Systematic Evaluation of Electrophile Reactivity and Stability for Covalent DNA‐Encoded Libraries

ABSTRACT DNA‐encoded Chemical Libraries (DEL) are increasingly being used for the discovery of new covalent drugs. In the work presented here, we describe a systematic study that investigates the suitability of a selection of 59 electrophilic compounds for the construction of versatile covalent DNA‐encoded libraries. We investigated six classes of electrophilic warheads with the potential to form irreversible covalent bonds with a nucleophilic target, that is, aryl halides, alkenes, alkynes, epoxides, α‐chloro carboxylates, and aromatic methylsulfonates, as well as two classes of electrophiles capable of forming reversible covalent bonds, that is, aldehydes and nitriles. The electrophiles were successively tested for their capability to be installed on DNA, their stability as DNA‐conjugates under various storage conditions, and, ultimately, for their on‐DNA reactivity and selectivity toward S‐nucleophiles (cysteine) and N‐nucleophiles (lysine). Eventually, 21 DNA‐linked electrophiles with favorable properties were identified, with over 50% coupling to DNA, excellent storage stability, and high reactivity toward either S‐ or both S‐ and N‐nucleophilic substrates.