Lipid Lowering Natural Products Targeting hPCSK9 May Prevent the Severity of COVID-19 Infection

Background: The deadly outbreak of COVID-19 disease caused by novel SARS CoV2 has created an unprecedented global health crisis affecting every sectors of human life and enor-mous damage to world's economy. With >16.1 million infections and >650,000 deaths worldwide as of July 27, 2020, there is no treatment for this disease neither is there any available vaccine. Seri-ous research efforts are ongoing on all fronts including treatment, prevention and diagnosis to combat the spread of this infection. A number of targets that include both viral and host proteins have been identified and became part of intense investigation. In this respect the viral surface spike (S) glycoprotein caught the attention most. It is cleaved by multiple host proteases to allow recognition by host receptor human Angiotensin Converting Enzyme2 (hACE2) leading to fusion and viral re-plication. Natural products, small compounds, antioxidants, peptides, proteins, oligonucleotides, antibodies and other compounds are under investigation for development of antiviral agents against COVID-19. Objective(s): Recently cholesterol lowering phytocompounds Quercetin, Swertiamarin and Berberine which promote human Low Density Lipoprotein Receptor (hLDLR) via inhibition of human Pro-protein Convertase Subtilisin Kexin9 (hPCSK9) have been shown to block viral infections caused by ebola, influenza, Respiratory Syncytial Virus (RSV), Hepatitis C virus (HCV) and other RNA type viruses. Since SARS CoV2 is a RNA virus with similar genetic structure and infection machin-ery, it is hypothesised that these phytocompounds may also exhibit antiviral property against COVID-19. Method(s): Our above concept is based on recently published studies as well as our herein presented in silico modeling and computational data which suggested strong interactions of hPCSK9 with above phytocompounds and most importantly with hACE2 following its complexation with receptor binding domain (RBD) of SARS CoV2 S protein. Result(s): These results and a proposed schematic model showing association of hPCSK9 with SARS CoV2 infection are presented in this manuscript. It is proposed that hPCSK9 plays the role of a co-receptor in binding with hACE2:RBD complex and thereby facilitates viral fusion. Conclusion(s): Our studies suggest that PCSK9 inhibitors may provide beneficial effect against COVID-19 infection by retarding viral fusion through displacement of bound hPCSK9 from its complex with ACE2:RBD of SARS CoV2 S protein.Copyright © 2021 Bentham Science Publishers.

Evaluation of the interaction between SARS-CoV-2 spike glycoproteins and the molecularly imprinted polypyrrole

The SARS-CoV-2 spike glycoprotein (SARS-CoV-2-S) was used as a template molecule and polypyrrole (Ppy) was applied as an electro-generated conducting polymer, which was acting as a matrix for the formation of molecular imprints. Two types of Ppy-layers: molecularly imprinted polypyrrole (MIP-Ppy) and non-imprinted polypyrrole (NIP-Ppy) were electrochemically deposited on the working platinum electrode. The performance of electrodes modified by MIP-Ppy and NIP-Ppy layers was evaluated by pulsed amperometric detection (PAD). During the assessment of measurement results registered by PAD, the integrated Cottrell equation (Anson plot) was used to calculate the amount of charge passed through the MIP-Ppy and NIP-Ppy layers. The interaction between SARS-CoV-2 spike glycoproteins and molecularly imprinted polypyrrole (MIP-Ppy) was assessed by the Anson plot based calculations. This assessment reveals that SARS-CoV-2-S glycoproteins are interacting with MIP-Ppy more strongly than with NIP-Ppy. [Display omitted] • The SARS-CoV-2 spike glycoprotein (SARS-CoV-2-S) was molecularly imprinted within polypyrrole (Ppy). • Molecularly imprinted polypyrrole (MIP-Ppy) and non-imprinted polypyrrole (NIP-Ppy) were electro-deposited on Pt electrode. • Performance of electrodes modified by MIP-Ppy and NIP-Ppy was evaluated by pulsed amperometric detection (PAD). • Cottrell equation (Anson plot) was applied for the calculation of passed charge. • Interaction between SARS-CoV-2 protein and MIP-Ppy and NIP-Ppy was evaluated using Anson plot. [ FROM AUTHOR]

Evaluation of the interaction between SARS-CoV-2 spike glycoproteins and the molecularly imprinted polypyrrole

