Identification of natural antimicrobial agents to treat dengue infection: In vitro analysis of latarcin peptide activity against dengue virus
© Rothan et al.; licensee BioMed Central Ltd. 2014
Received: 2 May 2014
Accepted: 21 May 2014
Published: 31 May 2014
Although there have been considerable advances in the study of dengue virus, no vaccines or anti-dengue drugs are currently available for humans. Therefore, new approaches are necessary for the development of potent anti-dengue drugs. Natural antimicrobial peptides (AMPs) with potent antiviral activities are potential hits-to-leads for antiviral drug discovery. We performed this study to identify and characterise the inhibitory potential of the latarcin peptide (Ltc 1, SMWSGMWRRKLKKLRNALKKKLKGE) against dengue virus replication in infected cells.
The Ltc 1 peptide showed a significantly inhibitory effect against the dengue protease NS2B-NS3pro at 37°C, a physiological human temperature, (IC50, 12.68 ± 3.2 μM), and greater inhibitory effect was observed at 40°C, a temperature similar to a high fever (IC50, 6.58 ± 4.1 μM). A greater reduction in viral load (p.f.u./ml) was observed at simultaneous (0.7 ± 0.3 vs. 7.2 ± 0.5 control) and post-treatment (1.8 ± 0.7 vs. 6.8 ± 0.6 control) compared to the pre-treatment (4.5 ± 0.6 vs. 6.9 ± 0.5 control). Treatment with the Ltc 1 peptide reduced the viral RNA in a dose-dependent manner with EC50 values of 8.3 ± 1.2, 7.6 ± 2.7 and 6.8 ± 2.5 μM at 24, 48 and 72 h, respectively.
The Ltc 1 peptide exhibited significant inhibitory effects against dengue NS2B-NS3pro and virus replication in the infected cells. Therefore, further investigation is necessary to develop the Ltc 1 peptide as a new anti-dengue therapeutic.
KeywordsLatarcin peptide Dengue virus NS2B-NS3 Protease Protease activity Viral inhibition
Dengue is a viral disease caused by four serotypes of the Flavivirus genus  and is prevalent in tropical and subtropical countries, ranging from Southeast Asia to the Americas . Over 390 million people are infected with dengue virus (DENV) annually in over 100 counties, resulting in approximately 12000 deaths . In Malaysia, the fatality rate of dengue infection is approximately 3.6% based on the total number of dengue infections. The majority of deaths caused by dengue infection occur after the mild infection develops into severe haemorrhagic fever and dengue shock syndrome . In addition to the global health problem caused by dengue infection, it also has an economic burden. The estimated cost of dengue infection is approximately US$ 950 million per year, which is higher than hepatitis B and Japanese encephalitis in Southeast Asia .
DENV is an enveloped virus with a positive stranded RNA genome of approximately 11 kb in length that encodes a single polypeptide. The host cell furin and the viral NS2B-NS3 serine protease NS2B-NS3pro cleave the viral polyprotein at different positions to release viral structural and non-structural proteins [6–9]. Therefore, the viral NS2B-NS3pro is a potential target for the design and development of antiviral drugs [10, 11]. NS2B acts as necessary a co-factor for the optimal catalytic activity of NS3 [10, 12]. NS2B-NS3pro consists of 185 residues from the N-terminal of the NS3 protein and the central 44 residues of the hydrophilic domain of NS2B [12, 13].
Despite the numerous studies about dengue virus, currently, no effective vaccine or antiviral therapeutics is available [14, 15]. It is difficult to develop anti-dengue treatments because of the incidence of the antibody-dependent enhancement due to the existence of four dengue serotypes, the unavailability of an actual animal model [16, 17] and the nature of the dengue protease, a promising target for dengue inhibitor development, which possesses a flat and hydrophilic active site that decreases the possibility of finding potent inhibitors to develop as antiviral therapeutics . These facts accentuate the need for new approaches to develop potent anti-dengue drugs.
Natural antimicrobial peptides (AMPs) are produced in the majority of living organisms as protection against various pathogens, including viruses. We hypothesise that AMPs that possess potent antiviral activities may be considered as hits-to-leads for developing new antiviral drugs. Therefore, the objective of this study was to identify and characterise the inhibitory potential of the latarcin peptide (Ltc 1, SMWSGMWRRKLKKLRNALKKKLKGE) against dengue virus replication in human cells. Ltc 1 is one of approximately seven latarcin peptides, which are produced in the venom gland of Lachesana tarabaeve, a central Asian spider. Recent studies showed considerable antimicrobial activities of the latarcin peptides against bacteria and yeast [19–21]. In particular, the Ltc 1 peptide showed moderate haemolytic activity and significant antimicrobial activity compared to the other latarcin analogues . However, there is a paucity of available data on the antiviral activities of Ltc 1 peptide. This study demonstrates for the first time significant inhibition by Ltc 1 against dengue NS2B-NS3pro and dengue virus replication in HepG2 cells.
