Cyclodextrin, a potent anti-tumor medication utilized predominantly in ovarian and breast cancer treatments, encounters significant challenges such as poor solubility, potential side effects, and resistance from tumor cells. Combining cyclodextrin with biocompatible substrates offers a promising strategy to address these obstacles. Understanding the atomic structure and physicochemical properties of cyclodextrin and its derivatives is essential for enhancing drug solubility, modification, targeted delivery, and controlled release. In this study, we investigate the topological indices of cyclodextrin using algebraic polynomials, specifically the degree-based M-polynomial and neighbor degree-based M-polynomial. By computing degree-based and neighbor degree-based topological indices, we aim to elucidate the structural characteristics of cyclodextrin and provide insights into its physicochemical behavior. The computed indices serve as predictive tools for assessing the health benefits and therapeutic efficacy of cyclodextrin-based formulations. In addition, we examined that the computed indices showed a significant relationship with the physicochemical characteristics of antiviral drugs. Graphical representations of the computed results further facilitate the visualization and interpretation of cyclodextrin's molecular structure, aiding researchers in designing novel drug delivery systems with improved pharmacological properties.