This study explored the antiviral potential of Tinosporaside, a natural compound found in Tinospora cordifolia, and its chemically modified versions, to identify a new treatment strategy against COVID-19. The research focused on two important viral enzymes-Mpro and PLpro, that are essential for the virus to replicate and weaken the immune response. This research employed a quantitative, computational methodology rather than a survey-based approach. Techniques such as molecular docking and molecular dynamics simulations were used to design and evaluate 56 Tinosporaside analogs. One particular derivative, T46, stood out for its strong and stable binding to both enzymes. It exhibited better performance than the original compound and possessed favorable druglike properties, including high absorption, low toxicity, and chemical stability. Small structural modifications to the compound, such as the addition of a pyrrole ring, carboxylic acid, and a bromine atom, played a crucial role in enhancing its effectiveness. Further computer simulations confirmed that T46 could interact effectively with both viral targets, potentially disrupting the virus’s ability to function. These findings suggest that T46 has strong potential as a lead compound for future antiviral drug development. While the results are based on computer simulations, they provide a solid starting point for laboratory experiments and, eventually, real-world applications. This work also highlights how natural compounds can be refined and repurposed using modern tools to fight emerging diseases like COVID-19.