| Literature DB >> 31453132 |
Abdullah A Elgazar1, Hamada Ramadan Knany1, Mohammed Soliman Ali1.
Abstract
BACKGROUND AND AIM: Traditional medicine is an important source for drug discovery. However, many challenges face the scientific community to develop novel drugs from it. To investigate the rationale behind the medical legacy of centuries of precious knowledge from traditional medicine, we aimed at performing virtual screening to identify potential leads from the middle-age textbook, The Canon of Medicine. EXPERIMENTAL PROCEDURE: A database of chemical constituents of plants mentioned within the book was built and docked against different molecular targets associated with inflammation such as phospholipase A2, p38 alpha mitogen activated protein kinase, cyclooxygenase-2 and leukotriene B4 dehydrogenase, after that literature survey was done to determine the consistency of traditional uses and molecular docking results with the current knowledge obtained from previous studies and reports. RESULTS ANDEntities:
Keywords: Anti-inflammatory; Avicenna; Traditional medicine; Virtual screening and drug discovery
Year: 2018 PMID: 31453132 PMCID: PMC6702150 DOI: 10.1016/j.jtcme.2018.09.004
Source DB: PubMed Journal: J Tradit Complement Med ISSN: 2225-4110
Validation of molecular docking software by redocking the co-crystallized ligands.
| PDB code | Co-crystallize Ligands | FlexX SCORE | RMSD | Interaction with essential amino acid/co-factors |
|---|---|---|---|---|
| 1db4 | 8In-200-A | −38.19 | 0.7598 | Gly29, Gly31, His47, |
| 1OUK | 084–501-A | −34 | 0.9218 | Met109, Asp168, Thr106 |
| 3NT1 | Naproxen | −29.23 | 0.7902 | Arg120, Tyr355 |
| 2DM6 | Indomethacin | −19.18 | 0.8632 | Arg56, Tyr262, Tyr273 |
Post-docking analysis of compounds achieving best binding energy with the selected targets.
| PLA2 | p38 alpha | COX-2 | LTB4DHDH | ||||||
|---|---|---|---|---|---|---|---|---|---|
| Plant | Compound | Binding energy ΔG (kcal/mol) | Interaction with amino acids | Binding energy ΔG (kcal/mol) | Interaction with amino acids | Binding energy ΔG (kcal/mol) | Interaction with amino acids | Binding energy ΔG (kcal/mol) | Interaction with amino acids |
| Mentha pulegium | Pedalitin | −22.75 | Asp48, Lys62, Leu2, Gly29 | −24.16 | Asp168,Ala34,Met109,His107,Gly110 | −18.20 | Arg 120, Tyr 355, Val349, Ala527, Leu352 | – | – |
| Jaceosidin | −22.75 | Asp48, Lys62, Leu2,Gly29 | −25.8 | Asp168,Ala34,Met109,Gly31,His107, Gly110 | – | – | −17.96 | Cys239,Tyr 245, Tyr262, Tyr273 | |
| Thymonin | – | – | −25.04 | Asp168,Ala34,Met109,His107,Gly110 | – | – | −17.18 | Cys239,Tyr 245, Tyr262, Val, 272, Tyr273 | |
| Rumex patientia | Emodin | −27.17 | Asp48, Gly31, Glu55, Thr61 | −27.1 | Met109,Gly110, Ala111, His107 | – | – | −18.14 | Cys239, Val 272 |
| Physcion | −23.81 | Gly31, Gly29, Thr61 | −27.85 | Met109,Gly110,His107,Ala111,Asp112 | – | – | – | – | |
| Rhabarberone | −22.5 | Lys52,Asp48,Gly31,Gly29 | – | – | −20.04 | Tyr 355, Ser 530 Val349, Ala527, Leu352 | – | – | |
| Chrysophanol | −27.32 | Met109,Gly110,Ala111,His107 | −21.03 | Tyr 355, Val349, Ala527, Leu352, Met 522 | – | – | |||
| Methylemodin | −28.19 | Gly31, Gly29, Glu 55, Thr61, Asp48 | – | – | – | – | – | – | |
| Taraxacum officinale | Cis-Caffeoyl Tartaric Acid | −25.81 | Lys52,Lys62,Asp48,His47,Gly29,Glu55 | – | – | −23.71 | Arg 120, Tyr 355, Val349, Ala527, Leu352 | −19.27 | Arg56, Tyr262, Val 272 |
| Caftaric Acid | −23.29 | Glu55,Gly29, Gly31,Lys62, Lys52 | – | – | −19.24 | Arg 120, Met 522, Val349, Ala527, Leu352 | −22.55 | Arg56, Tyr262, Val 272 | |
| Luteolin | – | – | −26.50 | Met109,Gly110,His107,Gly31,Ala34,Asp168 | −23.56 | Arg 120, Tyr 355, Val349, Ala527, Leu352 | −19.66 | Cys239, Tyr262, Tyr273 | |
| Hydroxycinnamic Acid | – | – | – | – | −20.77 | Arg 120, Tyr 355, Val349, Ala527, Leu352 | −18.06 | Ala53, Arg56, Tyr262 | |
Pharmacokinetic properties of compounds achieving best binding energy with the selected targets.
