S-protein Receptor-binding Domain Research Articles

Marine sulfated glycans inhibit the interaction of heparin with S-protein of SARS-CoV-2 Omicron XBB variant.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a worldwide COVID-19 pandemic, leading to 6.8million deaths. Numerous variants have emerged since its outbreak, resulting in its significantly enhanced ability to spread among humans. As with many other viruses, SARS‑CoV‑2 utilizes heparan sulfate (HS) glycosaminoglycan (GAG) on the surface of host cells to facilitate viral attachment and initiate cellular entry through the ACE2 receptor. Therefore, interfering with virion-HS interactions represents a promising target to develop broad-spectrum antiviral therapeutics. Sulfated glycans derived from marine organisms have been proven to be exceptional reservoirs of naturally existing HS mimetics, which exhibit remarkable therapeutic properties encompassing antiviral/microbial, antitumor, anticoagulant, and anti-inflammatory activities. In the current study, the interactions between the receptor-binding domain (RBD) of S-protein of SARS-CoV-2 (both WT and XBB.1.5 variants) and heparin were applied to assess the inhibitory activity of 10 marine-sourced glycans including three sulfated fucans, three fucosylated chondroitin sulfates and two fucoidans derived from sea cucumbers, sea urchin and seaweed Saccharina japonica, respectively. The inhibitory activity of these marine derived sulfated glycans on the interactions between RBD of S-protein and heparin was evaluated using Surface Plasmon Resonance (SPR). The RBDs of S-proteins from both Omicrion XBB.1.5 and wild-type (WT) were found to bind to heparin, which is a highly sulfated form of HS. All the tested marine-sourced sulfated glycans exhibited strong inhibition of WT and XBB.1.5S-protein binding to heparin. We believe the study on the molecular interactions between S-proteins and host cell glycosaminoglycans provides valuable insight for the development of marine-sourced, glycan-based inhibitors as potential anti-SARS-CoV-2 agents.

SARS-CoV-2 receptor a distinct genetic profile specific to the Iraqi Kurdish population.

SARS-CoV-2, the virus responsible for COVID-19, enters host cells by binding its spike protein's receptor-binding domain (RBD) to the human angiotensin-converting enzyme 2 (ACE2) receptor's peptidase domain (PD). This interaction plays a crucial role in the virus's ability to invade host cells and establish infection. Numerous studies have identified specific residues crucial for their binding interaction. Our objective was to determine whether natural variations in the ACE2 receptor could impact its affinity for the S-protein RBD. To explore this, we focused on investigating the effects of natural variations in the ACE2 PD residues on its binding affinity to the S-protein RBD interface of SARS-CoV-2. We conducted a genotyping study in the Iraqi Kurdish population and identified significant genetic variations in key binding residues of the ACE2 PD residues, including N330K, K353R, R357Q, P389H, and R393H. These variations suggest a distinct genetic profile specific to the Kurdish population regarding their interaction with the SARS-CoV-2 virus. Understanding the implications of these variations is essential for comprehending the mechanisms of viral infection, developing targeted therapeutics, and refining treatment strategies and vaccine design. Additionally, studying these variations can provide insights into population-specific vulnerabilities, help monitor viral evolution and transmission, and guide the development of effective interventions.

Combined biolistic and cell penetrating peptide delivery for the development of scalable intradermal DNA vaccines

Physical-based gene delivery via biolistic methods (such as the Helios gene gun) involve precipitation of nucleic acids onto microparticles and direct transfection through cell membranes of exposed tissue (e.g. skin) by high velocity acceleration. The glycosaminoglycan (GAG)-binding enhanced transduction (GET) system exploits novel fusion peptides consisting of cell-binding, nucleic acid condensing, and cell-penetrating domains, which enable enhanced transfection across multiple cell types. In this study, we combined chemical (GET) and physical (gene gun) DNA delivery systems, and hypothesized the combination would generate enhanced distribution and effective uptake in cells not initially transfected by biolistic penetration. Physicochemical characterization, optimization of bullet contents and transfection experiments in vitro in cell monolayers and engineered tissue demonstrated these formulations transfected efficiently, including DC2.4 dendritic cells. We incorporated these formulations into a biolistic format for gene gun by forming fireable dry bullets obtained via lyophilization (freeze drying). This system is simple and with enhanced scalability compared to conventional methods to generate bullets. Flushed GET bullet contents retained their ability to mediate transfection (17-fold greater and 13-fold greater reporter gene expression than standard spermidine bullets in the absence and presence of serum, respectively). Fired GET bullets in vitro (in cells and collagen gels) and in vivo (mice) showed increased reporter gene transfection compared to untreated controls, whilst maintaining cell viability in vitro and having no obvious toxicity in vivo. Lastly, a SARS-CoV-2 plasmid DNA vaccine with spike (S) protein-receptor binding domain (S-RBD) was delivered by gene gun using GET bullets. Specific T cell and antibody responses comparable to the conventional system were generated. The non-physical and physical combination of GET‑gold-DNA carriers using gene gun shows potential as an alternative DNA delivery method that is scalable for mass deployable vaccination and intradermal gene delivery.

