Peptide compounds exhibit the advantages of high target affinity, strong specificity, and low immunogenicity. Therefore, after clarifying the therapeutic target, peptide compounds can be obtained as lead compounds via the protein fragment truncation strategy. However, the inherent structural limitations of peptide compounds result in several drawbacks, such as poor stability, low oral bioavailability, and high production costs. In contrast, small-molecule compounds possess the prominent advantages of high oral bioavailability, metabolic stability, and low production costs. Thus, it is particularly important to screen small-molecule compounds that can mimic the action mode of peptides and retain biological activity by analyzing the interaction modes between peptide compounds and target proteins. Focusing on intractable brain diseases such as Alzheimer's disease, this paper systematically elaborates on the research and development pathway of deriving active peptide compounds from functional proteins, deciphering the interaction modes between peptides and target proteins, and further obtaining targeted small-molecule compounds through five typical transformation cases, which can provide a valuable reference for subsequent compound design.