This study is supported by funding from Taipei Medical University Hospital (102TMU-TMUH-19) and the Ministry of Science and Technology of Taiwan (MOST103-2320-B-038-031-MY3).

Note: Ensure that all procedures involving cell culture and virus infection are conducted in certified biosafety hoods that are appropriate for the biosafety level of the samples being handled. For the purpose of describing the protocols, Gaussia luciferase reporter-tagged HCV is used as a model virus32. In the context of the representative results, the compounds chebulagic acid (CHLA) and punicalagin (PUG) are used as candidate antivirals that target viral glycoprotein interactions with cell surface glycosaminoglycans during the early viral entry steps31. Heparin, which is known to interfere with the entry of many viruses30,31,33,34, is used as a positive control treatment in such context. For basic background on virology techniques, propagation of viruses, determination of virus titer, and expression of infectious dose in plaque forming units (PFU), focus forming units (FFU), or multiplicity of infection (MOI), the reader is referred to reference35. For prior examples and optimized conditions used for viruses shown in the representative results, the reader is referred to references30-32,36-39 as well as details listed in Table 1, Figure 1A, and Figure 2A.
1. Cell Culture, Compound Preparation, and Compound Cytotoxicity
<ol>
	<li>Grow the respective cell line for the virus infection system to be analyzed (Table 1). For HCV, grow the Huh-7.5 cells in Dulbecco&#8217;s modified Eagle&#8217;s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 200 U/ml penicillin G, 200 &#181;g/ml streptomycin, and 0.5 &#181;g/ml amphotericin B.</li>
	<li>Prepare the test compounds and controls using their respective solvents: for example, dissolve CHLA and PUG in dimethyl sulfoxide (DMSO); prepare heparin in sterile double-distilled water. For all subsequent dilutions, use culture media. 
	Note: The final concentration of DMSO in the test compound treatments is less than 1% in the experiments; 1% DMSO is included as a negative control treatment in the assays for comparison.</li>
	<li>Determine the cytotoxicity of the test compounds (e.g., CHLA and PUG) on the cells for the viral infection by using a cell viability determining reagent such as XTT (2,3-bis[2-methoxy-4-nitro-5-sulfophenyl]-5-phenylamino)-carbonyl]-2H-tetrazolium hydroxide):
	<ol>
		<li>For HCV, seed Huh-7.5 cells in a 96-well plate (1 &#215; 104 cells per well) and incubate at 37 &#176;C in a 5% CO2 incubator O/N to obtain a monolayer.</li>
		<li>Apply DMSO control (1%) or increasing concentrations of the test compounds CHLA and PUG (ex. 0, 10, 50, 100, and 500 &#956;M) to the culture wells in triplicate.</li>
		<li>Incubate at 37 &#176;C for 72 hr, then discard the medium in the plate and wash the cells with 200 &#956;l of phosphate buffered saline (PBS) twice.</li>
		<li>Add 100 &#181;l of assaying solution from the XTT-based in vitro toxicology assay kit to each well and incubate the plates at 37 &#176;C for another 3 hr to allow XTT formazan production.</li>
		<li>Determine the absorbance with a microplate reader at a test wavelength of 492 nm and a reference wavelength of 690 nm.</li>
		<li>Calculate the percentage of surviving cells using the following formula: cell viability (%) = At / As &#215; 100%, where &#8216;At&#8217; and &#8216;As&#8217; refer to the absorbance of the test compounds and the solvent control (ex. 1% DMSO) treatments, respectively. Determine the concentration of 50% cellular cytotoxicity (CC50) of the test compounds from an analytical software such as GraphPad Prism according to manufacturer&#8217;s protocol.</li>
	</ol>
	</li>
</ol>
2. Readout of Viral Infection
Note: The readout of viral infection depends on the virus system used and can involve methods such as plaque assays or measuring reporter signals from reporter-tagged viruses. The method for detecting reporter-HCV infection based on the luciferase reporter activity is described below.
<ol>
	<li>Collect the supernatants from the infected wells and clarify at 17,000 x g in a microcentrifuge for 5 min at 4 &#176;C.</li>
	<li>Mix 20 &#956;l of test supernatant to 50 &#956;l of luciferase substrate from the Gaussia luciferase assay kit and directly measure with a luminometer according to the manufacturer&#8217;s instructions.</li>
	<li>Express HCV infectivity as log10 of relative light units (RLU) for determining viral inhibition (%) and calculate the 50% effective concentration (EC50) of the test compounds against HCV infection using algorithms from GraphPad Prism software according to manufacturer&#8217;s protocol.</li>
</ol>
3. Viral Inactivation Assay
Note: Examples of incubation period and viral dose for various viruses are listed in Figure 1A. Higher concentrations of the virus can also be tested by increasing the MOI/PFU.
<ol>
	<li>Seed Huh-7.5 cells in a 96-well plate (1 &#215; 104 cells per well) and incubate at 37 &#176;C in a 5% CO2 incubator O/N to obtain a monolayer.</li>
	<li>Incubate the test compounds or controls (final concentrations are: CHLA = 50 &#956;M; PUG = 50 &#956;M; heparin = 1,000 &#956;g/ml; DMSO = 1%) with the HCV particles at 37 &#176;C (Figure 1A, &#8216;Long-Term&#8217;) in a 1:1 ratio. For example, to a 100 &#956;l virus inoculum containing 1 x 104 FFU, add 100 &#956;l of a 100 &#956;M CHLA working dilution; this yields CHLA treatment at a final concentration of 50 &#956;M.</li>
