Construction of Isoquinolone Scaffolds on DNA via Rhodium(III)-Catalyzed C-H Activation.

Isoquinolone is one of the most common heterocyclic core structures in countless natural products and many bioactive compounds. Here, a highly efficient approach to synthesize isoquinolone scaffolds on DNA via rhodium(III)-catalyzed C-H activation has been described. This chemistry transformation is robust and has shown good compatibility with DNA, which is suitable for DNA-encoded library synthesis.

Optimization of PROTAC Ternary Complex Using DNA Encoded Library Approach.

The proteolysis targeting chimera (PROTAC) strategy results in the down-regulation of unwanted protein(s) for disease treatment. In the PROTAC process, a heterobifunctional degrader forms a ternary complex with a target protein of interest (POI) and an E3 ligase, which results in ubiquitination and proteasomal degradation of the POI. While ternary complex formation is a key attribute of PROTAC degraders, modification of the PROTAC molecule to optimize ternary complex formation and protein degradation can be a labor-intensive and tedious process. In this study, we take advantage of DNA-encoded library (DEL) technology to efficiently synthesize a vast number of possible PROTAC molecules and describe a parallel screening approach that utilizes DNA barcodes as reporters of ternary complex formation and cooperative binding. We use a designed PROTAC DEL against BRD4 and CRBN to describe a dual protein affinity selection method and the direct discovery of novel, potent BRD4 PROTACs that importantly demonstrate clear SAR. Such an approach evaluates all the potential PROTACs simultaneously, avoids the interference of PROTAC solubility and permeability, and uses POI and E3 ligase proteins in an efficient manner.

PAC-FragmentDEL - photoactivated covalent capture of DNA-encoded fragments for hit discovery.

We describe a novel approach for screening fragments against a protein that combines the sensitivity of DNA-encoded library technology with the ability of fragments to explore what will bind. Each of the members of the library consists of a fragment which is linked to a photoactivatable diazirine moiety. Split and pool synthesis combines each fragment with a set of linkers with the version of the library reported here containing some 70k different compounds, each with an individual DNA code. Incubation of the library with a protein sample is followed by photoactivation, washing and subsequent PCR and sequencing which allows the individual fragment hits to be identified. We illustrate how the approach allows successful hit fragment identification using only microgram quantities of material for two targets. PAK4 is a kinase for which conventional fragment screening has generated many advance leads. The as yet undrugged target, 2-epimerase, presents a more challenging active site for identification of hit compounds. In both cases, PAC-FragmentDEL identified fragments validated as hits by ligand-observed NMR measurements and crystal structure determination of off-DNA sample binding to the proteins.

Photoredox Deaminative Alkylation in DNA-Encoded Library Synthesis.

Herein, we report an on-DNA photoredox-mediated deaminative alkylation method for diversifying DNA-tagged acrylamide substrate with amine-derived radicals. The radicals can be conveniently generated from sterically hindered primary amines, and the deaminative alkylation can tolerate a broad array of radical precursors. Furthermore, the methodology is applicable to Boc-protected diamines, free amino acids, and aryl halides, which bear functional groups enabling additional rounds of diversification. The method is believed to offer a high potential for constructing DNA-encoded libraries, as was demonstrated by the production of a mock library in a 2 × 3 matrix format and confirmation of DNA stability by UPLC-MS and qPCR experiments.

Palladium-Mediated Hydroamination of DNA-Conjugated Aryl Alkenes.

C-N bond formation is one of the most commonly used reactions in medicinal chemistry. Herein, we report an efficient Pd-promoted hydroamination reaction between DNA-conjugated aryl alkenes and a wide scope of aliphatic amines. The described reactions are demonstrated in good to excellent conversions to furnish C (sp3)-N bonds on DNA. This DNA-compatible transformation has strong potentials for the application into DNA-encoded library synthesis.

On-DNA Derivatization of Quinoxalin-2-ones by Visible-Light-Triggered Alkylation with Carboxylic Acids.

An efficient visible-light-induced alkylation of DNA-tagged quinoxaline-2-ones was described. The methodology demonstrated moderate-to-excellent conversions under mild conditions. The reaction was found to be tolerant with both N-protected α-amino acids and aliphatic carboxylic acids and could be applied to the synthesis of focused DNA-encoded quinoxalin-2-one libraries.

