Science of Synthesis

Willems, S.; Brunschweiger, A., Science of Synthesis: DNA-Encoded Libraries, (2024) 1, 351.

General Introduction

Isocyanide multicomponent reactions, commonly abbreviated to IMCRs, enable the synthesis of diverse molecular scaffolds, and thus, hold prominent roles in screening-library design and in medicinal chemistry.[‌1‌] Through clever combination of functionalized reaction partners, they provide access to a plethora of molecular-scaffold architectures.[‌2‌] However, slow reaction kinetics, the need for dry (anhydrous) reaction conditions in some cases, and the risk that nucleobases undergo reactions with isocyanides pose barriers to the adoption of IMCRs in solution-phase DNA-encoded library (DEL) synthesis.[‌3‌,‌4‌] These challenges can be overcome by performing the reactions on DNA oligonucleotides immobilized on a controlled-pore glass (CPG) solid phase (‌Figure 1‌ and ‌Figure 2‌, see also Section 2.11 by Raphael Franzini).[‌5‌–‌7‌] Prominent IMCRs that have been translated to DEL synthesis are the Ugi reaction (U-4CR, ‌Scheme 1‌), the Gröbke–Blackburn–Bienaymé reaction (GBB-3CR, ‌Scheme 1‌), the Ugi-azide reaction (UA-4CR, ‌Scheme 1‌), and the Ugi–aza-Wittig reaction (U-4CR/aza-Wittig, ‌Scheme 1‌). These reactions were all performed on DNA-tagged aldehydes,[‌5‌–‌7‌] and the Ugi reaction was additionally shown on a DNA-coupled carboxylic acid.[‌7‌] The first three reactions were tolerated by a native DNA strand, and could thus also be used for labeling DNA oligonucleotides, while the Ugi–aza-Wittig reaction caused significant DNA damage to a short DNA oligonucleotide,[‌5‌] requiring a DNA strand for barcoding that was chemically modified for greater stability to the reaction conditions, and termed csDNA (chemically stabilized DNA, ‌Figure 1‌).[‌6‌] The DNA strand used in this barcoding strategy was composed of three nucleobases: thymine; cytosine; and 7-deazaadenine, as a more depurination-resistant congener of adenine.[‌6‌] The barcodes were shown to tolerate a wider scope of reaction conditions, such as high loadings of transition-metal catalysts and strongly acidic conditions (that were, for instance, used to remove Boc groups from DNA-tagged products). Performing reactions on a CPG-coupled oligonucleotide, i.e. prior to cleavage of the oligomer from the solid phase, is a well-established strategy to append modifications to the sequence, and is commonly called “postsynthetic modification” (for further details, see Section 2.11).[‌5‌–‌10‌] Using this strategy in the initial steps of a DEL synthesis benefits from the option to perform reactions under anhydrous conditions and in organic solvents. Large excesses of reagents can be used to drive reactions to higher yields, and stringent washing conditions allow for the removal of contaminants. Importantly, protection of the nucleobase prevents chemical deamination that would cause barcode mutations. The significance of MCR chemistry approaches to DEL design was underpinned by recent publications by Satz et al.[‌11‌] and Lu et al.,[‌12‌] who published carbanion MCR reactions on a solubilized DNA tag containing all four natural nucleobases. The former group were able to translate the Van Leusen imidazole synthesis to DNA-tagged aldehyde ‌1‌ (‌Scheme 2‌). The central building block is 4-toluenesulfonylmethyl isocyanide (TosMIC; ‌3‌), a bivalent isocyanide that enables the formation of these important heterocycles in products ‌4‌ using a variety of primary amines (e.g. ‌2‌).[‌11‌] Instead of DNA-tagged aldehydes, Lu et al. attached Michael acceptor ‌5‌ to DNA. This was then reacted in a 1,3-dipolar addition reaction with azomethine ylides (‌Scheme 2‌).[‌12‌] These reactive carbanions were formed in a MCR fashion using isatins (e.g., ‌6‌) and proline (‌7‌), giving rise to spirocyclic DNA-tagged product ‌8‌.

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References