Virus neutralizing antibodies in pseudovirus particle neutralization reaction as a bioanalytical part of a Salnavac® vaccine clinical trial

Introduction. The SARS-CoV-2 coronavirus pandemic has been a major challenge for all areas of medical science, causing a surge of new developments in various fields ranging from diagnostic techniques to therapeutic and preventive approaches. Intranasal vaccination is an innovative approach to immunization against SARS-CoV-2, which has attracted the attention of many drug developers. Dynamics of blood virus-neutralizing antibodies (VNAs) in recovered COVID-19 patients or vaccinated healthy volunteers is one of the objective parameters for assessing vaccine immunological efficacy, which requires high standards of bioanalytical techniques within the framework of clinical trials. Immunogenicity data on the two-component Salnavak®(intranasal) and Gam-COVID-Vac®(intramuscular) vaccination obtained in randomized double-blind multicenter phase 3 clinical trial interim analysis are presented. The objective of the study was to assess immunogenicity of intranasal and intramuscular vaccination against COVID-19 using a neutralization reaction with pseudoviral particles and HEK293T-hACE2 cell culture.Materials and methods.A total of 137 healthy volunteers with a baseline anti-RBD IgG level not exceeding 100 BAU/ml received immunization by a two-component (Ad26 and Ad5 based) intranasal or intramuscular vaccine administered on day 1 and day 21. Immunogenicity level based on VNA quantitative analysis using a neutralization reaction with pseudoviral particles and a HEK293T-hACE2 cell culture as well as to SARS-CoV-2 S-protein receptor-binding domain (anti-RBD) IgG antibodies on days 21 and 42 after administration of component I was assessed.Results.The geometric mean VNA titer against SARS-CoV-2 on day 42 was 238.34±3.93 and 616.94±3.73 in the Salnavac®and Gam-COVID-Vac®groups, respectively. Trial data shows sufficient immunological efficacy of both intramuscular and intranasal vaccines based on a high protection level at VNA titer of more than 100 while using the pseudoviral neutralization method. The geometric mean of the anti-RBD IgG level by day 42 was 131.22±3.91 and 782.03±3.04 in the Salnavac®and Gam-COVID-Vak®groups, respectively. A direct moderate correlation was shown between VHA and anti-RBD IgG.Conclusion. Neutralization reaction using pseudoviral particles was successfully validated and used to determine the VNA titer during clinical trial. Trial interim data revealed that intranasal vaccine Salnavac®vs intramuscular vaccine Gam-COVID-Vak®resulted in lower but sufficient stringency of humoral immunity.

Synthesis of multivalent sialyllactose-conjugated PAMAM dendrimers: Binding to SARS-CoV-2 spike protein and influenza hemagglutinin

Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) and influenza viruses have spread around the world at an unprecedented rate. Despite multiple vaccines, new variants of SARS-CoV-2 and influenza have caused a remarkable level of pathogenesis. The development of effective antiviral drugs to treat SARS-CoV-2 and influenza remains a high priority. Inhibiting viral cell surface attachment represents an early and efficient means to block virus infection. Sialyl glycoconjugates, on the surface of human cell membranes, play an important role as host cell receptors for influenza A virus and 9-O-acetyl-sialylated glycoconjugates are receptors for MERS, HKU1 and bovine coronaviruses. We designed and synthesized multivalent 6′-sialyllactose-counjugated polyamidoamine dendrimers through click chemistry at room temperature concisely. These dendrimer derivatives have good solubility and stability in aqueous solutions. SPR, a real-time analysis quantitative method for of biomolecular interactions, was used to study the binding affinities of our dendrimer derivatives by utilizing only 200 micrograms of each dendrimer. Three SARS-CoV-2 S-protein receptor binding domain (wild type and two Omicron mutants) bound to multivalent 9-O-acetyl-6′-sialyllactose-counjugated and 6′-sialyllactose-counjugated dendrimers bound to a single H3N2 influenza A virus's HA protein (A/Hong Kong/1/1968), the SPR study results suggest their potential anti-viral activities.

