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Datta SS, Nagappan R, Biswas D, Basu D, Gupta K, Mondal PK, Tuzikov A, Bovin NV, Henry SM. A novel syphilis Treponema pallidum lipoprotein peptide antigen diagnostic assay using red cell kodecytes in routine blood centre column agglutination testing platforms. Vox Sang 2024. [PMID: 38946160 DOI: 10.1111/vox.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/16/2024] [Accepted: 03/18/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND AND OBJECTIVES The detection of treponemal antibodies, which are used to make a diagnosis of syphilis, is important both for diagnostic purposes and as a mandatory blood donor test in most countries. We evaluated the feasibility of using Kode Technology to make syphilis peptide red cell kodecytes for use in column agglutination serologic platforms. MATERIALS AND METHODS Candidate Kode Technology function-spacer-lipid (FSL) constructs were made for the Treponema pallidum lipoprotein (TmpA) of T. pallidum, using the peptide and FSL selection algorithms, and then used to make kodecytes. Developmental kodecytes were evaluated against a large range of syphilis antibody reactive and non-reactive samples in column agglutination platforms and compared against established methodologies. Overall, 150 reactive and 2072 non-reactive Syphicheck assay (a modified T. pallidum particle agglutination) blood donor samples were used to evaluate the agreement rate of the developed kodecyte assay. RESULTS From three FSL-peptide candidate constructs, one was found to be the most suitable for diagnostics. Of 150 Syphicheck assay reactive samples, 146 were TmpA-kodecyte reactive (97.3% agreement), compared with 58.0% with the rapid plasmin reagin (RPR) assay for the same samples. Against the 2072 expected syphilis non-reactive samples the agreement rate for TmpA-kodecytes was 98.8%. CONCLUSION TmpA-kodecytes are viable for use as cost-effective serologic reagent red cells for the detection of treponemal antibodies to diagnose syphilis with a high level of specificity in blood centres. This kodecyte methodology also potentially allows for introduction of the reverse-algorithm testing into low-volume laboratories, by utilizing existing transfusion laboratory infrastructure.
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Affiliation(s)
| | - Radhika Nagappan
- Department of Pathology and Laboratory Medicine, Auckland City Hospital, Auckland, New Zealand
- Kode Technology Laboratory, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland, New Zealand
| | - Durba Biswas
- Department of Transfusion Medicine, Tata Medical Center, Kolkata, India
| | - Debapriya Basu
- Department of Transfusion Medicine, Tata Medical Center, Kolkata, India
| | - Kaushik Gupta
- Department of Transfusion Medicine, Tata Medical Center, Kolkata, India
| | | | | | | | - Stephen M Henry
- Kode Technology Laboratory, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland, New Zealand
- Kode Biotech Limited, Auckland, New Zealand
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Kawashima T, Nakamura M, Sakono M. A one-process production of completely biotinylated proteins in a T7 expression system. Biotechnol Appl Biochem 2024. [PMID: 38770738 DOI: 10.1002/bab.2598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
Streptavidin is a tetrameric protein with high specificity and affinity for biotin. The interaction between avidin and biotin has become a valuable tool in nanotechnology. In recent years, the site-specific biotin modification of proteins using biotin ligases, such as BirA, has attracted attention. This study established an in vivo method for achieving the complete biotinylation of target proteins using a single plasmid co-expressing BirA and its target proteins. Specifically, a biotin-modified protein was produced in Escherichia coli strain BL21(DE3) using a single plasmid containing genes encoding both BirA and a protein fused to BirA's substrate sequence, Avitag. This approach simplifies the production of biotinylated proteins in E. coli and allows the creation of various biotinylated protein types through gene replacement. Furthermore, the biotin modification rate of the obtained target protein could be evaluated using Native-PAGE without performing complicated isolation operations of biotinylated proteins. In Native-PAGE, biotin-modified proteins and unmodified proteins were confirmed as clearly different bands, and it was possible to easily derive the modification rate from the respective band intensities.
