Network pharmacology, molecular docking, and molecular dynamics simulation in drug development: A comprehensive perspective
Hongyan Liu, Yuhua He, Bo Sun, Ziyi Xu, Yitao Fan, Jiachun Sun · Current Pharmaceutical Analysis · 2025
Drug development is a core area of modern medicine, and its history reflects the deep integration of multidisciplinary technologies. Current revolutionary breakthroughs in biotechnology and computational technologies are changing traditional drug research and development paradigms. In this transformation process, three key technologies underpin the research and development support system. First, network pharmacology (NP) combines analytical tools to construct drug-target-disease networks, identifying multiple targets and elucidating the mechanisms of drug action through network feature analysis[1]. Building on this, molecular docking technology utilizes computational tools to predict the static binding conformation and strength of ligand-target interactions, achieving high-throughput screening of biomacromolecule binding sites and significantly enhancing the discovery efficiency of lead compounds[2]. Complementing molecular docking, molecular dynamics (MD) simulation further supplements the spatiotemporal dimension of the interaction, revealing the dynamic changes in the binding process and target responses[3]. This stepwise technological integration framework employs a closed-loop research and development process involving target identification, molecular design, and dynamic validation. This approach not only improves the reliability of target validation but also significantly enhances the efficiency of lead compound optimization. Together, these advancements provide essential technical support for accelerating the clinical translation of innovative drug.