Publications by authors named "Alexander Ya Zherebker"

6 Publications

  • Page 1 of 1

Relation between lignin molecular profile and fungal exo-proteome during kraft lignin modification by Trametes hirsuta LE-BIN 072.

Bioresour Technol 2021 Sep 30;335:125229. Epub 2021 Apr 30.

A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russia.

The process of kraft lignin modification by the white-rot fungus Trametes hirsuta was investigated using electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS), and groups of systematically changing compounds were delineated. In the course of cultivation, fungus tended to degrade progressively more reduced compounds and produced more oxidized ones. However, this process was not gradual - the substantial discontinuity was observed between 6th and 10th days of cultivation. Simultaneously, the secretion of ligninolytic peroxidases by the fungus was changing in a cascade manner - new isoenzymes were added to the mixture of the already secreted ones, and once new isoenzyme appeared both its relative quantity and number of isoforms increased as cultivation proceeded. It was proposed, that the later secreted peroxidases (MnP7 and MnP1) possess higher substrate affinity for some phenolic compounds and act in more specialized manner than the early secreted ones (MnP5 and VP2).
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http://dx.doi.org/10.1016/j.biortech.2021.125229DOI Listing
September 2021

Fourier transform ion cyclotron resonance mass spectrometry for the analysis of molecular composition and batch-to-batch consistency of plant-derived polyphenolic ligands developed for biomedical application.

Rapid Commun Mass Spectrom 2020 Sep;34(18):e8850

Skolkovo Institute of Science and Technology, Skolkovo, Moscow region, 143025, Russia.

Complex plant-derived polyphenols are promising for biomedical application. Their high complexity prevents the use of conventional pharmacopoeia techniques to perform quality control. The goal of this study was to apply ultra-high-resolution mass spectrometry to evaluate the batch-to-batch consistency of the molecular composition of a polyphenolic ligand using appropriate statistical metrics.

Methods: Polyphenols were obtained by hydrolyzed-lignin oxidation. Manufacturing was performed under a range of reaction conditions: heating cycles, oxygen flows, purification. Direct-injection Fourier transform ion cyclotron resonance mass spectrometry (DI FTICR-MS) was applied to analyze reaction products. For pairwise comparison Jaccard and Tanimoto similarities calculations were proposed. In addition, principal component analysis (PCA) was applied for sample grouping based on the molecular class contributions.

Results: FTICR-MS analysis revealed moderate Jaccard similarity of products synthesized under the same conditions, which shared about 50% of the formulae calculated in each sample. The intensity-based Tanimoto index indicated high similarity of major components distribution of samples synthesized under standard conditions, while products obtained with variations in synthetic conditions were significantly different. PCA of molecular class contributions showed similar grouping with a high cumulative score.

Conclusions: FTICR-MS provides robust metrics for the examination of batch-to-batch consistency of synthetic polyphenol materials. This approach can be proposed for the analysis of reference samples and for development of complementary methods for quality control of medicinal agents based on various biologically active matrices.
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http://dx.doi.org/10.1002/rcm.8850DOI Listing
September 2020

Austalides V and W, new meroterpenoids from the fungus Aspergillus ustus and their antitumor activities.

Bioorg Med Chem Lett 2019 11 4;29(22):126708. Epub 2019 Oct 4.

G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, FSBIS FRC Pushchino Scientific Centre of Biological Research, Russian Academy of Sciences, Pushchino 142290, Russian Federation.

Two new austalide meroterpenoids, named austalides V and W (1 and 2), were isolated from the fungus Aspergillus ustus VKM F-4692. Their structures were elucidated by extensive spectroscopic analysis and by comparison with related known compounds. The main structural feature of both compounds is a tetrahydrofuranyl ring (G), a structural fragment, first found in austalides. Austalides V (1) and W (2) were able to inhibit the propagation of prostate and bladder cancer cells; this biologic activity is possibly related to the inhibition of a number of key pathways regulating cell growth and migration.
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http://dx.doi.org/10.1016/j.bmcl.2019.126708DOI Listing
November 2019

Dissection of the deep-blue autofluorescence changes accompanying amyloid fibrillation.

Arch Biochem Biophys 2018 08 24;651:13-20. Epub 2018 May 24.

