References supporting viral proteins as targets for CoViD

AIDS Res Hum Retroviruses. 2012 Jan; 28(1): 54–75.

HIV Type 1 Gag as a Target for Antiviral Therapy

Abdul A. Waheed and Eric O. Freed


The Gag proteins of HIV-1 are central players in virus particle assembly, release, and maturation, and also function in the establishment of a productive infection. Despite their importance throughout the replication cycle, there are currently no approved antiretroviral therapies that target the Gag precursor protein or any of the mature Gag proteins. Recent progress in understanding the structural and cell biology of HIV-1 Gag function has revealed a number of potential Gag-related targets for possible therapeutic intervention. In this review, we summarize our current understanding of HIV-1 Gag and suggest some approaches for the development of novel antiretroviral agents that target Gag.



Int J Med Sci. 2020; 17(12): 1803–1810.

Advances and challenges in the prevention and treatment of COVID-19

Yan-Jie Han,1,2,3,* Zhi-Guang Ren,1,2,* Xin-Xin Li,3 Ji-Liang Yan,3 Chun-Yan Ma,3 Dong-Dong Wu,1,2,4, and Xin-Ying Ji1,2,


Since the end of 2019, a new type of coronavirus pneumonia (COVID-19) caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has been spreading rapidly throughout the world. Previously, there were two outbreaks of severe coronavirus caused by different coronaviruses worldwide, namely Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the Middle East Respiratory Syndrome Coronavirus (MERS-CoV). This article introduced the origin, virological characteristics and epidemiological overview of SARS-CoV-2, reviewed the currently known drugs that may prevent and treat coronavirus, explained the characteristics of the new coronavirus and provided novel information for the prevention and treatment of COVID-19.



Intervirology. 1989;30(1):27-35. doi: 10.1159/000150073.

Processing and secretion of envelope glycoproteins of human immunodeficiency virus type 1 in the presence of trimming glucosidase inhibitor deoxynojirimycin

R Pal 1, V S Kalyanaraman, G M Hoke, M G Sarngadharan


The processing and secretion of the envelope glycoprotein of human immunodeficiency virus type 1 (HIV-1) were studied in chronically infected cells treated with the trimming glucosidase inhibitor deoxynojirimycin (DNM). In Molt3 cells infected with human T-lymphotropic virus type III (HTLV-IIIB), DNM inhibited the intracellular proteolytic processing of gp160 to gp120 and gp41. A clone of the HUT78 cell line called 6D5, when chronically infected with the HIV-1 isolate HTLV-III451 was shown to release both gp160 and gp120 into the culture medium. The secretion of envelope glycoproteins from these infected cells was not inhibited by DNM treatment. The secreted proteins had higher molecular weights than gp160 and gp120 from cultures not treated with DNM, presumably due to the presence of unprocessed carbohydrate residues on the polypeptide chain. These secreted glycoproteins from DNM-treated cells exhibited specific interaction with the CD4 molecule on the surface of target cells. However, the syncytium formation induced by HIV-1-infected cells on CD4+ cells was significantly inhibited in the presence of the glucosidase inhibitor. The minimal cytotoxicity of the DNM coupled with its strong inhibitory effect on the cell-to-cell spread of the virus suggest that it may be potentially useful in antiviral drug therapy of HIV-1 infection.



Trends Microbiol. 2011 Apr;19(4):191-7. doi: 10.1016/j.tim.2011.02.001. Epub 2011 Mar 4.

HIV envelope: challenges and opportunities for development of entry inhibitors

Michael Caffrey 1


The HIV envelope proteins glycoprotein 120 (gp120) and glycoprotein 41 (gp41) play crucial roles in HIV entry, therefore they are of extreme interest in the development of novel therapeutics. Studies using diverse methods, including structural biology and mutagenesis, have resulted in a detailed model for envelope-mediated entry, which consists of multiple conformations, each a potential target for therapeutic intervention. In this review, the challenges, strategies and progress to date for developing novel entry inhibitors directed at disrupting HIV gp120 and gp41 function are discussed.



The Science advisory board. Cell biology. CoViD-19. July 27, 2020

SARS-CoV-2 envelope protein identified as target for antiviral drugs

By Samantha Black, PhD, The Science Advisory Board editor in chief

Comparison of the SARS-CoV-2 genome with other betacoronaviruses can provide useful information on how drugs targeting other coronaviruses may improve outcomes for COVID-19 patients. The analysis was presented in a July 27 Frontiers in Cellular and Infection Microbiology article.

