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Keshk RM, Salama ZA, Elsaedany SK, ElRehim EMA, Beltagy DM. Synthesis, antimicrobial, anti-inflammatory, antioxidant and cytotoxicity of new pyrimidine and pyrimidopyrimidine derivatives. Sci Rep 2025; 15:9328. [PMID: 40102434 PMCID: PMC11920053 DOI: 10.1038/s41598-025-92066-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Accepted: 02/25/2025] [Indexed: 03/20/2025] Open
Abstract
A series of novel pyrimidine and pyrimidopyrimidine analogs were synthesized in good yield from 6-amino-4-aryl-2-oxo-pyrimidine-5-carbonitrile (1a-d). The synthesized compounds were characterized using various spectral studies, including FT-IR, 1H NMR, 13C NMR, mass spectrometry, and elemental analysis. Newly synthesized pyrimidopyrimidines and 2-(substituted-pyrazolyl)pyrimidine derivatives were assessed in vitro for their cytotoxic activities against three cancerous cell lines: colorectal carcinoma (HCT-116), mammary gland breast cancer (MCF-7), and hepatocellular carcinoma (HEPG-2), as well as normal fibroblasts (W138). The results indicated that compounds 3b, 10b, and 10c exhibited the highest cytotoxic activities, with IC50 values very close to those of the reference drug (doxorubicin) across all studied cancerous cell lines, while also demonstrating good safety effects on the normal human lung fibroblast cell line. Furthermore, all the synthesized compounds were examined for their antimicrobial activity against two Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis), one Gram negative bacterium (Escherichia coli) and two fungal species (Candida albicans and Aspergillus flavus). The antimicrobial results of the synthesized compounds, when compared with the reference drugs ampicillin and clotrimazole, revealed that compounds 3a, 3b, 3d, 4a-d, 9c and 10b exhibited excellent antimicrobial activities. Moreover, membrane stabilization or anti-hemolytic activity was employed as a method to study the in vitro anti-inflammatory activity of the prepared heterocyclic compounds. Antioxidant activities were also assessed by measuring the percentage of free radical scavenging. Compounds 4b, 10c and 11a-c demonstrated strong anti-hemolytic and antioxidant effects, which can be attributed to their ability to protect red blood cells from hemolysis.
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Affiliation(s)
- Reda Mohammed Keshk
- Chemistry Department, Faculty of Science, Damanhour University, Damanhour, 22511, Egypt.
| | - Zeinab Ahmed Salama
- Chemistry Department, Faculty of Science, Damanhour University, Damanhour, 22511, Egypt
| | - Samir Kamel Elsaedany
- Chemistry Department, Faculty of Science, Alexandaria University, Alexandaria, Egypt
| | | | - Doha Mohammad Beltagy
- Biochemistry Department, Faculty of Science, Damanhour University, Damanhour, 22511, Egypt
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2
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Ostroumova OS, Efimova SS, Zlodeeva PD, Alexandrova LA, Makarov DA, Matyugina ES, Sokhraneva VA, Khandazhinskaya AL, Kochetkov SN. Derivatives of Pyrimidine Nucleosides Affect Artificial Membranes Enriched with Mycobacterial Lipids. Pharmaceutics 2024; 16:1110. [PMID: 39339148 PMCID: PMC11435317 DOI: 10.3390/pharmaceutics16091110] [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: 07/22/2024] [Revised: 08/14/2024] [Accepted: 08/20/2024] [Indexed: 09/30/2024] Open
Abstract
The mechanisms of action of pyrimidine nucleoside derivatives on model lipid membranes of various compositions were studied. A systematic analysis of the tested agents' effects on the membrane physicochemical properties was performed. Differential scanning microcalorimetry data indicated that the ability of nucleoside derivatives to disorder membrane lipids depended on the types of nucleoside bases and membrane-forming lipids. The 5'-norcarbocyclic uracil derivatives were found to be ineffective, while N4-alkylcytidines demonstrated the most pronounced effects, significantly decreasing the dipalmitoylphosphocholine melting temperature and cooperativity of phase transition. The elongation of hydrophobic acyl radicals potentiated the disordering action of N4-alkylcytidines, while an increase in hydrophilicity due to replacing deoxyribose with ribose inhibited this effect. The ability of compounds to form transmembrane pores was also tested. It was found that 5-alkyluridines produced single, ion-permeable pores in phosphatidylglycerol membranes, and that methoxy-mycolic acid and trehalose monooleate potentiated the pore-forming activity of alkyloxymethyldeoxyuridines. The results obtained open up perspectives for the development of innovative highly selective anti-tuberculosis agents, which may be characterized by a low risk of developing drug resistance due to the direct action on the membranes of the pathogen.
