2026-10-12T10:11:17Z https://api.figshare.com/v2/oai

oai:figshare.com:article/34027521 2026-09-29T20:02:00Z category_4 category_13 category_14 category_873 category_46 category_734 category_64 portal_5 item_type_1 month_year_09_2026

<p>Reproducible molecular dynamics simulations and binding free energy analysis of the CZS-241–FABP5.</p> Rui An (636731) Shibing Hou (2288815) Min Hong (279203) Jiaorong Zhen (23973891) Zhijuan Wang (1900771) Haoming Huang (12791303) Weixuan Zhao (12058148) Mianmian Liao (10916520) Weiqu Yuan (23973893) Danping Huang (196661) Biochemistry Genetics Molecular Biology Chemical Sciences not elsewhere classified Immunology Biological Sciences not elsewhere classified Cancer xlink "> tcga predicted worse survival independent prognostic factor experimental validation confirmed nf -&# 954 epithelial &# 8211 protein &# 8211 xlink "> fabp5 fabp5 correlated positively immune checkpoint profiles higher tide scores b &# 945 b &# 8211 b pathway genes identify potential fabp5 characterize fabp5 expression duplicate md simulations fabp5 drives pd hcc cell proliferation &# 954 tide scores b pathway therapeutic potential protein docking decreased expression cell rna promising fabp5 fabp5 shapes fabp5 regulates fabp5 knockdown vitro assays targeting compound significantly upregulated seq datasets related pathways regulatory role molecular dynamics molecular docking mesenchymal transition lipid metabolism l1 via l1 upregulation l1 axis immunosuppressive microenvironment <p>(A-E)Molecular docking analysis between FABP5 and 5 potential drugs including XMD8–92, OCIFISERTIB, AXITINIB, RG-1530 and CZS-241. (F) RMSD profiles from duplicate molecular dynamics (MD) simulations showing that the CZS-241–FABP5 complex remained stable with fluctuations below 3 Å throughout the simulation. (G) Rg analysis indicating stable global compactness of the CZS-241–FABP5 complex with only minor conformational fluctuations during MD simulations. (H) SASA analysis showing slight variations, suggesting limited changes in the binding microenvironment upon ligand association. (I) Time-dependent evolution of the distance between CZS-241 and the key interacting residue THR56, illustrating transient fluctuations followed by convergence to a stable binding distance. (J) Hydrogen bond analysis demonstrating persistent intermolecular hydrogen bonding between CZS-241 and FABP5, with an average of approximately three hydrogen bonds maintained during the simulation.(K–L) RMSF profiles indicating low residue-level flexibility (<3 Å for most residues), consistent with a stable ligand–protein complex. (M) MM/PBSA binding free energy analysis showing a favorable average binding free energy (−48.48 kcal/mol) for the CZS-241–FABP5 complex, with per-residue energy decomposition identifying key amino acid residues contributing to ligand binding. (N) Free energy landscape (FEL) analyses of the FABP5–CZS-241 complex from two independent molecular dynamics simulations. The left panel represents replicate 1 and the right panel represents replicate 2.</p> 2026-09-29T20:01:47Z Image Figure 10.1371/journal.pone.0356359.g009 https://figshare.com/articles/figure/_p_Reproducible_molecular_dynamics_simulations_and_binding_free_energy_analysis_of_the_CZS-241_FABP5_p_/34027521 CC BY 4.0