The spike proteins of SARS-CoV-2 enable the virus to bind to the human angiotensin-converting enzyme 2 (ACE2). The spike proteins of SARS-CoV and SARS-CoV-2 are similar, but key structural differences in the receptor-binding domain prevent SARS-CoV-specific neutralizing antibodies from inhibiting infection by SARS-CoV-2.

“SARS-CoV-2 appears to have recently evolved from other related [betacoronaviruses], such as the ones causing SARS and Middle East respiratory syndrome (MERS),” explained author Intikhab Alam, PhD, a bioinformatician at King Abdullah University of Science and Technology in Saudi Arabia. “We wanted to understand the genetic makeup of SARS-CoV-2. Seeing what has changed might help find ways to detect the virus and understand its rapid spread. Seeing what remains conserved between these viruses might help predict if therapeutic approaches developed for other [betacoronaviruses] could work on SARS-CoV-2,” he said.

Core genomic features are required for the virus to be functional and are usually conserved among all strains of a species. For coronaviruses these include the spike protein, membrane glycoprotein (M), nucleocapsid (N), envelope protein (E), and the ORF1ab (a polyprotein known as replicase or protease). Alternatively, accessory features of the SARS-CoV-2 genome can provide insights into drivers of unique properties of the virus that explain its pathogenicity. Genome annotation and structural modeling can then be used to assess the effect of the accessory features and guide approaches to detection, treatment, and prevention.

This artistic representation of a SARS-CoV-2 virus

This artistic representation of a SARS-CoV-2 virus shows the membrane protein (green), the envelope protein (purple), and the characteristic spike protein (orange). Image courtesy of KAUST; Xavier Pita.

Researchers from the university applied a comparative pangenomic approach to data from all sequenced betacoronaviruses to detect core and accessory gene clusters and then annotated their functions through structural analysis. The team’s approach was unique because they first clustered all sequences and then calculated alignment to establish phylogeny. This allowed for higher sensitivity in the detection of gene clusters.

They found the E protein varied among betacoronaviruses, but that key features of the E protein are preserved between SARS-CoV and SARS-CoV-2. So, unlike previous analyses, the team classified the E protein, otherwise known as ORF3a or viroporin, as an accessory protein.

The E protein has ion channel activity (a multipass, transmembrane domain) and features a postsynaptic density protein 95 (PDZ)-binding motif (cytoplasmic β-barrel or β-sandwich fold and an N-terminal secretory-pathway signal peptide) that induces virulence. The E proteins from SARS-CoV-2 and SARS-CoV differ only by three substitutions and one deletion.

Therefore, the SARS-CoV-2 proteins are expected to act in the same way that they do for SARS-CoV, as accessory proteins localized in the endoplasmic reticulum-Golgi intermediate compartment and on the cell membrane, where they enhance viral pathogenicity through protein-protein interactions.

Previously, the E protein was identified as a determinant of pathogenicity for SARS-CoV and as a target of SARS-CoV antivirals. The E protein is thought to trigger cytokine storm that activates the inflammasome, resulting in acute respiratory distress syndrome (ARDS), a leading cause of death due to SARS-CoV-2 infection. The high degree of conservation of the ion channel and PDZ-binding motif between SARS-CoV and SARS-CoV-2 suggests that the E protein may be a good target for therapy and can possibly be inhibited with preexisting drugs.

“Drugs that inhibit the envelope protein E of previous SARS viruses should also block the protein in COVID-19,” Alam said. “Even though these drugs won’t stop the virus from spreading, we hope they could attenuate or prevent acute respiratory distress syndrome and help save lives.”

Do you have a unique perspective on your research related to genomics or virology? Contact the editor today to learn more.



Curr HIV Res. 2016; 14(3): 283–294.

Inhibition of HIV Entry by Targeting the Envelope Transmembrane Subunit gp41

Hyun Ah Yi,1 Brian C. Fochtman,2 Robert C. Rizzo,3 and Amy Jacobs*,1



The transmembrane subunit of the HIV envelope protein, gp41 is a vulnerable target to inhibit HIV entry. There is one fusion inhibitor T20 (brand name: Fuzeon, generic name: enfuvirtide) available by prescription. However, it has several drawbacks such as a high level of development of drug resistance, a short-half life in vivo, rapid renal clearance, low oral bioavailability, and it is only used as a salvage therapy. Therefore, investigators have been studying a variety of different modalities to attempt to overcome these limitations.


Comprehensive literature searches were performed on HIV gp41, inhibition mechanisms, and inhibitors. The latest structural information was collected, and multiple inhibition strategies targeting gp41 were reviewed.