	<li>Dilute the virus-drug mixture to &#8220;sub-therapeutic&#8221; (ineffective) concentration of the test compounds. For example, the ineffective concentration of CHLA and PUG against HCV is at 1 &#956;M31; therefore this requires a 50-fold dilution of the virus-drug mixture which can be accomplished with 9.8 ml of basal medium (cell culturing medium with 2% FBS). 
	Note: The dilution to sub-therapeutic concentration prevents significant interaction between the test compounds and the host cell surface and allows examination of treatment effect on the cell-free virions. Note that this dilution is dependent on the antiviral dose response of the test compounds against the particular viral infection, and is determined prior to performing this particular assay31.</li>
	<li>For comparison, mix the virus with the test compounds and immediately dilute (no incubation period) to sub-therapeutic concentration prior to infection (Figure 1A, &#8216;Short-Term&#8217;).</li>
	<li>Add 100 &#956;l of the diluted HCV-drug mixture onto the Huh-7.5 cell monolayer (the amount of virus is now at 1 x 102 FFU; final MOI = 0.01) and incubate for 3 hr at 37 &#176;C to allow viral adsorption.</li>
	<li>Following the infection, remove the diluted inocula and gently wash the wells with 200 &#956;l of PBS twice. 
	Note: Perform the washes gently to avoid lifting the cells.</li>
	<li>Apply 100 &#956;l of basal medium to each well and incubate at 37 &#176;C for 72 hr.</li>
	<li>Analyze the resulting infection by assaying the supernatant for luciferase activity as described in &#8216;2. Readout of Viral Infection&#8217;.</li>
</ol>
4. Viral Attachment Assay
Note: Examples of incubation period and viral dose for various viruses are listed in Figure 2A, &#8216;Attachment&#8217;. Higher concentrations of the virus can also be tested by increasing the MOI/PFU.
<ol>
	<li>Seed Huh-7.5 cells in a 96-well plate (1 &#215; 104 cells per well) and incubate at 37 &#176;C in a 5% CO2 incubator O/N to obtain a monolayer.</li>
	<li>Pre-chill the cell monolayers in plates at 4 &#176;C for 1 hr.</li>
	<li>Co-treat the cells with HCV inoculum (MOI = 0.01) and test compounds or controls (final concentrations are: CHLA = 50 &#956;M; PUG = 50 &#956;M; heparin = 1,000 &#956;g/ml; DMSO = 1%) at 4 &#176;C for 3 hr. For example, to a 90 &#956;l virus inoculum containing 1 x 102 FFU, add 10 &#956;l of a 500 &#956;M CHLA working dilution; this yields CHLA treatment at a final concentration of 50 &#956;M and an infection by HCV at MOI = 0.01 on the cell monolayer. 
	Note: It is important to carry out the experiment at 4 &#176;C since it allows for virus binding but precludes entry which most efficiently occurs at 37 &#176;C. Perform the addition of virus and test compounds on ice and the ensuing incubation in a 4 &#176;C refrigerator to ensure that the temperature is maintained at 4 &#176;C.</li>
	<li>Remove the supernatant and gently wash the cell monolayer with 200 &#956;l of ice-cold PBS twice. 
	Note: Perform the washes gently to avoid lifting the cells.</li>
	<li>Apply 100 &#956;l of basal medium to each well and incubate at 37 &#176;C for 72 hr.</li>
	<li>Analyze the resulting infection by assaying the supernatant for luciferase activity as described in &#8216;2. Readout of Viral Infection&#8217;.</li>
</ol>
5. Viral Entry/Fusion Assay
Note: Example of incubation periods and viral dose for various viruses are listed in Figure 2A &#8216;Entry/Fusion&#8217;. Higher concentrations of the virus can also be tested by increasing the MOI/PFU.
<ol>
	<li>Seed Huh-7.5 cells in a 96-well plate (1 &#215; 104 cells per well) and incubate at 37 &#176;C in a 5% CO2 incubator O/N to obtain a monolayer.</li>
	<li>Pre-chill the cell monolayers in plates at 4 &#176;C for 1 hr.</li>
	<li>Infect the cells with HCV (MOI = 0.01) at 4 &#176;C for 3 hr. For example, use a 100 &#956;l&#160;virus inoculum containing 1 x 102 FFU. 
	Note: Perform the addition of the viral inoculum on ice and the ensuing incubation in a 4 &#176;C refrigerator to maintain the temperature at 4 &#176;C, which permits viral binding but not entry.</li>
	<li>Remove the supernatant and gently wash the cell monolayers with 200 &#956;l of ice-cold PBS twice. 
	Note: Perform the washes gently to avoid lifting the cells.</li>
	<li>Treat the wells with the test compounds or controls (final concentrations are: CHLA = 50 &#956;M; PUG = 50 &#956;M; heparin = 1,000 &#956;g/ml; DMSO = 1%) and incubate at 37 &#176;C for 3 hr. For example, add 10 &#956;l of a 500 &#956;M CHLA working dilution to 90 &#956;l of media, mix, and treat the wells; this yields CHLA treatment at a final concentration of 50 &#956;M. 
	Note: The shift from 4 &#176;C to 37 &#176;C now facilitates the viral entry/fusion event and therefore allows assessment of test compounds&#8217; effect on this particular step.</li>
	<li>Aspirate the drug-containing supernatant and remove non-internalized extracellular viruses by either washing with 200 &#956;l of citrate buffer (50 mM sodium citrate, 4 mM potassium chloride, pH 3.0) or PBS. Apply 100 &#956;l of the basal medium before incubating at 37 &#176;C for 72 hr.</li>
	<li>Analyze the resulting infection by assaying the supernatant for luciferase activity as described in &#8216;2. Readout of Viral Infection&#8217;.</li>
</ol>

