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 (IC 50 ) 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 IC 50 value of 23.32 µmol/L.

A Modular Fluorescent Sensor Motif Used to Detect Opioids, Protein–Protein Interactions, and Protease Activity

“…During transfection of the mcherry-HCV protease and the cpGFP-CS-Nb39 protein components, we added BILN-2061 in a range of concentrations to the HEK293T cells and then fixed and imaged 24 h later. Image analysis and quantification showed that the IC 50 value of the SPOTon protease assay was 151 nM (Figure D), which is 3× higher than an IC 50 value reported in a fluorescence resonance energy transfer (FRET)-based in vitro assay . This is likely because the inhibitor needs to be added right after transfection and incubated for 24 h before imaging to inhibit HCV protease activity throughout the experiment.…”

Retraction Note: 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

“…This significant variation in the activity assay has altered the downstream inhibitory activities of extracts and natural products. Regrettably, this situation has forced us to retract our paper[ 2 ] to conduct more experimentation and make the major correction in data, before we can consider its rewriting and publication.…”