Many of the recent advances in inhibitors were peptide-based. Several creative modification strategies have also been performed to improve inhibitory efficacy of peptides and to overcome the drawbacks of T20 treatment. Small compounds have also been an area of intense research. There is a wide variety in development from those identified by virtual screens targeting specific regions of the protein to natural products. Finally, broadly neutralizing antibodies have also been important area of research. The inaccessible nature of the target regions for antibodies is a challenge, however, extensive efforts to develop better neutralizing antibodies are ongoing.


The fusogenic protein, gp41 has been extensively studied as a promising target to inhibit membrane fusion between the virus and target cells. At the same time, it is a challenging target because the vulnerable conformations of the protein are exposed only transiently. However, advances in biochemical, biophysical, structural, and immunological studies are coming together to move the field closer to an understanding of gp41 structure and function that will lead to the development of novel drugs and vaccines.,protein%20are%20exposed%20only%20transiently.



Curr Pharm Des. 2004;10(15):1805-25. doi: 10.2174/1381612043384448.

HIV-1 gp41 as a target for viral entry inhibition

Michael J Root 1, H Kirby Steger


The recent success of the fusion inhibitor T-20 (enfuvirtide) in clinical studies has ushered in a new chapter in the development of anti-HIV-1 therapeutics. T-20 is the first FDA-approved drug that targets the viral transmembrane protein gp41. This protein, along with gp120, promotes viral entry through a coordinated cascade of conformational transitions that lead to the fusion of the HIV-1 and target cell membranes. The interaction of gp120 with CD4 and a chemokine receptor stimulates gp41 to extend and bridge the space between the virus and cell. Subsequently, gp41 collapses into a trimer-of-hairpins structure that brings the viral and cellular membranes into close proximity necessary for fusion. Enfuvirtide targets the gp41 amino-terminal region exposed in the transient extended state, blocking the ultimate collapse into the trimer-of hairpins and inhibiting membrane fusion. The vulnerability of this transient extended state has stimulated the development of new agents, ranging from small molecules to large proteins, that bind to gp41 and inhibit its structural transformations. The discovery and characterization of these inhibitors have not only led to new antiviral strategies, but have also shed light on the accessibility of gp41 epitopes that might play a role in HIV-1 vaccine development.



Theochem. 2004 May; 677(1): 73–76.

Structural similarity between HIV-1 gp41 and SARS-CoV S2 proteins suggests an analogous membrane fusion mechanism

Xue Wu Zhang∗ and Yee Leng Yap


SARS-associated coronavirus (SARS-CoV) has been identified as the causal agent of a new emerging disease: severe acute respiratory syndrome (SARS). Its spike protein S2 is responsible for mediating fusion of viral and cellular membrane. In this study, we modeled the 3D structure of S2 subunit and compared this model with the core structure of gp41 from HIV-1. We found that SARS-CoV S2 and gp41 share the same two α helices, suggesting that the two viruses could follow an analogous membrane fusion mechanism. Further ligand-binding analysis showed that two inhibitors GGL and D-peptide from HIV-1 gp41 may serve as inhibitors for SARS-CoV entry.



BMC Microbiol. 2003; 3: 20.

Cloaked similarity between HIV-1 and SARS-CoV suggests an anti-SARS strategy

Yossef Kligercorresponding author1 and Erez Y Levanon1



Severe acute respiratory syndrome (SARS) is a febrile respiratory illness. The disease has been etiologically linked to a novel coronavirus that has been named the SARS-associated coronavirus (SARS-CoV), whose genome was recently sequenced. Since it is a member of the Coronaviridae, its spike protein (S2) is believed to play a central role in viral entry by facilitating fusion between the viral and host cell membranes. The protein responsible for viral-induced membrane fusion of HIV-1 (gp41) differs in length, and has no sequence homology with S2.


Sequence analysis reveals that the two viral proteins share the sequence motifs that construct their active conformation. These include (1) an N-terminal leucine/isoleucine zipper-like sequence, and (2) a C-terminal heptad repeat located upstream of (3) an aromatic residue-rich region juxtaposed to the (4) transmembrane segment.


This study points to a similar mode of action for the two viral proteins, suggesting that anti-viral strategy that targets the viral-induced membrane fusion step can be adopted from HIV-1 to SARS-CoV. Recently the FDA approved Enfuvirtide, a synthetic peptide corresponding to the C-terminal heptad repeat of HIV-1 gp41, as an anti-AIDS agent. Enfuvirtide and C34, another anti HIV-1 peptide, exert their inhibitory activity by binding to a leucine/isoleucine zipper-like sequence in gp41, thus inhibiting a conformational change of gp41 required for its activation. We suggest that peptides corresponding to the C-terminal heptad repeat of the S2 protein may serve as inhibitors for SARS-CoV entry.



