PTP-MEG2 plays a significant role in insulin production and is able to enhance insulin signaling and improve insulin sensitivity. So, PTP-MEG2 inhibitors are closely associated with type 2 diabetes therapy. A series of novel (R)-5-methylthiazolidin-4-one derivatives were designed and synthesized, and their PTP-MEG2 inhibitory activities (IC) were determined. Among the desired compounds, shares the highest inhibitory activity (IC = 1.34 μM) against PTP-MEG2. Additionally, various post-dynamic analyses confirmed that when compound bound to the PTP-MEG2, the protein conformations became unstable and the function of the pTyr recognition loop (Asn331-Cys338) would be disturbed. And thus, the ideal conformations needed for the catalytic activity was difficult to be maintained. In brief, these might be how the compound worked. Furthermore, we also found that the key residues Arg332 would play a critical role in disturbing the residue interactions. Abbreviations DCCM dynamic cross-correlation mapping DMF N,N-dimethylformamide DSSP definition of secondary structure of proteins FOXO forkhead transcription factors MD molecular dynamics PCA principal component analysis PDB protein data bank PTKs protein tyrosine kinases PTPs protein tyrosine phosphatases PTP-MEG2 megakaryocyte protein tyrosine phosphatase 2 RIN residue interaction network RING Residue Interaction Network Generator RMSD root means square deviation RMSF root mean square fluctuation Communicated by Ramaswamy H. Sarma.