Selective protease inhibitors from secondary metabolites of Philippine medicinal plants against porcine epidemic diarrhea virus: A computational veterinary drug discovery approach

Abstract

Background: Porcine epidemic diarrhea virus (PEDV) is a recurring coronavirus that causes severe diarrhea in pigs with high mortality and morbidity rates, especially in neonatal pigs. Despite the availability of vaccines, their efficacy is limited owing to antigenic differences between the vaccine and field strains, which poses a challenge to infection control. Antiviral drugs targeting conserved PEDV proteins show promise for complementing vaccination strategies. PEDV Nsp3 (PL2Pro) and Nsp5 (3CLPro) are essential proteases vital for viral replication, making them attractive targets for drug development against PEDV. Aim: To address the lack of therapeutics against recurring PEDV outbreaks and bridge the gap in the application of bioinformatics in veterinary drug discovery, this study aimed to discover compounds that inhibit PEDV proteases from Philippine medicinal plants by applying a modified virtual screening methodology that considers the physiology of swine hosts. Methods: This study employed a library of 690 metabolites from Philippine medicinal plants to screen for potential protease inhibitors targeting PEDV PL2Pro and 3CLPro. This includes evaluating the binding affinity, pharmacokinetics, dynamic stability, and critical binding site residues. Compounds demonstrating high affinity underwent a modified ADMET analysis, considering the enteric localization of the virus and potential toxicity to swine hosts. Furthermore, molecular dynamics simulations assessed compound stability under physiological swine conditions. Results: The study identified Bisandrographolide from Andrographis paniculata, CID 162866964 from Euphorbia neriifolia, and betulinic acid from Vitex negundo and Ocimum basilicum as metabolites that bind favorably and selectively to PEDV 3CLPro and have excellent pharmacokinetic properties and dynamic stability. In contrast, no selective inhibitor for PL2pro passed the same criteria. Conclusion: Employing the modified virtual screening protocol tailored for swine host considerations, the compounds identified in this study are anticipated to exert inhibitory effects against PEDV without off-target binding to analogous swine proteases and receptors. CID 162866964, bisandrographolide, and betulinic acid show promise for developing potent antivirals against PEDV.