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Affiliation(s)
| | | | | | | | - Dmitry A Makarov
- Engelhardt Institute of Molecular Biology, RAS, Moscow 119991, Russia
| | - Elena S Matyugina
- Engelhardt Institute of Molecular Biology, RAS, Moscow 119991, Russia
| | - Vera A Sokhraneva
- Engelhardt Institute of Molecular Biology, RAS, Moscow 119991, Russia
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3
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Shahab M, Danial M, Duan X, Khan T, Liang C, Gao H, Chen M, Wang D, Zheng G. Machine learning-based drug design for identification of thymidylate kinase inhibitors as a potential anti-Mycobacterium tuberculosis. J Biomol Struct Dyn 2024; 42:3874-3886. [PMID: 37232453 DOI: 10.1080/07391102.2023.2216278] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
The rise of antibiotic-resistant Mycobacterium tuberculosis (Mtb) has reduced the availability of medications for tuberculosis therapy, resulting in increased morbidity and mortality globally. Tuberculosis spreads from the lungs to other parts of the body, including the brain and spine. Developing a single drug can take several decades, making drug discovery costly and time-consuming. Machine learning algorithms like support vector machines (SVM), k-nearest neighbor (k-NN), random forest (RF) and Gaussian naive base (GNB) are fast and effective and are commonly used in drug discovery. These algorithms are ideal for the virtual screening of large compound libraries to classify molecules as active or inactive. For the training of the models, a dataset of 307 was downloaded from BindingDB. Among 307 compounds, 85 compounds were labeled as active, having an IC50 below 58 mM, while 222 compounds were labeled inactive against thymidylate kinase, with 87.2% accuracy. The developed models were subjected to an external ZINC dataset of 136,564 compounds. Furthermore, we performed the 100-ns dynamic simulation and post trajectories analysis of compounds having good interaction and score in molecular docking. As compared to the standard reference compound, the top three hits revealed greater stability and compactness. In conclusion, our predicted hits can inhibit thymidylate kinase overexpression to combat Mycobacterium tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Muhammad Shahab
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Muhammad Danial
- University of Chinese Academy of Sciences, Shenzhen Institute of Advanced Technology, Shenzhen, China
| | - Xiuyuan Duan
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Taimur Khan
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Chaoqun Liang
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Hanzi Gao
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Meiyu Chen
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Daixi Wang
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
| | - Guojun Zheng
- State Key Laboratories of Chemical Resources Engineering Beijing University of Chemical Technology, Beijing, China
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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: 1] [Impact Index Per Article: 0.5] [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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Leite DI, de Castro Bazan Moura S, da Conceição Avelino Dias M, Costa CCP, Machado GP, Pimentel LCF, Branco FSC, Moreira R, Bastos MM, Boechat N. A Review of the Development of Multitarget Molecules against HIV-TB Coinfection Pathogens. Molecules 2023; 28:molecules28083342. [PMID: 37110574 PMCID: PMC10143421 DOI: 10.3390/molecules28083342] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/23/2023] [Accepted: 03/30/2023] [Indexed: 04/29/2023] Open
Abstract
The human immunodeficiency virus (HIV) produces the pathologic basis of acquired immunodeficiency syndrome (AIDS). An increase in the viral load in the body leads to a decline in the number of T lymphocytes, compromising the patient's immune system. Some opportunistic diseases may result, such as tuberculosis (TB), which is the most common in seropositive patients. Long-term treatment is required for HIV-TB coinfection, and cocktails of drugs for both diseases are used concomitantly. The most challenging aspects of treatment are the occurrence of drug interactions, overlapping toxicity, no adherence to treatment and cases of resistance. Recent approaches have involved using molecules that can act synergistically on two or more distinct targets. The development of multitarget molecules could overcome the disadvantages of the therapies used to treat HIV-TB coinfection. This report is the first review on using molecules with activities against HIV and Mycobacterium tuberculosis (MTB) for molecular hybridization and multitarget strategies. Here, we discuss the importance and development of multiple targets as a means of improving adherence to therapy in cases of the coexistence of these pathologies. In this context, several studies on the development of structural entities to treat HIV-TB simultaneously are discussed.
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Affiliation(s)
- Debora Inacio Leite
- Laboratorio de Sintese de Farmacos (LASFAR), Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos (Farmanguinhos), Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro 21041-000, Brazil
| | - Stefany de Castro Bazan Moura
- Laboratorio de Sintese de Farmacos (LASFAR), Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos (Farmanguinhos), Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro 21041-000, Brazil
- Programa de Pos-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas (ICB), Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Filho, Rio de Janeiro 21941-902, Brazil
| | - Maria da Conceição Avelino Dias
- Laboratorio de Sintese de Farmacos (LASFAR), Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos (Farmanguinhos), Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro 21041-000, Brazil
| | - Carolina Catta Preta Costa
- Laboratorio de Sintese de Farmacos (LASFAR), Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos (Farmanguinhos), Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro 21041-000, Brazil
| | - Gustavo Peixoto Machado
- Laboratorio de Sintese de Farmacos (LASFAR), Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos (Farmanguinhos), Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro 21041-000, Brazil
| | - Luiz Claudio Ferreira Pimentel
- Laboratorio de Sintese de Farmacos (LASFAR), Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos (Farmanguinhos), Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro 21041-000, Brazil
| | - Frederico Silva Castelo Branco
- Laboratorio de Sintese de Farmacos (LASFAR), Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos (Farmanguinhos), Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro 21041-000, Brazil
| | - Rui Moreira
- Departamento de Química Medicinal, Faculdade de Farmácia, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisboa, Portugal
| | - Monica Macedo Bastos
- Laboratorio de Sintese de Farmacos (LASFAR), Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos (Farmanguinhos), Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro 21041-000, Brazil
| | - Nubia Boechat
- Laboratorio de Sintese de Farmacos (LASFAR), Fundacao Oswaldo Cruz, Instituto de Tecnologia em Farmacos (Farmanguinhos), Fiocruz, Rua Sizenando Nabuco, 100 Manguinhos, Rio de Janeiro 21041-000, Brazil
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Negrya SD, Jasko MV, Makarov DA, Karpenko IL, Solyev PN, Chekhov VO, Efremenkova OV, Vasilieva BF, Efimenko TA, Kochetkov SN, Alexandrova LA. Oligoglycol carbonate prodrugs of 5-modified 2'-deoxyuridines: synthesis and antibacterial activity. MENDELEEV COMMUNICATIONS 2022. [DOI: 10.1016/j.mencom.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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7
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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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Emerging impact of triazoles as anti-tubercular agent. Eur J Med Chem 2022; 238:114454. [PMID: 35597009 DOI: 10.1016/j.ejmech.2022.114454] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 05/04/2022] [Accepted: 05/08/2022] [Indexed: 01/08/2023]
Abstract
Tuberculosis, a disease of poverty is a communicable infection with a reasonably high mortality rate worldwide. 10 Million new cases of TB were reported with approx 1.4 million deaths in the year 2019. Due to the growing number of drug-sensitive and drug-resistant tuberculosis cases, there is a vital need to develop new and effective candidates useful to combat this deadly disease. Despite tremendous efforts to identify a mechanism-based novel antitubercular agent, only a few have entered into clinical trials in the last six decades. In recent years, triazoles have been well explored as the most valuable scaffolds in drug discovery and development. Triazole framework possesses favorable properties like hydrogen bonding, moderate dipole moment, enhanced water solubility, and also the ability to bind effectively with biomolecular targets of M. tuberculosis and therefore this scaffold displayed excellent potency against TB. This review is an endeavor to summarize an up-to-date innovation of triazole-appended hybrids during the last 10 years having potential in vitro and in vivo antitubercular activity with structure activity relationship analysis. This review may help medicinal chemists to explore the triazole scaffolds for the rational design of potent drug candidates having better efficacy, improved selectivity and minimal toxicity so that these hybrid NCEs can effectively be explored as potential lead to fight against M. tuberculosis.
