Aryl diazonium intermediates enable mild DNA-compatible C–C bond formation for medicinally relevant combinatorial library synthesis

Forging carbon–carbon (C–C) linkage in DNA-encoded combinatorial library synthesis represents a fundamental task for drug discovery, especially with broad substrate scope and exquisite functional group tolerance. Here we reported the palladium-catalyzed Suzuki–Miyaura, Heck and Hiyama type cross-coupling via DNA-conjugated aryl diazonium intermediates for DNA-encoded chemical library (DEL) synthesis. Starting from commodity arylamines, this synthetic route facilely delivers vast chemical diversity at a mild temperature and pH, thus circumventing damage to fragile functional groups. Given its orthogonality with traditional aryl halide-based cross-coupling, the aryl diazonium-centered strategy expands the compatible synthesis of complex C–C bond-connected scaffolds. In addition, DNA-tethered pharmaceutical compounds (e.g., HDAC inhibitor) are constructed without decomposition of susceptible bioactive warheads (e.g., hydroxamic acid), emphasizing the superiority of the aryl diazonium-based approach. Together with the convenient transformation into an aryl azide photo-crosslinker, aryl diazonium''s DNA-compatible diversification synergistically demonstrated its competence to create medicinally relevant combinatorial libraries and investigate protein–ligand interactions in pharmaceutical research.

Taking advantage of aryl diazonium intermediates, this work reported a DNA-compatible C–C bond formation strategy, achieving broad substrate scope, exquisite functional group tolerance, and orthogonality to aryl halide-based coupling reactions.     

In-solution direct oxidative coupling for the integration of sulfur/selenium into DNA-encoded chemical libraries

Sulfur/selenium-containing electron-rich arenes (ERAs) exist in a wide range of both approved and investigational drugs with diverse pharmacological activities. These unique chemical structures and bioactive properties, if combined with the emerging DNA-encoded chemical library (DEL) technique, would facilitate drug and chemical probe discovery. However, it remains challenging, as there is no general DNA-compatible synthetic methodology available for the formation of C–S and C–Se bonds in aqueous solution. Herein, an in-solution direct oxidative coupling procedure that could efficiently integrate sulfur/selenium into the ERA under mild conditions is presented. This method features simple DNA-conjugated electron-rich arenes with a broad substrate scope and a transition-metal free process. Furthermore, this synthetic methodology, examined by a scale-up reaction test and late-stage precise modification in a mock peptide-like DEL synthesis, will enable its utility for the synthesis of sulfur/selenium-containing DNA-encoded libraries and the discovery of bioactive agents.

DNA-compatible direct oxidative coupling using various sulfur/selenium sources has been achieved, featuring pre-functionalization-free substrates and transition metal-free condition.     

Streamlined construction of peptide macrocycles via palladium-catalyzed intramolecular S-arylation in solution and on DNA

A highly efficient and versatile method for construction of peptide macrocycles via palladium-catalyzed intramolecular S-arylation of alkyl and aryl thiols with aryl iodides under mild conditions is developed. The method exhibits a broad substrate scope for thiols, aryl iodides and amino acid units. Peptide macrocycles of a wide range of size and composition can be readily assembled in high yield from various easily accessible building blocks. This method has been successfully employed to prepare an 8-million-membered tetrameric cyclic peptide DNA-encoded library (DEL). Preliminary screening of the DEL library against protein p300 identified compounds with single digit micromolar inhibition activity.

A highly efficient and versatile method for construction of peptide macrocycles via palladium-catalyzed intramolecular S-arylation of alkyl and aryl thiols with aryl iodides under mild conditions is developed.     

Diversified strategy for the synthesis of DNA-encoded oxindole libraries

DNA-encoded library technology (DELT) employs DNA as a barcode to track the sequence of chemical reactions and enables the design and synthesis of libraries with billions of small molecules through combinatorial expansion. This powerful technology platform has been successfully demonstrated for hit identification and target validation for many types of diseases. As a highly integrated technology platform, DEL is capable of accelerating the translation of synthetic chemistry by using on-DNA compatible reactions or off-DNA scaffold synthesis. Herein, we report the development of a series of novel on-DNA transformations based on oxindole scaffolds for the design and synthesis of diversity-oriented DNA-encoded libraries for screening. Specifically, we have developed 1,3-dipolar cyclizations, cyclopropanations, ring-opening of reactions of aziridines and Claisen–Schmidt condensations to construct diverse oxindole derivatives. The majority of these transformations enable a diversity-oriented synthesis of DNA-encoded oxindole libraries which have been used in the successful hit identification for three protein targets. We have demonstrated that a diversified strategy for DEL synthesis could accelerate the application of synthetic chemistry for drug discovery.

