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The rapid development of vaccines is a crucial objective in modern biotechnology and molecular pharmacology. In this context, conducting research to expedite the selection of a potent immunogen is imperative. The candidate vaccine should induce the production of antibodies that can recognize the immunogenic epitopes of the target protein, resembling the ones found in recovered patients. One major challenge in vaccine development is the absence of straightforward and reliable techniques to determine the extent to which the spectrum of antibodies produced after vaccination corresponds to antibodies found after recovery. This paper describes a newly developed method to detect antibodies specific to immunogenic epitopes of the target protein in blood plasma and to compare them with antibody spectra generated post vaccination. Comparing the antibody pool generated in the human body after recovering from an infectious disease with the pool formed through vaccination can become a universal method for screening candidate vaccines. This method will enable the identification of candidate vaccines that can induce the production of antibodies similar to those generated in response to a natural infection. Implementing this approach will facilitate the rapid development of new vaccines, even when faced with a pandemic. [ABSTRACT FROM AUTHOR]

The S-protein is the major antigen of the SARS-CoV-2 virus, against which protective antibodies are generated. The S-protein gene was used in adenoviral vectors and mRNA vaccines against COVID-19. While the primary function of antibodies is to bind to antigens, catalytic antibodies can hydrolyze various substrates, including nucleic acids, proteins, oligopeptides, polysaccharides, and some other molecules. In this study, antibody fractions with affinity for RBD and S-protein (RBD-IgG and S-IgG) were isolated from the blood of COVID-19 patients vaccinated with Sputnik V. The fractions were analyzed for their potential to hydrolyze 18-mer oligopeptides corresponding to linear fragments of the SARS-CoV-2 S-protein. Here, we show that the IgG antibodies hydrolyze six out of nine oligopeptides efficiently, with the antibodies of COVID-19-exposed donors demonstrating the most significant activity. The IgGs of control donors not exposed to SARS-CoV-2 were found to be inactive in oligopeptide hydrolysis. The antibodies of convalescents and vaccinated patients were found to hydrolyze oligopeptides in a wide pH range, with the optimal pH range between 6.5 and 7.5. The hydrolysis of most oligopeptides by RBD-IgG antibodies is inhibited by thiol protease inhibitors, whereas S-IgG active centers generally combine several types of proteolytic activities. Ca2+ ions increase the catalytic activity of IgG preparations containing metalloprotease-like active centers. Thus, the proteolytic activity of natural antibodies against the SARS-CoV-2 protein is believed to be due to the similarity of catalytic antibodies' active centers to canonical proteases. This work raises the question of the possible physiological role of proteolytic natural RBD-IgG and S-IgG resulting from vaccination and exposure to COVID-19. [ABSTRACT FROM AUTHOR]

An effect of receptor‐binding domain (RBD) of SARS‐CoV‐2 S‐protein on structural parameters of model lipid membranes presented by dimyristoylphosphatidylcholine (DMPC) systems with cholesterol and melatonin impurities is studied by small angle neutron scattering (SANS). It is shown that an increase in melatonin concentration in the lipid membrane leads to a decrease in the thickness of the lipid bilayer, while an increase in the concentration of cholesterol leads to an increase in its thickness. It is suggested that increasing the concentration of melatonin in a membrane prevents the interaction of coronaviral S‐protein with a lipid membrane of a cell. In the presence of cholesterol in the system, the interaction of a lipid membrane with an active part of S‐protein occurs depending on a phase state of the lipid: in the case of a gel phase, there is no changes in structural parameters, but at higher temperatures in the case of a liquid crystal phase, an addition of RBD SARS‐CoV‐2 to the system causes a reduce in the membrane thickness. [ABSTRACT FROM AUTHOR]

The multistage purposeful synthesis of 5,15-bis(4′-l-N-tyrosinylamidophenyl)-10,20-bis(N-methylpyridin-3′-yl)porphine diiodide was carried out, and the optimum synthesis conditions were determined. 5,15-Bis(4′-nitrophenyl)-10,20-bis(pyridin-3′-yl)porphine served as the starting porphyrin. The structure, individual character, and purity of the target compound were proved by electron spectroscopy, 1H NMR spectroscopy, mass spectrometry (MALDI TOF), and TLC. Specific features of the interaction of the synthesized porphyrin with S-protein of SARS-CoV-2 were studied using spectral and thermochemical methods, including conditions of photoirradiation. The photoirradiation of the synthesized porphyrin in a complex with the SARS-CoV-2 S-protein can result in the partial oxidation of amino acid residues of the protein and distort its primary and secondary structures. The photoirradiation of the S-protein complex with the porphyrin decreases its thermal resistance to melting by 15 °C compared to the free S-protein and causes porphyrin release. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 infects humans through the binding of viral S-protein (spike protein) to human angiotensin I converting enzyme 2 (ACE2). The structure of the ACE2-S-protein complex has been deciphered and we focused on the 27 ACE2 residues that bind to S-protein. From human sequence databases, we identified nine ACE2 variants at ACE2–S-protein binding sites. We used both experimental assays and protein structure analysis to evaluate the effect of each variant on the binding affinity of ACE2 to S-protein. We found one variant causing complete binding disruption, two and three variants, respectively, strongly and mildly reducing the binding affinity, and two variants strongly enhancing the binding affinity. We then collected the ACE2 gene sequences from 57 nonhuman primates. Among the 6 apes and 20 Old World monkeys (OWMs) studied, we found no new variants. In contrast, all 11 New World monkeys (NWMs) studied share four variants each causing a strong reduction in binding affinity, the Philippine tarsier also possesses three such variants, and 18 of the 19 prosimian species studied share one variant causing a strong reduction in binding affinity. Moreover, one OWM and three prosimian variants increased binding affinity by >50%. Based on these findings, we proposed that the common ancestor of primates was strongly resistant to and that of NWMs was completely resistant to SARS-CoV-2 and so is the Philippine tarsier, whereas apes and OWMs, like most humans, are susceptible. This study increases our understanding of the differences in susceptibility to SARS-CoV-2 infection among primates. [ABSTRACT FROM AUTHOR]

Neuropilin-1 (NRP1) is a widely expressed cell surface receptor protein characterized by its pleiotropic function. Recent reports highlighted NRP1 as an additional entry point of the SARS-CoV-2 virus, enhancing viral infectivity by interacting with the S-protein of SARS-CoV-2. The ubiquitous distribution and mechanism of action of NRP1 enable the SARS-CoV-2 virus to attack multiple organs in the body simultaneously. Therefore, blocking NRP1 is a potential therapeutic approach against SARS-CoV-2 infection. The current study screened the South African natural compounds database (SANCDB) for molecules that can disrupt the SARS-CoV-2 S protein-NRP1 interaction as a potential antiviral target for SARS-CoV-2 cellular entry. Following excessive screening and validation analysis 3-O-Methylquercetin and Esculetin were identified as potential compounds to disrupt the S-protein-NRP1 interaction. Furthermore, to understand the conformational stability and dynamic features between NRP1 interaction with the selected natural products, we performed 200 ns molecular dynamics (MD) simulations. In addition, molecular mechanics-generalized Born surface area (MM/GBSA) was utilized to calculate the free binding energies of the natural products interacting with NRP1. 3-O-methylquercetin showed an inhibitory effect with binding energies ΔG of −25.52 ± 0.04 kcal/mol to NRP1, indicating the possible disruption of the NRP1-S-protein interaction. Our analysis demonstrated that 3-O-methylquercetin presents a potential antiviral compound against SARS-CoV-2 infectivity. These results set the path for future functional in-vitro and in-vivo studies in SARS-CoV-2 research. • Neuropilin-1 (NRP1) is a cell surface receptor protein interacting with the S-protein of the SARS-CoV-2 virus. • Furin-mediated proteolytic activity exposes the S1 protein C-terminal RRAR motif to the ligand-specific binding site of NRP1. • Therefore, blocking the S1-RRAR interactions with NRP1 with an antiviral drug would hinder virus infection of host cells. • Identifying natural compounds to block the RRAR-NRP1 complex are attractive therapeutic candidates for SARS-CoV-2 infection. [ABSTRACT FROM AUTHOR]

Ribonuclease S (RNase S) is a versatile model system to introduce non-canonical amino acids into a protein scaffold by self-assembly of the protein complex from S-protein and S-peptide. We have introduced two cysteines into the S-peptide replacing lysine-7 and glutamine-11 of the α-helical region of this peptide. The crystal structure of this variant was determined in the apo state and in complex with HgII ions. These structures serve as a template for the construction of artificial hybrid catalysts based on RNase S, e.g. for phosphanyl amino acids complexing transition metal ions for organometallic catalysis. [ABSTRACT FROM AUTHOR]

Abstract: Currently, there is an increasing interest in the use of probiotics as an alternative strategy to antimicrobial compounds. In this study, two high adhesive strains Lactobacillus crispatus K313 adhering to HT-29 cells as well as Lb. crispatus K243 adhering to collagen type IV were isolated from chicken intestines. SDS-PAGE analysis revealed the presence of the potential S-proteins SlpA and SlpB in Lb. crispatus K243 and K313. SlpA and SlpB, rich in hydrophobic amino acids, were proved to be involved in adhering to collagen type IV and HT-29 cells, respectively, based on the LiCl treatment assay. After removal of S-proteins, the viability and tolerance of the two Lb. crispatus strains to simulated gastric and small intestinal juice were reduced, indicating the protective role of S-proteins against the hostile environments. Lb. crispatus K313 exhibited the stronger autoaggregation ability and inhibitive activity against Salmonella braenderup H9812 adhesion to HT-29 cells than the strain K243. To elucidate the inhibitive mechanism, cultured epithelial cells were exposed with Lb. crispatus strains, and followed by a challenge with S. braenderup H9812. The pro-inflammatory signaling factors (IL-8, CXCL1 and CCL20) from HT-29 were detected by real-time PCR technology. The results showed that both of Lb. crispatus strains down-regulated the transcription level of those pro-inflammatory genes induced by S. braenderup H9812 by 36.2–58.8%. ELISA analysis was further confirmed that Lb. crispatus K243 and K313 inhibited the IL-8 secretion triggered by S. braenderup H9812 by 32.8% and 47.0%, indicating that the two isolates could attenuate the pro-inflammatory signaling induced by S. braenderup H9812, and have the potential application in clinical practice to prevent diarrhea. [Copyright &y& Elsevier]

Rapid, mass diagnosis of the coronavirus disease 2019 (COVID-19) is critical to stop the ongoing infection spread. The two standard screening methods to confirm the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are polymerase chain reaction (PCR), through the RNA of the virus, and serology by detecting antibodies produced as a response to the viral infection. However, given the detection complexity, cost and relatively long analysis times of these techniques, novel technologies are urgently needed. Here, we report an aptamer-based biosensor developed on a screen-printed carbon electrode platform for rapid, sensitive, and user-friendly detection of SARS-CoV-2. The aptasensor relies on an aptamer targeting the receptor-binding domain (RBD) in the spike protein (S-protein) of the SARS-CoV-2. The aptamer immobilization on gold nanoparticles, and the presence of S-protein in the aptamer-target complex, investigated for the first time by photo-induced force microscopy mapping between 770 and 1910 cm−1 of the electromagnetic spectrum, revealed abundant S-protein homogeneously distributed on the sensing probe. The detection of SARS-CoV-2 S-protein was achieved by electrochemical impedance spectroscopy after 40 min incubation with several analyte concentrations, yielding a limit of detection of 1.30 pM (66 pg/mL). Moreover, the aptasensor was successfully applied for the detection of a SARS-CoV-2 pseudovirus, thus suggesting it is a promising tool for the diagnosis of COVID-19. • Aptamer targeting the SARS-CoV-2 S-protein was immobilized on Au nanoparticles. • Aptamer-target complex on the probe was studied by photo-induce force microscopy. • PiFM revealed abundant S-protein present on the sensing probe. • LOD of aptasensor is lower than LOD of ELISA for SARS-CoV-2 S-protein. • The aptasensor can detect a SARS-CoV-2 pseudovirus. [ABSTRACT FROM AUTHOR]

Rapid molecular surveillance of SARS-CoV-2 S-protein variants leading to immune escape and/or increased infectivity is of utmost importance. Among global bottlenecks for variant monitoring in diagnostic settings are sequencing and bioinformatics capacities. In this study, we aimed to establish a rapid and user-friendly protocol for high-throughput S-gene sequencing and subsequent automated identification of variants. We designed two new primer pairs to amplify only the immunodominant part of the S-gene for nanopore sequencing. Furthermore, we developed an automated "S-Protein-Typer" tool that analyzes and reports S-protein mutations on the amino acid level including a variant of concern indicator. Validation of our primer panel using SARS-CoV-2-positive respiratory specimens covering a broad Ct range showed successful amplification for 29/30 samples. Restriction to the region of interest freed sequencing capacity by a factor of 12–13, compared with whole-genome sequencing. Using either the MinION or Flongle flow cell, our sequencing strategy reduced the time required to identify SARS-CoV-2 variants accordingly. The S-Protein-Typer tool identified all mutations correctly when challenged with our sequenced samples and 50 deposited sequences covering all VOCs (December 2021). Our proposed S-protein variant screening offers a simple, more rapid, and low-cost entry into NGS-based SARS-CoV-2 analysis, compared with current whole-genome approaches. [ABSTRACT FROM AUTHOR]