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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: 1.0] [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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Synthesis and Antiviral Evaluation of Nucleoside Analogues Bearing One Pyrimidine Moiety and Two D-Ribofuranosyl Residues. Molecules 2021; 26:molecules26123678. [PMID: 34208647 PMCID: PMC8234143 DOI: 10.3390/molecules26123678] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 12/02/2022] Open
Abstract
A series of 1,2,3-triazolyl nucleoside analogues in which 1,2,3-triazol-4-yl-β-d-ribofuranosyl fragments are attached via polymethylene linkers to both nitrogen atoms of the heterocycle moiety (uracil, 6-methyluracil, thymine, quinazoline-2,4-dione, alloxazine) or to the C-5 and N-3 atoms of the 6-methyluracil moiety was synthesized. All compounds synthesized were evaluated for antiviral activity against influenza virus A/PR/8/34/(H1N1) and coxsackievirus B3. Antiviral assays revealed three compounds, 2i, 5i, 11c, which showed moderate activity against influenza virus A H1N1 with IC50 values of 57.5 µM, 24.3 µM, and 29.2 µM, respectively. In the first two nucleoside analogues, 1,2,3-triazol-4-yl-β-d-ribofuranosyl fragments are attached via butylene linkers to N-1 and N-3 atoms of the heterocycle moiety (6-methyluracil and alloxazine, respectively). In nucleoside analogue 11c, two 1,2,3-triazol-4-yl-2′,3′,5′-tri-O-acetyl-β-d-ribofuranose fragments are attached via propylene linkers to the C-5 and N-3 atoms of the 6-methyluracil moiety. Almost all synthesized 1,2,3-triazolyl nucleoside analogues showed no antiviral activity against the coxsackie B3 virus. Two exceptions are 1,2,3-triazolyl nucleoside analogs 2f and 5f, in which 1,2,3-triazol-4-yl-2′,3′,5′-tri-O-acetyl-β-d-ribofuranose fragments are attached to the C-5 and N-3 atoms of the heterocycle moiety (6-methyluracil and alloxazine respectively). These compounds exhibited high antiviral potency against the coxsackie B3 virus with IC50 values of 12.4 and 11.3 µM, respectively, although both were inactive against influenza virus A H1N1. According to theoretical calculations, the antiviral activity of the 1,2,3-triazolyl nucleoside analogues 2i, 5i, and 11c against the H1N1 (A/PR/8/34) influenza virus can be explained by their influence on the functioning of the polymerase acidic protein (PA) of RNA-dependent RNA polymerase (RdRp). As to the antiviral activity of nucleoside analogs 2f and 5f against coxsackievirus B3, it can be explained by their interaction with the coat proteins VP1 and VP2.
