles

Discovery of electrophilic degraders that exploit SNAr chemistry.

Targeted covalent inhibition (TCI) and targeted protein degradation (TPD) have proven effective in pharmacologically addressing formerly 'undruggable' targets. Integration of both methodologies has resulted in the development of electrophilic degraders where recruitment of a suitable E3 ubiquitin ligase is achieved through formation of a covalent bond with a cysteine nucleophile. Expanding the scope of electrophilic degraders requires the development of electrophiles with tempered reactivity that enable selective ligase recruitment and reduce cross-reactivity with other cellular nucleophiles. In this study, we report the use of chemical moieties that enable nucleophilic aromatic substitution (SNAr) reactions in the rational design of electrophilic protein degraders. Appending an SNAr covalent warhead to several preexisting small molecule inhibitors transformed them into degraders, obviating the need for a defined E3 ligase recruiter. The SNAr covalent warhead is versatile; it can recruit various E3 ligases, including DDB1 and CUL4 associated factor 11 (DCAF11), DDB1 and CUL4 associated factor 16 (DCAF16), and possibly others. The incorporation of an SNAr covalent warhead into the BRD4 inhibitor led to the discovery of degraders with low picomolar degradation potency. Furthermore, we demonstrate the broad applicability of this approach through rational functional switching from kinase inhibitors into potent degraders.

Tuning Green Explosives through SNAr Chemistry.

Reactivity and regioselectivity of SNAr-type fluorine substitution with azide in polyfluorosubstituted nitrobenzenes was studied both theoretically and experimentally. The obtained polyazido-substituted nitrobenzene derivatives were extensively characterized by NMR, IR, HPLC, X-ray, and DFT methods. It was found that the substitution with the azide nucleophile occurs first at the para- and the ortho-positions to the NO2-group and that transazidation reactions also occur here. Thermal decomposition of prepared azidonitrobenzenes was studied both in controlled (kinetic decay) and uncontrolled (explosion) modes. In case of the controlled thermal decomposition of ortho-azidonitrobenzenes, benzofuroxans were found as major products of the reaction unless another azido group was adjacent to the furoxan moiety. The bursting power of azidonitrobenzenes was found to rise gradually with the number of the azide substituents in the aromatic ring.

Selective Arylation of RNA 2′‐OH Groups via SNAr Reaction with Trialkylammonium Heterocycles

AbstractSmall‐molecule reactions at the 2′‐OH groups of RNA enable useful applications for transcriptome technology and biology. To date, all reactions have involved carbonyl acylation and mechanistically related sulfonylation, limiting the types of modifications and properties that can be achieved. Here we report that electron‐deficient heteroaryl species selectively react with 2′‐OH groups of RNA in water via SNAr chemistry. In particular, trialkyl‐ammonium (TAA)‐activated aromatic heterocycles, prepared in one step from aryl chloride precursors, give high conversions to aryl ether adducts with RNAs in aqueous buffer in ~2–3 h. Remarkably, a TAA triazine previously used only for reaction with carboxylic acids, shows unprecedented selectivity for RNA over water, reacting rapidly with 2′‐OH groups while exhibiting a half‐life in water of >10 days. We further show that a triazine aryl species can be used as a probe at trace‐level yields to map RNA structure in vitro. Finally, we prepare a number of functionalized trialkylammonium triazine reagents and show that they can be used to covalently label RNA efficiently for use in vitro and in living cells. This direct arylation chemistry offers a simple and distinct structural scaffold for post‐synthetic RNA modification, with potential utility in multiple applications in transcriptome research.

Selective Arylation of RNA 2'-OH Groups via SNAr Reaction with Trialkylammonium Heterocycles.

