| Autor: |
Thaweesak Chieochansin, Kamonpan Sanachai, Nitchakan Darai, Wannasiri Chiraphapphaiboon, Kornkan Choomee, Pa-thai Yenchitsomanus, Chanitra Thuwajit, Thanyada Rungrotmongkol |
| Jazyk: |
angličtina |
| Rok vydání: |
2024 |
| Předmět: |
|
| Zdroj: |
Heliyon, Vol 10, Iss 17, Pp e36654- (2024) |
| Druh dokumentu: |
article |
| ISSN: |
2405-8440 |
| DOI: |
10.1016/j.heliyon.2024.e36654 |
| Popis: |
Our study employed molecular dynamics (MD) simulations to assess the binding affinity between short peptides derived from the tumor-associated antigen glypican 3 (GPC3) and the major histocompatibility complex (MHC) molecule HLA-A*11:01 in hepatocellular carcinoma. We aimed to improve the reliability of in silico predictions of peptide-MHC interactions, which are crucial for developing targeted cancer therapies. We used five algorithms to discover four peptides (TTDHLKFSK, VINTTDHLK, KLIMTQVSK, and STIHDSIQY), demonstrating the substantial potential for HLA-A11:01 presentation. The Anchored Peptide-MHC Ensemble Generator (APE-Gen) was used to create the initial structure of the peptide-MHC complex. This was followed by a 200 ns molecular dynamics (MD) simulation using AMBER22, which verified the precise positioning of the peptides in the binding groove of HLA-A*11:01, specifically at the A and F pockets. Notably, the 2nd residue, which serves as a critical anchor within the 2nd pocket, played a pivotal role in stabilising the binding interactions.VINTTDHLK (ΔGSIE = −14.46 ± 0.53 kcal/mol and ΔGMM/GBSA = −30.79 ± 0.49 kcal/mol) and STIHDSIQY (ΔGSIE and ΔGMM/GBSA = −14.55 ± 0.16 and −23.21 ± 2.23 kcal/mol) exhibited the most effective binding potential among the examined peptides, as indicated by both their binding free energies and its binding affinity on the T2 cell line (VINTTDHLK: IC50 = 0.45 nM; STIHDSIQY: IC50 = 0.35 nM). The remarkable concordance between in silico and in vitro binding affinity results was of particular significance, indicating that MD simulation is a potent instrument capable of bolstering confidence in in silico peptide predictions. By employing MD simulation as a method, our study provides a promising avenue for improving the prediction of potential peptide-MHC interactions, thereby facilitating the development of more effective and targeted cancer therapies. |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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