In silico study: Assessment of the inhibition of cyclo-oxygenase 2 by ibuprofen by validating molecular docking and cardiovascular effects reported during the COVID 19 pandemic

Introduction The Covid 19 pandemic has put the cardiovascular risk incurred when using nonsteroidal anti-inflammatory drugs at the heart of the discussion. Based on the information currently available, WHO does not recommend the use of ibuprofen. the objective is to evaluate the inhibition of cyclooxygenase 2 by ibuprofen by validating molecular docking. Method The crystallographic structure of ibuprofen bound to cyclooxygenase-2 was obtained from the Protein Data Bank (PDB) at a resolution <3.00 Å. The receiver was visualized using Discovery Studio Visualizer version 2.5.5. It was efficiently prepared using AutoDock / Vina software. The 3D structure of Ligand (Ibuprofen) was downloaded from the Drugbak database (https://www.drugbank.ca/): Accession number DB01050 Results Molecular docking was chosen as the first-line discrimination of the ibuprofen-COX2 intercation for the in silico study of putative competitors. The complex formed by Ibuprofen-COX 2 from the experimental model gives a docking score (Affinity: -7.3 (kcal / mol) with a mean square deviation of (RMSD = 23.884). Conclusion The evaluation of the inhibition of cyclo-oxygenase 2 by ibuprofen was validated by molecular docking. Cardiovascular effects already reported in patients treated with traditional non-steroidal antiinflammatory drugs and coxibs have been observed in patients with COVID 19. Molecular docking becomes an essential step in drug discovery to explore other drug targets


Materials and methods
To locate the sites of interaction, four different categories of COX inhibitors have been documented by Smith et al.,  . Several works have determined the crystal structures of COX-1 and COX-2 in complex with inhibitors and substrates (Kurumbail and al. 1996) , ) . Selinsky et al determined the crystal structure of IBP bound to COX-1. (Selinsky and al. 2001) . However, the analgesic and anti-inflammatory effects of ibuprofen (IBP) arise from inhibition of COX-2 rather than COX-1 (Laneuville and al. 1994) . In order to compare the mode of binding of IBP to COX-2 versus COX-1, and to reveal a possible mechanism of selective substrate inhibition mediated by IBP, Orlando et al determined the crystal structure murine (mu) COX-2 complexed with Ibuprofen (IBP) (Orlando and al. 2015). The coordinates of the X-ray crystals of COX-2 in complex with ibuprofen (IBP formula: C13 H18 O2) (PDB ID: 4PH9) in Table 1, 2, 3, were extracted from the RCSB database ( http: / /www.rcsb.org/pdb). This is selected for modeling studies.

2-2-Preparation of the ligand
The 3D structure of Ligand (Ibuprofen) was downloaded from the Drugbak database (https://www.drugbank.ca/): Accession number DB01050. Torsional connections have been verified. Ligand was saved in the same anchor folder in pdbqt format. The charges were then added.

3-Molecular docking protocol
Docking calculations were performed using standard AutoDock Vina defaults. The active site was placed in a 40 × 50 × 40 Å cubic box at the geometric center of the selected flexible residue set, which has 0.375 Å as the grid point spacing The values of the root mean square deviation (RMSD) between the mooring and the initial poses were calculated. The resulting best poses were ranked based on Vina scores (kcal / mol). assessed by free binding energies (S score, kcal / mol) and binding interactions between the ligand atom and the active site residues.

Result
Molecular docking was chosen as the first-line discrimination of the ibuprofen-COX2 intercation as a structural discrimination procedure based on the in silico prediction of putative competitors (Liu and al. 2017). The structural differences of each molecule also influence its interaction with COX2 (figure 1)  The active site was placed in a cubic box at the geometric center of the selected flexible residue set at 0.375 Å as the grid point spacing The coordinates of the Grid Box (number of points X, Y, Z dimensions and spacing) for the Ibuprofen-COX2 model (shown in Figure 3) were noted.      Looking at gastrointestinal outcomes as the primary endpoint, preliminary evidence has shown the link between COX inhibition and the risk of cardiovascular disease. The VioXX trial in patients with rheumatoid arthritis treated with Rofecoxib were five times more likely to have a myocardial infarction than patients on nonselective anti-inflammatory inhibitor Naproxen (Bombardier and al. 2000) . Following the results of the Adenomatous Polyp PRevention On Vioxx (APPROVe) study, rofecoxib was withdrawn from the market in 2004( Baron and al. 2008) A meta-analysis of 280 trials of nonsteroidal anti-inflammatory drugs versus placebo showed that high dose naproxen was associated with a risk, albeit a low one, of vascular events (Bhala and al. 2013). Furthermore, the risk of cardiovascular disease was not equal for all COX-2 inhibitors. Questions also remained about the dose and duration of use of nonsteroidal anti-inflammatory drugs associated with a high risk of cardiovascular disease.

Conclusion
Our docking validated the experimental results known in current practice concerning the inhibition of cyclo oxygenase by ibuprofen. Molecular docking becomes an essential step in drug discovery so that new exoges ligands can be identified