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<li>Isaacson, M. K., Compton, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Human+cytomegalovirus+glycoprotein+B+is+required+for+virus+entry+and+cell-to-cell+spread+but+not+for+virion+attachment%2C+assembly%2C+or+egress%5BTitle%5D)+AND+%22J+Virol%22%5BJournal%5D)">Human cytomegalovirus glycoprotein B is required for virus entry and cell-to-cell spread but not for virion attachment, assembly, or egress.</a> J Virol. 83, 3891-3903 (2009).</li>
<li>Leonard, V. H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Measles+virus+blind+to+its+epithelial+cell+receptor+remains+virulent+in+rhesus+monkeys+but+cannot+cross+the+airway+epithelium+and+is+not+shed%5BTitle%5D)+AND+%22J+Clin+Invest%22%5BJournal%5D)">Measles virus blind to its epithelial cell receptor remains virulent in rhesus monkeys but cannot cross the airway epithelium and is not shed.</a> J Clin Invest. 118, 2448-2458 (2009).</li>
<li>Ciesek, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((The+green+tea+polyphenol%2C+epigallocatechin-3-gallate%2C+inhibits+hepatitis+C+virus+entry%5BTitle%5D)+AND+%22Hepatology%22%5BJournal%5D)">The green tea polyphenol, epigallocatechin-3-gallate, inhibits hepatitis C virus entry.</a> Hepatology. 54, 1947-1955 (2011).</li>
<li>Lin, L. T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Saikosaponin+b2+is+a+naturally+occurring+terpenoid+that+efficiently+inhibits+hepatitis+C+virus+entry%5BTitle%5D)+AND+%22J+Hepatol%22%5BJournal%5D)">Saikosaponin b2 is a naturally occurring terpenoid that efficiently inhibits hepatitis C virus entry.</a> J Hepatol. 62, 541-548 (2015).</li>
<li>Atkins, C., Evans, C. W., White, E. L., Noah, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Screening+methods+for+influenza+antiviral+drug+discovery%5BTitle%5D)+AND+%22Expert+Opin+Drug+Discov%22%5BJournal%5D)">Screening methods for influenza antiviral drug discovery.</a> Expert Opin Drug Discov. 7, 429-438 (2012).</li>
<li>Zhang, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Identification+of+novel+virus+inhibitors+by+influenza+A+virus+specific+reporter+cell+based+screening%5BTitle%5D)+AND+%22Antiviral+Res%22%5BJournal%5D)">Identification of novel virus inhibitors by influenza A virus specific reporter cell based screening.</a> Antiviral Res. 93, 48-54 (2012).</li>
</ol>

The authors declare that no competing interests exist.

In this report the methods to identify and evaluate antiviral compounds based on a mechanistic approach of dissecting the early viral entry events were described. Specifically, the assays allowed us to examine the effect of test compounds on free virus particles, viral attachment, and viral entry/fusion. Critical steps were implemented to distinctly evaluate the drug effect on the specific stage of early viral entry. For instance, in the &#8216;viral inactivation assay&#8217;, the dilution of the virus-drug mixture to sub-therapeutic concentration prevents significant interaction between the test compound and the host cell surface by &#8216;titrating out&#8217; the drug. This ensures that the inhibitory effect observed on the subsequent infection of the host cell is due to a direct interaction between the test compound and the cell-free virions, rather than an effect from the test compound on host cell membrane or membrane-associated molecules, including viral receptors30. Similarly, the shift in temperature between 4 &#176;C (which allows for virus binding but not entry) and 37 &#176;C (which facilitates virus entry/fusion) in the &#8216;viral attachment assay&#8217; and &#8216;viral entry/fusion assay&#8217; are crucial to determine the test compound&#8217;s effect on each of these specific events. This is feasible due to the temperature sensitivity of enveloped viruses during these steps in the infection24-29. It is therefore important that the assays are performed at the indicated temperature to ensure the accuracy of the results; for example, by carrying out the experiment on ice to maintain at 4 &#176;C and by placing the sample directly in a 37 &#176;C incubator for the temperature shift. In addition, the use of negative (ex. DMSO solvent for drug preparation) and positive (ex. heparin treatment) controls also help further establish the assays&#8217; accuracy. The utility and applicability of such methods have been demonstrated in many antiviral studies26,30,31,40,41. Note that while heparin is included as a control for all three assays in the context of the representative results, it typically blocks the initial virus binding rather than the ensuing fusion/entry step (as reflected by the data in Figure 2). Additional controls could also be used, such as neutralizing antibodies directed against the virus (for viral inactivation assay), antibodies that mask the cell surface receptors for the virus (for viral attachment assay), and membrane fusion inhibitors (for viral fusion/entry assay). 
The assays described in this report, which are specific to the early stages of the viral infection, are useful in terms of application as secondary tests to characterize the mechanism of action of candidate drugs from primary screens which typically target the viral infection more broadly. Alternatively, they could also be incorporated in primary screens if one is specifically looking for inhibitors of early viral entry, including virus inactivating agents, viral attachment antagonists, and inhibitors to viral entry/fusion. In this case, their use allows a more focused and precise screen analysis for the identification of mechanism-specific antiviral candidates, which, in turn, would expedite downstream drug development. 
The use of cell-based assays in identifying antiviral agents provides several important advantages compared to biochemical assays, including revealing potential off-target effects (such as cytotoxicity) and adding physiological relevance to the bioactivity of the test agents42. These issues are important considerations for deciding whether a candidate agent is of value for continuation in subsequent phases of drug development. Similarly, the early viral entry-specific assays described in this report allow examination of the drug effect on the distinct viral entry stage at the cellular level, and more specifically in the context of an authentic viral infection in vitro. The results obtained from such assays would therefore help better predict the antiviral efficacy of the test compounds and also identify potentially unwanted off-target effects against the host cell. One potential limitation though, is that an in vitro cell-based assay may not completely reflect the actual in vivo entry step in the context of a natural viral infection. Nonetheless, the assays presented in this protocol do serve as an analytical platform for mechanism-based identification and evaluation of novel antiviral agents.
The development of reporter viruses or reporter cell systems to quantitate the amount of viral infection has greatly facilitated cell-based screening and evaluation of antiviral compounds. Examples include the use of recombinant viruses carrying a reporter gene or by means of recombinant human cell lines containing a reporter gene driven by the specific virus promoter31,43. In this report, the infection from luciferase-tagged HCV can be easily monitored by quantitating the reporter signal, thus facilitating data analysis. By incorporating these useful reporter-based tools, the early viral entry assays described here can essentially be adapted into high-throughput format for mechanism-based screening of small molecule libraries.
In conclusion, a protocol was described for assays dissecting the early viral entry as a means of identifying and evaluating mechanism-specific antiviral compounds. Such assays would be useful for discovering novel antagonists/inhibitors to viral entry and help expand the scope of antiviral agents for development as prophylactic and/or therapeutic treatments.