J Thorac Dis. 2013 Aug;5 Suppl 2(Suppl 2):S149-59. doi: 10.3978/j.issn.2072-1439.2013.06.14.

Novel hemagglutinin-based influenza virus inhibitors

Xintian Shen 1, Xuanxuan Zhang, Shuwen Liu


Influenza virus has caused seasonal epidemics and worldwide pandemics, which caused tremendous loss of human lives and socioeconomics. Nowadays, only two classes of anti-influenza drugs, M2 ion channel inhibitors and neuraminidase inhibitors respectively, are used for prophylaxis and treatment of influenza virus infection. Unfortunately, influenza virus strains resistant to one or all of those drugs emerge frequently. Hemagglutinin (HA), the glycoprotein in influenza virus envelope, plays a critical role in viral binding, fusion and entry processes. Therefore, HA is a promising target for developing anti-influenza drugs, which block the initial entry step of viral life cycle. Here we reviewed recent understanding of conformational changes of HA in protein folding and fusion processes, and the discovery of HA-based influenza entry inhibitors, which may provide more choices for preventing and controlling potential pandemics caused by multi-resistant influenza viruses.



J Virol. 2014 Feb;88(3):1447-60. doi: 10.1128/JVI.01225-13. Epub 2013 Nov 6.

New small molecule entry inhibitors targeting hemagglutinin-mediated influenza a virus fusion

Arnab Basu 1, Aleksandar Antanasijevic, Minxiu Wang, Bing Li, Debra M Mills, Jessica A Ames, Peter J Nash, John D Williams, Norton P Peet, Donald T Moir, Mark N Prichard, Kathy A Keith, Dale L Barnard, Michael Caffrey, Lijun Rong, Terry L Bowlin


Influenza viruses are a major public health threat worldwide, and options for antiviral therapy are limited by the emergence of drug-resistant virus strains. The influenza virus glycoprotein hemagglutinin (HA) plays critical roles in the early stage of virus infection, including receptor binding and membrane fusion, making it a potential target for the development of anti-influenza drugs. Using pseudotype virus-based high-throughput screens, we have identified several new small molecules capable of inhibiting influenza virus entry. We prioritized two novel inhibitors, MBX2329 and MBX2546, with aminoalkyl phenol ether and sulfonamide scaffolds, respectively, that specifically inhibit HA-mediated viral entry. The two compounds (i) are potent (50% inhibitory concentration [IC50] of 0.3 to 5.9 μM); (ii) are selective (50% cytotoxicity concentration [CC(50)] of >100 μM), with selectivity index (SI) values of >20 to 200 for different influenza virus strains; (iii) inhibit a wide spectrum of influenza A viruses, which includes the 2009 pandemic influenza virus A/H1N1/2009, highly pathogenic avian influenza (HPAI) virus A/H5N1, and oseltamivir-resistant A/H1N1 strains; (iv) exhibit large volumes of synergy with oseltamivir (36 and 331 μM(2) % at 95% confidence); and (v) have chemically tractable structures. Mechanism-of-action studies suggest that both MBX2329 and MBX2546 bind to HA in a nonoverlapping manner. Additional results from HA-mediated hemolysis of chicken red blood cells (cRBCs), competition assays with monoclonal antibody (MAb) C179, and mutational analysis suggest that the compounds bind in the stem region of the HA trimer and inhibit HA-mediated fusion. Therefore, MBX2329 and MBX2546 represent new starting points for chemical optimization and have the potential to provide valuable future therapeutic options and research tools to study the HA-mediated entry process.



Acta Pharmacologica Sinica volume 41, pages1141–1149(2020)Cite this article. Published: 03 August 2020. Review Article.

Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19

Yuan Huang, Chan Yang, Xin-feng Xu, Wei Xu & Shu-wen Liu


Coronavirus disease 2019 is a newly emerging infectious disease currently spreading across the world. It is caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The spike (S) protein of SARS-CoV-2, which plays a key role in the receptor recognition and cell membrane fusion process, is composed of two subunits, S1 and S2. The S1 subunit contains a receptor-binding domain that recognizes and binds to the host receptor angiotensin-converting enzyme 2, while the S2 subunit mediates viral cell membrane fusion by forming a six-helical bundle via the two-heptad repeat domain. In this review, we highlight recent research advance in the structure, function and development of antivirus drugs targeting the S protein.



