scholarly journals Covalent Inhibition of SARS-CoV-2 RBD-ACE2 Interaction by Aptamers with Multiple Sulfur(VI) Fluoride Exchange Modifications

2021 ◽  
Author(s):  
Zichen Qin ◽  
Yiying Zhu ◽  
Yu Xiang
Keyword(s):  
Human Serum ◽  
Covalent Bond ◽  
Covalent Bonding ◽  
Peptide Fragmentation ◽  
Host Cells ◽  
Great Promise ◽  
Enzyme Linked Immunosorbent Assay ◽  
Covalent Bonds ◽  
Target Proteins ◽  
Covalent Inhibitors

The SARS-CoV-2 spike protein uses its receptor-binding domain (RBD) to interact with the angiotensin-converting enzyme 2 (ACE2) receptor on host cells, establishing the first step of SARS-CoV-2 infection. Inhibitors of RBD-ACE2 interaction, therefore, have shown great promise in preventing SARS-CoV-2 infection. Currently known RBD-ACE2 inhibitors are all based on reversible binding and must compete with ACE2 or RBD at the equilibrium. On the other hand, covalent inhibitors, such as those based on sulfur(VI) fluoride exchange (SuFEx) chemistry, can form irreversible chemical bonds with target proteins and offer advantages including higher potency and longer duration of inhibition. Here, we report covalent aptamer inhibitors that can block RBD-ACE2 by forming covalent bonds with RBD. These covalent aptamer inhibitors were developed by equipping known RBD aptamers with multiple SuFEx (mSuFEx) modifications. The mSuFEx-aptamer 6C3-7SF underwent strong covalent bonding with RBD and some of its variants at fast rates (t1/2 = 20 ~ 29 min−1) and induced more efficient RBD-ACE2 inhibition (IC50 = 26 ~ 37 nM) than the original aptamer (IC50 > 200 nM) according to an in vitro enzyme-linked immunosorbent assay (ELISA). The covalent bond formation was highly selective to RBD over human serum albumin (HSA) and ACE2, and could occur efficiently in diluted human serum. Peptide fragmentation analyses of the RBD-6C3-7SF adducts revealed multiple sites of covalent bonding on RBD, including K378, R408, Y422, Y424, Y453, and K458. The surprising R408 suggests that context-specific non-N-terminal arginine could be a new type of targetable residue by SuFEx-based covalent inhibitors, which were never reported as reactive with any non-N-terminal arginine in target proteins. In addition, RBD R408 is responsible for binding with ACE2 N90 glycan, and this arginine is conserved in SARS-CoV-2 variants of concern or interest, suggesting that R408 could be the potential site of interest for developing SuFEx-based covalent inhibitors against threatening SARS-CoV-2 variants. Although the compatibility of mSuFEx-based covalent aptamers in cellular and in vivo systems should be further investigated, our study demonstrated the promise of mSuFEx chemistry in constructing potent covalent aptamers to inhibit important protein-protein interactions (PPIs).

scholarly journals Covalent Bonding Aptamer with Enhanced SARS-CoV-2 RBD-ACE2 Blocking and Pseudovirus Neutralization Activities

2021 ◽  
Author(s):  
Zichen Qin ◽  
Yiying Zhu ◽  
Yu Xiang
Keyword(s):  
Covalent Bonding ◽  
Host Cells ◽  
Receptor Binding Domain ◽  
Covalent Bonds ◽  
Angiotensin Converting Enzyme 2 ◽  
Drug Candidates ◽  
Chemically Modified ◽  
Binding Interface ◽  
Covalent Inhibition ◽  
Protein Receptor

SARS-CoV-2 uses its spike protein receptor-binding domain (RBD) to interact with the angiotensin-converting enzyme 2 (ACE2) receptor on host cells. Inhibitors of the RBD-ACE2 interaction are therefore promising drug candidates in treating COVID-19. Here, we report a covalent bonding aptamer that can block the RBD-ACE2 interaction and neutralize SARS-CoV-2 pseudovirus infection by forming covalent bonds on RBD, resulting in more than 25-fold enhancement of pseudovirus neutralization efficacy over the original binding aptamer. The chemically modified aptamer is equipped with sulfur(VI) fluoride exchange (SuFEx) modifications and covalently targets important RBD residues within the RBD-ACE2 binding interface, including Y453 and R408. The covalent bonding is highly specific to RBD over other proteins such as human serum albumin (HSA), ACE2 and immunoglobulin G1 (IgG1) Fc. Our study demonstrates the promise of introducing covalent inhibition mechanisms for developing robust RBD-ACE2 inhibitors against SARS-CoV-2 infection.

