Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin and provides insights into microtubule dynamic instability

Yang, J.; Yu, Y.; Li, Y.; Ye, H.; Yan, W.; Niu, L.; Zheng, Y.; Wang, Z.; Yang, Z.; Pei, H.; Wei, H.; Zhao, M.; Wen, J.; Yang, l.; Ouyang, L.; Wei, Y.; Chen, Q.; Li, W.; Chen, L.

doi:10.1101/2020.09.11.293563

bioRxiv · 10.1101/2020.09.11.293563

Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin and provides insights into microtubule dynamic instability

Yang, J.·Yu, Y.·Li, Y.·Ye, H.·Yan, W.·Niu, L.·Zheng, Y.·Wang, Z.·Yang, Z.·Pei, H.·Wei, H.·Zhao, M.·Wen, J.·Yang, l.·Ouyang, L.·Wei, Y.·Chen, Q.·Li, W.·Chen, L.

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Abstract

Microtubule, composed of {beta}-tubulin heterodimers, remains as one of the most popular anticancer targets for decades. To date, anti-microtubule drugs are mainly functionally divided into microtubule-destabilizing and microtubule-stabilizing agents while microtubule- or tubulin-degradation agents are rarely reported. Six known binding sites on tubulin dimer are identified with five sites on {beta}-tubulin and only one site on -tubulin (pironetin site), hinting compounds binding to -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 binding to the vinblastine site, cevipabulin also binds to a novel site on -tubulin (named the seventh site) which located near the nonexchangeable GTP. Interestingly, we find the binding of cevipabulin to the seventh site induces tubulin degradation. As the non-exchangeable GTP has structural role and is important for the stability of tubulin dimers, we propose and confirm the tubulin degradation mechanism as: Cevipabulin at the seventh site puts the T5 loop outward to make the non-exchangeable GTP exchangeable, which reduces the stability of tubulin and results in its destabilization and degradation. Our results confirm a novel agent binding site on -tubulin and shed light on the development of tubulin degraders as a new generation of anti-microtubule drugs targeting this novel site.

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Yang, J., Yu, Y., Li, Y., Ye, H., Yan, W., Niu, L., Zheng, Y., Wang, Z., Yang, Z., Pei, H., Wei, H., Zhao, M., Wen, J., Yang, l., Ouyang, L., Wei, Y., Chen, Q., Li, W., Chen, L.. 2020-09-11. Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin and provides insights into microtubule dynamic instability. https://doi.org/10.1101/2020.09.11.293563

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