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1.
Carbohydr Res ; 518: 108574, 2022 Aug.
Article in English | MEDLINE | ID: covidwho-1821162

ABSTRACT

Can envelope glycans be targeted to stop viral pandemics? Here we address this question by using molecular dynamics simulations to study the binding between 10 synthetic carbohydrate receptors (SCRs) and the 33 N-glycans most commonly found on the surfaces of enveloped viruses, including Zika virus and SARS-CoV-2. Based on association quotients derived from these simulations, we classified the SCRs as weak binders, promiscuous binders, or selective binders. The SCRs almost exclusively associate at the Man3GlcNAc2 core, which is common to all N-glycans, but the binding affinity between the SCR⋅glycan pair depends on the noncovalent interactions between the heterocycle rings and the glycan antennae. Systematic variations in the glycan and SCR structures reveal relationships that could guide the design of SCRs to attain affinity and selectivity towards a chosen envelope glycan target. With these results, envelope glycans, which are currently considered "undruggable", could become viable targets for new therapeutic strategies.


Subject(s)
COVID-19 , Receptors, Artificial , Zika Virus Infection , Zika Virus , Carbohydrates/chemistry , Humans , Molecular Dynamics Simulation , Polysaccharides/chemistry , Receptors, Artificial/chemistry , SARS-CoV-2 , Zika Virus/metabolism
2.
Viruses ; 14(2)2022 02 06.
Article in English | MEDLINE | ID: covidwho-1674826

ABSTRACT

An outbreak of SARS-CoV-2 coronavirus (COVID-19) first detected in Wuhan, China, has created a public health emergency all over the world. The pandemic has caused more than 340 million confirmed cases and 5.57 million deaths as of 23 January 2022. Although carbohydrates have been found to play a role in coronavirus binding and infection, the role of cell surface glycans in SARS-CoV-2 infection and pathogenesis is still not understood. Herein, we report that the SARS-CoV-2 spike protein S1 subunit binds specifically to blood group A and B antigens, and that the spike protein S2 subunit has a binding preference for Lea antigens. Further examination of the binding preference for different types of red blood cells (RBCs) indicated that the spike protein S1 subunit preferentially binds with blood group A RBCs, whereas the spike protein S2 subunit prefers to interact with blood group Lea RBCs. Angiotensin converting enzyme 2 (ACE2), a known target of SARS-CoV-2 spike proteins, was identified to be a blood group A antigen-containing glycoprotein. Additionally, 6-sulfo N-acetyllactosamine was found to inhibit the binding of the spike protein S1 subunit with blood group A RBCs and reduce the interaction between the spike protein S1 subunit and ACE2.


Subject(s)
Carbohydrates/chemistry , SARS-CoV-2/chemistry , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism , COVID-19/virology , Carbohydrates/genetics , China , Erythrocytes/metabolism , Humans , Ligands , Polysaccharides , Protein Array Analysis , Protein Binding , SARS-CoV-2/metabolism , Virus Internalization
3.
Comput Biol Chem ; 96: 107621, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1611674

ABSTRACT

Quantitative physicochemical perspective on life processes has been a great asset, in bioengineering and biotechnology. The quantitative physicochemical approach can be applied to practically all organisms, including viruses, if their chemical composition and thermodynamic properties are known. In this paper, a new method is suggested for determining elemental composition of viruses, based on atom counting. The atom counting method requires knowledge of genetic sequence, protein sequences and protein copy numbers. An algorithm was suggested for a program that finds elemental composition of various viruses (DNA or RNA, enveloped or non-enveloped). Except for the nucleic acid, capsid proteins, lipid bilayer and carbohydrates, this method includes membrane proteins, as well as spike proteins. The atom counting method has been compared with the existing molecular composition and geometric methods on 5 viruses of different morphology, as well as experimentally determined composition of the poliovirus. The atom counting method was found to be more accurate in most cases. The three methods were found to be complementary, since they require different kind of input information. Moreover, since the 3 methods rest on different assumptions, results of one model can be compared to those of the other two.


