1
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Wang Y, Chen KP. C and G are frequently mutated into T and A in coding regions of human genes. Mol Genet Genomics 2024; 299:23. [PMID: 38431687 DOI: 10.1007/s00438-024-02118-5] [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: 10/05/2023] [Accepted: 01/24/2024] [Indexed: 03/05/2024]
Abstract
Nucleotide mutations in human genes have long been a hot subject for study because some of them may lead to severe human diseases. Understanding the general mutational process and evolutionary trend of human genes could help answer such questions as why certain diseases occur and what challenges we face in protecting human health. In this study, we conducted statistics on 89,895 single-nucleotide variations identified in coding regions of 18,339 human genes. The results show that C and G are frequently mutated into T and A in human genes. C/G (C or G)-to-T/A mutations lead to reduction of hydrogen bonds in double-stranded DNA because C-G and T-A base pairs are maintained by three and two hydrogen bonds respectively. C-to-T and G-to-A mutations occur predominantly in human genes because they not only reduce hydrogen bonds but also belong to transition mutation. Reduction of hydrogen bonds could reduce energy consumption not only in separating double strands of mutated DNA for transcription and replication but also in disrupting stem-loop structure of mutated mRNA for translation. It is thus considered that to reduce hydrogen bonds (and thus to reduce energy consumption in gene expression) is one of the driving forces for nucleotide mutation. Moreover, codon mutation is positively correlated to its content, suggesting that most mutations are not targeted on changing any specific codons (amino acids) but are merely for reducing hydrogen bonds. Our study provides an example of utilizing single-nucleotide variation data to infer evolutionary trend of human genes, which can be referenced to conduct similar studies in other organisms.
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Affiliation(s)
- Yong Wang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China.
| | - Ke-Ping Chen
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, China
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2
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Wong XK, Ng CS, Yeong KY. Shaping the future of antiviral Treatment: Spotlight on Nucleobase-Containing drugs and their revolutionary impact. Bioorg Chem 2024; 144:107150. [PMID: 38309002 DOI: 10.1016/j.bioorg.2024.107150] [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: 11/08/2023] [Revised: 12/28/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024]
Abstract
Nucleobases serve as essential molecular frameworks present in both natural and synthetic compounds that exhibit notable antiviral activity. Through molecular modifications, novel nucleobase-containing drugs (NCDs) have been developed, exhibiting enhanced antiviral activity against a wide range of viruses, including the recently emerged SARS‑CoV‑2. This article provides a detailed examination of the significant advancements in NCDs from 2015 till current, encompassing various aspects concerning their mechanisms of action, pharmacology and antiviral properties. Additionally, the article discusses antiviral prodrugs relevant to the scope of this review. It fills in the knowledge gap by examining the structure-activity relationship and trend of NCDs as therapeutics against a diverse range of viral diseases, either as approved drugs, clinical candidates or as early-stage development prospects. Moreover, the article highlights on the status of this field of study and addresses the prevailing limitations encountered.
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Affiliation(s)
- Xi Khai Wong
- School of Science, Monash University (Malaysia Campus), Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Chen Seng Ng
- School of Science, Monash University (Malaysia Campus), Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia
| | - Keng Yoon Yeong
- School of Science, Monash University (Malaysia Campus), Jalan Lagoon Selatan, Bandar Sunway, 47500 Subang Jaya, Selangor, Malaysia.
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3
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Bellin L, Melzer M, Hilo A, Garza Amaya DL, Keller I, Meurer J, Möhlmann T. Nucleotide Limitation Results in Impaired Photosynthesis, