Brilacidin, a COVID-19 Drug Candidate, demonstrates broad-spectrum antiviral activity against human coronaviruses OC43, 229E and NL63 through targeting both the virus and the host cell

Brilacidin, a mimetic of host defense peptides (HDPs), is currently in phase 2 clinical trial as an antibiotic drug candidate. A recent study reported that brilacidin has antiviral activity against SARS-CoV-2 by inactivating the virus. In this work, we discovered an additional mechanism of action of brilacidin by targeting heparan sulfate proteoglycans (HSPGs) on host cell surface. Brilacidin, but not acetyl brilacidin, inhibits the entry of SARS-CoV-2 pseudovirus into multiple cell lines, and heparin, a HSPG mimetic, abolishes the inhibitory activity of brilacidin on SARS-CoV-2 pseudovirus cell entry. In addition, we found that brilacidin has broad-spectrum antiviral activity against multiple human coronaviruses (HCoVs) including HCoV-229E, HCoV-OC43, and HCoV-NL63. Mechanistic studies revealed that brilacidin has a dual antiviral mechanism of action including virucidal activity and binding to coronavirus attachment factor HSPGs on host cell surface. Brilacidin partially loses its antiviral activity when heparin was included in the cell cultures, supporting the host-targeting mechanism. Drug combination therapy showed that brilacidin has a strong synergistic effect with remdesivir against HCoV-OC43 in cell culture. Taken together, this study provides appealing findings for the translational potential of brilacidin as a broad-spectrum antiviral for coronaviruses including SARS-CoV-2.

As the third coronavirus that causes severe respiratory disease, SARS-CoV-2 associated COVID19 has led to more than 211 million infections and over 4. issued for Emergency Use Authorization. Although vaccine continues to be a mainstay for viral prophylaxis, the efficacy of vaccine might be compromised with emerging variants such as the delta variant [6][7][8] . For this reason, small molecular antiviral drugs are important complements of vaccines to help combat pandemics.
Host defense peptides (HDPs), also called antimicrobial peptides (AMPs), are typically small peptides (12-50 amino acids) that are expressed in neutrophils and mucosa and serve as the first line of defense against foreign pathogens 9 . HDPs have been extensively explored as antibiotics 10 , antivirals 11 , antifungals 12 and anticancer agents 13 . Most HDPs share an amphiphilic structure with a positively charged face and a hydrophobic face 14 . It is proposed that HDPs disrupt bacterial cell membranes by interacting with the negatively charged phospholipid headgroups [15][16][17] . Brilacidin is a small synthetic HDP mimetic 18 , and has potent antibacterial activity against both Grampositive and Gram-negative bacteria, and is currently in Phase 2 clinical trials (Clinical Trials NCT01211470, NCT020388, and NCT02324335). The antibacterial mechanisms of action of brilacidin include both membrane disruption and immunomodulation 19,20 .
Brilacidin is also in clinical trial (NCT04784897) as a SARS-CoV-2 antiviral drug candidate for hospitalized COVID-19 patients. A recent study showed that brilacidin exhibited potent inhibitory effect on SARS-CoV-2 replication (EC 50  In this work, we showed that brilacidin inhibits SARS-CoV-2 pseudovirus entry into multiple cell lines. However, acetyl brilacidin had no inhibition on SARS-CoV-2 pseudovirus entry, and heparin, a heparan sulfate proteoglycans (HSPGs) mimetic, diminished the inhibitory activity of brilacidin. This result suggests that brilacidin has an additional mechanism of action by binding to HSPGs on the host cell, thereby blocking viral attachment. HSPGs have been reported as an attachment factor for SARS-CoV-2 22,23 . In addition, we have shown that brilacidin has broad-spectrum antiviral activity against multiple HCoVs including HCoV-229E, HCoV-OC43, and HCoV-NL63. The antiviral mechanism against these viruses similarly involves both virucidal effects and binding to HSPGs. Brilacidin partially loses its antiviral activity against HCoV-229E, HCoV-OC43, HCoV-NL63 in the presence of heparin in cell culture. Drug time-ofaddition experiments provided additional evidence that brilacidin exerts its antiviral activity at both viral attachment and early entry stage of viral life cycle. Finally, drug combination therapy demonstrated that brilacidin has strong synergistic effect with remdesivir against HCoV-OC43 in cell culture. Overall, brilacidin appears to have appealing translational potential as a broad-spectrum antiviral for coronaviruses including SARS-CoV-2.

Brilacidin inhibits SARS-CoV-2 pseudovirus entry in multiple cell lines
To delineate whether brilacidin blocks SARS-CoV-2 viral entry, we generated pseudotyped HIV-1-derived lentiviral particles with SARS-CoV-2 spike protein 24 , which is widely used to study spike-mediated viral entry into host cells in biosafety level 2 facilities 25,26 . Brilacidin was tested in SARS-CoV-2 pseudovirus entry assay in several ACE2-expressing cell lines including Vero C1008, Calu-3, Huh-7, Caco-2, and 293T-ACE2. Vero C1008 and 293T-ACE2 express minimal levels of transmembrane serine proteinase 2 (TMPRSS2), therefore SARS-CoV-2 virus enters into these cell lines mainly through endocytosis and relies on endosomal cathepsin L for viral spike protein activation 27,28 . In contrast, Calu-3 and Caco-2 endogenously express TMPRSS2 29 , which activates SARS-CoV-2 spike protein on cell surface so virus gets into these cell lines through direct cell membrane fusion. Cathepsin L inhibitor E-64d and TMPRSS2 inhibitor camostat mesylate were included as controls 30 . Our results showed that brilacidin inhibited SARS-CoV-2 pseudovirus entry into all cell lines tested with IC 50 values ranging from 12.0 ± 1.7 to 23.0 ± 1.6 µM (Figure 1). Cytotoxicity assays showed that brilacidin was not toxic to all the cell lines tested at the concentrations examined ( Figure 1F). Overall, brilacidin inhibits SARS-CoV-2 pseudovirus entry into multiple cell lines. These results suggest the antiviral activity of brilacidin is independent of cathepsin L or TMPRSS2 inhibition. Brilacidin also inhibited HCoV-OC43 in the plaque assay with an EC 50 of 7.32 ± 0.15 µM ( Figure 2G, top panel). In contrast, brilacidin had no effect on the replication of either  EC 50 and CC 50 values were determined through curve fitting described in the "material and methods" section, and all data are mean ± standard deviation of three replicates.

Brilacidin targets both the virus and the host cell
To elucidate the antiviral mechanism of brilacidin, we first performed experiments to determine whether brilacidin directly targets the virus or the host cell. To assess the virucidal effect of brilacidin on human coronaviruses, we incubated HCoV-OC43, HCoV-229E or HCoV-NL63 with serial concentrations of brilacidin (25, 50, 100, 200 µM) or DMSO at 37 °C for 14 hrs. The mixture was then diluted 10 6 -fold to quantify the infectious viral titer. The final concentrations of brilacidin in each sample after dilution were 0.025, 0.05, 0.1 and 0.2 nM, respectively, which are far below its minimum inhibitory concentration (EC 50 s in the low µM range) and therefore had no effect on plaque formation. It was found that brilacidin treatment decreased the viral titers of all three human coronaviruses dose-dependently, and the viral titers were decreased by more than 1 log 10    Quantification of HCoV-OC43 (C) or HCoV-229E (D) virus released into the cell culture medium using plaque assay. *, p < 0.05; **, p < 0.01, ***, p < 0.001 (student's ttest). Data are mean ± standard deviation of duplicates.

