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Makarov DA, Negrya SD, Jasko MV, Karpenko IL, Solyev PN, Chekhov VO, Kaluzhny DN, Efremenkova OV, Vasilyeva BF, Chizhov AO, Avdanina DA, Zhgun AA, Kochetkov SN, Alexandrova LA. 5-Substituted Uridines with Activity against Gram-Positive Bacteria. ChemMedChem 2023; 18:e202300366. [PMID: 37707314 DOI: 10.1002/cmdc.202300366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023]
Abstract
The emergence of drug-resistant strains of pathogenic microorganisms necessitates the creation of new drugs. A series of uridine derivatives containing an extended substituent at the C-5 position as well as C-5 alkyloxymethyl, alkylthiomethyl, alkyltriazolylmethyl, alkylsulfinylmethyl and alkylsulfonylmethyl uridines were obtained in order to explore their antimicrobial properties and solubility. It has been shown that new ribonucleoside derivatives have an order of magnitude better solubility in water compared to their 2'-deoxy analogues and effectively inhibit the growth of a number of Gram-positive bacteria, including resistant strains of Mycobacterium smegmatis (MIC=15-200 μg/mL) and Staphylococcus aureus (MIC=25-100 μg/mL). Their activity is comparable to that of some antibiotics used in medicine.
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Affiliation(s)
- Dmitry A Makarov
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov str., Moscow, 119991, Russia
| | - Sergey D Negrya
- 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
| | - Pavel N Solyev
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov str., Moscow, 119991, Russia
| | - Vladimir O Chekhov
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov str., Moscow, 119991, Russia
| | - Dmitry N Kaluzhny
- 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
| | - Alexander O Chizhov
- Zelinsky Institute of Organic Chemistry RAS, 47 Leninsky Ave., Moscow, 119991, Russia
| | - Darya A Avdanina
- Research Center of Biotechnology RAS, 33 Leninsky Ave., Moscow, 119071, Russia
| | - Alexander A Zhgun
- Research Center of Biotechnology RAS, 33 Leninsky Ave., Moscow, 119071, Russia
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov str., Moscow, 119991, Russia
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Alexandrova LA, Khandazhinskaya AL, Matyugina ES, Makarov DA, Kochetkov SN. Analogues of Pyrimidine Nucleosides as Mycobacteria Growth Inhibitors. Microorganisms 2022; 10:microorganisms10071299. [PMID: 35889017 PMCID: PMC9322969 DOI: 10.3390/microorganisms10071299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 01/25/2023] Open
Abstract
Tuberculosis (TB) is the oldest human infection disease. Mortality from TB significantly decreased in the 20th century, because of vaccination and the widespread use of antibiotics. However, about a third of the world’s population is currently infected with Mycobacterium tuberculosis (Mtb) and the death rate from TB is about 1.4–2 million people per year. In the second half of the 20th century, new extensively multidrug-resistant strains of Mtb were identified, which are steadily increasing among TB patients. Therefore, there is an urgent need to develop new anti-TB drugs, which remains one of the priorities of pharmacology and medicinal chemistry. The antimycobacterial activity of nucleoside derivatives and analogues was revealed not so long ago, and a lot of studies on their antibacterial properties have been published. Despite the fact that there are no clinically used drugs based on nucleoside analogues, some progress has been made in this area. This review summarizes current research in the field of the design and study of inhibitors of mycobacteria, primarily Mtb.
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Alexandrova LA, Shevchenko OV, Jasko MV, Solyev PN, Karpenko IL, Negrya SD, Efremenkova OV, Vasilieva BF, Efimenko TA, Avdanina DA, Nuraeva GK, Potapov MP, Kukushkina VI, Kochetkov SN, Zhgun AA. 3′-Amino modifications enhance the antifungal properties of N4-alkyl-5-methylcytidines for potential biocides. NEW J CHEM 2022. [DOI: 10.1039/d1nj04312a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A set of 3′-modified N4-alkyl-5-methyl-2′-deoxycytidines has been synthesized and evaluated for biological activity. The replacement of the 3′-hydroxyl group with amino, aminoethyl and dialkylamino groups significantly enhances antifungal activity.