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Affiliation(s)
- Takuma Kawashima
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, Toyama, Toyama, Japan
| | - Mitsuki Nakamura
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, Toyama, Toyama, Japan
| | - Masafumi Sakono
- Department of Applied Chemistry, Faculty of Engineering, University of Toyama, Toyama, Toyama, Japan
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Vaskan I, Dimitreva V, Petoukhov M, Shtykova E, Bovin N, Tuzikov A, Tretyak M, Oleinikov V, Zalygin A. Effect of ligand and shell densities on the surface structure of core-shell nanoparticles self-assembled from function-spacer-lipid constructs. Biomater Sci 2024; 12:798-806. [PMID: 38180048 DOI: 10.1039/d3bm01704d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
Biomolecular corona is the major obstacle to the clinical translation of nanomedicines. Since corona formation is governed by molecular interactions at the nano-bio interface, nanoparticle surface properties such as topography, charge and surface chemistry can be tuned to manipulate biomolecular corona formation. To this end, as the first step towards a deep understanding of the processes of corona formation, it is necessary to develop nanoparticles employing various biocompatible materials and characterize their surface structure and dynamics at the molecular level. In this work, we applied molecular dynamics simulation to study the surface structure of organic core-shell nanoparticles formed by the self-assembly of synthetic molecules composed of a DOPE lipid, a carboxymethylglycine spacer and biotin. Lipid moieties form the hydrophobic core, spacer motifs serve as a hydrophilic shell and biotin residues function as a targeting ligand. By mixing such function-spacer-lipid, spacer-lipid and lipid-only constructs at various molar ratios, densities of the ligand and spacer on the nanoparticle surface were modified. For convenient analysis of the structure and dynamics of all regions of the nanoparticle surface, we compiled topography maps based on atomic coordinates. It was shown that an increase in the density of the shell does not reduce exposure of the core, but increases shell average thickness. Biotin, due to its alkyl valeric acid chain and spacer flexibility, is localized primarily near the hydrophobic core and its partial presentation on the surface occurs only in nanoparticles with higher ligand densities. However, an increase in biotin density leads to its clustering. In turn, ligand clustering diminishes the stealth properties of the shell and targeting efficiency. Based on nanoparticle surface structures, we determined the optimal density of biotin. Experimental studies reported in the literature confirm these conclusions. We also suggest design tips to achieve the preferred biotin presentation. Simulation results are consistent with the synchrotron SAXS profile. We believe that such studies will contribute to a better understanding of nano-bio interactions towards the rational design of efficient drug delivery systems.
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Affiliation(s)
- Ivan Vaskan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Veronika Dimitreva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
- National Research Nuclear University Moscow Engineering Physics Institute, Moscow, 115409, Russia
| | - Maxim Petoukhov
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, 119333, Russia
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences, Moscow, 119071, Russia
| | - Eleonora Shtykova
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow, 119333, Russia
| | - Nicolai Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Alexander Tuzikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Marina Tretyak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
| | - Vladimir Oleinikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
- National Research Nuclear University Moscow Engineering Physics Institute, Moscow, 115409, Russia
| | - Anton Zalygin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.
- National Research Nuclear University Moscow Engineering Physics Institute, Moscow, 115409, Russia
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4
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Vaskan IS, Prikhodko AT, Petoukhov MV, Shtykova EV, Bovin NV, Tuzikov AB, Oleinikov VA, Zalygin AV. Assessment of core-shell nanoparticles surface structure heterogeneity by SAXS contrast variation and ab initio modeling. Colloids Surf B Biointerfaces 2023; 224:113183. [PMID: 36764203 DOI: 10.1016/j.colsurfb.2023.113183] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023]
Abstract
For the biomedical applications of nanoparticles, the study of their structure is a major step towards understanding the mechanisms of their interaction with biological environment. Detailed structural analysis of particles' surface is vital for rational design of drug delivery systems. In particular, for core-shell or surface-modified nanoparticles surface structure can be described in terms of shell coating uniformity and shell thickness uniformity around the nanoparticle core. Taken together, these terms can be used to indicate degree of heterogeneity of nanoparticle surface structure. However, characterization of nanoparticle surface structure under physiological conditions is challenging due to limitations of experimental techniques. In this paper, we apply SAXS contrast variation combined with ab initio bead modeling for this purpose. Approach is based on the fact that nanoparticles under study are produced by self-assembly of phospholipid-conjugated molecules that possess moieties with significantly different electron densities enabling SAXS technique to be used to distinguish nanoparticle shell and study its structure. Ab initio single phase and ab initio multiphase modeling based on SAXS curve of nanoparticles in phosphate buffer solution allowed to reconstruct nanoparticle shell coating and assess its uniformity, while serial nanoparticle reconstructions from solutions with gradually increased solvent electron densities revealed relative shell coating thickness around nanoparticle core. Nanoparticle shell structure representation was verified by molecular dynamics simulation and derived full-atom nanoparticle shell structure showed good agreement with SAXS-derived representation. Obtained data indicate that studied nanoparticles exhibit highly heterogeneous surface structure.