Virus propagation in mosquito cells and titration
HepG2 cells with passage number less than 60 were maintained in DMEM medium supplemented with 10% FBS and incubated at 37°C in 5% CO2. HepG2 cells were used to study the peptide cytotoxicity and antiviral activity. Dengue virus serotype-2 (DENV2) was first propagated in C6/36 cells. The DENV2-infected cells that showed cytopathic effects (CPE) were lysed with a freeze and thaw cycle. The culture medium was then centrifuged at 1800 rpm for 10 min to remove the cell debris, filtered (0.2 μm), portioned into aliquots and stored at -80°C until use. The viral titre of the DENV2 suspension was established by serial dilutions on Vero cells using a plaque assay.
The Ltc 1 peptides were manufactured chemically using standard solid-phase peptide synthesis with a Symphony parallel synthesiser (Protein Technologies, Tucson, AZ, USA) as previously described . Briefly, the aqueous phase of the peptide synthesis was lyophilised to yield the crude peptide. The identity of the crude peptide was confirmed by LC-MS, and purification of the crude peptide was performed by RP-HPLC (Agilent 1200 series, USA). The identity of the 98% pure purified peptide was confirmed by LC-MS (Shimadzu LC/MS 2020, single quad, Japan). The purified peptide was then lyophilised using a Savant AES 2000 Automatic Environmental SpeedVac system. To prepare 2 mM pure peptide, 6.14 mg lyophilised peptide was dissolve into 1 ml filtered-deionised water for use as a stock solution.
The interaction between the Ltc 1 peptide and dengue NS2B-NS3pro was identified by protein-protein docking study. The Protein Data Bank (PDB) files of Ltc 1 (2PCO) and NS2BNS3pro (4M9F) were used in rigid global docking using an available online server (FireDoc, http://bioinfo3d.cs.tau.ac.il/FireDock/refs.html) as described previously [23, 24]. The results of the protein-protein docking were further analysed using Discovery Studio software version 3.5.
ELISA binding of Ltc 1 to dengue NS2B-NS3pro
Enzyme-linked immunosorbent assay (ELISA) was used to examine the binding affinity of Ltc 1 to dengue NS2B-NS3pro. Increasing concentrations of purified dengue NS2B-NS3pro (0, 20, 30 and 50 nM/well) in carbonate/bicarbonate buffer (Sigma, USA) were bound to black 96-well plate with transparent bottom at 4°C overnight in triplicates. The wells were blocked with PBS containing 0.05% Tween 20 (PBS-T) plus 0.5% BSA for 1 h at room temperature and washed three times with PBS-T. Increasing concentrations of the Ltc 1 peptide labeled with FITC fluorescence dye (0, 0.1, 0.5, 1, 5, 10, 20, 30, 50 nM) were prepared in PBS-T plus BSA; 100 μl of each dilution of the Ltc 1 bound to plates for 3 h on ice in dark place. After the plates were washed, the fluorescence signals of bound Ltc 1 were detected using Tecan Infinite M200 Pro fluorescence spectrophotometer (Tecan Group Ltd., Switzerland).
Dengue NS2B-NS3 protease (NS2B-NS3pro) assay
Ltc 1 peptide cytotoxicity
The cytotoxicity of the Ltc 1 peptides was evaluated by determining the maximal non-toxic dose (MNTD) and the 50% cytotoxic concentration (CC50) of the cells using the Non-Radioactive Cell Proliferation assay (Promega, USA) according to the manufacturer’s instructions. The peptide concentration of 25 μM showed 80% cell viability and was considered the MNTD value, assuming that approximately 80% of the cells were healthy. Vero cells were seeded at 1×104 cells/well in triplicate under optimal conditions (37°C, 5% CO2 in a humidified incubator) in 96-well plates with blank controls (media only) and cell controls (cells only). After an overnight incubation, the cells were treated with increasing concentrations of Ltc 1 peptide (0, 4, 8, 16, 32, 64 and 120 μM) with DMEM medium supplemented with 2% FBS and the cell culture was analysed after 72 h. The percentage of cell viability was calculated as follows: 100 - (absorbance of treated cells/absorbance of untreated cells) × 100. The MNTD and CC50 values were calculated from the dose-response curves.