Functionalization of DNA-Tagged Alkenes Enabled by Visible-Light-Induced C-H Activation of N-Aryl Tertiary Amines.

A highly efficient approach to C(sp3)-C(sp3) bond construction via on-DNA photoredox catalysis between on-DNA alkenes and N-aryl tertiary amines was developed. The methodology demonstrated 55%-95% conversions without obvious DNA damage, as seen by qPCR tests. Furthermore, various functional groups, such as carboxylic acids, aldehydes, and aryl halides, that can be used to create library diversities were shown to be tolerant of the C-H activation conditions.

Development of DNA-compatible hydroxycarbonylation reactions using chloroform as a source of carbon monoxide.

A robust palladium-catalyzed hydroxycarbonylation of aryl halides on DNA has been developed. Instead of Mo(CO)6 as a source of carbon monoxide as previously described in the literature, chloroform was used as a surrogate in this report for the purpose of avoiding to use a large excess of molybdenum reagent which is not totally soluble in aqueous reaction mixtures.

Cholesterol-Modified Oligonucleotides as Internal Reaction Controls during DNA-Encoded Chemical Library Synthesis.

We report two cholesterol-modified oligonucleotides for use as internal controls for on-DNA reactions during the pooled stages of a DNA-encoded chemical library (DECL) synthesis. As these cholesterol-tagged oligonucleotides are chromatographically separable from normal DECL intermediates, they can be directly monitored by mass spectrometry to track reaction progression within a complex pool of DNA. We observed similar product conversions for reactions on substrates linked to a standard DECL DNA headpiece, to the cholesterol-modified oligonucleotides, and to the cholesterol-modified oligonucleotides while in the presence of pooled DECL synthetic intermediates-validating their use as a representative control. We also highlight an example from a DECL production in which the use of the cholesterol-modified oligonucleotides provided quality control information that guided synthetic decisions. We conclude that the use of cholesterol-modified oligonucleotides as a regular control will significantly improve the quality of DECL productions.

C-S Coupling of DNA-Conjugated Aryl Iodides for DNA-Encoded Chemical Library Synthesis.

Thioethers have been widely found in biologically active compounds, including pharmaceuticals. In this report, a highly efficient approach to on-DNA construction of thioethers via Cu-promoted Ullmann cross-coupling between DNA-conjugated aryl iodides and thiols is developed. This methodology was demonstrated with medium to high yields, without obvious DNA damage. This reported reaction has strong potential for application in DNA-encoded chemical library synthesis.

Exploring Aldol Reactions on DNA and Applications to Produce Diverse Structures: An Example of Expanding Chemical Space of DNA-Encoded Compounds by Diversity-Oriented Synthesis.

A DNA-encoded chemical library (DECL) is built with combinatorial chemistry, which works by bringing chemical fragments together to generate diverse structures. However, chemical diversity of DNA-encoded chemical libraries is often limited by DNA compatible synthetic reactions. This report shows a conceptual strategy to expand chemical space of DNA-encoded chemical libraries by incorporation of diversity-oriented synthesis in DECL synthesis. We developed Aldol reactions on DNA in a combinatorial way. After obtaining DNA-tagged α, ß-unsaturated ketones which represent important chemical intermediates, many distinct structures with skeletal diversities are achieved by diversity-oriented synthesis.

A B2(OH)4-Mediated Synthesis of 2-Substituted Indazolone and Its Application in a DNA-Encoded Library.

Indazolone cores are among the most common structural components in medicinal chemistry and can be found in many biologically active molecules. In this report, a mild and efficient approach to 2-substituted indazolones via B2(OH)4-mediated reductive N-N bond formation is developed. This strategy features mild conditions, no request for a metal catalyst, and a wide scope for both aliphatic and aromatic amines. Meanwhile, this method was further successfully applied on DNA to construct indazolone cores for a DNA-encoded library. This will enable the production of a very attractive indazolone-cored library from simple amines and scaffolds, which will provide considerable diversity.

Synthesis of Multifunctional 2-Aminobenzimidazoles on DNA via Iodine-Promoted Cyclization.