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Affiliation(s)
- I S Vaskan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - A T Prikhodko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; National Research Nuclear University Moscow Engineering Physics Institute, Moscow 115409, Russia
| | - M V Petoukhov
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow 119333, Russia; A.N. Frumkin Institute of Physical Chemistry and Electrochemistry of Russian Academy of Sciences, Moscow 119071, Russia
| | - E V Shtykova
- A.V. Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of the Russian Academy of Sciences, Moscow 119333, Russia
| | - N V Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - A B Tuzikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - V A Oleinikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; National Research Nuclear University Moscow Engineering Physics Institute, Moscow 115409, Russia
| | - A V Zalygin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; National Research Nuclear University Moscow Engineering Physics Institute, Moscow 115409, Russia.
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5
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Slivka EV, Tuzikov AB, Khaidukov SV, Komarova VA, Henry SM, Bovin NV, Rapoport EM. Influence of the Lipid Moiety Structure on the Insertion/Release of Glycolipids in/from the Cell: A Study with Synthetic Analogs. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022050235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Perry H, Henry SM. Simulated red cell antibody identification training panels created using SARS-CoV-2 kodecytes and immune plasma. Transfusion 2022; 62:1630-1635. [PMID: 35761783 PMCID: PMC9349923 DOI: 10.1111/trf.17004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/18/2022] [Accepted: 06/04/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Training is essential to develop and maintain skills required to be a competent serologist, yet samples required to achieve this are often difficult to obtain. We evaluated the feasibility of SARS-CoV-2 peptide modified red cells (1144-kodecytes) to develop simulated antibody screening and identification panels of reagent red cells suitable for practical training the recognition and grading of serologic reactions. STUDY DESIGN AND METHODS Red cells from a single donor were modified into kodecytes using Kode Technology function-spacer-lipid constructs bearing a short SARS-CoV-2 peptide. Kodecytes and unmodified cells were then arranged in patterns representative of red cell antibody profiles as simulated antibody screening and identification reagent cell panels (SASID), and then tested against immune donor plasma samples containing SARS-CoV-2 antibodies. Manual tube and two different gel card serologic platforms were evaluated by routinue techniques. SASID exemplars were created for antibodies including D, Cw , f (ce), Jka (strong, weak, dosing), mixtures of D+E, Jka +K, Fya +E, high and low frequency antibodies and a warm IgG autoantibody. RESULTS Kodecytes (positive reactions) and unmodified cells (negative) when arranged and tested in appropriate patterns in SASID panels were able to mimic IgG antibody reactions, and were capable of measuring both accuracy and precision in reaction grading. CONCLUSIONS Kodecytes can be used to rapidly create in-house simulated yet realistic antibody screening and identification panels suitable for large scale training in the recognition and grading of serologic reactions.