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Affiliation(s)
| | - Oleg V. Shevchenko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991 Moscow, Russia
| | - Maxim V. Jasko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991 Moscow, Russia
| | - Pavel N. Solyev
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991 Moscow, Russia
| | - Inna L. Karpenko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991 Moscow, Russia
| | - Sergey D. Negrya
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991 Moscow, Russia
| | - Olga V. Efremenkova
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya St., 119021 Moscow, Russia
| | - Byazilya F. Vasilieva
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya St., 119021 Moscow, Russia
| | - Tatiana A. Efimenko
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya St., 119021 Moscow, Russia
| | - Darya A. Avdanina
- Research Center of Biotechnology RAS, 33 Leninsky Ave, 119071 Moscow, Russia
| | - Gulgina K. Nuraeva
- Research Center of Biotechnology RAS, 33 Leninsky Ave, 119071 Moscow, Russia
| | - Mark P. Potapov
- Research Center of Biotechnology RAS, 33 Leninsky Ave, 119071 Moscow, Russia
| | - Vera I. Kukushkina
- Research Center of Biotechnology RAS, 33 Leninsky Ave, 119071 Moscow, Russia
| | - Sergey N. Kochetkov
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991 Moscow, Russia
| | - Alexander A. Zhgun
- Research Center of Biotechnology RAS, 33 Leninsky Ave, 119071 Moscow, Russia
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Alexandrova LA, Jasko MV, Negrya SD, Solyev PN, Shevchenko OV, Solodinin AP, Kolonitskaya DP, Karpenko IL, Efremenkova OV, Glukhova AA, Boykova YV, Efimenko TA, Kost NV, Avdanina DA, Nuraeva GK, Volkov IA, Kochetkov SN, Zhgun AA. Discovery of novel N 4-alkylcytidines as promising antimicrobial agents. Eur J Med Chem 2021; 215:113212. [PMID: 33582576 DOI: 10.1016/j.ejmech.2021.113212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/18/2020] [Accepted: 01/12/2021] [Indexed: 10/22/2022]
Abstract
The emergence of drug-resistant strains of pathogenic microorganisms necessitates the creation of new drugs. In order to find new compounds that effectively inhibit the growth of pathogenic bacteria and fungi, we synthesized a set of N4-derivatives of cytidine, 2'-deoxycytidine and 5-metyl-2'-deoxycytidine bearing extended N4-alkyl and N4-phenylalkyl groups. The derivatives demonstrate activity against a number of Gram-positive bacteria, including Mycobacterium smegmatis (MIC = 24-200 μM) and Staphylococcus aureus (MIC = 50-200 μM), comparable with the activities of some antibiotics in medical use. The most promising compound appeared to be N4-dodecyl-5-metyl-2'-deoxycytidine 4h with activities of 24 and 48 μM against M. smegmatis and S. aureus, respectively, and high inhibitory activity of 0.5 mM against filamentous fungi that can, among other things, damage works of art, such as tempera painting. Noteworthy, some of other synthesized compounds are active against fungal growth with the inhibitory concentration in the range of 0.5-3 mM.
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Affiliation(s)
| | - Maxim V Jasko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Sergey D Negrya
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Pavel N Solyev
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia.
| | - Oleg V Shevchenko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Andrei P Solodinin
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Daria P Kolonitskaya
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Inna L Karpenko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Olga V Efremenkova
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya St., 119021, Moscow, Russia
| | - Alla A Glukhova
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya St., 119021, Moscow, Russia
| | - Yuliya V Boykova
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya St., 119021, Moscow, Russia
| | - Tatiana A Efimenko
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya St., 119021, Moscow, Russia
| | - Natalya V Kost
- Federal State Budgetary Scientific Institution "Mental Health Research Centre", 34 Kashirskoe Highway, 115522, Moscow, Russia
| | - Darya A Avdanina
- Research Center of Biotechnology RAS, 33 Leninsky Ave, 119071, Moscow, Russia
| | - Gulgina K Nuraeva
- Moscow Institute of Physics and Technology (National Research University), 9 Institutsky Alley, 141700, Dolgoprudny, Russia
| | - Ivan A Volkov
- Moscow Institute of Physics and Technology (National Research University), 9 Institutsky Alley, 141700, Dolgoprudny, Russia
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilova St., 119991, Moscow, Russia
| | - Alexander A Zhgun
- Research Center of Biotechnology RAS, 33 Leninsky Ave, 119071, Moscow, Russia
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Alexandrova LA, Efremenkova OV, Andronova VL, Galegov GA, Solyev PN, Karpenko IL, Kochetkov SN. 5-(4-alkyl-1,2,3-triazol-1-yl)methyl derivatives of 2′-deoxyuridine as inhibitors of viral and bacterial growth. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s1068162016050022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Malvezzi S, Sturla SJ, Tanasova M. Quantification of pyrophosphate as a universal approach to determine polymerase activity and assay polymerase inhibitors. Anal Biochem 2015; 478:1-7. [PMID: 25772306 DOI: 10.1016/j.ab.2015.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 02/24/2015] [Accepted: 03/03/2015] [Indexed: 11/17/2022]
Abstract
The importance of DNA polymerases in biology and biotechnology, and their recognition as potential therapeutic targets, drives development of methods for deriving kinetic characteristics of polymerases and their propensity to perform polynucleotide synthesis over modified DNA templates. Among various polymerases, translesion synthesis (TLS) polymerases enable cells to avoid the cytotoxic stalling of replicative DNA polymerases at chemotherapy-induced DNA lesions, thereby leading to drug resistance. Identification of TLS inhibitors to overcome drug-resistance necessitates the development of appropriate high-throughput assays. Since polymerase-mediated DNA synthesis involves the release of inorganic pyrophosphate (PPi), we established a universal and fast method for monitoring the progress of DNA polymerases based on the quantification of PPi with a fluorescence-based assay that we coupled to in vitro primer extension reactions. The established assay has a nanomolar detection limit in PPi and enables the evaluation of single nucleotide incorporation and DNA synthesis progression kinetics. The results demonstrated that the developed assay is a reliable method for monitoring TLS and identifying nucleoside and nucleotide-based TLS inhibitors.
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Affiliation(s)
- S Malvezzi
- Department of Health Sciences and Technology, ETH Zurich Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - S J Sturla
- Department of Health Sciences and Technology, ETH Zurich Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - M Tanasova
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA.
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Shmalenyuk ER, Kochetkov SN, Alexandrova LA. Novel inhibitors ofMycobacterium tuberculosisgrowth based on modified pyrimidine nucleosides and their analogues. RUSSIAN CHEMICAL REVIEWS 2013. [DOI: 10.1070/rc2013v082n09abeh004404] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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