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Gniech T, Humboldt A, Keith KA, James SH, Richert C. A ProTide of AZT Shows Activity Against Human Papillomaviruses. ChemMedChem 2024; 19:e202300661. [PMID: 38241205 DOI: 10.1002/cmdc.202300661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 01/18/2024] [Accepted: 01/18/2024] [Indexed: 01/21/2024]
Abstract
Infection by human papillomaviruses (HPV) can cause warts and tumors. So far, no small molecule antiviral has been approved for the treatment of infections with this DNA virus, although preclinical studies show activity for nucleosidic compounds, such as 9-(2-phosphonylmethoxy)ethylguanine (PMEG) or cidofovir. This prompted us to test new prodrug versions of the nucleoside analog 3'-azido-2',3'-dideoxythymidine (AZT), known to be active against reverse transcriptases and approved for the treatment of HIV. Here we report the synthesis of an ethylbutyl alaninyl ester phosphosphoramidate prodrug of AZT, dubbed AZAEB, and its activity against HPV, a target not known to be sensitive to AZT. A methyl ester derivative was found to be inactive against this and three other DNA viruses, while the phosphoramidate prodrug AZAEB showed a modest inhibitory effect against HPV types 6, 11, 18 and 31. Our results open up new avenues of study for the treatment of diseases caused by members of the papillomaviridae family.
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Affiliation(s)
- Tim Gniech
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Adrian Humboldt
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Kathy A Keith
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Scott H James
- Department of Pediatrics, Division of Pediatric Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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2
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Soter de Mariz e Miranda L, Schroeder Borges Gonçalves R, Uziel J, Obika S, Lubin-Germain N. Editorial: Nucleosides, nucleotides and nucleic acids: chemistry and biology. Front Chem 2024; 12:1401510. [PMID: 38660568 PMCID: PMC11040680 DOI: 10.3389/fchem.2024.1401510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 03/27/2024] [Indexed: 04/26/2024] Open
Affiliation(s)
| | | | - Jacques Uziel
- CY Cergy-Paris Université, BioCIS, CNRS, Cergy, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Japan
| | - Nadege Lubin-Germain
- CY Cergy-Paris Université, BioCIS, CNRS, Cergy, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
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3
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Flemmich L, Bereiter R, Micura R. Chemical Synthesis of Modified RNA. Angew Chem Int Ed Engl 2024:e202403063. [PMID: 38529723 DOI: 10.1002/anie.202403063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/16/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.
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Affiliation(s)
- Laurin Flemmich
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Raphael Bereiter
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria
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4
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Alexandrova LA, Oskolsky IA, Makarov DA, Jasko MV, Karpenko IL, Efremenkova OV, Vasilyeva BF, Avdanina DA, Ermolyuk AA, Benko EE, Kalinin SG, Kolganova TV, Berzina MY, Konstantinova ID, Chizhov AO, Kochetkov SN, Zhgun AA. New Biocides Based on N4-Alkylcytidines: Effects on Microorganisms and Application for the Protection of Cultural Heritage Objects of Painting. Int J Mol Sci 2024; 25:3053. [PMID: 38474298 DOI: 10.3390/ijms25053053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
The rapid increase in the antibiotic resistance of microorganisms, capable of causing diseases in humans as destroying cultural heritage sites, is a great challenge for modern science. In this regard, it is necessary to develop fundamentally novel and highly active compounds. In this study, a series of N4-alkylcytidines, including 5- and 6-methylcytidine derivatives, with extended alkyl substituents, were obtained in order to develop a new generation of antibacterial and antifungal biocides based on nucleoside derivatives. It has been shown that N4-alkyl 5- or 6-methylcytidines effectively inhibit the growth of molds, isolated from the paintings in the halls of the Ancient Russian Paintings of the State Tretyakov Gallery, Russia, Moscow. The novel compounds showed activity similar to antiseptics commonly used to protect works of art, such as benzalkonium chloride, to which a number of microorganisms have acquired resistance. It was also shown that the activity of N4-alkylcytidines is comparable to that of some antibiotics used in medicine to fight Gram-positive bacteria, including resistant strains of Staphylococcus aureus and Mycobacterium smegmatis. N4-dodecyl-5- and 6-methylcytidines turned out to be the best. This compound seems promising for expanding the palette of antiseptics used in painting, since quite often the destruction of painting materials is caused by joint fungi and bacteria infection.
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Affiliation(s)
| | - Ivan A Oskolsky
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Dmitry A Makarov
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Maxim V Jasko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Inna L Karpenko
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Olga V Efremenkova
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya, Moscow 119021, Russia
| | - Byazilya F Vasilyeva
- Gause Institute of New Antibiotics, 11 Bol'shaya Pirogovskaya, Moscow 119021, Russia
| | - Darya A Avdanina
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
| | - Anna A Ermolyuk
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
| | - Elizaveta E Benko
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
| | - Stanislav G Kalinin
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
| | | | - Maria Ya Berzina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Irina D Konstantinova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 16/10 Miklukho-Maklaya str., Moscow 117997, Russia
| | - Alexander O Chizhov
- Zelinsky Institute of Organic Chemistry RAS 47 Leninsky Ave, Moscow 119991, Russia
| | - Sergey N Kochetkov
- Engelhardt Institute of Molecular Biology RAS, 32 Vavilov Str., Moscow 119991, Russia
| | - Alexander A Zhgun
- Research Center of Biotechnology RAS, 33 Leninsky Ave, Moscow 119071, Russia
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5
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Tang P, Harding CJ, Dickson AL, da Silva RG, Harrison DJ, Czekster CM. Snapshots of the Reaction Coordinate of a Thermophilic 2'-Deoxyribonucleoside/ribonucleoside Transferase. ACS Catal 2024; 14:3090-3102. [PMID: 38449528 PMCID: PMC10913048 DOI: 10.1021/acscatal.3c06260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 03/08/2024]
Abstract
Nucleosides are ubiquitous to life and are required for the synthesis of DNA, RNA, and other molecules crucial for cell survival. Despite the notoriously difficult organic synthesis of nucleosides, 2'-deoxynucleoside analogues can interfere with natural DNA replication and repair and are successfully employed as anticancer, antiviral, and antimicrobial compounds. Nucleoside 2'-deoxyribosyltransferase (dNDT) enzymes catalyze transglycosylation via a covalent 2'-deoxyribosylated enzyme intermediate with retention of configuration, having applications in the biocatalytic synthesis of 2'-deoxynucleoside analogues in a single step. Here, we characterize the structure and function of a thermophilic dNDT, the protein from Chroococcidiopsis thermalis (CtNDT). We combined enzyme kinetics with structural and biophysical studies to dissect mechanistic features in the reaction coordinate, leading to product formation. Bell-shaped pH-rate profiles demonstrate activity in a broad pH range of 5.5-9.5, with two very distinct pKa values. A pronounced viscosity effect on the turnover rate indicates a diffusional step, likely product (nucleobase1) release, to be rate-limiting. Temperature studies revealed an extremely curved profile, suggesting a large negative activation heat capacity. We trapped a 2'-fluoro-2'-deoxyarabinosyl-enzyme intermediate by mass spectrometry and determined high-resolution structures of the protein in its unliganded, substrate-bound, ribosylated, 2'-difluoro-2'-deoxyribosylated, and in complex with probable transition-state analogues. We reveal key features underlying (2'-deoxy)ribonucleoside selection, as CtNDT can also use ribonucleosides as substrates, albeit with a lower efficiency. Ribonucleosides are the building blocks of RNA and other key intracellular metabolites participating in energy and metabolism, expanding the scope of use of CtNDT in biocatalysis.
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Affiliation(s)
- Peijun Tang
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Christopher J. Harding
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - Alison L. Dickson
- School
of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, United Kingdom
| | - Rafael G. da Silva
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
| | - David J. Harrison
- School
of Medicine, University of St Andrews, North Haugh, St Andrews KY16 9TF, United Kingdom
| | - Clarissa Melo Czekster
- School
of Biology, Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, United Kingdom
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6
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Sala S, Nitschke P, Masuda R, Gray N, Lawler NG, Wood JM, Buckler JN, Berezhnoy G, Bolaños J, Boughton BA, Lonati C, Rössler T, Singh Y, Wilson ID, Lodge S, Morillon AC, Loo RL, Hall D, Whiley L, Evans GB, Grove TL, Almo SC, Harris LD, Holmes E, Merle U, Trautwein C, Nicholson JK, Wist J. Integrative Molecular Structure Elucidation and Construction of an Extended Metabolic Pathway Associated with an Ancient Innate Immune Response in COVID-19 Patients. J Proteome Res 2024; 23:956-970. [PMID: 38310443 PMCID: PMC10913068 DOI: 10.1021/acs.jproteome.3c00654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/29/2023] [Indexed: 02/05/2024]
Abstract
We present compelling evidence for the existence of an extended innate viperin-dependent pathway, which provides crucial evidence for an adaptive response to viral agents, such as SARS-CoV-2. We show the in vivo biosynthesis of a family of novel endogenous cytosine metabolites with potential antiviral activities. Two-dimensional nuclear magnetic resonance (NMR) spectroscopy revealed a characteristic spin-system motif, indicating the presence of an extended panel of urinary metabolites during the acute viral replication phase. Mass spectrometry additionally enabled the characterization and quantification of the most abundant serum metabolites, showing the potential diagnostic value of the compounds for viral infections. In total, we unveiled ten nucleoside (cytosine- and uracil-based) analogue structures, eight of which were previously unknown in humans allowing us to propose a new extended viperin pathway for the innate production of antiviral compounds. The molecular structures of the nucleoside analogues and their correlation with an array of serum cytokines, including IFN-α2, IFN-γ, and IL-10, suggest an association with the viperin enzyme contributing to an ancient endogenous innate immune defense mechanism against viral infection.
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Affiliation(s)
- Samuele Sala
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Philipp Nitschke
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Reika Masuda
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Nicola Gray
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Nathan G. Lawler
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - James M. Wood
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovef Wellington, Welry, The University of Auckland, Auckland 1010, New Zealand
| | - Joshua N. Buckler
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
| | - Georgy Berezhnoy
- Department
of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Jose Bolaños
- Chemistry
Department, Universidad del Valle, Cali 76001, Colombia
| | - Berin A. Boughton
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Caterina Lonati
- Center
for Preclinical Research, Fondazione IRCCS
Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Titus Rössler
- Department
of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Yogesh Singh
- Institute
of Medical Genetics and Applied Genomics, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Ian D. Wilson
- Division
of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Burlington Danes Building, Du Cane Road, London W12 0NN, U.K.
| | - Samantha Lodge
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Aude-Claire Morillon
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Ruey Leng Loo
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Drew Hall
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Luke Whiley
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
| | - Gary B. Evans
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovef Wellington, Welry, The University of Auckland, Auckland 1010, New Zealand
| | - Tyler L. Grove
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Steven C. Almo
- Department
of Biochemistry, Albert Einstein College
of Medicine, Bronx, New York 10461, United States
| | - Lawrence D. Harris
- Ferrier
Research Institute, Victoria University
of Wellington, Wellington 6012, New Zealand
- The
Maurice Wilkins Centre for Molecular Biodiscovef Wellington, Welry, The University of Auckland, Auckland 1010, New Zealand
| | - Elaine Holmes
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
- Division
of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Burlington Danes Building, Du Cane Road, London W12 0NN, U.K.
| | - Uta Merle
- Department
of Internal Medicine IV, University Hospital
Heidelberg, 69120 Heidelberg, Germany
| | - Christoph Trautwein
- Department
of Preclinical Imaging and Radiopharmacy, Werner Siemens Imaging Center, University Hospital Tübingen, 72074 Tübingen, Germany
| | - Jeremy K. Nicholson
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
- Institute
of Global Health Innovation, Faculty of
Medicine, Imperial College London, Level 1, Faculty Building, South Kensington Campus, London SW7 2NA, U.K.
| | - Julien Wist
- The
Australian National Phenome Centre and Computational and Systems Medicine,
Health Futures Institute, Murdoch University, Harry Perkins Building, Perth WA6150, Australia
- Chemistry
Department, Universidad del Valle, Cali 76001, Colombia
- Faculty of Medicine, Department of Metabolism,
Digestion and Reproduction,
Division of Digestive Diseases at Imperial College, London SW7 2AZ, U.K.