Constructing DNA-encoded oxindole libraries by a diversified strategy.     

Merging C(sp3)–H activation with DNA-encoding

DNA-encoded library (DEL) technology has the potential to dramatically expedite hit identification in drug discovery owing to its ability to perform protein affinity selection with millions or billions of molecules in a few experiments. To expand the molecular diversity of DEL, it is critical to develop different types of DNA-encoded transformations that produce billions of molecules with distinct molecular scaffolds. Sequential functionalization of multiple C–H bonds provides a unique avenue for creating diversity and complexity from simple starting materials. However, the use of water as solvent, the presence of DNA, and the extremely low concentration of DNA-encoded coupling partners (0.001 M) have hampered the development of DNA-encoded C(sp³)–H activation reactions. Herein, we report the realization of palladium-catalyzed C(sp³)–H arylation of aliphatic carboxylic acids, amides and ketones with DNA-encoded aryl iodides in water. Notably, the present method enables the use of alternative sets of monofunctional building blocks, providing a linchpin to facilitate further setup for DELs. Furthermore, the C–H arylation chemistry enabled the on-DNA synthesis of structurally-diverse scaffolds containing enriched C(sp³) character, chiral centers, cyclopropane, cyclobutane, and heterocycles.

DNA-compatible C(sp³)–H activation reactions of aliphatic carboxylic acids, amides, and ketones were developed for efficient access to DEL synthesis.     

The Morita–Baylis–Hillman reaction for non-electron-deficient olefins enabled by photoredox catalysis

A strategy for overcoming the limitation of the Morita–Baylis–Hillman (MBH) reaction, which is only applicable to electron-deficient olefins, has been achieved via visible-light induced photoredox catalysis in this report. A series of non-electron-deficient olefins underwent the MBH reaction smoothly via a novel photoredox-quinuclidine dual catalysis. The in situ formed key β-quinuclidinium radical intermediates, derived from the addition of olefins with quinuclidinium radical cations, are used to enable the MBH reaction of non-electron-deficient olefins. On the basis of previous reports, a plausible mechanism is suggested. Mechanistic studies, such as radical probe experiments and density functional theory (DFT) calculations, were also conducted to support our proposed reaction pathways.

A strategy for overcoming the limitation of the Morita–Baylis–Hillman (MBH) reaction, which is only applicable to electron-deficient olefins, has been achieved via visible-light induced photoredox catalysis in this report.     

Highly efficient on-DNA amide couplings promoted by micelle forming surfactants for the synthesis of DNA encoded libraries

DNA encoded libraries (DELs) represent powerful new technology for finding small molecule ligands for proteins and are increasingly being applied to hit finding in medicinal chemistry. Crucial to the synthesis of high quality DELs is the identification of chemical reactions for their assembly that proceed with very high conversion across a range of different substrates, under conditions compatible with DNA-tagged substrates. Many current chemistries used in DEL synthesis do not meet this requirement, resulting in libraries of low fidelity. Amide couplings are the most commonly used reaction in synthesis of screening libraries and also in DELs. The ability to carry out highly efficient, widely applicable amide couplings in DEL synthesis would therefore be highly desirable. We report a method for amide coupling using micelle forming surfactants, promoted by a modified linker, that is broadly applicable across a wide range of substrates. Most significantly, this works exceptionally well for coupling of DNA-conjugated carboxylic acids (N-to-C) with amines in solution, a procedure that is currently very inefficient. The optimisation of separate procedures for coupling of DNA-conjugated acids and amines by reagent screening and statistically driven optimisation is described. The generality of the method is illustrated by the application to a wide range of examples with unprecedented levels of conversion. The utility of the (N-to-C) coupling of DNA-conjugated acids in DEL synthesis is illustrated by the three cycle synthesis of a fully DNA-encoded compound by two cycles of coupling of an aminoester, with intermediate ester hydrolysis, followed by capping with an amine. This methodology will be of great utility in the synthesis of high fidelity DELs.

Highly efficient forward and reverse on-DNA amide couplings were developed exploiting hydrophobic linkers in combination with the micelle forming surfactant TPGS-750M. The method is highly effective for a wide range of substrates in the synthesis of DNA-encoded libraries.     

