Chemomodeling analysis of C. sativa compounds as VKOR inhibitors

Overview

This repository contains code for analyzing and comparing molecular properties of various compounds, including Quercetin, Gallic Acid, Chlorogenic Acid, Catechol, Caffeic Acid, Coumaric Acid, Rosmarinic Acid, and Warfarin, with a control compound 4-Hydroxycoumarin. The analysis includes molecular weight, LogP, hydrogen bond donors, hydrogen bond acceptors, aromatic rings, and free energy (ΔG), with Tanimoto similarity calculations and Lipinski Rule-of-5 compliance checks.

Features

• Normalization of molecular descriptors.
• Calculation of Tanimoto similarity scores relative to Warfarin and 4-Hydroxycoumarin.
• Visualization of molecular structures and similarity scores.
• Drug-likeness assessment using Lipinski's Rule-of-5.

Requirements

• Python 3.x
• NumPy
• pandas
• RDKit
• matplotlib

Installation

1. Clone the repository:

   git clone https://github.com/virtualscreenlab/VKOR.git
   

2. Install the required packages:

   pip install numpy pandas rdkit matplotlib
   

Usage

Run the script Td.py or Ts.py to perform the analysis and generate visualizations:

python Td.py

or

python Ts.py

Output

• vkor_compounds.png: Grid image of compound structures.
• similarity_to_4_hydroxycoumarin.png: Bar plot of Tanimoto similarity to 4-Hydroxycoumarin.
• similarity_to_quercetin.png: Bar plot of Tanimoto similarity to Quercetin.

Contributing

Contributions are welcome! Please fork the repository and submit pull requests.

License

This project is licensed under the GNU General Public License.

Contact

For contact purposes, you may reach out to Prof. Sergey Shityakov via email at shityakoff@hotmail.com.