1. High efficiency transfection of HEK293T-derived cells using branched polyethyleneimine (PEI)
NOTE: Perform all steps in a biosafety cabinet using standard aseptic technique and BSL-2 procedures. Use HEK293T-derived cells for transfection and generation of pseudotyped viruses. In this Method cells are transfected in cell culture-treated 6 well plates. The PEI stock solution is prepared as previously described by Yang and colleagues (2017)12. Before proceeding to do the triple transfection to generate the pseudovirus, it is advisable to optimize the best PEI-plasmid DNA proportion to ensure a high transfection efficiency (more than 70-80%). This optimization should be done by transfection of a green fluorescent protein (GFP)-expressing plasmid and then checking the proportion of fluorescent cells using a fluorescence microscope. For this optimization, keep plasmid DNA constant at 2.5 µg per well and test several amounts of PEI, in the range of 1-20 µL. Here are the best conditions for these lots of cells and PEI, consisting of 5 µL of PEI stock solution (1 mg/mL) and 2.5 µg of GFP-expressing plasmid per well in a 6-well plate.
- Seed 7.5 x 105 HEK293-derived cells per well in a 6-well tissue culture plate, in a total volume of 2 mL per well of complete medium (DMEM-C: Dulbecco's Modified Eagle's Medium supplemented with 10% heat-inactivated fetal bovine serum (FBS), 20 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES), 100 IU/mL penicillin, and 100 µg/mL streptomycin) 24 h before transfection.
NOTE: When seeding cells, avoid moving the tissue culture plate in circular motions, since this may cause cell aggregation at the center of wells, resulting in irregular cell distribution and subsequently lower transfection efficiency. One 6-well plate is enough for one experiment, including one well as a cell control (non-transfected), and the rest of the plate for testing several proportions of PEI-plasmid DNA.
- Incubate the cells at 37 °C with 5% CO₂ overnight. Next day, ensure that the cells are approximately 50-60% confluent.
- On the day of transfection, prepare the PEI-plasmid DNA complexes in sterile, 1.5 mL microcentrifuge tubes.
- For each well, prepare a PEI solution tube containing 5 µL of PEI stock (1 mg/mL) in 50 µL of reduced serum medium, and one DNA solution tube containing 2.5 µg of the GFP-expressing plasmid, in 50 µL of the same medium.
- If several wells are to be transfected, solutions may be scaled up accordingly. Mix each tube briefly by vortex and spin down for 5 sec. Incubate tubes at room temperature (RT) for 10 min.
- During the time of this incubation, carefully remove the medium from each well of the 6-well plate, avoiding disruption of the cell monolayer. Replace carefully with 1 mL/well of complete transfection medium (DMEM-T, same as DMEM-C, but without antibiotics).
- Prepare the transfection complex. After the 10 min incubation, add the 50 µl of the DNA solution tube to the PEI solution tube. Mix quickly by pipetting up and down six times and incubate at RT for exactly 3 min. Immediately proceed to add complex dropwise to cells in each corresponding well.
- Seal the borders of the plate with parafilm and centrifuge at 1,000 x g for 30 min at RT, without brake, using a swing rotor and plate bucket.
- After centrifugation, remove parafilm gently and incubate the plate at 37 °C, 5% CO₂ for 3 h.
- After incubation, gently remove the transfection medium from each well and replace it slowly with 2 mL of pre-warmed DMEM-C per well.
- Incubate transfected cells at 37 °C with 5% CO₂ for 48 h.
- Assess transfection efficiency by GFP expression using fluorescence microscopy. The frequency of fluorescent cells should be higher than 70-80% (Figure 1). This is critical for the efficiency of the next method in section 2.