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Nascimento SMRD, Ferry A, Gallier F, Lubin-Germain N, Uziel J, Gonzales S, Miranda LSDME. Developments in the chemistry and biology of 1,2,3-triazolyl-C- nucleosides. Arch Pharm (Weinheim) 2024; 357:e2300580. [PMID: 38150650 DOI: 10.1002/ardp.202300580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/29/2023]
Abstract
In the last 50 years, nucleoside analogs have been introduced to drug therapy as antivirals for different types of cancer due to their interference in cellular proliferation. Among the first line of nucleoside treatment drugs, ribavirin (RBV) is a synthetic N-nucleoside with a 1,2,4-triazole moiety that acts as a broad-spectrum antiviral. It is on the World Health Organization (WHO) list of essential medicines. However, this important drug therapy causes several side effects due to its nonspecific mechanism of action. There is thus a need for a continuous study of its scaffold. A particular approach consists of connecting d-ribose to the nitrogen-containing base with a C-C bond. It provides more stability against enzymatic action and a better pharmacologic profile. The coronavirus disease (COVID) pandemic has increased the need for more solutions for the treatment of viral infections. Among these solutions, remdesivir, the first C-nucleoside, has been approved by the Food and Drug Administration (FDA) for clinical use against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It drew attention to the study of the C-nucleoside scaffold. Different C-nucleoside patterns have been synthesized over the years. They show many important activities against viruses and cancer cell lines. 1,2,3-Triazolyl-C-nucleoside derivatives are a prolific and efficient subclass of RBV analogs close to the already-known RBV with a C-C bond modification. These compounds are often prepared by alkynylation of the d-ribose ring followed by azide-alkyne cycloaddition. They are reported to be active against the Crimean-Congo hemorrhagic fever virus and several tumoral cell lines, showing promising biological potential. In this review, we explore such approaches to 1,2,3-triazolyl-C-nucleosides and their evolution over the years.
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Affiliation(s)
| | - Angélique Ferry
- CY Cergy Paris Université, CNRS, BioCIS, Cergy-Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Florian Gallier
- CY Cergy Paris Université, CNRS, BioCIS, Cergy-Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Nadège Lubin-Germain
- CY Cergy Paris Université, CNRS, BioCIS, Cergy-Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Jacques Uziel
- CY Cergy Paris Université, CNRS, BioCIS, Cergy-Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Simon Gonzales
- CY Cergy Paris Université, CNRS, BioCIS, Cergy-Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
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8
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Seliger H, Sanghvi YS. An Update on Protection of 5'-Hydroxyl Functions of Nucleosides and Oligonucleotides. Curr Protoc 2024; 4:e999. [PMID: 38439607 DOI: 10.1002/cpz1.999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
The synthesis of natural and chemically modified nucleosides and oligonucleotides is in great demand due to its increasing number of applications in diverse areas of research. These include tools for diagnostics and proteomics, research reagents for molecular biology, probes for functional genomics, and the design, discovery, development, and manufacture of new therapeutics. The likelihood of success in synthesizing these molecules is often dependent on the correct choice of a protection strategy to block the 5'-hydroxyl group of a carbohydrate moiety, nucleoside, or oligonucleotide. This topic was reviewed extensively in the year 2000. The purpose of this article is to complement and update the original review with recently published methodologies recommended for the protection and deprotection of the 5'-hydroxyl group. © 2024 Wiley Periodicals LLC.
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9
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Oshinowo M, Piccini M, Kociok-Köhn G, Marken F, Buchard A. Xylose- and Nucleoside-Based Polymers via Thiol-ene Polymerization toward Sugar-Derived Solid Polymer Electrolytes. ACS Appl Polym Mater 2024; 6:1622-1632. [PMID: 38357438 PMCID: PMC10862469 DOI: 10.1021/acsapm.3c02119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 01/07/2024] [Accepted: 01/08/2024] [Indexed: 02/16/2024]
Abstract
A series of copolymers have been prepared via thiol-ene polymerization of bioderived α,ω-unsaturated diene monomers with dithiols toward application as solid polymer electrolytes (SPEs) for Li+-ion conduction. Amorphous polyesters and polyethers with low Tg's (-31 to -11 °C) were first prepared from xylose-based monomers (with varying lengths of fatty acid moiety) and 2,2'-(ethylenedioxy)diethanethiol (EDT). Cross-linking by incorporation of a trifunctional monomer also produced a series of SPEs with ionic conductivities up to 2.2 × 10-5 S cm-1 at 60 °C and electrochemical stability up to 5.08 V, a significant improvement over previous xylose-derived materials. Furthermore, a series of copolymers bearing nucleoside moieties were prepared to exploit the complementary base-pairing interaction of nucleobases. Flexible, transparent, and reprocessable SPE films were thus prepared with improved ionic conductivity (up to 1.5 × 10-4 S cm-1 at 60 °C), hydrolytic degradability, and potential self-healing capabilities.
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Affiliation(s)
- Matthew Oshinowo
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K.
- University
of Bath Institute for Sustainability, Claverton Down, Bath BA2
7AY, U.K.
| | - Marco Piccini
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K.
- University
of Bath Institute for Sustainability, Claverton Down, Bath BA2
7AY, U.K.
| | - Gabriele Kociok-Köhn
- Materials
and Chemical Characterisation Facility (MC2), University of Bath, Claverton Down, Bath BA2
7AY, U.K.
| | - Frank Marken
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K.
- University
of Bath Institute for Sustainability, Claverton Down, Bath BA2
7AY, U.K.
| | - Antoine Buchard
- Department
of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY, U.K.
- University
of Bath Institute for Sustainability, Claverton Down, Bath BA2
7AY, U.K.
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10
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Sandei L, Cocconi E, Stingone C, Rapacciuolo MT, De Sio F, Vitelli R, Moreno Barreto A, Sutherland D, Hawkins J. Platelet hyperactivity: a comparison of water-soluble, bioactive compound levels in commercial tomato products and water-soluble tomato concentrate, a supplement with an approved EFSA antiplatelet health effect. Int J Food Sci Nutr 2024; 75:31-44. [PMID: 37867390 DOI: 10.1080/09637486.2023.2270782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/10/2023] [Indexed: 10/24/2023]
Abstract
The aim of this study was to evaluate and compare the concentration of water-soluble bioactive compounds in tomato products (polyphenols profile, water-soluble vitamins and nucleophilic substances) with the concentration of the same bioactive molecules existing in a water-soluble patented tomato extract, water-soluble tomato extract (WSTC), commercially available as FruitFlow®. This patented tomato extract has been recognised by EFSA (European Food Safety Authority) in a specific Health Claim declaration as having an "Antiplatelet health effect". More than 100 commercial tomato samples, coming from 18 different processing tomato companies worldwide, were analysed and compared with the FruitFlow® supplement. According to the multivariate statistical analyses applied to the data matrix, it is possible to conclude that the commercial tomato products measured (pastes, purees, others) show a significantly higher concentration of water-soluble bioactive molecules (nucleosides/nucleotides and polyphenols) responsible for an anti-platelet aggregation effect than the FruitFlow® dietary supplement.
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Affiliation(s)
- Luca Sandei
- SSICA - Stazione Sperimentale per l'Industria delle Conserve Alimentari, Parma, Italy
| | - Emanuela Cocconi
- SSICA - Stazione Sperimentale per l'Industria delle Conserve Alimentari, Parma, Italy
| | - Carlotta Stingone
- SSICA - Stazione Sperimentale per l'Industria delle Conserve Alimentari, Parma, Italy
| | | | - Francesco De Sio
- SSICA - Stazione Sperimentale per l'Industria delle Conserve Alimentari, Parma, Italy
| | - Rosanna Vitelli
- SSICA - Stazione Sperimentale per l'Industria delle Conserve Alimentari, Parma, Italy
| | - Andres Moreno Barreto
- SSICA - Stazione Sperimentale per l'Industria delle Conserve Alimentari, Parma, Italy
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11
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Anwar AF, Cain CF, Garza MJ, Degen D, Ebright RH, Del Valle JR. Stabilizing Pseudouridimycin: Synthesis, RNA Polymerase Inhibitory Activity, and Antibacterial Activity of Dipeptide-Modified Analogues. ChemMedChem 2024; 19:e202300474. [PMID: 37751316 PMCID: PMC10843019 DOI: 10.1002/cmdc.202300474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 09/28/2023]
Abstract
Pseudouridimycin (PUM) is a microbially produced C-nucleoside dipeptide that selectively targets the nucleotide addition site of bacterial RNA polymerase (RNAP) and that has a lower rate of spontaneous resistance emergence relative to current drugs that target RNAP. Despite its promising biological profile, PUM undergoes relatively rapid decomposition in buffered aqueous solutions. Here, we describe the synthesis, RNAP-inhibitory activity, and antibacterial activity of chemically stabilized analogues of PUM. These analogues feature targeted modifications that mitigate guanidine-mediated hydroxamate bond scission. A subset of analogues in which the central hydroxamate is replaced with amide or hydrazide isosteres retain the antibacterial activity of the natural product.
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Affiliation(s)
- Avraz F Anwar
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Christopher F Cain
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Michael J Garza
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - David Degen
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ, 08854, USA
| | - Richard H Ebright
- Waksman Institute and Department of Chemistry, Rutgers University, Piscataway, NJ, 08854, USA
| | - Juan R Del Valle
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, 46556, USA
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12
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Dong Z, Sun X. Chemical components in cultivated Cordyceps sinensis and their effects on fibrosis. Chin Herb Med 2024; 16:162-167. [PMID: 38375041 PMCID: PMC10874759 DOI: 10.1016/j.chmed.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/09/2022] [Accepted: 11/28/2022] [Indexed: 02/21/2024] Open
Abstract
Objective Cultivated Cordyceps sinensis powder has been used as clinical drug and healthy food to nourish the lung and kidney, which solves the problem of serious shortage of wild C. sinensis. This study aims to explore the chemical components and compared their anti-fibrotic effects in cultivated C. sinensis. Methods Nucleosides, sterols and polysaccharides were separated and purified from cultivated C. sinensis, and analyzed by high performance liquid chromatography, gas chromatography-mass spectrometry and chemical chromogenic methods, respectively. In high glucose-induced rat mesangial cell models, fibronectin and type 1 collagen were used as evaluation indicators. Results There were 10 kinds of nucleosides and one sterol in cultivated C. sinensis. The contents of nucleosides, sterols and polysaccharides in the cultivated C. sinensis were close to 2%, 0.55% and 4.4%, respectively. Furthermore, nucleoside, sterol and polysaccharide components exhibited varying degrees of anti-fibrotic activity. The nucleoside components and sterol components inhibited the expression of extracellular matrix more effectively in the three main components. Conclusion Cultivated C. sinensis remains the similar compounds with the wild C. sinensis, and nucleosides and sterols may be the main active substances that contribute to its anti-fibrotic effects. The project of this study may provide valuable information on further optimization of more effective remedies with few side effects based on cultivated C. sinensis.