Various reagent kits for comparatively analyzed effectiveness of humoral immune response after vaccination “Sputnik V"

Modern methods of vaccination have confirmed their high effectiveness in fighting against the pandemic of a novel coronavirus infection. However, the use of various types of vaccines requires studying the effectiveness of the post-vaccination immune response (PIO), first of all, assessing the specificity and amount of production of antibodies to the surface and internal antigens of the SARS-CoV-2 virus, in particular, after the use of the most promising domestic vaccine Gam-Covid-Vac (Sputnik V). In particular, the data on the effectiveness of PVIR (increased antibody level) for the most promising domestic vaccine Gam-Covid-Vac (Sputnik V) need to be confirmed. It is also necessary to evaluate the effectiveness of the laboratory methods used for this purpose. To assess the effectiveness of PVIR, samples of biomaterial (blood serum) obtained on the 2225 day after inoculation of the second component of the vaccine from 202 Sputnik V-vaccinated, not preimmunized subjects, lacking antibodies to SARS-CoV-2 before vaccination, were examined. The levels of IgG and IgM antibodies to the surface and nucleocapsid antigens of the SARS-CoV-2 virus were determined using several semi-quantitative and quantitative methods and reagent kits from national and foreign manufacturers. To assess the diagnostic effectiveness of the methods, a comparative analysis of the specificity and sensitivity of all the laboratory methods used and a data correlation for various quantitative methods (using the Spearman correlation coefficient) between antibodies specific to the full-sized trimerized S-protein and the receptor-binding domain (RBD) of the SARS-CoV-2 S-protein were carried out. During the study, it was determined that all the reagent kits used to study IgG antibodies against SARS-CoV-2 S-protein and S-protein RBD showed maximum (100%) specificity in in the majority subjects (from 186 to 202 samples). The relevance of the data (comparative specificity), both for semi-quantitative and quantitative ELISA as well as for both ILA test systems regarding qualitative characteristics (positivenegative) was also close to the maximum magnitude (98.499.4%). A post-vaccination immune response during Sputnik V vaccination analyzing production of specific IgG antibodies was observed in 98.9% of all vaccinated subjects. IgG antibody range was studied to assess related protective level. Data are presented that a protective level of more than 150 BAU/мл was observed in 59.390.5% of the subjects, above 500 BAU/ml in 22.052.4% of the subjects, depending on the method used and the set of reagents. Based on the data obtained, it is concluded that all the methods and kits of reagents used, including domestically manufactured semi-quantitative tests, can be considered adequate to assess effectiveness of the post-vaccination immune response analyzing production of SARS-CoV-2-specific antibodies.

Luteolin inhibits spike protein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) binding to angiotensin-converting enzyme 2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a respiratory illness that poses a serious threat to global public health. In an essential step during infection, SARS-CoV-2 uses the receptor-binding domain (RBD) of the spike (S) protein to engage with angiotensin-converting enzyme 2 (ACE2) in host cells. Chinese herbal medicines and their active components exhibit antiviral activity, with luteolin being a flavonoid that can significantly inhibit SARS-CoV infection. However, whether it can block the interaction between the S-protein RBD of SARS-CoV-2 and ACE2 has not yet been elucidated. Here, we investigated the effects of luteolin on the binding of the S-protein RBD to ACE2. By employing a competitive binding assay in vitro, we found that luteolin significantly blocked the binding of S-protein RBD to ACE2 with IC50 values of 0.61 mM, which was confirmed by the neutralized infection with SARS-CoV-2 pseudovirus in vivo. A surface plasmon resonance-based competition assay revealed that luteolin significantly affects the binding of the S-protein RBD to the ACE2 receptor. Molecular docking was performed to predict the binding sites of luteolin to the S-protein RBD-ACE2 complex. The active binding sites were defined based on published literature, and we found that luteolin might interfere with the mixture at residues including LYS353, ASP30, and TYR83 in the cellular ACE2 receptor and GLY496, GLN498, TYR505, LEU455, GLN493, and GLU484 in the S-protein RBD. These residues may together form attractive charges and destroy the stable interaction of S-protein RBD-ACE2. Luteolin also inhibits SARS-CoV-2 spike protein-induced platelet spreading, thereby inhibiting the binding of the spike protein to ACE2. Our results are the first to provide evidence that luteolin is an anti-SARS-CoV-2 agent associated with interference between viral S-protein RBD-ACE2 interactions.