Subject(s)
Viruses/chemistry , Algorithms , Animals , Carbohydrates/chemistry , Chemical Phenomena , Computational Biology , DNA, Viral/chemistry , DNA, Viral/genetics , Elements , Environmental Science , Humans , Lipids/chemistry , RNA, Viral/chemistry , RNA, Viral/genetics , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , Thermodynamics , Viral Proteins/chemistry , Viral Proteins/genetics , Viruses/genetics
4.
Biochem Soc Trans ; 49(5): 2411-2429, 2021 11 01.
Article in English | MEDLINE | ID: covidwho-1397910

ABSTRACT

The importance of vaccine-induced protection was repeatedly demonstrated over the last three decades and emphasized during the recent COVID-19 pandemic as the safest and most effective way of preventing infectious diseases. Vaccines have controlled, and in some cases, eradicated global viral and bacterial infections with high efficiency and at a relatively low cost. Carbohydrates form the capsular sugar coat that surrounds the outer surface of human pathogenic bacteria. Specific surface-exposed bacterial carbohydrates serve as potent vaccine targets that broadened our toolbox against bacterial infections. Since first approved for commercial use, antibacterial carbohydrate-based vaccines mostly rely on inherently complex and heterogenous naturally derived polysaccharides, challenging to obtain in a pure, safe, and cost-effective manner. The introduction of synthetic fragments identical with bacterial capsular polysaccharides provided well-defined and homogenous structures that resolved many challenges of purified polysaccharides. The success of semisynthetic glycoconjugate vaccines against bacterial infections, now in different phases of clinical trials, opened up new possibilities and encouraged further development towards fully synthetic antibacterial vaccine solutions. In this mini-review, we describe the recent achievements in semi- and fully synthetic carbohydrate vaccines against a range of human pathogenic bacteria, focusing on preclinical and clinical studies.


Subject(s)
Anti-Bacterial Agents/immunology , Bacteria/immunology , Bacterial Infections/immunology , Carbohydrates/immunology , Glycoconjugates/immunology , Vaccines, Synthetic/immunology , Anti-Bacterial Agents/chemistry , Anti-Bacterial Agents/therapeutic use , Bacteria/drug effects , Bacterial Infections/microbiology , Bacterial Infections/prevention & control , COVID-19/immunology , COVID-19/prevention & control , COVID-19/virology , COVID-19 Vaccines/immunology , COVID-19 Vaccines/therapeutic use , Carbohydrate Sequence , Carbohydrates/chemistry , Glycoconjugates/chemistry , Glycoconjugates/therapeutic use , Humans , Vaccines, Synthetic/chemistry , Vaccines, Synthetic/therapeutic use
5.
Expert Rev Vaccines ; 20(7): 797-810, 2021 07.
Article in English | MEDLINE | ID: covidwho-1260998

ABSTRACT

Introduction: Adjuvants are essential to vaccines for immunopotentiation in the elicitation of protective immunity. However, classical and widely used aluminum-based adjuvants have limited capacity to induce cellular response. There are increasing needs for appropriate adjuvants with improved profiles for vaccine development toward emerging pathogens. Carbohydrate-containing nanoparticles (NPs) with immunomodulatory activity and particulate nanocarriers for effective antigen presentation are capable of eliciting a more balanced humoral and cellular immune response.Areas covered: We reviewed several carbohydrates with immunomodulatory properties. They include chitosan, ß-glucan, mannan, and saponins, which have been used in vaccine formulations. The mode of action, the preparation methods, characterization of these carbohydrate-containing NPs and the corresponding vaccines are presented.Expert opinion: Several carbohydrate-containing NPs have entered the clinical stage or have been used in licensed vaccines for human use. Saponin-containing NPs are being evaluated in a vaccine against SARS-CoV-2, the pathogen causing the on-going worldwide pandemic. Vaccines with carbohydrate-containing NPs are in different stages of development, from preclinical studies to late-stage clinical trials. A better understanding of the mode of action for carbohydrate-containing NPs as vaccine carriers and as immunostimulators will likely contribute to the design and development of new generation vaccines against cancer and infectious diseases.