Viral infections are a constant threat to the public health and a significant cause of epidemic diseases, morbidity, and deaths worldwide. Specific modes of control against viral infections include vaccine development and antiviral therapies. While vaccine efforts have proven successful in immunizing against several viruses, many viral pathogens remain without a protective vaccine including dengue virus (DENV), human cytomegalovirus (HCMV), hepatitis C virus (HCV), human immunodeficiency virus (HIV), and respiratory syncytial virus (RSV)1-5. Antivirals, on the other hand, play an important role for the management of these viral infections when prophylactic vaccines are unavailable. However, to date, only few licensed and cost-effective antiviral drugs are available compared to the number of viral pathogens that threatens the public health. More importantly, due to an increase in global travel and rapid urbanization, the situation is aggravated by risks of epidemic outbreaks from emerging/re-emerging viral infections that are being introduced into non-indigenous areas6. Recent outbreaks caused by severe acute respiratory syndrome (SARS) virus, influenza viruses (H1N1, H5N1, H3N2, and H7N9), DENV, West Nile virus (WNV), measles virus (MV), Middle East Respiratory Syndrome (MERS) virus, and Ebola virus6-12 are among the examples reflecting the need for antivirals development when immunization and/or therapeutics are unavailable. In addition, there is always a potential risk of generating drug-resistant infections with currently used antivirals. Thus, the continuous development and expansion of the scope of antivirals to these emerging/re-emerging viral infections are necessary to provide better management strategies and safeguard the public health.
Most antiviral therapies consist of direct acting antivirals (DAAs) which target a specific viral protein or cofactor that mediates important steps in the viral life cycle. For example, the nucleoside analogue Acyclovir inhibits herpesvirus DNA polymerase, protease inhibitors Boceprevir and Telaprevir antagonize the HCV NS3, and Oseltamivir and Zanamivir are neuraminidase inhibitors that block the release of influenza virus particles from infected cells13-15. There are however very few licensed viral entry inhibitors including Enfuvirtide, which targets HIV gp41 to prevent fusion, and Maraviroc, which blocks the HIV co-receptor CCR5, thereby preventing viral entry16. Exploring novel antagonists/inhibitors to viral entry could help provide additional therapeutics for prophylactic or therapeutic use, such as in combination with other antivirals with a different mechanism of action to better manage viral infections17-19. 
Identification of antivirals can involve structure-guided drug design and candidate drug screening-based strategy. Methods for assessing antiviral activity of test agents include biochemical assays of enzymatic activity and evaluation by cell-based systems20-23. In cell-based systems, the viral life cycle can be dissected into distinct stages of infection, such as entry events (attachment, fusion, uncoating), the replication phase (viral genome replication and protein translation), and virion egress (assembly, maturation, and release). Since the assays can be adapted to investigate each specific stage using various tools and methods, this approach allows identification/examination of potential candidate antivirals with a specific mechanism of action targeting the distinct stage analyzed. For instance, to analyze drug effect specifically on the free virus particles prior to binding to the host cell, a &#8216;viral inactivation assay&#8217; can be performed. In this assay, the virus is allowed to incubate with the test drug and then diluted to titrate out the drug before infecting a cell monolayer. Additional steps such as viral attachment and entry/fusion stages can also be analyzed individually, by shifting the temperature during the infection. For many enveloped viruses, viral entry/fusion at the host cell membrane is greatly facilitated at 37 &#176;C, but is typically precluded at 4 &#176;C which does not affect virus binding24-29. Finally, the use of reporter viruses or cell systems could facilitate these studies and permit a high-throughput analysis.
We previously employed the cell-based approach and dissected the early entry of various enveloped viruses for the examination of antiviral compounds that potentially antagonize viral entry30,31. Herein, the various methods used, including viral inactivation, viral attachment, and viral entry/fusion assays, are described.

