Antitumor Activity and Mechanism of Robustic Acid from Dalbergia benthami Prain via Computational Target Fishing

Abstract

Dalbergia benthami Prain (D.benthami) is an important legume species of the Dalbergia family, due to the use of its trunk and root heart in traditional Chinese medicine (TCM). In the present study, we reported the isolation, characterization and pharmacological activities of robustic acid (RA) from the ethyl acetate extract of D. benthami Prain. The SwissADME prediction showed that the RA satisfied the Lipinski's rule of five (molecule weight (MW): 380.39 g/mol, lipid-water partition coefficient (log P): 3.72, hydrogen bond donors (Hdon): 1, hydrogen bond acceptors (Hacc): 6, rotatable bonds (Rbon): 3. Other chemical and pharmacological properties of this RA were also evaluated, including topological polar surface area (TPSA) = 78.13 Å and solubility (Log S) = -4.8. The probability values of the antineoplastic, anti-free radical activities and topoisomerase I (TopoⅠ) inhibitory activity were found to be 0.784, 0.644 and 0.379, respectively. The molecular docking experiment using the Surflex-Dock showed that the Total Score and C Score of RNA binding with the human DNA-Topo I complex were 7.80 and 4. The MTS assay experiment showed that the inhibitory rates of RA on HL-60, MT4, Hela, HepG2, SK-OV-3 and MCF-7 cells were 37.37%, 97.41%, 81.22%, 34.4%, 32.68% and 51.4%, respectively. In addition, RA exhibited an inhibitory effect on the angiogenesis of zebrafish embryo, a good TopoⅠ inhibitory activity at a 10 mM concentration and in a dose-dependent manner, excellent radical scavenging in the DPPH and ABTS assays, and the free radical scavenging rate was close to the positive control (BHT) at different concentrations (0.5-2.0 mg/mL). Furthermore, 18 potential targets were found for this RA by PharmMapper, including ANXA3, SRC, FGFR2, GSK3B, CSNK2B, YARS, LCK, EPHA2, MAPK14, RORA, CRABP2, PPP1CC, METAP2, MME, TTR, MET and KDR. The GO and KEGG pathway analysis revealed that the "protein tyrosine kinase activity", "rap1 signaling pathway" and "PI3K-Akt signaling pathway" were significantly enriched by the RA target genes. Our results will provide new insights into the pharmaceutical use of this species. More importantly, our data will expand our understanding of the molecular mechanisms of RA functions.

Keywords: Dalbergia benthami prain; anti-tumor activity; computational target fishing; robustic acid.

Figure 1

(a) The Chemical structure of RA; (b) The binding mode of RA with the DNA-Topo I complex (PDB:1T8I).

Figure 2

(a) The anticancer activities of RA in HL-60, MT4, Hela, HepG2, SK-OV-3and MCF-7 cell lines; (b) DNA Topo I inhibitory activity of RA using Camptothecin (0.1 mM) as a positive control; (c) Representative photographs of zebrafish SIVs. The SIVs of zebrafish embryos are indicated by a white rectangle; (d) Effects of the representative compounds and control on SIVs’ length of 72 hpf zebrafish embryos (x ± s, n = 12), * p < 0.05; (e) DPPH radical scavenging activity; (f) ABTS radical scavenging activity.

Figure 2

(a) The anticancer activities of RA in HL-60, MT4, Hela, HepG2, SK-OV-3and MCF-7 cell lines; (b) DNA Topo I inhibitory activity of RA using Camptothecin (0.1 mM) as a positive control; (c) Representative photographs of zebrafish SIVs. The SIVs of zebrafish embryos are indicated by a white rectangle; (d) Effects of the representative compounds and control on SIVs’ length of 72 hpf zebrafish embryos (x ± s, n = 12), * p < 0.05; (e) DPPH radical scavenging activity; (f) ABTS radical scavenging activity.

Figure 3

(a) The molecular mechanisms of RA via Computational Target Fishing; (b) GO analysis of potential targets; (c) KEGG pathway analysis of potential targets; (d) RA-target-pathway network.

Figure 3

(a) The molecular mechanisms of RA via Computational Target Fishing; (b) GO analysis of potential targets; (c) KEGG pathway analysis of potential targets; (d) RA-target-pathway network.