The oncogenic protein ARHGEF5/TIM has long been known to express specifically in human breast cancer and other tumors, which is an important member of Rho guanine nucleotide exchange factors that activate Rho-family GTPases by promoting GTP/GDP exchange. The activation capability of TIM is auto-inhibited by a putative helix N-terminal to Dbl homology (DH) domain, which is stabilized by intramolecular interaction of Src homology 3 domain with a poly-proline sequence that locates between the helix and DH domain. Here, we attempted to target TIM DH domain using the modified versions of its auto-inhibitory helix. In the procedure, bioinformatics techniques were used to investigate the intramolecular interaction of DH domain with auto-inhibitory helix and, based on obtained knowledge, to optimize physicochemical property and structural conformation for the helix. We also performed affinity assay to determine the binding strength of modified peptides to DH domain. Consequently, two modified peptides, namely, DALYEEYNLVV and EVLYEEYQLVV were found as good binders of DH domain with dissociation constants K d of 0.35 and 2 µM, respectively. Structural analysis revealed that the charge neutralization and electrostatic interaction confer additional stability for these two peptide complexes with DH domain.