| Literature DB >> 32384767 |
Annalisa Maruca1,2, Delia Lanzillotta3, Roberta Rocca2,3, Antonio Lupia2, Giosuè Costa1,2, Raffaella Catalano1,2, Federica Moraca2,4, Eugenio Gaudio5, Francesco Ortuso1,2, Anna Artese1,2, Francesco Trapasso3, Stefano Alcaro1,2.
Abstract
Essential oils (EOs) are popular in aromatherapy, a branch of alternative medicine that claims their curative effects. Moreover, several studies reported EOs as potential anti-cancer agents by inducing apoptosis in different cancer cell models. In this study, we have considered EOs as a potential resource of new kinase inhibitors with a polypharmacological profile. On the other hand, computational methods offer the possibility to predict the theoretical activity profile of ligands, discovering dangerous off-targets and/or synergistic effects due to the potential multi-target action. With this aim, we performed a Structure-Based Virtual Screening (SBVS) against X-ray models of several protein kinases selected from the Protein Data Bank (PDB) by using a chemoinformatics database of EOs. By evaluating theoretical binding affinity, 13 molecules were detected among EOs as new potential kinase inhibitors with a multi-target profile. The two compounds with higher percentages in the EOs were studied more in depth by means Induced Fit Docking (IFD) protocol, in order to better predict their binding modes taking into account also structural changes in the receptor. Finally, given its good binding affinity towards five different kinases, cinnamyl cinnamate was biologically tested on different cell lines with the aim to verify the antiproliferative activity. Thus, this work represents a starting point for the optimization of the most promising EOs structure as kinase inhibitors with multi-target features.Entities:
Keywords: SBVS; anti-cancer; essential oils; kinases; multi-target; polypharmacology
Mesh:
Substances:
Year: 2020 PMID: 32384767 PMCID: PMC7249159 DOI: 10.3390/molecules25092174
Source DB: PubMed Journal: Molecules ISSN: 1420-3049 Impact factor: 4.411
Name, CAS (Chemical Abstracts Service) number and 2D structure of essential oils (EOs) components selected after Structure-Based Virtual Screening (SBVS) are shown together with the Protein Kinases targets and their related best theoretical affinities (G-score in kcal/mol).
| Name | Structure | Target | G-Score |
|---|---|---|---|
| Psoralen |
| VEGFR2 | −8.09 |
| c-Met | −8.46 | ||
| 1-H-indol-2-ol |
| VEGFR2 | −8.00 |
| PDK1 | −8.64 | ||
| α-terpinen-7-al |
| VEGFR2 | −8.38 |
| PDK1 | −8.15 | ||
| ROCK1 | −8.00 | ||
| c-Met | −8.16 | ||
| Hinokitiol |
| VEGFR2 | −8.42 |
| c-Met | −8.20 | ||
| β-Vetivone |
| ROCK1 | −8.05 |
| c-Met | −8.26 | ||
| Precocene II |
| VEGFR2 | −8.02 |
| MEK2 | −8.08 | ||
| 1-H-benzochromene |
| VEGFR2 | −8.18 |
| PI3K-γ | −8.95 | ||
| c-Met | −8.88 | ||
| Piperonylacetone |
| VEGFR2 | −8.36 |
| ROCK1 | −8.33 | ||
| c-Met | −9.10 | ||
| Thymohydroquinone |
| SGK1 | −8.57 |
| VEGFR2 | −8.70 | ||
| PDK1 | −8.66 | ||
| CDK2 | −8.00 | ||
| GSK3β | −8.13 | ||
| ERK2 | −8.18 | ||
| 3-Phenil Benzaldeide |
| VEGFR2 | −9.47 |
| MEK2 | −8.41 | ||
| ROCK1 | −8.35 | ||
| B-Raf | −8.10 | ||
| c-Met | −8.07 | ||
| Cinnamyl cinnamate |
| EGFR | −8.12 |
| PDK1 | −8.19 | ||
| BMX | −8.06 | ||
| B-Raf | −8.02 | ||
| c-Met | −8.54 | ||
| Isoquinoline |
| VEGFR2 | −8.23 |
| PKA | −8.00 | ||
| ROCK1 | −8.04 | ||
| c-Met | −8.12 | ||
| Atronorin |
| SGK1 | −8.02 |
| EGFR | −9.69 | ||
| VEGFR2 | −10.97 | ||
| ABK | −8.17 | ||
| B-Raf | −8.01 | ||
| ERK1 | −9.06 | ||
| c-Met | −8.46 |
Figure 13D representations of the best docking pose of α-terpinen-7-al with the following anti-cancer targets: (A) c-Met (PDB: 2WGJ), represented as grey surface; (B) VEGFR2 (PDB: 3VHE), represented as green surface; (C) PDK1 (PDB: 3NAX), represented as orange surface; (D) ROCK1 (3TWJ), represented as pink surface. Ligands are shown in green carbon ball-and-sticks, while amino-acid residues involved in the molecular interactions are shown as carbon sticks with the correspondent color of protein’s surface. H-bonds is displayed as purple dashed lines.