Heparin decreases the inhibitory activity of brilacidin in SARS-CoV-2 pseudovirus cell entry and HCoV-OC43, HCoV-229E and HCoV-NL63 replication in cell culture
It was proposed that brilacidin binds to SARS-CoV-2 spike protein 30 . To test whether brilacidin blocks SARS-CoV-2 pseudovirus entry into host cells through interaction with the spike protein, we tested the direct binding of brilacidin to SARS-CoV-2 spike protein receptor binding domain (RBD) using differential scanning fluorimetry (DSF). The results demonstrated that brilacidin has no effect on the melting temperature (T m ) of SARS-CoV-2 spike protein RBD up to 100 µM (Table 1), indicating that there is no direct binding between brilacidin and SARS-CoV-2 spike protein RBD.  Figure 5A). It was found that acetyl brilacidin completely lost inhibitory activity in SARS-CoV-2 pseudovirus entry assay in Vero C1008, Calu-3 and Caco-2 cells (Figure 5B, 5C, 5D). This result suggests that the +4 charge on brilacidin is critical for the antiviral activity, and the antiviral mechanism of action might involve interaction with the binding to HSPGs.
If brilacidin binds to cell surface HSPGs in cell culture, exogenous addition of HSPG mimetics such as heparin will compete with HSPGs for binding of brilacidin, resulting in decreased inhibitory activity of brilacidin on SARS-CoV-2 pseudovirus entry and the replication of human coronaviruses in cell culture. We therefore performed the competition assay to evaluate the effect of heparin on the antiviral activity of brilacidin.
To test the effect of heparin on brilacidin activity in SARS-CoV-2 pseudovirus entry, heparin was first tested in SARS-CoV-2 pseudovirus entry assay in Vero C1008, Caco-2 and Calu-3 cells to determine proper concentrations in the competition assay. The highest concentration of heparin used in the competition assay was 100 µg/ml, which had no effect on SARS-CoV-2 pseudovirus entry ( Figure 5E)   (Figure 6A, 6B), and the amplified HCoV-229E, HCoV-NL63 and HCoV-OC43 viruses released into culture medium were quantified by plaque assay (Figure 6C, 6D  (student's t-test). All data are mean ± SD of two independent experiments.

Brilacidin has a strong synergistic antiviral effect with remdesivir in cell culture
Combination therapy is commonly used to slow down drug resistance development and reduce side effects 38,39 . The antiviral effect of brilacidin and remdesivir in combination therapy was evaluated in HCoV-OC43 plaque assay using the combination indices method (Figure 7)   The proposed antiviral mechanism of brilacidin is summarized in a model illustrated in Figure 8, which is supported by multiple lines of evidence. Our results showed that brilacidin has a dual antiviral mechanism against human coronaviruses including blocking viral attachment to host cells through binding to HSPGs and virucidal activity.
HCoV-OC43, HCoV-NL63 and HCoV-229E showed dose-dependent decrease of replication in cells pretreated with brilacidin, and viral particles lose infectivity after incubation with brilacidin (Figure 3). Drug time-of-addition experiment suggested that brilacidin exerted its antiviral activity at two individual steps: viral attachment to host cell and early entry after entering into the host cells (Figure 4). The inhibition of viral attachment by brilacidin was confirmed in SARS-CoV-2 pseudovirus entry assay (Figure 1). DSF assay results demonstrated that brilacidin has no direct binding to SARS-CoV-2 spike protein RBD ( Table 1). Competition experiment with heparin indicated that brilacidin binds to host cell surface HSPGs to block viral attachment to host cells. Addition of heparin dose-dependently decreased the inhibition of brilacidin in SARS-CoV-2 pseudovirus entry assay ( Figure 5) and the replication of HCoV-OC43, HCoV-NL63 and HCoV-229E in cell culture (Figure 6).

Antiviral assays
The antiviral activity of brilacidin was tested against HCoV-229E, HCoV-NL63 and HCoV-OC43 in Viral yield reduction (VYR) assays as previously described 30,[40][41][42] . The antiviral activity of brilacidin tested in HCoV-OC43 plaque assay was carried out similarly as described in VYR assay, except that about 100 PFU of HCoV-OC43 virus was used to infect the cells in each well of 6-well plate and serial concentrations of brilacidin (0, 3.13, 6.25, 12.5, 25, 50, 100 µM) was included in the Avicel overlay. The plaque areas were quantified using Image J and the EC 50 value was determined by plotting percentage of plaque area versus log 10 compound concentrations from best-fit dose response curves with variable slope in Prism 8.
The antiviral activity of brilacidin against influenza and enterovirus D68 was carried out in plaque assay as previously described 36,43,44 .

Cytotoxicity assay
Cytotoxicity of brilacidin was evaluated in different cell lines using the neutral red uptake assay as previously described 45,46

Time of addition
Drug time-of-addition experiment was performed as previously described 30,47 . Briefly, RD cells were seeded at 1 ×10 5 cells/well in 12-well plate with cover slip (Cat#: GG-12-

Combination therapy
The combination antiviral effects of brilacidin and remdesivir were evaluated in HCoV-