Real Time Cell Proliferation Assay (RTCA assay)
This assay was performed to test the real time effects of the Ltc 1 peptide on cell viability. Cell proliferation was measured using the xCELLigence Real-Time Cellular Analysis (RTCA) system (Roche, Germany) as described previously . Cell viability and growth were monitored continuously after applying increasing concentrations of the Ltc 1 peptide (0, 12.5, 25, 50, 100, 150, 200, 250 μM). Briefly, the background measurements were recorded after adding 100 μl culture medium to the wells. Next, the cells were seeded at a density of 1 × 104 cell/well in a 16-well plate with electrodes for 18 h to allow the cells to grow to log phase. The cells were treated with different concentrations of peptide dissolved in cell culture medium and continuously monitored for up to 100 h. The cell sensor impedance was expressed as an arbitrary unit named the cell index. The cell index was recorded every 5 minutes using a RTCA analyser. To eliminate variation between the wells, the cell index values were normalised to the value at the beginning of the treatment.
Treatment of DENV-infected cells with the Ltc 1 peptide
To infect the HepG2 cells with DENV2, the cells were cultured in 24-well plates (1.5 × 105 cells/well) for 24 h at 37°C and 5% CO2. The virus supernatant was added to the cells at a MOI of 2, followed by incubation for 1 h with gentle shaking every 15 min for optimal virus to cell contact. The cells were washed twice with fresh serum-free DMEM after removal of the virus supernatant. Then, fresh complete DMEM containing 25 μM Ltc 1 peptide was added to the cultures and incubated for 72 h. The HepG2 cells were then collected, and the virus particles and expression level of the viral NS1 protein were examined using immunostaining and western immunoblotting.
This assay was performed to identify the mode of antiviral activity of the Ltc 1 peptide against DENV2 entry, replication and release from the infected cells. Three independent experiments were performed in triplicate for pre-, simultaneous and post-infection treatments. HepG2 cells were grown in a 24-well tissue culture plate (1.5 × 105 cells/well), incubated 24 h under optimal conditions and infected with DENV2 at an MOI of 2. For pre-treatment infection, 25 μM peptide was added to the cells before virus inoculation and incubated for 24 h. After removal of the old medium containing the peptide, the DENV2 supernatant was added, followed by incubation for 1 h with gentle shaking every 10 min for optimal virus to cell contact. The virus supernatant was removed and the cells were washed twice with fresh serum-free DMEM medium to remove the residual virus. Fresh complete DMEM medium was added and the cultures were incubated for 72 h at 37°C, supplemented with 5% CO2. Identical applications were performed for the simultaneous treatment, except the peptide was mixed with the virus supernatant and incubated at 37°C for 1 h, and then inoculated onto the HepG2 cells. The post-treatment infection was performed after inoculation of the HepG2 cells with DENV2, and complete DMEM medium with the Ltc 1 peptide was then added. The cultures including the peptide were incubated for 72 h at 37°C and 5% CO2, and three wells of infected cells in each experiment were maintained without treatment as controls. The cell supernatants were collected and stored at −80°C for viral load determination using a plaque formation assay.
This assay was performed to evaluate the 50% effective concentration (EC50) of the Ltc 1 peptide against DENV2. HepG2 cells were grown in six-well microplates (1.5 × 106 cells/well) for 24 h in quadruplicate experiments. The cell culture media were removed and the cells were washed three times with PBS. Then, fresh medium containing the virus supernatant was added at MOI of 2, followed by incubation for 1 h with gentle shaking every 15 min. The viral residues were removed by washing with PBS, and serial dilutions of the Ltc 1 peptide (0, 2.5, 5, 10, 20, 40, 80 μM) were added. The cultures including the peptide were incubated for 72 h at 37°C and 5% CO2. The cell supernatants were collected and stored at −80°C for viral load determination using viral RNA and were quantified using one step qReal time-PCR.
Virus quantification by plaque formation assay
Cells lysates were prepared for immunoblotting against dengue viral antigen using ice-cold lysis buffer. The amount of protein in the cell lysates was quantified to ensure equal loading (20 μg) of the western blot gels using the 2-D Quant Kit (GE Healthcare Bio-Sciences, USA) according to the manufacturer’s instructions. The separated proteins were transferred onto nitrocellulose membranes and then blocked with blocking buffer. The membrane was incubated overnight with anti-DENV2 antibody specific to the viral NS1 protein (Abcam, UK, Cat. no. ab41616) and an anti-beta actin antibody (Abcam, UK, Cat. no. ab8226). After washing three times, the membranes were incubated with anti-mouse IgG conjugated to horseradish peroxidase (Dako, Denmark) at 1:1,000 for two h. Horseradish peroxidase substrate was added to for colour development.
