نوع مقاله : مقاله پژوهشی
عنوان مقاله English
نویسندگان English
Introduction
The angiotensin-converting enzyme 2 (ACE2) receptor is a key regulator of the renin–angiotensin system (RAS), which maintains vascular tone, electrolyte balance, and blood pressure. Beyond its physiological functions, ACE2 is recognized as the cellular entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19. The viral spike (S) glycoprotein binds directly to the extracellular domain of ACE2, initiating viral attachment and entry. Because of this, ACE2 represents a critical target for therapeutic intervention. Although vaccines and antiviral drugs have significantly reduced disease severity and transmission, the emergence of viral variants with mutations in the spike protein—such as Delta and Omicron—has limited the durability of immune protection. Furthermore, global disparities in vaccine access and the high production cost of monoclonal antibodies highlight the need for affordable, easily produced, and broadly effective antiviral agents. Peptide-based therapeutics have recently gained attention as promising alternatives to conventional antivirals. Their ability to mimic natural protein–protein interfaces allows for high target specificity with minimal off-target effects. Peptides are biocompatible, have low toxicity, and can be designed rapidly using computational methods. Advances in peptide stabilization and formulation have also improved their half-life and pharmacokinetic properties. Among peptide sources, animal-derived peptides stand out for their broad range of biological activities, including antimicrobial, antiviral, and immunomodulatory effects. These peptides, naturally found in milk, egg, venom, and marine organisms, can interfere with viral entry mechanisms or modulate host immunity. Given these properties, animal-derived peptides are excellent candidates for developing ACE2-targeting molecules that could block SARS-CoV-2 attachment. This study aimed to identify and computationally evaluate bioactive animal peptides capable of interacting with ACE2 as potential antiviral agents.
Methods
Twelve bioactive peptides from various animal sources were selected from the literature based on known antimicrobial or antiviral properties. An in silico screening pipeline was applied to assess their safety, stability, and pharmacological suitability. Toxicity and allergenicity were predicted using ToxinPred, hemolytic potential through HemoPI, inflammatory potential via ProInflam, and antigenicity using the Antigenic Peptide Predictor. Peptide stability and half-life were estimated using PEP-Life. Peptides passing all filters were considered non-toxic, non-hemolytic, and sufficiently stable for further analysis. The ACE2 receptor structure (PDB ID: 1R42) was obtained from the RCSB Protein Data Bank and refined with MODELLER 10.2 to rebuild missing residues. Energy minimization was performed using the YASARA server to optimize the structure. Three-dimensional peptide structures were predicted using PEP-FOLD3 and minimized under the same conditions. Protein–peptide docking was conducted with HPEPDOCK, and docking results were ranked based on binding energy. The PDBSUM server was used to analyze hydrogen bonding, hydrophobic interactions, and key residue contacts within the ACE2–peptide interface.
Results
Seven peptides passed all initial screening filters and were advanced to docking analysis. Among them, ELQACQQVMDR (Peptide 6), AQQLAAQLPAMCR (Peptide 7), and RRWQWRMKKLG (Peptide 12) exhibited the highest binding affinities toward ACE2. Peptide 12 showed the strongest binding, with a docking score of −246.510, forming stable hydrogen bonds and hydrophobic interactions with ACE2 residues Phe40, Gln98, Tyr202, Asp206, and Arg514. Notably, several of these residues are directly involved in binding the SARS-CoV-2 spike receptor-binding domain (RBD), suggesting that Peptide 12 may effectively compete with the viral spike for ACE2 occupancy. Peptide 7 formed eleven hydrogen bonds, indicating strong interface stabilization, while Peptide 6 showed compact binding within the ACE2 active pocket, suggesting structural efficiency and favorable energetics. All three peptides were predicted to be non-toxic, non-hemolytic, and non-inflammatory, with acceptable stability and half-life, suggesting favorable pharmacokinetic characteristics for potential therapeutic development.
Discussion
Docking analyses demonstrated that the top three peptides interact with ACE2 in a manner similar to known inhibitors such as the ACE2-derived peptide SBP1 and the engineered mini-protein LCB1, both of which block viral attachment by steric hindrance. Among these, Peptide 12 exhibited particularly strong and stable binding. Its cationic nature (+5 charge) enhances electrostatic attraction to the negatively charged ACE2 surface, strengthening the peptide–protein interaction without inducing hemolysis. The abundance of arginine and tryptophan residues in its sequence likely contributes to amphipathicity and tight binding. The engagement of residues Tyr202 and Asp206, which are known spike contact points, supports a competitive inhibition mechanism. Such peptides could block SARS-CoV-2 entry by directly occupying the spike-binding site on ACE2. Compared to synthetic inhibitors and monoclonal antibodies, animal-derived peptides have distinct advantages: they are inexpensive to produce, chemically stable, biodegradable, and cause minimal immune reactions. Furthermore, peptide therapeutics can be modified to improve resistance to proteolysis or enhance receptor affinity through sequence optimization and cyclization. The implications of these findings extend beyond COVID-19. Since ACE2 also plays roles in cardiovascular and inflammatory disorders, ACE2-binding peptides may be developed as modulators of ACE2 activity in other diseases, such as hypertension or acute respiratory distress syndrome (ARDS).
Conclusion
This in silico study provides strong evidence supporting the potential of animal-derived peptides as ACE2-targeting antiviral agents. Among the analyzed candidates, RRWQWRMKKLG (Peptide 12) demonstrated the highest binding affinity and the most extensive contact with critical residues involved in spike–ACE2 interaction. Peptides 6 and 7 also exhibited promising binding stability and safety, identifying them as additional leads for peptide-based antiviral research. These peptides possess favorable safety profiles, non-toxic and non-hemolytic characteristics, and reasonable predicted half-lives, suggesting they could be viable for therapeutic application. By directly targeting ACE2, they may prevent SARS-CoV-2 attachment and entry, providing an alternative strategy for antiviral development. Future research should focus on experimental validation, including: Surface plasmon resonance (SPR) or biolayer interferometry (BLI) to confirm binding affinity; In vitro viral inhibition assays to test entry blockade efficacy; Molecular dynamics (MD) simulations to evaluate complex stability under physiological conditions; and In vivo studies to assess pharmacokinetics and safety profiles. Overall, this study establishes a conceptual and computational framework for repurposing natural animal peptides as next-generation antiviral agents. These peptides, particularly Peptide 12, demonstrate a unique combination of safety, stability, and strong ACE2-binding potential. Their development could lead not only to effective peptide-based COVID-19 therapeutics but also to broader applications in treating other ACE2-mediated viral or inflammatory diseases.
کلیدواژهها English
