Anticervical cancer potential of root-derived compounds from Ekebergia senegalensis (Meliaceae): in vitro evaluation and computational insights

Abstract

DATA DESCRIPTION Supporting data repository documentation Article: Anticervical cancer potential of root-derived compounds from Ekebergia senegalensis (Meliaceae): in vitro evaluation and computational insights Dataset 1. Phytochemical isolation and structural characterization Description. This dataset contains experimental data generated during extraction, fractionation and isolation of compounds. Variables Variable Description Unit Sample_ID Sample identification Text Plant_part Plant material Root Fresh_weight Fresh material kg Extraction_solvent Extraction solvent % v/v Extraction_time Extraction duration h Crude_extract_weight Crude extract g Fraction_weight Fraction weight g Isolated_mass Purified compound mg Yield Isolation yield % TLC_profile Chromatographic profile Text Raw experimental information Fresh roots: 4 kg Ethanol/water (80:20, v/v) 6.5 L solvent Extraction repeated three times 48 h per extraction Crude extract: 85.0 g Ethyl acetate fraction: 45.0 g n-Butanol fraction: 4.01 g Silica gel chromatography 300 mL fractions; pooled A–H Software None (experimental laboratory procedures) Dataset 2. NMR and TOF-ES-MS characterization Description. Raw spectroscopic data for structural elucidation. Variables Variable Description Unit Compound Compound name Text NMR type 1H,13C,COSY,HSQC,HMBC - Chemical shift δ ppm Coupling constant J Hz m/z Mass peak Da Software Bruker TopSpin Instrument MS software Dataset 3. Molecular docking Description. Docking outputs against HPV16 E6 and E7. Variables Variable Description Unit Compound Ligand Text PDB_ID Protein target - Binding_energy Docking score kcal/mol Grid center Coordinates Å Grid size Dimensions Å Raw experimental information AutoDock Vina Exhaustiveness:20 UFF minimization (1000 steps) Software PyRx v0.8 AutoDock Vina AutoDock Tools Discovery Studio Dataset 4. ADMET prediction Description. Predicted pharmacokinetic descriptors. Variables Variable Description Unit Variable MW, TPSA, LogP, HIA, BBB, CYP, Clearance, Hepatotoxicity Various Software SwissADME pkCSM Dataset 5. Molecular dynamics simulations Description. Trajectory analysis of protein-ligand complexes. Variables Variable Description Unit Time Simulation time ns RMSD Deviation nm RMSF Fluctuation nm Rg Radius of gyration nm SASA Surface area nm² Binding energy MM/GBSA kJ/mol Raw experimental information 100 ns 300 K 1 bar 0.15 M TIP3P water 2 fs timestep 1001 MM/GBSA snapshots Software GROMACS v2025.1 gmx_MMPBSA SwissParam Dataset 6. In vitro cytotoxicity assay Description. MTT assay results. Variables Variable Description Unit Sample Extract/compound Text Cell_line HeLa/BJ - Concentration Test concentration µg/mL Absorbance OD570 AU Cell viability Viability % IC50 Half maximal inhibitory concentration µg/mL Raw experimental information 1×10⁴ cells/well 96-well plate 48 h incubation MTT 0.5 mg/mL 570 nm reading Doxorubicin control Triplicate experiments Software GraphPad Prism 10.0 Dataset 7. Statistical analysis Description. Statistical outputs. Variables Variable Description Unit Mean Arithmetic mean - SD Standard deviation - IC50 Nonlinear regression µg/mL ANOVA One-way ANOVA - p-value Significance - Software GraphPad Prism 10.0