This research aimed to use students' modeling processes as a means of scientific inquiry. Students constructed models to explain the interactions between felodipine R and S and protein. The approach encouraged active student participation in molecular interaction modeling and offered students a "model-based teaching" experience for developing explanations of chemical phenomena. The concept is built on four structural concepts in chemistry-molecular interactions, Gibbs free energy, chemical equilibria, and optical isomerism. This framework enabled the examination of medical students' ability to integrate general chemistry for developing models that can explain drug interactions. This proposal is part of a research cycle using design-based research for a qualitative methodology centered on modeling. This research provides evidence that constructivist teaching is possible as a model-based intervention in the classrooms, measured in a medical training context, allowing students to develop, evaluate, and constantly revise their chemical understanding.