Structural implications of SARS-CoV-2 Surface Glycoprotein N501Y mutation within receptor-binding domain [499-505] – computational analysis of the most frequent Asn501 polar uncharged amino acid mutations

The aim of this study was to evaluate the impact of the most frequent Asn501 polar uncharged amino acid mutations upon important structural properties of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) Surface Glycoprotein RBD – hACE2 (human angiotensin-converting enzyme 2) heterodimer. Mutations N501Y, N501T and N501S were considered and their impact upon complex solubility, secondary motifs formation and intermolecular hydrogen bonding interface was analyzed. Results and findings are reported based on 50 ns run in Gromacs molecular dynamics simulation software. Special attention is paid on the biomechanical shifts in the receptor-binding domain (RBD) [499-505]: ProThrAsn(Tyr)GlyValGlyTyr, having substituted Asparagine to Tyrosine at position 501. The main findings indicate that the N501S mutation increases SARS-CoV-2 S-protein RBD – hACE2 solubility over N501T, N501 (wild type): , . The N501Y mutation shifts -helix S-protein RBD [366-370]: SerValLeuTyrAsn into π-helix for t > 38.5 ns. An S-protein RBD [503-505]: ValGlyTyr shift from -helix into a turn is observed due to the N501Y mutation in t > 33 ns. An empirical proof for the presence of a Y501-binding pocket, based on RBD [499-505]: PTYGVGY ’s RMSF peak formation is presented. There is enhanced electrostatic interaction between Tyr505 (RBD) phenolic -OH group and Glu37 (hACE2) side chain oxygen atoms due to the N501Y mutation. The N501Y mutation shifts the hydrogen bond into permanent polar contact; ; .

Platelet αIIbβ3 integrin binds to SARS-CoV-2 spike protein of alpha strain but not wild type and omicron strains

Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 causes a pandemic infectious disease, Coronavirus disease 2019 (COVID-19). It causes respiratory infection. Then, it progresses into a systemic infection by involving other organs. This progression mechanism remains to be elucidated, although thrombus formation plays an important role in its progression. Platelets is involved in the thrombus formation by aggregating each other through association of activated αIIbβ3 integrin with the Arg-Gly-Asp (RGD) motif-containing its ligands such as fibrinogen and von Willebrand factor. SARS-CoV-2 enters host cells through association of the spike protein (S-protein) with its receptor, angiotensin-converting enzyme 2 (ACE-2), on the host cells. While presence of ACE2 in platelets is suspicious, S-protein harbors the RGD sequences within its receptor binding domain. Therefore, it could be possible SARS-CoV-2 enter platelets through association of S-protein with αIIbβ3. In this study, we found that receptor binding domain of S-protein of WT SARS-CoV-2 strain barely bound to isolated healthy human platelets. In contrast, highly toxic alpha-strain-based N501Y substitution strongly bound to platelets in a RGD dependent manner, although binding of S protein did not induce platelet aggregation or activation. This binding may serve for transferring the infection to systemic organs.

<i>In silico</i> phytochemical repurposing of natural molecules as entry inhibitors against RBD of the spike protein of SARS-CoV-2 using molecular docking studies

The receptor binding domain (RBD) of Spike-protein (S-protein) is responsible for virus entry via interaction with host protein ACE2 (angiotensin-converting enzyme 2), present on the cell surface of humans. Therefore, S-protein is an important target to block the entry of the SARS-CoV-2 into the cell for further growth. In the present study, phytochemical repurposing of natural molecules: narirutin, naringin, neohesperidin and hesperidin were performed against the RBD S-protein/ACE2 interface as well as the RBD of the S-protein using molecular docking. These natural molecules were found to have structural similarity to each other and had binding potential against the viral infections. It is first time reported here that the naringin and narirutin are having binding potential against both RBD S-protein/ACE2 interface and active site of RBD of S-protein using binding mode analysis. Hence, this study will open avenues for multitargeting similar natural molecules binding against the SARS-CoV-2 proteins as all reports are made in this single study.

Isolation of bio-molecule Baicalein (5, 6, 7-Trihydroxy flavone) from root of Oroxylum indicum L. Vent and its prospective interaction with COVID-19 Viral S-Protein Receptor Binding Domain

Newly emerged COVID-19 performs its activity through spike protein receptor binding domain (RBD). A strong competitive binding on this site can inhibit the COVID-19 (SARS-CoV-2) activity against host cells. A significant plant bioactive molecule, Baicalein (5,6,7-Trihydroxyflavone), has noteworthy effects on viral S protein. The biomolecule was isolated from an endangered medicinal tree Oroxylum indicum L. Vent. Therapeutic use various parts of Oroxylum have been mentioned in ancient literature, Ayurveda and is also being used a folklore medicine in many tribal areas of India. Molecular docking has been applied to screen the binding pattern and bond strength of biomolecule with ten amino acids. The binding site was defined with site findder algorithm. The residues were found Arg403, Glu406, Lys417, Tyr453, Ser494, Tyr495, Gly496, Phe497, Asn501, Tyr505. The biomolecule Baicalein showed effective binding capacity towards active site residues of SARS-CoV-2 spike receptor-binding domain. It was found to have a strong binding affinity with RBD of S-protein of viral residues with high negative binding free energy (-12.5545 kcal/mol). Such competitive interruption of hydrogen bond formation between the viral S- protein and biomolecules’ active sites would inhibit the potency of COVID-19 infectivity.

