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Targeting the glycan of receptor binding domain with jacalin as a novel approach to developing treatment against COVID-19

Citation

Veerappan, Anbazhagan; Rajendaran, Senthilnathan; Jothi, Arunchalam (2020), Targeting the glycan of receptor binding domain with jacalin as a novel approach to developing treatment against COVID-19, Dryad, Dataset, https://doi.org/10.5061/dryad.9kd51c5dk

Abstract

In silico analysis revealed that a lectin, jacalin from jackfurit seeds recognize glycosylated region of receptor binding domain (RBD) of COVID-19. Jacalin binding induce conformational changes in RBD and significantly affect its interaction with human angiotensin-converting enzyme 2. The result may open up exploration of lectins based strategies against COVID-19.In silico analysis revealed that a lectin, jacalin from jackfurit seeds recognize glycosylated region of receptor binding domain (RBD) of COVID-19. Jacalin binding induce conformational changes in RBD and significantly affect its interaction with human angiotensin-converting enzyme 2. The result may open up exploration of lectins based strategies against COVID-19.

Methods

protein-protein interaction was done through

https://alcazar.science.uu.nl/services/HADDOCK2.2/haddockserver-prediction.htmlhttps://alcazar.science.uu.nl/services/HADDOCK2.2/haddockserver-prediction.html

The recently solved structure of SARS-CoV-2 RBD complexed with ACE2 receptor (PDB ID: 6LZG) was used in our study. PDB ID: 1M26 of jacalin was used in the analysis.

The interacting residues were identified using Discovery Studio Visualization software and was also conformed using RING web server.

The secondary structure information for models was calculated using the web server ‘2Struc’, which uses DSSP (Dictionary of Secondary Structure of Proteins)

The structure of hydroxychloroquine (HCQ) drug is obtained from the pubchem database (PubChem ID: 3652). Molecular docking of HCQ was performed using AutoDock Vina with help of PyRx tool, and LigPlot+ program was used to identify the interacting residues between jacalin and HCQ.

Usage Notes

 

Active residues (Input given in HADDOCK)

 

First molecule

Second molecule

RBD vs Jacalin complex

RBD:

343,342,339,338,368

Jacalin:

1,47,121,122,123,125,78,80

RBD(N343G) vs Jacalin

RBD:

343,342,339,338,368

Jacalin:

1,47,121,122,123,125,78,80

Jacalin-RBD complex vs hACE2

hACE2: 31,19,24,34,41,42,353,83,30,38,35,82

RBD : 484,475,487,453,500,446,449,498,496,486,505,417,493,502,489