PPM1D Phosphatase: insights from crystal structure, kinetic analysis, and structure-based virtual screening

Authors

• JP Kumar
• D Kosek
• SR Durell
• N Tarasova
• LM Jenkins
• S Debnath
• NP Coussens
• MD Hall
• DH Appella
• F Dyda
• SJ Mazur
• E Appella

Abstract

The Wild-type p53-induced phosphatase (Wip1 or PPM1D) is a member of the serine/threonine metal-dependent protein phosphatase 2C (PP2C) family. PPM1D is induced by p53 during the DNA damage response and acts as an oncoprotein in various human cancers. Amplification or overexpression of PPM1D is linked to unfavorable outcomes in multiple types of cancer. Although PPM1D is a potential therapeutic target, gaining insights into its atomic structure is challenging due to the unique flexible regions of this family member. Here, we report the first crystal structure of the PPM1D catalytic domain to 1.8 Å resolution. The structure provides insights into the active site with two bound Mg2+ ions. The flap subdomain and B-loop, crucial for substrate recognition and catalysis, were also resolved. Surprisingly, we observed a nitrogen-oxygen-sulfur (NOS) bridge in the crystal structure, which might protect or stabilize the structure. While the NOS bridge is present in the crystal, its occurrence under biological conditions remains unproven. Molecular dynamics simulations and kinetic studies provided further mechanistic insights into the regulation of PPM1D catalytic activity. From this structure, we used an AI-based approach for virtual screening of over 7 million compounds to identify potential binders. This extensive screening suggested two compounds that bind to the allosteric site and one to the active site. We have validated that these molecules inhibit PPM1D and are currently developing analogs to further evaluate and improve their effectiveness. In conclusion, these results advance the understanding of PPM1D function and facilitate further development of specific inhibitors of PPM1D phosphatase.

Scientific Focus Area: Structural Biology

This page was last updated on Tuesday, August 6, 2024