7XZR

Crystal structure of TNIK-AMPPNP-thiopeptide TP15 complex

Summary for 7XZR

• Entry DOI: 10.2210/pdb7xzr/pdb
• Related: 7XZQ
• Related PRD ID: PRD_002381
• Descriptor: TRAF2 and NCK-interacting protein kinase, thiopeptide TP15, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, ... (7 entities in total)
• Functional Keywords: ripp, thiopeptide, kinase inhibition, complex, signaling protein, signaling protein-inhibitor complex, signaling protein/inhibitor
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 75452.07

Authors

Hamada, K.,Vinogradov, A.A.,Zhang, Y.,Chang, J.S.,Nishimura, H.,Goto, Y.,Onaka, H.,Suga, H.,Ogata, K.,Sengoku, T. (deposition date: 2022-06-03, release date: 2022-10-26, Last modification date: 2024-03-20)

Primary citation

Vinogradov, A.A.,Zhang, Y.,Hamada, K.,Chang, J.S.,Okada, C.,Nishimura, H.,Terasaka, N.,Goto, Y.,Ogata, K.,Sengoku, T.,Onaka, H.,Suga, H.
De Novo Discovery of Thiopeptide Pseudo-natural Products Acting as Potent and Selective TNIK Kinase Inhibitors.
J.Am.Chem.Soc., 144:20332-20341, 2022

PubMed Abstract: Bioengineering of ribosomally synthesized and post-translationally modified peptides (RiPPs) is an emerging approach to explore the diversity of pseudo-natural product structures for drug discovery purposes. However, despite the initial advances in this area, bioactivity reprogramming of multienzyme RiPP biosynthetic pathways remains a major challenge. Here, we report a platform for de novo discovery of functional thiopeptides based on reengineered biosynthesis of lactazole A, a RiPP natural product assembled by five biosynthetic enzymes. The platform combines in vitro biosynthesis of lactazole-like thiopeptides and mRNA display to prepare and screen large (≥10) combinatorial libraries of pseudo-natural products. We demonstrate the utility of the developed protocols in an affinity selection against Traf2- and NCK-interacting kinase (TNIK), a protein involved in several cancers, which yielded a plethora of candidate thiopeptides. Of the 11 synthesized compounds, 9 had high affinities for the target kinase (best = 1.2 nM) and 10 inhibited its enzymatic activity (best = 3 nM). X-ray structural analysis of the TNIK/thiopeptide interaction revealed the unique mode of substrate-competitive inhibition exhibited by two of the discovered compounds. The thiopeptides internalized to the cytosol of HEK293H cells as efficiently as the known cell-penetrating peptide Tat (4-6 μM). Accordingly, the most potent compound, TP15, inhibited TNIK in HCT116 cells. Altogether, our platform enables the exploration of pseudo-natural thiopeptides with favorable pharmacological properties in drug discovery applications.

PubMed: 36282922
DOI: 10.1021/jacs.2c07937

Experimental method

X-RAY DIFFRACTION (2.26 Å)