<table><tbody><tr><td>DMEM</td><td>GIBCO</td><td>11995-040</td><td></td></tr><tr><td>FBS</td><td>GIBCO</td><td>26140-079</td><td></td></tr><tr><td>Penicillin-Streptomycin</td><td>GIBCO</td><td>15070-063</td><td></td></tr><tr><td>Amphotericin B</td><td>GIBCO</td><td>15290-018</td><td></td></tr><tr><td>DMSO</td><td>Sigma</td><td>D5879</td><td></td></tr><tr><td>In vitro toxicology assay kit, XTT-based</td><td>Sigma</td><td>TOX2</td><td></td></tr><tr><td>PBS pH 7.4&amp;nbsp;</td><td>GIBCO</td><td>10010023</td><td></td></tr><tr><td>Microplate reader</td><td>Thermo Scientific</td><td>89087-320</td><td></td></tr><tr><td>Microcentrifuge</td><td>Thermo Scientific</td><td>75002420</td><td></td></tr><tr><td>BioLux Gaussia luciferase assay kit</td><td>New England Biolabs</td><td>E3300L&amp;nbsp;&amp;nbsp;&amp;nbsp;</td><td></td></tr><tr><td>Luminometer</td><td>Promega</td><td>GloMax-20/20</td><td></td></tr><tr><td>Sodium citrate, dihydrate</td><td>Sigma</td><td>71402</td><td></td></tr><tr><td>Potassium chloride</td><td>Sigma</td><td>P5405</td><td></td></tr></tbody></table>

early viral entry assays for the identification and evaluation of antiviral compounds

Cell-based systems are useful for discovering antiviral agents. Dissecting the viral life cycle, particularly the early entry stages, allows a mechanistic approach to identify and evaluate antiviral agents that target specific steps of the viral entry. In this report, the methods of examining viral inactivation, viral attachment, and viral entry/fusion as antiviral assays for such purposes are described, using hepatitis C virus as a model. These assays should be useful for discovering novel antagonists/inhibitors to early viral entry and help expand the scope of candidate antiviral agents for further drug development.

In Figure 1, the &#8216;viral inactivation assay&#8217; was performed to examine whether two specific natural compounds CHLA and PUG could inactivate the different enveloped viruses in cell-free state and prevent subsequent infection. The cytotoxicity and antiviral dose response of these compounds have been determined prior to performing the mechanistic study31. The viruses were pre-treated with the test compounds and then the virus-drug mixtures were diluted to sub-therapeutic concentrations before inoculation onto the respective cell monolayer for each virus system. As shown in Figure 1, both CHLA and PUG appeared to interact with the cell-free virions, resulting in irreversible effects that protected the cell monolayer from the subsequent infection. The two test compounds achieved a near 100% inhibition against HCMV, HCV, and DENV-2, whereas a 60 &#8211; 80% block was observed against MV and RSV. These results suggest that CHLA and PUG have direct impact on these free virus particles by inactivating them and neutralizing their infectivity.
In Figure 2, the attachment and entry/fusion assays were carried out to explore the effect of CHLA and PUG against these early viral entry-related events from HCMV, HCV, DENV-2, MV, and RSV. Both CHLA and PUG effectively prevented binding of the investigated viruses onto the respective host cell as shown by inhibition on the resulting viral infection (Figure 2, &#8216;Attachment&#8217;: light gray bars). The inhibitory effect on virus attachment by both compounds was similar against HCMV (Figure 2B), HCV (Figure 2C), DENV-2 (Figure 2D), and RSV (Figure 2F), ranging from 90 &#8211; 100%. On the other hand, PUG appeared to be more effective than CHLA against MV binding (Figure 2E), with the inhibition rate from the two compounds varying between 50 &#8211; 80%. The control treatment heparin, which is known to block entry of many viruses, also inhibited attachment of HCMV, DENV-2, RSV, ad MV, but was less efficient against HCV. The ensuing &#8216;viral entry/fusion assay&#8217; examined whether CHLA and PUG retained their activity during the virus entry/fusion phase (Figure 2, &#8216;Entry/Fusion&#8217;: dark gray bars). Again, both CHLA and PUG were observed to effectively impair the viral entry/fusion step of the viruses examined (Figure 2B &#8211; F), yielding a 50 &#8211; 90% protective effect on the respective cell monolayer. Heparin also potently inhibited entry/fusion in DENV-2 and RSV infections, but was less efficacious against HCMV, HCV, and MV (&#60; 40% inhibition on average).
<table border="0" cellpadding="0" cellspacing="0">
	<tbody>
		<tr>
			<td>Virus</td>
			<td>Cell Type</td>
		</tr>
		<tr>
			<td>HCMV</td>
			<td>HEL</td>
		</tr>
		<tr>
			<td>HCV</td>
			<td>Huh-7.5</td>
		</tr>
		<tr>
			<td>DENV-2</td>
			<td>Vero</td>
		</tr>
		<tr>
			<td>MV</td>
			<td>CHO-SLAM</td>
		</tr>
		<tr>
			<td>RSV</td>
			<td>HEp-2</td>
		</tr>
	</tbody>
</table>
Table 1: Host cell type for viral infection. The cell type used for each viral infection system described in the representative results is indicated. Additional details regarding the cells can be found in reference31.
<img alt="Figure 1" src="/files/ftp_upload/53124/53124fig1.jpg" /> 
Figure 1. Inactivation of viral infections by the test compounds CHLA and PUG. Different viruses were treated with the test compounds for a long period (incubated for 1.5 &#8211; 3 hr before titration; light gray bars) or short period (immediately diluted; dark gray bars) at 37 &#176;C before a dilution to sub-therapeutic concentration and subsequent analysis of infection on the respective host cells. (A) Schematics of the experiment (shown on the left) with the final virus concentration (PFU/well or MOI), long-term virus-drug incubation period (i), and subsequent incubation time (ii) indicated for each virus in the table on the right. Analyses for (B) HCMV, (C) HCV, (D) DENV-2, (E) MV, and (F) RSV are indicated in each additional panel. Results are plotted against the DMSO negative control treatment for virus infection and the data shown are the means&#160;&#177;&#160;standard errors of the mean (SEM) from three independent experiments. This figure has been modified from reference31. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/53124/53124fig1highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" src="/files/ftp_upload/53124/53124fig2.jpg" /> 
Figure 2. Evaluation of antiviral activities of the test compounds CHLA and PUG against virus attachment and entry/fusion. (A) The experimental procedure, virus concentration (PFU/well or MOI), and the time of addition and treatment with the test compounds (i, ii, iii) are presented for each virus in the schematics and the associated tables. In virus attachment analysis (light gray bars), monolayers of different cell types were pre-chilled at 4 &#176;C for 1 hr, then co-treated with the respective viruses and test compounds at 4 &#176;C (1.5 &#8211; 3 hr; i) before washing off the inoculates and test compounds for subsequent incubation (37 &#176;C; ii) and examination of virus infection. In virus entry/fusion analysis (dark gray bars), seeded cell monolayers were pre-chilled at 4 &#176;C for 1 hr and then challenged with the respective viruses at 4 &#176;C for 1.5 &#8211; 3 hr (i). Cells were then washed and treated with the test compounds for an additional incubation period (ii) during which the temperature was shifted to 37 &#176;C to facilitate the viral entry/fusion event. At the end of the incubation, extracellular viruses were removed by either citrate buffer (pH 3.0) or PBS washes and the cells were further incubated (iii) for analysis of virus infection. Results for (B) HCMV, (C) HCV, (D) DENV-2, (E) MV, and (F) RSV are indicated in each additional panel. Data are plotted against the DMSO negative control treatment of virus infection and are presented as means &#177;&#160;SEM from three independent experiments. This figure has been modified from reference31. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/53124/53124fig2highres.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Early Viral Entry Assays for the Identification and Evaluation of Antiviral Compounds at JoVE.com