Small-molecule reactions at the 2'-OH groups of RNA enable useful applications for transcriptome technology and biology. To date, all reactions have involved carbonyl acylation and mechanistically related sulfonylation, limiting the types of modifications and properties that can be achieved. Here we report that electron-deficient heteroaryl species selectively react with 2'-OH groups of RNA in water via SNAr chemistry. In particular, trialkyl-ammonium (TAA)-activated aromatic heterocycles, prepared in one step from aryl chloride precursors, give high conversions to aryl ether adducts with RNAs in aqueous buffer in ~2-3 h. Remarkably, a TAA triazine previously used only for reaction with carboxylic acids, shows unprecedented selectivity for RNA over water, reacting rapidly with 2'-OH groups while exhibiting a half-life in water of >10 days. We further show that a triazine aryl species can be used as a probe at trace-level yields to map RNA structure in vitro. Finally, we prepare a number of functionalized trialkylammonium triazine reagents and show that they can be used to covalently label RNA efficiently for use in vitro and in living cells. This direct arylation chemistry offers a simple and distinct structural scaffold for post-synthetic RNA modification, with potential utility in multiple applications in transcriptome research.

Development of a Decafluorobiphenyl Cyclized Peptide Targeting the NEMO-IKKα/β Interaction that Enhances Cell Penetration and Attenuates Lipopolysaccharide-Induced Acute Lung Injury.

Aberrant canonical NF-κB signaling has been implicated in diseases, such as autoimmune disorders and cancer. Direct disruption of the interaction of NEMO and IKKα/β has been developed as a novel way to inhibit the overactivation of NF-κB. Peptides are a potential solution for disrupting protein-protein interactions (PPIs); however, they typically suffer from poor stability in vivo and limited tissue penetration permeability, hampering their widespread use as new chemical biology tools and potential therapeutics. In this work, decafluorobiphenyl-cysteine SNAr chemistry, molecular modeling, and biological validation allowed the development of peptide PPI inhibitors. The resulting cyclic peptide specifically inhibited canonical NF-κB signaling in vitro and in vivo, and presented positive metabolic stability, anti-inflammatory effects, and low cytotoxicity. Importantly, our results also revealed that cyclic peptides had huge potential in acute lung injury (ALI) treatment, and confirmed the role of the decafluorobiphenyl-based cyclization strategy in enhancing the biological activity of peptide NEMO-IKKα/β inhibitors. Moreover, it provided a promising method for the development of peptide-PPI inhibitors.

Conversion of amino-terephthalonitriles to multi-substituted single benzene fluorophores with utility in bioimaging.

Substitution of two fluorine atoms of the tetrafluoroterephthalonitrile (TFTN) ring (ortho to each other) by amine nucleophiles through SNAr chemistry is achievable. However, tri- and tetra-substitution towards multi-substituted single benzene fluorophores (SBFs) is harder due to increased electron richness of the TFTN moiety. Tertiary amine donors promote the molecule towards such multi-substitution guided by the steric obstruction to intramolecular charge transfer to the TFTN ring. Contrarily, secondary amine substituents with better lone pair donation to the TFTN ring cannot induce the SNAr pathway and instead promote hydrolysis of the nitrile groups of the TFTN moiety. Theoretical investigations have helped unearth the reasons for this observed difference in chemical reactivities and also explain the differences in the emission spectra. Finally, the success of the synthetic method towards multi-substitution is showcased through creation of a highly lipophilic SBF bearing an octyl unit and demonstrating its utility in in vitro cellular imaging.

Synthesis of (thio)alkyloxy-substituted perfluorinated terphenyl derivatives: Optical properties, molecular docking and antioxidant activity