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Affiliation(s)
- Zhonghua Dong
- Department of Clinical Pharmacy, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Engineering and Technology Research Center for Pediatric Drug Development, Shandong Medicine and Health Key Laboratory of Clinical Pharmacy, Jinan 250014, China
| | - Xiao Sun
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan 250012, China
- Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan 250012, China
- Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Shandong Key Laboratory: Magnetic Field-free Medicine & Functional Imaging, Qilu Hospital of Shandong University, Jinan 250012, China
- NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan 250012, China
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13
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Makarov DA, Negrya SD, Jasko MV, Karpenko IL, Solyev PN, Chekhov VO, Kaluzhny DN, Efremenkova OV, Vasilyeva BF, Chizhov AO, Avdanina DA, Zhgun AA, Kochetkov SN, Alexandrova LA. 5-Substituted Uridines with Activity against Gram-Positive Bacteria. ChemMedChem 2023; 18:e202300366. [PMID: 37707314 DOI: 10.1002/cmdc.202300366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Fernandes da Silva C, Keeshan A, Cooper C. Hepatitis B virus genotypes influence clinical outcomes: A review. Can Liver J 2023; 6:347-352. [PMID: 38020195 PMCID: PMC10652982 DOI: 10.3138/canlivj-2023-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 03/28/2023] [Indexed: 12/01/2023]
Abstract
Hepatitis B virus (HBV) is a hepatotropic virus that affects approximately 296 million people worldwide. A crucial step to HBV replication is the transcription of its infectious DNA from its viral RNA intermediate. The production of the RNA intermediate hinges on reverse transcription, and therefore the lack of proofreading in that process commonly yields mutants and has led to nine well-described genotypes (A-I) and over 30 known sub-genotypes of the virus. The influence of genotype on HBV infection outcomes, which include fibrosis progression, cirrhosis, and hepatocellular carcinoma (HCC), remain uncertain. This review aims to analyze the influence of HBV genotype on the risk of development of these outcomes. The response to current and future HBV therapies is considered. Further study of larger and more diverse samples will hopefully resolve outstanding uncertainties.
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Affiliation(s)
| | - Alexa Keeshan
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
| | - Curtis Cooper
- Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, Ontario, Canada
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15
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Tosh D, Fisher CL, Salmaso V, Wan TC, Campbell RG, Chen E, Gao ZG, Auchampach JA, Jacobson KA. First Potent Macrocyclic A 3 Adenosine Receptor Agonists Reveal G-Protein and β-Arrestin2 Signaling Preferences. ACS Pharmacol Transl Sci 2023; 6:1288-1305. [PMID: 37705595 PMCID: PMC10496144 DOI: 10.1021/acsptsci.3c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Indexed: 09/15/2023]
Abstract
(N)-Methanocarba adenosine derivatives (A3 adenosine receptor (AR) agonists containing bicyclo[3.1.0]hexane replacing furanose) were chain-extended at N6 and C2 positions with terminal alkenes for ring closure. The resulting macrocycles of 17-20 atoms retained affinity, indicating a spatially proximal orientation of these receptor-bound chains, consistent with molecular modeling of 12. C2-Arylethynyl-linked macrocycle 19 was more A3AR-selective than 2-ether-linked macrocycle 12 (both 5'-methylamides, human (h) A3AR affinities (Ki): 22.1 and 25.8 nM, respectively), with lower mouse A3AR affinities. Functional hA3AR comparison of two sets of open/closed analogues in β-arrestin2 and Gi/o protein assays showed certain signaling preferences divergent from reference agonist Cl-IB-MECA 1. The potencies of 1 at all three Gαi isoforms were slightly less than its hA3AR binding affinity (Ki: 1.4 nM), while the Gαi1 and Gαi2 potencies of macrocycle 12 were roughly an order of magnitude higher than its radioligand binding affinity. Gαi2-coupling was enhanced in macrocycle 12 (EC50 2.56 nM, ∼40% greater maximal efficacy than 1). Di-O-allyl precursor 18 cyclized to form 19, increasing the Gαi1 potency by 7.5-fold. The macrocycles 12 and 19 and their open precursors 11 and 18 potently stimulated β-arrestin2 recruitment, with EC50 values (nM) of 5.17, 4.36, 1.30, and 4.35, respectively, and with nearly 50% greater efficacy compared to 1. This example of macrocyclization altering the coupling pathways of small-molecule (nonpeptide) GPCR agonists is the first for potent and selective macrocyclic AR agonists. These initial macrocyclic derivatives can serve as a guide for the future design of macrocyclic AR agonists displaying unanticipated pharmacology.
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Affiliation(s)
- Dilip
K. Tosh
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Courtney L. Fisher
- Department
of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Veronica Salmaso
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
- Molecular
Modeling Section, Department of Pharmaceutical and Pharmacological
Sciences, University of Padua, Padua 35131, Italy
| | - Tina C. Wan
- Department
of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Ryan G. Campbell
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Eric Chen
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - Zhan-Guo Gao
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
| | - John A. Auchampach
- Department
of Pharmacology & Toxicology and the Cardiovascular Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226, United States
| | - Kenneth A. Jacobson
- Laboratory
of Bioorganic Chemistry, National Institute of Diabetes and Digestive
and Kidney Disease, National Institutes
of Health, 9000 Rockville
Pike, Bethesda, Maryland 20892, United States
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16
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Pottie E, Suresh RR, Jacobson KA, Stove CP. Assay-Dependent Inverse Agonism at the A 3 Adenosine Receptor: When Neutral Is Not Neutral. ACS Pharmacol Transl Sci 2023; 6:1266-1274. [PMID: 37705594 PMCID: PMC10496142 DOI: 10.1021/acsptsci.3c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Indexed: 09/15/2023]
Abstract
The A3 adenosine receptor (A3AR) is implicated in a variety of (patho)physiological conditions. While most research has focused on agonists and antagonists, inverse agonism at A3AR has been scarcely studied. Therefore, this study aimed at exploring inverse agonism, using two previously engineered cell lines (hA3ARLgBiT-SmBiTβarr2 and hA3ARLgBiT-SmBiTminiGαi), both employing the NanoBiT technology. The previously established inverse agonist PSB-10 showed a decrease in basal signal in the β-arrestin 2 (βarr2) but not the miniGαi recruitment assay, indicative of inverse agonism in the former assay. Control experiments confirmed the specificity and reversibility of this observation. Evaluation of a set of presumed neutral antagonists (MRS7907, MRS7799, XAC, and MRS1220) revealed that all displayed concentration-dependent signal decreases when tested in the A3AR-βarr2 recruitment assay, yielding EC50 and Emax values for inverse agonism. Conversely, in the miniGαi recruitment assay, no signal decreases were observed. To assess whether this observation was caused by the inability of the ligands to induce inverse agonism in the G protein pathway, or rather by a limitation inherent to the employed A3AR-miniGαi recruitment assay, a GloSensor cAMP assay was performed. The outcome of the latter also suggests inverse agonism by the presumed neutral antagonists in this latter assay. These findings emphasize the importance of prior characterization of ligands in the relevant test system. Moreover, it showed the suitability of the NanoBiT βarr2 recruitment and the GloSensor cAMP assays to capture inverse agonism at the A3AR, as opposed to the NanoBiT miniGαi recruitment assay.
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Affiliation(s)
- Eline Pottie
- Laboratory
of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical
Sciences, Ghent University, Campus Heymans, Ottergemsesteenweg
460, B-9000 Ghent, Belgium
| | - R. Rama Suresh
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes & Digestive & Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20802, United States
| | - Kenneth A. Jacobson
- Laboratory
of Bioorganic Chemistry, National Institute
of Diabetes & Digestive & Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20802, United States
| | - Christophe P. Stove
- Laboratory
of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical
Sciences, Ghent University, Campus Heymans, Ottergemsesteenweg
460, B-9000 Ghent, Belgium
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17
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Bhattacharya S, Bhattacharyya T, Khanra S, Banerjee R, Dash J. Nucleoside-Derived Metallohydrogel Induces Cell Death in Leishmania Parasites. ACS Infect Dis 2023; 9:1676-1684. [PMID: 37606735 DOI: 10.1021/acsinfecdis.2c00635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Self-assembled hydrogels by virtue of their unique 3D network and tunability have extensively been explored for bio-medical applications like tissue engineering, delivery and release of therapeutic agents, etc. Herein, we demonstrate for the first-time nucleoside-based biocompatible hydrogels with a remarkable leishmanicidal effect against both Leishmania major promastigotes and amastigotes and no cytotoxic effect on the macrophage cell line. In this work, a series of biocompatible hydrogels have been synthesized by silver ion-driven self-assembly of natural nucleoside and nucleotide-like cytidine and 5'-GMP. The supramolecular metallogel obtained from the assembly of cytidine and boronic acid is capable of inducing apoptotic-like cell death of protozoan parasite by causing damage to the membrane as well as DNA. These hydrogels could find promising applications in combating cutaneous leishmaniasis by topical treatment.
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Affiliation(s)
- Semantee Bhattacharya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Tanima Bhattacharyya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Supriya Khanra
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Rahul Banerjee
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata 700064, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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18
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Perez-Molina JA, Cancio-Suárez MR, Moreno S. Is It Time for Treatment as Prevention of Chronic Hepatitis B? Pathogens 2023; 12:1137. [PMID: 37764945 PMCID: PMC10537200 DOI: 10.3390/pathogens12091137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Hepatitis B is a major global health problem with high morbidity and mortality. Approximately 296 million people are living with chronic HBV, and 1.5 million new infections are detected each year, even though a highly effective vaccine has been available for decades and viral replication and transmission can be contained with the use of drugs. Nucleoside therapy, while not curative in most cases, can control viral replication, improve prognosis, and prevent mother-to-child transmission safely. Current treatment guidelines do not include a significant number of chronically infected patients or pregnant women and are often complex to implement. Since these populations continue to have a detectable HVB viral load, they could perpetuate transmission. Expanding and facilitating treatment indications, including treatment as a public health intervention, could help control the spread of the HBV pandemic, thus bringing us closer to the goal of the United Nations General Assembly for the year 2030.
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Affiliation(s)
- Jose A. Perez-Molina
- National Reference Centre for Tropical Diseases, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
- IRYCIS, Carretera de Colmenar Km 9.1, 28034 Madrid, Spain; (M.R.C.-S.); (S.M.)
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Infectious Diseases Department, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Marta Rosas Cancio-Suárez
- IRYCIS, Carretera de Colmenar Km 9.1, 28034 Madrid, Spain; (M.R.C.-S.); (S.M.)
- Infectious Diseases Department, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
- Department of Medicine, Universidad de Alcalá, Alcalá de Henares, 28805 Madrid, Spain
| | - Santiago Moreno
- IRYCIS, Carretera de Colmenar Km 9.1, 28034 Madrid, Spain; (M.R.C.-S.); (S.M.)
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Infectious Diseases Department, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
- Department of Medicine, Universidad de Alcalá, Alcalá de Henares, 28805 Madrid, Spain
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19
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Du Y, Thanapipatsiri A, Yokoyama K. Biosynthesis and Genome Mining Potentials of Nucleoside Natural Products. Chembiochem 2023; 24:e202300342. [PMID: 37357819 PMCID: PMC10530009 DOI: 10.1002/cbic.202300342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
Nucleoside natural products show diverse biological activities and serve as leads for various application purposes, including human and veterinary medicine and agriculture. Studies in the past decade revealed that these nucleosides are biosynthesized through divergent mechanisms, in which early steps of the pathways can be classified into two types (C5' oxidation and C5' radical extension), while the structural diversity is created by downstream tailoring enzymes. Based on this biosynthetic logic, we investigated the genome mining discovery potentials of these nucleosides using the two enzymes representing the two types of C5' modifications: LipL-type α-ketoglutarate (α-KG) and Fe-dependent oxygenases and NikJ-type radical S-adenosyl-L-methionine (SAM) enzymes. The results suggest that this approach allows discovery of putative nucleoside biosynthetic gene clusters (BGCs) and the prediction of the core nucleoside structures. The results also revealed the distribution of these pathways in nature and implied the possibility of future genome mining discovery of novel nucleoside natural products.
