Emerging Applications of Aryl Trifluoromethyl Diazoalkanes and Diazirines in Synthetic Transformations

Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping

While photo-cross-linking (PXL) with alkyl diazirines can provide stringent distance restraints and offer insights into protein structures, unambiguous identification of cross-linked residues hinders data interpretation to the same level that has been achieved with chemical cross-linking (CXL). We address this challenge by developing an in-line system with systematic modulation of light intensity and irradiation time, which allows for a quantitative evaluation of diazirine photolysis and photo-reaction mechanism. Our results reveal a two-step pathway with mainly sequential generation of diazo and carbene intermediates. Diazo intermediate preferentially targets buried polar residues, many of which are inaccessible with known CXL probes for their limited reactivity. Moreover, we demonstrate that tuning light intensity and duration enhances selectivity towards polar residues by biasing diazo-mediated cross-linking reactions over carbene ones. This mechanistic dissection unlocks the full potential of PXL, paving the way for accurate distance mapping against protein structures and ultimately, unveiling protein dynamic behaviors.

Evaluation of Antibacterial Functionalized Dihydropyrimidine Photoaffinity Probes Toward Mechanism of Action Studies

Antibiotic-resistant bacteria are a global health concern, necessitating the development of antibiotics working through new or underutilized mechanisms. Functionalized amino dihydropyrimidines have previously demonstrated potential as antibacterial agents, but they had limited potency, and their biological mechanism was not understood. To further evaluate their potential, focused libraries were prepared and screened for bacterial growth inhibition, and these compounds provided additional insights into the structure-activity relationships, allowing for the preparation of compounds that inhibited all strains of Staphylococcus aureus with an MIC of 2 μg/mL. After eliminating the proposed mechanism of dihydrofolate reductase inhibition, trifluoromethyl diazirine photoaffinity probes were synthesized to investigate their mechanism, and these were tested to ensure the photolabile group did not impact the antibacterial activity. Finally, the compounds were screened for hemolysis and mammalian cytotoxicity. While they lacked nonspecific membrane rupturing activity, many of the compounds showed significant mammalian cytotoxicity, indicating further development will be required to render them selective for bacteria.

Tougher Bioadhesives through Dual Stimulation Strategies

Carbene-based bioadhesives have favourable attributes for tissue adhesion, including non-specific bonding to wet and dry tissues, but suffer from relatively weak fracture strength after photocuring. Light irradiation of carbene-precursor (diazirine) also creates inert side products that are absent under thermal activation. Herein, a dual activation method combines light irradiation at elevated temperatures for the evaluation of diazirine depletion and effects on cohesive properties. A customized photo/thermal-rheometer evaluates viscoelastic properties, correlated to the kinetics of carbene:diazoalkane ratios via 19F NMR). The latter exploits the sensitive -CF3 functional group to determine joule-based light/temperature kinetics on trifluoroaryl diazirine consumption. The combination of heat and photoactivation produced bioadhesives that are 3× tougher compared to control. Dual thermal/light irradiation may be a strategy to improve viscoelastic dissipation and toughness of photo-activated adhesive resins.

Unveiling the Selectivity of Ru(II)-Catalyzed C-H Activation for Defluorinative Cyclization of 2-Arylbenzimidazole and Trifluoromethyl Diazo: A DFT Study

The synthesis of monofluorinated heterocyclic compounds by C-H activation combined with defluorination is useful. Studies on the reaction mechanism and selectivity have shown that these processes play a positive role in promoting the development of monofluorinated reactions. Density functional theory (DFT) calculations were performed to investigate the mechanism and selectivity of Ru(II)-catalyzed 2-arylbenzimidazole with trifluoromethyl diazo. DFT calculations showed that C-H activation occurs through a concerted metalation/deprotonation (CMD) mechanism. After that, deprotonation and defluorinative cyclization are assisted by acetate and trifluoroethanol (TFE). Further mechanistic insights through noncovalent interaction (NCI) analysis were also obtained to elucidate the origin of the selectivity in the defluorination process.

Cyclopropanation of Alkenes with Halodiazirines as Halocarbene Precursors in Continuous Flow

The cyclopropanation reaction of alkenes with photolytically-generated chlorocarbenes from chlorodiazirines is reported as an effective way to prepare substituted 3-chloro-3-aryl-cyclopropanes. This practical and efficient approach allows the synthesis of various 3-chloro-3-aryl-cyclopropanes (32 examples) in continuous flow in 5-minute residence time under light-emitting diode (LED) irradiation. The conditions using 380 nm LED irradiation were successfully extended to the synthesis of substituted 3-bromo-3-aryl-cyclopropanes (3 examples).

Copper-catalyzed multicomponent reaction of β-trifluoromethyl β-diazo esters enabling the synthesis of β-trifluoromethyl N,N-diacyl-β-amino esters

An efficient multicomponent reaction of newly designed β-trifluoromethyl β-diazo esters, acetonitrile, and carboxylic acids via an interrupted esterification process under copper-catalyzed conditions has been developed, which affords various unsymmetrical β-trifluoromethyl N,N-diacyl-β-amino esters in good to excellent yields. The reaction features mild conditions, a wide scope of β-amino esters and carboxylic acids, and also applicability to large-scale synthesis, thus providing an efficient way for the synthesis of β-trifluoromethyl β-diacylamino esters. Furthermore, this reaction represents the first example of a Mumm rearrangement of β-trifluoromethyl β-diazo esters.