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Affiliation(s)
- Holly Perry
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland, New Zealand.,School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Stephen M Henry
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland, New Zealand
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Centurion F, Basit AW, Liu J, Gaisford S, Rahim MA, Kalantar-Zadeh K. Nanoencapsulation for Probiotic Delivery. ACS NANO 2021; 15:18653-18660. [PMID: 34860008 DOI: 10.1021/acsnano.1c09951] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Gut microbiota dynamically participate in diverse physiological activities with direct impact on the host's health. A range of factors associated with the highly complex intestinal flora ecosystem poses challenges in regulating the homeostasis of microbiota. The consumption of live probiotic bacteria, in principle, can address these challenges and confer health benefits. In this context, one of the major problems is ensuring the survival of probiotic cells when faced with physical and chemical assaults during their intake and subsequent gastrointestinal passage to the gut. Advances in the field have focused on improving conventional encapsulation techniques in the microscale to achieve high cell viability, gastric and temperature resistance, and longer shelf lives. However, these microencapsulation approaches are known to have limitations with possible difficulties in clinical translation. In this Perspective, we present a brief overview of the current progress of different probiotic encapsulation methods and highlight the contemporary and emerging single-cell encapsulation strategies using nanocoatings for individual probiotic cells. Finally, we discuss the relative advantages of various nanoencapsulation approaches and the future trend toward developing coated probiotics with advanced features and health benefits.
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Affiliation(s)
- Franco Centurion
- School of Chemical Engineering, University of New South Wales (UNSW), Sydney, New South Wales 2052, Australia
| | - Abdul W Basit
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Jinyao Liu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Simon Gaisford
- UCL School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Md Arifur Rahim
- School of Chemical Engineering, University of New South Wales (UNSW), Sydney, New South Wales 2052, Australia
| | - Kourosh Kalantar-Zadeh
- School of Chemical Engineering, University of New South Wales (UNSW), Sydney, New South Wales 2052, Australia
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Klaczko ME, Lucas K, Salminen AT, McCloskey MC, Ozgurun B, Ward BM, Flax J, McGrath JL. Rapid and specific detection of intact viral particles using functionalized microslit silicon membranes as a fouling-based sensor. Analyst 2021; 147:213-222. [PMID: 34933322 DOI: 10.1039/d1an01504d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The COVID-19 pandemic demonstrated the public health benefits of reliable and accessible point-of-care (POC) diagnostic tests for viral infections. Despite the rapid development of gold-standard reverse transcription polymerase chain reaction (RT-PCR) assays for SARS-CoV-2 only weeks into the pandemic, global demand created logistical challenges that delayed access to testing for months and helped fuel the spread of COVID-19. Additionally, the extreme sensitivity of RT-PCR had a costly downside as the tests could not differentiate between patients with active infection and those who were no longer infectious but still shedding viral genomes. To address these issues for the future, we propose a novel membrane-based sensor that only detects intact virions. The sensor combines affinity and size based detection on a membrane-based sensor and does not require external power to operate or read. Specifically, the presence of intact virions, but not viral debris, fouls the membrane and triggers a macroscopically visible hydraulic switch after injection of a 40 μL sample with a pipette. The device, which we call the μSiM-DX (microfluidic device featuring a silicon membrane for diagnostics), features a biotin-coated microslit membrane with pores ∼2-3× larger than the intact virus. Streptavidin-conjugated antibody recognizing viral surface proteins are incubated with the sample for ∼1 hour prior to injection into the device, and positive/negative results are obtained within ten seconds of sample injection. Proof-of-principle tests have been performed using preparations of vaccinia virus. After optimizing slit pore sizes and porous membrane area, the fouling-based sensor exhibits 100% specificity and 97% sensitivity for vaccinia virus (n = 62). Moreover, the dynamic range of the sensor extends at least from 105.9 virions per mL to 1010.4 virions per mL covering the range of mean viral loads in symptomatic COVID-19 patients (105.6-107 RNA copies per mL). Forthcoming work will test the ability of our sensor to perform similarly in biological fluids and with SARS-CoV-2, to fully test the potential of a membrane fouling-based sensor to serve as a PCR-free alternative for POC containment efforts in the spread of infectious disease.
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Affiliation(s)
- Michael E Klaczko
- Department of Chemistry, University of Rochester, Rochester, NY, 14627 USA
| | - Kilean Lucas
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627 USA.
| | - Alec T Salminen
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627 USA.
| | - Molly C McCloskey
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627 USA.
| | - Baturay Ozgurun
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627 USA.
| | - Brian M Ward
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, 14642 USA
| | - Jonathan Flax
- Department of Urology, University of Rochester Medical Center, Rochester, NY, 14642 USA
| | - James L McGrath
- Department of Biomedical Engineering, University of Rochester, Rochester, NY, 14627 USA.