Nucleophilic aromatic substitution (SNAr) has been known to be a strongly para-selective reaction for various multifunctional perfluoroaryls. In the current study, we report the application of SNAr chemistry to synthesize different derivatives of optically active symmetrical and asymmetrical perfluorinated fluoroterphenyl analogues. The synthesis procedures include a Cu-assisted decarboxylation of perfluorinated fluorobenzoate derivatives and SNAr reaction to produce (thio)alkyloxy-substituted perfluorinated fluoroterphenyls in respectable yield and superb purity starting from the potassium salt of perfluorobenzoate and aryl iodide. The synthesized adducts were inspected by FT-IR and 1H/13C/19F NMR spectroscopy. The optical properties of the synthesized perfluorinated adducts were explored. The absorption and fluorescence spectra showed solvatochromic properties. The DPPH procedure was utilized to inspect the synthesized perfluoroterphenyl analogues for their antioxidant activity. The results demonstrated that the perfluoroterphenyl adducts with asymmetrical hydrocarbon chain exhibited maximum efficiency over an IC50 =10.25±0.24 µg/mL. Moreover, the perfluoroterphenyl adducts were employed in molecular docking using (PDB: 5IKQ) protein.

Genetically encoded discovery of perfluoroaryl macrocycles that bind to albumin and exhibit extended circulation in vivo

Peptide-based therapeutics have gained attention as promising therapeutic modalities, however, their prevalent drawback is poor circulation half-life in vivo. In this paper, we report the selection of albumin-binding macrocyclic peptides from genetically encoded libraries of peptides modified by perfluoroaryl-cysteine SNAr chemistry, with decafluoro-diphenylsulfone (DFS). Testing of the binding of the selected peptides to albumin identified SICRFFC as the lead sequence. We replaced DFS with isosteric pentafluorophenyl sulfide (PFS) and the PFS-SICRFFCGG exhibited KD = 4–6 µM towards human serum albumin. When injected in mice, the concentration of the PFS-SICRFFCGG in plasma was indistinguishable from the reference peptide, SA-21. More importantly, a conjugate of PFS-SICRFFCGG and peptide apelin-17 analogue (N3-PEG6-NMe17A2) showed retention in circulation similar to SA-21; in contrast, apelin-17 analogue was cleared from the circulation after 2 min. The PFS-SICRFFC is the smallest known peptide macrocycle with a significant affinity for human albumin and substantial in vivo circulation half-life. It is a productive starting point for future development of compact macrocycles with extended half-life in vivo.

Cu(I)-catalyzed Synthesis of Symmetrical Perfluoroterphenyl Analogues; Fluorescence, Antioxidant and Molecular Docking studies.

Pentafluoroaryl analogues have been found to exhibit para specific nucleophilic aromatic substitution (SN Ar). Herein, we describe the use of SN Ar chemistry to create luminous perfluorinated symmetrical terphenyls. Both of SN Ar chemistry and Cu(I)-catalyzed decarboxylative cross-coupling were applied for the synthesis of those perfluorinated symmetrical terphenyls in high yields from the corresponding derivatives of aryl iodide and potassium salt of fluorobenzoate. A series of perfluorinated symmetrical terphenyls with different para alkoxy chains were synthesized. The synthesized perfluorinated terphenyl adducts were confirmed via elemental analysis, FT-IR, 1 H/13 C NMR, and 19 F NMR spectra. The absorbance and fluorescence spectra showed solvatochromic activities. The new synthesized fluoroterphenyl hybrids were screened against antioxidant inspection over DPPH performance, in assessment to Vitamin C and BHT as standard drugs exposed that fluoroterphenyl hybrid covering decyl hydrocarbons exhibited highest effectiveness through IC50 values 21.74 μg/mL. Additionally, molecular docking procedures of the synthesized fluoro-terphenyl hybrids were employed by using (PDB ID: 5IKQ) protein. The docking simulation was displayed convenient and recognized findings with the antioxidant examination.

Synthesis, molecular docking and antioxidant activity of new fluorescent tetrafluoroterphenyl analogues.

