The need for new and innovative analytical methods that may shed information towards the composition of complex natural mixtures is a keystone on bioprospection programs. Dereplication methodologies associated to state-of-the-art spectroscopic techniques, have been successful in the selection of biologically active extracts. Our research group „NuBBE“ has incorporated the use of those methods as well as molecular virtual design using Nuclear Magnetic Resonance (NMR) aiming to increase the understanding of molecular relationships on dynamic natural matrixes and synergism effects of bioactive crude extracts. Highly active crude extracts, from Abarema lusoria and Calea pinnatifida, previously in vitro screened using human cell lineages such as HL-60 (Leukemia), MDA-MB435 (Melanoma), HCT-8 (Colon) and SF-295 (Glioblastoma), were analyzed using HPLC/DAD-HRMS and compared with in silico databases aiming to detect known plant metabolites. NMR data from the crude extracts was processed and compared with an NMR molecular virtual designed environment containing all known compounds for each species. Flavonoids, such as 8-methyl-naringenine, 4′,5,7-trihydroxy-3′,6-dimethoxy-8-methylflavanone, 3′,4′,5,6,7-pentahydroxy-8-methyldihydroflavonol and the benzophenone bis (2-hydroxy-4,6-dimethoxy-3-methylphenyl) metanone, were detected in A. lusoria. From C. pinnatifida we were able to detect flavonoids, such as 4′,5,7-trihydroxy-3-methoxy-6,8-dimethylflavanone, 4′,7-dihydroxy-5-methoxy-6-methyldihydroflavonol, 5,6,7-trihydroxy-3′,4′-dimethoxy-8-methylflavanone and, 3′,4′-dimethoxy-5,7-dihydroxy-6,8-dimethyldihydroflavonol. The occurrence of flavonoids may be associated to the original activity revealed in the in vitro assays. However, further studies must be performed in order to establish molecular synergism effects since there is no significant antineoplasic activity reported for those metabolites once isolated.