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11
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Negrya SD, Jasko MV, Makarov DA, Solyev PN, Karpenko IL, Shevchenko OV, Chekhov OV, Glukhova AA, Vasilyeva BF, Efimenko TA, Sumarukova IG, Efremenkova OV, Kochetkov SN, Alexandrova LA. Glycol and Phosphate Depot Forms of 4- and/or 5-Modified Nucleosides Exhibiting Antibacterial Activity. Mol Biol 2021. [DOI: 10.1134/s002689332101012x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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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: 7] [Impact Index Per Article: 1.8] [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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13
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Andreeva OV, Garifullin BF, Zarubaev VV, Slita AV, Yesaulkova IL, Saifina LF, Shulaeva MM, Belenok MG, Semenov VE, Kataev VE. Synthesis of 1,2,3-triazolyl nucleoside analogues and their antiviral activity. Mol Divers 2020; 25:473-490. [PMID: 32930935 PMCID: PMC7490575 DOI: 10.1007/s11030-020-10141-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 09/03/2020] [Indexed: 12/20/2022]
Abstract
Abstract Based on the fact that a search for influenza antivirals among nucleoside analogues has drawn very little attention of chemists, the present study reports the synthesis of a series of 1,2,3-triazolyl nucleoside analogues in which a pyrimidine fragment is attached to the ribofuranosyl-1,2,3-triazol-4-yl moiety by a polymethylene linker of variable length. Target compounds were prepared by the Cu alkyne-azide cycloaddition (CuAAC) reaction. Derivatives of uracil, 6-methyluracil, 3,6-dimethyluracil, thymine and quinazolin-2,4-dione with ω-alkyne substituent at the N1 (or N5) atom and azido 2,3,5-tri-O-acetyl-D-β-ribofuranoside were used as components of the CuAAC reaction. All compounds synthesized were evaluated for antiviral activity against influenza virus A/PR/8/34/(H1N1) and coxsackievirus B3. The best values of IC50 (inhibiting concentration) and SI (selectivity index) were demonstrated by the lead compound 4i in which the 1,2,3-triazolylribofuranosyl fragment is attached to the N1 atom of the quinazoline-2,4-dione moiety via a butylene linker (IC50 = 30 μM, SI = 24) and compound 8n in which the 1,2,3-triazolylribofuranosyl fragment is attached directly to the N5 atom of the 6-methyluracil moiety (IC50 = 15 μM, SI = 5). According to theoretical calculations, the antiviral activity of the 1,2,3-triazolyl nucleoside analogues 4i and 8n against H1N1 (A/PR/8/34) influenza virus can be explained by their influence on the functioning of the polymerase acidic protein (PA) of RNA-dependent RNA polymerase (RdRP). Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s11030-020-10141-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Olga V Andreeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str., 8, Kazan, Russian Federation, 420088
| | - Bulat F Garifullin
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str., 8, Kazan, Russian Federation, 420088
| | - Vladimir V Zarubaev
- Pasteur Institute of Epidemiology and Microbiology, Mira Str., 14, Saint Petersburg, Russian Federation, 197101
| | - Alexander V Slita
- Pasteur Institute of Epidemiology and Microbiology, Mira Str., 14, Saint Petersburg, Russian Federation, 197101
| | - Iana L Yesaulkova
- Pasteur Institute of Epidemiology and Microbiology, Mira Str., 14, Saint Petersburg, Russian Federation, 197101
| | - Liliya F Saifina
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str., 8, Kazan, Russian Federation, 420088
| | - Marina M Shulaeva
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str., 8, Kazan, Russian Federation, 420088
| | - Maya G Belenok
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str., 8, Kazan, Russian Federation, 420088
| | - Vyacheslav E Semenov
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str., 8, Kazan, Russian Federation, 420088.
| | - Vladimir E Kataev
- Arbuzov Institute of Organic and Physical Chemistry, FRC Kazan Scientific Center, Russian Academy of Sciences, Arbuzov Str., 8, Kazan, Russian Federation, 420088
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14
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Venugopala KN, Tratrat C, Pillay M, Chandrashekharappa S, Al-Attraqchi OHA, Aldhubiab BE, Attimarad M, Alwassil OI, Nair AB, Sreeharsha N, Venugopala R, Morsy MA, Haroun M, Kumalo HM, Odhav B, Mlisana K. In silico Design and Synthesis of Tetrahydropyrimidinones and Tetrahydropyrimidinethiones as Potential Thymidylate Kinase Inhibitors Exerting Anti-TB Activity Against Mycobacterium tuberculosis. DRUG DESIGN DEVELOPMENT AND THERAPY 2020; 14:1027-1039. [PMID: 32214795 PMCID: PMC7082623 DOI: 10.2147/dddt.s228381] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 02/20/2020] [Indexed: 01/03/2023]
Abstract
Background and Purpose Tuberculosis has been reported to be the worldwide leading cause of death resulting from a sole infectious agent. The emergence of multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis has made the battle against the infection more difficult since most currently available therapeutic options are ineffective against these resistant strains. Therefore, novel molecules need to be developed to effectively treat tuberculosis disease. Preliminary docking studies revealed that tetrahydropyrimidinone derivatives have favorable interactions with the thymidylate kinase receptor. In the present investigation, we report the synthesis and the mycobacterial activity of several pyrimidinones and pyrimidinethiones as potential thymidylate kinase inhibitors. Methods The title compounds (1a-d) and (2a-b) were synthesized by a one-pot three-component Biginelli reaction. They were subsequently characterized and used for whole-cell anti-TB screening against H37Rv and multidrug-resistant (MDR) strains of Mycobacterium tuberculosis (MTB) by the resazurin microplate assay (REMA) plate method. Molecular modeling was conducted using the Accelry's Discovery Studio 4.0 client program to explain the observed bioactivity of the compounds. The pharmacokinetic properties of the synthesized compounds were predicted and analyzed. Results Of the compounds tested for anti-TB activity, pyrimidinone 1a and pyrimidinethione 2a displayed moderate activity against susceptible MTB H37Rv strains at 16 and 32 µg/mL, respectively. Only compound 2a was observed to exert modest activity at 128 µg/mL against MTB strains with cross-resistance to rifampicin and isoniazid. The presence of the trifluoromethyl group was essential to retain the inhibitory activity of compounds 1a and 2a. Molecular modeling studies of these compounds against thymidylate kinase targets demonstrated a positive correlation between the bioactivity and structure of the compounds. The in-silico ADME (absorption, distribution, metabolism, and excretion) prediction indicated favorable pharmacokinetic and drug-like properties for most compounds. Conclusion Pyrimidinone 1a and pyrimidinethione 2a were identified as the leading compounds and can serve as a starting point to develop novel anti-TB therapeutic agents.
