Diversified strategy for the synthesis of DNA-encoded oxindole libraries

Abstract

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.

Fig. 1. The workflow of oxindole-scaffold DNA-encoded library.

Fig. 2. Design and synthesis of diversified oxindole DNA-encoded libraries. (a) Isatin derivatives were commercially available or synthesized via Sandmeyer isatin synthesis. (b) On-DNA three-component cycloaddition reaction. (c) 3-Diazoisatin derivatives were transformed by 3-N-tosylhydrazone isatin derivatives under basic conditions. (d) PdCl_2-promoted on-DNA cyclopropanation reaction. (e) Spiroaziridine isatin derivatives were transformed by aza-Corey–Chaykovsky reaction. (f) On-DNA amidation reaction conditions. (g) On-DNA ring-opening reaction. (h) Oxindole derivatives were commercially available. (i) On-DNA Claisen–Schmidt condensation.

Fig. 3. On-DNA three-component cyclization using three DNA-tagging points. (A) Three types of DNA-tagged spiropyrrolizidine centered modes. (B) Optimization of on-DNA three-component cyclization from acrylamide linked DNA oligonucleotides. Scope of substituted isatins, prolines and amino acids. (C) on-DNA reactions from DNA-linked 6. (a) Isatin (200 equiv.), proline (300 equiv.), 80 °C, 3 h. (D) On-DNA cyclization reaction from DNA-linked 8. (b) Acryl ester (200 equiv.), proline (200 equiv.), rt, 3 h. (E) On-DNA cyclization reaction from DNA-linked 10. (c) Acryl ester (200 equiv.), proline (200 equiv.), rt, 3 h. Conversions determined by LCMS.

Fig. 4. On-DNA cyclopropanation reaction.

Fig. 5. On-DNA ring-opening reactions by nucleophiles.

Fig. 6. On-DNA Claisen–Schmidt condensation reaction.

Fig. 7. (A) The structures of DNA-encoded libraries. DNA-encoded library A, which was divided into five sub-libraries: DEL-A1, a di-synthon library; DEL-A2, a tri-synthon library contained a Heck coupling reaction; DEL-A3, a tri-synthon library contained a Suzuki coupling reaction; DEL-A4, a tri-synthon library contained an amidation reaction, reductive amination reaction and urea formation; DEL-A5, a tri-synthon library contained an amidation reaction, these reaction schemes are listed in S6 of ESI; DNA-encoded library C based on DNA-compatible ring-opening methodology; DNA-encoded library D based on DNA compatible Claisen condensation methodology. (B) Physicochemical property distribution of DELs, including AlogP, HBA, HBD, MW, RB, TPSA and PCA. For PCA, PC means principal component, and it's a linear combination of variables (e.g. MW, AlogP, etc.). Each PC value accounts for the percentage of the total variance around the PCs. When PC1 & PC2 accounts for the majority of the variation (>70%), we could use a 2D graph to represent the chemical space.

Fig. 8. Selection outcomes of DELs-A3–5. (A) Selection data analysis of DEL-A3 for BRD4-BD1. (B) Selection data analysis of DEL-A4 for BRD4-BD1. (C) Selection data analysis of DEL-A5 for BRD4-BD1. (D) Selection data analysis of DEL-A3 for Aurora. (E) Selection data analysis of DEL-A4 for P300. (F) Validation of three compounds 21, 22, and 23 by off-DNA resynthesis and biochemical assay data. (G) Validation of two compounds 24 and 25 by off-DNA resynthesis and IC₅₀ assay data.