2. Generation of SARS-CoV-2 spike- and VSV-G pseudotyped pseudoviral particles
NOTE: This Method uses the same procedure as section 1, except that instead of using the GFP plasmid, cells will be co-transfected with the three plasmids required to generate pseudotyped viruses, using the optimal transfection conditions to assure high transfection efficiency. The protocol also uses HEK293T-derived cells in 6-well plates, sufficient for the following three required conditions: a) non transfected cells (one well), b) cells transfected only with the MLV packaging plasmid and the luciferase reporter transfer vector (one well; spike-less pseudoviruses) and c) cells transfected with these two plasmids and the spike-expressing plasmid to generate SARS-CoV-2 pseudotyped viruses (four wells). The spike-expressing plasmid used here codes for the spike of the SARS-CoV-2, Wuhan strain, and contains sequence modifications to allow for an efficient presentation of the protein in PVs. The spike-less pseudovirus will be required as a control later during infections, to validate the spike-dependent entry in permissive cells. Similarly, VSV-G-PVs are generated using the same experimental design to be used later as a counter-screening of potential inhibitory compounds. If a larger volume of pseudovirus is required, the protocol may be scaled up to two 6-well plates, which may also be practical for the plate centrifugation step.
- The day before transfection, seed HEK293T-derived cells into two 6-well plates, as described in section 1. Use one plate for the generation of spike-PVs and the other for the VSV-G-PVs.
- The day of transfection, prepare the transfection mixes as shown in Table 1, following step 1.3.
NOTE: PEI solution is prepared as previously reported12. Plasmids pCMV-MLVgagpol and pTG-Luc were obtained from Millet and Whittaker8. Plasmid pVSV-G was obtained from Gee et al 202013. All plasmids should be prepared in advance as high-quality preps, free of endotoxins. It is recommended to use commercially available maxiprep kits, with a final step of sterile filtration through low-binding, 0.2 µm syringe filter.
- Mix each tube as described in section 1 and incubate at RT for 10 min.
- During this incubation, carefully remove the medium from each well of the 6-well plates, avoiding disruption of the cell monolayer. Slowly replace with 1 mL of pre-warmed DMEM-T medium to each well, ensuring the medium runs down the wall of the well and not directly onto the cells.
- Prepare transfection complexes as described in section 1 and transfect cells using the previously described protocol.
- After the 48-h incubation post-transfection, collect the supernatants, transfer them to 50 mL sterile conical centrifuge tubes, and centrifuge at 290 x g for 7 min at 4 °C. Collect the cell-free supernatant, and filter it using a polyvinylidene fluoride (PVDF), sterile 0.45 µm top bottle filter unit. Prepare aliquots of 1 mL and store them at -80 °C.
NOTE: Pseudotyped particles are stable at -80 °C for several months. Avoid repeated freeze-thaw cycles to preserve infectivity.
| For SARS-CoV-2 spike-PVs (per well) | For VSV-G-PVs (per well) | For spike-less PVs (per well) |
| PEI solution: | | | |
| PEI (1 mg/ml)1 | 5 µL | 5 µL | 5 µL |
| Reduced serum medium | 45 µL | 45 µL | 45 µL |
| Plasmid DNA solution:2 | | | |
| pCMV-MLVgagpol | 0.79 µg | 0.79 µg | 0.79 µg |
| pTG-luc | 0.92 µg | 0.92 µg | 0.92 µg |
| pUNO1-spike | 0.79 µg | - | - |
| pVSV-G | - | 0.79 µg | - |
| Reduced serum medium | to 50 µL | to 50 µL | To 50 µL |
Table 1: Preparation of transfection mixes for the generation of PVs.
3. Titration of SARS-CoV-2 and VSV-G pseudotyped particles
NOTE: This step is essential to confirm that the produced pseudotyped particles are infectious and to determine the minimum effective volume required for downstream applications such as compound screening. The titration should be done for every new batch of pseudovirus. To this purpose, cells highly susceptible to infection with SARS-CoV-2 (HSI cells) are infected with decreasing amounts of the pseudotyped viruses. The entry of the pseudoviruses, mediated by the spike-human ACE2 interaction, or by VSV-G with other cellular receptors, is monitored 72 h later by the detection of the luciferase activity in a luminescence assay.
- The day before the transduction, seed 2.5 x 104 HSI cells per well in a 96-well tissue culture plate, in 50 µL of complete medium (DMEM-C). Prepare three wells for each amount of pseudovirus to test, and include wells for infection, also with spike-less pseudoviruses, and for non-infected cells. Incubate the plate at 37 °C with 5% CO₂ overnight.