Cell Discovery volume 6, Article number: 28 (2020)

The anti-influenza virus drug, arbidol is an efficient inhibitor of SARS-CoV-2 in vitro

Xi Wang, Ruiyuan Cao, Huanyu Zhang, Jia Liu, Mingyue Xu, Hengrui Hu, Yufeng Li, Lei Zhao, Wei Li, Xiulian Sun, Xinglou Yang, Zhengli Shi, Fei Deng, Zhihong Hu, Wu Zhong & Manli Wang

Dear editor,

Since December 2019, a novel disease COVID-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) rapidly spread to over 200 countries and infected over 1.50 million people including 92,798 deaths (data as of April 10, 2020). On March 11, the World Health Organization (WHO) characterized COVID-19 as a pandemic, and called for accelerating diagnostics, vaccines, and drugs developments to combat this novel disease. Apart of the new coronavirus, influenza virus infections have been a consistent threat to the global public health over the years. In the United States alone, the Centers for Disease Control and Prevention (CDC) estimates that, so far during the 2019–2020 winter season, there have been at least 39 million illnesses, 400,000 hospitalizations and 24,000 deaths from influenza ( Considering the current concomitant circulation of SARS-CoV-2 and influenza virus infections, the exploration of available and viable anti-influenza drugs to treat both diseases is of great interest.

Actually, in the early stages of the outbreak of COVID-19, some anti-flu drugs (for example, oseltamivir) have been applied for the treatment of COVID-19 patients1,2. Previously, we reported that favipiravir (T705), an anti-influenza drug approved in Japan and China, showed a certain efficacy against SARS-CoV-2 in vitro3. In addition, arbidol, an anti-influenza drug targeting the viral hemagglutinin (HA) is being used in a clinical trial against COVID-19 (ChiCTR2000029573) and has been recently added to the Guidelines for the Diagnosis and Treatment of COVID-19 (sixth and seventh editions) in China. A recent retrospective study suggested that arbidol treatment showed tendency to improve the discharging rate and decrease the mortality rate of COVID-19 patients4. However, to our knowledge, there has been no systematical analysis about the efficacy of anti-influenza drugs against SARS-CoV-2.

In this study, we evaluated six currently available and licensed anti-influenza drugs against SARS-CoV-2. The drugs include arbidol, baloxavir, laninamivir, oseltamivir, peramivir, and zanamivir5,6. The M2 inhibitors (amantadine and rimantadine) were not considered in this study since they were not recommended for treating influenza by WHO due to drug resistance. First, the cytotoxicity of the compounds in African green monkey kidney cells, Vero E6 (ATCC-1586) was measured by a standard cell counting kit-8 (CCK8) assay. Then, the cells were infected with SARS-CoV-2 at a multiplicity of infection (MOI) of 0.05 in the presence of either compound or dimethyl sulfoxide (DMSO) control. The dose–response curves were determined by quantification of viral RNA copy numbers in the supernatant of infected cell at 48 h post infection (p.i.). As demonstrated in Fig. 1a, arbidol efficiently inhibited virus infection in vitro. The 50% maximal effective concentration (EC50) and the 50% cytotoxic concentration (CC50) of arbidol was 4.11 (3.55–4.73) and 31.79 (29.89–33.81) μM, respectively, and the selectivity index (SI = CC50/EC50) was 7.73. Baloxavir partially inhibited SARS-CoV-2 infection (~29%) at a high concentration of 50 μM (Fig. 1a). In contrast, laninamivir, oseltamivir, peramivir, and zanamivir did not exhibit anti-SARS-CoV-2 activity even at the highest drug concentrations (Fig. 1a). The antiviral effect of the compounds was also evaluated by observing cytopathic effects (CPE) and immunofluorescence staining of infected cells. As shown in Supplementary Fig. S1, at 48 h p.i. only in cells treated with arbidol, but not with the other five drugs, viral NP expression and CPE due to SARS-CoV-2 was substantially reduced. To be noted, we also tried some human lung cell lines, for example human embryo lung fibroblasts MRC-5 and lung cancer cell line Calu-3, however, they were not very efficient for SARS-CoV-2 replication, and therefore were not used for this study.

