9MLF image
Deposition Date 2024-12-19
Release Date 2025-11-12
Last Version Date 2025-11-12
Entry Detail
PDB ID:
9MLF
Title:
TUBULIN-RB3_SLD IN COMPLEX WITH COMPOUND QW-4-183-llb
Biological Source:
Source Organism:
Rattus norvegicus (Taxon ID: 10116)
Sus scrofa (Taxon ID: 9823)
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.40 Å
R-Value Free:
0.23
R-Value Work:
0.19
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tubulin alpha-1B chain
Gene (Uniprot):TUBA1B
Chain IDs:A, C
Chain Length:438
Number of Molecules:2
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Tubulin beta chain
Chain IDs:B, D
Chain Length:433
Number of Molecules:2
Biological Source:Sus scrofa
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Stathmin-4
Gene (Uniprot):Stmn4
Chain IDs:E
Chain Length:143
Number of Molecules:1
Biological Source:Rattus norvegicus
Primary Citation
Design and synthesis of novel 4-aryl-2-benzoyl-imidazoles as colchicine binding site inhibitors.
Eur.J.Med.Chem. 298 118021 118021 (2025)
PMID: 40763661 DOI: 10.1016/j.ejmech.2025.118021

Abstact

Highly potent tubulin inhibitors serve as critical payloads in several FDA-approved antibody-drug conjugates (ADCs). However, all these compounds are natural products with complex structures, which limit the ability to adjust their physicochemical properties for the optimal balance between payload release and ADC stability during systemic circulation, as well as efficient tumor penetration. Although taxanes are widely used in cancer therapy, they are unsuitable for ADCs due to insufficient potency and a high tendency to develop acquired drug resistance. Colchicine binding site inhibitors (CBSIs) are attractive alternatives, offering tunable properties and the potential to overcome multidrug resistance associated with the use of many existing tubulin inhibitors. However, most CBSIs lack sufficient potency for viable ADC applications. In our pursuit of a highly potent CBSI suitable for ADC use, we identified a novel series of sabizabulin derivatives. These compounds were evaluated in vitro across four cancer cell lines, including one with high resistance to taxanes. Among them, compound 11b emerged as the most promising one with IC50 values ranging from 0.6 nM to 1.3 nM in cancer cells, entering the potency range as a potential ADC payload. Importantly, 11b also effectively overcame taxane-associated drug resistance. Mechanistic studies confirmed that 11b directly binds to the colchicine site on tubulin, as demonstrated by its high-resolution crystal structure in a complex with tubulin protein. In vivo efficacy studies using a taxane-resistant prostate cancer xenograft model (PC-3/TxR) revealed that 11b significantly suppressed tumor growth, disrupted angiogenesis, and induced apoptosis. Together, these findings highlight 11b as a highly potent CBSI with the capability of overcoming acquired drug resistance to taxanes, suggesting its strong potential as a next-generation ADC payload.

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Primary Citation of related structures
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