| Literature DB >> 28293075 |
Ranjith Kumavath1, Manan Azad1, Pratap Devarapalli1, Sandeep Tiwari2, Shreya Kar3, Debmalya Barh4, Vasco Azevedo2, Alan Prem Kumar5.
Abstract
Aromatase (CYP19A1) the key enzyme of estrogen biosynthesis, is often deregulated in breast cancer patients. It catalyzes the conversion of androgen to estrogen, thus responsible for production of estrogen in human body. However, it causes over-production of estrogen which eventually leads to proliferation of breast cancer cells. Identification of new small molecule inhibitors targeted against CYP19A1 therefore, facilitates to increase drug sensitivity of cancer cells. In this scenario, the present study aims to identify new molecules which could block or suppress the activity of aromatase enzyme by molecular docking studies using Schrödinger-Maestro v9.3. In this study we used in silico approach by modeling CYP19A1 protein the strcture was subjected to protein preparation wizard; to add hydrogen and optimize the protonation states of Thr310 and Ser478 and Asp309 residues. Active site of the CYP19A1 protein was identified using SiteMap tool of Scchrodinger package. We further carried out docking studies by means of Glid, with various ligands. Based on glid score, potential ligands were screeened and their interaction with CYP19A1 was identified. The best hits were further screened for Lipinski's rule for drug-likeliness and bioactivity scoring properties. Thus, we report two rubivivaxin and rhodethrin compounds that have successfully satisfied all in silico parameters, necessitating further in vitro and in vivo studies.Entities:
Keywords: anticancer drug; aromatase inhibitors; breast cancer; molecular docking
Year: 2016 PMID: 28293075 PMCID: PMC5320928 DOI: 10.6026/97320630012324
Source DB: PubMed Journal: Bioinformation ISSN: 0973-2063
Induced Fit docking results of drug molecules and reference ligand ASD showing Glide gScore, Glide energy and IFD score with CYP19A1
| Drug Bank ID | Ligand | Glide gScore (Kcal/mol) | Glide Energy (Kcal/mol) | IFD Score (Kcal/mol) |
| DB00197 | Troglitazone | -13.24 | -63.51 | -981.61 |
| DB00539 | Toremifene (SERM) | -10.97 | -52.09 | -976.98 |
| DB000894 | Testolactone | -10.85 | -50.76 | -976.54 |
| DB01406 | Danazol | -10.88 | -60.43 | -975.58 |
| Nil | Rubivivaxin | -11.04 | -49.96 | -975.58 |
| DB01536 | Androstenedione (ASD) | -11.06 | -50.31 | -974.5 |
| DB04839 | Cyproterone | -10.32 | -47.21 | -974.36 |
| DB00882 | Clomifene | -10.79 | -52.1 | -974.21 |
| DB00367 | Levonorgestrel | -11.21 | -43.14 | -974.09 |
| DB00675 | Tamoxifen (SERM) | -8.95 | -59.11 | -974.08 |
| DB03784 | Liarozole hydrochloride | -10.54 | -50.28 | -973.99 |
| DB06710 | Methyltestosterone | -11.07 | -57.21 | -973.85 |
| DB03749 | Plome stane | -9.78 | -43.75 | -973.17 |
| DB00269 | Chlorotrianisene | -10.44 | -49.88 | -972.83 |
| DB03781 | Liarozolefumarate | -9.32 | -50.27 | -972.83 |
| Nil | Rhodethrin | -9.53 | -42.34 | -972.74 |
| DB00351 | Megestrol | -10.75 | -52.38 | -972.68 |
| DB00255 | Diethylstilbestrol | -9.21 | -44.85 | -972.03 |
| DB01234 | Dexamethasone | -11.83 | -51.78 | -971.93 |
| DB00531 | Cyclophosphamide | -6.38 | -33.83 | -971.68 |
| DB00987 | Cytarabine | -8.87 | -47.05 | -969.89 |
| DB01168 | Procarbazine | -7.01 | -35.71 | -969.9 |
| DB02451 | Fadrozole hydrochloride | -7.43 | -40.94 | -969.4 |
| DB03778 | Fadrozole hydrochloride hydrate | -7.46 | -41.7 | -969.37 |
| DB01101 | Capecitabne | -10.84 | -59.63 | -968.72 |
| DB00201 | Caffeine | -6.2 | -33.91 | -966.93 |
| Nil | p-Bromophenol | -6.46 | -26.26 | -966.91 |
| DB00441 | Gemcitabine | -6.95 | -36.03 | -966.63 |
| DB01169 | Arsenic trioxide | -3.82 | -25.69 | -964.89 |
| DB00958 | Carboplatin | -5.7 | -32.73 | -964.89 |
| DB00544 | Fluorouracil | -4.36 | -14.75 | -961.49 |
Figure 1Molecular interaction of natural substrate Androstenedione (ASD) with CYP19A1 protein.