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Affiliation(s)
- Yanan Du
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 27710, USA
| | - Anyarat Thanapipatsiri
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 27710, USA
| | - Kenichi Yokoyama
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 27710, USA
- Department of Chemistry, Duke University, 307 Research Drive, Durham, NC 27710, USA
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20
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Serrano-García I, Domínguez-García J, Hurtado-Fernández E, González-Fernández JJ, Hormaza JI, Beiro-Valenzuela MG, Monasterio R, Pedreschi R, Olmo-García L, Carrasco-Pancorbo A. Assessing the RP-LC-MS-Based Metabolic Profile of Hass Avocados Marketed in Europe from Different Geographical Origins (Peru, Chile, and Spain) over the Whole Season. Plants (Basel) 2023; 12:3004. [PMID: 37631215 PMCID: PMC10458757 DOI: 10.3390/plants12163004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
Spain dominates avocado production in Europe, with the Hass variety being the most prominent. Despite this, Spanish production satisfies less than 10% of the overall avocado demand in Europe. Consequently, the European avocado market heavily relies on imports from overseas, primarily sourced from Peru and Chile. Herein, a comprehensive characterization of the metabolic profile of Hass avocado fruits from Spain, Peru, and Chile, available in the European market throughout the year, was carried out. The determination of relevant substances was performed using high- and low-resolution RP-LC-MS. Remarkable quantitative differences regarding phenolic compounds, amino acids, and nucleosides were observed. Principal component analysis revealed a natural clustering of avocados according to geographical origin. Moreover, a specific metabolic pattern was established for each avocado-producing country using supervised partial least squares discriminant analysis. Spanish fruits exhibited high levels of coumaric acid malonyl-hexose II, coumaric acid hexose II, and ferulic acid hexose II, together with considerably low levels of pantothenic acid and uridine. Chilean avocado fruits presented high concentrations of abscisic acid, uridine, ferulic acid, succinic acid, and tryptophan. Fruits from Peru showed high concentrations of dihydroxybenzoic acid hexose, alongside very low levels of p-coumaric acid, ferulic acid, coumaric acid malonyl-hexose I, and ferulic acid hexose II.
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Affiliation(s)
- Irene Serrano-García
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Ave. Fuentenueva S/N, 18071 Granada, Spain; (I.S.-G.); (J.D.-G.); (M.G.B.-V.); (R.M.); (A.C.-P.)
| | - Joel Domínguez-García
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Ave. Fuentenueva S/N, 18071 Granada, Spain; (I.S.-G.); (J.D.-G.); (M.G.B.-V.); (R.M.); (A.C.-P.)
| | - Elena Hurtado-Fernández
- Department of Biological and Health Sciences, Faculty of Health Sciences, University of Loyola, Campus Sevilla, Avda. de las Universidades S/N, 41704 Dos Hermanas, Spain;
| | - José Jorge González-Fernández
- Institute for Mediterranean and Subtropical Horticulture (IHSM La Mayora-UMA-CSIC), 29750 Algarrobo-Costa, Spain; (J.J.G.-F.); (J.I.H.)
| | - José Ignacio Hormaza
- Institute for Mediterranean and Subtropical Horticulture (IHSM La Mayora-UMA-CSIC), 29750 Algarrobo-Costa, Spain; (J.J.G.-F.); (J.I.H.)
| | - María Gemma Beiro-Valenzuela
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Ave. Fuentenueva S/N, 18071 Granada, Spain; (I.S.-G.); (J.D.-G.); (M.G.B.-V.); (R.M.); (A.C.-P.)
| | - Romina Monasterio
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Ave. Fuentenueva S/N, 18071 Granada, Spain; (I.S.-G.); (J.D.-G.); (M.G.B.-V.); (R.M.); (A.C.-P.)
- Instituto de Biología Agrícola de Mendoza (IBAM), UNCuyo-CONICET, Facultad de Ciencias Agrarias, Chacras de Coria, Mendoza 5505, Argentina
| | - Romina Pedreschi
- Escuela de Agronomía, Facultad de Ciencias Agronómicas y de los Alimentos, Pontificia Universidad Católica de Valparaíso, Calle San Francisco S/N, La Palma, Quillota 2260000, Chile;
- Millennium Institute Center for Genome Regulation (CRG), Santiago 8331150, Chile
| | - Lucía Olmo-García
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Ave. Fuentenueva S/N, 18071 Granada, Spain; (I.S.-G.); (J.D.-G.); (M.G.B.-V.); (R.M.); (A.C.-P.)
| | - Alegría Carrasco-Pancorbo
- Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Ave. Fuentenueva S/N, 18071 Granada, Spain; (I.S.-G.); (J.D.-G.); (M.G.B.-V.); (R.M.); (A.C.-P.)
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21
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Zheng W, Wang M, Chai X, Pan F, Xu M, Wang Y, Lan L, Hu F, Zhang Z, Chen Z. Targeted metabolomics analysis of nucleosides and the identification of biomarkers for colorectal adenomas and colorectal cancer. Front Mol Biosci 2023; 10:1163089. [PMID: 37441164 PMCID: PMC10334214 DOI: 10.3389/fmolb.2023.1163089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/29/2023] [Indexed: 07/15/2023] Open
Abstract
The morbidity and mortality of colorectal cancer (CRC) have been increasing in recent years, and early detection of CRC can improve the survival rate of patients. RNA methylation plays crucial roles in many biological processes and has been implicated in the initiation of various diseases, including cancer. Serum contains a variety of biomolecules and is an important clinical sample for biomarker discovery. In this study, we developed a targeted metabolomics method for the quantitative analysis of nucleosides in human serum samples by using liquid chromatography with tandem mass spectrometry (LC-MS/MS). We successfully quantified the concentrations of nucleosides in serum samples from 51 healthy controls, 37 patients with colorectal adenomas, and 55 patients with CRC. The results showed that the concentrations of N 6-methyladenosine (m6A), N 1-methyladenosine (m1A), and 3-methyluridine (m3U) were increased in patients with CRC, whereas the concentrations of N 2-methylguanosine (m2G), 2'-O-methyluridine (Um), and 2'-O-methylguanosine (Gm) were decreased in patients with CRC, compared with the healthy controls and patients with colorectal adenomas. Moreover, the levels of 2'-O-methyluridine and 2'-O-methylguanosine were lower in patients with colorectal adenomas than those in healthy controls. Interestingly, the levels of Um and Gm gradually decreased in the following order: healthy controls to colorectal adenoma patients to CRC patients. These results revealed that the aberrations of these nucleosides were tightly correlated to colorectal adenomas and CRC. In addition, the present work will stimulate future investigations about the regulatory roles of these nucleosides in the initiation and development of CRC.
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Affiliation(s)
- Weifang Zheng
- Lanxi Hospital of Traditional Chinese Medicine, Jinhua, China
| | - Mingwei Wang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, China
| | | | - Fuzhen Pan
- Lanxi Hospital of Traditional Chinese Medicine, Jinhua, China
| | - Meihui Xu
- Lanxi Hospital of Traditional Chinese Medicine, Jinhua, China
| | - Yingchen Wang
- Lanxi Hospital of Traditional Chinese Medicine, Jinhua, China
| | | | - Feiran Hu
- Lanxi Hospital of Traditional Chinese Medicine, Jinhua, China
| | - Zhe Zhang
- Lanxi Red Cross Hospital, Jinhua, China
| | - Zhu Chen
- Lanxi Hospital of Traditional Chinese Medicine, Jinhua, China
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22
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Zhang M, Li Q, Yu K, Li J, Wu J, Li S, Chen Y, Cai W, Ma J. Systemic chemical characterization of Lemna minor by UHPLC-Q-Exactive Orbitrap MS coupled with parallel reaction monitoring. J Mass Spectrom 2023; 58:e4923. [PMID: 37177835 DOI: 10.1002/jms.4923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Lemna minor L. (LM) has been used for measles opacity, rubella itching, edema, and oliguria, and the main active ingredients were flavonoids, namely, apigenin, apigenin-7-O-glucoside, and luteolin-7-O-glucoside. However, few systematic analyses of their constituents have been performed; thus, it was necessary to establish a fast and efficient method to identify the chemical composition of LM. In this study, the UHPLC-Q-Exactive Orbitrap mass spectrometry coupled with parallel reaction monitoring was established. Finally, a total of 112 constituents, including 30 dipeptides, 28 nucleosides, 11 amino acids, 10 organic acids, 10 flavonoids, and 23 other compounds, were identified by MS, diagnostic fragment ions, and retention time. One hundred one of those chemicals were first found in LM, which was very beneficial for the further development and utilization of nutriments and the medicinal use of LM.
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Affiliation(s)
- Min Zhang
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, China
| | - Qing Li
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, China
| | - Kaiquan Yu
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, China
| | - Jiaxin Li
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, China
| | - Jili Wu
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, China
| | - Shani Li
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, China
| | - Yuqi Chen
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, China
| | - Wei Cai
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, China
| | - Jieyao Ma
- School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, China
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23
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Dembek M, Bocian S. Phosphodiester Stationary Phases as Universal Chromatographic Materials for Separation in RP LC, HILIC, and Pure Aqueous Mobile Phase. Materials (Basel) 2023; 16:ma16093539. [PMID: 37176421 PMCID: PMC10180384 DOI: 10.3390/ma16093539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/11/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023]
Abstract
Modern analytical chemistry techniques meet the need for greater attention to ecological and economic aspects. It is becoming necessary to seek solutions to reduce harmful waste production, especially in large quantities. High-performance liquid chromatography is a technique widely used in many industries, including mainly pharmaceuticals, and requires an approach to reduce the significant amount of organic solvent waste. One of the green chemistry solutions is using environmentally benign substitutes, such as pure water, supercritical dioxide, and ethanol. Our work focuses on the preparation and application of new stationary phases with embedded hydrophilic groups for separations using pure water in liquid chromatography. Polar-embedded stationary phases are obtained by attaching a phosphodiester group and 4 different hydrophobic molecules. The studies consisted of hydrophobicity measurements, concentration dependence of retention of the organic additive to the mobile phase, and chromatographic separations of polar and non-polar substance mixtures in RP-LC and HILIC systems. Three mixtures were studied: purine alkaloids, benzene, and polycyclic aromatic hydrocarbons and nucleosides. The stationary phases interact differently with the analytes depending on the attached hydrophobic group. It is possible to use pure water to separate each mixture under study. It is also significant that it has been possible to separate a mixture of completely non-polar compounds using pure water for the first time. The research being carried out is crucial in synthesizing new polar-embedded stationary phases, providing work versatility and high environmental performance.
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Affiliation(s)
- Mikołaj Dembek
- Chair of Environmental Chemistry and Bioanalysis, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100 Torun, Poland
| | - Szymon Bocian
- Chair of Environmental Chemistry and Bioanalysis, Faculty of Chemistry, Nicolaus Copernicus University, 7 Gagarina Str., 87-100 Torun, Poland
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24
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Negi I, Singh B, Singh Mahmi A, Sharma P. Structural Properties of Hachimoji Nucleic Acids and Their Building Blocks: Comparison of Genetic Systems with Four, Six and Eight Alphabets. Chemphyschem 2023; 24:e202200714. [PMID: 36315394 DOI: 10.1002/cphc.202200714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/29/2022] [Indexed: 11/07/2022]
Abstract
Expansion of the genetic alphabet is an ambitious goal. A recent breakthrough has led to the eight-base (hachimoji) genetics having canonical and unnatural bases. However, very little is known on the molecular-level features that facilitate the candidature of unnatural bases as genetic alphabets. Here we amalgamated DFT calculations and MD simulations to analyse the properties of the constituents of hachimoji DNA and RNA. DFT reveals the dominant syn conformation for isolated unnatural deoxyribonucleosides and at the 5'-end of oligonucleotides, although an anti/syn mixture is predicted at the nonterminal and 3'-terminal positions. However, isolated ribonucleotides prefer an anti/syn mixture, but mostly prefer anti conformation at the nonterminal positions. Further, the canonical base pairing combinations reveals significant strength, which may facilitate replication of hachimoji DNA. We also identify noncanonical base pairs that can better tolerate the substitution of unnatural pairs in RNA. Stacking strengths of 51 dimers reveals higher average stacking stabilization of dimers of hachimoji bases than canonical bases, which provides clues for choosing energetically stable sequences. A total of 14.4 μs MD simulations reveal the influence of solvent on the properties of hachimoji oligonucleotides and point to the likely fidelity of replication of hachimoji DNA. Our results pinpoint the features that explain the experimentally observed stability of hachimoji DNA.
