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Differences in Presentation of SARS-CoV-2 Omicron Strain Variant BA.1–BA.5 Peptides by HLA Molecules
Doklady Biochemistry and Biophysics. 2022. Vol. 507. No. 1. P. 298 – 301.
In this work, we analyzed the binding affinities of mutated peptides of Omicron strain variants BA.1–BA.5 and the worldwide prevalent HLA alleles. Bioinformatics analysis was conducted with the use of T-CoV web portal. We showed that, for all five viral variants, mutations cause a significant reduction in the number of tightly binding peptides for HLA-B*07:02 and HLA-C*01:02 molecules. At the same time, there were novel potential mutant epitopes (binding affinity less than 50 nM) in case of HLA-A*32:01 allele. Interestingly, mutations caused multidirectional effect on the binding affinities of the viral peptides and HLA-DRB1*03:01. Specifically, Spike protein mutations in the BA.1 variant caused more than 100-fold decrease in PINLVRDLPQGFSAL binding affinity, 10-fold decrease in affinity in the case of BA.2, BA.4, and BA.5 variants, and 30% increase in affinity for the BA.3 variant.
Publication based on the results of:
Aliper E., Ryzhov I., Obukhova P. et al., Biochimica et Biophysica Acta - Biomembranes 2026 Vol. 1868 No. 1 Article 184472
Antibodies to peptide 1147 (amino acids 1147-61) of the SARS-CoV-2 protein S are highly diagnostic. Peptide 1147, although located in a region that is partly spatially hidden in the intact protein, is not subject to mutations, suggesting therapeutic potential. The aim of this study was to elucidate the architecture of this region and the way ...
Added: October 20, 2025
Bhimani K. R., Peresadina A., Burmak K. et al., 2026 Vol. 519 Article 117532
Database-searching based precursor ion identification in tandem mass spectrometry data analysis is limited to the search space. Once a single amino acid variation (SAAV) or a modification is not included to the search space, then its observed spectra will not be annotated correctly. Several methods have been developed to identify and localize post-translational modifications (PTMs); ...
Added: October 2, 2025
Chang C., Wu C., Shkurnikov M. et al., Journal of Biomedical Science 2025 Vol. 32 Article 44
Background
The evolution of SARS-CoV-2, particularly through new variants, presents significant global health challenges due to their potential for immune evasion and reduced vaccine effectiveness. This study aims to investigate the impact of mutations in the Spike protein of Omicron EG.5 and XBB.1.16 variants on the binding affinities of viral peptides to common human leukocyte antigen ...
Added: May 6, 2025
Amaro R., Åqvist J., Bahar I. et al., Nature Methods 2025 Vol. 22 P. 641–645
The communities that embraced data archiving efforts decades ago are now, in the era of data-driven biology, gaining the most from the AI revolution. The structural biology community was a pioneer in this regard, establishing the Protein Data Bank in 1971 and making data accessible using the FAIR principles even before these were articulated1,2. The ...
Added: April 18, 2025
The COVID-19 Host Genetics Initiative .., Rakitko A., Nature 2023 Vol. 621 No. 7977 P. Е7–Е26
Investigating the role of host genetic factors in COVID-19 severity and susceptibility can inform our understanding of the underlying biological mechanisms that influence adverse outcomes and drug development 1, 2. Here we present a second updated genome-wide association study (GWAS) on COVID-19 severity and infection susceptibility to SARS-CoV-2 from the COVID-19 Host Genetic Initiative (data ...
Added: March 4, 2025
Lomakin Y., Ovchinnikova L., Terekhov S. et al., Communications Biology 2024 Vol. 7 Article 842
Identifying high-affinity antibodies in human serum is challenging due to extremely low number of circulating B cells specific to the desired antigens. Delays caused by a lack of information on the immunogenic proteins of viral origin hamper the development of therapeutic antibodies. We propose an efficient approach allowing for enrichment of high-affinity antibodies against pathogen ...
Added: January 19, 2025
Kudryavtsev D., Mozhaeva V., Ivanov I. et al., Nanoscale 2024 Vol. 16 No. 26 P. 12424–12430
Existing methods for the mass detection of viruses are limited to the registration of small amounts of a viral genome or specific protein markers. In spite of high sensitivity, the applied methods cannot distinguish between virulent virus particles and non-infectious virus particle debris. We report an approach to solve this long-standing challenge using the SARS-CoV-2 ...
Added: January 10, 2025
M.Yu. Shkurnikov, S.A. Tonevitskaya, E.V. Stepanova et al., Doklady Biochemistry and Biophysics 2023 Vol. 512 No. 1 P. 266–269
Conducting preclinical studies of mRNA vaccines is complicated by the lack of relevant animal models of the human immune system. Immunocompetent mice are widely used in biomedical research. However, critical differences in the genetics and immune system of mice and humans prevent the study of unique human immune responses in mice. Within the framework of ...