Antiviral activities of the drugs. The antiviral efficacy was evaluated in Vero E6 cells by qRT-PCR analysis of virus yield at 48 h p.i. Data represent the mean ± standard deviation (SD) from two independent repeats. b, c Time-of-addition experiment of arbidol. Three experimental groups (Full-time, Entry, and Post-entry) were set up as described in the Supplementary Methods. At 16 h p.i., virus yield in the cell supernatant was quantified by qRT-PCR (b), and the expression of NP in infected cells was analyzed by western blots (c). The values below the blot represent the relative band intensity (NP/GAPDH) normalized to that of the DMSO group. d Impact of arbidol on SARS-CoV-2 binding. Vero E6 cells were treated with arbidol (10 μM) or DMSO for 1 h prior to infection with SARS-CoV-2 at 4 °C for 1 h. The supernatant (unbound virions) and the cells containing bound virions (bound virions) were collected for quantification of viral RNA copies by qRT-PCR. e, f Effect of arbidol on intracellular trafficking of SARS-CoV-2. The co-localization of virions with EEs or LEs was analyzed by immunofluorescence assays as described in the Supplementary Methods. e The portion of virions that co-localized with EEs or ELs in each group (n > 150 cells) was quantified by Image J. f Representative confocal microscopic images of virions (red) and LAMP1+ ELs (green) in each group. The nuclei (blue) were stained with Hoechst 33258 dye. White arrows: virions co-localized with ELs; bars: 10 μm. For (b) and (e), statistical analysis was performed using a one-way analysis of variance (ANOVA) with GraphPad Prism. For (d), statistical analysis was performed and calculated by unpaired two-tailed t test. *P < 0.05; ***P < 0.001; ns, not significant.

Apart from influenza virus, arbidol was reported to inhibit a wide array of viruses by interfering with multiple steps of the virus replication cycle7. The stage of SARS-CoV-2 replication targeted by arbidol was explored by conducting a preliminary time-of-addition experiment using virus at an MOI of 0.05. Arbidol was incubated with cells during the virus entry process (Entry), the post-entry stages (Post-entry), or the entire process of infection (Full-time) and progeny virus yield was quantified by qRT-PCR. The data revealed that arbidol efficiently blocked both viral entry and post-entry stages. It had a profound impact on virus Entry (~75% inhibition) with a lesser effect on Post-entry events (~55% inhibition rate) (Fig. 1b). In addition, western blot analysis (Fig. 1c) and immunofluorescence microscopy (Supplementary Fig. S2) confirmed that the expression level of viral NP was reduced drastically at Full-time (13% of the DMSO group, Fig. 1c), and showed more inhibitory effect at the Entry stage (41%) than at the Post-entry stage (61%).

The details of how arbidol blocks the entry of SARS-CoV-2 into cells were further investigated. Virus (MOI = 0.05) was allowed to bind to Vero E6 cells at 4 °C for 1 h in the presence of arbidol (10 μM) or DMSO control. Virus particles bound to the cell (bound virions) and those in the supernatant (unbound virions) were analyzed by qRT-PCR. The results showed that arbidol treatment led to a significantly decreased binding efficiency (67%) compared with the control group (P < 0.05) (Fig. 1d). Correspondingly, the portion of unbound virions increased significantly to 156% of the control group after arbidol treatment (P < 0.001) (Fig. 1d).

Next, we analyzed viral intracellular trafficking. As we reported recently, within infected cells, SARS-CoV-2 underwent vesicle transportation, which was first carried out by early endosomes (EEs) then further transported to endolysosomes (ELs)8. Co-localization of virions with EEs or ELs was visualized by immunofluorescence microscopy and statistically analyzed (n > 150 cells). As shown in Fig. 1e and Supplementary Fig. S3, in each tracked time points, there was no significant difference in the amounts of virions co-localized with EEs when comparing the DMSO- and arbidol-treated groups, although as time of infection went on (30, 60, and 90 min p.i.), the levels of co-localization considerably decreased in both DMSO- (24.0%, 5.1%, and 3.2%) and arbidol- (21.4%, 4.1%, and 2.8%) treated groups, suggesting that some virions were already transported from EEs to the next stage of vesicle transportation. By contrast, at 60 min p.i., a slightly higher percentage of virions were transported to ELs in the arbidol-treated group (22.4%) than in the DMSO group (18.3%) (P < 0.05) (Fig. 1e, f). At 90 min p.i., significantly fewer virions (~13.5%) were detected in ELs in the DMSO group; whereas significantly higher proportions of virions (~23.6%) remained within ELs in the arbidol-treated group, suggesting the drug trapped the virus in the ELs (P < 0.001) (Fig. 1e, f). Taken together, these results suggested that arbidol impeded not only viral attachment, but also release of SARS-CoV-2 from intracellular vesicles (ELs).

Among the drugs tested, laninamivir, oseltamivir, peramivir, and zanamivir are neuraminidase (NA) inhibitors, which are most widely prescribed for prophylaxis and treatment of influenza. Although no NA analog exists in SARS-CoV-2, NA inhibitors such as oseltamivir nevertheless are being used clinically in treating COVID-19 patients1,2. Our data showed these NA inhibitors were not active against SARS-CoV-2 (Fig. 1a), which is consistent with the finding that oseltamivir and zanamivir were ineffective in inhibiting SARS-CoV9. Baloxavir marboxil is a new anti-influenza drug, which selectively inhibits the endonuclease activity of the viral polymerase responsible for snatching capped primers from host mRNAs to initiate viral mRNA transcription. However, this “cap-snatching” mechanism of the endonuclease is not shared by coronaviruses that encode their own enzymes to form 5ʹ-mRNA cap structures10. This may explain why baloxavir failed to block SARS-CoV-2 infection (Fig. 1a). During the review process of this study, Choy et al. also showed that oseltamivir and baloxavir failed to inhibit SARS-CoV-2 in vitro11.


