Exploring the cause of the inhibitor 4AX attaching to binding site disrupting protein tyrosine phosphatase 4A1 trimerization by molecular dynamic simulation

Abstract

Ectopic overexpression of protein tyrosine phosphatase of liver regeneration-1 (PTP4A1, also called PRL-1) markedly enhanced hepatocellular carcinoma (HCC) cells migration and invasion. The PTP4A1 trimerization played a vital role in mediating cell proliferation and motility. Biochemical and structural studies have proved that the compound 4AX, a well-known inhibitor for PRL1, directly binds to the PTP4A1 trimer interface and obstructs trimer formation of PTP4A1. However, the molecular basis of the ligand-4AX inhibition on PTP4A1 trimer conformations remains unclear. In this study, the docking analysis and the molecular dynamics simulation (MD simulation) study were performed to investigate how the molecule binding at each interface disrupted the trimer formation. The results suggested that the ligand-4AX attaching to the binding site changed the conformation of A:Q131, A:Q135 in the AC interface, C:R18, C:P96 in the CA interface and B:Q131 in the BA interface, leading to the weak interactions between subunits and thus resulting in the disruption of the PTP4A1 trimerization.

Keywords:

• PTP4A1 trimer
• HCC
• molecular docking
• MD simulation
• post-dynamic analysis

Disclosure statement

The authors report no conflicts of interest in this work.

Additional information

Funding

This study was supported by the National Natural Science Foundation of China (Grant No. 81273361),the National Natural Science Foundation of China (Grant No. 81773569), the Natural Science Foundation of Tianjin (Grant No. 16JCZDJC32500), the Natural Science Foundation of Tianjin (Grant No. 18JCQNJC13700), the Cooperation and Exchange Project of the National Natural Science Foundation of China (Grant No. 81611130090) and the Science & Technology Development Fund of Tianjin Education Commission for Higher Education (Grant No. 2017KJ229).