Added: July 1, 2024
Vladimir Staroverov, Alexei Galatenko, Evgeny Knyazev et al., PeerJ 2024 Vol. 12 Article e16964
Within-host infection dynamics of Omicron dramatically differs from previous variants of SARS-CoV-2. However, little is still known about which parameters of virus-cell interplay contribute to the observed attenuated replication and pathogenicity of Omicron. Mathematical models, often expressed as systems of differential equations, are frequently employed to study the infection dynamics of various viruses. Adopting such ...
Added: March 20, 2024
Tamazian G., Komissarov A., Kobak D. et al., , in: Bioinformatics Research and Applications: 18th International Symposium, ISBRA 2022, Haifa, Israel, November 14–17, 2022, ProceedingsVol. 13750.: [б.и.], 2022. Ch. n/a P. 255–262.
Since the beginning of the COVID-19 pandemic, whole-genome sequences of SARS-CoV-2 have been continuously added to public databases, such as NCBI Virus and GISAID. As of July 2022, the SARS-CoV-2 Data Hub of the
NCBI Virus database stored more than one million complete whole-genome sequences of the coronavirus. For navigating the SARS-CoV-2 genome sequences, the Pango ...
Added: February 8, 2024
Knyazev S. N., Chhugani K., Sarwal V. et al., Nature Methods 2022 Vol. 19 No. 4 P. 374–380
During the COVID-19 pandemic, genomics and bioinformatics have emerged as essential public health tools. The genomic data acquired using these methods have supported the global health response, facilitated the development of testing methods and allowed the timely tracking of novel SARS-CoV-2 variants. Yet the virtually unlimited potential for rapid generation and analysis of genomic data ...
Added: February 8, 2024
Borisevich S., Khamitov E., Maxim A. Gureev et al., Viruses 2022 Vol. 14 No. 1 Article 119
In this work, we evaluated the antiviral activity of Arbidol (Umifenovir) against SARS-CoV-2 using a pseudoviral system with the glycoprotein S of the SARS-CoV-2 virus on its surface. In order to search for binding sites to protein S of the virus, we described alternative binding sites of Arbidol in RBD and in the ACE-2-RBD complex. ...
Added: February 8, 2024
Yarovaya O., Shcherbakov D., Borisevich S. et al., Viruses 2022 Vol. 14 No. 6 Article 1295
In the present work we studied the antiviral activity of the home library of monoterpenoid derivatives using the pseudoviral systems of our development, which have glycoproteins of the SARS-CoV-2 virus strains Wuhan and Delta on their surface. We found that borneol derivatives with a tertiary nitrogen atom can exhibit activity at the early stages of ...
Added: February 8, 2024
Sidorova M. V., Bibilashvili R. S., Avdeev D. V. et al., Doklady Biochemistry and Biophysics 2022 Vol. 507 P. 237–241
The aim of this work was to design and characterize peptides based on the α-helices h1 and h2 of the ACE2 receptor, forming the interaction interface between the receptor-binding domain (RBD) of the SARS-CoV-2 S protein and the cellular ACE2 receptor. Monomeric and heterodimeric peptides connected by disulfide bonds at different positions were synthesized. Solubility, RBD-binding ...
Added: February 8, 2024
Popkov A., Dubnov Y. A., Popkov Y., Информационные технологии и вычислительные системы 2022 № 3 С. 67–78
The work is devoted to application of the theory of Randomized Machine Learning to forecasting of the COVID-19 pandemic based on SIR epidemiological model. We propose two modelling variants, the first is based on estimation of SIR model using real case data, the second is based on the idea of modelling transmission coefficient and its prediction. Comparative study ...
Added: February 5, 2024
Yarovaya O., Filimonov A., Baev D. et al., Viruses 2024 Vol. 16 No. 2 Article 215
Although the COVID-19 pandemic caused by SARS-CoV-2 viruses is officially over, the search for new effective agents with activity against a wide range of coronaviruses is still an important task for medical chemists and virologists. We synthesized a series of thiazolo-thiophenes based on (+)- and (−)-usnic acid and studied their ability to inhibit the main ...
Added: January 31, 2024
Klink G. V., Danilenko D., Komissarov A. et al., Viruses 2023 Vol. 15 No. 7 Article 1415
The Omicron variant of SARS-CoV-2 rapidly spread worldwide in late 2021–early 2022, displacing the previously prevalent Delta variant. Before 16 December 2021, community transmission had already been observed in tens of countries globally. However, in Russia, the majority of reported cases at that time had been sporadic and associated with travel. Here, we report an ...
Added: November 30, 2023
Staroverov V., Nersisyan S., Galatenko A. V. et al., PeerJ 2023 Vol. 11 Article e14828
Mathematical modeling is widely used to study within-host viral dynamics. However, to the best of our knowledge, for the case of SARS-CoV-2 such analyses were mainly conducted with the use of viral load data and for the wild type (WT) variant of the virus. In addition, only few studies analyzed models for in vitro data, ...
Added: July 27, 2023