Delving into the Latest Updates on Institute of Chemical Biology and Fundamental Medicine SB RAS with Synapse

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Neoplasms

Skin and Musculoskeletal Diseases

Oncolytic virus

Disease domain score

A glimpse into the focused therapeutic areas

Technology Platform

Most used technologies in drug development

Targets

Most frequently developed targets

Disease Domain	Count

Neoplasms	2

Top 5 Drug Type	Count

Oncolytic virus	2

Top 5 Target	Count

CSF-2R(Granulocyte-macrophage colony-stimulating factor receptor)	1
GM-CSF x RYBP	1

New phosphate-modified nucleic acid derivatives are of great significance in basic research and biomedical applications. We have recently developed a new class of phosphoramide benzoazole oligonucleotides (PABAOs). In this work, th properties of N-benzoxazole oligodeoxyribonucleotides have been thoroughly examined. We have demonstrated the convenient automated solid-phase synthesis of oligomers with a different number of modifications (up to six) at various positions. Optical properties, thermal stability, structure, and dynamics of PABAO/DNA complexes have been investigated. The N-benzoxazole-modified phosphate group is uncharged at neutral pH and has a pKa value of 8.52. Structural analysis performed by the CD spectroscopy and MD simulation indicate B-form of PABAO/DNA duplexes. The thermal stability of PABAO/DNA complexes bearing N-benzoxazole is reduced by 2.5-6.2° per modification compared to native duplexes at standard and near physiological buffer conditions. The performed study underlines a great potential of phosphoramide benzoazole oligonucleotides for basic research, applied sciences, and biotechnology.

01 Nov 2024·World Journal of Microbiology and Biotechnology

DNA-metabarcoding of cyanobacteria and microalgae in chernozem soils of temperate continental climate of the forest-steppe zone of Eurasia under different degrees of agrotechnology intensification

Article

Author: Tupikin, Alexey ; Renganathan, Prabhaharan ; Lukyanov, Vyacheslav ; Bukin, Yurij ; Gaysina, Lira

Chernozem soil is a valuable resource and contains a great diversity of microorganisms that play a global role in the process of soil formation, the species diversity of which has changed over the last five years under the influence of different agrotechnologies. For the first time, under the conditions of the Central Chernozem region, grain and fallow crop rotation, studies using the DNA-metabarcoding method were carried out to study the taxonomic structure of bacteria, fungi, cyanobacteria, and microalgae communities in the arable horizon of typical medium loamy chernozem under winter wheat cultivation. A comparative analysis of the composition of the genotypes showed significant differences in the presented level of mineral nutrition of the soil NPK (60) and NPK (100) compared with the control variant. After processing the 16S and 18S rRNA datasets, a similar trend of decreasing numbers of pro- and eukaryotic species was found from 6296 (control without MF) to 5310 with NPK (60) and to 4643 with NPK (100), respectively. The Chao1 index indicated that the expected diversity within the prokaryotic group was higher in the control without MF at 211, but decreased to 182 and 193 with NPK (60) and NPK (100) fertilizers, respectively. Analysis of the eukaryotic group revealed a 2.6- and 2.9-fold decrease in diversity by class and genus, respectively, depending on the nutritional levels in agrotechnologies, owing to the use of MF. In the prokaryotic community, Alphaproteobacteria microorganisms predominated at an amount of 14.20-14.46%, with Cyanophyceae accounting for 5.2-9.9%. The diversity of eukaryotes was smaller than the number of classes of prokaryotes; the main dominant were Zygnematophyceae 19.5-41%, Chlorophyceae occupied 10.4-15.8%. On the other hand, the doses of fertilizers used contributed to the emergence of dominant species adapted to high doses of mineral nutrients for plants.

01 Oct 2024·Russian Journal of Bioorganic Chemistry

An Approach to the Synthesis of Cyclic Photocleavable RNA for Photoactivatable CRISPR/Cas9 System

Author: Zharkov, D. O. ; Vorobyeva, M. A. ; Novopashina, D. S. ; Ivanskaya, E. V. ; Meschaninova, M. I.

Abstract: Objective: The development of controllable gene editing systems based on the CRISPR/Cas technol. is a problem of immediate interest in modern mol. biol. and genetic engineering.An interesting solution of this problem is modification of guide RNA by introduction of photocleavable linkers.Methods: We developed an approach to the synthesis of cyclic photocleavable guide crRNA for the CRISPR/Cas9 system with a photolinker based on 1-(2-nitrophenyl)-1,2-ethanediol (PL).In cyclic form, such guide RNA is not functional.Upon irradiation by UV-light, such guide RNA is linearized and CRISPR/Cas9 system is activated.Two chem. methods for the cyclization of RNA were tested: Michael reaction (thiol-maleimide condensation) and Cu-catalyzed azide-alkyne cycloaddition (CuAAC, click-chem. reaction).For this purpose, 5′,3′-modified RNA containing reactive groups were preparedResults and Discussion: The advantages of the CuAAC reaction for cyclic RNA preparation was demonstrated.Efficiency of cyclic RNA depends on their secondary structure and on the ability of reactive groups to move closer.A series of photocleavable and control non-cleavable cyclic crRNA was obtained.It was shown that cyclic crRNAs guide Cas9 nuclease for plasmid cleavage less efficiently, but linearization of photocleavable cyclic crRNA increases the extent of plasmid cleavage.Conclusions: The developed approach allows to synthesize cyclic photocleavable RNA that can be used for spatiotemporal activation of guide RNA for gene editing.Photoregulation of gene editing will allow minimizing the off-target effects.

100 Deals associated with Institute of Chemical Biology and Fundamental Medicine SB RAS

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100 Translational Medicine associated with Institute of Chemical Biology and Fundamental Medicine SB RAS

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Pipeline

Pipeline Snapshot as of 03 May 2025

The statistics for drugs in the Pipeline is the current organization and its subsidiaries are counted as organizations,Early Phase 1 is incorporated into Phase 1, Phase 1/2 is incorporated into phase 2, and phase 2/3 is incorporated into phase 3

Preclinical

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Current Projects

Drug(Targets)	Indications	Global Highest Phase

VV-GMCSF-Apo(Institute of Chemical Biology and Fundamental Medicine) ( GM-CSF x RYBP )	Neoplasms More	Preclinical
VV-GMCSF-Lact(Oncostar) ( CSF-2R )	Breast Cancer More	Preclinical