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Novgorodtseva AI, Vorob'ev AY, Lomzov AA, Vasilyeva SV. Synthesis and physicochemical properties of new phosphoramide oligodeoxyribonucleotides. I. N-caffeine derivatives. Bioorg Chem 2025; 157:108313. [PMID: 40024199 DOI: 10.1016/j.bioorg.2025.108313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2025] [Revised: 02/14/2025] [Accepted: 02/22/2025] [Indexed: 03/04/2025]
Abstract
Herein, we report the synthesis of new oligonucleotide derivatives containing an internucleotide N-caffeine phosphoramide (PN-caffeine) group. This modification was introduced via Staudinger's reaction with an appropriate caffeine azide during standard solid-phase oligonucleotide synthesis. Modified hexathymidylates and oligonucleotides with a heteronucleotide sequence were obtained with a yield of ∼90 %. Physicochemical properties of the new oligonucleotides were analyzed next. UV spectral determination of pKa showed that the PN-caffeine group is neutral at pH < 5 and is negatively charged at pH > 8. The modified oligonucleotides emit weak fluorescence, and the same is true for different charge states of the PN-caffeine moiety and its positions in the DNA strand. A decrease in melting temperature of DNA/DNA and DNA/RNA duplexes was observed after the modification introduction into the DNA. Circular dichroism analysis indicated that the modification does not significantly disrupt either a DNA/DNA or DNA/RNA duplex at either low or high temperatures. This modification expands the existing classes of phosphoramide derivatives of nucleic acids and can be used for various biomedical applications.
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Affiliation(s)
- Alina I Novgorodtseva
- Institute of Chemical Biology & Fundamental Medicine, SB RAS, 8 Akad. Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Aleksey Y Vorob'ev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, SB RAS, 9 Akad. Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Alexander A Lomzov
- Institute of Chemical Biology & Fundamental Medicine, SB RAS, 8 Akad. Lavrentiev Avenue, Novosibirsk 630090, Russia.
| | - Svetlana V Vasilyeva
- Institute of Chemical Biology & Fundamental Medicine, SB RAS, 8 Akad. Lavrentiev Avenue, Novosibirsk 630090, Russia.
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2
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Khoury W, Trus R, Chen X, Baghaie L, Clark M, Szewczuk MR, El-Diasty M. Parsimonious Effect of Pentoxifylline on Angiogenesis: A Novel Pentoxifylline-Biased Adenosine G Protein-Coupled Receptor Signaling Platform. Cells 2023; 12:cells12081199. [PMID: 37190108 DOI: 10.3390/cells12081199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/13/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Angiogenesis is the physiological process of developing new blood vessels to facilitate the delivery of oxygen and nutrients to meet the functional demands of growing tissues. It also plays a vital role in the development of neoplastic disorders. Pentoxifylline (PTX) is a vasoactive synthetic methyl xanthine derivative used for decades to manage chronic occlusive vascular disorders. Recently, it has been proposed that PTX might have an inhibitory effect on the angiogenesis process. Here, we reviewed the modulatory effects of PTX on angiogenesis and its potential benefits in the clinical setting. Twenty-two studies met the inclusion and exclusion criteria. While sixteen studies demonstrated that pentoxifylline had an antiangiogenic effect, four suggested it had a proangiogenic effect, and two other studies showed it did not affect angiogenesis. All studies were either in vivo animal studies or in vitro animal and human cell models. Our findings suggest that pentoxifylline may affect the angiogenic process in experimental models. However, there is insufficient evidence to establish its role as an anti-angiogenesis agent in the clinical setting. These gaps in our knowledge regarding how pentoxifylline is implicated in host-biased metabolically taxing angiogenic switch may be via its adenosine A2BAR G protein-coupled receptor (GPCR) mechanism. GPCR receptors reinforce the importance of research to understand the mechanistic action of these drugs on the body as promising metabolic candidates. The specific mechanisms and details of the effects of pentoxifylline on host metabolism and energy homeostasis remain to be elucidated.