The SARS-CoV-2 spike glycoprotein (SARS-CoV-2-S) was used as a template molecule and polypyrrole (Ppy) was applied as an electro-generated conducting polymer, which was acting as a matrix for the formation of molecular imprints. Two types of Ppy-layers: molecularly imprinted polypyrrole (MIP-Ppy) and non-imprinted polypyrrole (NIP-Ppy) were electrochemically deposited on the working platinum electrode. The performance of electrodes modified by MIP-Ppy and NIP-Ppy layers was evaluated by pulsed amperometric detection (PAD). During the assessment of measurement results registered by PAD, the integrated Cottrell equation (Anson plot) was used to calculate the amount of charge passed through the MIP-Ppy and NIP-Ppy layers. The interaction between SARS-CoV-2 spike glycoproteins and molecularly imprinted polypyrrole (MIP-Ppy) was assessed by the Anson plot based calculations. This assessment reveals that SARS-CoV-2-S glycoproteins are interacting with MIP-Ppy more strongly than with NIP-Ppy.

A potent virucidal activity of functionalized TiO2 nanoparticles adsorbed with flavonoids against SARS-CoV-2.

The coronavirus SARS-CoV-2 has caused a pandemic with > 550 millions of cases and > 6 millions of deaths worldwide. Medical management of COVID-19 relies on supportive care as no specific targeted therapies are available yet. Given its devastating effects on the economy and mental health, it is imperative to develop novel antivirals. An ideal candidate will be an agent that blocks the early events of viral attachment and cell entry, thereby preventing viral infection and spread. This work reports functionalized titanium dioxide (TiO2)-based nanoparticles adsorbed with flavonoids that block SARS-CoV-2 entry and fusion. Using molecular docking analysis, two flavonoids were chosen for their specific binding to critical regions of the SARS-CoV-2 spike glycoprotein that interacts with the host cell angiotensin-converting enzyme-2 (ACE-2) receptor. These flavonoids were adsorbed onto TiO2 functionalized nanoparticles (FTNP). This new nanoparticulate compound was assayed in vitro against two different coronaviruses; HCoV 229E and SARS-CoV-2, in both cases a clear antiviral effect was observed. Furthermore, using a reporter-based cell culture model, a potent antiviral activity is demonstrated. The adsorption of flavonoids to functionalized TiO2 nanoparticles induces a ~ threefold increase of that activity. These studies also indicate that FTNP interferes with the SARS-CoV-2 spike, impairing the cell fusion mechanism. KEY POINTS/HIGHLIGHTS: • Unique TiO2 nanoparticles displaying flavonoid showed potent anti-SARS-CoV-2 activity. • The nanoparticles precisely targeting SARS-CoV-2 were quantitatively verified by cell infectivity in vitro. • Flavonoids on nanoparticles impair the interactions between the spike glycoprotein and ACE-2 receptor.

Accurate prediction of virus-host protein-protein interactions via a Siamese neural network using deep protein sequence embeddings.

Prediction and understanding of virus-host protein-protein interactions (PPIs) have relevance for the development of novel therapeutic interventions. In addition, virus-like particles open novel opportunities to deliver therapeutics to targeted cell types and tissues. Given our incomplete knowledge of PPIs on the one hand and the cost and time associated with experimental procedures on the other, we here propose a deep learning approach to predict virus-host PPIs. Our method (Siamese Tailored deep sequence Embedding of Proteins [STEP]) is based on recent deep protein sequence embedding techniques, which we integrate into a Siamese neural network. After showing the state-of-the-art performance of STEP on external datasets, we apply it to two use cases, severe acute respiratory syndrome coronavirus 2 and John Cunningham polyomavirus, to predict virus-host PPIs. Altogether our work highlights the potential of deep sequence embedding techniques originating from the field of NLP as well as explainable artificial intelligence methods for the analysis of biological sequences.

The STING Ligand and Delivery System Synergistically Enhance the Immunogenicity of an Intranasal Spike SARS-CoV-2 Vaccine Candidate.

