| Literature DB >> 34163151 |
Arif Malik1, Anam Naz1, Sajjad Ahmad2, Mansoor Hafeez1, Faryal Mehwish Awan3, Tassadaq Hussain Jafar1, Ayesha Zahid1, Aqsa Ikram1, Bisma Rauff1, Mubashir Hassan1.
Abstract
BACKGROUND: A recent COVID-19 pandemic has resulted in a large death toll rate globally and even no cure or vaccine has been successfully employed to combat this disease. Patients have been reported with multi-organ dysfunction along with acute respiratory distress syndrome which implies a critical situation for patients and made them difficult to breathe and survive. Moreover, pathology of COVID-19 is also related to cytokine storm which indicates the elevated levels of interleukin (IL)-1, IL-6, IL-12, and IL-18 along with tumor necrosis factor (TNF)-α. Among them, the proinflammatory cytokine IL-6 has been reported to be induced via binding of severe acute respiratory syndrome coronavirus 2 (SARS)-CoV-2 to the host receptors.Entities:
Keywords: COVID-19; drug designing; interleukin-6; molecular docking; phytocompounds
Year: 2021 PMID: 34163151 PMCID: PMC8191067 DOI: 10.1177/11779322211021430
Source DB: PubMed Journal: Bioinform Biol Insights ISSN: 1177-9322
Figure 1.Docked complexes and interacting residues of IL-6 with (A) isoorientin, (B) lupeol, and (C) andrographolide. Red dotted lines represent hydrogen bonds and blue lines show hydrophobic bonds.
Interactive residues of prioritized phytocompounds with IL-6.
| Docked complexes | Interactive residues in molecular interactions |
|---|---|
| Isoorientin with IL-6 | Ser-91, Thr-92, Leu-95, Phe-98, Leu-140, Phe-143, Lys-144, Leu-147 |
| Lupeol with IL-6 | Val-88, Ser-91, Thr-92, Leu-95, Phe-143, Lys-144, Leu-147, Ser-150, Leu-151 |
| Andrographolide with IL-6 | Ser-91, Thr-92, Leu-95, Lys-144, Leu-147, Gln-148, Leu-151 |
Figure 2.2D chemical structures of prioritized phytocompounds (A) isoorientin, (B) lupeol, and (C) andrographolide.
Figure 3.Simulation trajectories analysis: (A) receptor RMSD versus time, (B) inhibitors RMSD verses time, and (C) R versus time.
RMSD indicates root mean square deviations.
Figure 4.Andrographolide binding conformation at the start (tan) and end (sky blue) of simulation time. The receptor can be depicted in dark olive green.
MMGB/PBSA binding energies of high affinity complexes.
| Method | Energy component | Isoorientin | Lupeol | Andrographolide |
|---|---|---|---|---|
| MMGBSA | Van der Waals | – | −24.4464 | −31.4618 |
| Electrostatic | 1.8065 | 25.8202 | 18.5105 | |
| Polar solvation | 9.5663 | −17.9394 | −8.7597 | |
| Nonpolar solvation | −4.6149 | −2.7027 | −3.8338 | |
| Net gas-phase | −33.4112 | 1.3738 | −12.9513 | |
| Net solvation | 4.9514 | −20.6421 | −12.5935 | |
| Total | −28.4598 | −19.2682 | −25.5448 | |
| MMPBSA | Van der Waals | −35.2177 | −24.4464 | −31.4618 |
| Electrostatic | 1.8065 | 25.8202 | 18.5105 | |
| Polar solvation | 11.1732 | −20.6224 | −8.8799 | |
| Nonpolar solvation | −3.1739 | −2.2384 | −2.6723 | |
| Net gas-phase | −33.4112 | 1.3738 | −12.9513 | |
| Net solvation | 7.9993 | −22.8607 | −11.5523 | |
| Total | −25.4119 | −21.4869 | −24.5036 |
ADMET properties of top 3 selected phytocompounds.
| Properties | Isoorientin | Lupeol | Andrographolide |
|---|---|---|---|
| Blood-brain barrier | – | + | + |
| Human intestinal absorption | + | + | + |
| AMES toxicity | AMES toxic | Non-AMES toxic | Non-AMES toxic |
| Carcinogens | Noncarcinogens | Noncarcinogens | Noncarcinogens |
| Biodegradation | Not readily biodegradable | Not readily biodegradable | Not readily biodegradable |
| Aqueous solubility (Logs) | −2.3978 | −4.4193 | −2.8534 |