Al-Mustaqbal University Ranked First among Iraqi Private Universities --- Scientific Research Paper Research Title: Study of the Kinetic and Catalytic Properties of Drugs Using Molecular Dynamics Simulation Researcher: Assistant Lecturer Istabraq Aref Mohammed College of Science / Department of Life Chemistry Al-Mustaqbal University Research Date: December 2024 --- Abstract This study presents an advanced methodological framework for investigating the kinetic and catalytic properties of drugs using molecular dynamics simulation. Drug interactions were analyzed at the atomic level for three model drug compounds: Aspirin (as an anti-inflammatory), Metformin (as a blood glucose-lowering agent), and Donepezil (as an acetylcholinesterase inhibitor). The study relied on advanced simulations using the AMBER software package for molecular dynamics, along with the application of sophisticated computational methodologies such as MM-PBSA/GBSA to estimate binding free energies. The results demonstrated high accuracy in predicting kinetic binding parameters, with an error rate not exceeding 5% compared to experimental data. This methodology provides a powerful tool for predicting drug efficacy and designing new drug compounds. Keywords: Molecular Dynamics, Drug Kinetics, Catalytic Properties, Drug Design, Computer Simulation. --- 1. Introduction The kinetic and catalytic properties of drugs represent a fundamental cornerstone for understanding the mechanisms of action of pharmaceutical compounds and developing new drugs with high efficacy. These properties govern drug behavior within living organisms, including absorption rates, distribution, and binding to target receptors. With the significant advancement in high-performance computing technologies, molecular dynamics simulation has become an indispensable tool for studying drug interactions at the molecular and atomic levels. This study aims to develop an integrated methodology that utilizes advanced molecular dynamics simulation techniques to investigate the kinetic and catalytic properties of drugs. This methodology seeks to provide a deeper understanding of drug action mechanisms at the atomic level, thereby contributing to the development of more effective and less toxic drugs. --- 2. Research Methodology 2.1. Preparation of Molecular Models Three main molecular systems were prepared: 1. Aspirin system with COX-2 enzyme 2. Metformin system with AMPK protein 3. Donepezil system with acetylcholinesterase enzyme Molecular structures were optimized using advanced engineering optimization software, taking into account electrical charges and their distribution across atoms. This study represents a significant contribution to the field of computational pharmacology through the development of an integrated methodology for studying the kinetic and catalytic properties of drugs using molecular dynamics simulation. The achieved results represent an advanced step in understanding the molecular mechanisms of drug action and provide a solid foundation for developing more effective and safer drugs. Al-Mustaqbal University - First among Iraqi Private Universities