Figure 23D representations of the best docking pose of cinnamyl cinnamate with the following anti-cancer targets: (A) EGFR (PDB: 3POZ), represented as blue surface; (B) PDK1 (PDB: 3NAX), represented as orange surface; (C) c-Met (PDB: 2WGJ), represented as grey surface; (D) BMX (PDB: 3SXR), represented as red surface; (E) B-Raf (PDB: 2FB8), represented as yellow surface. Ligands are shown in green carbon ball-and-sticks, while amino-acid residues involved in the molecular interactions are shown as carbon sticks with the correspondent color of protein’s surface. H-bonds and π-π interactions are displayed as purple and cyan dashed lines, respectively.
Figure 3Re-docked best poses of the relative co-crystallized ligands in the Protein Data Bank (PDB) models: (A) BMX (PDB code: 3SXR), represented as red surface; (B) B-Raf (PDB code: 2FB8), represented as yellow surface; (C) c-Met (PDB code: 2WGJ), represented as grey surface; (D) EGFR (PDB code: 3POZ), represented as blue surface; (E) PDK1 (PDB code: 3NAX), represented as orange surface; (F) ROCK1 (PDB code: 3TWJ), represented as pink surface; (G) VEGFR2 (PDB code: 3VHE), represented as green surface. Ligands are shown in green carbon ball-and-sticks, while amino-acid residues involved in the molecular interactions are shown as carbon sticks with the correspondent color of protein’s surface. H-bonds, π-π and halogen interactions are displayed as purple, cyan and yellow-gold dashed lines, respectively.
G-score and Induced Fit Docking (IFD) scores, expressed in kcal/mol, of α-terpinen-7-al and cinnamyl cinnamate complexed with kinase proteins selected by SBVS.
| Name | Target | G-Score | IFD Score |
|---|---|---|---|
| α-terpinen-7-al | VEGFR2 | −8.82 | −665.28 |
| PDK1 | −8.52 | −603.38 | |
| ROCK1 | −8.18 | −870.20 | |
| c-Met | −8.62 | −633.60 | |
| Cinnamyl cinnamate | EGFR | −8.31 | −654.13 |
| PDK1 | −9.46 | −605.92 | |
| BMX | −8.72 | −575.64 | |
| B-Raf | −8.64 | −563.84 | |
| c-Met | −9.50 | −635.95 |
Figure 4Effects of cinnamyl cinnamate treatment on cell proliferation of (A) MCF7, (B) A549, (C) HL60, and (D) Hela malignant cells. 500 cells were plated, in triplicate, in 384-well plates and treated with cinnamyl cinnamate at concentration of 10 μM for 24, 48 and 72 h; cells treated with DMSO were used as control. Cell proliferation was measured performing a cell titer assay and expressed as a percentage of control (** p < 0.005; *** p < 0.0005). Each column represents the mean ± SD of three different wells.