Investigation into Cyclopeptide-Based Antitumor Agents: Design, Precision Synthesis, Virtual Target Screening, and Experimental Verification

Computer-aided exploration of antitumor agents has garnered significant attention in recent years and has been demonstrated to be highly effective in accelerating drug discovery processes. Constrained peptides combine the advantages of both biological macromolecules and small molecules, offering significant benefits in addressing “difficult-to-target” targets. Cyclic peptides represent the central class of constrained peptides, wherein their cyclic topological structure restricts molecular conformation, inhibits protease hydrolysis, and enhances metabolic stability. Natural marine monocyclic peptides such as Phakellistatin 13 have been shown to possess broad-spectrum biological activities. In this study, we designed and prepared three novel Phakellistatin 13 analogs aiming to investigate the impact of minor structural modifications on the biological activities of cyclic peptides. ECD spectroscopy and theoretical simulations were utilized to investigate the chirality. AI-assisted target screening was conducted to identify the potential targets of the synthesized peptides, revealing that cyclic peptide 3 exhibited a high affinity for lysine-specific demethylase 1 (LSD1). This interaction was subsequently validated through theoretical molecular docking, molecular dynamics simulations, and experimental biological layer interferometry. Extensive in vitro and in vivo biological experiments demonstrated that cyclic peptide 3 effectively inhibited tumor cell proliferation and induced apoptosis and autophagy. To improve the membrane permeability of the designed cyclic peptides, we further explored liposomal encapsulation to enhance their stability and cellular uptake, thereby improving therapeutic efficacy. This research not only provides valuable insights into chemical structure modification but also deepens our understanding of the biological action mechanisms and protein targets of natural cyclic peptide-based drugs.