A potent and selective PROTAC degrader of CDK9 as effective inhibitor of HIV-1 RNA synthesis.

Cyclin-dependent kinase (CDK) 9 plays a role in the transcription elongation of HIV-1 promoter. Functional inactivation of CDK9 could attenuate HIV-1 replication. However, high homology of CDK family members poses significant challenges in developing CDK9-specific inhibitors, as promiscuous inhibition often leads to off-target toxicities. In this work, a series of novel heterobifunctional compounds was designed and synthesized by conjugating a multitargeted CDK inhibitor with the ligand of different E3 ligases via a chemical linker. A VHL-recruiting heterobifunctional compound (9g) was identified as a highly selective PROTAC degrader of CDK9 by both western blotting and MS-based proteomics analyses. This novel PROTAC compound effectively reduced HIV-1 RNA synthesis by blocking CDK9-mediated transcription elongation. Furthermore, it exhibited significantly lower cytotoxicity and higher anti-HIV-1 therapeutic index than its CDK9 binding warhead. In conclusion, the identification of a selective CDK9-targeted degrader provides a novel anti-HIV-1 lead and highlights the potential of the PROTAC approach for developing host-directed, broad-spectrum antiviral agent candidates.