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561 results on '"Tuzikov, Alexander"'

1. Identification of Potential SARS-CoV-2 Main Protease Inhibitors Using Drug Repurposing and Molecular Modeling

Author

Andrianov, Alexander M., Furs, Konstantin V., Gonchar, Anna V., Xie, Xiong, Karpenko, Anna D., Laikov, Yan V., Varabyeu, Danila A., Liu, Hong, Tuzikov, Alexander V., Goos, Gerhard, Series Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Peng, Wei, editor, Cai, Zhipeng, editor, and Skums, Pavel, editor

Published
2024
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2. Path Tracking Control of a Spherical Robot with Pendulum-Like Driver

Author

Balandin, Dmitry V., Biryukov, Ruslan S., Tuzikov, Alexander M., Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Balandin, Dmitry, editor, Barkalov, Konstantin, editor, and Meyerov, Iosif, editor

Published
2024
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4. Generative Autoencoders for Designing Novel Small-Molecule Compounds as Potential SARS-CoV-2 Main Protease Inhibitors

Author

Shuldau, Mikita A., Yushkevich, Artsemi M., Bosko, Ivan P., Tuzikov, Alexander V., Andrianov, Alexander M., Filipe, Joaquim, Editorial Board Member, Ghosh, Ashish, Editorial Board Member, Prates, Raquel Oliveira, Editorial Board Member, Zhou, Lizhu, Editorial Board Member, Tuzikov, Alexander V., editor, Belotserkovsky, Alexei M., editor, and Lukashevich, Marina M., editor

Published
2022
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7. Deep Learning Approach with Rotate-Shift Invariant Input to Predict Protein Homodimer Structure

Author

Hadarovich, Anna, Kalinouski, Alexander, Tuzikov, Alexander V., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Cai, Zhipeng, editor, Mandoiu, Ion, editor, Narasimhan, Giri, editor, Skums, Pavel, editor, and Guo, Xuan, editor

Published
2020
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8. Development of a Neural Network-Based Approach for Prediction of Potential HIV-1 Entry Inhibitors Using Deep Learning and Molecular Modeling Methods

Author

Nikolaev, Grigory I., Shuldov, Nikita A., Anischenko, Arseny I., Tuzikov, Alexander V., Andrianov, Alexander M., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Cai, Zhipeng, editor, Mandoiu, Ion, editor, Narasimhan, Giri, editor, Skums, Pavel, editor, and Guo, Xuan, editor

Published
2020
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9. In Silico-Guided Discovery of Potential HIV-1 Entry Inhibitors Mimicking bNAb N6: Virtual Screening, Docking, Molecular Dynamics, and Post-Molecular Modeling Analysis

Author

Andrianov, Alexander M., Nikolaev, Grigory I., Kornoushenko, Yuri V., Karpenko, Anna D., Bosko, Ivan P., Tuzikov, Alexander V., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Cai, Zhipeng, editor, Mandoiu, Ion, editor, Narasimhan, Giri, editor, Skums, Pavel, editor, and Guo, Xuan, editor

Published
2020
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11. A novel syphilis Treponema pallidum lipoprotein peptide antigen diagnostic assay using red cell kodecytes in routine blood centre column agglutination testing platforms.

Author

Datta, Suvro Sankha, Nagappan, Radhika, Biswas, Durba, Basu, Debapriya, Gupta, Kaushik, Mondal, Pradip Kumar, Tuzikov, Alexander, Bovin, Nicolai V., and Henry, Stephen M.

Subjects
TREPONEMA pallidum, ERYTHROCYTES, PEPTIDES, AGGLUTINATION tests, COMMUNICABLE diseases, SYPHILIS
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. [ABSTRACT FROM AUTHOR]

Published
2024
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13. Labeling of Polysaccharides with Biotin and Fluorescent Dyes

Author

Tuzikov, Alexander, primary, Shilova, Nadezhda, additional, Ovchinnikova, Tatiana, additional, Nokel, Alexey, additional, Patova, Olga, additional, Knirel, Yuriy, additional, Chernova, Tatiana, additional, Gorshkova, Tatiana, additional, and Bovin, Nicolai, additional

Published
2023
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17. Ensemble-based characterization of unbound and bound states on protein energy landscape

Author

Ruvinsky, Anatoly M., Kirys, Tatsiana, Tuzikov, Alexander V., and Vakser, Ilya A.