Variations in Cell Surface ACE2 Levels Alter Direct Binding of SARS-CoV-2 Spike Protein and Viral Infectivity: Implications for Measuring Spike Protein Interactions with Animal ACE2 Orthologs.

ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19), the most severe pandemic in a century. The virus gains access to host cells when the viral spike protein (S-protein) binds to the host cell surface receptor angiotensin-converting enzyme 2 (ACE2). Studies have attempted to understand SARS-CoV-2 S-protein interactions with vertebrate orthologs of ACE2 by expressing ACE2 orthologs in mammalian cells and measuring viral infection or S-protein binding. Often, these cells only transiently express ACE2 proteins, and the levels of ACE2 at the cell surface are not quantified. Here, we describe a cell-based assay that uses stably transfected cells expressing ACE2 proteins in a bicistronic vector with an easy-to-quantify reporter protein, Thy1.1. We found that both the binding of the S-protein receptor-binding domain (RBD) and infection with a SARS-CoV-2 pseudovirus are proportional to the amount of human ACE2 expressed at the cell surface, which can be inferred by quantifying the level of Thy1.1. We also compared different ACE2 orthologs, which were expressed in stably transfected cells expressing equivalent levels of Thy1.1. When ranked for either viral infectivity or RBD binding, mouse ACE2 had a weak to undetectable affinity for S-protein, while human ACE2 had the highest level detected, and feline ACE2 had an intermediate phenotype. The generation of stably transfected cells whose ACE2 level can be normalized for cross-ortholog comparisons allows us to create a reusable cellular library useful for measuring emerging SARS-CoV-2 variants’ abilities to potentially infect different animals.IMPORTANCE SARS-CoV-2 is a zoonotic virus responsible for the worst global pandemic in a century. An understanding of how the virus can infect other vertebrate species is important for controlling viral spread and understanding the natural history of the virus. Here, we describe a method to generate cells stably expressing different orthologs of ACE2, the receptor for SARS-CoV-2, on the surface of a human cell line. We find that both the binding of the viral spike protein receptor-binding domain (RBD) and infection of cells with a SARS-CoV-2 pseudovirus are proportional to the ACE2 levels at the cell surface. This method will allow the creation of a library of stably transfected cells expressing similar levels of different vertebrate ACE2 orthologs, which can be used repeatedly for identifying vertebrate species that may be susceptible to infection with SARS-CoV-2 and its many variants.

Inhibition of SARS-CoV-2 wild-type (Wuhan-Hu-1) and Delta (B.1.617.2) strains by marine sulfated glycans.

The Coronavirus disease pandemic has steered the global therapeutic research efforts toward the discovery of potential anti-severe acute respiratory syndrome coronavirus (SARS-CoV-2) molecules. The role of the viral spike glycoprotein (S-protein) has been clearly established in SARS-CoV-2 infection through its capacity to bind to the host cell surface heparan sulfate proteoglycan (HSPG) and angiotensin-converting enzyme-2. The antiviral strategies targeting these 2 virus receptors are currently under intense investigation. However, the rapid evolution of the SARS-CoV-2 genome has resulted in numerous mutations in the S-protein posing a significant challenge for the design of S-protein-targeted inhibitors. As an example, the 2 key mutations in the S-protein receptor-binding domain (RBD), L452R, and T478K in the SARS-CoV-2 Delta variant (B.1.617.2) confer tighter binding to the host epithelial cells. Marine sulfated glycans (MSGs) demonstrate excellent inhibitory activity against SARS-CoV-2 via competitive disruption of the S-protein RBD-HSPG interactions and thus have the potential to be developed into effective prophylactic and therapeutic molecules. In this study, 7 different MSGs were evaluated for their anti-SARS-CoV-2 activity in a virus entry assay utilizing a SARS-CoV-2 pseudovirus coated with S-protein of the wild-type (Wuhan-Hu-1) or the Delta (B.1.617.2) strain. Although all tested MSGs showed strong inhibitory activity against both strains, no correlations between MSG structural features and virus inhibition could be drawn. Nevertheless, the current study provides evidence for the maintenance of inhibitory activity of MSGs against evolving SARS-CoV-2 strains.

Peptide-Antibody Fusions Engineered by Phage Display Exhibit an Ultrapotent and Broad Neutralization of SARS-CoV-2 Variants.

The spread of COVID-19 has been exacerbated by the emergence of variants of concern (VoC). Many VoC contain mutations in the spike protein (S-protein) and are implicated in infection and response to therapeutics. Bivalent neutralizing antibodies (nAbs) targeting the S-protein receptor-binding domain (RBD) are promising therapeutics for COVID-19, but they are limited by low potency and vulnerability to RBD mutations in VoC. To address these issues, we used naïve phage-displayed peptide libraries to isolate and optimize 16-residue peptides that bind to the RBD or the N-terminal domain (NTD) of the S-protein. We fused these peptides to the N-terminus of a moderate-affinity nAb to generate tetravalent peptide–IgG fusions, and we showed that both classes of peptides were able to improve affinities for the S-protein trimer by >100-fold (apparent KD < 1 pM). Critically, cell-based infection assays with a panel of six SARS-CoV-2 variants demonstrated that an RBD-binding peptide was able to enhance the neutralization potency of a high-affinity nAb >100-fold. Moreover, this peptide–IgG was able to neutralize variants that were resistant to the same nAb in the bivalent IgG format, including the dominant B.1.1.529 (Omicron) variant that is resistant to most clinically approved therapeutic nAbs. To show that this approach is general, we fused the same peptide to a clinically approved nAb drug and showed that it enabled the neutralization of a resistant variant. Taken together, these results establish minimal peptide fusions as a modular means to greatly enhance affinities, potencies, and breadth of coverage of nAbs as therapeutics for SARS-CoV-2.

Understanding the Driving Forces That Trigger Mutations in SARS-CoV-2: Mutational Energetics and the Role of Arginine Blockers in COVID-19 Therapy.

SARS-CoV-2 is a global challenge due to its ability to mutate into variants that spread more rapidly than the wild-type virus. Because the molecular biology of this virus has been studied in such great detail, it represents an archetypal paradigm for research into new antiviral drug therapies. The rapid evolution of SARS-CoV-2 in the human population is driven, in part, by mutations in the receptor-binding domain (RBD) of the spike (S-) protein, some of which enable tighter binding to angiotensin-converting enzyme (ACE2). More stable RBD-ACE2 association is coupled with accelerated hydrolysis of furin and 3CLpro cleavage sites that augment infection. Non-RBD and non-interfacial mutations assist the S-protein in adopting thermodynamically favorable conformations for stronger binding. The driving forces of key mutations for Alpha, Beta, Gamma, Delta, Kappa, Lambda and Omicron variants, which stabilize the RBD-ACE2 complex, are investigated by free-energy computational approaches, as well as equilibrium and steered molecular dynamic simulations. Considered also are the structural hydropathy traits of the residues in the interface between SARS-CoV-2 RBD and ACE2 protein. Salt bridges and π-π interactions are critical forces that create stronger complexes between the RBD and ACE2. The trend of mutations is the replacement of non-polar hydrophobic interactions with polar hydrophilic interactions, which enhance binding of RBD with ACE2. However, this is not always the case, as conformational landscapes also contribute to a stronger binding. Arginine, the most polar and hydrophilic among the natural amino acids, is the most aggressive mutant amino acid for stronger binding. Arginine blockers, such as traditional sartans that bear anionic tetrazoles and carboxylates, may be ideal candidate drugs for retarding viral infection by weakening S-protein RBD binding to ACE2 and discouraging hydrolysis of cleavage sites. Based on our computational results it is suggested that a new generation of “supersartans”, called “bisartans”, bearing two anionic biphenyl-tetrazole pharmacophores, are superior to carboxylates in terms of their interactions with viral targets, suggesting their potential as drugs in the treatment of COVID-19. In Brief: This in silico study reviews our understanding of molecular driving forces that trigger mutations in the SARS-CoV-2 virus. It also reports further studies on a new class of “supersartans” referred to herein as “bisartans”, bearing two anionic biphenyltetrazole moieties that show potential in models for blocking critical amino acids of mutants, such as arginine, in the Delta variant. Bisartans may also act at other targets essential for viral infection and replication (i.e., ACE2, furin cleavage site and 3CLpro), rendering them potential new drugs for additional experimentation and translation to human clinical trials.

Development of a rapid neutralizing antibody test for SARS-CoV-2 and its application for neutralizing antibody screening and vaccinated serum testing

BackgroundSince the outbreak of coronavirus disease (COVID-19), the high infection rate and mutation frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent, have contributed to the ongoing global pandemic. Vaccination has become the most effective means of controlling COVID-19. Traditional neutralizing tests of sera are complex and labor-intensive, therefore, a rapid test for detecting neutralizing antibodies and antibody status post-immunization is needed. MethodsBased on the fact that antibodies exhibit neutralizing activity by blocking the binding of the S protein receptor-binding domain (S-RBD) to ACE2, we developed a rapid neutralizing antibody test, ACE2-Block-ELISA. To evaluate the sensitivity and specificity, we used 54 positive and 84 negative serum samples. We also tested the neutralizing activities of monoclonal antibodies (mAbs) and 214 sera samples from healthy individuals immunized with the inactivated SARS-CoV-2 vaccine. ResultsThe sensitivity and specificity of the ACE2-Block ELISA were 96.3% and 100%, respectively. For neutralizing mAb screening, ch-2C5 was selected for its ability to block the ACE2–S-RBD interaction. A plaque assay confirmed that ch-2C5 neutralized SARS-CoV-2, with NT50 values of 4.19, 10.63, and 1.074 µg/mL against the SARS-CoV-2 original strain, and the Beta and Delta variants, respectively. For the immunized sera samples, the neutralizing positive rate dropped from 82.14% to 32.16% within 4 months post-vaccination. ConclusionsThis study developed and validated an ACE2-Block-ELISA to test the neutralizing activities of antibodies. As a rapid, inexpensive and easy-to-perform method, this ACE2-Block-ELISA has potential applications in rapid neutralizing mAb screening and SARS-CoV-2 vaccine evaluation.

Potential Anti-SARS-CoV-2 Activity of Pentosan Polysulfate and Mucopolysaccharide Polysulfate.

With the increased prevalence of new SARS-CoV-2 variants of concern, such as Delta and Omicron, the COVID-19 pandemic has become an ongoing human health disaster, killing millions worldwide. SARS-CoV-2 invades its host through the interaction of its spike (S) protein with a host cell receptor, angiotensin-converting enzyme 2 (ACE2). In addition, heparan sulfate (HS) on the surface of host cells plays an important role as a co-receptor for this viral pathogen–host cell interaction. Our previous studies demonstrated that many sulfated glycans, such as heparin, fucoidans, and rhamnan sulfate have anti-SARS-CoV-2 activities. In the current study, a small library of sulfated glycans and highly negatively charged compounds, including pentosan polysulfate (PPS), mucopolysaccharide polysulfate (MPS), sulfated lactobionic acid, sulodexide, and defibrotide, was assembled and evaluated for binding to the S-proteins and inhibition of viral infectivity in vitro. These compounds inhibited the interaction of the S-protein receptor-binding domain (RBD) (wild type and different variants) with immobilized heparin, a highly sulfated HS, as determined using surface plasmon resonance (SPR). PPS and MPS showed the strongest inhibition of interaction of heparin and S-protein RBD. The competitive binding studies showed that the IC50 of PPS and MPS against the S-protein RBD binding to immobilized heparin was ~35 nM and ~9 nM, respectively, much lower than the IC50 for soluble heparin (IC50 = 56 nM). Both PPS and MPS showed stronger inhibition than heparin on the S-protein RBD or spike pseudotyped lentiviral particles binding to immobilized heparin. Finally, in an in vitro cell-based assay, PPS and MPS exhibited strong antiviral activities against pseudotyped viral particles of SARS-CoV-2 containing wild-type or Delta S-proteins.

Efficacy of defensins as neutralizing agents against the deadly SARS-CoV-2

SARS-CoV-2 infection causes asymptomatic to severe human respiratory diseases. Vaccinations are effective only to a certain extent, and the disease recurs with milder symptoms even after booster doses. Hence, we hypothesize that antiviral therapy in conjunction with vaccination is the need of the hour for containing the disease. SARS-CoV-2 enters the host cell through interaction between viral spike (S) protein and human Angiotensin II converting enzyme2 (ACE2). So, any S-protein neutralizing molecule could be a potential antiviral moiety. The interaction-interface architecture indicates that cationic peptides effectively bind to anionic interface residues of S protein-receptor binding domain (S-RBD). Subsequently, we adopted molecular docking and simulation approaches to examine the binding affinity of cationic human α and β defensins, HNP1 and HBD2 with S-RBD. We observed strong hydrogen bonds, electrostatic, salt bridge, and hydrophobic interactions between these defensins and S-RBD with binding energy (BE) of −10.7 kcal/mol. Interestingly, defensins from Zea mays (ZmD32), Solanum lycopersicum (TPP3), and Sorghum bicolor (DEF1_SORBI) exhibited approximately similar BE of −11.1 kcal/mol, −11.9 kcal/mol, and −12.6 kcal/mol respectively, comparable to ACE2 (BE= −11.9 kcal/mol). Molecular dynamics simulation of S-RBD complexes formed with HBD2, ZmD32 and TPP3, showed stable associations for 100 ns. Results of in-silico studies demonstrated higher binding affinity of more positively-charged peptides with S-RBD, suggesting the potential of plant defensins to block ACE2 binding of S-RBD. These results warrant experimental validation. However these findings indicate the usefulness of plant defensin homologues as neutralizing antiviral agents for use as ideal prophylactic and therapeutic drugs for COVID-19. Communicated by Ramaswamy H. Sarma

