Multiple advancements have been introduced to combat cancer by improving current treatments. This includes the use of natural compounds, including quercetin. While quercetin is well-documented and has shown induction of apoptosis against cancer, it lacks crucial properties such as permeability and bioavailability. This study aimed to model quercetin and a quercetin analogue, 3,6,2',4',5'-pentahydroxyflavone, functionalized with l-amino acids to improve their drug potency to provide insights on novel cancer treatments. Specifically, the study focused on the molecular docking of functionalized quercetin and 3,6,2',4',5'-pentahydroxyflavone with two apoptosis-regulating proteins: caspase-3 and bcl-2.Quercetin and 3,6,2',4',5'-pentahydroxyflavone were functionalized with 20 l-amino acids and modified to improve their binding affinities. 315 modified complexes were created, prepared, and docked. Of these, six leads, three modified quercetin complexes and three modified analogue complexes, were chosen for evaluation of their interaction profiles and ADMET properties. These leads had greatly enhanced binding affinities compared to their base compounds. Modified quercetin functionalized with asparagine obtained binding affinities of -10.8 kcal/mol and -9.8 kcal/mol for caspase-3 and bcl-2, respectively, while modified 3,6,2',4',5'-pentahydroxyflavone functionalized with asparagine obtained binding affinities of -10.3 kcal/mol and -11.1 kcal/mol for caspase-3 and bcl-2, respectively. The results suggest the potential use of the compounds in cancer drug development via induction of apoptosis due to their strong binding affinities. Further in vitro studies could explore the efficacy of such in different routes of administration.