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Molecular Docking Studies Of Natural Phenolic Compound and Derivates With Phospholipase A2
Pablo Henrique Delmondes
* ,
Ricardo Stefani
1  Laboratório de Estudos em Materiais (LEMAT), Instituto de Ciências Exatas e da Terra, Campus Universitário do Araguaia, Universidade Federal de Mato Grosso
Published: 12 December 2016 by MDPI in MOL2NET'16, Conference on Molecular, Biomed., Comput. & Network Science and Engineering, 2nd ed. congress CHEMBIOINFO-02: Chem-Bioinformatics Congress Cambridge, UK-Chapel Hill and Richmond, USA, 2016.
https://doi.org/10.3390/mol2net-02-03830
Abstract:

The enzym phospholipase A2 (PLA2) catalyzes the conversion of membrane phospholipids in the inflammatory mediators, such as prostaglandins and leukotrienes. Because of this role, substances with inhibitory activity of PLA2 enzyme, has gained prominence in the scientific community like possible anti-inflammatory. Several studies have shown that phenolic compounds such as flavonoids, phenolic acids and other, has, among various biological activities, anti-inflammatory activity by inhibition of the enzyme PLA2. Based on this context, this study aimed to conduct a molecular docking study of various natural phenolic compounds and some of their derivatives forward to the enzyme PLA2. The crystallographic structure of PLA 2 was obtained from Target Database Protein Data Bank [PDB ID: 1KPM] and the ligands were obtained from PubChem Database. The docking was performed using the AutoDock 4.0 software. It was observed that among the phenolic compounds included in the study, those with better interaction with the enzyme were rosmarinic acid 3'-O-beta-glucoside, 4-nerolidylcatechol, rosmarinic acid methyl ester, quercetin 3-O-malonylglucoside, quercetin pentaacetate and rosmarinic acid, respectively. The present study provides a better understanding of the inhibition of PLA2 by phenolic compounds, which may contribute to the development of new anti-inflammatories.

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Comments on this paper
Marcus Scotti
10 January 2017
kind of interactions
I congratulate the authors for the nice work. Regarding the interactions: Do the authors realize some more important kind of interaction? I mean, what the residues and structural pattern in tested phenolic compounds that are suitable for the binding?

Thanks,

Marcus
Ricardo Stefani
10 January 2017
Dear Marcus,

Hope you are doing well. Thank you for your interest in our work. We did not conduct studies to find residues and structural pattern suitable for binding, that is, we did not conduct any Q/SAR study. We have visually inspected the sites of interaction and realized that hydroxyl patterns are important for interactions of binding site. This will be discussed in detail in a full paper.

Cheers,

Ricardo.
Ihosvany Camps
20 January 2017
Re-score and protein resolution
Dear Authors,

How did you select your protein? Which is its resolution? It is from x-ray or RMN?

Also, did you re-score your poses with other score function? The AutoDock software is not among the must reliable docking software used by community.

Regards,

Camps
Ricardo Stefani
21 January 2017
Dear Dr. Camps,

Thank you for your comments. The enzyme was elucidated by X-ray crystallography, with a resolution of 1.80 Å. Gasteiger charge and polar hydrogens required for the potential calculations were added considering the target structure, and the water molecules removed. The redocking presented value of RMSD = 1.89 Å, considering the most stable pose of the more populous cluster. This result is considered satisfactory, sincde the RMSD (which measures the deviation) between the best pose and the ligand is less than 2.0 Å. Although Autodock is not the most reliable docking software, it is still one of the most reliable and is a free docking software, being a good alternative for research groups with limited financial resources.


Regards,

Ricardo.


 
 
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