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Khandazhinskaya A, Eletskaya B, Mironov A, Konstantinova I, Efremenkova O, Andreevskaya S, Smirnova T, Chernousova L, Kondrashova E, Chizhov A, Seley-Radtke K, Kochetkov S, Matyugina E. New Flexible Analogues of 8-Aza-7-deazapurine Nucleosides as Potential Antibacterial Agents. Int J Mol Sci 2023; 24:15421. [PMID: 37895100 PMCID: PMC10607158 DOI: 10.3390/ijms242015421] [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: 10/02/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
A variety of ribo-, 2'-deoxyribo-, and 5'-norcarbocyclic derivatives of the 8-aza-7-deazahypoxanthine fleximer scaffolds were designed, synthesized, and screened for antibacterial activity. Both chemical and chemoenzymatic methods of synthesis for the 8-aza-7-deazainosine fleximers were compared. In the case of the 8-aza-7-deazahypoxanthine fleximer, the transglycosylation reaction proceeded with the formation of side products. In the case of the protected fleximer base, 1-(4-benzyloxypyrimidin-5-yl)pyrazole, the reaction proceeded selectively with formation of only one product. However, both synthetic routes to realize the fleximer ribonucleoside (3) worked with equal efficiency. The new compounds, as well as some 8-aza-7-deazapurine nucleosides synthesized previously, were studied against Gram-positive and Gram-negative bacteria and M. tuberculosis. It was shown that 1-(β-D-ribofuranosyl)-4-(2-aminopyridin-3-yl)pyrazole (19) and 1-(2',3',4'-trihydroxycyclopent-1'-yl)-4-(pyrimidin-4(3H)-on-5-yl)pyrazole (9) were able to inhibit the growth of M. smegmatis mc2 155 by 99% at concentrations (MIC99) of 50 and 13 µg/mL, respectively. Antimycobacterial activities were revealed for 4-(4-aminopyridin-3-yl)-1H-pyrazol (10) and 1-(4'-hydroxy-2'-cyclopenten-1'-yl)-4-(4-benzyloxypyrimidin-5-yl)pyrazole (6). At concentrations (MIC99) of 40 and 20 µg/mL, respectively, the compounds resulted in 99% inhibition of M. tuberculosis growth.
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Affiliation(s)
- Anastasia Khandazhinskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St. 32, 119991 Moscow, Russia; (A.K.); (E.K.); (S.K.)
| | - Barbara Eletskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia; (B.E.); (A.M.); (I.K.)
| | - Anton Mironov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia; (B.E.); (A.M.); (I.K.)
- Institute of Biochemical Technology and Nanotechnology, Peoples’ Friendship University of Russia Named after Patrice Lumumba, Miklukho-Maklaya St. 6, 117198 Moscow, Russia
| | - Irina Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya St. 16/10, 117997 Moscow, Russia; (B.E.); (A.M.); (I.K.)
| | - Olga Efremenkova
- Gause Institute of New Antibiotics, Bol’shaya Pirogovskaya St. 11, 119021 Moscow, Russia;
| | - Sofya Andreevskaya
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, 107564 Moscow, Russia; (S.A.); (T.S.); (L.C.)
| | - Tatiana Smirnova
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, 107564 Moscow, Russia; (S.A.); (T.S.); (L.C.)
| | - Larisa Chernousova
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, 107564 Moscow, Russia; (S.A.); (T.S.); (L.C.)
| | - Evgenia Kondrashova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St. 32, 119991 Moscow, Russia; (A.K.); (E.K.); (S.K.)
| | - Alexander Chizhov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky pr. 47, 119991 Moscow, Russia;
| | - Katherine Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA;
| | - Sergey Kochetkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St. 32, 119991 Moscow, Russia; (A.K.); (E.K.); (S.K.)
| | - Elena Matyugina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov St. 32, 119991 Moscow, Russia; (A.K.); (E.K.); (S.K.)