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Affiliation(s)
- Katharigatta N Venugopala
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia.,Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
| | - Christophe Tratrat
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Melendhran Pillay
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban 4001, South Africa
| | | | | | - Bandar E Aldhubiab
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Mahesh Attimarad
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Osama I Alwassil
- Department of Pharmaceutical Sciences, College of Pharmacy, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Anroop B Nair
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Nagaraja Sreeharsha
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Rashmi Venugopala
- Department of Public Health Medicine, University of KwaZulu-Natal, Howard College Campus, Durban 4001, South Africa
| | - Mohamed A Morsy
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia.,Department of Pharmacology, Faculty of Medicine, Minia University, El-Minia 61511, Egypt
| | - Michelyne Haroun
- Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Kingdom of Saudi Arabia
| | - Hezekiel M Kumalo
- Department of Medical Biochemistry, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Medical School, Durban 4001, South Africa
| | - Bharti Odhav
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
| | - Koleka Mlisana
- Department of Microbiology, National Health Laboratory Services, KZN Academic Complex, Inkosi Albert Luthuli Central Hospital, Durban 4001, South Africa
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15
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Khandazhinskaya AL, Matyugina ES, Alexandrova LA, Kezin VA, Chernousova LN, Smirnova TG, Andreevskaya SN, Popenko VI, Leonova OG, Kochetkov SN. Interaction of 5-substituted pyrimidine nucleoside analogues and M.Tuberculosis: A view through an electron microscope. Biochimie 2020; 171-172:170-177. [PMID: 32147512 DOI: 10.1016/j.biochi.2020.03.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/03/2020] [Indexed: 01/17/2023]
Abstract
The data of transmission electron microscopy (TEM) on morphology of M. tuberculosis H37Rv bacterial cells treated with four analogues of pyrimidine nucleosides with different substituents at 5 position of base are presented. We showed that the growth of M. tuberculosis H37Rv cells effectively inhibited by each of these compounds. This process is accompanied with the accumulation of lipid intracellular vacuole-like inclusions in the cells, appearance of deep protrusions and indentations on the surface, partial and/or complete destruction of the three-layered cell envelope. The exact molecular mechanism of action of 5-substituted pyrimidine nucleosides on M. tuberculosis cells remains to be proved. However, one can suggest that mechanism of action for these compounds is related either to their direct interactions with bacteria cell walls or to interactions with enzymes participating in the process of cell wall formation.
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Affiliation(s)
- Anastasia L Khandazhinskaya
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia.
| | - Elena S Matyugina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia.
| | - Liudmila A Alexandrova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia.
| | - Vasiliy A Kezin
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia
| | - Larisa N Chernousova
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow, 107564, Russia.
| | - Tatiana G Smirnova
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow, 107564, Russia.
| | - Sofya N Andreevskaya
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow, 107564, Russia.
| | - Vladimir I Popenko
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia.
| | - Olga G Leonova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia.
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow, 119991, Russia.
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16
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Negrya SD, Makarov DA, Solyev PN, Karpenko IL, Chekhov OV, Glukhova AA, Vasilyeva BF, Sumarukova IG, Efremenkova OV, Kochetkov SN, Alexandrova LA. 5-Alkylthiomethyl Derivatives of 2'-Deoxyuridine: Synthesis and Antibacterial Activity. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1068162020010070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Negrya SD, Jasko MV, Solyev PN, Karpenko IL, Efremenkova OV, Vasilyeva BF, Sumarukova IG, Kochetkov SN, Alexandrova LA. Synthesis of water-soluble prodrugs of 5-modified 2ʹ-deoxyuridines and their antibacterial activity. J Antibiot (Tokyo) 2020; 73:236-246. [DOI: 10.1038/s41429-019-0273-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 12/09/2019] [Accepted: 12/15/2019] [Indexed: 12/14/2022]
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18
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Sharipova RR, Saifina LF, Belenok MG, Semenov VE, Kataev VE. First Analog of Pyrimidine Nucleosides with Two D-Ribofuranose Residues. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2020. [DOI: 10.1134/s1070428020010285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Andreeva OV, Belenok MG, Saifina LF, Shulaeva MM, Dobrynin AB, Sharipova RR, Voloshina AD, Saifina AF, Gubaidullin AT, Khairutdinov BI, Zuev YF, Semenov VE, Kataev VE. Synthesis of novel 1,2,3-triazolyl nucleoside analogues bearing uracil, 6-methyluracil, 3,6-dimethyluracil, thymine, and quinazoline-2,4-dione moieties. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.151276] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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20
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Khanapurmath N, Kulkarni MV, Joshi SD, Anil Kumar G. A click chemistry approach for the synthesis of cyclic ureido tethered coumarinyl and 1-aza coumarinyl 1,2,3-triazoles as inhibitors of Mycobacterium tuberculosis H37Rv and their in silico studies. Bioorg Med Chem 2019; 27:115054. [DOI: 10.1016/j.bmc.2019.115054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/23/2019] [Accepted: 08/21/2019] [Indexed: 12/11/2022]
