It is important to avoid promiscuous binding between an anticancer peptide and multiple proteins with SH3 domain, so as to minimize the risks of unpredictable toxic and side effects. In the present study, we applied bioinformatics methods to optimize amino acid sequences, in order to reduce the probability of promiscuous binding. Relevant peptide databases and bioinformatics tools were utilized to summarize the rules of promiscuous binding between peptides and SH3 domains. Based on that, we specifically optimized the amino acid sequences of the peptides. The results suggest that most of the modified amino acid sequences exhibit lower level of binding promiscuity, which significantly improves the overall binding specificity and reduces safety risks (P<0.05). This study provides a reference for designing targeted peptide drugs with high binding specificity and low toxicity.