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Affiliation(s)
- Indu Negi
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Bimaldeep Singh
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Amanpreet Singh Mahmi
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India.,Department of Chemistry and Biochemistry, University of Windsor, 401 Sunset Ave., Windsor, ON, N9B 3P4, Canada
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25
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Itzhakov R, Tworowski D, Sadot N, Sayas T, Fallik E, Kleiman M, Poverenov E. Nucleoside-Based Cross-Linkers for Hydrogels with Tunable Properties. ACS Appl Mater Interfaces 2023; 15:7359-7370. [PMID: 36701767 DOI: 10.1021/acsami.2c19525] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Herein, we report bioderived cross-linkers to create biopolymer-based hydrogels with tunable properties. Nucleosides (inosine and uridine) and ribose (pentose sugar lucking the nitrogenous base) were partially oxidized to yield inosine dialdehyde (IdA), uridine dialdehyde (UdA), and ribose dialdehyde (RdA). The dialdehydes were further used as cross-linkers with polysaccharide chitosan to form hydrogels. Depending on the cross-linker type and concentration, the hydrogels showed tunable rheological, mechanical, and liquid holding properties allowing the preparation of injectable, soft, and moldable hydrogels. Computational modeling and molecular dynamics simulations shed light on hydrogel formation and revealed that, in addition to covalent bonding, noncovalent interactions (π-π stacking, cation-π, and H-bonding) also significantly contributed to the cross-linking process. To demonstrate various application possibilities, the prepared hydrogels were used as a growth platform for plant cells, as injectable inks for layer-by-layer 3D printing applications, and as moldable hydrogels for soft lithography to replicate the microstructure of the plant. These findings suggest that the obtained tunable biocompatible hydrogels have the potential to be good candidates for various biotechnological applications.
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Affiliation(s)
- Rafael Itzhakov
- Agro-Nanotechnology and Advanced Materials Research Center, Department of Food Sciences, Agricultural Research Organization, Volcani Institute, Rishon LeZion7505101, Israel
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Biochemistry and Food Sciences, The Hebrew University of Jerusalem, Rehovot76100, Israel
| | - Dmitry Tworowski
- Department of Structural Biology, Weizmann Institute of Science, Rehovot76100, Israel
| | - Noy Sadot
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Biochemistry and Food Sciences, The Hebrew University of Jerusalem, Rehovot76100, Israel
- Plant Sciences Institute, Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Institute, Rishon LeZion7505101, Israel
| | - Tali Sayas
- Plant Sciences Institute, Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Institute, Rishon LeZion7505101, Israel
| | - Elazar Fallik
- Agro-Nanotechnology and Advanced Materials Research Center, Department of Food Sciences, Agricultural Research Organization, Volcani Institute, Rishon LeZion7505101, Israel
| | - Maya Kleiman
- Plant Sciences Institute, Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Institute, Rishon LeZion7505101, Israel
| | - Elena Poverenov
- Agro-Nanotechnology and Advanced Materials Research Center, Department of Food Sciences, Agricultural Research Organization, Volcani Institute, Rishon LeZion7505101, Israel
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26
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Eyberg J, Ringenberg M, Richert C. Caging of a Strongly Pairing Fluorescent Thymidine Analog with Soft Nucleophiles. Chemistry 2023; 29:e202203289. [PMID: 36395348 PMCID: PMC10107337 DOI: 10.1002/chem.202203289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022]
Abstract
Controlling the pairing strength of nucleobases in DNA through reactions with compounds found inside the cell is a formidable challenge. Here we report how a thiazolyl substituent turns a strongly pairing ethynylpyridone C-nucleoside into a reactive residue in oligonucleotides. The thiazolyl-bearing pyridone reacts with soft nucleophiles, such as glutathione, but not with hard nucleophiles like hydroxide or carbonate. The addition products pair much more weakly with adenine in a complementary strand than the starting material, and also change their fluorescence. This makes oligonucleotides containing the new deoxynucleoside interesting for controlled release. Due to its reactivity toward N, P, S, and Se-nucleophiles, and the visual signal accompanying chemical conversion, the fluorescent nucleotide reported here may also have applications in chemical biology, sensing and diagnostics.
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Affiliation(s)
- Juri Eyberg
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Mark Ringenberg
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
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27
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Wang F, Lin H, Tong J, Tai J, Wu J, Yao Y, Liu Y. Effects of Morphology and Solvent/Temperature on THz Spectra: Take Nucleosides as Example. Molecules 2023; 28:molecules28041528. [PMID: 36838517 PMCID: PMC9965851 DOI: 10.3390/molecules28041528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/18/2023] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
Water molecules were easy to combine with organic molecules and embed into the lattice of solid molecules to form a hydrate. Compared with anhydrous compounds, a hydrate has completely different physical and chemical properties. In this paper, terahertz (THz) spectra of five nucleosides in the solid and liquid phases were studied experimentally by Fourier-transform infrared spectroscopy (FTIR) in the frequency of 0.5-9 THz. In addition, the lattice energy, geometric structure, and vibration spectrum of the molecular crystal of the nucleosides were analyzed theoretically by the generalized energy-based fragmentation approach under periodic boundary conditions (denoted as PBC-GEBF). Furthermore, different nucleoside molecular morphology (monomer, polymer, and crystal), solvent (implicit and explicit water), and temperature/theoretical model effect on the THz spectra were mainly investigated. It was found that in the low-frequency band, the vibrational modes were generally originated from the collective vibration of all molecules involved (more than 99% of them were vibration; only less than 1% of them were rotation and translation), which can reflect the molecular structure and spatial distribution of different substances. The Gibbs free energy of thymidine monomer, dimer, tetramer, and crystal was studied. It was found that the cell-stacking energy had the greatest influence on the spectrum, indicating that only the crystal structure constrained by the periodic boundary conditions could well describe the experimental results. In addition, hydrophobic forces dominated the formation of new chemical bonds and strong inter-molecular interactions; the free water had little contribution to the THz spectrum of nucleosides, while crystalline water had a great influence on the spectrum.
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Affiliation(s)
- Fang Wang
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Haifeng Lin
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
- Correspondence:
| | - Jiawen Tong
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Junbin Tai
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Jiaen Wu
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Yaru Yao
- College of Electronic Engineering, Nanjing XiaoZhuang University, Nanjing 211171, China
| | - Yunfei Liu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China
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28
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Roche TP, Fialho DM, Menor-Salván C, Krishnamurthy R, Schuster GB, Hud NV. A Plausible Prebiotic Path to Nucleosides: Ribosides and Related Aldosides Generated from Ribulose, Fructose, and Similar Abiotic Precursors. Chemistry 2023; 29:e202203036. [PMID: 36261321 DOI: 10.1002/chem.202203036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Indexed: 12/12/2022]
Abstract
The prebiotic origins of ribose, nucleosides, and eventually RNA are enduring questions whose answers are central to the RNA world hypothesis. The abiotic synthesis of sugars was first demonstrated over a century ago, but no known prebiotic reaction produces ribose (an aldose sugar) selectively and in good yield. In contrast, ribulose, and fructose (ketose sugars) and other monosaccharides are formed in high yield by several robust abiotic reactions. It is reported here that ketose sugars - both ketopentoses and ketohexoes - serve as precursors for the formation of ribosides and other aldosides, as demonstrated by glycoside-forming reactions involving barbituric acid, a plausibly prebiotic nucleobase. Moreover, a one-pot reaction of glyceraldehyde and barbituric acid was discovered which under mild conditions, and without special minerals or other catalysts, results in the formation of glycosides. These results reveal that an exclusive or high-yielding generation of free ribose was not required for its incorporation into processes that provided the foundations for life.
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Affiliation(s)
- Tyler P Roche
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - David M Fialho
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Cesar Menor-Salván
- Departmento de Biología de Sistemas/IQAR, Universidad de Alcalá, Madrid, 28806, Spain
| | | | - Gary B Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Nicholas V Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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29
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Van Giesen KJ, Thompson MJ, Meng Q, Lovelock SL. Biocatalytic Synthesis of Antiviral Nucleosides, Cyclic Dinucleotides, and Oligonucleotide Therapies. JACS Au 2023; 3:13-24. [PMID: 36711092 PMCID: PMC9875237 DOI: 10.1021/jacsau.2c00481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/11/2022] [Accepted: 11/11/2022] [Indexed: 05/27/2023]
Abstract
Nucleosides, nucleotides, and oligonucleotides modulate diverse cellular processes ranging from protein production to cell signaling. It is therefore unsurprising that synthetic analogues of nucleosides and their derivatives have emerged as a versatile class of drug molecules for the treatment of a wide range of disease areas. Despite their great therapeutic potential, the dense arrangements of functional groups and stereogenic centers present in nucleic acid analogues pose a considerable synthetic challenge, especially in the context of large-scale manufacturing. Commonly employed synthetic methods rely on extensive protecting group manipulations, which compromise step-economy and result in high process mass intensities. Biocatalytic approaches have the potential to address these limitations, enabling the development of more streamlined, selective, and sustainable synthetic routes. Here we review recent achievements in the biocatalytic manufacturing of nucleosides and cyclic dinucleotides along with progress in developing enzymatic strategies to produce oligonucleotide therapies. We also highlight opportunities for innovations that are needed to facilitate widespread adoption of these biocatalytic methods across the pharmaceutical industry.
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Affiliation(s)
| | | | | | - Sarah L. Lovelock
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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30
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Fàbrega C, Clua A, Eritja R, Aviñó A. Oligonucleotides Carrying Nucleoside Antimetabolites as Potential Prodrugs. Curr Med Chem 2023; 30:1304-1319. [PMID: 34844535 DOI: 10.2174/0929867328666211129124039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/07/2021] [Accepted: 09/27/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Nucleoside and nucleobase antimetabolites are an important class of chemotherapeutic agents for the treatment of cancer as well as other diseases. INTRODUCTION In order to avoid undesirable side effects, several prodrug strategies have been developed. In the present review, we describe a relatively unknown strategy that consists of using oligonucleotides modified with nucleoside antimetabolites as prodrugs. METHODS The active nucleotides are generated by enzymatic degradation once incorporated into cells. This strategy has attracted large interest and is widely utilized at present due to the continuous developments made in therapeutic oligonucleotides and the recent advances in nanomaterials and nanomedicine. RESULTS A large research effort was made mainly in the improvement of the antiproliferative properties of nucleoside homopolymers, but recently, chemically modified aptamers, antisense oligonucleotides and/or siRNA carrying antiproliferative nucleotides have demonstrated a great potential due to the synergetic effect of both therapeutic entities. In addition, DNA nanostructures with interesting properties have been built to combine antimetabolites and enhancers of cellular uptake in the same scaffold. Finally, protein nanoparticles functionalized with receptor-binders and antiproliferative oligomers represent a new avenue for a more effective treatment in cancer therapy. CONCLUSION It is expected that oligonucleotides carrying nucleoside antimetabolites will be considered as potential drugs in the near future for biomedical applications.