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21
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Pozzi C, Lopresti L, Tassone G, Mangani S. Targeting Methyltransferases in Human Pathogenic Bacteria: Insights into Thymidylate Synthase (TS) and Flavin-Dependent TS (FDTS). Molecules 2019; 24:molecules24081638. [PMID: 31027295 PMCID: PMC6514825 DOI: 10.3390/molecules24081638] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/18/2019] [Accepted: 04/25/2019] [Indexed: 01/10/2023] Open
Abstract
In cells, thymidylate synthases provide the only de novo source of 2′-deoxythymidine-5′-monophosphate (dTMP), required for DNA synthesis. The activity of these enzymes is pivotal for cell survival and proliferation. Two main families of thymidylate synthases have been identified in bacteria, folate-dependent thymidylate synthase (TS) and flavin-dependent TS (FDTS). TS and FDTS are highly divergent enzymes, characterized by exclusive catalytic mechanisms, involving different sets of cofactors. TS and FDTS mechanisms of action have been recently revised, providing new perspectives for the development of antibacterial drugs targeting these enzymes. Nonetheless, some catalytic details still remain elusive. For bacterial TSs, half-site reactivity is still an open debate and the recent evidences are somehow controversial. Furthermore, different behaviors have been identified among bacterial TSs, compromising the definition of common mechanisms. Moreover, the redox reaction responsible for the regeneration of reduced flavin in FDTSs is not completely clarified. This review describes the recent advances in the structural and functional characterization of bacterial TSs and FDTSs and the current understanding of their mechanisms of action. Furthermore, the recent progresses in the development of inhibitors targeting TS and FDTS in human pathogenic bacteria are summarized.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Ludovica Lopresti
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
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22
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Khandazhinskaya AL, Alexandrova LA, Matyugina ES, Solyev PN, Efremenkova OV, Buckheit KW, Wilkinson M, Buckheit RW, Chernousova LN, Smirnova TG, Andreevskaya SN, Leonova OG, Popenko VI, Kochetkov SN, Seley-Radtke KL. Novel 5'-Norcarbocyclic Pyrimidine Derivatives as Antibacterial Agents. Molecules 2018; 23:E3069. [PMID: 30477147 PMCID: PMC6321083 DOI: 10.3390/molecules23123069] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/16/2018] [Accepted: 11/20/2018] [Indexed: 11/16/2022] Open
Abstract
A series of novel 5'-norcarbocyclic derivatives of 5-alkoxymethyl or 5-alkyltriazolyl-methyl uracil were synthesized and the activity of the compounds evaluated against both Gram-positive and Gram-negative bacteria. The growth of Mycobacterium smegmatis was completely inhibited by the most active compounds at a MIC99 of 67 μg/mL (mc²155) and a MIC99 of 6.7⁻67 μg/mL (VKPM Ac 1339). Several compounds also showed the ability to inhibit the growth of attenuated strains of Mycobacterium tuberculosis ATCC 25177 (MIC99 28⁻61 μg/mL) and Mycobacterium bovis ATCC 35737 (MIC99 50⁻60 μg/mL), as well as two virulent strains of M. tuberculosis; a laboratory strain H37Rv (MIC99 20⁻50 μg/mL) and a clinical strain with multiple drug resistance MS-115 (MIC99 20⁻50 μg/mL). Transmission electron microscopy (TEM) evaluation of M. tuberculosis H37Rv bacterial cells treated with one of the compounds demonstrated destruction of the bacterial cell wall, suggesting that the mechanism of action for these compounds may be related to their interactions with bacteria cell walls.
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Affiliation(s)
- Anastasia L Khandazhinskaya
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia.
| | - Liudmila A Alexandrova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia.
| | - Elena S Matyugina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia.
| | - Pavel N Solyev
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia.
| | - Olga V Efremenkova
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya St., Moscow 119021, Russia.
| | - Karen W Buckheit
- ImQuest BioSciences, 7340 Executive Way Suite R, Frederick, MD 21704, USA.
| | - Maggie Wilkinson
- ImQuest BioSciences, 7340 Executive Way Suite R, Frederick, MD 21704, USA.
| | - Robert W Buckheit
- ImQuest BioSciences, 7340 Executive Way Suite R, Frederick, MD 21704, USA.
| | - Larisa N Chernousova
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow 107564, Russia.
| | - Tatiana G Smirnova
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow 107564, Russia.
| | - Sofya N Andreevskaya
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow 107564, Russia.
| | - Olga G Leonova
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia.
| | - Vladimir I Popenko
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia.
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia.
| | - Katherine L Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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23
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Ben Othman R, Fer MJ, Le Corre L, Calvet-Vitale S, Gravier-Pelletier C. Effect of uridine protecting groups on the diastereoselectivity of uridine-derived aldehyde 5'-alkynylation. Beilstein J Org Chem 2017; 13:1533-1541. [PMID: 28845198 PMCID: PMC5550804 DOI: 10.3762/bjoc.13.153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/20/2017] [Indexed: 12/17/2022] Open
Abstract
The 5'-alkynylation of uridine-derived aldehydes is described. The addition of alkynyl Grignard reagents on the carbonyl group is significantly influenced by the 2',3'-di-O-protecting groups (R1): O-alkyl groups led to modest diastereoselectivities (65:35) in favor of the 5'R-isomer, whereas O-silyl groups promoted higher diastereoselectivities (up to 99:1) in favor of the 5'S-isomer. A study related to this protecting group effect on the diastereoselectivity is reported.
