Data supporting the study: Dual ACE2-Inflammation Modulation by R. palmarum Fatty Acids: Computational Analysis

================================================================================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 ([e-mail])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# 数据集说明文档：棕榈象鼻虫（Rhynchophorus palmarum）脂肪酸对ACE2与炎症的双重调控：计算分析 提交日期：2025年7月17日 仓库作者：William Daniel Lituma-González（[e-mail]） 作者：William Daniel Lituma-González、Santiago Ballaz、Tanishque Verma、J. M. Sasikumar、Shanmugamurthy Lakshmanan ## 简要说明 本数据集包含支撑题为《棕榈象鼻虫（Rhynchophorus palmarum）脂肪酸靶向血管紧张素转换酶2（ACE2）与炎症的双重作用：一项具备抗病毒潜力的计算研究》论文发现的全部输入文件、配置脚本与核心输出数据。 本研究采用全面的**in silico（计算机模拟）**方法，评估了9种来自棕榈象鼻虫幼虫的脂肪酸作为双功能治疗剂的潜力。研究内容涵盖ADMET（吸收、分布、代谢、排泄与毒性）与生物活性预测、针对人类血管紧张素转换酶2（ACE2）受体8个关键区域的柔性分子对接，以及100 ns分子动力学（MD）模拟，以评估候选复合物的稳定性与动态特性。本研究的核心目标是评估这些化合物既能干扰ACE2介导的病毒入侵，又能同时调控宿主炎症通路的潜力。 ## 方法学概述 本计算流程包括： 1. **蛋白质制备**：使用UCSF ChimeraX、WinCoot与MolProbity对人类血管紧张素转换酶2（ACE2）受体结构（蛋白质数据库编号PDB ID: 6M0J）进行优化与验证。 2. **配体制备**：从PubChem获取简化分子线性输入规范（SMILES）字符串，并使用Avogadro（MMFF94s力场）与Open Babel进行三维结构优化。 3. **ADMET/生物活性预测**：通过Way2Drug（PASS Online等）、pkCSM、SwissADME与Deep-PK服务器开展分析。 4. **分子对接**：使用SwissDock服务器针对ACE2上8个预定义结合区域执行柔性对接。 5. **分子动力学（MD）**：使用GROMACS（v. 2023.4）开展100 ns全原子MD模拟。 6. **结合自由能计算**：使用gmx_MMPBSA工具，通过MM/PBSA（分子力学-泊松-玻尔兹曼表面积）方法完成结合自由能计算。 ## 文件与文件夹说明 本数据集按以下文件夹组织，每个文件夹均包含专属的README.txt文件以提供详细说明。 **/01_Protein_Preparation/**：存放ACE2受体制备的“处理前后”文件，包括原始PDB结构（6M0J）以及用于所有模拟的最终分离、优化后ACE2结构，同时附带验证报告。 **/02_Ligand_Preparation/**：存放9种脂肪酸的输入结构，包括SMILES代码列表，以及一个子文件夹，其中包含以.sdf格式保存的最终能量最小化三维结构。 **/03_ADMET_Bioactivity_Predictions/**：包含9个独立的Microsoft Excel工作簿，每个工作簿对应一种脂肪酸，整合了来自各所用服务器的该化合物的全部预测结果（ADMET、生物活性、靶点信息）。 **/04_Molecular_Docking/**：包含汇总Excel文件`Docking_Results_Summary.xlsx`，收录了全部72次对接模拟的最佳得分与相互作用残基；同时包含子文件夹`SwissDock_Raw_Outputs/`，存放SwissDock服务器生成的所有模拟的完整原始输出文件。 **/05_Molecular_Dynamics/**：包含12个选定MD模拟的GROMACS输入文件，数据按12个子文件夹组织（例如`Alphalinoleic_Region_1/`）。每个子文件夹包含GROMACS拓扑文件`topol.top`、结构文件（.gro）、参数文件（.mdp）、索引文件（.ndx）、完整力场目录`toppar/`，以及子文件夹`Data_Analysis/`，存放最终分析数据（.xvg格式文件）。 **/06_Binding_Free_Energy_MMPBSA/**：存放MM/PBSA计算的结果，按12个子文件夹组织，结构与05号文件夹一致。每个子文件夹包含`gmx_MMPBSA`工具生成的输入（.in）与输出（.csv、.dat）文件。 **/07_Manuscript_Data/**：包含用于生成论文及其补充材料中所有图表与表格的基础数值数据，数据按对应图表/表格命名的子文件夹组织（例如`/Figure_1_Data/`）。 ## 本数据集引用方式 若您在自身研究中使用本仓库提供的任何数据，请同时引用原始论文与本数据集。 1. **原始论文**：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. **本数据集**：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