Virtual Screening of Potential Drug Molecules Against Covid-19 Targets: A Drug Repurposing Approach

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shattered normal life across the world. This deadly virus displays many variants and has claimed many lives in various countries. Spike protein plays a major role in the transmission and infectivity of this virus. The scientific community is trying hard to reign this virus and save human lives. In this effort, drug repurposing has emerged as a reliable tool to screen FDA-approved drugs. In the present study, we did a virtual screening of 265 FDA-approved drugs against two important covid-19 targets (Non-structural protein & main protease) with PDB IDs 6W4H, 6LU7, and 6W63. A comparative analysis of the best drugs based on docking score, binding energy, and effective hits was done against both targets. Out of 265 molecules, the best 7 molecules showed reliable hits against both targets. Best seven drugs namely Saquinavir, Indinavir, Tenofovir Alafenamide, Ritonavir, Nelfinavir mesylate, Cefiderocol and Plazomicin. Our results suggest that these ligands, in combination or individually, can be taken as novel prospects for developing a drug against SARS CoV-2.

The FDA-Approved Drug Nelfinavir Inhibits Lytic Cell-Free but Not Cell-Associated Nonlytic Transmission of Human Adenovirus

ABSTRACT Adenoviruses (AdVs) are prevalent and give rise to chronic and recurrent disease. Human AdV (HAdV) species B and C, such as HAdV-C2, -C5, and -B14, cause respiratory disease and constitute a health threat for immunocompromised individuals. HAdV-Cs are well known for lysing cells owing to the E3 CR1-β-encoded adenovirus death protein (ADP). We previously reported a high-throughput image-based screening framework and identified an inhibitor of HAdV-C2 multiround infection, nelfinavir mesylate. Nelfinavir is the active ingredient of Viracept, an FDA-approved inhibitor of human immunodeficiency virus (HIV) aspartyl protease that is used to treat AIDS. It is not effective against single-round HAdV infections. Here, we show that nelfinavir inhibits lytic cell-free transmission of HAdV, indicated by the suppression of comet-shaped infection foci in cell culture. Comet-shaped foci occur upon convection-based transmission of cell-free viral particles from an infected cell to neighboring uninfected cells. HAdV lacking ADP was insensitive to nelfinavir but gave rise to comet-shaped foci, indicating that ADP enhances but is not required for cell lysis. This was supported by the notion that HAdV-B14 and -B14p1 lacking ADP were highly sensitive to nelfinavir, although HAdV-A31, -B3, -B7, -B11, -B16, -B21, -D8, -D30, and -D37 were less sensitive. Conspicuously, nelfinavir uncovered slow-growing round HAdV-C2 foci, independent of neutralizing antibodies in the medium, indicative of nonlytic cell-to-cell transmission. Our study demonstrates the repurposing potential of nelfinavir with postexposure efficacy against different HAdVs and describes an alternative nonlytic cell-to-cell transmission mode of HAdV.

The FDA-approved drug Nelfinavir inhibits lytic cell-free transmission of human adenoviruses

Adenoviruses (AdVs) are prevalent and give rise to chronic and recurrent disease. The human AdV (HAdV) species B and C, such as HAdV-C2, C5 and B14, cause respiratory disease, and constitute a health threat for immuno-compromised individuals. HAdV-Cs are well known for lysing cells, owing to the E3 CR1-β-encoded adenovirus death protein (ADP). We previously reported a high-throughput image-based screening framework and identified an inhibitor of HAdV-C2 multi-round infection, Nelfinavir Mesylate. Nelfinavir is the active ingredient of Viracept, an FDA-approved inhibitor of the human immuno-deficiency virus (HIV) aspartyl protease, and used to treat acquired immunodeficiency syndrome (AIDS). It is not effective against single round HAdV infections. Here, we show that Nelfinavir inhibits the lytic cell-free transmission of HAdV, indicated by the suppression of comet-shaped infection foci in cell culture. Comet-shaped foci occur upon convection-based transmission of cell-free viral particles from an infected cell to neighbouring uninfected cells. HAdV lacking ADP was insensitive to Nelfinavir, but gave rise to comet-shaped foci indicating that ADP enhances but is not required for cell lysis. This was supported by the notion that HAdV-B14 and B14p1 lacking ADP were highly sensitive to Nelfinavir, although HAdV-A31, B3, B7, B11, B16, B21, D8, D30 or D37 were less sensitive. Conspicuously, Nelfinavir uncovered slow-growing round-shaped HAdV-C2 foci, independent of neutralizing antibodies in the medium, indicative of non-lytic cell-to-cell transmission. Our study demonstrates the repurposing potential of Nelfinavir with post-exposure efficacy against different HAdVs, and describes an alternative non-lytic cell-to-cell transmission mode of HAdV.Graphical AbstractFigure 1.

