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Ryzhov I, Tuzikov A, Obukhova P, Sablina M, Popova I, Anisimova D, Galanina O, Shilova N, Khaidukov S, Chizhov A, Henry S, Bovin N. Antigen Presentation in an Artificial and Cell Membrane: Blood Group A Glycan Recognition. Chembiochem 2025; 26:e202400843. [PMID: 39584413 DOI: 10.1002/cbic.202400843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2024] [Revised: 11/05/2024] [Accepted: 11/25/2024] [Indexed: 11/26/2024]
Abstract
Glycosphingolipids (GSL) are functionally important components of the cell membrane and recognition of their glycan "head" by the immune system is a key part of normal and pathological processes. Recognition of glycolipid antigens on a living cell, their structure, "context" (microenvironment and clustering), presentation including orientation and distance from the plasma membrane, as well as molecular dynamics are important. GSL antigens are targets for the development of anticancer vaccines and therapeutic antibodies, therefore, control of the presentation of their glycans by synthetic methods opens up new possibilities in medicine. In this work, we synthesized 13 GSL analogues as function-spacer-lipids (FSLs) with the same head (blood group A tetrasaccharide, ABO system) but each either differing in the structure of the lipid tail, or the length of the region between the head and the tail, or cluster organization of the head (from 2 to 4 tetrasaccharides in a cluster). The insertion of these FSLs into an artificial and erythrocyte membranes was compared, and their interaction with antibodies was studied, including erythrocyte agglutination. The results give further insight into knowledge of the membrane presentation of GSLs (some results can be extrapolated to glycoproteins) and factors involved in their interaction with antibodies.
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Affiliation(s)
- Ivan Ryzhov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander Tuzikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Polina Obukhova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov of the Ministry of Healthcare of the Russian Federation, Moscow, Russian Federation
| | - Marina Sablina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Inna Popova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Darya Anisimova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Oxana Galanina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Nadezhda Shilova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V. I. Kulakov of the Ministry of Healthcare of the Russian Federation, Moscow, Russian Federation
| | - Sergey Khaidukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander Chizhov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Stephen Henry
- School of Engineering, AUT University, Auckland, New Zealand
| | - Nicolai Bovin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
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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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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: 0.5] [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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