Natural bioactive peptides have emerged as pivotal candidates in modern science due to their multifaceted biological activities and versatile applications across biomedicine, biotechnology, and nutraceuticals. These molecules exhibit a broad pharmacological spectrum including antimicrobial, antiplatelet, antioxidant, antihypertensive, and antitumor properties, positioning them as potent therapeutic agents and essential functional food constituents. Compared to synthetic alternatives, their inherent structural diversity, biocompatibility, and biodegradability offer a superior safety profile by minimizing systemic toxicity and adverse effects. This review provides a comprehensive analysis of the primary natural reservoirs of these peptides, which encompass terrestrial flora and fauna as well as marine organisms and microorganisms, while elucidating their complex mechanisms of action and structure–function relationships. Furthermore, we evaluate contemporary methodologies for peptide identification and optimization, such as high-throughput proteomics, computational modeling, and strategic chemical modifications aimed at enhancing metabolic stability and bioavailability. Although bottlenecks in extraction, scalable production, and proteolytic susceptibility persist, recent breakthroughs in recombinant technology and rational design are facilitating their industrial translation. Finally, we discuss future perspectives focused on the synergy between artificial intelligence, nanotechnology, and sustainable circular economy strategies to maximize the therapeutic accessibility and functional efficacy of natural peptides.

Extracellular protein disulfide isomerase (PDI) is a critical mediator of thrombus formation and a promising target for novel antithrombotic therapies aiming to overcome the bleeding risks associated with current antiplatelet agents. This study aimed to design and evaluate novel, targeted peptide-based PDI inhibitors with a safe physiological profile. We utilized a bioinformatics-driven rational design approach, based on the evolutionary conservation of the PDI active site, to generate a library of 34 targeted peptides. The inhibitory mechanism and biological efficacy of the lead candidate, peptide p23, were evaluated using 500 ns molecular dynamics (MD) simulations, flow cytometry, and in vitro microfluidic thrombosis models under arterial shear stress. Based on bioinformatic analyses, p23 is predicted to interact with the PDI catalytic cleft and potentially form a highly stable inhibitory complex. Functionally, p23 maintained consistent antiplatelet efficacy in the complex matrix of human platelet-rich plasma. Flow cytometry demonstrated that p23 selectively suppresses integrin GPIIb/IIIa conformational activation without impairing P-selectin and CD63 surface expression. Crucially, p23 significantly reduced collagen-dependent three-dimensional thrombus formation in whole blood under biomimetic arterial flow, while still allowing for necessary residual platelet adhesion. Unlike direct integrin antagonists, p23 preserved physiological clot retraction and did not prolong plasma coagulation parameters. These findings validate the rational design of covalent PDI inhibitors and highlight peptide p23 as a promising candidate for preclinical in vivo evaluation, offering a favorable preliminary hemostatic profile and the potential for a reduced impact on hemostasis.

Extracellular protein disulfide isomerase (PDI) is a critical mediator of thrombus formation and a promising target for novel antithrombotic therapies aiming to overcome the bleeding risks associated with current antiplatelet agents. This study aimed to design and evaluate novel, targeted peptide-based PDI inhibitors with a safe physiological profile. We utilized a bioinformatics-driven rational design approach, based on the evolutionary conservation of the PDI active site, to generate a library of 34 targeted peptides. The inhibitory mechanism and biological efficacy of the lead candidate, peptide p23, were evaluated using 500 ns molecular dynamics (MD) simulations, flow cytometry, and in vitro microfluidic thrombosis models under arterial shear stress. MD simulations revealed that p23 navigates the PDI catalytic cleft to establish a highly stable inhibitory complex via a targeted covalent bond with the critical Cys400 residue. Functionally, p23 maintained consistent antiplatelet efficacy in the complex matrix of human platelet-rich plasma. Flow cytometry demonstrated that p23 selectively suppresses integrin GPIIb/IIIa conformational activation without impairing P-selectin and CD63 surface expression. Crucially, p23 significantly reduced collagen-dependent three-dimensional thrombus formation in whole blood under biomimetic arterial flow, while still allowing for necessary residual platelet adhesion. Unlike direct integrin antagonists, p23 preserved physiological clot retraction and did not prolong plasma coagulation parameters. These findings validate the rational design of covalent PDI inhibitors and highlight peptide p23 as a promising candidate for preclinical in vivo evaluation, offering a favorable hemostatic profile and a significantly wider safety margin.