Subject(s)
Adjuvants, Immunologic/chemistry , COVID-19 Vaccines/chemistry , COVID-19/prevention & control , Carbohydrates/chemistry , Nanoparticles/chemistry , Adjuvants, Immunologic/administration & dosage , Animals , COVID-19/immunology , COVID-19 Vaccines/administration & dosage , COVID-19 Vaccines/immunology , Carbohydrates/administration & dosage , Carbohydrates/immunology , Chitosan/administration & dosage , Chitosan/chemistry , Chitosan/immunology , Humans , Mannans/administration & dosage , Mannans/chemistry , Mannans/immunology , Nanoparticles/administration & dosage , beta-Glucans/administration & dosage , beta-Glucans/chemistry , beta-Glucans/immunology
6.
Sci Rep ; 11(1): 7880, 2021 04 12.
Article in English | MEDLINE | ID: covidwho-1180278

ABSTRACT

Since the pandemic outbreak of Covid-19 in December 2019, several lateral flow assay (LFA) devices were developed to enable the constant monitoring of regional and global infection processes. Additionally, innumerable lateral flow test devices are frequently used for determination of different clinical parameters, food safety, and environmental factors. Since common LFAs rely on non-biodegradable nitrocellulose membranes, we focused on their replacement by cellulose-composed, biodegradable papers. We report the development of cellulose paper-based lateral flow immunoassays using a carbohydrate-binding module-fused to detection antibodies. Studies regarding the protein binding capacity and potential protein wash-off effects on cellulose paper demonstrated a 2.7-fold protein binding capacity of CBM-fused antibody fragments compared to the sole antibody fragment. Furthermore, this strategy improved the spatial retention of CBM-fused detection antibodies to the test area, which resulted in an enhanced sensitivity and improved overall LFA-performance compared to the naked detection antibody. CBM-assisted antibodies were validated by implementation into two model lateral flow test devices (pregnancy detection and the detection of SARS-CoV-2 specific antibodies). The CBM-assisted pregnancy LFA demonstrated sensitive detection of human gonadotropin (hCG) in synthetic urine and the CBM-assisted Covid-19 antibody LFA was able to detect SARS-CoV-2 specific antibodies present in serum. Our findings pave the way to the more frequent use of cellulose-based papers instead of nitrocellulose in LFA devices and thus potentially improve the sustainability in the field of POC diagnostics.


Subject(s)
Antibodies, Viral/analysis , COVID-19 Serological Testing/methods , COVID-19/diagnosis , Carbohydrates/chemistry , Collodion/chemistry , Immunoassay/methods , Biocompatible Materials , Chorionic Gonadotropin/chemistry , Clostridium thermocellum/immunology , Humans , Immunoglobulin Fragments/chemistry , Immunoglobulin G/chemistry , Point-of-Care Systems , Protein Binding , SARS-CoV-2/immunology , Urinalysis
7.
Biomolecules ; 11(3)2021 03 22.
Article in English | MEDLINE | ID: covidwho-1151739

ABSTRACT

Global processes, such as climate change, frequent and distant travelling and population growth, increase the risk of viral infection spread. Unfortunately, the number of effective and accessible medicines for the prevention and treatment of these infections is limited. Therefore, in recent years, efforts have been intensified to develop new antiviral medicines or vaccines. In this review article, the structure and activity of the most promising antiviral cyanobacterial products are presented. The antiviral cyanometabolites are mainly active against the human immunodeficiency virus (HIV) and other enveloped viruses such as herpes simplex virus (HSV), Ebola or the influenza viruses. The majority of the metabolites are classified as lectins, monomeric or dimeric proteins with unique amino acid sequences. They all show activity at the nanomolar range but differ in carbohydrate specificity and recognize a different epitope on high mannose oligosaccharides. The cyanobacterial lectins include cyanovirin-N (CV-N), scytovirin (SVN), microvirin (MVN), Microcystisviridis lectin (MVL), and Oscillatoria agardhii agglutinin (OAA). Cyanobacterial polysaccharides, peptides, and other metabolites also have potential to be used as antiviral drugs. The sulfated polysaccharide, calcium spirulan (CA-SP), inhibited infection by enveloped viruses, stimulated the immune system's response, and showed antitumor activity. Microginins, the linear peptides, inhibit angiotensin-converting enzyme (ACE), therefore, their use in the treatment of COVID-19 patients with injury of the ACE2 expressing organs is considered. In addition, many cyanobacterial extracts were revealed to have antiviral activities, but the active agents have not been identified. This fact provides a good basis for further studies on the therapeutic potential of these microorganisms.


