M01 tool: An automated, comprehensive computational tool for generating small molecule-peptide hybrids and docking them into curated protein structures

The field of computational drug design is rapidly advancing, necessitating innovative methods to enhance the efficiency and accuracy of ligand-receptor interactions. We introduce M01 tool, a comprehensive computational package designed to facilitate the generation and docking of small molecule-peptide hybrids. M01 tool integrates several established tools, including RDKit and EasyDock, into a user-friendly platform that automates the workflow from hybrid generation to docking simulations. Key features include an intuitive interface for visualizing molecules and selecting connection points, automated receptor preparation from UniProt or PDB IDs, generation of default docking configuration files, ligand preparation and docking using EasyDock, and calculation of molecular descriptors related to ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties. M01 tool aims to simplify the use of advanced computational tools for researchers with limited chemistry expertise, providing a robust and streamlined solution for hybrid design and docking studies. Validation using peptide-alkoxyamine hybrids demonstrated M01 tool's capability to generate and dock over 8,000 unique hybrid molecules, confirming its potential as a powerful tool in drug design.