The anti-HIV Drug Nelfinavir Mesylate (Viracept) is a Potent Inhibitor of Cell Fusion Caused by the SARS-CoV-2 Spike (S) Glycoprotein Warranting further Evaluation as an Antiviral against COVID-19 infections

Coronaviruses belong to a group of enveloped, positive-single stranded RNA viruses that are known to cause severe respiratory distress in animals and humans. The current SARS coronavirus-2 (SARS CoV-2) pandemic has caused more than 2,000,000 infections globally and nearly 200,000 deaths. Coronaviruses enter susceptible cells via fusion of the viral envelope with the plasma membrane and/or via fusion of the viral envelope with endosomal membranes after endocytosis of the virus into endosomes. Previous results with SARS and MERS CoV have shown that the Spike (S) glycoprotein is a major determinant of virus infectivity and immunogenicity. Herein, we show that expression of SARS CoV-2 S (S-n) glycoprotein after transient transfection of African green monkey kidney (Vero) cells caused extensive cell fusion in comparison to limited cell fusion caused by the SARS S (S-o) glycoprotein. S-n expression was detected intracellularly and on transfected Vero cell surfaces and caused the formation of very large multinucleated cells (syncytia) by 48 hours post transfection. These results are in agreement with published pathology observations of extensive syncytial formation in lung tissues of COVID-19 patients. This differential S-n versus S-o-mediated cell fusion suggests that SARS-CoV-2 is able to spread from cell-to-cell much more efficiently than SARS effectively avoiding extracellular spaces and neutralizing antibodies. A systematic screening of several drugs for ability to inhibit S-n and S-o cell fusion revealed that the FDA approved HIV-protease inhibitor, nelfinavir mesylate (Viracept) drastically inhibited S-n and S-o-mediated cell fusion in a dose-dependent manner. Complete inhibition of cell fusion was observed at a 10 micromolar concentration. Computational modeling and in silico docking experiments suggested the possibility that nelfinavir may bind inside the S trimer structure, proximal to the S2 amino terminus directly inhibiting S-n and S-o-mediated membrane fusion. Also, it is possible that nelfinavir mesylate acts on cellular processes to inhibit S proteolytic processing. These results warrant further investigations of the potential of nelfinavir mesylate as an antiviral drug, especially at early times after SARS-CoV-2 symptoms appear.

Nelfinavir Is Active Against SARS-CoV-2 in Vero E6 Cells

Utilizing an integrative computational drug discovery approach, we predicted that nelfinavir is a potential inhibitor of SARS-CoV-2 main protease. Further docking nelfinavir to 30 potential target proteins of COVID-19, we found that nelfinavir is most probably a multi-target agent. The half-maximal effective concentration (EC₅₀) of nelfinavir mesylate against SARS-CoV-2 was 2.89±0.65 μM while that of remdesivir was 1.00±0.34 μM, both drugs showed similar dose-response curves. Based on its high potency against SARS-CoV-2 at cellular level, its higher exposure in lung than in plasma, its good safe profile and its potential to reduce inflammation, nelfinavir deserves further exploration for the treatment of COVID-19.

Nelfinavir Is Active Against SARS-CoV-2 in Vero E6 Cells

Utilizing an integrative computational drug discovery approach, we predicted that nelfinavir is a potential inhibitor of SARS-CoV-2 main protease. Further docking nelfinavir to 30 potential target proteins of COVID-19, we found that nelfinavir is most probably a multi-target agent. The half-maximal effective concentration (EC₅₀) of nelfinavir mesylate against SARS-CoV-2 was 2.89±0.65 μM while that of remdesivir was 1.00±0.34 μM, both drugs showed similar dose-response curves. Based on its high potency against SARS-CoV-2 at cellular level, its higher exposure in lung than in plasma, its good safe profile and its potential to reduce inflammation, nelfinavir deserves further exploration for the treatment of COVID-19.