Expanding the scope of native chemical ligation – templated small molecule drug synthesis via benzanilide formation

We describe a reaction system that enables the synthesis of Bcr–Abl tyrosine kinase inhibitors (TKI) via benzanilide formation in water. The reaction is based on native chemical ligation (NCL). In contrast to previous applications, we used the NCL chemistry to establish aromatic rather than aliphatic amide bonds in coupling reactions between benzoyl and o-mercaptoaniline fragments. The method was applied for the synthesis of thiolated ponatinib and GZD824 derivatives. Acid treatment provided benzothiazole structures, which opens opportunities for diversification. Thiolation affected the affinity for Abl1 kinase only moderately. Of note, a ponatinib-derived benzothiazole also showed nanomolar affinity. NCL-enabled benzanilide formation may prove useful for fragment-based drug discovery. To show that benzanilide synthesis can be put under the control of a template, we connected the benzoyl and o-mercaptoaniline fragments to DNA and peptide nucleic acid (PNA) oligomers. Complementary RNA templates enabled adjacent binding of reactive conjugates triggering a rapid benzoyl transfer from a thioester-linked DNA conjugate to an o-mercaptoaniline-DNA or -PNA conjugate. We evaluated the influence of linker length and unpaired spacer nucleotides within the RNA template on the product yield. The data suggest that nucleic acid-templated benzanilide formation could find application in the establishment of DNA-encoded combinatorial libraries (DEL).

The templated native chemical ligation between benzoyl thioesters and o-mercaptoaniline fragments proceeds in water and provides benzanilides that have nanomolar affinity for Abl1 kinase.     

Rapid access to t-butylalkylated olefins enabled by Ni-catalyzed intermolecular regio- and trans-selective cross-electrophile t-butylalkylation of alkynes

Among the carbo-difunctionalization of alkynes, the stereoselective dialkylation of alkynes is the most challenging transformation due to associated competitive side reactions and thus remains underdeveloped. Herein, we report the first Ni-catalyzed regio- and trans-selective cross-dialkylation of alkynes with two distinct alkyl bromides to afford olefins with two aliphatic substituents. The reductive conditions circumvent the use of organometallic reagents, enabling the cross-dialkylation process to occur at room temperature from two different alkyl bromides. This operationally simple protocol provides a straightforward and practical access to a wide range of stereodefined dialkylated olefins with broad functional group tolerance from easily available starting materials.

A direct reductive cross-dialkylation of alkynes is achieved to afford trans-dialkylated olefins using two distinct alkyl bromides. The reaction undergoes with exclusive chemo-, regio- and stereoselectivity without the use of organometallic reagents.     

Asymmetric [3 + 2] photocycloadditions of cyclopropylamines with electron-rich and electron-neutral olefins

Radical addition to olefins is a common and useful chemical transformation. In the context of offering enantioenriched three-dimensional molecules via such a highly reactive process, chiral hydrogen-bonding (H-bonding) catalysis has been widely used to provide enantiocontrol. The current strategies for operating H-bonding induction are confined to following that are prevalent in ionic-type manifolds. Here, we report a novel protocol towards electron-rich olefins based on converting these species from acting as H-bonding donors to acceptors. It facilitates the first development of asymmetric [3 + 2] photocycloadditions with cyclopropylamines. The method is also effective for electron-neutral olefins, in which the successful construction of all-carbon quaternary stereocentres from 1,1-diaryl ethylenes that feature two structurally similar aryl substituents demonstrates the versatility of this new chiral H-bonding catalytic strategy. Furthermore, the importance of the obtained six kinds of products in pharmaceuticals and asymmetric catalysis underscores the practicability of this work.

Radical addition to olefins is a common and useful chemical transformation.     

Palladium-catalyzed difluoroalkylative carbonylation of styrenes toward difluoropentanedioates

The introduction of fluorine atoms into organic molecules is an attractive but challenging topic. In this work, an interesting palladium-catalyzed difluoroalkylative carbonylation of aryl olefins has been developed. A wide range of aryl olefins were transformed into the corresponding difluoropentanedioate compounds with good functional-group tolerance and excellent regioselectivity. Inexpensive ethyl bromodifluoroacetate acts both as a difluoroalkyl precursor and a nucleophile here. Additionally, a scale–up reaction was also performed successfully, and further transformations of the obtained product were shown as well.