Nucleophilic aromatic substitution (SN Ar) chemistry has been applied to develop many functionalized pentafluorobenzene derivatives. Those compounds are highly specific at the para position of the fluorinated ring. Therefore, they are typical adducts for the preparation of antioxidant molecular systems. In this context, we report the use of SN Ar chemistry as a suitable and simple synthetic approach for fluorescent antioxidant perfluorinated materials bearing ether bonds of various para-substituted alkoxy chains in high purity and excellent yields. The fluoroterphenyl core was prepared via alkylation, decarboxylated through Cu(I)-assisted, and cross-coupled by potassium salt of fluorobenzoate followed by reaction with different alcohols. The structures of the synthesized fluoroterphenyl adducts were proved by FT-IR, 1 H NMR, 13 C NMR, and 19 F NMR. The emission plus absorption spectra showed solvatochromism. In contrast to ascorbic acid and BHT as references, newly prepared tetrafluoroterphenyl analogues were investigated toward antioxidant examination through the DPPH process, which revealed that tetrafluoroterphenyl analogue containing the decyl chain had the highest activity over IC50 value =22.36±0.19 g/mL. Also, using the protein (PDB ID: 5IKQ) through molecular docking strategies of the produced tetrafluoroterphenyl analogues were used. The antioxidant investigations and docking results were offered convergent results to each other.

Two birds one stone: β-fluoropyrrolyl-cysteine SNAr chemistry enabling functional porphyrin bioconjugation.

Bioconjugation, a synthetic tool that endows small molecules with biocompatibility and target specificity through covalent attachment of a biomolecule, holds promise for next-generation diagnosis or therapy. Besides the establishment of chemical bonding, such chemical modification concurrently allows alteration of the physicochemical properties of small molecules, but this has been paid less attention in designing novel bioconjugates. Here, we report a "two birds one stone" methodology for irreversible porphyrin bioconjugation based on β-fluoropyrrolyl-cysteine SNAr chemistry, in which the β-fluorine of porphyrin is selectively replaced by a cysteine in either peptides or proteins to generate novel β-peptidyl/proteic porphyrins. Notably, due to the distinct electronic nature between fluorine and sulfur, such replacement makes the Q band red-shift to the near-infrared region (NIR, >700 nm). This facilitates intersystem crossing (ISC) to enhance the triplet population and thus singlet oxygen production. This new methodology features water tolerance, a fast reaction time (15 min), good chemo-selectivity, and broad substrate scope, including various peptides and proteins under mild conditions. To demonstrate its potential, we applied porphyrin β-bioconjugates in several scenarios, including (1) cytosolic delivery of functional proteins, (2) metabolic glycan labeling, (3) caspase-3 detection, and (4) tumor-targeting phototheranostics.

Synthesis, self-assembly and optical properties of novel fluorescent alkoxy-substituted fluoroaryl 1, 3, 4-oxadiazole organogelator

Aromatic nucleophilic substitution (SNAr) reactions have been known to be regioselective to the para position on a variety of substituted perfluorobenzenes. In the current study, a series of fluoroaryl 1, 3, 4-oxadiazole derivatives substituted with different para terminal ethers were synthesized using SNAr chemistry to afford fluorescent and thermally reversible low molecular weight organogelators (LMWOs). SNAr was used to synthesize these highly fluorinated organogelators in high purity and good yields starting from pentafluorobenzoic acid and 4′-hydroxy-4-biphenylcarbonitrile. These fluorinated 1, 3, 4-oxadiazole derivatives were characterized by elemental analysis, FTIR, and 1H, 13C, and 19F NMR spectroscopy. The photophysical properties of those organogelators were described. Both UV–visible absorption and fluorescence spectral profiles displayed a solvatochromic and solvatofluorochromic properties. The absorption maxima for the developed organogelators were monitored in the range of 260–289 nm, whereas the emission maxima were monitored in the range of 278–305 nm. The best gelation properties were monitored for the hexyloxy-substituted 2-(biphenylyl)-5-(perflurophenyl)-1, 3, 4-oxadiazole gelator in different solvents with critical gel concentrations in the range of 1.86–5.07 mM. The self-assembly process was monitored to occur via van der Waals forces and π-π stacks to result in gelation of solvents. Scanning electron microscope (SEM) demonstrated nanofiber-like structures (350–550 nm). The thermal stability of the hexyloxy-substituted organogel was monitored at 48 °C. Both cytotoxicity and antimicrobial activity of the produced fluoroaryl 1, 3, 4-oxadiazole derivatives were explored to verify their potential use for biomedical applications, such as drug delivery and bioimaging.