Conceptual integration of covalent bond models by Algerian students

2014 ◽  
Vol 15 (4) ◽  
pp. 675-688 ◽  
Author(s):  
Hazzi Salah ◽  
Alain Dumon
Keyword(s):  
Covalent Bond ◽  
Covalent Bonding ◽  
Quantum Model ◽  
Covalent Bonds ◽  
Conceptual Integration ◽  
Knowledge Framework ◽  
Chemistry Learning ◽  
Valence Electrons ◽  
Lewis Structures ◽  
Hybrid Orbitals

The concept of covalent bonding is characterized by an interconnected knowledge framework based on Lewis and quantum models of atoms and molecules. Several research studies have shown that students at all levels of chemistry learning find the quantum model to be one of the most difficult subjects to understand. We have tried in this paper to analyze the extent to which Algerian students, at the end of their training, have integrated the covalent bonding theories based on the quantum model of atom theory and are able to interpret Lewis structures using the quantum model. The analysis of the responses to a written questionnaire showed that this integration was not achieved by our students and that they are not able to correctly describe covalent bonds in a Lewis structure using the concepts of the quantum model. They have a “quantum box” conception of atomic or hybrid orbitals. This conception acts as a “pedagogical learning impediment” to the integration of the geometrical representations of atomic and hybrid orbitals, the conditions of their overlapping to give bonds and consequently the description of covalent bonds using the quantum model. So, the students use an alternative conceptual framework based on the use of Lewis model paired valence electrons to form covalent bonds that we have named the: “electrons pair framework”. Furthermore, the students restricted the denomination of a covalent bond to the sharing of one electron (either s or p but not spn) from each atom to give one “electron pair σ”, and thought that σ bonds are only formed in single bonds.

MANY-ATOM VAN DER WAALS INTERACTIONS LEAD TO DIRECTION-SENSITIVE INTERACTIONS OF COVALENT BONDS

2008 ◽  
Vol 06 (04) ◽  
pp. 693-707 ◽  
Author(s):  
ALEXEI V. FINKELSTEIN ◽  
MICHAEL Y. LOBANOV ◽  
NIKITA V. DOVIDCHENKO ◽  
NATALIA S. BOGATYREVA
Keyword(s):  
Physical Theory ◽  
Van Der Waals ◽  
Protein Structures ◽  
Covalent Bond ◽  
Covalent Bonding ◽  
Van Der Waals Interactions ◽  
Binding Affinities ◽  
Dispersion Interactions ◽  
Energy Effect ◽  
Covalent Bonds

Strict physical theory and numerical calculations show that a specific coupling of many-atom van der Waals interactions with covalent bonding can significantly (half as much) increase the strength of attractive dispersion interactions when the direction of interaction coincides with the direction of the covalent bond, and decrease this strength when the direction of interaction is perpendicular to the direction of the covalent bond. The energy effect is comparable to that caused by the replacement of atoms (e.g. N by C or O ) in conventional pairwise van der Waals interactions. Analysis of protein structures shows that they bear an imprint of this effect. This means that many-atom van der Waals interactions cannot be ignored in refinement of protein structures, in simulations of their folding, and in prediction of their binding affinities.

EFEKTIVITAS MODEL PEMBELAJARAN KOOPERATIF TIPE TEAMS GAMES TOURNAMENT (TGT) BERBANTUAN MEDIA KARTU SOAL PADA SUB MATERI IKATAN KOVALEN KELAS X MIA DI SMA ISLAM HARUNIYAH PONTIANAK

2018 ◽  
Vol 6 (2) ◽  
Author(s):  
Zulfadhli Abdillah
Keyword(s):  
Student Learning ◽  
Learning Outcomes ◽  
Covalent Bond ◽  
Student Learning Outcomes ◽  
Learning Model ◽  
Covalent Bonds ◽  
Team Games ◽  
Bonding Material ◽  
Before And After ◽  
Tenth Grade