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Tuzikov AB, Ryabukhina EV, Paramonov AS, Chizhov AO, Bovin NV, Vodovozova EL. A convenient route to conjugates of 1,2-diglycerides with functionalized oligoethylene glycol spacer arms. MENDELEEV COMMUNICATIONS 2021. [DOI: 10.1016/j.mencom.2021.07.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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10
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Ryzhov IM, Tuzikov AB, Nizovtsev AV, Baidakova LK, Galanina OE, Shilova NV, Ziganshina MM, Dolgushina NV, Bayramova GR, Sukhikh GT, Williams EC, Nagappan R, Henry SM, Bovin NV. SARS-CoV-2 Peptide Bioconjugates Designed for Antibody Diagnostics. Bioconjug Chem 2021; 32:1606-1616. [PMID: 34181851 DOI: 10.1021/acs.bioconjchem.1c00186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In the near future, the increase in the number of required tests for COVID-19 antibodies is expected to be many hundreds of millions. Obviously, this will be done using a variety of analytical methods and using different antigens, including peptides. In this work, we compare three method variations for detecting specific immunoglobulins directed against peptides of approximately 15-aa of the SARS-CoV-2 spike protein. These linear peptide epitopes were selected using antigenicity algorithms, and were synthesized with an additional terminal cysteine residue for their bioconjugation. In two of the methods, constructs were prepared where the peptide (F, function) is attached to a negatively charged hydrophilic spacer (S) linked to a dioleoylphosphatidyl ethanolamine residue (L, lipid) to create a function-spacer-lipid construct (FSL). These FSLs were easily and controllably incorporated into erythrocytes for serologic testing or in a lipid bilayer deposited on a polystyrene microplate for use in an enzyme immunoassays (EIA). The third method, also an EIA, used polyacrylamide conjugated peptides (peptide-PAA) prepared by controlled condensation of the cysteine residue of the peptide with the maleimide-derived PAA polymer which were immobilized on polystyrene microplates by physisorption of the polymer. In this work, we describe the synthesis of the PAA and FSL peptide bioconjugates, design of test systems, and comparison of the bioassays results, and discuss potential reasons for higher performance of the FSL conjugates, particularly in the erythrocyte-based serologic assay.
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Affiliation(s)
- Ivan M Ryzhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russian Federation
| | - Alexander B Tuzikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russian Federation
| | - Alexey V Nizovtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russian Federation
| | - Ludmila K Baidakova
- Branch of the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russian Federation
| | - Oxana E Galanina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russian Federation
| | - Nadezhda V Shilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russian Federation.,National Medical Research Center for Obstetrics, Gynecology and Perinatology named after V.I. Kulakov of the Ministry of Health of Russian Federation, Moscow 117997, Russian Federation
| | - Marina M Ziganshina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after V.I. Kulakov of the Ministry of Health of Russian Federation, Moscow 117997, Russian Federation
| | - Nataliya V Dolgushina
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after V.I. Kulakov of the Ministry of Health of Russian Federation, Moscow 117997, Russian Federation
| | - Guldana R Bayramova
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after V.I. Kulakov of the Ministry of Health of Russian Federation, Moscow 117997, Russian Federation
| | - Gennady T Sukhikh
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after V.I. Kulakov of the Ministry of Health of Russian Federation, Moscow 117997, Russian Federation
| | - Eleanor C Williams
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland 1010, New Zealand
| | - Radhika Nagappan
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland 1010, New Zealand
| | - Stephen M Henry
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland 1010, New Zealand
| | - Nicolai V Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow 117997, Russian Federation.,Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland 1010, New Zealand
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11
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Nagappan R, Flegel WA, Srivastava K, Williams EC, Ryzhov I, Tuzikov A, Galanina O, Shilova N, Sukhikh G, Perry H, Bovin NV, Henry SM. COVID-19 antibody screening with SARS-CoV-2 red cell kodecytes using routine serologic diagnostic platforms. Transfusion 2021; 61:1171-1180. [PMID: 33590501 PMCID: PMC8014685 DOI: 10.1111/trf.16327] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 12/23/2022]
