DOI: 10.5281/zenodo.16043418
title: Data supporting the study: Dual ACE2-Inflammation Modulation by R. palmarum Fatty Acids: Computational Analysis

description: ================================================================================README for the Dataset: Dual ACE2-Inflammation Modulation by R. palmarum Fatty Acids: Computational Analysis

================================================================================

Date of deposit: July 17, 2025

Author of Repository: William Daniel Lituma-González (william.lituma@yachaytech.edu.ec)Authors: William Daniel Lituma-González, Santiago Ballaz, Tanishque Verma, J. M. Sasikumar, Shanmugamurthy Lakshmanan

================================================================================BRIEF DESCRIPTION================================================================================

This dataset contains all the input files, configuration scripts, and key output data supporting the findings of the manuscript titled: "Dual Targeting of ACE2 and Inflammation with Rhynchophorus palmarum Fatty Acids: A Computational Study with Antiviral Potential".

This study employed a comprehensive in silico approach to evaluate the potential of nine fatty acids from Rhynchophorus palmarum larvae as dual-action therapeutic agents. The investigation involved ADMET and bioactivity predictions, flexible molecular docking against eight key regions of the human ACE2 receptor, and 100 ns molecular dynamics (MD) simulations to assess the stability and dynamics of promising complexes. The primary goal was to assess the potential of these compounds to interfere with ACE2-mediated viral entry while simultaneously modulating host inflammatory pathways.

================================================================================METHODOLOGICAL OVERVIEW================================================================================

The computational workflow included:1.  **Protein Preparation:** Optimization and validation of the ACE2 receptor structure (PDB ID: 6M0J) using UCSF ChimeraX, WinCoot, and MolProbity.2.  **Ligand Preparation:** Retrieval of SMILES strings from PubChem and 3D structure optimization using Avogadro (MMFF94s force field) and Open Babel.3.  **ADMET/Bioactivity Prediction:** Analysis using Way2Drug (PASS Online, etc.), pkCSM, SwissADME, and Deep-PK web servers.4.  **Molecular Docking:** Flexible docking performed with the SwissDock web server against eight predefined binding regions on ACE2.5.  **Molecular Dynamics (MD):** 100 ns all-atom MD simulations performed with GROMACS (v. 2023.4).6.  **Binding Free Energy:** Calculations performed using the MM/PBSA method with the gmx_MMPBSA tool.

================================================================================DESCRIPTION OF FILES AND FOLDERS================================================================================

The data is organized into the following folders, each containing its own specific README.txt file for detailed explanations.

**/01_Protein_Preparation/**-   Contains the "before and after" files for the ACE2 receptor preparation. Includes the raw PDB structure (6M0J) and the final, isolated, and optimized ACE2 structure used for all simulations, along with validation reports.

**/02_Ligand_Preparation/**-   Contains the input structures for the nine fatty acids. Includes a list of SMILES codes and a subfolder with the final, energy-minimized 3D structures in `.sdf` format.

**/03_ADMET_Bioactivity_Predictions/**-   Contains nine separate Microsoft Excel workbooks. Each workbook corresponds to one fatty acid and consolidates all prediction results (ADMET, bioactivity, targets) for that specific compound from the various web servers used.

**/04_Molecular_Docking/**-   Contains a summary Excel file (`Docking_Results_Summary.xlsx`) with the best scores and interacting residues for all 72 simulations. It also includes a subfolder (`SwissDock_Raw_Outputs/`) with the complete, raw output files from the SwissDock server for each simulation.

**/05_Molecular_Dynamics/**-   Contains the GROMACS input files for the 12 selected MD simulations. The data is organized into 12 subfolders (e.g., `Alphalinoleic_Region_1/`). Each subfolder contains the GROMACS topology (`topol.top`), structure (`.gro`), parameters (`.mdp`), index (`.ndx`), the complete force field directory (`toppar/`), and a subfolder (`Data_Analysis/`) with the final analysis data (`.xvg` files).

**/06_Binding_Free_Energy_MMPBSA/**-   Contains the results from the MM/PBSA calculations, organized into 12 subfolders that mirror the structure of folder 05. Each subfolder contains the input (`.in`) and output (`.csv`, `.dat`) files from the `gmx_MMPBSA` tool.

**/07_Manuscript_Data/**-   Contains the underlying numerical data used to generate every figure and table in the manuscript and its supplementary information. The data is organized into subfolders named after each figure/table (e.g., `/Figure_1_Data/`).

================================================================================HOW TO CITE THIS DATASET================================================================================

If you use any of the data provided in this repository in your own research, please cite both the original manuscript and this dataset.

**1. Original Manuscript:**Lituma-González, W. D., Ballaz, S., Verma, T., Sasikumar, J. M., & Lakshmanan, S. (2025). Dual Targeting of ACE2 and Inflammation with Rhynchophorus palmarum Fatty Acids: A Computational Study with Antiviral Potential. [Journal Name, Volume, Pages].

**2. This Dataset:**Lituma-González, W. D., Ballaz, S., Verma, T., Sasikumar, J. M., & Lakshmanan, S. (2025). Data supporting the study: Dual Targeting of ACE2 and Inflammation with Rhynchophorus palmarum Fatty Acids [Data set]. Zenodo. https://doi.org/10.5281/zenodo.16043419