Early Viral Entry Assays for the Identification and Evaluation of Antiviral Compounds

Here, we present a protocol that examines specific steps of the viral entry to identify and evaluate novel antiviral agents.

Cell-based systems are useful for discovering antiviral agents. Dissecting the viral life cycle, particularly the early entry stages, allows a mechanistic ...

early-viral-entry-assays-for-identification-evaluation-antiviral

Nanyang Technological University

Research

JoVE Journal

Immunology and Infection

30.2K Views.  Taipei Medical University Hospital. Here, we present a protocol that examines specific steps of the viral entry to identify and evaluate novel antiviral agents.

Video: Early Viral Entry Assays for the Identification and Evaluation of Antiviral Compounds

Quantitative Analyses of all Influenza Type A Viral Hemagglutinins and Neuraminidases using Universal Antibodies in Simple Slot Blot Assays

Hemagglutinin (HA) and neuraminidase (NA) are two surface proteins of influenza viruses which are known to play important roles in the viral life cycle and the induction of protective immune responses1,2. As the main target for neutralizing antibodies, HA is currently used as the influenza vaccine potency marker and is measured by single radial immunodiffusion (SRID)3. However, the dependence of SRID on the availability of the corresponding subtype-specific antisera causes a minimum of 2-3 months delay for the release of every new vaccine. Moreover, despite evidence that NA also induces protective immunity4, the amount of NA in influenza vaccines is not yet standardized due to a lack of appropriate reagents or analytical method5. Thus, simple alternative methods capable of quantifying HA and NA antigens are desirable for rapid release and better quality control of influenza vaccines.
Universally conserved regions in all available influenza A HA and NA sequences were identified by bioinformatics analyses6-7. One sequence (designated as Uni-1) was identified in the only universally conserved epitope of HA, the fusion peptide6, while two conserved sequences were identified in neuraminidases, one close to the enzymatic active site (designated as HCA-2) and the other close to the N-terminus (designated as HCA-3)7. Peptides with these amino acid sequences were synthesized and used to immunize rabbits for the production of antibodies. The antibody against the Uni-1 epitope of HA was able to bind to 13 subtypes of influenza A HA (H1-H13) while the antibodies against the HCA-2 and HCA-3 regions of NA were capable of binding all 9 NA subtypes. All antibodies showed remarkable specificity against the viral sequences as evidenced by the observation that no cross-reactivity to allantoic proteins was detected. These universal antibodies were then used to develop slot blot assays to quantify HA and NA in influenza A vaccines without the need for specific antisera7,8. Vaccine samples were applied onto a PVDF membrane using a slot blot apparatus along with reference standards diluted to various concentrations. For the detection of HA, samples and standard were first diluted in Tris-buffered saline (TBS) containing 4M urea while for the measurement of NA they were diluted in TBS containing 0.01% Zwittergent as these conditions significantly improved the detection sensitivity. Following the detection of the HA and NA antigens by immunoblotting with their respective universal antibodies, signal intensities were quantified by densitometry. Amounts of HA and NA in the vaccines were then calculated using a standard curve established with the signal intensities of the various concentrations of the references used. 
Given that these antibodies bind to universal epitopes in HA or NA, interested investigators could use them as research tools in immunoassays other than the slot blot only.

A simple slot blot method was developed for the quantification of influenza viral hemagglutinin and neuraminidase using universal antibodies targeting their most conserved sequences identified through bioinformatics analyses. This innovative approach may provide a useful alternative to quantitative determination of all viral hemagglutinin and neuraminidase.

