9OK6 image
Deposition Date 2025-05-09
Release Date 2025-07-23
Last Version Date 2025-08-27
Entry Detail
PDB ID:
9OK6
Keywords:
Title:
Crystal structure of TNF alpha in complex with compound 19
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.78 Å
R-Value Free:
0.24
R-Value Work:
0.18
R-Value Observed:
0.19
Space Group:
C 1 2 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tumor necrosis factor
Gene (Uniprot):TNF
Chain IDs:A, B, C, D, E, F
Chain Length:158
Number of Molecules:6
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation

Abstact

Tumor necrosis factor α (TNFα) plays a critical role in inflammatory and autoimmune diseases. While biologic drugs have improved patient outcomes in conditions like rheumatoid arthritis by disrupting TNFα signaling, small molecule targeting has been challenging due to the strong TNF-receptor binding and difficulty in disrupting the TNF trimer. This research presents small molecule TNFα inhibitors with a novel bridged-piperazine core, developed through molecular dynamics simulation and scaffold hopping. The initial hit was optimized using structure-based design, leading to the discovery of a lead molecule with similar potency to the prototype but enhanced physicochemical properties. This lead demonstrated oral efficacy in a mouse glucose-6-phosphate isomerase-induced paw swelling model, comparable to the effects of a TNFα antibody. The estimated effective human dose is 200 mg once daily, highlighting the potential for clinical development of these compounds.

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Disease

Primary Citation of related structures