In silico simulation of hyperoside, isoquercetin, quercetin, and quercitrin as potential antivirals against the pNP868R protein of African swine fever virus

Research (Published online: 20-01-2024)

19. In silico simulation of hyperoside, isoquercetin, quercetin, and quercitrin as potential antivirals against the pNP868R protein of African swine fever virus

Putri Pandarangga, Yohanes T. R. M. R. Simarmata, Adi Berci Handayani Liu, and Dwi Ari Fitri Haryati

Veterinary World, 17(1): 171-178

Putri Pandarangga: Department of Clinic, Reproduction, Pathology, and Nutrition, Faculty of Medicine and Veterinary Medicine, Universitas Nusa Cendana, Kupang, 85001, Indonesia.

Yohanes T. R. M. R. Simarmata: Department of Clinic, Reproduction, Pathology, and Nutrition, Faculty of Medicine and Veterinary Medicine, Universitas Nusa Cendana, Kupang, 85001, Indonesia.

Adi Berci Handayani Liu: Department of Chemistry, Faculty of Math and Science, Gadjah Mada University, Yogyakarta, 55281, Indonesia.

Dwi Ari Fitri Haryati: Department of Chemistry, Faculty of Math and Science, Gadjah Mada University, Yogyakarta, 55281, Indonesia.

Background and Aim: African swine fever (ASF) causes disease in pigs with up to 100% mortality rates. There is no effective vaccine to protect against it. This study aimed to perform in silico docking of ASF virus (ASFV) pNP868R protein with potential flavonoid ligands to identify ligands that interfere with mRNA cap formation.

Materials and Methods: The ASFV pNP868R protein was tested with hyperoside, isoquercetin, quercetin, and quercitrin in this in silico simulation. ASFV pNP868R protein was extracted from the Research Collaboration for Structural Bioinformatics P rotein Data Bank (RCSB PDB) database with PDB ID 7D8U (https://www.rcsb.org/structure/7D8U). Standard ligands were separated from proteins using UCSF Chimera 1.13. The standard ligand was redocked to protein using AutoDockTools 1.5.6 with the AutoDock4 method for validation. In the docking process, the grid box size was 40 × 40 × 40 Å3 with x, y, and z coordinates of 16.433, −43.826, and −9.496, respectively. The molecular docking process of the proposed ligand–protein complex can proceed if the standard ligand position is not significantly different from its original position in the viral protein’s pocket. The root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (RoG) of the hyperoside with the lowest energy binding need to be analyzed with molecular dynamics using Groningen machine for chemical simulation 5.1.1.

Results: Molecular docking and dynamic simulation revealed that hyperoside had the most stable and compact binding to the pNP868R protein. Hyperoside binds to the protein at the minimum energy of −9.07 KJ/mol. The RMSD, RMSF, and RoG values of 0.281 nm, 0.2 nm, and 2.175 nm, respectively, indicate the stability and compactness of this binding.

Conclusion: Hyperoside is the most likely antiviral candidate to bind to the pNP868R protein in silico. Therefore, it is necessary to test whether this flavonoid can inhibit mRNA capping in vitro and elicit the host immune response against uncapped viral mRNA.

Keywords: hyperoside, isoquercetin, molecular docking, pNP868R, quercetin, quercitrin.