To examine the efficacy of the Ltc 1 peptide for reducing viral particles, HepG2 cells were grown on cover slips in 6-well plates and infected with DENV2 at an MOI of 2. The DENV2-infected cells were then treated with 25 μM peptide for 24 h. The cells were washed three times with PBS to remove the peptide residues and then fixed with ice-cold methanol for 15 min at -20°C. After washing, the cells were incubated with coating buffer for 1 h at room temperature. A mouse antibody specific to the dengue envelop glycoprotein (Abcam, UK, Cat. no. ab41349) was added, and the cells were incubated overnight at 4°C. The cells were washed three times with PBS and incubated for 30 min with an anti-mouse IgG labelled with FITC fluorescent dye (Invitrogen, USA, Cat. no. 62-6511). To stain the cell nuclei, Hoechst dye was added (Invitrogen, USA, Cat. no. H1399) for the last 15 min of the incubation.
Viral RNA quantification
The DENV2 copy number was quantified in the culture supernatants using one-step quantitative real-time PCR. Known copies of the viral RNA were 10-fold serially diluted to generate a standard curve. The viral RNA was extracted using the QIAmp viral RNAmini kit (QIAGEN, Germany), and the qRT-PCR was performed using a SYBR Green Master Kit (Qiagen, Germany). Triplicate reactions were performed for each sample, and a no template control was included as a negative control. Absolute quantification was performed using an ABI7500 machine (Applied Biosystems, Foster City, CA). The results were analysed using Sequence Detection Software Version 1.3 (Applied Biosystems, Foster City, CA). The percentage of viral inhibition (%) was calculated as follows: 100 – (viral copy number of treated cells/viral copy number of untreated cells) × 100.
All the assays were performed in triplicate, and the statistical analyses were performed using GraphPad Prism version 5.01 (GraphPad Software, San Diego, CA). P values <0.05 were considered significant. The error bars are expressed as ± SD.
The inhibitory potential of the Ltc 1 peptide against the DENV2 protease NS2B-NS3pro
The effect of the Ltc 1 peptide on cell proliferation and assessment of antiviral activity
Determination of antiviral inhibitory dose
Quantitative real-time PCR was used to determine the viral copy numbers in the infected cells after treatment with the Ltc 1 peptide. The infected cells were treated with increasing concentrations of the Ltc 1 peptide for 24, 48 and 72 h. The Ltc 1 peptide showed dose-dependent inhibition of DENV2 replication in HepG2 cells. However, the results showed insignificant effects for the time points on peptide activity (Figure 4). The inhibitory effects of the Ltc 1 peptide were dependent on increasing concentrations of the peptide at the three time points. The Ltc 1 peptide inhibited DENV2 replication at EC50 values of 8.3 ± 1.2 μM for 24 h, 7.6 ± 2.7 μM for 48 h and 6.8 ± 2.5 μM for 72 h (Figure 4).
The mode of inhibition
We performed this study to identify and characterise the inhibitory potential of the latarcin peptide (Ltc 1) against dengue virus propagation in human cells. The results of the protein-protein docking study showed that the Ltc 1 peptide bound to the NS3 by hydrophobic residue interactions of the peptide, primarily Leu 11, 14, 18 and Trp 3 and 7 that interact with the surrounding hydrophobic residues of NS3 (Leu 28, Phe 30, Trp 50, Val 154 and Tyr 161). The binding of Ltc 1 to NS3 may effectively inhibit binding of the substrate to the active site or decrease the contribution of the NS2B co-factor active site formation. This observations were further considered by ELISA binding assay that showed significant binding affinity of Ltc 1 peptide to dengue NS2B-NS3pro.
The result of this study was further verified using a dengue NS2B-NS3pro assay that showed significant inhibition by the Ltc 1 peptide against dengue protease. Dengue NS2B-NS3pro cleaves the viral polyprotein at the positions between the capsid, NS2A-NS2B, NS2B-NS3, NS3-NS4A and NS4B-NS5, which lead to the release of mature individual viral structural (S) and non-structural (NS) proteins [6–9]. Therefore, inhibition of dengue NS2B-NS3pro may directly lead to inhibition of the post-translational processing of the viral polyprotein and subsequent virus replication [10, 11].
