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Alexandrova LA, Oskolsky IA, Makarov DA, Jasko MV, Karpenko IL, Efremenkova OV, Vasilyeva BF, Avdanina DA, Ermolyuk AA, Benko EE, Kalinin SG, Kolganova TV, Berzina MY, Konstantinova ID, Chizhov AO, Kochetkov SN, Zhgun AA. New Biocides Based on N4-Alkylcytidines: Effects on Microorganisms and Application for the Protection of Cultural Heritage Objects of Painting. Int J Mol Sci 2024; 25:3053. [PMID: 38474298 DOI: 10.3390/ijms25053053] [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: 02/15/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
The rapid increase in the antibiotic resistance of microorganisms, capable of causing diseases in humans as destroying cultural heritage sites, is a great challenge for modern science. In this regard, it is necessary to develop fundamentally novel and highly active compounds. In this study, a series of N4-alkylcytidines, including 5- and 6-methylcytidine derivatives, with extended alkyl substituents, were obtained in order to develop a new generation of antibacterial and antifungal biocides based on nucleoside derivatives. It has been shown that N4-alkyl 5- or 6-methylcytidines effectively inhibit the growth of molds, isolated from the paintings in the halls of the Ancient Russian Paintings of the State Tretyakov Gallery, Russia, Moscow. The novel compounds showed activity similar to antiseptics commonly used to protect works of art, such as benzalkonium chloride, to which a number of microorganisms have acquired resistance. It was also shown that the activity of N4-alkylcytidines is comparable to that of some antibiotics used in medicine to fight Gram-positive bacteria, including resistant strains of Staphylococcus aureus and Mycobacterium smegmatis. N4-dodecyl-5- and 6-methylcytidines turned out to be the best. This compound seems promising for expanding the palette of antiseptics used in painting, since quite often the destruction of painting materials is caused by joint fungi and bacteria infection.
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Affiliation(s)
| | - Ivan A Oskolsky
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Dmitry A Makarov
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Maxim V Jasko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Inna L Karpenko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Olga V Efremenkova
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya, Moscow 119021, Russia
| | - Byazilya F Vasilyeva
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya, Moscow 119021, Russia
| | - Darya A Avdanina
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
| | - Anna A Ermolyuk
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
| | - Elizaveta E Benko
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
| | - Stanislav G Kalinin
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
| | | | - Maria Ya Berzina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Irina D Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Alexander O Chizhov
- Zelinsky Institute of Organic Chemistry RAS 47 Leninsky Ave, Moscow 119991, Russia
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Alexander A Zhgun
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
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Kreutter D, Schwaller P, Reymond JL. Predicting enzymatic reactions with a molecular transformer. Chem Sci 2021; 12:8648-8659. [PMID: 34257863 PMCID: PMC8246114 DOI: 10.1039/d1sc02362d] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 05/24/2021] [Indexed: 11/29/2022] Open
Abstract
The use of enzymes for organic synthesis allows for simplified, more economical and selective synthetic routes not accessible to conventional reagents. However, predicting whether a particular molecule might undergo a specific enzyme transformation is very difficult. Here we used multi-task transfer learning to train the molecular transformer, a sequence-to-sequence machine learning model, with one million reactions from the US Patent Office (USPTO) database combined with 32 181 enzymatic transformations annotated with a text description of the enzyme. The resulting enzymatic transformer model predicts the structure and stereochemistry of enzyme-catalyzed reaction products with remarkable accuracy. One of the key novelties is that we combined the reaction SMILES language of only 405 atomic tokens with thousands of human language tokens describing the enzymes, such that our enzymatic transformer not only learned to interpret SMILES, but also the natural language as used by human experts to describe enzymes and their mutations.
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Affiliation(s)
- David Kreutter
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Philippe Schwaller
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
- IBM Research Europe Säumerstrasse 4 8803 Rüschlikon Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern Freiestrasse 3 3012 Bern Switzerland
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Il’icheva IA, Polyakov KM, Mikhailov SN. Strained Conformations of Nucleosides in Active Sites of Nucleoside Phosphorylases. Biomolecules 2020; 10:E552. [PMID: 32260512 PMCID: PMC7226091 DOI: 10.3390/biom10040552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 11/28/2022] Open
Abstract
Nucleoside phosphorylases catalyze the reversible phosphorolysis of nucleosides to heterocyclic bases, giving α-d-ribose-1-phosphate or α-d-2-deoxyribose-1-phosphate. These enzymes are involved in salvage pathways of nucleoside biosynthesis. The level of these enzymes is often elevated in tumors, which can be used as a marker for cancer diagnosis. This review presents the analysis of conformations of nucleosides and their analogues in complexes with nucleoside phosphorylases of the first (NP-1) family, which includes hexameric and trimeric purine nucleoside phosphorylases (EC 2.4.2.1), hexameric and trimeric 5'-deoxy-5'-methylthioadenosine phosphorylases (EC 2.4.2.28), and uridine phosphorylases (EC 2.4.2.3). Nucleosides adopt similar conformations in complexes, with these conformations being significantly different from those of free nucleosides. In complexes, pentofuranose rings of all nucleosides are at the W region of the pseudorotation cycle that corresponds to the energy barrier to the N↔S interconversion. In most of the complexes, the orientation of the bases with respect to the ribose is in the high-syn region in the immediate vicinity of the barrier to syn ↔ anti transitions. Such conformations of nucleosides in complexes are unfavorable when compared to free nucleosides and they are stabilized by interactions with the enzyme. The sulfate (or phosphate) ion in the active site of the complexes influences the conformation of the furanose ring. The binding of nucleosides in strained conformations is a characteristic feature of the enzyme-substrate complex formation for this enzyme group.
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Affiliation(s)
| | | | - Sergey N. Mikhailov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov Str. 32, 119991 Moscow, Russia; (I.A.I.); (K.M.P.)
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Kulikova IV, Drenichev MS, Solyev PN, Alexeev CS, Mikhailov SN. Enzymatic Synthesis of 2-Deoxyribose 1-Phosphate and Ribose 1 Phosphate and Subsequent Preparation of Nucleosides. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Irina V. Kulikova
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; 32 Vavilov St. 119991 Moscow Russian Federation
| | - Mikhail S. Drenichev
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; 32 Vavilov St. 119991 Moscow Russian Federation
| | - Pavel N. Solyev
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; 32 Vavilov St. 119991 Moscow Russian Federation
| | - Cyril S. Alexeev
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; 32 Vavilov St. 119991 Moscow Russian Federation
| | - Sergey N. Mikhailov
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences; 32 Vavilov St. 119991 Moscow Russian Federation
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