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Progress in medicine is driven by a deeper understanding of human biology and is enabled by ligand discovery. The search for molecules capable of specific binding to validated biological targets is a formidable challenge mastered by many actors from diverse fields of expertise and empowered by the combinations of different methodologies. As some biological targets are still resisting these colossal efforts, novel technologies have been developed, and among them stand DNA-encoded chemical libraries (DELs). In the last decade, DELs have been gaining momentum for the facilitated discovery of ligands from large collections of small molecules. This work aimed at further developing dual-display DEL technology and at overcoming some of its limitations to pursue difficult targets, especially those presenting extended binding surfaces. Our ambition was to display and encode pharmacophores in the chemical space between small molecules and biologics. The general context of ligand discovery and how DEL research has become an active part of it is exposed in the introduction. Then more precise perspectives of dual-display DELs and of macrocyclic DELs are presented, as this work intends to bring them together to create the next-generation dual-display DELs. In the first part of this thesis, an extended encoding platform for dual-display DELs that allows for the simultaneous display of an unprecedented number of building blocks was established. The novel system, termed “large encoding design” (LED), was optimized until its reliability and robustness could be thoroughly demonstrated. Then it was successfully compared to a previously established encoding system and validated through the recovery of known binders in model experiments. In the second part of this work, highly combinatorial libraries supported by the novel LED platform were synthesized. These libraries display combinations of macrocycles, comparable to the recognition regions of antibodies or nanobodies, but still at a smaller molecular scale. The macrocyclic architectures are endowed by an originally designed tetra-functionalized scaffold and the stringent selection of highly reactive and diverse sets of building blocks. Finally, both a dual-display DEL comprising 56,250,000 unique combinations of macrocycles and its non-cyclized correlate counting 6,250,000 members were constructed. The obtained DELs of high purity were employed for a screening campaign against twenty biological targets of pharmaceutical relevance. Preliminary results showed positive outcomes for the model systems and promising fingerprints for de novo ligand discovery, paving the way for next-generation dual-display DELs to become a valuable modality for drug discovery. |