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Affiliation(s)
- Carme Fàbrega
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
| | - Anna Clua
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Barcelona, Spain.,Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), E-08034 Barcelona, Spain
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31
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Fan J, Liu XQ, Meng CXN, Jiao S, Feng WH, Yan LH, Wang ZM. [Quality evaluation of Galli Gigerii Endothelium Corneum based on HPLC fingerprints and content determination of nucleosides]. Zhongguo Zhong Yao Za Zhi 2023; 48:114-125. [PMID: 36725264 DOI: 10.19540/j.cnki.cjcmm.20220425.201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Galli Gigerii Endothelium Corneum(GGEC), the dried gizzard membrane of Gallus gallus domesticus is a Chinese medicinal material commonly used for digestion. However, due to the particularity of texture and composition, its active ingre-dients have not been clarified so far, and there is also a lack of quality evaluation indicators. In this study, UPLC-Q-TOF-MS was used to analyze the chemical components from the water extract of GGEC, and ten nucleosides were identified for the first time. HPLC fingerprints of the water extracts of GGEC were established and the content of seven nucleosides was determined. The fingerprint similarities of 40 batches of GGEC samples ranged from 0.765 to 0.959, indicating that there were great differences among the GGEC products processed with different methods. In addition, SPSS 22.0 and SIMCA 14.1 were used for hierarchical cluster analysis(HCA) and principal component analysis(PCA) on the 19 common peaks of the HPLC fingerprints of GGEC, and the 40 batches of samples were divided into three categories: raw GGEC, fried GGEC and vinegar-processed GGEC. Eight differential components in GGEC were marked by orthogonal partial least squares discrimination analysis(OPLS-DA), two of which were adenine and thymine. The results of content determination showed that the total content of the seven nucleosides in raw GGEC, fried GGEC and vinegar-processed GGEC were 182.5-416.8, 205.3-368.7, and 194.2-283.0 μg·g~(-1), respectively. There were significant differences in the content of hypoxanthine, thymine and thymidine among the GGEC products processed with different methods(P<0.05), which were graded in the order of fried GGEC>vinegar-processed GGEC>raw GGEC. This suggested that the content of hypoxanthine, thymine and thymidine tended to increase during the frying process, and the variation range might be related to the degree of heat exposure. The established methods in this study were simple and reproducible, and could be used for qualitative and quantitative analysis of GGEC and its processed pro-ducts. This study also provided reference for the establishment of quality standards of GGEC with chemical components as control index.
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Affiliation(s)
- Jia Fan
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China
| | - Xiao-Qian Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China
| | - Chen-Xiao-Ning Meng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China
| | - Sen Jiao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China
| | - Wei-Hong Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China
| | - Li-Hua Yan
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China
| | - Zhi-Min Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences Beijing 100700, China
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32
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Palafox MA, Pedraza Velasco MLD, Marín JI, Posada-Moreno P. How proton transfer affects the helical parameters in DNA:DNA microhelices. J Biomol Struct Dyn 2022; 40:13759-13777. [PMID: 34806548 DOI: 10.1080/07391102.2021.1994880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Proton transfer reactions are a widespread phenomenon in many areas of the life sciences and it is one of the origins of the spontaneous point mutations during DNA replication. Because of its importance, many studies have been reported on these reactions. However, the present work is the first one focused on the structural geometrical changes by double proton transfer (DPT). Thus, different Watson-Crick (WC) pairs were optimized first in a simple model with one nucleoside base pair, and in a microhelix form with three nucleoside base pairs. The canonical and few tautomeric forms were considered in DNA:DNA microhelices with A-type and B-type helical forms. The stability of these structures and how the DPT process affects the main geometrical parameters was analyzed, in particular the deformation of the helical parameters. The M06-2X DFT method was used for this purpose. The purine/pyrimidine ring in the keto form appears easier to be deformed than when it is in the enol form. The weaker WC base pair formed with mixed microhelices than with nucleobases alone and the significant deformation of the helical and backbone parameters with the DPT appears to complicate this process in microhelices.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mauricio Alcolea Palafox
- Departamento de Química-Fisica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid. Ciudad Universitaria s/n, Madrid, Spain
| | | | - Josefa Isasi Marín
- Departamento de Química Inorgánica, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Paloma Posada-Moreno
- Departamento de Enfermería, Facultad de Enfermería, Fisioterapia y Podología, Universidad Complutense de Madrid, Madrid, Spain.,Departamento de Enfermería, UCM, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Madrid, Spain
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Serrano JL. Water-Soluble Pd-Imidate Complexes as Versatile Catalysts for the Modification of Unprotected Halo nucleosides. CHEM REC 2022; 22:e202200179. [PMID: 36094784 DOI: 10.1002/tcr.202200179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/24/2022] [Indexed: 12/15/2022]
Abstract
Modification of unprotected nucleosides has been attracting continuous interest, since these building blocks themselves and their phosphate-upgraded corresponding nucleotides have shown a plethora of uses in fields like biochemistry or pharmacy. Pd-catalyzed cross-coupling reactions, conducted in water or its mixtures with polar organic solvents, have frequently been the researchers' choice for the functionalization of the purine/pyrimidine base of the unprotected nucleosides. In this scenario, the availability of hydrophilic ligands and its water-soluble palladium complexes has markedly set the pace of the advances. The approach of our group to the synthesis of such complexes, Pd-imidates specifically, has faced critical stages, namely the jump to synthesize water soluble complexes from our experience working in conventional solvents, the preparation of phosphine free complexes and the overall goal of getting catalytic systems able to work close to room temperature. The continuous feedback with Kapdi's group, experienced in the chemistry of nucleosides, has produced over the last decade the interesting results in both fields presented here.
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Affiliation(s)
- José Luis Serrano
- Departamento de Ingeniería Química y Ambiental., Área de Química Inorgánica, Universidad Politécnica de Cartagena member of European University of Technology, 30203, Cartagena, Spain
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Kumar RK, Sanghvi YS, Reddy PY, Banerjee S. An Improved Scalable Synthesis of the Potent Antiviral (S)-HPMPA. Curr Protoc 2022; 2:e602. [PMID: 36440983 DOI: 10.1002/cpz1.602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We present an improved synthesis of (S)-HPMPA (1) from an easily accessible and commercially available compound, (S)-3-(benzyloxy)propane-1,2-diol (10). Tritylation of primary alcohol 10 was highly selective, and pure product was isolated in good yield. Alkylation of (R)-1-(benzyloxy)-3-(trityloxy)propan-2-ol (11) with diethyl p-toluenesulfonyloxymethyl phosphonate (6) using sodium hydride in tetrahydrofuran followed by detritylation afforded the desired chiral synthon 12. Tosylation of the primary alcohol and subsequent reaction with sodium adeninate afforded protected S-HPMPA (14). Global deprotection using concentrated hydrochloric acid in a sealed tube afforded S-HPMA (1), and the deprotected 1 was crystallized from water and acetone to obtain a 99% pure product. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Preparation of (R)-1-(benzyloxy)-3-(trityloxy)propan-2-ol (11) Basic Protocol 2: Preparation of diethyl (S)-(((1-(benzyloxy)-3-hydroxypropan-2-yl)oxy)methyl)phosphonate (12) Basic Protocol 3: Preparation of (R)-3-(benzyloxy)-2-((diethoxyphosphoryl)methoxy)propyl-4-methylbenzenesulfonate (13) Basic Protocol 4: Preparation of diethyl (S)-(((1-(6-amino-9H-purin-9-yl)-3-(benzyloxy)propan-2-yl)oxy)methyl)phosphonate (14) Support Protocol 1: Preparation of sodium adeninate Basic Protocol 5: Preparation of (S)-(((1-(6-amino-9H-purin-9-yl)-3-hydroxypropan-2-yl)oxy)methyl)phosphonic acid (1).
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Affiliation(s)
| | - Yogesh S Sanghvi
- Sapala Organics Pvt. Ltd, Hyderabad, Telangana, India
- Rasayan Inc., Encinitas, California, USA
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Kennelly SA, Moorthy R, Otero RS, Harki DA. Expanding Catch and Release DNA Decoy (CRDD) Technology with Pyrimidine Mimics. Chemistry 2022; 28:e202201355. [PMID: 35849314 PMCID: PMC9588621 DOI: 10.1002/chem.202201355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Indexed: 01/05/2023]
Abstract
Catch and release DNA decoys (CRDDs) utilize photochemically responsive nucleoside analogues that generate abasic sites upon exposure to light. Herein, we describe the synthesis and evaluation of four candidate CRDD monomers containing nucleobases that mimic endogenous pyrimidines: 2-nitroimidazole (2-NI), 2-nitrobenzene (2-NB), 2-nitropyrrole (2-NP) and 3-nitropyrrole (3-NP). Our studies reveal that 2-NI and 2-NP can function as CRDDs, whereas 3-NP and 2-NB undergo decomposition and transformation to a higher-ordered structure upon photolysis, respectively. When incorporated into DNA, 2-NP undergoes rapid photochemical cleavage of the anomeric bond (1.8 min half-life) to yield an abasic site. Finally, we find that all four pyrimidine mimics show significantly greater stability when base-paired against the previously reported 7-nitroindole CRDD monomer. Our work marks the expansion of CRDD technology to both purine and pyrimidine scaffolds.
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Affiliation(s)
- Samantha A. Kennelly
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
| | - Ramkumar Moorthy
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
| | - Ruben Silva Otero
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
| | - Daniel A. Harki
- Department of Medicinal ChemistryUniversity of Minnesota2231 6th Street SEMinneapolis, MN 55455USA
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Shiu PH, Li J, Zheng C, Rangsinth P, Li R, Cheung QT, Lau AH, Chan JC, Kwan YW, Cheung TM, Leung GP. Amauroderma rugosum Extract Suppresses Inflammatory Responses in Tumor Necrosis Factor Alpha/Interferon Gamma-Induced HaCaT Keratinocytes. Molecules 2022; 27. [PMID: 36235070 DOI: 10.3390/molecules27196533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/25/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022]
Abstract
Keratinocytes form the physical barrier of the skin and play an important role in the inflammatory process. Amauroderma rugosum is an edible mushroom; however, its pharmacological properties have seldom been studied. Although the anti-inflammatory effect of the organic solvent extract of Amauroderma rugosum has been previously reported, it is not known whether the aqueous extract has a similar effect. In addition, the effect of Amauorderma rugosum extract on skin has never been explored. Therefore, the objectives of the present study were to evaluate the anti-inflammatory effects of the aqueous extract of Amauroderma rugosum on HaCaT keratinocytes, to explore its mechanisms of action, and to study the possible active ingredients involved. The results showed that the aqueous extract of Amauroderm rugosum at a concentration of 1.5 mg/mL was non-toxic to HaCaT cells and inhibited the release of cytokine interleukin-1β, and chemokines interleukin-8 and monocyte chemoattractant protein-1 in tumor necrosis factor (TNF)-α- and interferon (IFN)-γ-stimulated HaCaT cells. Amauroderma rugosum extract reduced the intracellular levels of reactive oxygen species. In addition, Amauroderma rugosum extract reduced the total protein expression of nuclear factor-kappa B (NF-κB) and B-cells inhibitor alpha in HaCaT keratinocytes and inhibited the phosphorylation of mitogen-activated protein kinase kinase (MEK) 1/2, extracellular signal-regulated kinase (ERK) 1/2, protein kinase B (Akt), and mammalian target of rapamycin (mTOR) in TNF-α- and INF-γ-stimulated HaCaT keratinocytes. Chemical analysis revealed that the aqueous extract of Amauroderma rugosum contains polysaccharides, triterpenes, and phenolic compounds. Anti-inflammatory compounds, such as gallic acid, guanosine, and uridine, were also present. The anti-inflammatory effect of Amauroderma rugosum could be mimicked by a combination of gallic acid, guanosine, and uridine. In conclusion, our study suggests that the aqueous extract of Amauroderma rugosum exerts anti-inflammatory effects on keratinocytes through its antioxidant and inhibitory effects on MEK/ERK-, Akt/mTOR-, and NF-κB-dependent signaling pathways.
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Jin YT, Qi YQ, Jin M, Sun JF, Diao SB, Zhou W, Zhao LX, Li G. Synthesis, antitumor and antibacterial activities of cordycepin derivatives. J Asian Nat Prod Res 2022; 24:849-859. [PMID: 34657548 DOI: 10.1080/10286020.2021.1982907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Twelve novel cordycepin derivatives were designed and synthesized with modification at positions of 2', 5'-hydroxyl and N6 amino groups of cordycepin. The results showed that the inhibitory activities of 3, 4b, 6c and 6d on A549 were comparable to the positive control gefitinib, and the inhibitory activity of 6a on A549 was better than that of gefitinib. Also, the inhibitory activities of twelve cordycepin derivatives against E. coli 1924, S. aureus 4220 and S. mutans 3289 were studied. Among them, 4b showed certain inhibitory on S. mutans 3289, while 6b showed certain inhibition on S. aureus 4220.