 This  study  is  motivated  by  the  low  learning  outcomes  in  the  Sub-covalent  Bond class of tenth-grade students, SMA Islam Haruniyah Pontianak. This problem is due to the  lack  of  students'  understanding  of  the  concept  of  Covalent  Bonds.  Therefore,  a proper learning model is required to improve students’ understanding of Covalent Bond concepts  based  on  the  characteristics  of  both  learning  materials    and  students.  This study  aimed  to  investigate  the  differences  in  the  student  learning  outcomes  and  the effectiveness of the question card-based on TGT learning in the Sub-covalent Bonding material. Using the pre-experimental method of one-group pretest-posttest design, the tenth-grade  students  of  Math  and  Science  Class  of  SMS  Islam  Haruniyah  Pontianak participated in this study. The data collection tools used were learning outcomes tests, observation sheets, and interview sheets. The results of data analysis revealed that the average  pretest  score  was  36  and  the  posttest  was  62.94.  In  addition,  the  t-test statistical  analysis  indicated  a  significance  value  of  0.00  (0.00  <0.05)  which  meanth that there were differences in student learning outcomes between before and after the question  card-based  TGT  learning  model  implemented.  The  gain  value  was  0.42.  In other words, the  question card-based on TGT learning model is effective in improving the student  learning outcomes with good category. Keywords: Covalent Bond, Question Card, Team Games Tournament (TGT)

Serum Albumins Guided Plasmonic Nanoassemblies with Opposite Chiralities

Soft Matter ◽  
2021 ◽  
Author(s):  
Zhaoyi Wang ◽  
Ningning Zhang ◽  
Jincheng Li ◽  
Jun Lu ◽  
Li Zhao ◽  
...  
Keyword(s):  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Great Promise ◽  
Plasmonic Nanostructures ◽  
Serum Albumins ◽  
Catalytic Applications

Chiral assemblies by combining natural biomolecules with plasmonic nanostructures hold great promise for plasmonic enhanced sensing, imaging, and catalytic applications. Herein, we demonstrate that human serum albumin (HSA) and porcine...

Structure study of the chalcogens and chalcogenides by X-ray absorption fine structure

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Hiroyuki Ikemoto ◽  
Takafumi Miyanaga
Keyword(s):  
Fine Structure ◽  
Covalent Bond ◽  
Narrow Channel ◽  
Structure Study ◽  
Chain Structure ◽  
Covalent Bonds ◽  
X Ray ◽  
Absorption Fine ◽  
Amorphous States ◽  
X Ray Absorption

AbstractIn this review, we make a survey of the structure studies for the chalcogen elements and several chalcogenides in liquid, amorphous and nanosized state by using X-ray absorption fine structure (XAFS). The chalcogen elements have hierarchic structures; the chain structure constructed with the strong covalent bond as a primary structure, and the weaker interaction between chains as a secondary one. Existence of these two kinds of interactions induces exotic behaviors in the liquid, amorphous and nanosized state of the chalcogen and chalcogenides. XAFS is a powerful structure analysis technique for multi-element systems and the disordered materials, so it is suitable for the study of such as liquid, amorphous and nanosized mixtures. In section 2, the structures for the liquid state are discussed, which show the interesting semiconductor-metal transition depending on their temperatures and components. In section 3, the structure for the amorphous states are discussed. Especially, some of chalcogens and chalcogenides present the photostructural change, which is important industrial application. In section 4, the structures of nanosized state, nanoparticles and isolated chain confined into the narrow channel, are discussed. The studies of the nanoparticle and the isolated chain reveal the alternative role between the intrachain covalent bonds and the interchain interaction.

scholarly journals Bone marrow stromal fibroblasts secrete interleukin-6 and granulocyte- macrophage colony-stimulating factor in the absence of inflammatory stimulation: demonstration by serum-free bioassay, enzyme-linked immunosorbent assay, and reverse transcriptase polymerase chain reaction

Blood ◽  
1992 ◽  
Vol 80 (5) ◽  
pp. 1190-1198 ◽  
Author(s):  
SC Guba ◽  
CI Sartor ◽  
LR Gottschalk ◽  
YH Jing ◽  
T Mulligan ◽  
...  
Keyword(s):  
Human Serum ◽  
Enzyme Linked Immunosorbent Assay ◽  
Stromal Fibroblasts ◽  
Gm Csf ◽  
Normal Human ◽  
Macrophage Colony Stimulating Factor ◽  
Polymerase Chain ◽  
Macrophage Colony ◽  
Stimulating Factor