It has been assumed that S-protein (vitronectin) associates with terminal C5b-9 complement complexes only when the latter fail to attach to target lipid bilayers, thereby forming inactive fluidphase SC5b-9 complexes. Using monoclonal anti-S-protein antibodies, we show here that a minor portion of C5b-9 complexes associated with both homologous and heterologous cells contain S-protein. This conclusion derives from Western blot analyses, from the sedimentation behaviour of solubilized S-protein, and from the fad that the protein co-immunoprecipitates with C5b-9(m). Association of S-protein with C5b-9(m) takes place primarily al the stage of C9-binding. An average of ⩽0.4 moles of S-protein are estimated to be present per mole C5b-9(m). Hence, only a fraction of C5b-9 complexes contain S-protein. The function of cell-bound S-protein is unknown. Haemolytic titrations with purified components failed to demonstrate any protective effect of S-protein on the lysis of sheep or human erythrocytes by C5b-9. S-protein bound to complement-lysed homologous or heterotogous cells is readily detectable by conventional immunocytochemical staining. We conclude that differentiation between tissue-deposited fluid-phase C5b-9 and membrane C5b-9 complexes cannot be made on the basis of immunohistological stainings for S-protein alone. [ABSTRACT FROM AUTHOR]

ABSTRACT- Characteristics of primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC) are bile duct destruction and portal inflammation. Increased levels of circulating complement activation products are also present. This raises the possibility of involvement of complement-dependent cytotoxic mechanisms in the pathogenesis. Therefore, we investigated liver biopsy specimens from 21 patients with PBC, six patients with PSC and six controls for complement deposits by immunohistochemistry using polyclonal and monoclonal antibodies against C3d, the terminal complement complex (TCC) and vitronectin (S-protein). We found C3d, TCC and vitronectin deposits only in the portal tracts. C3d and TCC were present in the walls of the hepatic arteries and in the connective tissue stroma but never around the bile ducts. We found vitronectin deposits throughout the connective tissue, often independent of the TCC deposits. When vitronectin and TCC were co-localized, the staining patterns were inverse; that is, intense staining for TCC accompanied weak staining for vitronectin and vice versa. Occasionally complete dissociation between TCC and vitronectin staining was observed. Deposits of TCC and vitronectin showed a focal distribution leaving many portal tracts free of TCC. Our results question whether complement-dependent cytotoxic mechanisms take part in the bile duct destruction in PBC and PSC. [ABSTRACT FROM AUTHOR]

When SC5b-7 was prepared from the C8-depleted serum activated with inulin, it contained SP-40,40 as well as S-protein. From the densitometry of each component in SC5b-9 after SDS - PAGE, it was estimated that SC5b-9 was constituted of one molecule each of C5b, C6, C7, C8, S-protein, and SP-40,40 and two molecules of C9. SP-40,40 was depleted from normal serum with an affinity column using mouse monoclonal anti-SP-40,4O antibody. When the resulting SP-40,40-depleted serum was activated with inulin, SC5b-9 lacking SP-40,40 could be formed. S-Protein-depleted serum was also prepared with an affinity column using mouse monoclonal anti-S-protein antibody. Similarly, SC5b-9 lacking S-protein could be formed by the inulin activation of the S-protein-depleted serum. These results indicate that either SP-40,40 or S-protein should be able to form a soluble C5b-9 complex. [ABSTRACT FROM PUBLISHER]

The thymus plays an integral role in the development and production of T lymphocytes.However, thymocytes differ markedly in their phenotypic characteristics from the T cells normally found in the peripheral lymphoid organs. We have examined the phenotypic characteristics of recent thymic emigrants and compared them with both mature phenotype thymocytes (CD4© CD8-CD3 and CD4-CD8©CD3 ) and lymph node T cells. Recent thymic emigrants were defined as those fluorescein-positive cells found in the lymph node up to 16 h after intrathymic injection of fluorescein. Most cells emigrating from the thymus expressed CD and either CD4 or CD8, indicating maturity. Recent thymic emigrants, like mature phenotype thymocytes, were slightly larger on average than peripheral T cells, but this differential was lost within 24 h of emigration. Also like mature thymocytes but unlike peripheral T cells, some recent emigrants expressed heat-stable antigen. This did not change within 24 h of emigration. The antigen CD44 (Pgp-1, Ly-24) was expressed on a proportion of mature thymocytes, recent thymic emigrants, and peripheral T cells, and its expression did not show any clear relationship to maturity. The antigen CD45R also did not show marked changes associated with maturity, but our data do not parallel the published data of the expression of CD45R in the human. We conclude that recent thymic emigrants are phenotypically mature with respect to some antigens but not others. None of the antigens we investigated could have been used to uniquely distinguish recent thymic emigrants from peripheral T cells or from mature thymocytes [ABSTRACT FROM PUBLISHER]