In this study, the Ltc 1 peptide inhibited dengue NS2B-NS3pro in the low micromolar range (IC50 values of 12.68 μM at 37°C and 6.58 μM at 40°C). We hypothesise that the activity of the dengue protease decreased at the high fever temperature (40°C) because of the instability of the structural complex. Therefore, the Ltc 1 peptide showed higher inhibition, which is an approximately one fold reduction in the IC50 value compared to the inhibitory potential at 37°C. The activity of the NS2B-NS3pro primarily depends on the interaction between NS3 with the cofactor NS2B, which stabilises the enzyme structure and contributes to the formation of the active site [27, 28].
Previous studies reported various inhibitors against dengue protease, including standard serine protease inhibitors , substrate based inhibitors , and non-substrate based inhibitors [31, 32]. For example, aprotinin, a 58 amino acid protein, showed the highest inhibitory effect against the dengue protease at picomolar levels compared to the other standard serine protease inhibitors . The peptidic α-keto amide  and cyclopeptide inhibitors  showed significant inhibition against dengue NS2B-NS3pro at micromolar dose ranges compared to the other peptidic inhibitors. In addition, the non-substrate based inhibitors, such as small molecule inhibitors, showed significant inhibitory activities at low micromolar concentrations against the flavivirus proteases [31, 32]. Although several of these compounds are potent inhibitors of the dengue NS2b-NS3 protease, some showed poor stability in solution. Furthermore, several studies did not use cell-based assays to evaluate the toxicity and antiviral efficacy of the identified compounds . The nature of the dengue protease, which possesses a flat and hydrophilic active site, decreases the possibility of identifying potent inhibitors to develop as antiviral therapeutics . Based on the results of this study, we postulate that the hydrophobic residues of Ltc 1 are important for stabilising the binding to the hydrophilic active site of the dengue protease.
In this study, the inhibitory potential of the Ltc 1 peptide against the dengue protease was further verified using cell based assays. Previously, other characteristics of the latarcin family peptides, such as anti-neoplastic cells activities , were examined. The latarcin peptides can alter the lipid bilayers of the cell membrane, may induce the apoptosis of mammalian cells . Because of this, the possible effect of the Ltc 1 peptide on cell proliferation was removed to avoid false interpretation of the antiviral activity. Subsequently, the antiviral activity of the Ltc 1 peptide was evaluated at the doses with minimal effects on cell proliferation as determined by MTT assay and Real-Time Cellular Analysis (RTCA). The results of the immunostaining and western blot analyses showed that the Ltc 1 peptide significantly reduced the viral particles and non-structural protein NS1 in DENV-infected cells. Furthermore, the results of the time-of-addition assay showed that the Ltc 1 peptide inhibited dengue virus replication at both the simultaneous and post-treatments compared to the pre-treatment. The mechanism of antimicrobial activity of the latarcin peptides depends on the helix-hinge-helix structure that is important for lysing bacterial cell membranes [35, 36]. This finding emphasised that the direct incubation of DENV with the Ltc 1 peptide during the simultaneous treatment may led to lysis of the viral particles by the peptide. The results of the post-treatment and dose-response assays showed that the viral load was significantly deceased after treatment with the Ltc 1 peptide. Based on this finding, we hypothesise that the Ltc 1 peptide may interrupt the dengue life cycle in HepG2 cells during post-translational processing of the polyprotein by inhibiting the dengue serine protease. This inhibition may hinder flavivirus replication and virion assembly, as evidenced by the lack of infectious virion production in mutants carrying inactivating viral proteases . However, other α-helical peptides, similar to Ltc 1, have significant inhibitory effects against HIV-1 because of an actual interference with the virus assembly stage of the viral life cycle . Therefore, other mechanisms may be responsible for the observed effects, such as the interruption of virus assembly and release from the infected cells because of Ltc 1 interaction with other viral or host cell proteins; however, this warrants additional studies.
The Ltc 1 peptide exhibited significant inhibition of the dengue protease and virus replication in HepG2 cells. Therefore, Ltc1 may act as a lead structure for developing therapies against DENV.
- Ltc 1:
Latarcin-1 peptide analogue
Dengue virus serotype 2
NS2B cofactor amino acids sequence 49–95 in DENV2 NS2B and 1394–1440 in DENV2 polyprotein
NS3 protease amino acids sequence 1–185 in NS3 protease and 1476–1660 in DENV2 polyprotein
NS2B fused to NS3pro via 9 amino acids (G4-T-G4)
Fluorogenic peptide substrate (Boc-Gly-Arg-Arg-AMC).
This project was funded by the Ministry of Science, Technology and Innovation-Malaysia (ERGS grant ER016-2013A).
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