Hemagglutinin (HA) and neuraminidase (NA) are two surface proteins of influenza viruses which are known to play important roles in the viral life cycle ...

Assays for the Identification of Novel Antivirals against Bluetongue Virus

To identify potential antivirals against BTV, we have developed, optimized and validated three assays presented here. The CPE-based assay was the first assay developed to evaluate whether a compound showed any antiviral efficacy and have been used to screen large compound library. Meanwhile, cytotoxicity of antivirals could also be evaluated using the CPE-based assay. The dose-response assay was designed to determine the range of efficacy for the selected antiviral, i.e. 50% inhibitory concentration (IC50) or effective concentration (EC50), as well as its range of cytotoxicity (CC50). The ToA assay was employed for the initial MoA study to determine the underlying mechanism of the novel antivirals during BTV viral lifecycle or the possible effect on host cellular machinery. These assays are vital for the evaluation of antiviral efficacy in cell culture system, and have been used for our recent researches leading to the identification of a number of novel antivirals against BTV.

Three assays, including the cytopathic effect (CPE)-based assay, dose-response assay and Time-of-Addition (ToA) assay have been developed, optimized, validated and utilized to identify novel antivirals against Bluetongue virus (BTV), as well as to determine the possible Mechanism-of-Action (MoA) for newly identified antivirals.

To identify potential antivirals against BTV, we have  developed, optimized and validated three assays presented here. The CPE-based  assay was the first ...

High-throughput Screening for Broad-spectrum Chemical Inhibitors of RNA Viruses

RNA viruses are responsible for major human diseases such as flu, bronchitis, dengue, Hepatitis C or measles. They also represent an emerging threat because of increased worldwide exchanges and human populations penetrating more and more natural ecosystems. A good example of such an emerging situation is chikungunya virus epidemics of 2005-2006 in the Indian Ocean. Recent progresses in our understanding of cellular pathways controlling viral replication suggest that compounds targeting host cell functions, rather than the virus itself, could inhibit a large panel of RNA viruses. Some broad-spectrum antiviral compounds have been identified with host target-oriented assays. However, measuring the inhibition of viral replication in cell cultures using reduction of cytopathic effects as a readout still represents a paramount screening strategy. Such functional screens have been greatly improved by the development of recombinant viruses expressing reporter enzymes capable of bioluminescence such as luciferase. In the present report, we detail a high-throughput screening pipeline, which combines recombinant measles and chikungunya viruses with cellular viability assays, to identify compounds with a broad-spectrum antiviral profile.

In vitro assays to measure virus replication have been greatly improved by the development of recombinant RNA viruses expressing luciferase or other enzymes capable of bioluminescence. Here we detail a high-throughput screening pipeline that combines such recombinant strains of measles and chikungunya viruses to isolate broad-spectrum antivirals from chemical libraries.

RNA viruses are responsible for major human diseases such as flu, bronchitis, dengue, Hepatitis C or measles. They also represent an emerging threat ...

Rapid Screening of HIV Reverse Transcriptase and Integrase Inhibitors

Although a number of anti HIV drugs have been approved, there are still problems with toxicity and drug resistance. This demonstrates a need to identify new compounds that can inhibit infection by the common drug resistant HIV-1 strains with minimal toxicity. Here we describe an efficient assay that can be used to rapidly determine the cellular cytotoxicity and efficacy of a compound against WT and mutant viral strains.
The desired target cell line is seeded in a 96-well plate and, after a 24 hr incubation, serially dilutions of the compounds to be tested are added. No further manipulations are necessary for cellular cytotoxicity assays; for anti HIV assays a predetermined amount of either a WT or drug resistant HIV-1 vector that expresses luciferase is added to the cells. Cytotoxicity is measured by using an ATP dependent luminescence assay and the impact of the compounds on infectivity is measured by determining the amount of luciferase in the presence or the absence of the putative inhibitors.
This screening assay takes 4 days to complete and multiple compounds can be screened in parallel. Compounds are screened in triplicate and the data are normalized to the infectivity/ATP levels in absence of target compounds. This technique provides a quick and accurate measurement of the efficacy and toxicity of potential anti HIV compounds.

Here we describe cellular cytotoxicity and single round infectivity assays that allow for the rapid and accurate screening of compounds to determine their cellular cytotoxicity (CC50) and IC50 values against WT and drug resistant HIV-1.

Although a number of anti HIV drugs have been approved, there are still problems with toxicity and drug resistance. This demonstrates a need to identify ...

Highly Sensitive Assay for Measurement of Arenavirus-cell Attachment

Arenaviruses are a family of enveloped RNA viruses that cause severe human disease. The first step in the arenavirus life cycle is attachment of viral particles to host cells. While virus-cell attachment can be measured through the use of virions labeled with biotin, radioactive isotopes, or fluorescent dyes, these approaches typically require high multiplicities of infection (MOI) to enable detection of bound virus. We describe a quantitative (q)RT-PCR-based assay that measures Junin virus strain Candid 1 attachment via quantitation of virion-packaged viral genomic RNA. This assay has several advantages including its extreme sensitivity and ability to measure attachment over a large dynamic range of MOIs without the need to purify or label input virus. Importantly, this approach can be easily tailored for use with other viruses through the use of virus-specific qRT-PCR reagents. Further, this assay can be modified to permit measurement of particle endocytosis and genome uncoating. In conclusion, we describe a simple, yet robust assay for highly sensitive measurement of arenavirus-cell attachment.

