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Título:

Modelling of Hepatitis E virus RNA-dependent RNA polymerase genotype 3 from a chronic patient and in silico interaction analysis by molecular docking with Ribavirin

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Autor:

Cancela D'Angelo, Florencia
Rendon Marín, S
Quintero Gil, C
Houston, DR
Gumbis, G
Panzera Crespo, Yanina
Arbiza, Juan
Mirazo, Santiago
Pérez Crossa, Ruben Gustavo

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Tipo de documento:

Preprint

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Palabras clave:

Hepatitis E virus
RNA polymerase
Ribavirin
Molecular docking
Interaction
Structure.

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Año de publicación:

2021

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Resumen:

Hepatitis E Virus (HEV) infection is an emergent zoonotic disease, where chronic hepatitis E associated to solid organ transplant (SOT) recipients, related to genotype 3, is the clinical manifestation of major concern. In this setting, ribavirin (RBV) treatment is the only available therapy, though drug-resistant variants could emerge leading to a therapeutic failure. Crystallographic structures have not been reported for most of the HEV proteins, including the RNA-polymerase (RdRp). Therefore, the mechanism of action of RBV against HEV and the molecular interactions between this drug and RdRp are largely unknown. In this work, we aimed to model in silico the 3 D structure of a novel HEV3 RdRp (HEV_C1_Uy) from a chronically HEV infected-SOT recipient treated with RBV and to perform a molecular docking simulation between RBV triphosphate (RBVT), 7-methyl-guanosine-5'-triphosphate and the modelled protein. The models were generated using I-TASSER server and validated with multiple bioinformatics tools. The docking analysis were carried out with AutoDock Vina and LeDock software. We obtained a suitable model for HEV_C1_Uy (C-Score=-1.33, RMSD = 10.4 ± 4.6 Å). RBVT displayed a binding affinity of −7.6 ± 0.2 Kcal/mol by molecular docking, mediated by 6 hydrogen-bonds (Q195-O14, S198-O11, E257-O13, S260-O2, O3, S311-O11) between the finger’s-palm-domains and a free binding energy of 31.26 ± 16.81 kcal/mol by molecular dynamics simulations. We identified the possible HEV RdRp interacting region for incoming nucleotides or analogs and provide novel insights that will contribute to better understand the molecular interactions of RBV and the enzyme and the mechanism of action of this antiviral drug.

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Versión permitida: Preprint. The University of Edinburgh
Publicado también en: Journal of Biomolecular Structure and Dynamics, 2023, 41(2): 705-721. DOI: 10.1080/07391102.2021.2011416

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CSIC: I+D_2018_245

Citación:

Cancela D'Angelo, F, Rendon Marín, S, Quintero Gil, C, y otros. "Modelling of Hepatitis E virus RNA-dependent RNA polymerase genotype 3 from a chronic patient and in silico interaction analysis by molecular docking with Ribavirin" [Preprint]. Publicado en: Edinburgh Research Explorer. 2021, 26 h. https://www.pure.ed.ac.uk/ws/portalfiles/portal/243181490/Manuscript_002_.pdf

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Licencia Creative Commons Atribución - No Comercial (CC - By-NC 4.0)

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