| NO. | Compound | OB (%) | Caco-2 | DL |
|---|---|---|---|---|
| 1 | Pedalitin | 34.02 | 0.38 | 0.31 |
| 2 | Jaceosidin | 2.14 | 0.42 | 0.34 |
| 3 | Thymonin | 1.97 | 0.65 | 0.41 |
| 4 | Emodin | 24.40 | 0.22 | 0.24 |
| 5 | Physcion | 22.29 | 0.52 | 0.27 |
| 6 | Rhabarberone | 83.38 | −0.12 | 0.24 |
| 7 | Chrysophanol | 18.64 | 0.62 | 0.21 |
| 8 | Methylemodin | 20.44 | 0.43 | 0.27 |
| 9 | Cis-Caffeoyl Tartaric Acid | 11.33 | −1.42 | 0.20 |
| 10 | Caftaric Acid | N/A | N/A | N/A |
| 11 | Luteolin | 36.16 | 0.19 | 0.25 |
| 12 | Hydroxycinnamic Acid | 53.60 | 0.48 | 0.04 |
* OB(%): oral bioavailability, CaCo-2: intestinal permeability, DL: Drug likeness.
Fig. 1Ligand interaction diagram of compounds with PLA2 (PDB ID: 1db4). A) PLA2/Methylemodin complex (B) PLA2/Emodin complex (C) PLA2/cis-caffeoyl tartaric acid complex.
Fig. 2Ligand interaction diagram of compounds with p38 α MAPK (PDB ID: 2QD9). A) P38 α/Physcion complex (b) P38α/Chrysophanol complex (c) P38 α/Emodin complex.
Fig. 3Ligand interaction diagram of compounds with COX-2 (PDB ID: 1NT3). A) COX-2/Cis-caffeoyl tartaric acidcomplex (b) COX-2/Luteolin complex (c) COX-2/Chrysophanol complex.
Fig. 4Ligand interaction diagram of compounds with COX-2 (PDB ID: 1NT3). A) LTB4DHR/Cafteric acid complex (b) LTB4DHR/Luteolin complex (c) LTB4DHR/Cis-caffeoyl tartaric acid complex.
Fig. 5Molecular interaction of the best ranking compounds (Superimposed) with the binding site of targets under investigation (A) Binding of Physcion (blue), Chrysophanol (Red) and Emodin (White) in the active site of p38α MAPK (B) Binding of Methyl Emodin (Green), Cis-caffeoyl tartaric acid (White), Emodin (Blue) in the active site of PLA2 (C) binding of Luteolin (Green), Chrysophanol (White) and Cis-caffeoyl tartaric acid (Blue) in the active site of COX-2 (D) Cis-caffeoyl tartaric acid (Green), Caftaric acid (RED), Luteolin (blue) in the active site of LTB4DHR.
Fig. 6Scheme of the proposed Anti-inflammatory mechanism for compounds derived from the formula. The compounds inhibit different steps in the inflammation pathway. MAPKS: Mitogen activated protein kinase, PLA2: Phospholipase A2, 5-LOX: 5-Lipoxygenase, Cox-2: Cyclooxygenase-2, HETES: Hydroxyeicosatetraenoic acid, LTB4DHR: Leukotriene B4 dehydrogenase, TNF-α: Tumor necrosis alpha 4) Emodin 5) Physcion 7) Chrysophanol 8) Cis-caffeoyl tartaric acid 9) Caftaric acid 10) Luteolin 12) Methylemodin.