Subject(s)
Antiviral Agents/chemistry , Cyanobacteria/chemistry , HIV/drug effects , Lectins/pharmacology , Polysaccharides/pharmacology , SARS-CoV-2/drug effects , Simplexvirus/drug effects , Anti-HIV Agents/pharmacology , Antineoplastic Agents/pharmacology , Antiviral Agents/pharmacology , Bacterial Proteins/chemistry , Bacterial Proteins/pharmacology , COVID-19/drug therapy , Carbohydrates/chemistry , Carbohydrates/pharmacology , Cyanobacteria/metabolism , HIV Infections/drug therapy , Humans , Lectins/chemistry , Lectins/metabolism , Polysaccharides/chemistry , Polysaccharides/metabolism
8.
Viruses ; 13(2)2021 02 02.
Article in English | MEDLINE | ID: covidwho-1154509

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally. Although measures to control SARS-CoV-2, namely, vaccination, medication, and chemical disinfectants are being investigated, there is an increase in the demand for auxiliary antiviral approaches using natural compounds. Here we have focused on hydroxytyrosol (HT)-rich aqueous olive pulp extract (HIDROX®) and evaluated its SARS-CoV-2-inactivating activity in vitro. We showed that the HIDROX solution exhibits time- and concentration-dependent SARS-CoV-2-inactivating activities, and that HIDROX has more potent virucidal activity than pure HT. The evaluation of the mechanism of action suggested that both HIDROX and HT induced structural changes in SARS-CoV-2, which changed the molecular weight of the spike proteins. Even though the spike protein is highly glycosylated, this change was induced regardless of the glycosylation status. In addition, HIDROX or HT treatment disrupted the viral genome. Moreover, the HIDROX-containing cream applied on film showed time- and concentration-dependent SARS-CoV-2-inactivating activities. Thus, the HIDROX-containing cream can be applied topically as an antiviral hand cream. Our findings suggest that HIDROX contributes to improving SARS-CoV-2 control measures.


Subject(s)
Antiviral Agents/pharmacology , Olea , Phenylethyl Alcohol/analogs & derivatives , Plant Extracts/pharmacology , SARS-CoV-2/drug effects , Administration, Topical , Animals , Antiviral Agents/chemistry , Carbohydrates/chemistry , Chlorocebus aethiops , Coronavirus Nucleocapsid Proteins/chemistry , Genome, Viral/drug effects , Glycosylation , Microbial Sensitivity Tests , Phenylethyl Alcohol/administration & dosage , Phenylethyl Alcohol/pharmacology , Phosphoproteins/chemistry , Plant Extracts/chemistry , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Skin Cream , Spike Glycoprotein, Coronavirus/chemistry , Vero Cells , Virus Inactivation/drug effects
9.
Prog Biophys Mol Biol ; 161: 39-53, 2021 05.
Article in English | MEDLINE | ID: covidwho-894160

ABSTRACT

A variety of coronaviruses (CoVs) have infected humans and caused mild to severe respiratory diseases that could result in mortality. The human CoVs (HCoVs) belong to the genera of α- and ß-CoVs that originate in rodents and bats and are transmitted to humans via zoonotic contacts. The binding of viral spike proteins to the host cell receptors is essential for mediating fusion of viral and host cell membranes to cause infection. The SARS-CoV-2 originated in bats (RaTG13 SARS-CoV) and is transmitted to humans via pangolins. The presence of 'PRRA' sequence motif in SARS-CoV-2 spike proteins from human, dog, cat, mink, tiger and lion suggests a common viral entry mechanism into host cells. In this review, we discuss structural features of HCoV spike proteins and recognition of host protein and carbohydrate receptors.