The respiratory organ serves as a primary target site for SARS-CoV-2. Thus, the vaccine-stimulating immune response of the respiratory tract is significant in controlling SARS-CoV-2 transmission and disease development. In this study, mucoadhesive nanoparticles were used to deliver SARS-CoV-2 spike proteins (S-NPs) into the nasal tracts of mice. The responses in the respiratory organ and the systemic responses were monitored. The administration of S-NPs along with cGAMP conferred a robust stimulation of antibody responses in the respiratory tract, as demonstrated by an increase of IgA and IgG antibodies toward the spike proteins in bronchoalveolar lavages (BALs) and the lungs. Interestingly, the elicited antibodies were able to neutralize both the wild-type and Delta variant strains of SARS-CoV-2. Significantly, the intranasal immunization also stimulated systemic responses. This is evidenced by the increased production of circulating IgG and IgA, which were able to neutralize and bind specifically to the SARS-CoV-2 virion and spike protein. Additionally, this intranasal administration potently activated a splenic T cell response and the production of Th-1 cytokines, suggesting that this vaccine may well activate a cellular response in the respiratory tract. The results demonstrate that STING agonist strongly acts as an adjuvant to the immunogenicity of S-NPs. This platform may be an ideal vaccine against SARS-CoV-2.

Molecularly imprinted polypyrrole based sensor for the detection of SARS-CoV-2 spike glycoprotein.

This study describes the application of a polypyrrole-based sensor for the determination of SARS-CoV-2-S spike glycoprotein. The SARS-CoV-2-S spike glycoprotein is a spike protein of the coronavirus SARS-CoV-2 that recently caused the worldwide spread of COVID-19 disease. This study is dedicated to the development of an electrochemical determination method based on the application of molecularly imprinted polymer technology. The electrochemical sensor was designed by molecular imprinting of polypyrrole (Ppy) with SARS-CoV-2-S spike glycoprotein (MIP-Ppy). The electrochemical sensors with MIP-Ppy and with polypyrrole without imprints (NIP-Ppy) layers were electrochemically deposited on a platinum electrode surface by a sequence of potential pulses. The performance of polymer layers was evaluated by pulsed amperometric detection. According to the obtained results, a sensor based on MIP-Ppy is more sensitive to the SARS-CoV-2-S spike glycoprotein than a sensor based on NIP-Ppy. Also, the results demonstrate that the MIP-Ppy layer is more selectively interacting with SARS-CoV-2-S glycoprotein than with bovine serum albumin. This proves that molecularly imprinted MIP-Ppy-based sensors can be applied for the detection of SARS-CoV-2 virus proteins.

Plant-based vaccines: Potentiality against severe acute respiratory syndrome coronavirus 2

The pandemic of novel coronavirus disease-19 caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has stimulated scientists from different backgrounds to gear up on developing vaccines against the virus. Several antigenic epitopes of the virus have the potential to induce an immunogenic response, among which viral spike protein ("S" protein) is considered to be the most suitable vaccine candidate. In this review, the latest progress in the field of plant molecular pharming (PMF), its application, limitations, and commercial initiatives toward the production of the SARS-CoV-2 vaccine have been discussed. Vaccine production by PMF has gained considerable attention these days and can be used for large-scale commercial production of antigenic proteins, antibodies, and other biopharmaceuticals. New age plant breeding techniques facilitated by CRISPR-Cas-based genome editing technology and next-generation sequencing methods also help to achieve greater precision and rapidity. Several unique advantages are offered by plant-based vaccine production techniques over that of the microbial or mammalian cell culture system. Virus-like particles and Agrobacterium-mediated transient somatic expression systems have a high potential for the large scale, cost-effective, and robust production of plant-derived vaccines against SARS-CoV-2.

Peritoneal Administration of a Subunit Vaccine Encapsulated in a Nanodelivery System Not Only Augments Systemic Responses against SARS-CoV-2 but Also Stimulates Responses in the Respiratory Tract.

The COVID-19 pandemic has currently created an unprecedented threat to human society and global health. A rapid mass vaccination to create herd immunity against SARS-CoV-2 is a crucial measure to ease the spread of this disease. Here, we investigated the immunogenicity of a SARS-CoV-2 subunit vaccine candidate, a SARS-CoV-2 spike glycoprotein encapsulated in N,N,N-trimethyl chitosan particles or S-TMC NPs. Upon intraperitoneal immunization, S-TMC NP-immunized mice elicited a stronger systemic antibody response, with neutralizing capacity against SARS-CoV-2, than mice receiving the soluble form of S-glycoprotein. S-TMC NPs were able to stimulate the circulating IgG and IgA as found in SARS-CoV-2-infected patients. In addition, spike-specific T cell responses were drastically activated in S-TMC NP-immunized mice. Surprisingly, administration of S-TMC NPs via the intraperitoneal route also stimulated SARS-CoV-2-specific immune responses in the respiratory tract, which were demonstrated by the presence of high levels of SARS-CoV-2-specific IgG and IgA in the lung homogenates and bronchoalveolar lavages of the immunized mice. We found that peritoneal immunization with spike nanospheres stimulates both systemic and respiratory mucosal immunity.