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Affiliation(s)
- William Khoury
- School of Medicine, Queen's University, Kingston, ON K7L 3L4, Canada
| | - Ryan Trus
- Faculty of Arts and Science, Queen's University, Kingston, ON K7L 3N9, Canada
- School of Medicine, The Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Xingyu Chen
- School of Medicine, Queen's University, Kingston, ON K7L 3L4, Canada
| | - Leili Baghaie
- Department of Biomedical & Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Mira Clark
- Faculty of Arts and Science, Queen's University, Kingston, ON K7L 3N9, Canada
- Department of Biomedical & Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Myron R Szewczuk
- Department of Biomedical & Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Mohammad El-Diasty
- Division of Cardiac Surgery, Queen's University, Kingston, ON K7L 2V7, Canada
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3
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Reshetnikov DV, Ivanov ID, Baev DS, Rybalova TV, Mozhaitsev ES, Patrushev SS, Vavilin VA, Tolstikova TG, Shults EE. Design, Synthesis and Assay of Novel Methylxanthine-Alkynylmethylamine Derivatives as Acetylcholinesterase Inhibitors. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248787. [PMID: 36557921 PMCID: PMC9788520 DOI: 10.3390/molecules27248787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/01/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Abstract
Xanthine derivatives have been a great area of interest for the development of potent bioactive agents. Thirty-eight methylxanthine derivatives as acetylcholinesterase inhibitors (AChE) were designed and synthesized. Suzuki-Miyaura cross-coupling reactions of 8-chlorocaffeine with aryl(hetaryl)boronic acids, the CuAAC reaction of 8-ethynylcaffeine with several azides, and the copper(I) catalyzed one-pot three-component reaction (A3-coupling) of 8-ethynylcaffeine, 1-(prop-2-ynyl)-, or 7-(prop-2-ynyl)-dimethylxanthines with formaldehyde and secondary amines were the main approaches for the synthesis of substituted methylxanthine derivatives (yield 53-96%). The bioactivity of all new compounds was evaluated by Ellman's method, and the results showed that most of the synthesized compounds displayed good and moderate acetylcholinesterase (AChE) inhibitory activities in vitro. The structure-activity relationships were also discussed. The data revealed that compounds 53, 59, 65, 66, and 69 exhibited the most potent inhibitory activity against AChE with IC50 of 0.25, 0.552, 0.089, 0.746, and 0.121 μM, respectively. The binding conformation and simultaneous interaction modes were further clarified by molecular docking studies.
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Affiliation(s)
- Danila V. Reshetnikov
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave, 9, 630090 Novosibirsk, Russia
| | - Igor D. Ivanov
- The Federal Research Center Institute of Molecular Biology and Biophysics, Timakov Str., 2/12, 630117 Novosibirsk, Russia
| | - Dmitry S. Baev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave, 9, 630090 Novosibirsk, Russia
| | - Tatyana V. Rybalova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave, 9, 630090 Novosibirsk, Russia
| | - Evgenii S. Mozhaitsev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave, 9, 630090 Novosibirsk, Russia
| | - Sergey S. Patrushev
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave, 9, 630090 Novosibirsk, Russia
- Novosibirsk State University, Pirogova Str., 1, 630090 Novosibirsk, Russia
| | - Valentin A. Vavilin
- The Federal Research Center Institute of Molecular Biology and Biophysics, Timakov Str., 2/12, 630117 Novosibirsk, Russia
- Novosibirsk State University, Pirogova Str., 1, 630090 Novosibirsk, Russia
| | - Tatyana G. Tolstikova
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave, 9, 630090 Novosibirsk, Russia
- Novosibirsk State University, Pirogova Str., 1, 630090 Novosibirsk, Russia
| | - Elvira E. Shults
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, Lavrentyev Ave, 9, 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-(383)-3308533
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Ovais Dar M, Kapse RY, Dubey G, Singh T, Thiruvenkatam V, Bharatam PV. Electronic Structure Analysis and Synthesis of Nitroso
N
‐Heterocyclic Imines. ChemistrySelect 2022. [DOI: 10.1002/slct.202203613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Mohammad Ovais Dar
- Department of Medicinal Chemistry National Institute of Pharmaceutical Education and Research Sector 67, S.A.S. Nagar 160062 Punjab India
| | - Rahul Y. Kapse
