
Affinity screenings with encoded libraries are transformative tools for rapid hit discovery from vast compound collections. Yet the adaptation of established chemical reactions to DNA-encoded libraries (DELs) remains challenging due to DNA-compatibility constraints and mismatches between barcode and chemical structure in case of incomplete reactions or side product formation. Recently, we introduced self-encoded libraries (SELs) as a barcode-free alternative to DELs, offering unmatched flexibility in reaction conditions. The SEL platform decodes screening hits directly from their chemical structure, avoiding the problem of mismatched barcode-compound pairs. Here, we expand the SEL platform to Buchwald-Hartwig aminations, enabling the construction of high diversity SELs. We performed a thorough reaction condition optimization and tested a scope of > 170 different building blocks, including diverse aryl bromides and a broad spectrum of aromatic and aliphatic amines. We adapted our automated MS/MS-based decoding methodology SIRIUS-COMET to the resulting scaffolds, enabling accurate hit decoding from complex mixtures. A 25,725-member library was synthesized and screened all at once against carbonic anhydrase IX (CAIX), resulting in robust enrichment of hits with specific building block patterns and yielding several nanomolar-affinity binders. This work showcases the seamless integration of palladium-catalyzed cross-couplings into SELs, expanding the chemical space of this technology and accelerating hit discovery with high synthetic versatility.
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