8YMB

The crystal structure of SHD931 in complex with Brd4-BD2 and VCB

This is a non-PDB format compatible entry.

Summary for 8YMB

• Entry DOI: 10.2210/pdb8ymb/pdb
• Descriptor: Bromodomain-containing protein 4, Elongin-B, Elongin-C, ... (7 entities in total)
• Functional Keywords: complex, protac, macrocyclic, ligase
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 8
• Total formula weight: 117937.69

Authors

Huang, W.X.,Chen, Y.H.,Li, C.G.,Ding, K. (deposition date: 2024-03-08, release date: 2025-02-12)

Primary citation

Li, C.,Chen, Y.,Huang, W.,Qiu, Y.,Huang, S.,Zhou, Y.,Zhou, F.,Xu, J.,Ren, X.,Zhang, J.,Wang, Z.,Ding, M.,Ding, K.
Structure-Based Design of "Head-to-Tail" Macrocyclic PROTACs.
Jacs Au, 4:4866-4882, 2024

PubMed Abstract: Macrocyclization is a compelling strategy for conventional drug design for improving biological activity, target specificity, and metabolic stability, but it was rarely applied to the design of PROTACs possibly due to the mechanism and structural complexity. Herein, we report the rational design of the first series of "Head-to-Tail" macrocyclic PROTACs. The resulting molecule exhibited pronounced Brd4 protein degradation with low nM DC values while almost totally dismissing the "hook effect", which is a general character and common concern of a PROTAC, in multiple cancer cell lines. Further biological evaluation revealed that the compound exhibited positive cooperativity and induced protein-protein interactions (PPIs) in both biophysical and cellular NanoBRET assays and outperformed macroPROTAC-1 that is the first reported macrocyclic Brd4 PROTAC, in cellular assays. liver microsomal stability evaluation suggested that demonstrated improved metabolic stability in different species compared with the linear counterpart. The co-crystal structure of Brd4: : VCB (VHL, Elongin C and Elongin B) complex determination and molecular dynamics (MD) simulation also elucidated details of the chemical-induced PPIs and highlighted the crucial contribution of restricted conformation of to the ternary complex formation. These results collectively support that macrocyclization could be an attractive and feasible strategy for a new PROTAC design.

PubMed: 39735913
DOI: 10.1021/jacsau.4c00831

Experimental method

X-RAY DIFFRACTION (2.95 Å)