Aspects of the physiochemical properties of SARS-CoV-2 to prevent S-protein receptor binding using Arabic gum

Abstract With the number of people infected with the new coronavirus exceeding millions of confirmed infections, the world is turning to scientists and researchers, everyone is waiting – impatiently – for the results of the research that is being carried out in full swing to find an effective treatment for the virus. The recent development of the virus has witnessed at least 17 mutations that may affect its external shape, especially on the S-protein receptor-binding domain (RBD), which helps it attach to human cells’ receptor angiotensin-converting enzyme-2 (ACE2) to make RBD–ACE2 interaction and entry to host cell. This interaction becomes stronger in the new strains of the coronavirus due to a mutation that occurs in the S-proteins that attach to human cells. For researchers and scientists to be able to confront this pandemic that has spread in the world like wildfire, they must be armed with accurate understanding and clear knowledge about coronavirus. This study focuses on polysaccharides, specifically negatively polysaccharides, that can interfere with the positive charge of the surface of the SARS-CoV-2 and ACE2, thus inhibiting the virus’s infectivity and destroying it. In addition, polysaccharides will boost the immune function of the vaccine, thereby fostering nonspecific immunity of the body and specific immunity of the body, cellular immunity, mucosal immunity, humoral immunity, and decreased pro-inflammatory expression. This research aims to reduce the attachment power and modify the pulling apart of the RBD and the angiotensin-converting enzyme 2 (ACE2) by polysaccharide molecules such as Arabic gum (AG) and carrageenan. The adapted fluorometric assay is used to investigate the probability of Arabic gum and ACE2 interactions. The obtained results confirmed that the interaction could take place between Arabic gum and ACE2. Several literature studies promote the use of the urchin egg as antiviral, especially for SARS-CoV-2, because it has sulfated fucan polysaccharide molecules that prevent interaction of SARS-CoV-2 with a host cell. But, to the best of our knowledge, we found that the effect of urchin egg as antiviral, especially for SARS-CoV-2 is very difficult due to the presence of immunoglobulin G (IgG) in the human cells containing sugars that terminate with N-glycolylneuraminic (Neu5Ac) as found in the sperm of sea urchin. So, s most probably an interaction has occurred between Neu5Ac in IgG of human cells and sulfated fucan polysaccharide molecules of urchin egg.

Extracellular vimentin is an attachment factor that facilitates SARS-CoV-2 entry into human endothelial cells

SARS-CoV-2 entry into host cells is a crucial step for virus tropism, transmission, and pathogenesis. Angiotensin-converting enzyme 2 (ACE2) has been identified as the primary entry receptor for SARS-CoV-2; however, the possible involvement of other cellular components in the viral entry has not yet been fully elucidated. Here we describe the identification of vimentin (VIM), an intermediate filament protein widely expressed in cells of mesenchymal origin, as an important attachment factor for SARS-CoV-2 on human endothelial cells. Using liquid chromatography-tandem mass spectrometry, we identified VIM as a protein that binds to the SARS-CoV-2 spike (S) protein. We showed that the S-protein receptor binding domain (RBD) is sufficient for S-protein interaction with VIM. Further analysis revealed that extracellular VIM binds to SARS-CoV-2 S-protein and facilitates SARS-CoV-2 infection, as determined by entry assays performed with pseudotyped viruses expressing S and with infectious SARS-CoV-2. Coexpression of VIM with ACE2 increased SARS-CoV-2 entry in HEK-293 cells, and shRNA-mediated knockdown of VIM significantly reduced SARS-CoV-2 infection of human endothelial cells. Moreover, incubation of A549 cells expressing ACE2 with purified VIM increased pseudotyped SARS-CoV-2-S entry. CR3022 antibody, which recognizes a distinct epitope on SARS-CoV-2-S-RBD without interfering with the binding of the spike with ACE2, inhibited the binding of VIM with CoV-2 S-RBD, and neutralized viral entry in human endothelial cells, suggesting a key role for VIM in SARS-CoV-2 infection of endothelial cells. This work provides insight into the pathogenesis of COVID-19 linked to the vascular system, with implications for the development of therapeutics and vaccines.