- Department of Medicinal Chemistry National Institute of Pharmaceutical Education and Research Sector 67, S.A.S. Nagar 160062 Punjab India
| | - Gurudutt Dubey
- Department of Medicinal Chemistry National Institute of Pharmaceutical Education and Research Sector 67, S.A.S. Nagar 160062 Punjab India
- Current address Discipline of Chemistry Indian Institute of Technology Gandhinagar Palaj Gandhinagar 382355 Gujarat India
| | - Tejender Singh
- Department of Medicinal Chemistry National Institute of Pharmaceutical Education and Research Sector 67, S.A.S. Nagar 160062 Punjab India
- Current address Tata Institute of Fundamental Research (TIFR) Hyderabad Gopanpally Hyderabad 500046 Telangana India
| | - Vijay Thiruvenkatam
- Discipline of Biological Engineering Indian Institute of Technology Gandhinagar Palaj Gandhinagar 382355 Gujarat India
| | - Prasad V. Bharatam
- Department of Medicinal Chemistry National Institute of Pharmaceutical Education and Research Sector 67, S.A.S. Nagar 160062 Punjab India
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Reshetnikov DV, Burova LG, Rybalova TV, Bondareva EA, Patrushev SS, Evstropov AN, Shults EE. Synthesis and Antibacterial Activity of Caffeine Derivatives Containing Amino-Acid Fragments. Chem Nat Compd 2022. [DOI: 10.1007/s10600-022-03826-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mellado M, Reyna-Jeldes M, Weinstein-Oppenheimer C, Covarrubias AA, Aguilar LF, Coddou C, Mella J, Cuellar MA. QSAR-driven synthesis of antiproliferative chalcones against SH-SY5Y cancer cells: Design, biological evaluation, and redesign. Arch Pharm (Weinheim) 2022; 355:e2200042. [PMID: 35435270 DOI: 10.1002/ardp.202200042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 11/10/2022]
Abstract
Neuroblastoma is one of the most frequent types of cancer found in infants, and traditional chemotherapy has limited efficacy against this pathology. Thus, the development of new compounds with higher activity and selectivity than traditional drugs is a current challenge in medicinal chemistry research. In this study, we report the synthesis of 21 chalcones with antiproliferative activity and selectivity against the neuroblastoma cell line SH-SY5Y. Then, we developed three-dimensional quantitative structure-activity relationship models (comparative molecular field analysis and comparative molecular similarity index analysis) with high-quality statistical values (q2 > 0.7; r2 > 0.8; r2 pred > 0.7), using IC50 and selectivity index (SI) data as dependent variables. With the information derived from these theoretical models, we designed and synthesized 16 new molecules to prove their consistency, finding good antiproliferative activity against SH-SY5Y cells on these derivatives, with three of them showing higher SI than the referential drugs 5-fluorouracil and cisplatin, displaying also a proapoptotic effect comparable to these drugs, as proven by measuring their effects on executor caspases 3/7 activity induction, Bcl-2/Bax messenger RNA levels alteration, and DNA fragmentation promotion.
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Affiliation(s)
- Marco Mellado
- Instituto de Investigación y Postgrado, Facultad de Ciencias de la Salud, Universidad Central de Chile, Santiago, Chile
| | - Mauricio Reyna-Jeldes
- Laboratorio de Señalización Purinérgica, Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad Católica del Norte, Coquimbo, Chile.,Millennium Nucleus for the Study of Pain (MiNuSPain), Santiago, Chile
| | - Caroline Weinstein-Oppenheimer
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile.,Centro de Investigación Farmacopea Chilena (CIFAR), Universidad de Valparaíso, Valparaíso, Chile
| | - Alejandra A Covarrubias
- Laboratorio de Neurotoxicología Ambiental, Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad Católica del Norte, Coquimbo, Chile
| | - Luis F Aguilar
- Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Claudio Coddou
- Laboratorio de Señalización Purinérgica, Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad Católica del Norte, Coquimbo, Chile.,Millennium Nucleus for the Study of Pain (MiNuSPain), Santiago, Chile
| | - Jaime Mella
- Centro de Investigación Farmacopea Chilena (CIFAR), Universidad de Valparaíso, Valparaíso, Chile.,Instituto de Química y Bioquímica, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
| | - Mauricio A Cuellar
- Escuela de Química y Farmacia, Facultad de Farmacia, Universidad de Valparaíso, Valparaíso, Chile.,Centro de Investigación Farmacopea Chilena (CIFAR), Universidad de Valparaíso, Valparaíso, Chile
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