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Matyugina ES, Novikov MS, Kozlovskaya LI, Volok VP, Shustova EY, Ishmukhametov AA, Kochetkov SN, Khandazhinskaya AL. Evaluation of the Antiviral Potential of Modified Heterocyclic Base and 5'-Norcarbocyclic Nucleoside Analogs Against SARS-CoV-2. Acta Naturae 2021; 13:78-81. [PMID: 35127150 PMCID: PMC8807529 DOI: 10.32607/actanaturae.11479] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/10/2021] [Indexed: 12/31/2022] Open
Abstract
The pandemic caused by the novel betacoronavirus SARS-CoV-2 has already claimed more than 3.5 million lives. Despite the development and use of anti-COVID-19 vaccines, the disease remains a major public health challenge throughout the world. Large-scale screening of the drugs already approved for the treatment of other viral, bacterial, and parasitic infections, as well as autoimmune, oncological, and other diseases is currently underway as part of their repurposing for development of effective therapeutic agents against SARS-CoV-2. In this work, we present the results of a phenotypic screening of libraries of modified heterocyclic bases and 5'-norcarbocyclic nucleoside analogs previously synthesized by us. We identified two leading compounds with apparent potential to inhibit SARS-CoV-2 replication and EC50 values in a range of 20-70 μM. The structures of these compounds can be further optimized to develop an antiviral drug.
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Affiliation(s)
- E. S. Matyugina
- Engelhardt Institute of Molecular Biology, Moscow, 119991 Russia
| | - M. S. Novikov
- Volgograd State Medical University, Volgograd, 400131 Russia
| | - L. I. Kozlovskaya
- FSBSI “Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of the Russian Academy of Sciences”, Moscow, 108819 Russia
- Sechenov Moscow State Medical University, Moscow, 119991 Russia
| | - V. P. Volok
- FSBSI “Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of the Russian Academy of Sciences”, Moscow, 108819 Russia
| | - E. Y. Shustova
- FSBSI “Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of the Russian Academy of Sciences”, Moscow, 108819 Russia
| | - A. A. Ishmukhametov
- FSBSI “Chumakov Federal Scientific Center for Research and Development of Immune and Biological Products of the Russian Academy of Sciences”, Moscow, 108819 Russia
- Sechenov Moscow State Medical University, Moscow, 119991 Russia
| | - S. N. Kochetkov
- Engelhardt Institute of Molecular Biology, Moscow, 119991 Russia
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Zhang L, Jiang Y, Pang X, Hua P, Gao X, Li Q, Li Z. Simultaneous Optimization of Ultrasound-Assisted Extraction for Flavonoids and Antioxidant Activity of Angelica keiskei Using Response Surface Methodology (RSM). Molecules 2019; 24:E3461. [PMID: 31554203 PMCID: PMC6804174 DOI: 10.3390/molecules24193461] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/06/2019] [Accepted: 09/18/2019] [Indexed: 02/02/2023] Open
Abstract
Angelica keiskei Koidzumi (A. keiskei), as a Japanese edible herbal plant, enjoys a variety of biological activities due to the presence of numerous active compounds, especially flavonoids. This study aims for the optimization of ultrasound-assisted extraction (UAE) for flavonoids in A. keiskei and their antioxidant activity by using the response surface methodology (RSM). Single-factor experiments and a four-factor three-level Box-Behnken design (BBD) were performed to explore the effects of the following parameters on flavonoid extraction and antioxidant activity evaluation: ultrasonic temperature (X1), ultrasonic time (X2), ethanol concentration (X3) and liquid-solid ratio (X4). The optimum conditions of the combination of total flavonoid content (TFC), 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging capacity (DPPH-RSC) and ferric-reducing antioxidant power (FRAP) were as follows: X1 = 80 °C, X2 = 4 min, X3 = 78%, X4 = 35 mL/g, respectively. The experimental results provide a theoretical basis for the extensive utilization of A. keiskei and flavonoids extraction from A. keiskei as a potential source of antioxidants.
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Affiliation(s)
- Lei Zhang
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao 266071, China.
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
| | - Yuhuan Jiang
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
- Institute of Advanced Cross-Field Science, College of Life Sciences, Qingdao University, Qingdao 266071, China.
| | - Xuening Pang
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
- Institute of Advanced Cross-Field Science, College of Life Sciences, Qingdao University, Qingdao 266071, China.
| | - Puyue Hua
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
- Institute of Advanced Cross-Field Science, College of Life Sciences, Qingdao University, Qingdao 266071, China.
| | - Xiang Gao
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
- Institute of Advanced Cross-Field Science, College of Life Sciences, Qingdao University, Qingdao 266071, China.
| | - Qun Li
- College of Chemistry and Chemical Engineering, Qingdao University, Qingdao 266071, China.