Subject(s)
COVID-19/immunology , Receptors, Virus/chemistry , Spike Glycoprotein, Coronavirus/chemistry , Amino Acid Motifs , Animals , Carbohydrates/chemistry , Chiroptera , Cryoelectron Microscopy , Databases, Protein , Drug Repositioning , Genome, Viral , Humans , Middle East Respiratory Syndrome Coronavirus , Pangolins , Phylogeny , Protein Binding , Protein Conformation , Protein Interaction Mapping , SARS-CoV-2 , Species Specificity
10.
Chemistry ; 26(51): 11782-11795, 2020 Sep 10.
Article in English | MEDLINE | ID: covidwho-777429

ABSTRACT

Synthetic carbohydrate receptors (SCRs) that selectively recognize cell-surface glycans could be used for detection, drug delivery, or as therapeutics. Here we report the synthesis of seven new C2h symmetric tetrapodal SCRs. The structures of these SCRs possess a conserved biaryl core, and they vary in the four heterocyclic binding groups that are linked to the biaryl core via secondary amines. Supramolecular association between these SCRs and five biologically relevant C1 -O-octyloxy glycans, α/ß-glucoside (α/ß-Glc), α/ß-mannoside (α/ß-Man), and ß-galactoside (ß-Gal), was studied by mass spectrometry, 1 H NMR titrations, and molecular modeling. These studies revealed that selectivity can be achieved in these tetrapodal SCRs by varying the heterocyclic binding group. We found that SCR017 (3-pyrrole), SCR021 (3-pyridine), and SCR022 (2-phenol) bind only to ß-Glc. SCR019 (3-indole) binds only to ß-Man. SCR020 (2-pyridine) binds ß-Man and α-Man with a preference to the latter. SCR018 (2-indole) binds α-Man and ß-Gal with a preference to the former. The glycan guests bound within their SCR hosts in one of three supramolecular geometries: center-parallel, center-perpendicular, and off-center. Many host-guest combinations formed higher stoichiometry complexes, 2:1 glycan⋅SCR or 1:2 glycan⋅SCR, where the former are driven by positive allosteric cooperativity induced by glycan-glycan contacts.


Subject(s)
Carbohydrates/chemical synthesis , Lectins, C-Type/chemistry , Mannose-Binding Lectins/chemistry , Mannose/chemical synthesis , Polysaccharides/chemistry , Receptors, Artificial/chemistry , Receptors, Cell Surface/chemistry , Carbohydrates/chemistry , Magnetic Resonance Spectroscopy , Mannose/chemistry , Models, Molecular , Molecular Structure
11.
Med Hypotheses ; 144: 110155, 2020 Nov.
Article in English | MEDLINE | ID: covidwho-716870

ABSTRACT

The world is experiencing one of the most difficult moments in history with the COVID-19 pandemic, a disease caused by SARS-CoV-2, a new type of coronavirus. Virus infectivity is mediated by the binding of Spike transmembrane glycoprotein to specific protein receptors present on cell host surface. Spike is a homotrimer that emerges from the virion, each monomer containing two subunits named S1 and S2, which are related to cell recognition and membrane fusion, respectively. S1 is subdivided in domains S1A (or NTD) and S1B (or RBD), with experimental and in silico studies suggesting that the former binds to sialic acid-containing glycoproteins, such as CD147, whereas the latter binds to ACE2 receptor. Recent findings indicate that the ABO blood system modulates susceptibility and progression of infection, with type-A individuals being more susceptible to infection and/or manifestation of a severe condition. Seeking to understand the molecular mechanisms underlying this susceptibility, we carried out an extensive bibliographic survey on the subject. Based on this survey, we hypothesize that the correlation between the ABO blood system and susceptibility to SARS-CoV-2 infection can be presumably explained by the modulation of sialic acid-containing receptors distribution on host cell surface induced by ABO antigens through carbohydrate-carbohydrate interactions, which could maximize or minimize the virus Spike protein binding to the host cell. This model could explain previous sparse observations on the molecular mechanism of infection and can direct future research to better understand of COVID-19 pathophysiology.


Subject(s)
ABO Blood-Group System , COVID-19/blood , COVID-19/diagnosis , Carbohydrates/chemistry , Disease Susceptibility , Spike Glycoprotein, Coronavirus/chemistry , Angiotensin-Converting Enzyme 2/chemistry , Animals , Basigin/chemistry , Binding Sites , COVID-19/epidemiology , Humans , Models, Theoretical , Molecular Dynamics Simulation , Protein Binding , Protein Domains , SARS-CoV-2 , Virus Internalization
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