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Affiliation(s)
- Raja Ben Othman
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité (USPC), Centre Interdisciplinaire Chimie Biologie-Paris (CICB-Paris), 45 rue des Saints Pères, 75270 Paris 06, France
| | - Mickaël J Fer
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité (USPC), Centre Interdisciplinaire Chimie Biologie-Paris (CICB-Paris), 45 rue des Saints Pères, 75270 Paris 06, France
| | - Laurent Le Corre
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité (USPC), Centre Interdisciplinaire Chimie Biologie-Paris (CICB-Paris), 45 rue des Saints Pères, 75270 Paris 06, France
| | - Sandrine Calvet-Vitale
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité (USPC), Centre Interdisciplinaire Chimie Biologie-Paris (CICB-Paris), 45 rue des Saints Pères, 75270 Paris 06, France
| | - Christine Gravier-Pelletier
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR 8601 CNRS, Université Paris Descartes, Sorbonne Paris Cité (USPC), Centre Interdisciplinaire Chimie Biologie-Paris (CICB-Paris), 45 rue des Saints Pères, 75270 Paris 06, France
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Dual-targeted anti-TB/anti-HIV heterodimers. Antiviral Res 2017; 145:175-183. [PMID: 28743447 DOI: 10.1016/j.antiviral.2017.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/16/2017] [Accepted: 07/19/2017] [Indexed: 01/12/2023]
Abstract
HIV and M. tuberculosis are two intersecting epidemics making the search for new dual action drugs against both pathogens extremely important. Here, we report on the synthesis and suppressive activities of five dual-targeted HIV/TB compounds. These compounds are heterodimers of AZT, as anti-HIV molecules, and 5-substituted uracil derivatives, as anti-TB molecules. We found that these compounds inhibit the growth of M. tuberculosis and suppress the replication of HIV in human cell cultures and human lymphoid tissues ex vivo. We identified one particular heterodimer that inhibited both HIV and the drug-resistant TB strain MS-115 most potently. This compound demonstrated low toxicity and had no cytostatic effect on cells in culture, constituting an ideal candidate for future development and further in vivo testing.
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25
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Triazole derivatives and their anti-tubercular activity. Eur J Med Chem 2017; 138:501-513. [PMID: 28692915 DOI: 10.1016/j.ejmech.2017.06.051] [Citation(s) in RCA: 330] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 05/20/2017] [Accepted: 06/25/2017] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) remains one of the most widespread and leading deadliest diseases, threats one-third of the world's population. Although numerous efforts have been undertaken to develop new anti-TB agents, only a handful of compounds have entered human trials in the past 5 decades. Triazoles including 1,2,3-triazole and 1,2,4-triazole are one of the most important classes of nitrogen containing heterocycles that exhibited various biological activities. Triazole derivatives are regarded as a new class of effective anti-TB candidates owing to their potential anti-TB potency. Thus, molecules containing triazole moiety may show promising in vitro and in vivo anti-TB activities and might be able to prevent the drug resistant to certain extent. This review outlines the advances in the application of triazole-containing hybrids as anti-TB agents, and discusses the structure-activity relationship of these derivatives.
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Borsari C, Ferrari S, Venturelli A, Costi MP. Target-based approaches for the discovery of new antimycobacterial drugs. Drug Discov Today 2017; 22:576-584. [DOI: 10.1016/j.drudis.2016.11.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 11/07/2016] [Accepted: 11/15/2016] [Indexed: 12/24/2022]
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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: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Purine and pyrimidine nucleoside and nucleotide analogs have been extensively studied as anticancer and antiviral agents. In addition to this, they have recently shown great potential against Mycobacterium Tuberculosis, the causative agent of TB. TB ranks as the tenth most common cause of death in the world. The current treatment for TB infection is limited by side effects and cost of the drugs and most importantly by the development of resistance to the therapy. Therefore the development of novel drugs, capable of overcoming the drawbacks of the existing treatments, has become the focus of many research programs. In parallel to that, a tremendous effort has been made to elucidate the unique metabolism of this pathogen with the aim to identify new possible targets. This review presents the state of the art in nucleoside and nucleotide analogs in the treatment of TB. In particular, we report on the inhibitory activity of this class of compounds, both in enzymatic and whole-cell assays, providing a brief insight to which reported target these novel compounds are hitting.
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Synthesis and evaluation of C-5 modified 2'-deoxyuridine monophosphates as inhibitors of M. tuberculosis thymidylate synthase. Bioorg Med Chem 2015; 23:7131-7. [PMID: 26482569 DOI: 10.1016/j.bmc.2015.09.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 09/30/2015] [Indexed: 11/20/2022]
Abstract
A series of 5'-monophosphates of 5-substituted 2'-deoxyuridine analogs, which recently demonstrated in vitro substantial suppression of two strains of Mycobacterium tuberculosis growth (virulent laboratory H37Rv and multiple resistant MS-115), has been synthesized and evaluated as potential inhibitors of M. tuberculosis thymidylate synthases: classical (ThyA) and flavin dependent thymidylate synthase (ThyX). A systematic SAR study and docking revealed 5-undecyloxymethyl-2'-deoxyuridine 5'-monophosphate 3b, displaying an IC50 value against ThyX of 8.32 μM. All derivatives lack activity against the ThyA. It can be assumed that the mechanism of action of 3b may be partially associated with the inhibition of the ThyX.
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Negria SD, Karpenko IL, Efremenkova OV, Chizhov AO, Kochetkov SN, Alexandrova LA. Synthesis and antimicrobial properties of 5,5′-modified 2′,5′-dideoxyuridines. HETEROCYCL COMMUN 2015. [DOI: 10.1515/hc-2015-0166] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
AbstractAn effective method of synthesis of 5,5′-modified 2′,5′-dideoxyuridine derivatives is based on sequential 5′-iodination and azidation of 5-[4-(1-decyl)-1,2,3-triazol-1-yl]methyl-2′-deoxyuridine followed by 1,3-dipolar cycloaddition of the intermediate azide with an olefin under the catalysis of Cu(I) resulting in 75–85% yield of 5′-[4-substituted (1,2,3-triazol-1-yl]-5-[4-(1-decyl)-1,2,3-triazol-1-yl]methyl-2′,5′-dideoxyuridine. The compounds were shown to possess low cytotoxicity in Vero, A549 cells and Jurkat cell cultures and did not demonstrate noticeable antimicrobial activity.
