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Timofeeva AM, Shayakhmetova LS, Nikitin AO, Sedykh TA, Matveev AL, Shanshin DV, Volosnikova EA, Merkuleva IA, Shcherbakov DN, Tikunova NV, Sedykh SE, Nevinsky GA. Natural Antibodies Produced in Vaccinated Patients and COVID-19 Convalescents Hydrolyze Recombinant RBD and Nucleocapsid (N) Proteins. Biomedicines 2024; 12:1007. [PMID: 38790969 PMCID: PMC11118737 DOI: 10.3390/biomedicines12051007] [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: 03/20/2024] [Revised: 04/30/2024] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Antibodies are protein molecules whose primary function is to recognize antigens. However, recent studies have demonstrated their ability to hydrolyze specific substrates, such as proteins, oligopeptides, and nucleic acids. In 2023, two separate teams of researchers demonstrated the proteolytic activity of natural plasma antibodies from COVID-19 convalescents. These antibodies were found to hydrolyze the S-protein and corresponding oligopeptides. Our study shows that for antibodies with affinity to recombinant structural proteins of the SARS-CoV-2: S-protein, its fragment RBD and N-protein can only hydrolyze the corresponding protein substrates and are not cross-reactive. By using strict criteria, we have confirmed that this proteolytic activity is an intrinsic property of antibodies and is not caused by impurities co-eluting with them. This discovery suggests that natural proteolytic antibodies that hydrolyze proteins of the SARS-CoV-2 virus may have a positive impact on disease pathogenesis. It is also possible for these antibodies to work in combination with other antibodies that bind specific epitopes to enhance the process of virus neutralization.
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Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
- Advanced Engineering School, Novosibirsk State University, 630090 Novosibirsk, Russia
| | | | - Artem O. Nikitin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
- Advanced Engineering School, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Tatyana A. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
| | - Andrey L. Matveev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
| | - Daniil V. Shanshin
- State Research Center of Virology and Biotechnology Vector, 630559 Koltsovo, Russia (D.N.S.)
| | | | - Iuliia A. Merkuleva
- State Research Center of Virology and Biotechnology Vector, 630559 Koltsovo, Russia (D.N.S.)
| | - Dmitriy N. Shcherbakov
- State Research Center of Virology and Biotechnology Vector, 630559 Koltsovo, Russia (D.N.S.)
- Department of Physical-Chemistry, Biology and Biotechnology, Altay State University, 656049 Barnaul, Russia
| | - Nina V. Tikunova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
- Advanced Engineering School, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
- Advanced Engineering School, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Georgy A. Nevinsky
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia (S.E.S.)
- Advanced Engineering School, Novosibirsk State University, 630090 Novosibirsk, Russia
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Timofeeva AM, Sedykh SE, Dmitrenok PS, Nevinsky GA. Identification of Antibody-Mediated Hydrolysis Sites of Oligopeptides Corresponding to the SARS-CoV-2 S-Protein by MALDI-TOF Mass Spectrometry. Int J Mol Sci 2023; 24:14342. [PMID: 37762643 PMCID: PMC10531968 DOI: 10.3390/ijms241814342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/10/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Antibodies recognizing RBD and the S-protein have been previously demonstrated to be formed in humans after SARS-CoV-2 infection and vaccination with the Sputnik V adenovirus vaccine. These antibodies were found to be active when hydrolyzing FITC-labeled oligopeptides corresponding to linear epitopes of the S-protein. The thin-layer chromatography method allows the relative accumulation of the reaction product to be estimated but cannot identify hydrolysis sites. This study used the MALDI-TOF MS method to establish oligopeptide hydrolysis sites. Using the MALDI-TOF MS method in combination with the analysis of known hydrolysis sites characteristic of canonical proteases allowed us to establish the unique hydrolysis sites inherent only to catalytically active antibodies. We have discovered two 12-mer oligopeptides to have six hydrolysis sites equally distributed throughout the oligopeptide. The other three oligopeptides were found to have two to three closely spaced hydrolysis sites. In contrast to trypsin and chymotrypsin proteases, the catalytically active antibodies of COVID-19 patients have their peptide bond hydrolyzed mainly after proline, threonine, glycine, or serine residues. Here, we propose a new high-throughput experimental method for analyzing the proteolytic activity of natural antibodies produced in viral pathology.
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Affiliation(s)
- Anna M. Timofeeva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Sergey E. Sedykh
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Pavel S. Dmitrenok
- Elyakov Pacific Institute of Bioorganic Chemistry of Far East Branch RAS, 100 let Vladivostoku Ave. 159, Vladivostok 690022, Russia
| | - Georgy A. Nevinsky
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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