Jun Hyung Park, Jungyeon Kim, Chang Deok Seo, Hee Myeong Wang, Yeongju Lee, Hyun-Suk Lim

Organic Letters

DOI: 10.1021/acs.orglett.6c02366 

Abstract

Peptide nucleic acid (PNA) offers superior chemical stability relative to DNA, enabling encoded library synthesis under conditions incompatible with conventional DNA-based systems. Here, we report a robust PNA encoding strategy for the construction of large single-pharmacophore PNA-encoded libraries through enhanced discrimination between perfectly matched PNA/DNA duplexes and mismatches. This approach integrates a mismatch-destabilizing codon design with optimized hybridization conditions that selectively favor formation of perfectly matched duplexes.

Daniela Schaub, Alice Lessing, Fabian Meyer, Peter Stockinger, Miquel Estévez-Gay, Michael Eichenberger, Gerlis von Haugwitz, Andreas Gloger, Jörg Scheuermann, Rebecca Buller

Nature Catalysis

DOI: 10.1038/s41929-026-01576-x

Abstract

DNA-encoded chemical library (DEL) technology is a powerful tool in early-stage drug discovery. Although widely applied in industry and academia, challenges persist in generating DELs with high quality and chemical diversity. Low yields in building-block incorporation, limited selectivity and, most importantly, DNA damage from harsh reaction conditions compromise library quality, reduce signal-to-noise in affinity selections and ultimately hinder drug discovery. Here we show that tailored enzymes can be harnessed for the effective construction of molecular diversity on DNA under mild conditions. Targeting amide bond formation, we designed a cascade of complementary coenzyme A ligases and rationally tailored N -acyltransferases to access a broad amide scope on-DNA (>120 examples), identifying structural elements that optimize the biocatalysts’ DNA compatibility in the process. Integrating the enzymatic cascade with chemical synthesis led to the construction of a diverse DEL without damage to the DNA barcode, highlighting the biocatalysts’ applicability for early scaffold construction and late-stage functionalization.

Bailey McIntosh, Yen Chin Koay

Current Opinion in Chemical Biology

DOI: 10.1016/j.cbpa.2026.102726

Abstract

Natural product (NP)-inspired scaffolds occupy a privileged position in interface-centric drug discovery, as their preorganised three-dimensional architectures, multivalent contact surfaces, and covalent anchoring potential enable them to engage extended, topographically complex protein-protein and protein-nucleic acid interfaces. This review argues that modern platforms are now making these interactions systematically accessible, shifting NP drug discovery from occupancy-based inhibition toward interface stabilisation and induced proximity at targets previously considered undruggable. We evaluate how trillion-scale DNA-encoded libraries, RaPID-based macrocycle selection, and covalent chemoproteomics interrogate vast chemical spaces to identify compounds with non-classical binding modes relevant to proximity-driven therapeutic discovery, assessing both their demonstrated strengths and current limitations in the context of interface-centric therapeutics. We further discuss how AI-based tools support network prioritisation, interface hotspot prediction, and ternary complex modelling, while noting that computational predictions require independent experimental validation and do not yet replace biochemical evidence. We propose that systematic integration of NP-inspired scaffolds with modern discovery platforms and computational tools, represents the most productive current framework for targeting disease-relevant complexes previously considered inaccessible, expanding the boundary of druggability across oncology, cardiovascular, and metabolic medicine.

Qigui Nie, Junshan Fan, Xianfu Fang, Xiaoyue Yang, Gong Zhang, Yangfeng Li, Yizhou Li

Organic Letters

DOI: 10.1021/acs.orglett.6c02792

Abstract

We report a DNA-compatible linchpin strategy for the construction and late-stage diversification of macrocyclic peptide DNA-encoded libraries (MPDELs). Treatment of DNA-conjugated linear peptides with 1,5-dichloropentane-2,4-dione (DPD) enabled highly efficient macrocyclization while introducing a versatile 1,3-diketone linchpin. Subsequent DNA-compatible late-stage diversification afforded four classes of heterocycle-embedded DNA-conjugated macrocycles, including pyrazoles, azolopyrimidines, 2-aminonicotinamides, and 2-hydroxynicotinonitriles, with a broad substrate scope and high conversion. A scale-up test, cross-substrate scope study, and enzymatic ligation demonstrated excellent compatibility with DNA-encoded library synthesis, providing a versatile platform for expanding the chemical space of macrocyclic peptide DNA-encoded libraries.

