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- Title
Computational design of anti-cancer peptides tailored to target specific tumor markers.
- Authors
Naeem, Aisha; Noureen, Nighat; Al-Naemi, Shaikha Khalid; Al-Emadi, Jawaher Ahmed; Khan, Muhammad Jawad
- Abstract
Anti-cancer peptides (ACPs) are short peptides known for their ability to inhibit tumor cell proliferation, migration, and the formation of tumor blood vessels. In this study, we designed ACPs to target receptors often overexpressed in cancer using a systematic in silico approach. Three target receptors (CXCR1, DcR3, and OPG) were selected for their significant roles in cancer pathogenesis and tumor cell proliferation. Our peptide design strategy involved identifying interacting residues (IR) of these receptors, with their natural ligands serving as a reference for designing peptides specific to each receptor. The natural ligands of these receptors, including IL8 for CXCR1, TL1A for DcR3, and RANKL for OPG, were identified from the literature. Using the identified interacting residues (IR), we generated a peptide library through simple permutation and predicted the structure of each peptide. All peptides were analyzed using the web-based prediction server for Anticancer peptides, AntiCP. Docking simulations were then conducted to analyze the binding efficiencies of peptides with their respective target receptors, using VEGA ZZ and Chimera for interaction analysis. Our analysis identified HPKFIKELR as the interacting residues (IR) of CXCR-IL8. For DcR3, we utilized three domains from TL1A (TDSYPEP, TKEDKTF, LGLAFTK) as templates, along with two regions (SIKIPSS and PDQDATYP) from RANKL, to generate a library of peptide analogs. Subsequently, peptides for each receptor were shortlisted based on their predicted anticancer properties as determined by AntiCP and were subjected to docking analysis. After docking, peptides that exhibited the least binding energy were further analyzed for their detailed interaction with their respective receptors. Among these, peptides C9 (HPKFELY) and C7 (HPKFEWL) for CXCR1, peptides D6 (ADSYPQP) and D18 (AFSYPFP) for DcR3, and peptides P19 (PDTYPQDP) and p16 (PDQDATYP) for OPG, demonstrated the highest affinity and stronger interactions compared to the other peptides. Although in silico predictions indicated a favorable binding affinity of the designed peptides with target receptors, further experimental validation is essential to confirm their binding affinity, stability and pharmacokinetic characteristics. Highlights: An in silico strategy to design anti-cancer peptides with high affinity for differentially expressed receptors (targets) on cancer cells, specifically CXCR1, DcR3, and OPG receptors. Interacting residues of natural ligands and their receptors as a guide to creating a peptide library. AntiCP to assess the anti-cancer properties of the designed peptides. Docking simulations to analyze the binding efficiencies of the peptides with their respective target receptors.
- Subjects
TUMOR markers; PEPTIDES; INHIBITION of cellular proliferation; CHEMOKINE receptors; BINDING energy; P16 gene
- Publication
BMC Chemistry, 2024, Vol 18, Issue 1, p1
- ISSN
2661-801X
- Publication type
Article
- DOI
10.1186/s13065-024-01143-0