2-Aminobenzimidazole cores are among the most common structural components in medicinal chemistry and can be found in many biologically active molecules. Herein, we report a mild protocol for the synthesis of multifunctional 2-aminobenzimidazoles on-DNA with broad substrate scopes. The reaction conditions expand our ability to design and synthesize 2-aminobenzimidazole core-focused DNA-encoded libraries.

Synthesis of C3-Alkylated Indoles on DNA via Indolyl Alcohol Formation Followed by Metal-Free Transfer Hydrogenation.

3-Alkylated indole cores have been found in countless natural products and many biologically active compounds, including pharmaceuticals. In this report, a highly efficient approach to C3-alkylated indole derivatives on DNA via indolyl alcohol formation followed by metal-free transfer hydrogenation is developed. This on-DNA C3 alkylation approach is attractive because library compounds can be constructed from simple aldehydes or acid functionalized aldehydes, which are widely commercially available.

Iron(II)-catalyzed intramolecular olefin aminofluorination.

An iron(II)-catalyzed diastereoselective olefin aminofluorination is reported (dr up to >20:1). This new transformation applies a functionalized hydroxylamine and Et3N·3HF as the nitrogen and fluorine source, which facilitates the efficient synthesis of ß-fluoro primary amines and amino acids from allylic alcohol derivatives. Preliminary mechanistic studies reveal that an iron-nitrenoid is a possible intermediate and that its reactivity and enantioselectivity can be efficiently modulated by ligands.

Iron(II)-catalyzed asymmetric intramolecular aminohydroxylation of indoles.

An enantioselective intramolecular indole aminohydroxylation reaction is catalyzed by iron(II)-chiral bisoxazoline (BOX) complexes (ee up to 99%, dr > 20:1). This discovery enables expedient asymmetric synthesis of a series of biologically active 3-amino oxindoles and 3-amino indolanes.

Iron(II)-catalyzed intramolecular aminohydroxylation of olefins with functionalized hydroxylamines.

A diastereoselective aminohydroxylation of olefins with a functionalized hydroxylamine is catalyzed by new iron(II) complexes. This efficient intramolecular process readily affords synthetically useful amino alcohols with excellent selectivity (dr up to > 20:1). Asymmetric catalysis with chiral iron(II) complexes and preliminary mechanistic studies reveal an iron nitrenoid is a possible intermediate that can undergo either aminohydroxylation or aziridination, and the selectivity can be controlled by careful selection of counteranion/ligand combinations.

Highly enantioselective cyclizations of conjugated trienes with low catalyst loadings: a robust chiral N-heterocyclic carbene enabled by acetic acid cocatalyst.

Densely functionalized cyclopentenones are useful synthetic intermediates. We report herein a new method to synthesize this important class of compounds through a highly enantioselective (98 → 99% ee) triene cyclization that is cocatalyzed by acetic acid and a chiral N-heterocyclic carbene (NHC). We discovered that acetic acid not only could coexist with NHCs but also could greatly stabilize the active catalyst, which enables a long-lived catalyst with high reactivity and selectivity.

Efficient total synthesis of (S)-14-azacamptothecin.

An efficient total synthesis of (S)-14-azacamptothecin has been accomplished in 10 steps and 56% overall yield from 5H-pyrano[4,3-d]pyrimidine 8. A mild Hendrickson reagent-triggered intramolecular cascade cyclization, a highly enantioselective dihydroxylation, and an efficient palladium-catalyzed transformation of an O-allyl into N-allyl group are the key steps in the synthesis. This work provides a much higher overall yield than the previous achievement and shows sound flexibility for the further applications that will lead to new bioactive analogues.

Expeditious total syntheses of camptothecin and 10-hydroxycamptothecin.

New expeditious total syntheses of (S)-camptothecin (16% overall yield, 95% ee) and (S)-10-hydroxycamptothecin (14% overall yield, 99% ee) have been accomplished, respectively, starting from readily available and inexpensive materials. Development, optimization, and successful application of the cascade reaction consisting of a pyrrolidine-catalyzed Michael addition, an intramolecular aldol condensation, and an oxidative aromatization, the intramolecular oxa Diels-Alder cycloaddition, and the Sharpless asymmetric dihydroxylation make these two new syntheses more efficient and straightforward.