Abstract
Background The Coronavirus disease 2019 (COVID‐19) pandemic is having a major global impact, and the resultant response in the development of new diagnostics is unprecedented. The detection of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has a role in managing the pandemic. We evaluated the feasibility of using SARS‐CoV‐2 peptide Kode Technology‐modified red cells (C19‐kodecytes) to develop an assay compatible with existing routine serologic platforms. Study Design and Methods A panel of eight unique red cells modified using Kode Technology function‐spacer‐lipid constructs and bearing short SARS‐CoV‐2 peptides was developed (C19‐kodecyte assay). Kodecytes were tested against undiluted expected antibody‐negative and ‐positive plasma samples in manual tube and three column agglutination technology (CAT) platforms. Parallel analysis with the same peptides in solid phase by enzyme immunoassays was performed. Evaluation samples included >120 expected negative blood donor samples and >140 COVID‐19 convalescent plasma samples, with independent serologic analysis from two centers. Results Specificity (negative reaction rate against expected negative samples) in three different CAT platforms against novel C19‐kodecytes was >91%, which correlated with published literature. Sensitivity (positive reaction rate against expected positive convalescent, PCR‐confirmed samples) ranged from 82% to 97% compared to 77% with the Abbott Architect SARS‐CoV‐2 IgG assay. Manual tube serology was less sensitive than CAT. Enzyme immunoassay results with some Kode Technology constructs also had high sensitivity. Conclusions C19‐kodecytes are viable for use as serologic reagent red cells for the detection of SARS‐CoV‐2 antibody with routine blood antibody screening equipment.
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Affiliation(s)
- Radhika Nagappan
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland, New Zealand
| | - Willy A Flegel
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Kshitij Srivastava
- Department of Transfusion Medicine, NIH Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Eleanor C Williams
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland, New Zealand
| | - Ivan Ryzhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Alexander Tuzikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Oxana Galanina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Nadezhda Shilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Gennady Sukhikh
- Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Holly Perry
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland, New Zealand.,School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Nicolai V Bovin
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland, New Zealand.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Stephen M Henry
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative Technologies, Auckland University of Technology, Auckland, New Zealand
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Zalygin A, Solovyeva D, Vaskan I, Henry S, Schaefer M, Volynsky P, Tuzikov A, Korchagina E, Ryzhov I, Nizovtsev A, Mochalov K, Efremov R, Shtykova E, Oleinikov V, Bovin N. Structure of Supramers Formed by the Amphiphile Biotin-CMG-DOPE. ChemistryOpen 2020; 9:641-648. [PMID: 32499990 PMCID: PMC7266497 DOI: 10.1002/open.201900276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 03/02/2020] [Indexed: 11/10/2022] Open
Abstract
The synthetic function-spacer-lipid (FSL) amphiphile biotin-CMG-DOPE is widely used for delicate ligation of living cells with biotin residues under physiological conditions. Since this molecule has an "apolar-polar-hydrophobic" gemini structure, the supramolecular organization is expected to differ significantly from the classical micelle. Its organization is investigated with experimental methods and molecular dynamics simulations (MDS). Although the linear length of a single biotin-CMG-DOPE molecule is 9.5 nm, the size of the dominant supramer globule is only 14.6 nm. Investigations found that while the DOPE tails form a hydrophobic core, the polar CMG spacer folds back upon itself and predominantly places the biotin reside inside the globule or planar layer. MDS demonstrates that <10 % of biotin residues on the highly water dispersible globules and only 1 % of biotin residues in layer coatings are in an linear conformation and exposing biotin into the aqueous medium. This explains why in biotin-CMG-DOPE apolar biotin residues both in water dispersible globules and coatings on solid surfaces are still capable of interacting with streptavidin.