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Affiliation(s)
- Yu-Ting Jin
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, China
| | - Yan-Qiu Qi
- Key Laboratory of Natural Resources of Changbai Mountain and Functional Molecules, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Mei Jin
- Key Laboratory of Natural Resources of Changbai Mountain and Functional Molecules, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Jin-Feng Sun
- Key Laboratory of Natural Resources of Changbai Mountain and Functional Molecules, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Sheng-Bao Diao
- Key Laboratory of Natural Resources of Changbai Mountain and Functional Molecules, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Wei Zhou
- Key Laboratory of Natural Resources of Changbai Mountain and Functional Molecules, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
| | - Long-Xuan Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, China
| | - Gao Li
- Key Laboratory of Natural Resources of Changbai Mountain and Functional Molecules, Ministry of Education, College of Pharmacy, Yanbian University, Yanji 133002, China
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38
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Tan YC, Lee GH, Huang DQ, Lim SG. Future anti-HDV treatment strategies, including those aimed at HBV functional cure. Liver Int 2022; 43:1157-1169. [PMID: 35946084 DOI: 10.1111/liv.15387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/11/2022] [Accepted: 08/08/2022] [Indexed: 02/13/2023]
Abstract
HDV is a defective virus that uses the HBV surface antigen to enter hepatocytes. It is associated with an accelerated course of liver fibrosis progression and an increased risk of hepatocellular carcinoma. Negative HDV RNA 24 weeks after the end of therapy has been proposed as an endpoint but late relapses make this endpoint suboptimal, hence HBsAg loss appears to be more appropriate. Current HBV antiviral agents have poor activity against HDV hence the search for improved therapy. Drugs only active against HDV, such as lonafarnib, have shown efficacy in combination with nucleoside analogues and peginterferon, but do not lead to HBsAg loss. HBsAg loss sustained 24 weeks after the end of therapy with negative HBV DNA is termed functional cure. Agents that are being investigated for functional cure include those that inhibit replication such as entry inhibitors, polymerase inhibitors and capsid assembly modulators but seldom lead to functional cure. Agents that reduce HBV antigen load such as RNA interference and inhibitors of HBsAg secretion are promising. Immunomodulators on their own seldom achieve functional cure, hence these agents in combination to assess the optimal combination are being investigated. Consequently, agents leading to functional cure of HBV are ideal for both HBV and HDV.
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Affiliation(s)
- Yong Chuan Tan
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Guan Huei Lee
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Daniel Q Huang
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Seng Gee Lim
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Gastroenterology and Hepatology, National University Health System, Singapore
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Pastor-Anglada M, Mata-Ventosa A, Pérez-Torras S. Inborn Errors of Nucleoside Transporter (NT)-Encoding Genes ( SLC28 and SLC29). Int J Mol Sci 2022; 23:8770. [PMID: 35955904 PMCID: PMC9369021 DOI: 10.3390/ijms23158770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/29/2022] Open
Abstract
The proper regulation of nucleotide pools is essential for all types of cellular functions and depends on de novo nucleotide biosynthesis, salvage, and degradation pathways. Despite the apparent essentiality of these processes, a significant number of rare diseases associated with mutations in genes encoding various enzymes of these pathways have been already identified, and others are likely yet to come. However, knowledge on genetic alterations impacting on nucleoside and nucleobase transporters is still limited. At this moment three gene-encoding nucleoside and nucleobase transporter proteins have been reported to be mutated in humans, SLC29A1, SLC29A3, and SLC28A1, impacting on the expression and function of ENT1, ENT3, and CNT1, respectively. ENT1 alterations determine Augustine-null blood type and cause ectopic calcification during aging. ENT3 deficiency translates into various clinical manifestations and syndromes, altogether listed in the OMIM catalog as histiocytosis-lymphoadenopathy plus syndrome (OMIM#602782). CNT1 deficiency causes uridine-cytidineuria (URCTU) (OMIM#618477), a unique type of pyrimidineuria with an as yet not well-known clinical impact. Increasing knowledge on the physiological, molecular and structural features of these transporter proteins is helping us to better understand the biological basis behind the biochemical and clinical manifestations caused by these deficiencies. Moreover, they also support the view that some metabolic compensation might occur in these disturbances, because they do not seem to significantly impact nucleotide homeostasis, but rather other biological events associated with particular subtypes of transporter proteins.
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Affiliation(s)
- Marçal Pastor-Anglada
- Departament de Bioquímica i Biomedicina Molecular, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institut de Recerca Sant Joan de Déu (IR SJD), Esplugues de Llobregat, 08950 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBER EHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Aida Mata-Ventosa
- Departament de Bioquímica i Biomedicina Molecular, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institut de Recerca Sant Joan de Déu (IR SJD), Esplugues de Llobregat, 08950 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBER EHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Sandra Pérez-Torras
- Departament de Bioquímica i Biomedicina Molecular, Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, 08028 Barcelona, Spain
- Institut de Recerca Sant Joan de Déu (IR SJD), Esplugues de Llobregat, 08950 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBER EHD), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Wang Y, Huang X, Zhang X, Wang J, Li K, Liu G, Lu K, Zhang X, Xie C, Zheng T, Cheng YY, Wang Q. Synthesis and Biological Evaluation of Novel Allobetulon/Allobetulin-Nucleoside Conjugates as AntitumorAgents. Molecules 2022; 27:4738. [PMID: 35897914 DOI: 10.3390/molecules27154738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/26/2022] Open
Abstract
Allobetulin is structurally similar tobetulinic acid, inducing the apoptosis of cancer cells with low toxicity. However, both of them exhibited weak antiproliferation against several tumor cell lines. Therefore, the new series of allobetulon/allobetulin–nucleoside conjugates 9a–10i were designed and synthesized for potency improvement. Compounds 9b, 9e, 10a, and 10d showed promising antiproliferative activity toward six tested cell lines, compared to zidovudine, cisplatin, and oxaliplatin based on their antitumor activity results. Among them, compound 10d exhibited much more potent antiproliferative activity against SMMC-7721, HepG2, MNK-45, SW620, and A549 human cancer cell lines than cisplatin and oxaliplatin. In the preliminary study for the mechanism of action, compound 10d induced cell apoptosis and autophagy in SMMC cells, resulting in antiproliferation and G0/G1 cell cycle arrest by regulating protein expression levels of Bax, Bcl-2, and LC3. Consequently, the nucleoside-conjugated allobetulin (10d) evidenced that nucleoside substitution was a viable strategy to improve allobetulin/allobetulon’s antitumor activity based on our present study.
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Dziuba D. Environmentally sensitive fluorescent nucleoside analogues as probes for nucleic acid - protein interactions: molecular design and biosensing applications. Methods Appl Fluoresc 2022; 10. [PMID: 35738250 DOI: 10.1088/2050-6120/ac7bd8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are indispensable in studying the interactions of nucleic acids with nucleic acid-binding proteins. By replacing one of the poorly emissive natural nucleosides, FNAs enable real-time optical monitoring of the binding interactions in solutions, under physiologically relevant conditions, with high sensitivity. Besides that, FNAs are widely used to probe conformational dynamics of biomolecular complexes using time-resolved fluorescence methods. Because of that, FNAs are tools of high utility for fundamental biological research, with potential applications in molecular diagnostics and drug discovery. Here I review the structural and physical factors that can be used for the conversion of the molecular binding events into a detectable fluorescence output. Typical environmentally sensitive FNAs, their properties and applications, and future challenges in the field are discussed.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Université de Strasbourg, 74 Route du Rhin, Illkirch-Graffenstaden, Grand Est, 67401, FRANCE
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Kitzenberg DA, Lee JS, Mills KB, Kim JS, Liu L, Vázquez-Torres A, Colgan SP, Kao DJ. Adenosine Awakens Metabolism to Enhance Growth-Independent Killing of Tolerant and Persister Bacteria across Multiple Classes of Antibiotics. mBio 2022;:e0048022. [PMID: 35575513 DOI: 10.1128/mbio.00480-22] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Metabolic and growth arrest are primary drivers of antibiotic tolerance and persistence in clinically diverse bacterial pathogens. We recently showed that adenosine (ADO) suppresses bacterial growth under nutrient-limiting conditions. In the current study, we show that despite the growth-suppressive effect of ADO, extracellular ADO enhances antibiotic killing in both Gram-negative and Gram-positive bacteria by up to 5 orders of magnitude. The ADO-potentiated antibiotic activity is dependent on purine salvage and is paralleled with a suppression of guanosine tetraphosphate synthesis and the massive accumulation of ATP and GTP. These changes in nucleoside phosphates coincide with transient increases in rRNA transcription and proton motive force. The potentiation of antibiotic killing by ADO is manifested against bacteria grown under both aerobic and anaerobic conditions, and it is exhibited even in the absence of alternative electron acceptors such as nitrate. ADO potentiates antibiotic killing by generating proton motive force and can occur independently of an ATP synthase. Bacteria treated with an uncoupler of oxidative phosphorylation and NADH dehydrogenase-deficient bacteria are refractory to the ADO-potentiated killing, suggesting that the metabolic awakening induced by this nucleoside is intrinsically dependent on an energized membrane. In conclusion, ADO represents a novel example of metabolite-driven but growth-independent means to reverse antibiotic tolerance. Our investigations identify the purine salvage pathway as a potential target for the development of therapeutics that may improve infection clearance while reducing the emergence of antibiotic resistance. IMPORTANCE Antibiotic tolerance, which is a hallmark of persister bacteria, contributes to treatment-refractory infections and the emergence of heritable antimicrobial resistance. Drugs that reverse tolerance and persistence may become part of the arsenal to combat antimicrobial resistance. Here, we demonstrate that salvage of extracellular ADO reduces antibiotic tolerance in nutritionally stressed Escherichia coli, Salmonella enterica, and Staphylococcus aureus. ADO potentiates bacterial killing under aerobic and anaerobic conditions and takes place in bacteria lacking the ATP synthase. However, the sensitization to antibiotic killing elicited by ADO requires an intact NADH dehydrogenase, suggesting a requirement for an energized electron transport chain. ADO antagonizes antibiotic tolerance by activating ATP and GTP synthesis, promoting proton motive force and cellular respiration while simultaneously suppressing the stringent response. These investigations reveal an unprecedented role for purine salvage stimulation as a countermeasure of antibiotic tolerance and the emergence of antimicrobial resistance.
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Benítez‐Mateos AI, Paradisi F. Sustainable Flow-Synthesis of (Bulky) Nucleoside Drugs by a Novel and Highly Stable Nucleoside Phosphorylase Immobilized on Reusable Supports. ChemSusChem 2022; 15:e202102030. [PMID: 34726353 PMCID: PMC9298701 DOI: 10.1002/cssc.202102030] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/29/2021] [Indexed: 05/02/2023]
Abstract
The continuous synthesis of valuable nucleoside drugs was achieved in up to 99 % conversion by using a novel halotolerant purine nucleoside phosphorylase from Halomonas elongata (HePNP). HePNP showed an unprecedented tolerance to DMSO, usually required for substrate solubility, and could be immobilized on agarose microbeads through disulfide bonds, via a genetically fused Cystag. This covalent yet reversible binding chemistry showcased the reusability of agarose microbeads in a second round of enzyme immobilization with high reproducibility, reducing waste and increasing the sustainability of the process. Finally, the flow synthesis of a Nelarabine analogue (6-O-methyl guanosine) was optimized to full conversion on a 10 mm scale within 2 min residence time, obtaining the highest space-time yield (89 g L-1 h-1 ) reported to date. The cost-efficiency of the system was further enhanced by a catch-and-release strategy that allowed to recover and recirculate the excess of sugar donor from the downstream water waste.