Diarylamine Synthesis via Desulfinylative Smiles Rearrangement.

Diarylamines are obtained directly from sulfinamides through a novel rearrangement sequence. The transformation is transition metal-free and proceeds under mild conditions, providing facile access to highly sterically hindered diarylamines that are otherwise inaccessible by traditional SNAr chemistry. The reaction highlights the distinct reactivity of the sulfinamide group in Smiles rearrangements versus that of the more common sulfonamides.

Synthesis and self-assembly of new fluorescent cholesteryloxy-substituted fluorinated terphenyls with gel formation and mesogenic phases

Fluorescent mesogenic compounds have been reported as suitable materials for electronic displays with low energy consumption. Aromatic nucleophilic substitution (SNAr) reactions have been extremely para selective on various pentafluorophenyl derivatives, which is ideal to build up fluorescent calamitic (rod-like) liquid crystals. In the current study, we report the use of SNAr strategy toward the synthesis of emissive low molecular mass organogels (LMMOs) with mesogenic phases. The synthesis of these new cholesteryloxy-substituted fluorinated terphenyls was carried out through decarboxylative cross-coupling reaction catalyzed by copper iodide, followed by the application of SNAr chemistry. The produced organogelator was obtained in excellent purity and high yield starting from aryl iodides and pentafluorobenzoate. A series of asymmetric fluorinated terphenyls were synthesized with different terminal alkoxides. The molecular structures were studied by elemental analysis, 1H, 13C and 19F NMR, and infrared spectroscopic methods. The liquid crystalline phases were explored by differential scan calorimeter (DSC) and optical polarizing microscopy (POM) demonstrating at least one mesogenic phase. The absorbance and fluorescence spectral curves exhibited solvatochromic properties. The morphological properties were studied by scan electron microscope (SEM), which showed nanofibrous scaffolds generated from the assembly of cholesteryloxy-substituted terphenyls. This self-assembly process was supported by π-stack packing and van der Waals forces.

Photoacoustic imaging of elevated glutathione in models of lung cancer for companion diagnostic applications.

Companion diagnostics (CDx) are powerful tests that can provide physicians with crucial biomarker information that can improve treatment outcomes by matching therapies to patients. Here, we report a photoacoustic imaging-based CDx (PACDx) for the selective detection of elevated glutathione (GSH) in a lung cancer model. GSH is abundant in most cells, so we adopted a physical organic chemistry approach to precisely tune the reactivity to distinguish between normal and pathological states. To evaluate the efficacy of PACDx in vivo, we designed a blind study where photoacoustic imaging was used to identify mice bearing lung xenografts. We also employed PACDx in orthotopic lung cancer and liver metastasis models to image GSH. In addition, we designed a matching prodrug, PARx, that uses the same SNAr chemistry to release a chemotherapeutic with an integrated PA readout. Studies demonstrate that PARx can inhibit tumour growth without off-target toxicity in a lung cancer xenograft model.