- The day of the transduction, thaw one aliquot of each pseudovirus batch to test on ice and gently mix by inversion. Include also one aliquot of the spike-less control. Add directly to each well several amounts of the pseudovirus preparation (100, 50, 25, 12.5, 6.2, 3.1, 1.5, and 0.8 µL). Adjust the volumes of all wells to 150 µL with DMEM-C.
- Seal the plate with parafilm and centrifuge at 2,500 × g for 45 min at RT, with no brake.
- Remove the parafilm seal and incubate the plate for 72 h at 37 °C, 5% CO₂.
- After incubation, prepare for the luciferase assay following the instructions of the manufacturer. Thaw luciferase substrate (stored at -80 °C) and 5x luciferase assay lysis buffer (stored at -20 °C) and equilibrate at RT (10-15 min).
- Dilute the luciferase assay lysis buffer to 1x with sterile water. Prepare at least 3 mL.
- Slowly and carefully aspirate and discard the supernatant of each well using a multichannel pipette.
- Add 30 µL of 1x lysis buffer to each well using a multichannel pipette. Place the plate in a plate shaker for 10 min at 150 rpm, at RT. Verify complete lysis under an inverted microscope (all cells should be lysed and not distinguishable upon visual examination).
NOTE: Prepare the microplate reader in advance to perform luminescence detection immediately after substrate addition to ensure consistency and avoid signal decay.
- Transfer the lysates to an opaque, white 96-well plate.
- Add 50 µL of luciferase substrate to each well and mix briefly by moving the plate in a circular motion. Place the plate in the luminometer and measure luminescence.
- Analyze the data obtained.
- Verify that controls give the expected luminescence values. Ensure that the non-infected cells give very low background luminescence values.
NOTE: Cells infected with spike-less pseudovirus should give values at the level of non-infected cells, and cells infected with decreasing amounts of spike-presenting pseudovirus should show high, dose-dependent values of luminescence (Figure 2). The luminescence values generated by the VSV-G-PVs are usually much higher than those of spike-PVs, about one or two orders of magnitude.
- For subsequent screenings, select the amount of pseudovirus that generates a signal at least one hundred to one thousand times that of the non-infected cells.
4. Screening of compounds for pseudoviral entry inhibition using spike-PVs
- Seed 2.5 x 104 HSI cells per well in 50 µL of complete medium (DMEM-C) in a 96-well plate, as described in section 3. Incubate overnight at 37 °C, 5% CO₂.
- Consider a plate design that includes columns 1 to 11 for compounds plus pseudovirus, and column 12 for controls. In column 12, allocate four wells for virus control (pseudovirus only) and four wells for non-infected, non-treated cells.
- The next day, prepare serial dilutions (1:3) of compounds to be tested, starting at 50 µM (final concentrations during infections: 50, 16.6, 5.5, 1.8, 0.6, 0.2, and 0.06 µM), in DMEM-C containing 0.5% DMSO.
- For convenience, prepare dilutions in a separate 96-well "dilution plate", where serial dilutions are first made and then transferred (50 µL) to the plate containing the cells.
- If the number of compounds is very large, in the order of hundreds or more, reduce this first dilution series to about 4 points, using a single well per dilution point, and consider a prescreening. Then, re-test the potential hits using 7-point serial dilutions, 1:3, with three replicates, starting at the same concentration of 50 µM.
- Once dilutions of compounds are ready, gently aspirate the medium of cells using a multichannel pipette and add 50 µL of compound dilutions to the corresponding wells. Incubate for 1 h at 37 °C, 5% CO₂. For controls in column 12, add DMEM-C only.
- Without removing the compounds, add to each well the predetermined amount of pseudotyped SARS-CoV-2 pseudovirus, in a volume of 50 µL of complete medium, containing the compounds at the same concentrations. Seal the plates with parafilm.
- Centrifuge the plate at 2,500 × g for 45 min at RT without brake, then remove parafilm and incubate at 37 °C, 5% CO2 for 72 h.
- Proceed with luciferase-based infectivity quantification as described in section 3.
- Perform data analysis.
- Export luminescence values into a spreadsheet to format the data for subsequent import into data analysis and graphing software.