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Affiliation(s)
- Ana I. Benítez‐Mateos
- Department of ChemistryBiochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
| | - Francesca Paradisi
- Department of ChemistryBiochemistry and Pharmaceutical SciencesUniversity of BernFreiestrasse 33012BernSwitzerland
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44
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Dettori R, Yang Q, Achenie LEK, Schwarz RD. Retraction: A Temperature-, pH- and Voltage-Responsive Nanogate with a Remarkably High Factor of Change in Ion Currents due to ON/OFF Switching. Chemistry 2021; 28:e202104138. [PMID: 34936150 DOI: 10.1002/chem.202104138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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45
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Rodríguez Lara A, Mesa-García MD, Medina KAD, Quirantes Piné R, Casuso RA, Segura Carretero A, Huertas JR. Assessment of the Phytochemical and Nutrimental Composition of Dark Chia Seed ( Salvia hispánica L.). Foods 2021; 10:3001. [PMID: 34945556 PMCID: PMC8702123 DOI: 10.3390/foods10123001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/24/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022] Open
Abstract
Chia seeds are rich sources of different macro and micronutrients associated with health benefits; thus, they may be considered as a functional food. However, the composition depends on the variety, origin, climate and soil. Here, we show a comprehensive characterization of extractable and non-extractable phenolic compounds of dark chia seed Salvia hispanica L. using high-performance liquid chromatography-electrospray ionization-quadrupole time-of-flight (HPLC-ESI-QTOF) and discuss potential health benefits associated with the presence of a number of nutritional and bioactive compounds. We report that dark chia from Jalisco is a high-fiber food, containing omega-3 polyunsaturated fatty acids, essential amino acids (phenylalanine and tryptophan), and nucleosides (adenosine, guanidine and uridine), and rich in antioxidant phenolic compounds, mainly caffeic acid metabolites. Our data suggest that chia seeds may be used as ingredients for the development of functional foods and dietary supplements.
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Affiliation(s)
- Avilene Rodríguez Lara
- Department of Physiology, Biomedical Research Center, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Parque Tecnológico de la Salud, Avenida del Conocimiento s/n, 18100 Granada, Spain; (A.R.L.); (R.A.C.)
| | - María Dolores Mesa-García
- Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology “José Mataix”, Biomedical Research Center, University of Granada, Parque Tecnológico de la Salud, Avenida del Conocimiento s/n, 18100 Granada, Spain;
- Ibs.GRANADA, Biosanitary Research Institute of Granada, 18012 Granada, Spain
| | - Karla Alejandra Damián Medina
- University Center of Tonala, University of Guadalajara, Av 555 Ejido San José Tateposco, Nuevo Periferico Oriente, Tonala 45425, Mexico;
| | - Rosa Quirantes Piné
- Technological Centre for Research and Development of Functional Foods, Avenida del Conocimiento, 37, 18100 Granada, Spain; (R.Q.P.); (A.S.C.)
| | - Rafael A. Casuso
- Department of Physiology, Biomedical Research Center, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Parque Tecnológico de la Salud, Avenida del Conocimiento s/n, 18100 Granada, Spain; (A.R.L.); (R.A.C.)
| | - Antonio Segura Carretero
- Technological Centre for Research and Development of Functional Foods, Avenida del Conocimiento, 37, 18100 Granada, Spain; (R.Q.P.); (A.S.C.)
| | - Jesús Rodríguez Huertas
- Department of Physiology, Biomedical Research Center, Institute of Nutrition and Food Technology “José Mataix”, University of Granada, Parque Tecnológico de la Salud, Avenida del Conocimiento s/n, 18100 Granada, Spain; (A.R.L.); (R.A.C.)
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46
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Khan AM, Agnihotri NK, Singh VK, Mohapatra SC, Mathur D, Kumar M, Kumar R. Biocatalyst-mediated selective acylation and deacylation chemistry on the secondary hydroxyl/amine groups of nucleosides. Nucleosides Nucleotides Nucleic Acids 2021; 40:1220-1236. [PMID: 34636267 DOI: 10.1080/15257770.2021.1986222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Nucleosides play a pivotal role in biological systems and therefore have attracted a lot of interest as chemotherapeutic agents in drug discovery. Over the years biocatalysts have emerged as a sustainable alternative to conventional synthetic catalysts. As a nature's catalyst, they exhibit excellent selectivity, remarkable tolerance, and help in carrying out eco-friendly benign processes. The use of a biocatalyst as a regio- and enantioselective catalyst is particularly relevant in the transformations of nucleosides and their analogs because of the presence of multiple chiral centres. Herein, we discuss the recent advances in the Pseudomonas Cepacia Lipase mediated selective acylation and deacylation reactions of the secondary hydroxyl and amino groups of nucleosides and their analogs.
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Affiliation(s)
- Amarendra Mohan Khan
- Department of Chemistry, Motilal Nehru College, University of Delhi, Delhi, India
| | | | - Vinay Kumar Singh
- Department of Chemistry, Sri Aurobindo College, University of Delhi, Delhi, India
| | | | - Divya Mathur
- Department of Chemistry, Daulat Ram College, University of Delhi, Delhi, India
| | - Manish Kumar
- Department of Chemistry, Motilal Nehru College, University of Delhi, Delhi, India
| | - Rajesh Kumar
- Department of Chemistry, R.D.S. College, B. R. A. Bihar University, Muzaffarpur, India
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Parker WB, Thottassery JV. 5-Aza-4'-thio-2'-deoxycytidine, a new orally bioavailable non-toxic "best-in-class" DNMT1 depleting agent in clinical development. J Pharmacol Exp Ther 2021; 379:211-222. [PMID: 34503994 DOI: 10.1124/jpet.121.000758] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/01/2021] [Indexed: 11/22/2022] Open
Abstract
DNA methyltransferase 1 (DNMT1) is an enzyme that functions as a maintenance methyltransferase during DNA replication, and depletion of this enzyme from cells is considered to be a rational goal in DNA methylation dependent disorders. Two DNMT1 depleting agents aza-dCyd (5-aza-2'-deoxycytidine, decitabine) and aza-Cyd (5-aza-cytidine, azacitidine) are currently used for the treatment of myelodysplastic syndromes and acute myeloid leukemia, and have also been investigated for non-oncology indications such as sickle cell disease. However, these agents have several off-target activities leading to significant toxicities that limit dosing and duration of treatment. Development of more selective inhibitors of DNMT1 could therefore afford treatment for long durations at effective doses. We have discovered that 5-aza-4'-thio-2'-deoxycytidine (aza-T-dCyd) is as effective as aza-dCyd in depleting DNMT1 in mouse tumor models, but with markedly low toxicity. In this review we describe the preclinical studies that led to the development of aza-T-dCyd as a superior DNMT1 depleting agent with respect to aza-dCyd, and will describe its pharmacology, metabolism, and mechanism of action. In an effort to understand why aza-T-dCyd is a more selective DNMT1 depleting agent than aza-dCyd, we will also compare and contrast the activities of these two agents. Significance Statement Aza-T-dCyd is a potent DNMT1 depleting agent. Although similar in structure to decitabine (aza-dCyd) its metabolism and mechanism of action is different than that of aza-dCyd, resulting in less off target activity and less toxicity. The larger therapeutic index of aza-T-dCyd (DNMT1 depletion vs toxicity) in mice suggests that it would be a better clinical candidate to selectively deplete DNMT1 from target cells and determine whether or not depletion of DNMT1 is an effective target for various diseases.
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49
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Sun YJ, Cheng L. The Chemistry behind ThiC Rearrangement. Chembiochem 2021; 23:e202100385. [PMID: 34494352 DOI: 10.1002/cbic.202100385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/03/2021] [Indexed: 11/06/2022]
Abstract
Thiamine (vitamin B1) is crucial for life and plays a central role in metabolism. It contains thiazole and pyrimidine moieties that are constructed independently and then assembled together to generate thiamine phosphate. The study of the thiazole moiety is relatively clear, but deciphering the mechanistic enzymology of thiamine pyrimidine is more difficult. This review aims to summarize the recent research progress on ThiC rearrangement, mainly including the mechanism, related enzymes, and genes involved in the rearrangement.
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Affiliation(s)
- Ying-Jie Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
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50
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Wang Q, Liu R, Zhu Y, Yang B, Ding YH, Bai JD, Wen HJ, Wu HR, Duan JA, Zhao M. [Regional differences of nucleosides and amino acids in Elaphuri Davidiani Cornu]. Zhongguo Zhong Yao Za Zhi 2021; 46:3494-3503. [PMID: 34402271 DOI: 10.19540/j.cnki.cjcmm.20210310.304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In order to reveal the regional characteristics of nucleosides and amino acids in Elaphuri Davidiani Cornu,39 samples of Elaphuri Davidiani Cornu collected from 4 different regions were analyzed by UPLC-QTRAP ~®/MS2 method followed by orthogonal partial least-squares discrimination analysis( OPLS-DA) and cluster analysis( CA). The results showed all the samples contained abundant nucleosides and amino acids,with the total content of 45. 09 μg·g~(-1) and 634. 80 μg·g-1,respectively. The samples presented significant regional differences in the contents of individual components,and the main differential components included Ura,Hpro,Thr,Glu,G5 P,2'-dG,Adeno,Met,Ade,Gln,Orni,Phe,2'-dA,Hit,Lys,and Ile. Among them,Ura,Met,Glu,and Ile had the highest content in the samples from Dafeng in Jiangsu,Qinhu in Jiangsu,Beijing,and Shishou in Hubei,respectively. OPLS-DA and CA demonstrated that all the samples of Elaphuri Davidiani Cornu could be divided into three categories,reflecting the regional characteristics. The results indicated that the accumulation of nucleosides and amino acids in Elaphuri Davidiani Cornu was closely related to its habitat,providing a useful reference for the research on the quality formation,quality evaluation and control,as well as the comprehensive utilization of Elaphuri Davidiani Cornu. The findings suggested that the content factors of Ura,Met,Glu,and Ile could be included into the quality standard system of Elaphuri Davidiani Cornu as the characteristics of medicinal materials from different regions.
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Affiliation(s)
- Qian Wang
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization,Key Laboratory of Chinese Medicinal Resources Recycling Utilization under National Administration of Traditional Chinese Medicine,National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine,Nanjing University of Chinese Medicine Nanjing 210023,China
| | - Rui Liu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization,Key Laboratory of Chinese Medicinal Resources Recycling Utilization under National Administration of Traditional Chinese Medicine,National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine,Nanjing University of Chinese Medicine Nanjing 210023,China Jiangsu Key Laboratory of Research and Development in Marine Bio-Resource Pharmaceutics Nanjing 210023,China
| | - Yue Zhu
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization,Key Laboratory of Chinese Medicinal Resources Recycling Utilization under National Administration of Traditional Chinese Medicine,National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine,Nanjing University of Chinese Medicine Nanjing 210023,China
| | - Bin Yang
- Institute of Chinese Materia Medica,China Academy of Chinese Medical Sciences Beijing 100700,China
| | - Yu-Hua Ding
- Dafeng Milu National Nature Reserve Dafeng 224136,China
| | - Jia-de Bai
- Beijing Milu Ecological Research Center Beijing 100076,China
| | - Hua-Jun Wen
- Shishou Milu National Nature Reserve Shishou 434407,China
| | - Hai-Rong Wu
- Qinhu Milu National Wetland Park Taizhou 225500,China
| | - Jin-Ao Duan
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization,Key Laboratory of Chinese Medicinal Resources Recycling Utilization under National Administration of Traditional Chinese Medicine,National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine,Nanjing University of Chinese Medicine Nanjing 210023,China
| | - Ming Zhao
- Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization,Key Laboratory of Chinese Medicinal Resources Recycling Utilization under National Administration of Traditional Chinese Medicine,National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine,Nanjing University of Chinese Medicine Nanjing 210023,China
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