key: cord-0948767-q22vy1ij
authors: Saleem Basha, S; Tripathi, Dhirendra; Koora, Sravanthi; Satyanarayana, K; Jayaraman, Selvaraj
title: Molecular docking analysis of potential compounds from an Indian medicinal soup "kabasura kudineer" extract with IL-6
date: 2021-05-31
journal: Bioinformation
DOI: 10.6026/97320630017568
sha: 12269e11f3aa84320a320438d89338c1b639b46c
doc_id: 948767
cord_uid: q22vy1ij

The use of "kabasura kudineer" (liquid soup made from Indian medicinal plants) for combating COVID-19 has been common in the states of Tamilnadu and Puducherry, India during the pandemic. Therefore, it is of interest to document the molecular docking analysis of IL-6 inhibitors with potential antiviral compounds from "kabasura kudineer" extract. We show the optimal binding features of gallic acid and luteolin with the Interleukin-6 protein for further consideration.

Symptoms of the novel corona virus are similar to normal flu linked to CoVid-19 in structure and cause [1] [2] [3] [4] [5] [6] [7] [8] . Jing Liu et al. [7] reported that CoVid-19 patients sustained decrease in the proportion of lymphocytes with increase in the inflammatory cytokines (interleukin) in the peripheral blood. It is also known that IL-6 binds with gp130 to initiate downstream signal transduction, gene expression, and intracellular signal transduction [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] . The design, development and evaluation of compounds to combat the viral pandemic are gaining momentum. The use of "kabasura kudineer" (liquid soup from Indian medicinal plants) for combating CoVid-19 has been common in the states of Tamilnadu and Puducherry during the pandemic. Therefore, it is of interest to ©Biomedical Informatics (2021) 569 document the molecular docking analysis of compounds from an Indian medicinal soup "kabasura kudineer" extract with IL-6. 

Protein structure of IL-6 (PDB IDs: 3L5I, having resolution < 1.90 ▌, R-value free <0.222, R-Value Work <0.181) was downloaded from the Protein Data Bank (http://www.rscb.org) [27] . Assigned bonds orders and hydrogen atoms were added. Water molecules were removed within 3▌ of HET groups [20] . OPLS3 force field in Schrodinger, LLC, NY, USA, 2009 was used for energy minimization [28] . The receptor grid boxes were generated using Glide's Receptor Grid Generation module at the active site (with the radius of 20 around the crystal structure) of co-crystallized ligand with the computing cubic box of 14.74 × 53.85 × 73.53 .

Flexible docking with GLIDE Extra precision (XP) convention was used for calculating the binding affinity and ligand efficiency as an inhibitor of Corona virus target [29] [30] . Maestro interface (Schrodinger Suite, LLC, NY) was used as the visualization tool for docked ligands. 

The use of "kabasura kudineer" (liquid soup from Indian medicinal plants) for combating COVID-19 has been common in the states of Tamilnadu and Puducherry during the pandemic. Therefore, it is of interest to document the molecular docking analysis of IL-6 inhibitors with potential antiviral compounds from "kabasura kudineer" extract ( Table 1) . The potential binding residues in IL-6 are TYR, ALA, VAL, LYS, TRY, THR, and ASP. 38 molecules were docked with IL-6 and ranked based on their dock score. Compounds with optimal binding features are given in Table 2 . Table 2 shows that compounds (gallic acid and luteolin) showed good binding interactions with IL-6 structures compared to known standard compounds. Compound 1 (gallic acid) has one salt bridge interaction with LYS430 and three hydrogen bonding interactions with VAL477, TRY478, and ALA79 (Figure 1) . It also has more lipophilic interactions and non-bonded interactions against IL-6. When comparing to other compounds including the standard anti-HIV drugs, gallic acid has a more binding affinity towards IL-6 and it showed best hydrogen bonding interactions. Compound 2 (luteolin) has one pi-stacking interaction with LYS430 and four hydrogen-bonding interactions with LYS429, THR393, TYR478, and ALA479 ( Figure 2) . It also has more lipophilic interactions and nonbonded interactions against IL-6. When comparing to other compounds including standard anti-HIV drugs, Luteolin has good binding affinity, hydrogen bond towards IL-6. Thus, data show that they are involved in non-bonded interaction with IL-6. 

We report that gallic acid and luteolin have good binding features with the Interleukin-6 protein for further consideration. Thus, kabasura kuduneer extract containing gallic acid and luteolin used in combating COVID-19 is of importance.

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