Subjects
Physics - Biological Physics, Quantitative Biology - Biomolecules
Abstract

Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their binding mechanisms and characterize the energy landscapes in implicit solvent. First, results show that bound and unbound spectra often significantly overlap. Moreover, the larger the overlap the smaller the RMSD between bound and unbound conformational ensembles. Second, the analysis of the unbound-to-bound changes points to conformational selection as the binding mechanism for four of the proteins. Third, the center of the unbound spectrum has a higher energy than the center of the corresponding bound spectrum of the dimeric and multimeric states for most of the proteins. This suggests that the unbound states often have larger entropy than the bound states considered outside of the complex. Fourth, the exhaustively long minimization, making small intra-rotamer adjustments, dramatically reduces the distance between the centers of the bound and unbound spectra as well as the spectra extent. It condenses unbound and bound energy levels into a thin layer at the bottom of the energy landscape with the energy spacing that varies between 0.8-4.6 and 3.5-10.5 kcal/mol for the unbound and bound states correspondingly. At the same time, the energy gap between the two lowest states in the full ensemble varies between 0.9 and 12.1 kcal/mol. Finally, the analysis of protein energy fluctuations showed that protein vibrations itself can excite the inter-state transitions, thus supporting the conformational selection theory., Comment: 12 pages, 5 figures, 2 tables, supporting material

Published
2012

18. Structure fluctuations and conformational changes in protein binding

Author

Ruvinsky, Anatoly M., Kirys, Tatsiana, Tuzikov, Alexander V., and Vakser, Ilya A.

Subjects
Physics - Biological Physics, Quantitative Biology - Biomolecules
Abstract

Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers of mass in proteins and a statistical analysis of conformation changes in the side-chains upon binding. Normal mode analysis and an elastic network model were applied to a set of protein complexes to calculate the residue fluctuations and develop the residue classification. Comparison with a classification based on normalized B-factors suggests that the B-factors may underestimate protein flexibility in solvent. Our classification shows that protein loops and disordered fragments are enriched with highly fluctuating residues and depleted with weakly fluctuating residues. To calculate the dihedral angles distribution functions, the configuration space was divided into cells by a cubic grid. The effect of protein association on the distribution functions depends on the amino acid type and a grid step in the dihedral angles space. The changes in the dihedral angles increase from the near-backbone dihedral angle to the most distant one, for most residues. On average, one fifth of the interface residues change the rotamer state upon binding, whereas the rest of the interface residues undergo local readjustments within the same rotamer., Comment: 13 pages, 6 figures

Published
2011
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19. Side-chain conformational changes upon protein-protein association

Author

Ruvinsky, Anatoly M., Kirys, Tatsiana, Tuzikov, Alexander V., and Vakser, Ilya A.

Subjects
Quantitative Biology - Biomolecules, Physics - Biological Physics
Abstract

Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short and long side chains have different propensities for the conformational changes. Long side chains with three or more dihedral angles are often subject to large conformational transition. Shorter residues with one or two dihedral angles typically undergo local conformational changes not leading to a conformational transition. The relationship between the local readjustments and the equilibrium fluctuations of a side chain around its unbound conformation is suggested. Most of the side chains undergo larger changes in the dihedral angle most distant from the backbone. The amino acids with symmetric aromatic (Phe and Tyr) and charged (Asp and Glu) groups show the opposite trend where the near-backbone dihedral angles change the most. The frequencies of the core-to-surface interface transitions of six nonpolar residues and Tyr exceed the frequencies of the opposite, surface-to-core transitions. The binding increases both polar and nonpolar interface areas. However, the increase of the nonpolar area is larger for all considered classes of protein complexes. The results suggest that the protein association perturbs the unbound interfaces to increase the hydrophobic forces. The results facilitate better understanding of the conformational changes in proteins and suggest directions for efficient conformational sampling in docking protocols., Comment: 21 pages, 6 figures

