ResultsSix compounds from C. affinis and C. gigantea were isolated and characterized from the dichloromethane (DCM)-soluble fractions of the methanolic extracts of these two species. Three of the compounds were from C. gigantea and proposed as penduletin (C1), a mixture of α-amyrin (C2a), β-amyrin (C2b), and monoglyceride of stearic acid (C3), while the remaining three compounds were from C. affinis and proposed as penduletin (C4) (which was also isolated from C. gigantea), 7,8-(3″,3″-dimethyl-pyrano)-4′-hydroxy flavonol (C5), and lastly a mixture of 7,8-(3″,3″-dimethyl-pyrano)-4′-hydroxy flavonol (C5) and 4′,7,8-trihydroxy flavonol (C6). These compounds showed promising zones of inhibition against Gram-positive and Gram-negative bacteria and fungi. In the antidiarrheal test, C5 demonstrated the highest reduction in castor oil-induced diarrhea (44.44%) at a dose of 20 mg/kg compared to loperamide’s 77.78% reduction. However, the analgesic assessment showed a noteworthy inhibition of acetic acid-induced writhing by C1/C4 and C2 (56.52%) at a dose of 20 mg/kg compared to the 76.09% by diclofenac sodium. In comparison, C2 showed pronounced anti-inflammatory action by 68.15% and 52.06% reduction, respectively, in the early and later phases compared to the ibuprofen’s outcomes of 73.54% and 74.68%. Plausible targets such as dihydrofolate reductase (DHFR) for antimicrobial, kappa opioid receptor (KOR) for antidiarrheal, and cyclooxygenase 2 (COX-2) for anti-inflammatory and analgesic activities showed a noteworthy binding affinity with isolated compounds, and ADME/T studies displayed these phytochemicals’ drug-likeness profiles.