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
| | - Zichao Li
- Institute of Angelica keiskei Health Industry Technology, Qingdao University, Qingdao 266071, China.
- Institute of Advanced Cross-Field Science, College of Life Sciences, Qingdao University, Qingdao 266071, China.
- Qingdao Balanson Biotech Co., Ltd., Qingdao 266071, China.
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Khandazhinskaya AL, Matyugina ES, Solyev PN, Wilkinson M, Buckheit KW, Buckheit RW, Chernousova LN, Smirnova TG, Andreevskaya SN, Alzahrani KJ, Natto MJ, Kochetkov SN, de Koning HP, Seley-Radtke KL. Investigation of 5'-Norcarbocyclic Nucleoside Analogues as Antiprotozoal and Antibacterial Agents. Molecules 2019; 24:E3433. [PMID: 31546633 PMCID: PMC6804079 DOI: 10.3390/molecules24193433] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/16/2019] [Accepted: 09/19/2019] [Indexed: 11/17/2022] Open
Abstract
Carbocyclic nucleosides have long played a role in antiviral, antiparasitic, and antibacterial therapies. Recent results from our laboratories from two structurally related scaffolds have shown promising activity against both Mycobacterium tuberculosis and several parasitic strains. As a result, a small structure activity relationship study was designed to further probe their activity and potential. Their synthesis and the results of the subsequent biological activity are reported herein.
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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; (E.S.M.); (P.N.S.); (S.N.K.)
| | - Elena S. Matyugina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (E.S.M.); (P.N.S.); (S.N.K.)
| | - Pavel N. Solyev
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (E.S.M.); (P.N.S.); (S.N.K.)
| | - Maggie Wilkinson
- ImQuest BioSciences, 7340 Executive Way Suite R, Frederick, MD 21704, USA; (M.W.); (K.W.B.)
| | - Karen W. Buckheit
- ImQuest BioSciences, 7340 Executive Way Suite R, Frederick, MD 21704, USA; (M.W.); (K.W.B.)
| | - Robert W. Buckheit
- ImQuest BioSciences, 7340 Executive Way Suite R, Frederick, MD 21704, USA; (M.W.); (K.W.B.)
| | - Larisa N. Chernousova
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow 107564, Russia; (L.N.C.); (T.G.S.); (S.N.A.)
| | - Tatiana G. Smirnova
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow 107564, Russia; (L.N.C.); (T.G.S.); (S.N.A.)
| | - Sofya N. Andreevskaya
- Central Tuberculosis Research Institute, 2 Yauzskaya Alley, Moscow 107564, Russia; (L.N.C.); (T.G.S.); (S.N.A.)
| | - Khalid J. Alzahrani
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK; (K.J.A.); (M.J.N.); (H.P.d.K.)
- Department of Clinical Laboratory, College of Applied Medical Sciences, Taif University, Taif 21974, Saudi Arabia
| | - Manal J. Natto
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK; (K.J.A.); (M.J.N.); (H.P.d.K.)
| | - Sergey N. Kochetkov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, 32 Vavilov St., Moscow 119991, Russia; (E.S.M.); (P.N.S.); (S.N.K.)
| | - Harry P. de Koning
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Sir Graeme Davies Building, 120 University Place, Glasgow G12 8TA, UK; (K.J.A.); (M.J.N.); (H.P.d.K.)
| | - Katherine L. Seley-Radtke
- Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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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: 1.7] [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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Evaluation of the antiprotozoan properties of 5′-norcarbocyclic pyrimidine nucleosides. Bioorg Med Chem Lett 2017; 27:3081-3086. [DOI: 10.1016/j.bmcl.2017.05.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 12/11/2022]
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HIV-1 non-nucleoside reverse transcriptase inhibitors: incorporation of benzylphosphonate moiety for solubility improvement. MENDELEEV COMMUNICATIONS 2016. [DOI: 10.1016/j.mencom.2016.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Matyugina ES, Valuev-Elliston VT, Geisman AN, Novikov MS, Chizhov AO, Kochetkov SN, Seley-Radtke KL, Khandazhinskaya AL. Structure-activity evaluation of new uracil-based non-nucleoside inhibitors of HIV reverse transcriptase. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00225j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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