Molecular Docking Interaction of drug molecules with CYP19A1.aNumber of hydrogen bonds formed between the CYP19A1 binding domain and the drug compounds. bThe interacting active site residues of CYP19A1 protein with the drug molecules in the ligand-receptor complex.
| Ligand-enzyme complex | No.of H-bonds | Interacting residuesb | Atom of the ligand | Bond length A0 |
| Troglitazone-CYP19A1 | 2 | Leu 372, Met 374 | H of NH, O of C=O | 1.932, 1.654 |
| Toremifene-CYP19A1 | Nil | Nil | Nil | Nil |
| Testolactone--CYP19A1 | 2 | Ash 309, Met 374 | O of C=O, O of C=O | 1.689, 1.845 |
| Danazol-CYP19A1 | 2 | Ash 309, Met 375 | N of , O of -OH | 1.990, 2.071 |
| Rubivivaxin-CYP19A1 | 6 | Arg 115, Ala 306, Ala 306, Thr 310, Leu 372, Met 374 | O of -COOH, H of -OH, H of -OH, O of -OH, H of -OH, O of -COOH | 1.834, 1.906, 1.575, 2.136, 1.773, 1.705 |
| Androstenedione-CYP19A1 | 2 | Ash 309, Met 374 | O of C=O, O of C=O | 1.689, 1.888 |
| Cyproterone-CYP19A1 | 2 | Met 374, Hem 600 | O of C=O, H of -OH | 1.71 |
| Clomifene-CYP19A1 | Nil | Nil | Nil | Nil |
| Levonorgestrel-CYP19A1 | 2 | Thr 310, Met 374 | H of -OH, O of C=O | 1.895, 1.635 |
| Tamoxifen-CYP19A1 | 1 | Ash 309 | H of N-H | 1.687 |
| Liarozole hydrochloride-CYP19A1 | 2 | Leu 477, Hem 600 | H of NH, H of N-H | 1.771 |
| Methyltestosterone-CYP19A1 | 3 | Ala 306, Thr 310, Met 374 | H of -OH, O of -OH, O of C=O | 1.938, 1.787, 1.759 |
| Plome stane-CYP19A1 | 1 | Met 374 | O of C=O | 1.976 |
| Chlorotrianisene-CYP19A1 | 1 | Met 374 | O of | 2.058 |
| Liarozolefumarate-CYP19A1 | 2 | Leu 372, Ser 473 | H of NH, H of N-H | 1.94 |
| Rhodethrin-CYP19A1 | 3 | Thr 310, Leu 477, Hem 600 | O of -COOH, H of NH, H of -OH | 1.940, 2.011, 2.458 |
| Megestrol-CYP19A1 | 2 | Leu 372, Met 374 | H of -OH, O of C=O | 1.938, 1.804 |
| Diethylstilbestrol-CYP19A1 | 2 | Glu 302, Leu 477 | H of -OH, H of -OH | 1.787, 1.548 |
| Dexamethasone-CYP19A1 | 3 | Ash 309, Met 374, Ser 478 | O of -OH, O of C=O, H of -OH | 2.193, 1.712, 1.805 |
| Cyclophosphamide-CYP19A1 | 1 | Met 374 | O of O=P | 2.132 |
| Cytarabine-CYP19A1 | 4 | Ala 306, Thr 310, Leu 372, Leu 477 | H of -OH, O of -OH, H of NH2, H of NH2 | 1.870, 1.861, 1.960, 1.907 |
| Procarbazine-CYP19A1 | 2 | Hem 600, Hem 600 | N of N-NH2, N of NH | 2.003 |
| Fadrozole hydrochloride-CYP19A1 | 1 | Met 374 | N of C=N | 1.876 |
