7EMJ image
Deposition Date 2021-04-14
Release Date 2022-04-20
Last Version Date 2024-07-10
Entry Detail
PDB ID:
7EMJ
Title:
Crystal structure of T2R-TTL-Barbigerone complex
Biological Source:
Source Organism:
Rattus norvegicus (Taxon ID: 10116)
Gallus gallus (Taxon ID: 9031)
Sus scrofa (Taxon ID: 9823)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.33 Å
R-Value Free:
0.24
R-Value Work:
0.19
R-Value Observed:
0.19
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Tubulin alpha-1B chain
Gene (Uniprot):TUBA1B
Chain IDs:A, C
Chain Length:451
Number of Molecules:2
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:Tubulin beta chain
Chain IDs:B, D
Chain Length:445
Number of Molecules:2
Biological Source:Sus scrofa
Polymer Type:polypeptide(L)
Molecule:Stathmin-4
Gene (Uniprot):Stmn4
Chain IDs:E
Chain Length:189
Number of Molecules:1
Biological Source:Rattus norvegicus
Polymer Type:polypeptide(L)
Molecule:Tubulin tyrosine ligase
Chain IDs:F
Chain Length:384
Number of Molecules:1
Biological Source:Gallus gallus
Primary Citation
Crystal structure of tubulin-barbigerone complex enables rational design of potent anticancer agents with isoflavone skeleton.
Phytomedicine 109 154550 154550 (2023)
PMID: 36610121 DOI: 10.1016/j.phymed.2022.154550

Abstact

BACKGROUND Isoflavones possess many biological activities, including anti-inflammatory and anticancer effects. Microtubules (composed of αβ-tubulin heterodimers) are described as one possible cellular target of some of these isoflavones. However, the binding of tubulin to isoflavones has not been extensively studied, and until now, no crystal structure of the tubulin-isoflavone complex has been solved, and details of the isoflavone-tubulin interaction remain elusive. PURPOSE Barbigerone is an isoflavone mainly found in the genus Milletti, such as the edible leguminous plant Millettia ferruginea, with anticancer activity. This study aims to confirm the cellular target of barbigerone and to study its anticancer mechanism. METHOD Surface plasmon resonance assays and X-ray crystallography were used to study the interaction of barbigerone with tubulin protein. Immunofluorescence, in-cell and in vitro tubulin polymerization assays were employed to investigate the mechanism. MTT assays, cell clonal formation assays, wound healing assays, tube formation assays and H460 xenograft models were conducted to evaluate the in vitro and in vivo anticancer activities of barbigerone and one of its derivatives, 0412. RESULTS Here, we found that barbigerone binds to tubulin to inhibit tubulin polymerization. Moreover, we solved the X-ray crystal structure of the tubulin-barbigerone complex at 2.33 Å resolution, which unambiguously determined the orientation and position of barbigerone in the colchicine-binding site. Illuminated by the X-ray data, we synthetized and obtained a more active isoflavone, 0412. Both barbigerone and 0412 inhibit cancer cell proliferation, tubulin polymerization, migration of HeLa cells and capillary-like tube formation of HUVECs, induce G2/M phase cell cycle arrest and apoptosis, and exhibit anticancer activity in an H460 xenograft model. CONCLUSION In all, through biochemical and X-ray crystal structure results, we identified tubulin as the cellular target of one isoflavone, barbigerone, and proved that the tubulin-barbigerone complex plays a guiding role in obtaining a more active compound, 0412. These studies provide a crucial research basis for the development of isoflavones as anticancer candidate compounds.

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Primary Citation of related structures