The first step in the arenavirus life cycle is attachment of viral particles to host cells. We report a quantitative (q)RT-PCR-based assay for ultrasensitive detection and quantitation of arenavirus attachment events.

Arenaviruses are a family of enveloped RNA viruses that cause severe human disease. The first step in the arenavirus life cycle is attachment of viral ...

Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16

Antiviral assays that mechanistically examine viral entry are pertinent to discern at which step the evaluated agents are most effective, and allow for the identification of candidate viral entry inhibitors. Here, we present the experimental approaches for the identification of small molecules capable of blocking infection by the non-enveloped coxsackievirus A16 (CVA16) through targeting the virus particles or specific steps in early viral entry. Assays include the time-of-drug-addition analysis, flow cytometry-based viral binding assay, and viral inactivation assay. We also present a molecular docking protocol utilizing virus capsid proteins to predict potential residues targeted by the antiviral compounds. These assays should help in the identification of candidate antiviral agents that act on viral entry. Future directions can explore these possible inhibitors for further drug development.

The goal of the protocol is to illustrate the different assays relating to viral entry that can be used to identify candidate viral entry inhibitors.

Antiviral assays that mechanistically examine viral entry are pertinent to discern at which step the evaluated agents are most effective, and allow for ...

High-throughput Antiviral Assays to Screen for Inhibitors of Zika Virus Replication

Antiviral drug discovery requires the development of reliable biochemical and cellular assays that can be performed in high-throughput screening (HTS) formats. The flavivirus non-structural (NS) proteins are thought to co-translationally assemble on the endoplasmic reticulum (ER) membranes, forming the replication complex (RC). The NS3 and NS5 are the most studied enzymes of the RC and constitute the main targets for drug development due to their crucial roles in viral genome replication. NS3 protease domain, which requires NS2B as its cofactor, is responsible for the cleavage of the immature viral polyprotein into the mature NS proteins, whereas NS5 RdRp domain is responsible for the RNA replication. Herein, we describe in detail the protocols used in replicon-based screenings and enzymatic assays to test large compound libraries for inhibitors of the Zika virus (ZIKV) replication. Replicons are self-replicating subgenomic systems expressed in mammalian cells, in which the viral structural genes are replaced by a reporter gene. The inhibitory effects of compounds on viral RNA replication can be easily evaluated by measuring the reduction in the reporter protein activity. The replicon-based screenings were performed using a BHK-21 ZIKV replicon cell line expressing Renilla luciferase as a reporter gene. To characterize the specific targets of identified compounds, we established in-vitro fluorescence-based assays for recombinantly expressed NS3 protease and NS5 RdRp. The proteolytic activity of the viral protease was measured by using the fluorogenic peptide substrate Bz-nKRR-AMC, while the NS5 RdRp elongation activity was directly detected by the increase of the fluorescent signal of SYBR Green I during RNA elongation, using the synthetic biotinylated self-priming template 3&#8242;UTR-U30 (5&#39;-biotin-U30-ACUGGAGAUCGAUCUCCAGU-3&#39;).

In this work, we describe the protocols used in replicon-based and viral enzyme-based assays to screen for inhibitors of Zika virus replication in a high-throughput screening format.

Antiviral drug discovery requires the development of reliable biochemical and cellular assays that can be performed in high-throughput screening (HTS) ...

Assessing the Effectiveness of an Antiviral Test Compound through a Viral Inactivation Assay

Source: Tai, C. et al., <a href="https://app-jove-com.remotexs.ntu.edu.sg/v/53124">Early Viral Entry Assays for the Identification and Evaluation of Antiviral Compounds.</a> J. Vis. Exp. (2015)
This video demonstrates the viral inactivation assay, showcasing the evaluation of the impact of antiviral agents on viral particles.

1. Viral Inactivation Assay
Note: Examples of incubation period and viral dose for various viruses are listed in Figure 1A. Higher concentrations of the ...

JoVE Encyclopedia of Experiments

Immunology

Immunodiagnostics

Specialized Assays

A Viral Attachment Assay for Screening of Antiviral Compounds

Source: Tai, C. et al., <a href="https://app-jove-com.remotexs.ntu.edu.sg/v/53124">Early Viral Entry Assays for the Identification and Evaluation of Antiviral Compounds.</a> J. Vis. Exp.&#160;(2015)
This video demonstrates a viral attachment assay for screening antiviral compounds. Using genetically modified hepatitis C virus and luciferase, it assesses inhibitory effects on viral attachment, as indicated by lower light intensity in co-treated wells compared to wells treated with the virus alone.

NOTE: Ensure that all procedures involving cell culture and virus infection are conducted in certified biosafety hoods that are appropriate for the ...

An Assay to Evaluate the Effect of Test Compounds on Viral Entry and Fusion in Host Cells

Source: Tai, C., et al. <a href="https://app-jove-com.remotexs.ntu.edu.sg/v/53124">Early Viral Entry Assays for the Identification and Evaluation of Antiviral Compounds.</a> J. Vis. Exp. (2015).
This video demonstrates an assay to evaluate antiviral agents that target specific steps of the viral entry into host cells and fusion with the endosome. The cells are incubated at a low temperature and then infected with HCV. The low temperature permits viral binding to host cells but inhibits internalization via endocytosis. The test antiviral compound is added, and the cells are incubated at physiological temperature. This shift to a higher temperature facilitates viral entry and allows assessment of the impact of the test compound on viral envelope fusion with endosomes.

Note: Ensure that all procedures involving cell culture and virus infection are conducted in certified biosafety hoods that are appropriate for the ...