| Literature DB >> 26597878 |
Sarbani Dey Ray1,2, Supratim Ray3, Muhammad Zia-Ul-Haq4, Vincenzo De Feo5, Saikat Dewanjee6.
Abstract
BACKGROUND: The root bark of Zizyphus nummularia (Rhamnaceae) is traditionally used as an anti-inflammatory agent. The current study aimed to explore the anti-inflammatory activity (in vivo) of a crude ethanolic extract (EE) and the pure identified octadecahydro-picene-2,3,14,15-tetranone (IC) in the root bark of Z. nummularia. IC was further subjected to suitable in vitro and in silico studies to find out the mechanistic pharmacology.Entities:
Mesh:
Substances:
Year: 2015 PMID: 26597878 PMCID: PMC4657250 DOI: 10.1186/s12906-015-0942-7
Source DB: PubMed Journal: BMC Complement Altern Med ISSN: 1472-6882 Impact factor: 3.659
Fig. 1The structure of isolated picene compound, octadecahydro-picene-2,3,14,15-tetraone
The Qikprop® properties and descriptors
| Sl no. | Descriptor | Description | Recommended range |
|---|---|---|---|
| 1 | mol_MW | Molecular weight of the molecule | 130.0–725.0 |
| 2 | SASA | Total solvent accessible surface area (SASA) in square angstroms using a probe with a 1.4 A0 radius | 300.0–1000.0 |
| 3 | FOSA | Hydrophobic component of the SASA (saturated carbon and attached hydrogen) | 0.0–750.0 |
| 4 | FISA | Hydrophilic component of the SASA (SASA on N, O and hydrogen on heteroatom) | 7.0–330.0 |
| 5 | PISA | Π (carbon and attached hydrogen) component of SASA | 0.0–450.0 |
| 6 | Volume | Total solvent-accessible volume in cubic angstroms using a probe with 1.4 A0 radius | 500.0–2000.0 |
| 7 | donorHB | Estimated number of hydrogen bonds that would be donated by the solute to water molecules in an aqueous solution. Values are averages taken over a number of configurations, so they can be non-integer | 0.0–6.0 |
| 8 | accptHB | Estimated number of hydrogen bonds that would be accepted by the solute to water molecules in an aqueous solution. Values are averages taken over a number of configurations, so they can be non-integer | 2.0–20.0 |
| 9 | QPlogP o/w | Predicted octanol/water partition coefficient | −2.0-6.5 |
| 10 | Human oral absorption | Predictive qualitative human oral absorption. The assessment uses a knowledge-based set of rules, including checking for suitable values percent human oral absorption, number of metabolites, number of rotatable bonds logP, solubility and cell permeability | 1, 2, 3 for low, medium and high absorption respectively |
| 11 | % human oral absorption | It predicts human oral absorption on 0 to 100 % scale. The prediction is based on a quantitative multiple linear regression model. This property usually correlates well with human oral absorption. | >80 % is high <25 % is poor |
| 12 | #rtvFG | This particular descriptor indicates the number of reactive functional groups. The presence of these groups can lead to decomposition, reactivity, or toxicity problems in vivo. | 0 to 2.0 |
| 13 | CNS | Predictive central nervous activity on a −2 (inactive) to +2 (active) scale. | −2.0 to 2.0 |
| 14 | Lipinski’s rule of five | Lipinski’s rules of five are: mol_MW < 500, QPlogPo/w < 5, donorHB ≤ 5, accptHB ≤ 10. Compounds that satisfy these rules are considered drug like. (The “five” refers to the limits, which are multiples of 5). | Maximum is 4 |
Top-ranked SiteMap® prediction for receptor binding sites
| Sl. no | Title | Site score |
|---|---|---|
| 1 | Sitemap_site1 | 0.643 |
| 2 | Sitemap_site2 | 0.566 |
Fig. 2The centroid of the sitemap_site1 used in the generation of grid of TNF-α receptor. Hydrophobic map: yellow mesh; hydrogen bond (HB) donor map: blue mesh; HB acceptor map: red mesh. White points indicate generated site points
Fig. 3The centroid of the sitemap_site1 within the TNF-α receptor site
Fig. 4Effect of EE and IC in acute and chronic inflammations in mice. Panel a: Effect on carrageenan induced paw edema in mice. Panel b: Effect on xylene and arachidonic acid-induced mouse ear model. Percent of oedema weight = 100 x (WR-WL)/WL; where WR is the mass of right ear, WL mass left ear. Panel c: Effect on cotton pellet granumola in experimental mice. Values are expressed as mean ± SE (n = 6). *p < 0.05 compared with control group. **p < 0.01 compared with control group
Fig. 5Effect of IC in NO, PGE-2 and TNF-α production in PBS stimulated RAW 264.7 cells. Values are expressed as mean ± SE (n = 3)
Pharmacokinetic prediction of selected compound (IC) by QikProp® 3.2
| Sl no. | Descriptor | Predicted values of IC |
|---|---|---|
| 1 | mol_MW | 356.46 |
| 2 | SASA | 603.7 |
| 3 | FOSA | 326.13 |
| 4 | FISA | 209.07 |
| 5 | PISA | 68.5 |
| 6 | Volume | 1115.35 |
| 7 | donorHB | 2 |
| 8 | accptHB | 5.5 |
| 9 | QPlogPo/w | 2.498 |
| 10 | Human oral absorption | 3 |
| 11 | % human oral absorption | 77.61 |
| 12 | #rtvFG | 0 |
| 13 | CNS | −2.0 |
| 14 | Lipinski’s rule of five | 0 |
Fig. 63D view of docking pose of minimum energy structure complex of IC docked at the predicted active site of TNF-α (PDB ID: 1A8M) viewed using Glide XP visualizer of Schrödinger Maestro. Hydrogen bond is shown as yellow dash and bonded with GLN 47
Fig. 7Hydrophilic-lipophilic contour (White portion include Hydrophilic domain of TNF-α and brown portion indicate Hydrophobic domain of TNF-α)
Fig. 8The key amino acids were shown within the active site of TNF-α after docking