Screening and identification of bioactive compounds from citrus against non-structural protein 3 protease of hepatitis C virus genotype 3a by fluorescence resonance energy transfer assay and mass spectrometry

Abstract

BACKGROUND

Hepatitis C virus genotype 3a (HCV G3a) is highly prevalent in Pakistan. Due to the elevated cost of available Food and Drug Administration-approved drugs against HCV, medicinal natural products of potent antiviral activity should be screened for the cost-effective treatment of the disease. Furthermore, from natural products, active compounds against vital HCV proteins like non-structural protein 3 (NS3) protease could be identified to prevent viral proliferation in the host.

AIM

To develop cost-effective HCV genotype 3a NS3 protease inhibitors from citrus fruit extracts.

METHODS

Full-length NS3 without co-factor non-structural protein 4A (NS4A) and codon optimized NS3 protease in fusion with NS4A were expressed in Escherichia coli. The expressed protein was purified by metal ion affinity chromatography and gel filtration. Citrus fruit extracts were screened using fluorescence resonance energy transfer (FRET) assay against the protease and polyphenols were identified as potential inhibitors using electrospray ionization-mass spectrometry (MS)/MS technique. Among different polyphenols, highly potent compounds were screened using molecular modeling approaches and consequently the most active compound was further evaluated against HCV NS4A-NS3 protease domain using FRET assay.

RESULTS

NS4A fused with NS3 protease domain gene was overexpressed and the purified protein yield was high in comparison to the lower yield of the full-length NS3 protein. Furthermore, in enzyme kinetic studies, NS4A fused with NS3 protease proved to be functionally active compared to full-length NS3. So it was concluded that co-factor NS4A fusion is essential for the purification of functionally active protease. FRET assay was developed and validated by the half maximal inhibitory concentration (IC₅₀) values of commercially available inhibitors. Screening of citrus fruit extracts against the native purified fused NS4A-NS3 protease domain showed that the grapefruit mesocarp extract exhibits the highest percentage inhibition 91% of protease activity. Among the compounds identified by LCMS analysis, hesperidin showed strong binding affinity with the protease catalytic triad having S-score value of -10.98.

CONCLUSION

Fused NS4A-NS3 protease is functionally more active, which is effectively inhibited by hesperidin from the grapefruit mesocarp extract with an IC₅₀ value of 23.32 µmol/L.

Keywords: Hepatitis C virus genotype 3a, Non-structural protein 3 protease, Fluorescence resonance energy transfer assay, Citrus extract, Mass spectrometry, Hesperidin

Core Tip: The manuscript describes the screening of active metabolites in citrus fruit extracts against hepatitis C virus genotype3a non-structural protein 3 (HCV-G3a NS3) protease. In this study, conditions have been optimized to get highly purified and functionally active protein HCV NS3. Further, fluorescence resonance energy transfer assay was used to screen the citrus extracts against NS3 protease. By using liquid chromatography coupled with tandem mass spectrometry/mass spectrometry analysis and bioinformatics modeling approaches, the observed activity of citrus extracts against HCV genotype3a NS3 protease was ascribed to hesperidin. Fluorescence resonance energy transfer assay confirmed the inhibitory potential of hesperidin against NS4A-NS3 protease domain with an half maximal inhibitory concentration value of 23.32 µmol/L.