- Prepare bar graphs plotting the mean of each concentration point, including the standard error of the mean bars. Plot also the values obtained from positive (PVs alone) and negative controls (non-infected cells).
NOTE: The results of the assay are considered valid if 1) non-infected cells show very low values, 2) PVs controls show high values, 3) positive control of inhibition (i.e., arbidol or hACE2-Fc) shows inhibition of infection, in a dose-dependent manner (Figure 3A, B).
- Then, observe the values produced by unknown compounds to assess if there is inhibition and if there is a dose-dependent effect. If so, then subject these compounds to further confirmatory analyses.
NOTE: For further confirmation of potential hits, follow the next steps. First, retest the potential hits compounds as suggested in step 4.2. If the dose response effect is confirmed, then perform a counter screening using the same dilution series but infecting with the VSV-G-PVs. This test is important to check if the inhibition of entry is specific for the spike-ACE2 interaction, and not due to interference at any other step later during the production of the luciferase in the infected cells (Figure 3A, B). Here, the positive compound should not show inhibitory activity against the VSV-G-PVs. If this is the case, then the same series of concentrations should be tested for cytotoxicity using a cell viability assay (MTT assay, shown in section 5). As a summary, a potential hit compound should show inhibition of SARS-CoV-2-spike-PVs, and no or less inhibition of VSV-G-PVs, and no, or at least a much weaker inhibition of the viability of the cells. Adjusting a dose-response curve using the luminescence data will allow the estimation of the half-maximal inhibitory concentration (IC50) for the inhibition of the PVs, and a half-maximal cytotoxic concentration (CC50) from the viability assay. The ratio CC50 / IC50 is used to calculate the selectivity index (SI), which is an important indicator of the potential usefulness of the positive compound. For the analysis of the dose-response curves and the estimation of the IC50 and CC50 very detailed procedures have been described14.
5. MTT-based cell viability assay
- Seed 2.5 x 104 HSI cells per well in 50 µL of DMEM-C in a 96-well plate. Incubate the plate overnight at 37 °C, 5% CO₂. Ensure the cells are about 50% confluency the next day. Prepare enough wells, considering all different concentrations of the compound to be evaluated, untreated cells, and blank wells containing only medium, in triplicate. Test the potential hit compounds at the same concentrations evaluated in the PV entry inhibition assay.
- After incubation, carefully remove the medium and replace it with 100 µL of complete medium containing different concentrations of the compound to evaluate, in 0.5% DMSO.
- Centrifuge the plate at 2,500 × g for 45 min at RT without brake and incubate for 72 h at 37 °C, 5% CO₂. This step is included to handle the cells exactly as done in the previous section, except for the addition of the PVs.
- Prepare a 0.5 mg/mL MTT solution using DMEM. Sterilize by filtering through 0.2 µm and keep in the dark.
NOTE: 3-(4,5-Dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) is light sensitive. It should be kept frozen, in the dark.
- Carefully remove the medium from each well and replace it with 100 µL of MTT solution. Incubate for 2 h at 37 °C, 5% CO2.
- During this incubation, prepare a solubilization solution containing 40 mM HCl in isopropyl alcohol.
- Carefully remove the MTT solution using a multichannel pipette, without disturbing the formazan crystals at the bottom of each well.
- Add 100 µL of the solubilization solution to each well. Wrap the plate in aluminum foil and place it on a plate shaker at 150 rpm for 15 min.
- Record absorbance at 570 nm and 630 nm.
- Perform data analysis.
- Using the raw values of optical density, subtract the values obtained at 630 nm from those obtained at 570 nm for each well. Then average the corrected values of the untreated cell wells. Consider these untreated cells 100% viable.
- Then normalize treated cells' values against the untreated cells' wells, using the formula:
Viability (%) = 
- Plot viability percentages as bars representing the mean of replicates ±± standard error of the mean. Perform further statistical analysis to compare groups using procedures implemented in a data analysis and graphing software, comparing viabilities at different concentrations with the untreated cells control.
- Compare means of each concentration point to that of the DMSO-only treated cells using nonparametric Kruskal-Wallis with Dunn post-test (differences are considered significant at p-values < 0.05). For plotting a dose-response curve and estimating the CC50 out of OD values, check the procedure reported elsewere14.