An interesting palladium-catalyzed difluoroalkylative carbonylation of aryl olefins has been developed. A wide range of aryl olefins were transformed into the corresponding difluoropentanedioate compounds with good functional-group tolerance and excellent regioselectivity.     

Light-driven reduction of aromatic olefins in aqueous media catalysed by aminopyridine cobalt complexes

A catalytic system based on earth-abundant elements that efficiently hydrogenates aryl olefins using visible light as the driving-force and H₂O as the sole hydrogen atom source is reported. The catalytic system involves a robust and well-defined aminopyridine cobalt complex and a heteroleptic Cu photoredox catalyst. The system shows the reduction of styrene in aqueous media with a remarkable selectivity (>20 000) versus water reduction (WR). Reactivity and mechanistic studies support the formation of a [Co–H] intermediate, which reacts with the olefin via a hydrogen atom transfer (HAT). Synthetically useful deuterium-labelled compounds can be straightforwardly obtained by replacing H₂O with D₂O. Moreover, the dual photocatalytic system and the photocatalytic conditions can be rationally designed to tune the selectivity for aryl olefin vs. aryl ketone reduction; not only by changing the structural and electronic properties of the cobalt catalysts, but also by modifying the reduction properties of the photoredox catalyst.

A dual catalytic system based on earth-abundant elements reduces aryl olefins to alkanes in aqueous media under visible light. Mechanistic studies allow for rational tunning of the system for the selective reduction of aryl olefins vs ketones and vice versa.     

Fe-catalyzed Fukuyama-type indole synthesis triggered by hydrogen atom transfer

Fe, Co, and Mn hydride-initiated radical olefin additions have enjoyed great success in modern synthesis, yet the extension of other hydrogen radicalophiles instead of olefins remains largely elusive. Herein, we report an efficient Fe-catalyzed intramolecular isonitrile–olefin coupling reaction delivering 3-substituted indoles, in which isonitrile was firstly applied as the hydrogen atom acceptor in the radical generation step by MHAT. The protocol features low catalyst loading, mild reaction conditions, and excellent functional group tolerance.

A mild and efficient method has been developed to synthesize 3-substituted indoles via an Fe-catalyzed radical isonitrile–olefin coupling reaction initiated by MHAT to isonitriles.     

Desymmetrization of pibrentasvir for efficient prodrug synthesis

A novel and practical desymmetrization tactic is described to access a new class of pibrentasvir prodrugs. The homotopic benzimidazoles of pibrentasvir (PIB) are differentiated via a one-pot di-Boc/mono-de-Boc selective N-Boc protection and formaldehyde adduct formation sequence, both enabled by crystallization-induced selectivity. The first step represents the only known application of the Horeau principle of statistical amplification for C₂-symmetric polyheterocycle regioselective functionalization. The resulting versatile intermediate is employed in the high-yielding preparation of several pibrentasvir prodrug candidates.

Horeau principle statistical amplification and solubility-driven selectivities allow C₂-desymmetrization of pibrentasvir without typically required internal functionalization or steric proximity effects.     

Asymmetrically bridged aroyl-S,N-ketene acetal-based multichromophores with aggregation-induced tunable emission

Asymmetrically bridged aroyl-S,N-ketene acetals and aroyl-S,N-ketene acetal multichromophores can be readily synthesized in consecutive three-, four-, or five-component syntheses in good to excellent yields by several successive Suzuki-couplings of aroyl-S,N-ketene acetals and bis(boronic)acid esters. Different aroyl-S,N-ketene acetals as well as linker molecules yield a library of 23 multichromophores with substitution and linker pattern-tunable emission properties. This allows control of different communication pathways between the chromophores and of aggregation-induced emission (AIE) and energy transfer (ET) properties, providing elaborate aggregation-based fluorescence switches.

A library of 23 asymmetrically linked aroyl-S,N-ketene acetal solid-state emissive multichromophores accessed by one-pot multicomponent reactions exhibits AIE- and AIEE-active behavior as well as dual emission and potential energy transfer.     

An induced-fit model for asymmetric organocatalytic reactions: a case study of the activation of olefins via chiral Brønsted acid catalysts

We elucidate the stereo-controlling factors of the asymmetric intramolecular hydroalkoxylation of terminal olefins catalyzed by bulky Brønsted acids [Science2018, 359 (6383), 1501–1505] using high-level electronic structure methods. The catalyst–substrate interaction is described using a dispersion-driven induced-fit model, in which the conformational changes of the catalyst and of the substrate in the transition states are governed to a large extent by London dispersion forces. The distortion energy of the catalyst is dominated by the change in the intramolecular dispersion interactions, while intermolecular catalyst–substrate dispersion interactions are the major stabilizing contribution in the transition state. This model provides a new general framework in which to discuss the stereoselectivity of transformations catalyzed by such confined organocatalysts.