Arbidol, an indole-derivative, has been licensed for decades in Russia and China against influenza. It is a broad-spectrum drug against a wide range of enveloped and non-enveloped viruses. Arbidol interacts preferentially with aromatic amino acids, and it affects multiple stages of the virus life cycle, either by direct targeting viral proteins or virus-associated host factors7. For example, in influenza virus, crystal structures showed that arbidol inserted into a hydrophobic pocket of the fusion subunit of HA, thus hindering low-pH conformational change of HA and blocking the fusion process12. In hepatitis C virus, arbidol impaired both virus attachment and intracellular vesicle trafficking13. Likewise, we found arbidol plays a role in interfering SAS-CoV-2 binding (Fig. 1d) and intracellular vesicle trafficking (Fig. 1e, f). Arbidol can also bind to lipid membranes and may alter membrane configuration of the cytoplasm or the endosome, which are crucial for viral attachment and fusion7. It could be further investigated whether arbidol targets virus or/and cells by using published method14.

In summary, among the six anti-influenza drugs, only arbidol efficiently inhibited SARS-CoV-2 infection. Functionally, it appears to block virus entry by impeding viral attachment and release from the ELs. Although the SI of arbidol is relatively low (SI = 7.73), as a repurposed drug, its pharmacokinetics profile such as maximal concentration (Cmax) is more important for predicting efficacy. It is generally believed that if the Cmax achieves EC90, the drug is very likely to be effective; while if the Cmax achieves EC50, the drug is possibly effective in vivo. In humans, a single oral administration of 800 mg of arbidol results in Cmax of ~4.1 μM15, and this dosage is efficacious and safe against different influenza viruses with EC50 values ranging from 2.5–20 μM7,16. Arbidol also showed anti-inflammatory activity, which may enhance its efficacy in vivo16. Considering the EC50 (4.11 μM) of arbidol against SARS-CoV-2 is comparable to, or even lower than those of influenza viruses, we, therefore, suggest that arbidol is potentially effective to treat COVID-19 patients. However, the current dose of arbidol (200 mg, 3 times/day) recommended by the Chinese Guidelines may not be able to achieve an ideal therapeutic efficacy to inhibit SARS-CoV-2 infection, and should be elevated. This needs to be verified by clinical trials.



Clinical Epidemiology and Global Health. Volume 9, January–March 2021, Pages 90-98

Antivirals for COVID-19: A critical review

Andri Frediansyah, Ruchi Tiwari, Khan Sharun, Kuldeep Dhama, Harapan Harapan


No specific drugs have been approved for coronavirus disease 2019 (COVID-19) to date as the development of antivirals usually requires time. Therefore, assessment and use of currently available antiviral drugs is critical for a timely response to the current pandemic. Here, we have reviewed anti-SARS-CoV-2 potencies of available antiviral drug groups such as fusion inhibitors, protease inhibitors, neuraminidase inhibitors, and M2 ion-channel protein blockers. Although clinical trials to assess the efficacy of these antivirals are ongoing, this review highlights important information including docking and modeling analyses, in vitro studies, as well as results from clinical uses of these antivirals against COVID-19 pandemic.



Life Sci. 2020 May 1; 248: 117477.

Anti-HCV, nucleotide inhibitors, repurposing against COVID-19

Abdo A. Elfiky⁎



A newly emerged Human Coronavirus (HCoV) is reported two months ago in Wuhan, China (COVID-19). Until today >2700 deaths from the 80,000 confirmed cases reported mainly in China and 40 other countries. Human to human transmission is confirmed for COVID-19 by China a month ago. Based on the World Health Organization (WHO) reports, SARS HCoV is responsible for >8000 cases with confirmed 774 deaths. Additionally, MERS HCoV is responsible for 858 deaths out of about 2500 reported cases. The current study aims to test anti-HCV drugs against COVID-19 RNA dependent RNA polymerase (RdRp).

Materials and methods

In this study, sequence analysis, modeling, and docking are used to build a model for Wuhan COVID-19 RdRp. Additionally, the newly emerged Wuhan HCoV RdRp model is targeted by anti-polymerase drugs, including the approved drugs Sofosbuvir and Ribavirin.