Abstract Bone marrow (BM) stromal fibroblasts produce hematopoietic growth factors (HGFs) in response to inflammatory mediators such as tumor necrosis factor-alpha or interleukin-1 alpha (IL-1 alpha). In the absence of such inflammatory stimuli, production of HGFs by BM stromal cells has been problematic and controversial. In vivo, however, basal hematopoiesis maintains blood counts within a normal homeostatic range even in the absence of inflammation, and HGFs are required for progenitor cell differentiation in vitro. To better ascertain the contribution of BM stromal fibroblasts to basal hematopoiesis, we therefore studied HGF production in quiescent BM stromal fibroblasts by three sensitive assays: serum-free bioassay, enzyme-linked immunosorbent assay, and reverse transcriptase polymerase chain reaction. Stromal fibroblasts were cultured in the presence or absence of normal human serum to determine if serum factor(s) present in the noninflammatory (basal) state induce secretion of HGFs. Human serum was found to induce or enhance transcription and secretion of granulocyte- macrophage colony-stimulating factor (GM-CSF) and enhance secretion of constitutively expressed IL-6. In contrast, no secretion of either granulocyte-CSF (G-CSF) or IL-3 was found. These data indicate that factors in normal human serum are active in enhancing GM-CSF and IL-6 production by stromal fibroblasts and suggest that these growth factors contribute to the maintainance of normal, basal hematopoiesis in vivo.

scholarly journals Protein Turnover Measurements in Human Serum by Serial Immunoaffinity LC-MS/MS

2018 ◽  
Vol 64 (2) ◽  
pp. 279-288 ◽  
Author(s):  
Vahid Farrokhi ◽  
Xiaoying Chen ◽  
Hendrik Neubert
Keyword(s):  
Mass Spectrometry ◽  
Cell Adhesion ◽  
Human Serum ◽  
Adhesion Molecule ◽  
Protein Turnover ◽  
Cell Adhesion Molecule ◽  
Analytical Sensitivity ◽  
Target Proteins ◽  
Cell Adhesion Molecule 1 ◽  
Sample Set

Abstract BACKGROUND The half-life of target proteins is frequently an important parameter in mechanistic pharmacokinetic and pharmacodynamic (PK/PD) modeling of biotherapeutics. Clinical studies for accurate measurement of physiologically relevant protein turnover can reduce the uncertainty in PK/PD model-based predictions, for example, of the therapeutic dose and dosing regimen in first-in-human clinical trials. METHODS We used a targeted mass spectrometry work flow based on serial immunoaffinity enrichment ofmultiple human serum proteins from a [5,5,5-2H3]-L-leucine tracer pulse-chase study in healthy volunteers. To confirm the reproducibility of turnover measurements from serial immunoaffinity enrichment, multiple aliquots from the same sample set were subjected to protein turnover analysis in varying order. Tracer incorporation was measured by multiple–reaction-monitoring mass spectrometry and target turnover was calculated using a four-compartment pharmacokinetic model. RESULTS Five proteins of clinical or therapeutic relevance including soluble tumor necrosis factor receptor superfamily member 12A, tissue factor pathway inhibitor, soluble interleukin 1 receptor like 1, soluble mucosal addressin cell adhesion molecule 1, and muscle-specific creatine kinase were sequentially subjected to turnover analysis from the same human serum sample. Calculated half-lives ranged from 5–15 h; however, no tracer incorporation was observed for mucosal addressin cell adhesion molecule 1. CONCLUSIONS The utility of clinical pulse-chase studies to investigate protein turnover can be extended by serial immunoaffinity enrichment of target proteins. Turnover analysis from serum and subsequently from remaining supernatants provided analytical sensitivity and reproducibility for multiple human target proteins in the same sample set, irrespective of the order of analysis.

scholarly journals C-Terminal Invariable Domain of VlsE Is Immunodominant but Its Antigenicity Is Scarcely Conserved among Strains of Lyme Disease Spirochetes

2001 ◽  
Vol 69 (5) ◽  
pp. 3224-3231 ◽  
Author(s):  
Fang Ting Liang ◽  
Lisa C. Bowers ◽  
Mario T. Philipp
Keyword(s):  
Lyme Disease ◽  
Antibody Response ◽  
Human Serum ◽  
Synthetic Peptide ◽  
Species Complex ◽  
Enzyme Linked Immunosorbent Assay ◽  
Serum Samples ◽  
Variable Surface ◽  
Entire Sequence ◽  
Carboxyl Terminal

