PROXINAUT: An Automation Platform for Rapid Hit-to-Degrader Discovery
- 1Leiden University
Abstract
Massive library-based platforms enable rapid early hit discovery, yet subsequent hit resynthesis and validation remain major bottlenecks in drug discovery. This delay is amplified when optimizing hits, or elaborating structures towards more advanced modalities, such as chemical inducers of proximity (CIPs). Here, we report PROXINAUT, an end-to-end workflow integrating self-encoded library-based hit discovery with an automated parallel solid-phase synthesis platform to streamline hit discovery, validation, optimization, and degrader development. As a demonstration, screening a 176k-member benzimidazole library against BRD4 yielded six hit candidates, which were obtained via parallel automated synthesis and validated as submicromolar binders. The automation workflow empowered a rapid structure activity relationship exploration around the whole scaffold and resulted in a variant with six fold improved binding affinity. Next, we aimed to automatize the development of bifunctional degraders. Solid phase synthesis typically leaves a C-terminal amide as a synthetic artifact that can compromise druglike properties. We developed a strategy to repurpose this resin-attachment site, converting it into functional degrons featuring either FBXO31-targeting C-terminal amides or cereblon-binding cyclic imides. Operating without human intervention, our automated platform executes up to 16 synthetic steps across multiple parallel structures, enabling true de novo synthesis of full bifunctional scaffolds, where ligand, linker and E3 recruiter variations can all be explored within the same workflow. This resulted in cell-active BRD4 degraders with subnanomolar to nanomolar potency. Overall, we show how library selections can merge with multi-step parallel automation to convert hits directly into validated leads and advanced degrader modalities.
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BibTeX
@misc{mckenna2026proxinaut,
title = {{PROXINAUT: An Automation Platform for Rapid Hit-to-Degrader Discovery}},
author = {S. M. McKenna and M. T. Gnatzy and E. van der Nol and F. J. Boxman and C. Zhang and X. Jin and J. Liu and J. Kortekaas and X. Zhang and S. Pomplun},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.22.753586},
url = {https://www.biorxiv.org/content/10.64898/2026.09.22.753586v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - PROXINAUT: An Automation Platform for Rapid Hit-to-Degrader Discovery
AU - S. M. McKenna
AU - M. T. Gnatzy
AU - E. van der Nol
AU - F. J. Boxman
AU - C. Zhang
AU - X. Jin
AU - J. Liu
AU - J. Kortekaas
AU - X. Zhang
AU - S. Pomplun
PY - 2026
DA - 2026/09/22
PB - bioRxiv
DO - 10.64898/2026.09.22.753586
UR - https://www.biorxiv.org/content/10.64898/2026.09.22.753586v1
AB - Massive library-based platforms enable rapid early hit discovery, yet subsequent hit resynthesis and validation remain major bottlenecks in drug discovery. This delay is amplified when optimizing hits, or elaborating structures towards more advanced modalities, such as chemical inducers of proximity (CIPs). Here, we report PROXINAUT, an end-to-end workflow integrating self-encoded library-based hit discovery with an automated parallel solid-phase synthesis platform to streamline hit discovery, validation, optimization, and degrader development. As a demonstration, screening a 176k-member benzimidazole library against BRD4 yielded six hit candidates, which were obtained via parallel automated synthesis and validated as submicromolar binders. The automation workflow empowered a rapid structure activity relationship exploration around the whole scaffold and resulted in a variant with six fold improved binding affinity. Next, we aimed to automatize the development of bifunctional degraders. Solid phase synthesis typically leaves a C-terminal amide as a synthetic artifact that can compromise druglike properties. We developed a strategy to repurpose this resin-attachment site, converting it into functional degrons featuring either FBXO31-targeting C-terminal amides or cereblon-binding cyclic imides. Operating without human intervention, our automated platform executes up to 16 synthetic steps across multiple parallel structures, enabling true de novo synthesis of full bifunctional scaffolds, where ligand, linker and E3 recruiter variations can all be explored within the same workflow. This resulted in cell-active BRD4 degraders with subnanomolar to nanomolar potency. Overall, we show how library selections can merge with multi-step parallel automation to convert hits directly into validated leads and advanced degrader modalities.
ER -