Qigui Nie, Xufeng Li, Xianfu Fang, Junshan Fan, Xia Yang, Gong Zhang, Yangfeng Li, Yizhou Li

Chinese Journal of Chemistry

DOI: 10.1002/cjoc.70673

Abstract

Comprehensive Summary DNA‐encoded library (DEL) technology has emerged as a powerful platform for peptide drug discovery by enabling the rapid construction and screening of vast chemical space through on‐DNA amino acid coupling. However, despite the critical role of unnatural amino acids (UAAs) in improving peptide stability, bioavailability, and target specificity, the limited availability of structurally diverse DNA‐compatible UAA building blocks remains a major bottleneck for expanding the chemical diversity of DNA‐encoded peptide libraries. Herein, we report a robust and DNA‐compatible strategy for the on‐DNA generation of dehydroalanine (Dha) through the mild elimination of DNA‐conjugated cysteine under biocompatible conditions. Acting as a highly versatile synthetic linchpin, Dha enables the divergent installation of a broad spectrum of UAAs featuring sulfur‐, nitrogen‐, carbon‐, phosphorus‐containing, and cyclic side chains, thereby substantially enriching accessible peptide chemical space. Beyond serving as a diversification handle, the utility of this platform was demonstrated in multiple settings, including mock combinatorial peptide library synthesis, late‐stage functionalization of bioactive peptide motifs, and on‐DNA peptide macrocyclization, highlighting its broad synthetic scope and operational flexibility. Importantly, Dha also functions as an electrophilic covalent warhead for ligand‐directed protein crosslinking, expanding its application beyond library diversification. Leveraging this unique reactivity, we further established a cysteine “unmasking” strategy that enables crosslinking‐assisted DEL selection. As a proof of concept, a Dha‐containing DEL screened against carbonic anhydrase II successfully identified target binders through covalent capture. Collectively, this work introduces a generalizable approach for expanding the structural diversity and functional complexity of DNA‐encoded peptide libraries while integrating crosslinking‐assisted selection capabilities, thereby providing new opportunities for peptide ligand discovery and covalent probe development.

Hangke Ma, Peng Chen, Siyue Chen, Han Zhang, Fanming Zeng, Zhijun Han, Li Chen, Ayun Luo, Huanqing Zhang, Zhaomei Sun, Kehan Zhou, Lijun Xue, Kexin Yang, Yun Jin Hu

ACS Medicinal Chemistry Letters

DOI: 10.1021/acsmedchemlett.6c00278

Abstract

High-throughput screening (HTS) and DNA-encoded library (DEL) selection are cornerstones of drug discovery but suffer from high operational infrastructure requirements or constraints to affinity-only selections. Herein we report a robust on-DNA compound screening method that bridges this gap, enabling direct functional evaluation of DNA-linked small molecules while bypassing plate-based or selection-wash limitations. To validate this platform, a focused collection of trisubstituted benzamides was synthesized and screened directly on-DNA against p38α MAPK. This methodology rapidly prioritized advanced structures, culminating in the seamless identification of compound I-13. Upon off-DNA synthesis, I-13 was confirmed as a potent p38α inhibitor (IC50 = 65 nM), demonstrating 4-fold selectivity over p38β and excellent selectivity over p38γ and p38δ (>461 fold). While achieving reasonable p38α/β isoform selectivity remains a subject for future optimization, this platform offers a powerful, low-barrier alternative to traditional HTS and DEL for rapid, functional hit-to-lead discovery.