Simultaneous Detection of SARS-CoV-2 IgG/IgM Antibodies, Using Gold Nanoparticles-Based Lateral Flow Immunoassay.

The novel coronavirus disease (COVID-19), known as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), exhibits a strong human-to-human transmission infectivity and could cause acute respiratory infections. Therefore, simple and rapid serological testing is urgently needed to recognize positive cases. In this study, a point-of-care serological test based on lateral flow immunoassay (LFIA) was developed and its application for the simultaneous detection of IgM/IgG antibodies against SARS-CoV-2 was evaluated. The recombinant SARS-CoV-2 antigens were conjugated to the produced colloidal gold nanoparticles and used as the detection reagent. This test required only 10-15 minutes to achieve simultaneous qualitative detection of IgM/IgG antibodies specific to SARS-CoV-2 in 20 µL of serum or plasma samples. The clinical performance and reliability of the assay were evaluated by performing the test with 60 samples and comparing the results of these tests with those obtained via real-time polymerase chain reaction. The sensitivity and specificity of our assay were defined to be 90% and 96.6%, respectively. The presented LFIA was sufficiently sensitive and accurate to be used for the rapid diagnosis of coronavirus disease 2019 in laboratories or in patient care settings, particularly in emergency conditions, in which many samples require to be evaluated on time.

De novo design, retrosynthetic analysis and combinatorial synthesis of a hybrid antiviral (VTAR-01) to inhibit the interaction of SARS-CoV2 spike glycoprotein with human angiotensin-converting enzyme 2.

SARS-like coronavirus (SARS-CoV2) has emerged as a global threat to humankind and is rapidly spreading. The infectivity, pathogenesis and infection of this virus are dependent on the interaction of SARS-CoV2 spike protein with human angiotensin converting enzyme 2 (hACE2). Spike protein contains a receptor-binding domain (RBD) that recognizes hACE-2. In the present study, we are reporting a de novo designed novel hybrid antiviral 'VTAR-01' molecule that binds at the interface of RBD-hACE2 interaction. A series of antiviral molecules were tested for binding at the interface of RBD-hACE2 interaction. In silico screening, molecular mechanics and molecular dynamics simulation (MDS) analysis suggest ribavirin, ascorbate, lopinavir and hydroxychloroquine have strong interaction at the RBD-hACE2 interface. These four molecules were used for de novo fragment-based antiviral design. De novo designing, docking and MDS analysis identified a 'VTAR' hybrid molecule that has better interaction with this interface than all of the antivirals used to design it. We have further used retrosynthetic analysis and combinatorial synthesis to design 100 variants of VTAR molecules. Retrosynthetic analysis and combinatorial synthesis, along with docking and MDS, identified that VTAR-01 interacts with the interface of the RBD-ACE2 complex. MDS analysis confirmed its interaction with the RBD-ACE2 interface by involving Glu35 and Lys353 of ACE2, as well as Gln493 and Ser494 of RBD. Interaction of spike protein with ACE2 is essential for pathogenesis and infection of this virus; hence, this in silico designed hybrid antiviral molecule (VTAR-01) that binds at the interface of RBD-hACE2 may be further developed to control the infection of SARS-CoV2.

Induction of Exaggerated Cytokine Production in Human Peripheral Blood Mononuclear Cells by a Recombinant SARS-CoV-2 Spike Glycoprotein S1 and Its Inhibition by Dexamethasone.