Published
2010

20. Labeling of Polysaccharides with Biotin and Fluorescent Dyes.

Author

Tuzikov, Alexander, Shilova, Nadezhda, Ovchinnikova, Tatiana, Nokel, Alexey, Patova, Olga, Knirel, Yuriy, Chernova, Tatiana, Gorshkova, Tatiana, and Bovin, Nicolai

Subjects
*POLYSACCHARIDES, *BIOTIN, *FLUORESCEIN isothiocyanate, *CARBOXYL group, *HYALURONIC acid, *GLYCOLIPIDS, *FLUORESCENT dyes
Abstract

Examples of labeling polysaccharides at hydroxyl groups are described in this paper, which are especially in demand for molecules with a blocked reducing end. The protocols presented are suitable for the microscale synthesis of labeled polysaccharides that do not require a chromatography step for isolation. Examples of hydroxyl labeling include (1) direct modification with fluorescein isothiocyanate; (2) reaction with a fluorescein-dichlorotriazine derivative; (3) reaction with biotin-dichlorotriazine; (4) indirect two-step modification (given for glycosphingolipid) with glutaric anhydride followed by amidation with aminospacered BODIPY or SuCy5. The labeling of carboxyl groups of hyaluronic acid with BODIPY is also described. The staining of plant tissue sections with biotinylated polysaccharide versus being fluorescein labeled is compared. [ABSTRACT FROM AUTHOR]

Published
2024
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26. Methods for Genome-Wide Analysis of MDR and XDR Tuberculosis from Belarus

Author

Sergeev, Roman, Kavaliou, Ivan, Gabrielian, Andrei, Rosenthal, Alex, Tuzikov, Alexander, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Bourgeois, Anu, editor, Skums, Pavel, editor, Wan, Xiang, editor, and Zelikovsky, Alex, editor

Published
2016
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27. Genome-Wide Structural Modeling of Protein-Protein Interactions

Author

Anishchenko, Ivan, Badal, Varsha, Dauzhenka, Taras, Das, Madhurima, Tuzikov, Alexander V., Kundrotas, Petras J., Vakser, Ilya A., Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Bourgeois, Anu, editor, Skums, Pavel, editor, Wan, Xiang, editor, and Zelikovsky, Alex, editor

Published
2016
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34. Repurposing Navitoclax to block SARS‐CoV‐2 fusion and entry by targeting heptapeptide repeat sequence 1 in S2 protein.

Author

Jiao, Fanke, Andrianov, Alexander M., Wang, Lijue, Furs, Konstantin V., Gonchar, Anna V., Wang, Qian, Xu, Wei, Lu, Lu, Xia, Shuai, Tuzikov, Alexander V., and Jiang, Shibo

Subjects
SARS-CoV-2, DRUG counterfeiting, SARS-CoV-2 Omicron variant, CLINICAL trials
Abstract

Along with the long pandemic of COVID‐19 caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has come the dilemma of emerging viral variants of concern (VOC), particularly Omicron and its subvariants, able to deftly escape immune surveillance and the otherwise protective effect of current vaccines and antibody drugs. We previously identified a peptide‐based pan‐CoV fusion inhibitor, termed as EK1, able to bind the HR1 region in viral spike (S) protein S2 subunit. This effectively blocked formation of the six‐helix bundle (6‐HB) fusion core and, thus, showed efficacy against all human coronaviruses (HCoVs). EK1 is now in phase 3 clinical trials. However, the peptide drug generally lacks oral availability. Therefore, we herein performed a structure‐based virtual screening of the libraries of biologically active molecules and identified nine candidate compounds. One is Navitoclax, an orally active anticancer drug by inhibition of Bcl‐2. Like EK1 peptide, it could bind HR1 and block 6‐HB formation, efficiently inhibiting fusion and infection of all SARS‐CoV‐2 variants tested, as well as SARS‐CoV and MERS‐CoV, with IC50 values ranging from 0.5 to 3.7 μM. These findings suggest that Navitoclax is a promising repurposed drug candidate for development as a safe and orally available broad‐spectrum antiviral drug to combat the current SARS‐CoV‐2 and its variants, as well as other HCoVs. [ABSTRACT FROM AUTHOR]

