DNA-encoded libraries (DELs) are powerful drug discovery tools, enabling rapid hit generation against immobilized protein targets. However, translating these hits is often hampered by synthetic inefficiency and, for libraries of "beyond-Rule-of-5" compounds such as macrocyclic peptides, by enrichment of poorly cell-permeable members. Here we introduce LC-seq, a sequencing-based chromatographic strategy that simultaneously assesses synthetic fidelity and permeability-relevant lipophilicity for individual library members. Applying LC-seq to a proof-of-concept 120,000-member peptide library, we mapped reaction efficiency across all synthetic cycles and measured each member's lipophilicity from sequencing-count-derived retention times. We identified building-block-specific structure-reactivity trends, and the on-DNA lipophilicities of resynthesized members correlated strongly with their off-DNA lipophilicities and passive permeability in artificial membranes. This simple approach enables direct, per-member assessment of compound quality and lipophilicity, with projected scalability to libraries of millions.
Grant Koch, M. F. Lawler, Adam Murray et al.· Journal of Medicinal Chemist...· 0 citations
The LC3/GABARAP protein family is a promising target for selective inhibition of autophagy. Further, LC3/GABARAP ligands have been used as targeted degraders of soluble proteins, protein aggregates, mitochondria, lipid droplets, and RNA. However, the small molecules used for such applications have poor binding affinity and known off-target effects. LC3/GABARAP proteins are challenging targets for small-molecule drug development due to their long, shallow binding grooves. In this work, we evaluate multiple approaches to stabilizing the extended structure of the native binding motif, producing N-methylated peptides and stapled peptides with low nanomolar affinity. A crystal structure and molecular dynamics simulations support a model where the N-methylation pre-organizes the motif into an extended, strand-like structure. N-methylation allowed minimization of the binding motif to a tetrapeptide that retained sub-micromolar affinity while minimizing charge and overall molecular weight. The truncated, N-methylated tetrapeptide showed passive permeability in artificial membrane and cell-based transwell assays. These results highlight new drug-like space for LC3/GABARAP ligands with high affinity and subfamily selectivity. Table of Contents Graphic Drawn and developed by Mollie McGibbon and Joshua Kritzer
Imani McDonald, Joana A. Wilms, Nicholas Cardi et al.· bioRxiv· 0 citations
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