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Exploring the dynamic mechanism of allosteric drug SHP099 inhibiting SHP2E69K

Abstract

The E69K mutation is one of the most frequent protein tyrosine phosphatase-2 (SHP2) mutations in leukemia, and it can cause the increase in the protein activity. Recent studies have shown that the E69K mutation was fairly sensitive to the allosteric inhibitor of SHP2 (SHP099). However, the molecular mechanism of the allosteric drug SHP099 inhibiting SHP2E69K remains unclear. Thus, the molecular dynamic simulations and the post-dynamics analyses (RMSF, PCA, DCCM, RIN and the binding free energies) for SHP2WT, SHP2WT-SHP099, SHP2E69K and SHP2E69K-SHP099 were carried out, respectively. Owing to the strong binding affinity of SHP099 to residues Thr219 and Arg220, the flexibility of linker region (residues Val209-Arg231) was reduced. Moreover, the presence of SHP099 kept the autoinhibition state of the SHP2 protein through enhancing the interactions between the linker region and Q loop in PTP domain, such as Thr219/Val490, Thr219/Asn491, Arg220/Ile488 and Leu254/Asn491. In addition, it was found that the residues (Thr219, Arg220, Leu254 and Asn491) might be the key residues responsible for the conformational changes of protein. Overall, this study may provide an important basis for understanding how the SHP099 effectively inhibited the SHP2E69K activity at the molecular level.

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Acknowledgements

This study was supported by the National Natural Science Foundation of China (Grant No. 81773569), the Natural Science Foundation of Tianjin (Grant No. 18JCQNJC13700), the Science & Technology Development Fund of Tianjin Education Commission for Higher Education (Grant No. 2017KJ229).

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Correspondence to Ying Ma or Run-Ling Wang.

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Du, S., Lu, Xh., Li, WY. et al. Exploring the dynamic mechanism of allosteric drug SHP099 inhibiting SHP2E69K. Mol Divers 25, 1873–1887 (2021). https://doi.org/10.1007/s11030-020-10179-y

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Keywords

  • E69K mutation
  • Allosteric inhibitor SHP099
  • Molecular dynamic simulation
  • Protein tyrosine phosphatase-2
  • Post-dynamics analyses