ABSTRACT VlsE, the variable surface antigen of Borrelia burgdorferi, contains two invariable domains located at the amino and carboxyl terminal ends, respectively, and a central variable domain. In this study, both immunogenicity and antigenic conservation of the C-terminal invariable domain were assessed. Mouse antiserum to a 51-mer synthetic peptide (Ct) which reproduced the entire sequence of the C-terminal invariable domain of VlsE from B. burgdorferi strain B31 was reacted on immunoblots with whole-cell lysates extracted from spirochetes of 12 strains from the B. burgdorferi sensu lato species complex. The antiserum recognized only VlsE from strain B31, indicating that epitopes of this domain differed among these strains. When Ct was used as enzyme-linked immunosorbent assay (ELISA) antigen, all of the seven monkeys and six mice that were infected with B31 spirochetes produced a strong antibody response to this peptide, indicating that the C-terminal invariable domain is immunodominant. None of 12 monkeys and only 11 of 26 mice that were infected with strains other than B31 produced a detectable anti-Ct response, indicating a limited antigenic conservation of this domain among these strains. Twenty-six of 33 dogs that were experimentally infected by tick inoculation were positive by the Ct ELISA, while only 5 of 18 serum samples from dogs clinically diagnosed with Lyme disease contained detectable anti-Ct antibody. Fifty-seven of 64 serum specimens that were collected from American patients with Lyme disease were positive by the Ct ELISA, while only 12 of 21 European samples contained detectable anti-Ct antibody. In contrast, antibody to the more conserved invariable region IR6 of VlsE was present in all of these dog and human serum samples.

scholarly journals Development and Validation of 13-plex Luminex-Based Assay for Measuring Human Serum Antibodies to Streptococcus pneumoniae Capsular Polysaccharides

mSphere ◽  
2018 ◽  
Vol 3 (4) ◽  
pp. e00128-18 ◽  
Author(s):  
Danka Pavliakova ◽  
Peter C. Giardina ◽  
Soraya Moghazeh ◽  
Shite Sebastian ◽  
Maya Koster ◽  
...  
Keyword(s):  
Human Serum ◽  
Lower Limit ◽  
Immunosorbent Assay ◽  
Enzyme Linked Immunosorbent Assay ◽  
Igg Antibodies ◽  
Igg Antibody ◽  
Correlate Of Protection ◽  
Immune Correlate ◽  
Relative Standard ◽  
Limit Of Quantitation

ABSTRACT A Luminex-based direct immunoassay (dLIA) platform has been developed to replace the standardized pneumococcal enzyme-linked immunosorbent assay platform. The multiplex dLIA simultaneously measures the concentration of serum immunoglobulin G (IgG) antibodies specific for pneumococcal capsular polysaccharide (PnPS) serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, and 23F. The assay uses poly-l-lysine (PLL)-conjugated PnPS, chemically coupled to spectrally distinct Luminex microspheres. Assay validation experiments were performed using residual human serum samples obtained from 13-valent pneumococcal conjugate vaccine (13vPnC) clinical studies. Assay results are expressed as IgG antibody concentrations in micrograms per milliliter using the international reference serum, 007sp. The lower limit of quantitation (LLOQ) for all serotypes covered in the 13-plex dLIA fell within the range of 0.002 to 0.038 µg/ml serum IgG. The difference between the lower limit and upper limit of the assay range was >500-fold for all serotypes, and assay variability was <20% relative standard deviation (RSD) for all serotypes. IgG antibody measurements were shown to be serotype-specific (some cross-reactivity was observed only between the structurally related serotypes 6A and 6B as well as 19A and 19F), and no interference was observed between the serotypes when the assay was performed in the 13-plex format compared to the singleplex assays. The 13-plex dLIA platform developed by Pfizer Inc. generates up to 143 test results in a single 96-well plate and is a suitable replacement of the enzyme-linked immunosorbent assay (ELISA) platform for evaluating vaccine clinical trials. IMPORTANCE The pneumococcal enzyme-linked immunosorbent assay (ELISA) measures IgG antibodies in human serum, and it is an important assay that supports licensure of pneumococcal vaccines. The immune correlate of protection, 0.35 µg/ml of IgG antibodies, was determined by the ELISA method. Pfizer has developed a new Luminex-based assay platform to replace the ELISA. These papers describe the important work of (i) validating the Luminex-based assay and (ii) bridging the immune correlate of protection (0.35 µg/ml IgG) to equivalent values reported by the Luminex platform.

Sign in / Sign up

Export Citation Format

Share Document