Photocatalytic Activation of Aryl(trifluoromethyl) Diazos to Carbenes for High-Resolution Protein Labeling with Red Light

State-of-the-art methods in photoproximity labeling center on the targeted generation and capture of short-lived reactive intermediates to provide a snapshot of local protein environments. Diazirines are the current gold standard for high-resolution proximity labeling, generating short-lived aryl(trifluoromethyl) carbenes. Here, we present a method to access aryl(trifluoromethyl) carbenes from a stable diazo source via tissue-penetrable, deep red to near-infrared light (600-800 nm). The operative mechanism of this activation involves Dexter energy transfer from photoexcited osmium(II) photocatalysts to the diazo, thus revealing an aryl(trifluoromethyl) carbene. The labeling preferences of the diazo probe with amino acids are studied, showing high reactivity toward heteroatom-H bonds. Upon the synthesis of a biotinylated diazo probe, labeling studies are conducted on native proteins as well as proteins conjugated to the Os photocatalyst. Finally, we demonstrate that the conjugation of a protein inhibitor to the photocatalyst also enables selective protein labeling in the presence of spectator proteins and achieves specific labeling of a membrane protein on the surface of mammalian cells via a two-antibody photocatalytic system.

Functionalization of Polydimethylsiloxane with Diazirine-Based Linkers for Covalent Protein Immobilization

Biomolecule attachment to solid supports is critical for biomedical devices, such as biosensors and implants. Polydimethylsiloxane (PDMS) is commonly used for these applications due to its advantageous properties. To enhance the biomolecule immobilization on PDMS, a novel technique is demonstrated using newly synthesized diazirine molecules for the surface modification of PDMS. This nondestructive process involves a reaction between diazirine molecules and PDMS through C-H insertion with thermal or ultraviolet activation. The success of the PDMS modification is confirmed by various surface characterization techniques. Bovine serum albumin (BSA) and immunoglobulin G (IgG) are strongly attached to the modified PDMS surfaces, and the amount of protein is quantified using iodine-125 radiolabeling. The results demonstrate that PDMS is rapidly functionalized, and the stability of the immobilized proteins is significantly improved with multiple types of diazirine molecules and activation methods. Confocal microscopy provides three-dimensional images of the distribution of immobilized IgG on the surfaces and the penetration of diazirine-based linkers through the PDMS substrate during the coating process. Overall, this study presents a promising new approach for functionalizing PDMS surfaces to enhance biomolecule immobilization, and its potential applications can extend to multimaterial modifications for various diagnostic and medical applications such as microfluidic devices and immunoassays with relevant bioactive proteins.

Discovery of a Novel Trifluoromethyl Diazirine Inhibitor of SARS-CoV-2 Mpro

SARS-CoV-2 M^pro is a chymotrypsin-like cysteine protease playing a relevant role during the replication and infectivity of SARS-CoV-2, the coronavirus responsible for COVID-19. The binding site of M^pro is characterized by the presence of a catalytic Cys145 which carries out the hydrolytic activity of the enzyme. As a consequence, several M^pro inhibitors have been proposed to date in order to fight the COVID-19 pandemic. In our work, we designed, synthesized and biologically evaluated MPD112, a novel inhibitor of SARS-CoV-2 M^pro bearing a trifluoromethyl diazirine moiety. MPD112 displayed in vitro inhibition activity against SARS-CoV-2 M^pro at a low micromolar level (IC₅₀ = 4.1 μM) in a FRET-based assay. Moreover, an inhibition assay against PL^pro revealed lack of inhibition, assuring the selectivity of the compound for the M^pro. Furthermore, the target compound MPD112 was docked within the binding site of the enzyme to predict the established intermolecular interactions in silico. MPD112 was subsequently tested on the HCT-8 cell line to evaluate its effect on human cells' viability, displaying good tolerability, demonstrating the promising biological compatibility and activity of a trifluoromethyl diazirine moiety in the design and development of SARS-CoV-2 M^pro binders.

Application of Aromatic Substituted 2,2,2-Trifluoro Diazoethanes in Organic Reactions

Abstract:

This review provides an overview of metal-, nonmetal-, light-, or catalyst free-promoting reactions of aromatic substituted 2,2,2-trifluoro diazoethanes with organic molecules for the synthesis of trifluoromethyl-substituted compounds. Several approaches will be reviewed and divided into (i) copper-, iron-, Trop(BF4)-, B(C6F5)3-, light-, or rhodium-promoted reactions of aromatic substituted 2,2,2-trifluoro diazoethanes with silanes, amines, mercaptans, phosphonates, p-cyanophenol, benzoic acid, diphenylphosphinic acid, boranes and nBu3SnH, (ii) rhodium-catalyzed reactions of aromatic substituted 2,2,2-trifluoro diazoethanes with amides and phenylhydroxylamine, (iii) copper-, rhodium-, silver-, and light-catalyzed reactions of aromatic substituted 2,2,2-trifluoro diazoethanes with alkynes, (iv) palladium-, copper-, rhodium- and iron-catalyzed reactions of aromatic substituted 2,2,2-trifluoro diazoethanes with alkenes, (v) BF3·OEt2-, copper-, tin- or TBAB-catalyzed reactions of aromatic substituted 2,2,2-trifluoro diazoethanes with HF·Py, (difluoroiodo)toluene (p-TolIF2), TMSCF3, AgSCF3, TMSCF2Br or 1,3-dicarbonyl compounds, (vi) palladium-, copper-, gold/silver- or rhodium-catalyzed reactions of aromatic substituted 2,2,2-trifluoro diazoethanes with indoles, benzene compounds or pyridines, and (vii) palladium-catalyzed reaction of aromatic substituted 2,2,2-trifluoro diazoethanes with benzyl or allyl bromides.

Electronically optimized diazirine-based polymer crosslinkers

Electronically optimized bis-diazirine crosslinkers allow aliphatic polymers to be crosslinked with up to 10-fold improved efficacy, relative to earlier designs. Activation is achieved using modest temperatures or through UV or visible light.