Published
2023
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36. Watershed Segmentation with Chamfer Metric

Author

Goncharenko, Vasily, Tuzikov, Alexander, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Kuba, Attila, editor, Nyúl, László G., editor, and Palágyi, Kálmán, editor

Published
2006
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39. Poly-L-Lysine-Based αGal-Glycoconjugates for Treating Anti-αGal IgE-Mediated Diseases

Author

Olivera-Ardid, Sara, Bello-Gil, Daniel, Tuzikov, Alexander, Araujo, Ricardo N., Ferrero-Alves, Yara, García Figueroa, Blanca Esther, Labrador Horrillo, Moises, García-Pérez, Ana L., Bovin, Nicolai, Mañez, Rafael, Universitat Autònoma de Barcelona. Departament de Medicina, Institut Català de la Salut, [Olivera-Ardid S, Bello-Gil D, Ferrero-Alves Y] RemAb Therapeutics, Mòdul de Recerca B, Universitat Autònoma de Barcelona, Bellaterra, Spain. [Tuzikov A] Department of Chemical Biology of Glycans and Lipids, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry Russian Academy of Sciences (RAS), Moscow, Russia. [Araujo RN] Laboratório de Artrópodes Hematófagos, Departamento de Parasitologia, ICB/UFMG, Belo Horizonte, Brazil. [García Figueroa BE] MEGA: Asthma Inception and Progression Mechanisms, Complejo Hospitalario de Navarra (CHN), Pamplona, Spain. Instituto de investigación sanitaria de Navarra (IdiSNA), Pamplona, Spain. ARADyAL Research Network, Instituto de Salud Carlos III (ISCIII), Madrid, Spain. [Labrador-Horrillo M] ARADyAL Research Network, Instituto de Salud Carlos III (ISCIII), Madrid, Spain. Departament de Medicina, Universitat Autònoma de Barcelona, Bellaterra, Spain. Secció d’Al•lèrgia, Servei de Medicina Interna, Vall d’Hebron Hospital Universitari, Barcelona, Spain. Àrea de Malalties Immunomediades i Teràpies Innovadores, Vall d’Hebron Institut de Recerca (VHIR), Barcelona, Spain, and Vall d'Hebron Barcelona Hospital Campus

Subjects
Al·lèrgia, Allergy, Immunology, Immunoteràpia, αGal-syndrome, Immunotheraphy, Poly-l-lysine-based αGal-glycoconjugates, Mice, Immunology and Allergy, Animals, Humans, Polylysine, Ratolins, Eukaryota::Animals::Chordata::Vertebrates::Mammals::Eutheria::Rodentia::Muridae::Murinae::Mice [ORGANISMS], hidratos de carbono::glicoconjugados [COMPUESTOS QUÍMICOS Y DROGAS], Immune System Diseases::Hypersensitivity::Hypersensitivity, Immediate::Food Hypersensitivity [DISEASES], GalT-KO mice, Anti-αgal IgE inhibition, Immunoglobulin E, Carbohydrates::Glycoconjugates [CHEMICALS AND DRUGS], Al·lèrgia alimentària, Immunoglobulin M, Glicoconjugats, Immunoglobulin G, Immunotherapy, Eukaryota::animales::Chordata::vertebrados::mamíferos::Eutheria::Rodentia::Muridae::Murinae::ratones [ORGANISMOS], Glycoconjugates, Food Hypersensitivity, enfermedades del sistema inmune::hipersensibilidad::hipersensibilidad inmediata::hipersensibilidad a los alimentos [ENFERMEDADES]
Abstract

