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Abstract

Infectious myonecrosis virus (IMNV) disease causes mass mortality and decreased shrimp production. The RdRp region projects to the interior, where it may function in transcription. The focus of this study was to determine the effect of amino acid polymorphisms from several countries on the structure of RdRp and identify the potential of watercress in inhibiting IMNV by targeting the RdRp protein of IMNV through an in silico approach. The results showed that the structure of the IMNV RdRp protein from Indonesia was similar to Mexico, and the protein structure from India_QDN was identical to India_QIL. Ligand binding affinity values showed that Rhamnetin 3-sophoroside in RdRp samples from Indonesia and India_QDN had the lowest values of -7.8 kcal/mol and -8.7 kcal/mol. Meanwhile, Rhamnazin 3-sophoroside had the lowest binding affinity value of -8.2 kcal/mol in RdRp protein samples from Mexico and India_QIL. The structure of the RdRp protein is still stable after interacting with rhamnetin and rhamnazin as indicated by the RMSD backbone value, ligand structure, and number of hydrogen bonds. Polymorphisms of amino acids from various countries have altered the structure of the RdRp protein of IMNV. The bioactive constituents in watercress N. officinale, specifically, rhamnetin and rhamnazin, have shown stable binding to RdRp protein. This suggests that the compound might inhibit the viral activity of the RdRp protein of IMNV from several countries.

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Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

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