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How does nintedanib overcome cancer drug-resistant mutation of RET protein-tyrosine kinase: insights from molecular dynamics simulations

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Abstract

Targeted drug therapies represent a therapeutic breakthrough in the treatment of human cancer. However, the emergence of acquired resistance inevitably compromises therapeutic drugs. Rearranged during transfection (RET) proto-oncogene, which encodes a receptor tyrosine kinase, is a target for several kinds of human cancer such as thyroid, breast, and colorectal carcinoma. A single mutation L881V at the RET kinase domain was found in familial medullary thyroid carcinoma. Nintedanib can effectively inhibit the RET L881V mutant, whereas its analog compound 1 is unable to combat this mutant. However, the underlying mechanism was still unexplored. Here, molecular dynamics (MD) simulations, binding free energy calculations, and structural analysis were performed to uncover the mechanism of overcoming the resistance of RET L881V mutant to nintedanib. Energetic analysis revealed that the L881V mutant remained sensitive to the treatment of nintedanib, whereas it was insensitive to the compound 1. Structural analysis further showed that the distribution of K758, D892, and N879 network had a detrimental effect on the binding of compound 1 to the L881V mutant. The obtained results may provide insight into the mechanism of overcoming resistance in the RET kinase.

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The relevant data are available from the corresponding author upon reasonable request.

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Acknowledgements

The authors highly thank the Supercomputer Center at Wuhan University for providing computational resources.

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    Authors and Affiliations

    1. Department of Urology, Ezhou Central Hospital, Hubei, 436000, China

      Shu Cao, Changbin Tan, Ming Fu & Wenqing Xiong

    2. Department of Interventional Therapy, Changhai Hospital Affiliated To Navy Medical University, Shanghai, 200433, China

      Xu Jiang

    3. Department of Anesthesiology, Changhai Hospital, The Second Military Medical University, Shanghai, 200433, China

      Dong Ji

    4. Department of Neurology, Ezhou Central Hospital, Hubei, 436000, China

      Jun Lv

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    SC, XJ, CT, MF, and WX performed molecular docking and MD simulations and wrote the manuscript. JL and DJ revised the manuscript.

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    Correspondence to Dong Ji or Jun Lv.

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    Shu Cao and Xu Jiang contributed equally to this work.

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    Cao, S., Jiang, X., Tan, C. et al. How does nintedanib overcome cancer drug-resistant mutation of RET protein-tyrosine kinase: insights from molecular dynamics simulations. J Mol Model 27, 337 (2021). https://doi.org/10.1007/s00894-021-04964-1

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