An understanding of the pathological inflammatory mechanisms involved in SARS-CoV-2 virus infection is necessary in order to discover new molecular pharmacological targets for SARS-CoV-2 cytokine storm. In this study, the effects of a recombinant SARS-CoV-2 spike glycoprotein S1 was investigated in human peripheral blood mononuclear cells (PBMCs). Stimulation of PBMCs with spike glycoprotein S1 (100 ng/mL) resulted in significant elevation in the production of TNFα, IL-6, IL-1ß and IL-8. However, pre-treatment with dexamethasone (100 nM) caused significant reduction in the release of these cytokines. Further experiments revealed that S1 stimulation of PBMCs increased phosphorylation of NF-κB p65 and IκBα, and IκBα degradation. DNA binding of NF-κB p65 was also significantly increased following stimulation with spike glycoprotein S1. Treatment of PBMCs with dexamethasone (100 nM) or BAY11-7082 (1 µM) resulted in inhibition of spike glycoprotein S1-induced NF-κB activation. Activation of p38 MAPK by S1 was blocked in the presence of dexamethasone and SKF 86002. CRID3, but not dexamethasone pre-treatment, produced significant inhibition of S1-induced activation of NLRP3/caspase-1. Further experiments revealed that S1-induced increase in the production of TNFα, IL-6, IL-1ß and IL-8 was reduced in the presence of BAY11-7082 and SKF 86002, while CRID3 pre-treatment resulted in the reduction of IL-1ß production. These results suggest that SARS-CoV-2 spike glycoprotein S1 stimulated PBMCs to release pro-inflammatory cytokines through mechanisms involving activation of NF-κB, p38 MAPK and NLRP3 inflammasome. It is proposed that the clinical benefits of dexamethasone in COVID-19 are possibly due to its anti-inflammatory activity in reducing SARS-CoV-2 cytokine storm.

The screening and evaluation of potential clinically significant HIV drug combinations against the SARS-CoV-2 virus.

Spike glycoprotein is essential for the reproduction of the SARS-CoV-2 virus, and its inhibition using already approved antiviral drugs may open new avenues for treatment of patients with the COVID-19 disease. Because of that we analyzed the inhibition of SARS-CoV-2 spike glycoprotein with FDA-approved antiviral drugs and their double and triple combinations. We used the VINI in silico model of cancer to perform this virtual drug screening, showing HIV drugs to be the most effective. Besides, the combination of cobicistat-abacavir-rilpivirine HIV drugs demonstrated the highest in silico efficacy of inhibiting SARS-CoV-2 spike glycoprotein. Therefore, a clinical trial of cobicistat-abacavir-rilpivirine on a limited number of COVID-19 patients in moderately severe and severe condition is warranted.

Comparative molecular docking analysis of the SARS CoV-2 Spike glycoprotein with the human ACE-2 receptors and thrombin.

Comparative molecular docking and vixualization analysis of the human thrombin with the SARS CoV-2 Spike glycoprotein and the human ACE-2 receptors is of interest. The data shows that residues spanning positions 30-41 in the ACE-2 have interaction with the spike glycoprotein (UniProt ID: Q9BYF1). Results also shows that thrombin binds with SER494 in the spike protein, and GLU37 in the ACE2 receptor. SER494 in the viral receptor-binding domain provides support for hotspot-353 reported elsewhere. These preliminary data provide insights for further probe.

In silico screening of known small molecules to bind ACE2 specific RBD on Spike glycoprotein of SARS-CoV-2 for repurposing against COVID-19.

Background: Human coronavirus (SARS-CoV-2) is causing a pandemic with significant morbidity and mortality. As no effective novel drugs are available currently, drug repurposing is an alternative intervention strategy. Here we present an  in silico drug repurposing study that implements successful concepts of computer-aided drug design (CADD) technology for repurposing known drugs to interfere with viral cellular entry via the spike glycoprotein (SARS-CoV-2-S), which mediates host cell entry via the hACE2 receptor. Methods: A total of 4015 known and approved small molecules were screened for interaction with SARS-CoV-2-S through docking studies and 15 lead molecules were shortlisted. Additionally, streptomycin, ciprofloxacin, and glycyrrhizic acid (GA) were selected based on their reported anti-viral activity, safety, availability and affordability. The 18 molecules were subjected to molecular dynamics (MD) simulation. Results: The MD simulation results indicate that GA of plant origin may be repurposed for SARS-CoV-2 intervention, pending further studies. Conclusions: Repurposing is a beneficial strategy for treating COVID-19 with existing drugs. It is aimed at using docking studies to screen molecules for clinical application and investigating their efficacy in inhibiting SARS-CoV-2-S. SARS-CoV-2-S is a key pathogenic protein that mediates pathogen-host interaction. Hence, the molecules screened for inhibitory properties against SARS-CoV-2-S can be clinically used to treat COVID-19 since the safety profile is already known.