Anti-αGal IgE antibodies mediate a spreading allergic condition known as αGal-syndrome (AGS). People exposed to hard tick bites are sensitized to αGal, producing elevated levels of anti-αGal IgE, which are responsible for AGS. This work presents an immunotherapy based on polymeric αGal-glycoconjugates for potentially treating allergic disorders by selectively inhibiting anti-αGal IgE antibodies. We synthesized a set of αGal-glycoconjugates, based on poly-L-lysine of different degrees of polymerization (DP1000, DP600, and DP100), to specifically inhibit in vitro the anti-αGal IgE antibodies in the serum of αGal-sensitized patients (n=13). Moreover, an animal model for αGal sensitization in GalT-KO mice was developed by intradermal administration of hard tick’ salivary gland extract, mimicking the sensitization mechanism postulated in humans. The in vitro exposure to all polymeric glycoconjugates (5-10-20-50-100 µg/mL) mainly inhibited anti-αGal IgE and IgM isotypes, with a lower inhibition effect on the IgA and IgG, respectively. We demonstrated a differential anti-αGal isotype inhibition as a function of the length of the poly-L-lysine and the number of αGal residues exposed in the glycoconjugates. These results defined a minimum of 27 αGal residues to inhibit most of the induced anti-αGal IgE in vitro. Furthermore, the αGal-glycoconjugate DP1000-RA0118 (10 mg/kg sc.) showed a high capacity to remove the anti-αGal IgE antibodies (≥75% on average) induced in GalT-KO mice, together with similar inhibition for circulating anti-αGal IgG and IgM. Our study suggests the potential clinical use of poly-L-lysine-based αGal-glycoconjugates for treating allergic disorders mediated by anti-αGal IgE antibodies. Copyright © 2022 Olivera-Ardid, Bello-Gil, Tuzikov, Araujo, Ferrero-Alves, García Figueroa, Labrador-Horrillo, García-Pérez, Bovin and Mañez.

Published
2022

40. Minkowski Sum Volume Minimization for Convex Polyhedra

Author

Tuzikov, Alexander V., Sheynin, Stanislav A., Viergever, Max A., editor, Bajcsy, Ruzena, editor, Brady, Mike, editor, Faugeras, Olivier D., editor, Koenderink, Jan J., editor, Pizer, Stephen M., editor, Tsuji, Saburo, editor, Zucker, Steven W., editor, Goutsias, John, editor, Vincent, Luc, editor, and Bloomberg, Dan S., editor

Published
2000
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42. Antibodies against hyaluronan oligosaccharides in xenotransplantation.

Author

Bello‐Gil, Daniel, Olivera‐Ardid, Sara, Tuzikov, Alexander B., Costa, Cristina, Bovin, Nicolai V., and Mañez, Rafael

Subjects
XENOTRANSPLANTATION, OLIGOSACCHARIDES, IMMUNOGLOBULINS, LABORATORY rats, ERYTHROCYTES
Abstract

Carbohydrate‐specific antibodies are significant mediators of xenograft rejection. This study analyzed the carbohydrate specificity of antibodies in baboons before and after xenotransplantation of organs or injection of porcine red blood cells from hDAF transgenic pigs, using a glycan array with structurally defined glycans. Antibodies against hyaluronic acid disaccharide (HA2) showed the highest reactivity at baseline and rose after xenogeneic exposure. We also investigated in the serum of baboons that underwent xenotransplantation with either hDAF or hDAF/hMCP transgenic pig organs and Lewis rats after hamster‐skin xenotransplantation the specificity of anti‐HA antibodies on a glycan microarray representing HA oligosaccharides containing from two to 40 saccharides. Notably, the HA oligosaccharides ranging from 32 to 40 saccharides exhibited the highest antibody binding intensities at baseline in baboon and rat sera. After xenotransplantation, antibodies against HA38 and HA40 in baboons, and HA32, HA34, and HA36 in rats showed the highest titer increases. The changes of anti‐HA IgM and IgG antibodies in rats after skin xenotransplantation was also confirmed by an ELISA specific for HA2, HA24, and HA85 antibodies. Thus, xenotransplantation is associated with increased antibodies against HA‐oligosaccharides, which may represent a new target for intervention. [ABSTRACT FROM AUTHOR]

Published
2023
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