Exploring chemical space based on Transformation to design broad-spectrum 3CL^pro inhibitors against coronavirus

How to efficiently explore chemical space to discover new compounds remains an important challenge in drug discovery. In this work, we introduce a Transformation strategy that enables efficient, scaffold-guided exploration of sub-chemical space around known bioactive molecules to obtain broad-spectrum inhibitors capable of targeting multiple proteins with related binding pockets. The core concept is to retain a validated binding scaffold responsible for essential target interactions, while systematically modifying peripheral regions to rapidly access nearby chemical space associated with target variability and functional optimization. We applied this strategy to the 3C-like protease (3CL^pro), a conserved enzyme present in multiple coronaviruses and a key target for broad-spectrum antiviral development. Key pharmacophoric features of the SARS-CoV-2 3CL^pro inhibitor Leritrelvir were preserved as the core scaffold to maintain critical active-site interactions, while non-essential regions were iteratively transformed within a defined sub-chemical space to generate structurally diverse analogues. Using this, several novel compounds were designed, synthesized and evaluated. Compounds 7c and 7d exhibited potent inhibition of SARS-CoV-2 3CL^pro. Notably, compound 7c showed broad-spectrum antiviral activity, maintaining potency comparable to Leritrelvir against β-coronavirus 3CL^pro, while demonstrating improved inhibition against α-coronavirus HCoV-NL63 3CL^pro. Its anti-SARS-CoV-2 activity was essentially equivalent to Leritrelvir, while its anti-HCoV-NL63 activity was superior. Overall, these results demonstrate that the Transformation strategy is an effective and generalizable framework for scaffold-guided chemical space exploration, particularly suitable for multi-target systems such as viral proteases, where conserved scaffolds maintain baseline activity, while sub-chemical space exploration enables optimization of potency, spectrum coverage, and resistance mitigation.