We elucidate the stereo-controlling factors of the asymmetric intramolecular hydroalkoxylation of terminal olefins catalyzed by bulky Brønsted acids [Science2018, 359 (6383), 1501–1505] using high-level electronic structure methods.     

Intramolecular photochemical [2 + 1]-cycloadditions of nucleophilic siloxy carbenes

Visible light induced singlet nucleophilic carbenes undergo rapid [2 + 1]-cycloaddition with tethered olefins to afford unique bicyclo[3.1.0]hexane and bicyclo[4.1.0]heptane scaffolds. This cyclopropanation process requires only visible light irradiation to proceed, circumventing the use of exogenous (photo)catalysts, sensitisers or additives and showcases a vastly underexplored mode of reactivity for nucleophilic carbenes in chemical synthesis. The discovery of additional transformations including a cyclopropanation/retro-Michael/Michael cascade process to afford chromanones and a photochemical C–H insertion reaction are also described.

Visible light induced singlet nucleophilic carbenes undergo rapid [2 + 1]-cycloaddition with tethered olefins to afford unique bicyclo[3.1.0]hexane and bicyclo[4.1.0]heptane scaffolds.     

Catalyst-free arylation of sulfonamides via visible light-mediated deamination

A novel arylation of sulfonamides with boronic acids to afford numerous diaryl sulfones via a visible light-mediated N–S bond cleavage other than the typical transition-metal-catalyzed C(O)–N bond activation is described. This methodology, which represents the first catalyst-free protocol for the sulfonylation of boronic acids, is characterized by its simple reaction conditions, good functional group tolerance and high efficiency. Several successful examples for the late-stage functionalization of diverse sulfonamides indicate the high potential utility of this method in pharmaceutical science and organic synthesis.

The simple, catalyst-free sulfonylation of boronic acids with sulfonamides via a visible light-mediated N–S bond cleavage is described, affording diaryl sulfones with high efficiency. Late-stage functionalization of sulfonamide drugs was shown.     

Exploring a new class of singlet fission fluorene derivatives with high-energy triplets

In this study, we report strong experimental evidence for singlet fission (SF) in a new class of fluorene-based molecules, exhibiting two-branched donor–acceptor structures. The time-resolved spectroscopic results disclose ultrafast formation of a double triplet state (occurring in few picoseconds) and efficient triplet exciton separation (up to 145% triplet yield). The solvent polarity effect and the role of intramolecular charge transfer (ICT) on the SF mechanism have been thoroughly investigated with several advanced spectroscopies. We found that a stronger push–pull character favors SF, as long as the ICT does not act as a trap by opening a competitive pathway. Within the context of other widely-known SF chromophores, the unconventional property of generating high-energy triplet excitons (ca. 2 eV) via SF makes these materials outstanding candidates as photosensitizers for photovoltaic devices.

We found that a stronger push–pull character favours SF, as long as the ICT does not act as a trap. The unique property of generating high-energy triplets (ca. 2 eV) via SF makes these materials outstanding candidates for photovoltaic applications.     

Development of a fluorescent probe library enabling efficient screening of tumour-imaging probes based on discovery of biomarker enzymatic activities

Fluorescent probes that can selectively detect tumour lesions have great potential for fluorescence imaging-guided surgery. Here, we established a library-based approach for efficient screening of probes for tumour-selective imaging based on discovery of biomarker enzymes. We constructed a combinatorial fluorescent probe library for aminopeptidases and proteases, which is composed of 380 probes with various substrate moieties. Using this probe library, we performed lysate-based in vitro screening and/or direct imaging-based ex vivo screening of freshly resected clinical specimens from lung or gastric cancer patients, and found promising probes for tumour-selective visualization. Further, we identified two target enzymes as novel biomarker enzymes for discriminating between tumour and non-tumour tissues. This library-based approach is expected to be an efficient tool to develop tumour-imaging probes and to discover new biomarker enzyme activities for various tumours and other diseases.

Efficient methodology to develop tumor-imaging fluorescent probes based on screening with our newly constructed probe library for aminopeptidase/protease (380 probes) and clinical samples has been established.