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

Jianhong Yang, Yamei Yu, Yong Li, Haoyu Ye, Wei Yan, Lu Niu, Yunhua Zheng, Zhoufeng Wang, Zhuang Yang, Heying Pei, Haoche Wei, Min Zhao, Jiaolin Wen, Linyu Yang, Liang Ouyang, Yuquan Wei, Qiang Chen, Weimin Li, Lijuan Chen
doi: https://doi.org/10.1101/2020.09.11.293563
Jianhong Yang
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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  • For correspondence: chenlijuan125@163.com weimi003@scu.edu.cn yjh1988@scu.edu.cn
Yamei Yu
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Yong Li
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Haoyu Ye
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Wei Yan
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Lu Niu
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Yunhua Zheng
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Zhoufeng Wang
2Department of Respiratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
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Zhuang Yang
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Heying Pei
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Haoche Wei
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Min Zhao
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Jiaolin Wen
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Linyu Yang
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Liang Ouyang
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Yuquan Wei
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Qiang Chen
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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Weimin Li
2Department of Respiratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
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  • For correspondence: chenlijuan125@163.com weimi003@scu.edu.cn yjh1988@scu.edu.cn
Lijuan Chen
1State Key Laboratory of Biotherapy and Cancer Center, West China Hospital of Sichuan University, Chengdu 610041, China
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  • For correspondence: chenlijuan125@163.com weimi003@scu.edu.cn yjh1988@scu.edu.cn
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Abstract

Microtubule, composed of αβ-tubulin heterodimers, remains as one of the most popular anticancer targets for decades. To date, anti-microtubule drugs mainly target β-tubulin to inhibit microtubule dynamic instability (MDI) while agents binding to α-tubulin are less well characterized and also the molecular mechanism of MDI is far from being articulated. Cevipabulin, an oral microtubule-active antitumor clinical candidate, is widely accepted as a microtubule stabilizing agent (MSA) but binds to the microtubule-destabilization vinblastine site on β-tubulin and this unusual phenomenon has so far failed to be explained. Our X-ray crystallography study reveals that, in addition binding to the vinblastine site, cevipabulin also binds to a novel site on α-tubulin (named the seventh site) which located at the region spatially corresponding to the vinblastine site on β-tubulin. Interestingly, cevipabulin exhibits two unique site-dependent functions. Cevipabulin binding to the seventh site promotes tubulin degradation through interaction of the non-exchengeable GTP to reduce tubulin stability. Cevipabulin binding to the vinblastine site enhances longitudinal interactions but inhibits lateral interactions of tubulins, thus inducing tubulin protofilament polymerization (but not microtubule polymerization like MSAs), and then tangling into irregular tubulin aggregates. Importantly, the tubulin-cevipabulin structure is an intermediate between “bent” and “straight” tubulins and the involved bent-to-straight conformation change will be helpful to fully understand the molecular mechanism of tubulin assembly. Our findings confirm cevipabulin is not an MSA and shed light on the development of a new generation of anti-microtubule drugs targeting the novel site on α-tubulin and also provide new insights into MDI.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted September 11, 2020.
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Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin and provides insights into microtubule dynamic instability
Jianhong Yang, Yamei Yu, Yong Li, Haoyu Ye, Wei Yan, Lu Niu, Yunhua Zheng, Zhoufeng Wang, Zhuang Yang, Heying Pei, Haoche Wei, Min Zhao, Jiaolin Wen, Linyu Yang, Liang Ouyang, Yuquan Wei, Qiang Chen, Weimin Li, Lijuan Chen
bioRxiv 2020.09.11.293563; doi: https://doi.org/10.1101/2020.09.11.293563
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Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin and provides insights into microtubule dynamic instability
Jianhong Yang, Yamei Yu, Yong Li, Haoyu Ye, Wei Yan, Lu Niu, Yunhua Zheng, Zhoufeng Wang, Zhuang Yang, Heying Pei, Haoche Wei, Min Zhao, Jiaolin Wen, Linyu Yang, Liang Ouyang, Yuquan Wei, Qiang Chen, Weimin Li, Lijuan Chen
bioRxiv 2020.09.11.293563; doi: https://doi.org/10.1101/2020.09.11.293563

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