Reversible binding of the anticancer drug KXO1 (tirbanibulin) to the colchicine-binding site of β-tubulin explains KXO1's low clinical toxicity

Li, Niu; Yang, Jianhong; Yan, Wei; Yu, Yamei; Zheng, Yunhua; Ye, Haoyu; Chen, Qiang; Chen, Lijuan

doi:10.1074/jbc.ra119.010732

Cited by 46 publications

(69 citation statements)

References 36 publications

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“…Protein expression and purification were described in detail in our precious study ( 25 ). Tubulin, RB3, and TTL (2:1.3:1.2 molar ratio) were mixed together, then 5 mM tyrosine, 10 mM DTT, and 1 mM AMPPCP were added, and then the mixture was concentrated to about 15 mg/ml at 4°C.…”

Section: Methodsmentioning

confidence: 99%

Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin with tubulin degradation effect

Yang

et al. 2021

Sci. Adv.

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Microtubules, composed of αβ-tubulin heterodimers, have remained popular anticancer targets for decades. Six known binding sites on tubulin dimers have been identified thus far, with five sites on β-tubulin and only one site on α-tubulin, hinting that compounds binding to α-tubulin are less well characterized. Cevipabulin, a microtubule-active antitumor clinical candidate, is widely accepted as a microtubule-stabilizing agent by binding to the vinblastine site. Our x-ray crystallography study reveals that, in addition to binding to the vinblastine site, cevipabulin also binds to a new site on α-tubulin. We find that cevipabulin at this site pushes the αT5 loop outward, making the nonexchangeable GTP exchangeable, which reduces the stability of tubulin, leading to its destabilization and degradation. Our results confirm the existence of a new agent binding site on α-tubulin and shed light on the development of tubulin degraders as a new generation of antimicrotubule drugs targeting this novel site.

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Section: Methodsmentioning

confidence: 99%

Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin with tubulin degradation effect

Yang

et al. 2021

Sci. Adv.

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“…Some positions of these aromatic structures were further substituted with low hydrophilic and hydrophobic groups that could contribute to the interaction with this hydrophobic site. Like tirbanibulin, it is intended that the designed compounds occupy NZ and COL binding sites to promote microtubule destabilization …”

Section: Introductionmentioning

confidence: 99%

Design, Synthesis and Evaluation of 2,4‐Diaminoquinazoline Derivatives as Potential Tubulin Polymerization Inhibitors

et al. 2020

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Microtubules are highly dynamic polymers composed of αand β-tubulin proteins that have been shown to be potential therapeutic targets for the development of anticancer drugs. Currently, a wide variety of chemically diverse agents that bind to β-tubulin have been reported. Nocodazole (NZ) and colchicine (COL) are well-known tubulin-depolymerizing agents that have close binding sites in the β-tubulin. In this study, we designed and synthesized a set of nine 2,4-diaminoquinazoline derivatives that could occupy both NZ and COL binding sites. The synthesized compounds were evaluated for their antiproliferative activities against five cancer cell lines (PC-3, HCT-15, MCF-7, MDA-MB-231, and SK-LU-1), a noncancerous one (COS-7), and peripheral blood mononuclear cells (PBMC). The effect of compounds 4 e and 4 i on tubulin organization and polymerization was analyzed on the SK-LU-1 cell line by indirect immunofluorescence, western blotting, and tubulin polymerization assays. Our results demonstrated that both compounds exert their antiproliferative activity by inhibiting tubulin polymerization. Finally, a possible binding pose of 4 i in the NZ/COL binding site was determined by using molecular docking and molecular dynamics (MD) approaches. To our knowledge, this is the first report of non-N-substituted 2,4-diaminoquinazoline derivatives with the ability to inhibit tubulin polymerization.

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“…Second, our approach allows the replacement of an MTA or a self-assembled protein of interest, to be fully characterized for its effect on normal cell functions. Thus, all the colchicine-derivatives and CSIs, which have recently gained interest in treating multi-drug resistant cell lines (104)(105)(106)(107)(108), can be potentially tested for their efficacy and toxicity on MT dynamics and cell functions and compared to the narrow therapeutic window of colchicine.…”

Section: Discussionmentioning

confidence: 99%

Poisson poisoning as the mechanism of action of the microtubule-targeting agent colchicine

Hemmat

Braman

Escalante

et al. 2020

Preprint

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Microtubule-directed anti-cancer drugs, such as paclitaxel, vinblastine, and colchicine, disrupt cell mitosis through suppression of microtubule dynamics ("kinetic stabilization"). However, while the molecular mechanisms of paclitaxel and vinblastine act as pseudoand true-kinetic stabilizers, respectively, the molecular mechanism of colchicine has remained enigmatic since it requires explanation of both the slow kinetics of the drug and suppression of microtubule dynamics. In this work, we applied an integrated multi-scale modeling-experimental approach to systematically characterize the microtubule targeting agent (MTA) colchicine. We found that colchicine stabilizes microtubule dynamics significantly both in vivo and in vitro in a time and concentration-dependent manner. Molecular modeling results suggest that tubulin's binding pocket is accessible to the drug for only 15% of the simulation trajectory time in straight and 82% in curved conformation on average, confirming that colchicine mainly binds to free tubulin. Molecular dynamics simulations show that there are conformational changes at longitudinal and lateral residues of GTP-tubulin-colchicine compared to a lattice tubulin structure, explaining why further incorporation of tubulin dimers to a tubulin-colchicine complex at a protofilament tip is unfavorable. Thermokinetic modeling of microtubule assembly shows that colchicine bound at fractions as low as ~0.008 to free tubulin can poison the ends of protofilaments with a Poisson distribution and thus, reduce the microtubule growth rate, while stabilizing the tubulin lateral bond and reducing the microtubule shortening rate, i.e. true kinetic stabilization. This study suggests new strategies for colchicine administration to improve the therapeutic window in the treatment of cancer and inflammatory diseases. Significance StatementColchicine is an ancient microtubule targeting agent (MTA) known to attenuate microtubule (MT) dynamics but its cancer treatment efficacy is often limited by lack of a detailed understanding of the drug's mechanism of action. The primary goal of this study was to perform a multi-scale systematic analysis of molecular mechanism of action of colchicine. The analysis indicates that unlike paclitaxel and vinblastine, colchicine poisons the ends of protofilaments of MTs at low fractions bound to tubulin, in a time-dependent manner. Our results suggest new insights into improvement of the clinical administration of colchicine and new colchicine-site inhibitors.

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Reversible binding of the anticancer drug KXO1 (tirbanibulin) to the colchicine-binding site of β-tubulin explains KXO1's low clinical toxicity

Cited by 46 publications

References 36 publications

Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin with tubulin degradation effect

Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin with tubulin degradation effect

Design, Synthesis and Evaluation of 2,4‐Diaminoquinazoline Derivatives as Potential Tubulin Polymerization Inhibitors

Poisson poisoning as the mechanism of action of the microtubule-targeting agent colchicine

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