Objective ·To establish various in vitro screening systems for the discovery of peptide inhibitors targeting the interaction between small ubiquitin-like modifier (SUMO)-activating enzyme subunit 1 (SAE1) and subunit 2 (SAE2), as well as to evaluate their advantages, disadvantages, and applicability to this research. Methods ·The DNA fragments encoding human SAE1 and SAE2 were cloned into vector pET-28a, respectively, to generate protein SAE1 and SAE2. Purified proteins were used to establish screening assays, including isothermal calorimetry (ITC), fluorescence polarization (FP), surface plasmon resonance (SPR) and a fluorescence assay based on the SAE enzyme activity. The inhibitory activity of peptide candidates in different screening systems was examined, and their performance in terms of sensitivity, robustness, throughput and cost was evaluated. Results ·The dissociation constant (K_d) of in vitro SAE1 and SAE2 interaction was determined to be 0.96 μmol/L by ITC, and PEPT7 was identified as the most potent peptide. However, the tracer of FP, which was derived from PEPT7, was not up to snuff due to its low affinity with SAE2. In the SPR assay, the K_d value (=1.13 μmol/L) of SAE1 and SAE2 interaction was in line with the results from ITC. The SAE enzyme activity-based screening assay revealed that HP1B, the most effective peptide, inhibited SAE with an half-maximal inhibitory concentration (IC₅₀) of 15.72 μmol/L. The affinity of HP1B for SAE1 was determined to be 34.4 μmol/L by SPR. Conclusion ·Several common screening systems for protein-protein interation (PPI) inhibitors are established and compared. Among them, ITC does not allow for high-throughput screening and it is difficult to accurately evaluate the low-affinity polypeptides with insignificant binding heat. The feasibility of FP relies heavily on the strong affinity between a tracer peptide and the protein target, making it unsuitable for the screening and optimization of low-affinity peptides. SPR is highly sensitive but the cost is high. The SAE enzyme activity-based assay stands out because it is a combination of high sensitivity, robustness, throughput and acceptable cost.