Automated Solid-Phase Flow Synthesis for Scaffold Diversification of a High-Throughput Screening Hit

High-throughput screening (HTS) enables rapid hit identification, yet subsequent analogue synthesis and structure-activity relationship exploration remain constrained by labor-intensive multistep workflows. Here, we describe an automated solid-phase flow synthesis (SPS-flow) platform for diversity-oriented analogue generation of an HTS-derived, non-peptidic small-molecule hit scaffold. A benzodiazepine hit against cyclin-dependent kinase 11B (CDK11B) was selected as a proof-of-concept and translated into a modular 10-11-step synthetic sequence through fragment-guided retrosynthetic design. A sterically tuned triazene linker on 2-chlorotrityl resin was developed to tolerate diverse reaction conditions while enabling traceless cleavage and post-synthetic diazonium diversification, and Chemical Recipe File (CRF)-based control coordinated continuous-, circulation-, and stop-flow operations within a unified automated workflow. The platform enabled the synthesis of 42 benzodiazepine analogues in 5%-33% overall yields, with each sequence completed within approximately 45-48 h from a common resin-bound precursor. Within the explored first-generation design space, the library rapidly defined the synthetic accessibility and preliminary structure-activity landscape of the scaffold under SPS-flow conditions, supporting early triage of the series and demonstrating that SPS-flow can be used as a programmable platform for automated multistep diversification and early-stage drug optimization.