Structure-based design of potent and selective inhibitors of the HECT ligase NEDD4
Among the human E3 ubiquitin ligases, NEDD4 (Neural precursor cell expressed developmentally down-regulated 4) plays a critical role in development and cancer, making it a compelling therapeutic target. However, no specific NEDD4 inhibitors have advanced in drug development. In this study, we reveal the inhibitory mechanism of Norclomipramine, a tricyclic antidepressant, which inhibits NEDD4-mediated ubiquitin chain elongation by binding to a hydrophobic pocket in the Ub exosite of the N-lobe. Building on this mechanism, we conducted a focused medicinal chemistry campaign, resulting in the development of covalent inhibitors that specifically target the non-catalytic cysteine C627. These compounds exhibit selective binding to NEDD4 over other family members, effectively inhibiting NEDD4-mediated polyubiquitination while leaving monoubiquitinated substrates unaffected. Among these, compound 32 emerged as a potent lead (IC<sub>50</sub> = 0.12 µM) with favorable pharmacokinetic properties, including oral bioavailability, paving the way for future in vivo efficacy studies.
Authors
- Agostino Bruno (ORCID: https://orcid.org/0000-0002-2731-980X)
- Raffaella Amici
- Simona Polo (ORCID: https://orcid.org/0000-0001-5536-9399)
- Elena Maspero (ORCID: https://orcid.org/0000-0001-6468-4796)
- Alessia Romussi (ORCID: https://orcid.org/0000-0003-4915-5903)
- Ciro Mercurio (ORCID: https://orcid.org/0000-0001-6240-4607)
- Paolo Trifiró
- Manuela Villa
- Marco Cirò
- Vincenzo Taibi
- Janine Weber (ORCID: https://orcid.org/0000-0002-7639-4830)
- Maurizio Pasi (ORCID: https://orcid.org/0000-0002-3624-4571)
- Sebastiano Pasqualato (ORCID: https://orcid.org/0000-0002-9038-7768)
- Giuseppe Meroni (ORCID: https://orcid.org/0000-0003-4378-0388)
- Paolo Soffientini (ORCID: https://orcid.org/0000-0002-1730-5615)
- Luca Sartori
- Stefania Vultaggio
- Brian Leuzzi (ORCID: https://orcid.org/0000-0001-5237-2920)
- Valentina Cecatiello (ORCID: https://orcid.org/0000-0003-4015-7160)
- Anna Cappa
- Angela Bachi (ORCID: https://orcid.org/0000-0003-4842-6556)
- Raimondo Fattori
- Giovanni Fagà (ORCID: https://orcid.org/0000-0002-7674-2583)
- Mario Rossi (ORCID: https://orcid.org/0000-0001-6349-8895)
- Mario Varasi (ORCID: https://orcid.org/0000-0003-0367-8290)
- Shakti Dahe (ORCID: https://orcid.org/0009-0009-8909-240X)
- L Lombardo (ORCID: https://orcid.org/0000-0002-8900-3560)
Institutions
- University of Parma (IT)
- Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
- University of Milan (IT)
- Austral University (AR)
- IFOM (IT)
- Human Technopole (IT)
- Recordati (Italy) (IT)
- Policlinico San Matteo Fondazione (IT)
- Vifor Pharma (United States) (US)
- European Institute of Oncology (IT)
Publication Details
- Journal
- Communications Chemistry
- Published
- 2025-05-28
- DOI
- https://doi.org/10.1038/s42004-025-01557-4
- Citations
- 3
- Primary Topic
- Protein Degradation and Inhibitors
- Type
- article
- Field-Weighted Citation Impact
- 2.42
Funders
- Worldwide Cancer Research
- Fondazione Cariplo