MOLECULAR DOCKING AS A TOOL FOR STRUCTURAL ELUCIDATION OF BIOACTIVE COMPOUNDS: A REVIEW

Abstract

Structural elucidation is an important step in chemical, pharmaceutical, biochemical, and natural product research because it helps researchers identify a compound and understand how its atoms are arranged. Traditional techniques such as nuclear magnetic resonance spectroscopy, mass spectrometry, infrared spectroscopy, ultraviolet spectroscopy, and X-ray crystallography remain the main methods used for structure determination. However, these methods may sometimes face difficulties, especially when compounds have closely related structures, are unstable, or are obtained in very small quantities. Molecular docking has become a useful computational tool that can support structural elucidation by providing information on how an identified or proposed compound may interact with a biological target. It does not replace experimental methods, but it can help explain the possible relationship between chemical structure and biological activity. In docking studies, a ligand is placed into the binding site of a protein to predict its binding pose, interaction pattern, and possible binding strength. This is useful in natural product research, drug discovery, and studies involving bioactive compounds, where researchers often need to understand how a compound may produce its observed activity. Molecular docking can also support the comparison of related compounds, interpretation of structure–activity relationships, and selection of promising molecules for further testing. Despite its usefulness, docking has limitations, including issues with protein flexibility, scoring accuracy, ligand preparation, and binding site selection. Therefore, docking results should be interpreted carefully and supported with experimental data, validation methods, molecular dynamics simulation, and biological assays where possible. This review discusses the principles, workflow, applications, limitations, and future relevance of molecular docking as a complementary tool in structural elucidation.