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Affiliation(s)
- Anton Zalygin
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Daria Solovyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Ivan Vaskan
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute)Kashirskoe shosse 31Moscow115409Russian Federation
| | - Stephen Henry
- School of EngineeringComputer & Mathematical SciencesAuckland University of TechnologyAuckland1010New Zealand
| | - Marcel Schaefer
- School of EngineeringComputer & Mathematical SciencesAuckland University of TechnologyAuckland1010New Zealand
| | - Pavel Volynsky
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Alexander Tuzikov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Elena Korchagina
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Ivan Ryzhov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Alexey Nizovtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Konstantin Mochalov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
| | - Roman Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
- National Research University Higher School of EconomicsMyasnitskaya Str. 20Moscow101000Russian Federation
| | - Eleonora Shtykova
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre 'Crystallography and Photonics' of Russian Academy of SciencesMoscow119333Russian Federation
- Semenov Institute of Chemical PhysicsRussian Academy of SciencesMoscow119991Russian Federation
| | - Vladimir Oleinikov
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute)Kashirskoe shosse 31Moscow115409Russian Federation
| | - Nicolai Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of Sciences16/10 Miklukho-Maklaya str.Moscow117997Russia
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Affiliation(s)
- Stephen Henry
- Centre for Kode Technology Innovation School of Engineering, Computer and Mathematical Sciences Auckland University of Technology Auckland New Zealand
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14
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E Perry H, Ryzhov I, Galanina O, V Bovin N, M Henry S. Incidence in plasma of low level antibodies against three xenotransplantation and immunotherapeutic glycan antigens. AIMS ALLERGY AND IMMUNOLOGY 2020. [DOI: 10.3934/allergy.2020007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Perry H, Bovin N, Henry S. A standardized kodecyte method to quantify ABO antibodies in undiluted plasma of patients before ABO‐incompatible kidney transplantation. Transfusion 2019; 59:2131-2140. [DOI: 10.1111/trf.15247] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 02/18/2019] [Accepted: 02/20/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Holly Perry
- School of Science, Faculty of Health and Environmental SciencesAuckland University of Technology Auckland New Zealand
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative TechnologiesAuckland University of Technology Auckland New Zealand
| | - Nicolai Bovin
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative TechnologiesAuckland University of Technology Auckland New Zealand
- Shemyakin Institute of Bioorganic Chemistry Moscow Russian Federation
| | - Stephen Henry
- Centre for Kode Technology Innovation, School of Engineering, Computer and Mathematical Sciences, Faculty of Design and Creative TechnologiesAuckland University of Technology Auckland New Zealand
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Affiliation(s)
- Stephen M. Henry
- Center for Kode Technology Innovation, School of Engineering, Computer & Mathematical Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Nicolai V. Bovin
- Center for Kode Technology Innovation, School of Engineering, Computer & Mathematical Sciences, Auckland University of Technology, Auckland, New Zealand
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
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Ryzhov IM, Tuzikov AB, Perry H, Korchagina EY, Bovin NV. Blood Group O→A Transformation by Chemical Ligation of Erythrocytes. Chembiochem 2018; 20:131-133. [PMID: 30019804 DOI: 10.1002/cbic.201800289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Indexed: 12/14/2022]
Abstract
Agglutination of red blood cells (RBCs) remains the only practical method for routine use for ABH typing in clinical practice. However, exact mechanistic details of agglutination are not yet thoroughly studied. In this research, RBCs of blood group O were converted to blood group A through two approaches: by chemical ligation of the cells' glycocalyx with synthetic blood group A tetrasaccharide, and by insertion of synthetic glycolipid carrying the same A antigen into the cells' membranes. The O→A ligated RBCs and natural A RBCs showed comparable agglutination characteristics with antibodies. As expected, RBCs with inserted glycolipid showed lower agglutination scores. This approach could help cell biologists in site-specific and cell-friendly modification of glycocalyx by other ligands.
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Affiliation(s)
- Ivan M Ryzhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - Alexander B Tuzikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - Holly Perry
- Centre for Kode Technology Innovation, School of Engineering, Computer & Mathematical Sciences, Auckland University of Technology, Auckland, 1010, New Zealand
| | - Elena Yu Korchagina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - Nicolai V Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia.,Centre for Kode Technology Innovation, School of Engineering, Computer & Mathematical Sciences, Auckland University of Technology, Auckland, 1010, New Zealand
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