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Affiliation(s)
- Sergey D. Negria
- 1Engelhardt Institute of Molecular Biology RAS, Vavilov str. 32, Moscow 119991, Russia
| | - Inna L. Karpenko
- 1Engelhardt Institute of Molecular Biology RAS, Vavilov str. 32, Moscow 119991, Russia
| | - Olga V. Efremenkova
- 2Gause Institute of New Antibiotics RAMS, Bol’shaya Pirogovskaya str. 11, Moscow 119867, Russia
| | - Alexander O. Chizhov
- 3Zelinsky Institute of Organic Chemistry RAS, Leninsky pr. 47, Moscow 119991, Russia
| | - Sergey N. Kochetkov
- 1Engelhardt Institute of Molecular Biology RAS, Vavilov str. 32, Moscow 119991, Russia
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Verbitskiy EV, Cheprakova EM, Slepukhin PA, Kravchenko MA, Skornyakov SN, Rusinov GL, Chupakhin ON, Charushin VN. Synthesis, and structure-activity relationship for C(4) and/or C(5) thienyl substituted pyrimidines, as a new family of antimycobacterial compounds. Eur J Med Chem 2015; 97:225-34. [PMID: 25982331 DOI: 10.1016/j.ejmech.2015.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/03/2015] [Accepted: 05/05/2015] [Indexed: 10/23/2022]
Abstract
Combination of the Suzuki cross-coupling and nucleophilic aromatic substitution of hydrogen (SN(H)) reactions proved to be a convenient method for the synthesis of C(4) and/or C(5) mono(thienyl) and di(thienyl) substituted pyrimidines from commercially available 5-bromopyrimidine. All new pyrimidines were found to be active in micromolar concentrations in vitro against H37Rv, avium, terrae, rifampicin and isoniazid-resistance strains of Mycobacterium tuberculosis. The data for acute in vivo toxicity in mice have been obtained for these compounds which appear to be promising antitubercular agents.
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Affiliation(s)
- Egor V Verbitskiy
- I. Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, S. Kovalevskoy Str., 22, Ekaterinburg, 620137, Russia; Ural Federal University, Mira St. 19, Ekaterinburg, 620002, Russia.
| | - Ekaterina M Cheprakova
- I. Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, S. Kovalevskoy Str., 22, Ekaterinburg, 620137, Russia; Ural Federal University, Mira St. 19, Ekaterinburg, 620002, Russia
| | - Pavel A Slepukhin
- I. Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, S. Kovalevskoy Str., 22, Ekaterinburg, 620137, Russia; Ural Federal University, Mira St. 19, Ekaterinburg, 620002, Russia
| | - Marionella A Kravchenko
- Ural Research Institute for Phthisiopulmonology, 22 Parts'ezda St., 50, Ekaterinburg, 620039, Russia
| | - Sergey N Skornyakov
- Ural Research Institute for Phthisiopulmonology, 22 Parts'ezda St., 50, Ekaterinburg, 620039, Russia
| | - Gennady L Rusinov
- I. Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, S. Kovalevskoy Str., 22, Ekaterinburg, 620137, Russia; Ural Federal University, Mira St. 19, Ekaterinburg, 620002, Russia
| | - Oleg N Chupakhin
- I. Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, S. Kovalevskoy Str., 22, Ekaterinburg, 620137, Russia; Ural Federal University, Mira St. 19, Ekaterinburg, 620002, Russia
| | - Valery N Charushin
- I. Postovsky Institute of Organic Synthesis, Ural Branch of the Russian Academy of Sciences, S. Kovalevskoy Str., 22, Ekaterinburg, 620137, Russia; Ural Federal University, Mira St. 19, Ekaterinburg, 620002, Russia
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Shmalenyuk ER, Karpenko IL, Chernousova LN, Chizhov AO, Smirnova TG, Andreevskaya SN, Alexandrova LA. New 5-modified 2′-deoxyuridine derivatives: synthesis and antituberculosis activity. Russ Chem Bull 2015. [DOI: 10.1007/s11172-014-0572-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Synthesis and antituberculosis activity of novel 5-styryl-4-(hetero)aryl-pyrimidines via combination of the Pd-catalyzed Suzuki cross-coupling and S(N)(H) reactions. Bioorg Med Chem Lett 2014; 24:3118-20. [PMID: 24856062 DOI: 10.1016/j.bmcl.2014.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 05/02/2014] [Accepted: 05/05/2014] [Indexed: 11/23/2022]
Abstract
Combination of the Suzuki cross-coupling and nucleophilic aromatic substitution of hydrogen (SN(H)) reactions proved to be a convenient method for the synthesis of 5-styryl-4-(hetero)aryl substituted pyrimidines from commercially available 5-bromopyrimidine. All intermediate 5-bromo-4-(hetero)aryl substituted pyrimidines and also the targeted 5-styryl-4-(hetero)arylpyrimidines were found to be active in micromolar concentrations in vitro against Mycobacterium tuberculosis H37Rv, avium, terrae, and multi-drug-resistant strain isolated from tuberculosis patients in Ural region (Russia). It has been found that some of these compounds possess a low toxicity and have a bacteriostatic effect, comparable and even higher with that of first-line antituberculosis drugs.
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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: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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