| Fadrozole hydrochloride hydrate-CYP19A1 | 2 | Met 374, Hem 600 | N of C=N, N of N-H | 1.961 |
| Capecitabne-CYP19A1 | 2 | Leu 372, Met 374 | H of -OH, O of | 2.100, 1.859 |
| Caffeine-CYP19A1 | 1 | Met 374 | O of C=O | 2.011 |
| p-Bromophenol-CYP19A1 | 2 | Arg 115, Met 374 | H of -OH, O of -OH | 2.045 |
| Gemcitabine-CYP19A1 | 3 | Thr 310, Met 374, Leu 477 | H of NH2, O of -OH, H of -OH | 2.307, 2.081, 1.722 |
| Arsenic trioxide-CYP19A1 | 2 | Arg 115, Met 374 | O of O=As, O of O=As | 1.988, 1.654 |
| Carboplatin-CYP19A1 | 1 | Met 374 | O of C=O | 1.911 |
| Fluorouracil-CYP19A1 | 1 | Met 374 | N of | 2.017 |
Molinspiration and Osiris results of compounds
| Compounds | cLogP | Solubility | Mol.Weight | TPSA | Drug-Likeness | Drug-Score | Toxicity Risk |
| Troglitazone | 4.39 | -5.46 | 441 | 110.1 | 3.55 | 0.47 | No Risk |
| Toremifene | 4.95 | -4.8 | 405 | 12.47 | 4.33 | 0.15 | High Risk |
| Testolactone | 2.71 | -3.74 | 300 | 43.37 | -2.73 | 0.43 | No Risk |
| Danazol | 3.46 | -4.88 | 337 | 46.26 | 2.07 | 0.62 | No Risk |
| Rubivivaxin | 1.03 | -1.73 | 298 | 124.2 | 3.46 | 0.55 | No Risk |
| Rhodethrin | 1.55 | -2.62 | 263 | 82.55 | -1.21 | 0.56 | No Risk |
Figure 4Close view, Binding mode and interacted ligands of Troglitazone with CYP19A1. A. Close view of Troglitazone with CYP19A1. B. Binding mode of Troglitazone with CYP19A1. C. Interaction with ligands.
Figure 5Close view, Binding mode and interacted ligands of Toremifene with CYP19A1. A. Close view of Toremifene with CYP19A1. B. Binding mode of Toremifene with CYP19A1929. C. Interaction with ligands 5929.
Figure 6Close view, Binding mode and interacted ligands of Testolactone with CYP19A1. A. Close view of Testolactone with CYP19A1. B. Binding mode of Testolactone with CYP19A1. C. Interaction with ligands.
Figure 7Close view, Binding mode and interacted ligands of Danazol with CYP19A1.A. Close view of Danazol with CYP19A1 B. Binding mode of Danazol with CYP19A1. C. Interaction with ligands.
Figure 3Close view, Binding mode and interacted ligands of Rubrivivaxin with CYP19A1. A. Close view of Rubrivivaxin with CYP19A1. B. Binding mode of Rubrivivaxin with CYP19A1. C. Interaction with ligands
Figure 2Close view, Binding mode and interacted ligands of Rhodethrin with CYP19A1. A. Close view of Rhodethrin with CYP19A1. B. Binding mode of Rhodethrin with CYP19A1. C. Interaction with ligands.