Faculty of Physics, M.V. Lomonosov Moscow State University, Leninskie Gory, Moscow, 119991, Russia. Electronic address:

Pathogenesis of numerous diseases is associated with the formation of amyloid fibrils. Extrinsic fluorescent dyes, including Thioflavin T (ThT), are used to follow the fibrillation kinetics. It has recently been reported that the so-called deep-blue autofluorescence (dbAF) is changing during the aggregation process. However, the origin of dbAF and the reasons for its change remain debatable. Here, the kinetics of fibril formation in model proteins were comprehensively analyzed using fluorescence lifetime and intensity of ThT, intrinsic fluorescence of proteinaceous fluorophores, and dbAF. For all systems, intensity enhancement of the dbAF band with similar spectral parameters (∼350 nm excitation; ∼450 nm emission) was observed. Although the time course of ThT lifetime (indicative of protofibrils formation) coincided with that of tyrosine residues in insulin, and the kinetic changes in the ThT fluorescence intensity (reflecting formation of mature fibrils) coincided with changes in ThT absorption spectrum, the dbAF band started to increase from the beginning of the incubation process without a lag-phase. Our mass-spectrometry data and model experiments suggested that dbAF could be at least partially related to oxidation of amino acids. This study scrutinizes the dbAF features in the context of the existing hypotheses about the origin of this spectral band.
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http://dx.doi.org/10.1016/j.abb.2018.05.019DOI Listing
August 2018

Synthesis of model humic substances: a mechanistic study using controllable H/D exchange and Fourier transform ion cyclotron resonance mass spectrometry.

Analyst 2015 Jul;140(13):4708-19

Department of Chemistry, Lomonosov Moscow State University, Leninskie gory 1-3, 119991 Moscow, Russia.

The products of the oxidative coupling of phenols are frequently used as synthetic analogues to natural humic substances (HS) for biomedical research. However, their molecular compositions and exact structures remain largely unknown. The objective of this study was to develop a novel approach for the molecular-level analysis of phenolic polymerisates that is capable of inventorying molecular constituents and resolving their distinct structural formulas. For this purpose, we have synthesized the model HS using the oxidative coupling of a specifically designed phenylpropanoic monomer, 3-(4-hydroxy-3-methoxyphenyl)-3-oxopropionic acid, to hydroquinone. We have characterized the synthesized model HS using high resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS), (1)H NMR spectroscopy, and controllable hydrogen/deuterium (H/D) exchange. We succeeded in the molecular inventory of the model HS. The assigned molecular formulas occupied the substantial space of CHO compositions in the Van Krevelen diagram with a maximum density found in the regions of tannins and lignins, resembling those of natural HS. To identify the exact structural formulas of the individual constituents in the model HS, we have applied selective H/D exchange of non-labile backbone protons by a choice of basic or acidic catalytic conditions followed by FTICR MS. The determined formulas allowed us to verify the proposed pathways of hydroxylation and carboxylation in the course of the phenolic coupling and to identify the acetylation of aromatic rings as an important side reaction. We conclude that the proposed analytical approach may be used to identify the molecular carriers of biological activity within the phenolic polymerisates and eventually within natural HS.
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http://dx.doi.org/10.1039/c5an00602cDOI Listing
July 2015

Molecular mapping of sorbent selectivities with respect to isolation of Arctic dissolved organic matter as measured by Fourier transform mass spectrometry.

Environ Sci Technol 2014 Jul 12;48(13):7461-8. Epub 2014 Jun 12.

Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 1-3, 119991 Moscow, Russia.

The objectives of this study were to identify molecular features characteristic to arctic DOM from the Kolyma River basin and to elucidate structural imprints induced by a choice of the sorption technique. To achieve this goal, DOM was isolated from the Kolyma River basin with a use of three nonionic sorbents: Amberlite XAD-8 resin, PPL- and C18 - SPE cartridges, and one anion exchanging resin-diethylaminoethyl (DEAE) -cellulose. The structural studies were conducted with a use of electrospray ionization Fourier Transform Ion Cyclotron Resonance (ESI FT-ICR) mass spectrometry and liquid state (1)H NMR spectroscopy. The DOM isolates obtained with a use of PPL and C18 cartridges were characterized with higher content of aliphatic compounds as compared to XAD-8 and DEAE-isolates. In total, for all arctic DOM isolates we observed predominance of hydrogen saturated compounds with high H/C values of identified formulas from FT-ICR MS data. (1)H NMR spectroscopy studies have confirmed this trend and revealed high contribution of alkyl-chain protons into the spectral density of the arctic DOM reaching 43% for PPL isolates.
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http://dx.doi.org/10.1021/es5015423DOI Listing
July 2014
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