Synthesis, characterization, and self‐assembly of fluorescent fluorine‐containing liquid crystals

SN Ar has been used to synthesize various functionalized derivatives of pentafluorobenzenes which are highly specific at the para position; and consequently are ideal for building calamitic (rod-like) liquid crystalline molecular systems. Here, we display the effectiveness of SN Ar chemistry as a convenient method toward the synthesis of fluorescent liquid crystalline perfluorinated comprising ethers and thioethers in excellent yields and high purity. In the current work, we describe the synthesis, self-assembly, and mesogenic properties of new perfluorinated para-terphenyls bearing various para-substituted alkoxy and thioalkoxy chains. The terphenyl core was prepared using Cu(I) (or Cu(I)/phenanthroline)-catalyzed decarboxylative carbon-carbon (or carbon-oxygen [sulfur]) cross-coupling from the analogous aromatic iodide and fluorobenzoate potassium salt. The molecular structures of the prepared perfluorinated terphenyls were demonstrated with 1 H, 13 C, and 19 F NMR, as well as FT-IR and X-ray crystallography. The liquid crystalline properties and mesogenic phases were characterized with differential scanning calorimetry and high-resolution polarized optical microscope. Both UV-visible absorbance and emission spectra demonstrated solvatochromism. Supramolecular self-assembly of the generated perfluorinated para-terphenyls was monitored by van der Waals and π-π stacking interaction forces. The creation of nanofibrous architectures was monitored by scanning electron microscopy.

Arene C−H Activation at Aluminium(I): meta Selectivity Driven by the Electronics of SNAr Chemistry

AbstractThe reactivity of the electron‐rich anionic AlI aluminyl compound K2[(NON)Al]2 (NON=4,5‐bis(2,6‐diisopropylanilido)‐2,7‐di‐tert‐butyl‐9,9‐dimethylxanthene) towards mono‐ and disubstituted arenes is reported. C−H activation chemistry with n‐butylbenzene gives exclusively the product of activation at the arene meta position. Mechanistically, this transformation proceeds in a single step via a concerted Meisenheimer‐type transition state. Selectivity is therefore based on similar electronic factors to classical SNAr chemistry, which implies the destabilisation of transition states featuring electron‐donating groups in either ortho or para positions. In the cases of toluene and the three isomers of xylene, benzylic C−H activation is also possible, with the product(s) formed reflecting the feasibility (or otherwise) of competing arene C−H activation at a site which is neither ortho nor para to a methyl substituent.

Arene C-H Activation at Aluminium(I): meta Selectivity Driven by the Electronics of SN Ar Chemistry.

The reactivity of the electron‐rich anionic AlI aluminyl compound K2[(NON)Al]2 (NON=4,5‐bis(2,6‐diisopropylanilido)‐2,7‐di‐tert‐butyl‐9,9‐dimethylxanthene) towards mono‐ and disubstituted arenes is reported. C−H activation chemistry with n‐butylbenzene gives exclusively the product of activation at the arene meta position. Mechanistically, this transformation proceeds in a single step via a concerted Meisenheimer‐type transition state. Selectivity is therefore based on similar electronic factors to classical SNAr chemistry, which implies the destabilisation of transition states featuring electron‐donating groups in either ortho or para positions. In the cases of toluene and the three isomers of xylene, benzylic C−H activation is also possible, with the product(s) formed reflecting the feasibility (or otherwise) of competing arene C−H activation at a site which is neither ortho nor para to a methyl substituent.

Organophotochemical SNAr Reactions of Mildly Electron‐Poor Fluoroarenes

C–F functionalization of arenes with a range of alcohol and pyrazole nucleophiles has been achieved without the need for metal catalysts or highly electron‐poor substrates. Treatment of fluoroarenes with alcohols or pyrazoles and DDQ under irradiation by blue LED light provides the corresponding substituted products. The procedure is complementary to classical SNAr chemistry which generally requires basic reaction conditions and high temperatures, and provides products under non‐basic conditions at ≈ 40 °C.

Synthesis of azido-substituted benzaldehydes via SNAr chemistry

Conditions for the formation of azidobenzaldehydes and azidobenzonitriles using sodium azide in DMSO under typical SNAr conditions are described. This simplifies access to these valuable building blocks compared to the more common sequences reported in the literature. Interestingly, fluorosubstituted aryl ketones and esters do not afford azides, but instead amine products.