Key findings

The results suggest the effectiveness of Sofosbuvir, IDX-184, Ribavirin, and Remidisvir as potent drugs against the newly emerged HCoV disease.


The present study presents a perfect model for COVID-19 RdRp enabling its testing in silico against anti-polymerase drugs. Besides, the study presents some drugs that previously proved its efficiency against the newly emerged viral infection.



This article is a preprint.  doi:

Discovery of SARS-CoV-2 antiviral synergy between remdesivir and approved drugs in human lung cells

Xammy Nguyenla, Eddie Wehri, Erik Van Dis, Scott B. Biering, Livia H. Yamashiro, Julien Stroumza, Claire Dugast-Darzacq, Thomas Graham, Sarah Stanley, Julia Schaletzky


The SARS coronavirus 2 (SARS-CoV-2) has caused an ongoing global pandemic with currently 29 million confirmed cases and close to a million deaths. At this time, there are no FDA-approved vaccines or therapeutics for COVID-19, but Emergency Use Authorization has been granted for remdesivir, a broad-spectrum antiviral nucleoside analog. However, remdesivir is only moderately efficacious against SARS-CoV-2 in the clinic, and improved treatment strategies are urgently needed. To accomplish this goal, we devised a strategy to identify compounds that act synergistically with remdesivir in preventing SARS-CoV-2 replication. We conducted combinatorial high-throughput screening in the presence of submaximal remdesivir concentrations, using a human lung epithelial cell line infected with a clinical isolate of SARS-CoV-2. We identified 20 approved drugs that act synergistically with remdesivir, many with favorable pharmacokinetic and safety profiles. Strongest effects were observed with established antivirals, Hepatitis C virus nonstructural protein 5 A (HCV NS5A) inhibitors velpatasvir and elbasvir. Combination with their partner drugs sofosbuvir and grazoprevir further increased efficacy, increasing remdesivir’s apparent potency 25-fold. We therefore suggest that the FDA-approved Hepatitis C therapeutics Epclusa (velpatasvir/sofosbuvir) and Zepatier (elbasvir/grazoprevir) should be fast-tracked for clinical evaluation in combination with remdesivir to improve treatment of acute SARS-CoV-2 infections.



Preprint from bioRxiv, 16 Jun 2020. DOI: 10.1101/2020.06.15.153411 PPR: PPR176779

The in vitro antiviral activity of the anti-hepatitis C virus (HCV) drugs daclatasvir and sofosbuvir against SARS-CoV-2

Sacramento CQ, Fintelman-Rodrigues N, Temerozo JR, de Paula Dias Da Silva A, da Silva Gomes Dias S, dos Santos da Silva C, Ferreira AC, Mattos M, Pão CRR, de Freitas CS, Soares VC, Hoelz LVB, Fernandes TVA, Branco FSC, Bastos MM, Boechat N, Saraiva FB, Ferreira MA, Rajoli RKR, Pedrosa CSG … Souza TML


Current approaches of drugs repurposing against 2019 coronavirus disease (COVID-19) have not proven overwhelmingly successful and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic continues to cause major global mortality. Daclatasvir (DCV) and sofosbuvir (SFV) are clinically approved against hepatitis C virus (HCV), with satisfactory safety profile. DCV and SFV target the HCV enzymes NS5A and NS5B, respectively. NS5A is endowed with pleotropic activities, which overlap with several proteins from SARS-CoV-2. HCV NS5B and SARS-CoV-2 nsp12 are RNA polymerases that share homology in the nucleotide uptake channel. We thus tested whether SARS-COV-2 would be susceptible these anti-HCV drugs. DCV consistently inhibited the production of infectious SARS-CoV-2 in Vero cells, in the hepatoma cell line (HuH-7) and in type II pneumocytes (Calu-3), with potencies of 0.8, 0.6 and 1.1 μM, respectively. Although less potent than DCV, SFV and its nucleoside metabolite inhibited replication in Calu-3 cells. Moreover, SFV/DCV combination (1:0.15 ratio) inhibited SARS-CoV-2 with EC 50 of 0.7:0.1 μM in Calu-3 cells. SFV and DCV prevented virus-induced neuronal apoptosis and release of cytokine storm-related inflammatory mediators, respectively. Both drugs inhibited independent events during RNA synthesis and this was particularly the case for DCV, which also targeted secondary RNA structures in the SARS-CoV-2 genome. Concentrations required for partial DCV in vitro activity are achieved in plasma at Cmax after administration of the approved dose to humans. Doses higher than those approved may ultimately be required, but these data provide a basis to further explore these agents as COVID-19 antiviral candidates.