Vitronectin is a major cell-adhesive protein in animal sera for tissue culture. This report describes an easy, inexpensive, and rapid method to purify vitronectins from a variety of animal sera and plasmas. [ABSTRACT FROM AUTHOR]

The present study attempts to decipher the site-specific amino acid alterations at certain positions experiencing preferential selectivity and their effect on proteins' stability and flexibility. The study examines the selection preferences by considering pair-wise non-bonded interaction energies of adjacent and interacting amino acids present at the interacting site, along with their evolutionary history. For the study, variations in the interacting residues of spike protein (S-Protein) receptor-binding domain (RBD) of different coronaviruses were examined. The MD simulation trajectory analysis revealed that, though all the variants studied were structurally stable at their native and bound confirmations, the RBD of 2019-nCoV/SARS-CoV-2 was found to be more flexible and more dynamic. Furthermore, a noticeable change observed in the non-bonded interaction energies of the amino acids interacting with the receptor corroborated their selection at respective positions. The conformational changes exerted by the altered amino acids could be the reason for a broader range of interacting receptors among the selected proteins. The results envisage a strong indication that the residue selection at certain positions is governed by a well-orchestrated feedback mechanism, which follows increased stability and flexibility in the folded structure compared to its evolutionary predecessor. [Display omitted] [ABSTRACT FROM AUTHOR]

The D614G variant of SARS-CoV-2 S-protein emerged in early 2020 and quickly became the dominant circulating strain in Europe and its environs. The variant was characterized by the higher viral load, which is not associated with disease severity, higher incorporation into the virion, and high cell entry via ACE-2 and TMPRSS2. Previous strains of the coronavirus and the current SARS-CoV-2 have demonstrated the selection of mutations as a mechanism of escaping immune responses. In this study, we used molecular dynamics simulation and MM-PBSA binding energy analysis to provide insights into the behaviour of the D614G S-protein at the molecular level and describe the neutralization mechanism of this variant. Our results show that the D614G S-protein adopts distinct conformational dynamics which is skewed towards the open-state conformation more than the closed-state conformation of the wild-type S-protein. Residue-specific variation of amino acid flexibility and domain-specific RMSD suggest that the mutation causes an allosteric conformational change in the RBD. Evaluation of the interaction energies between the S-protein and neutralizing antibodies show that the mutation may enhance, reduce or not affect the neutralizing interactions depending on the neutralizing antibody, especially if it targets the RBD. The results of this study have shed insights into the behaviour of the D614G S-protein at the molecular level and provided a glimpse of the neutralization mechanism of this variant. • The D614G S-protein adopts distinct conformation dynamics compared to the wild-type. • Structural dynamics of the D614G S-protein is skewed towards the open-state conformation of wild-type S-protein. • The mutation induces an allosteric conformation change in the receptor-binding domain of the S-protein. • The potency of neutralizing the D614G variant may depend on the type of neutralizing antibody. [ABSTRACT FROM AUTHOR]

Background: The outbreak of coronavirus disease (COVID-19) was caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), through its surface spike glycoprotein (S-protein) recognition on the receptor Angiotensin-converting enzyme 2 (ACE2) in humans. However, it remains unclear how genetic variations in ACE2 may affect its function and structure, and consequently alter the recognition by SARS-CoV-2.Methods: We have systemically characterized missense variants in the gene ACE2 using data from the Genome Aggregation Database (gnomAD; N = 141,456). To investigate the putative deleterious role of missense variants, six existing functional prediction tools were applied to evaluate their impact. We further analyzed the structural flexibility of ACE2 and its protein-protein interface with the S-protein of SARS-CoV-2 using our developed Legion Interfaces Analysis (LiAn) program.Results: Here, we characterized a total of 12 ACE2 putative deleterious missense variants. Of those 12 variants, we further showed that p.His378Arg could directly weaken the binding of catalytic metal atom to decrease ACE2 activity and p.Ser19Pro could distort the most important helix to the S-protein. Another seven missense variants may affect secondary structures (i.e. p.Gly211Arg; p.Asp206Gly; p.Arg219Cys; p.Arg219His, p.Lys341Arg, p.Ile468Val, and p.Ser547Cys), whereas p.Ile468Val with AF = 0.01 is only present in Asian.Conclusions: We provide strong evidence of putative deleterious missense variants in ACE2 that are present in specific populations, which could disrupt the function and structure of ACE2. These findings provide novel insight into the genetic variation in ACE2 which may affect the SARS-CoV-2 recognition and infection, and COVID-19 susceptibility and treatment. [ABSTRACT FROM AUTHOR]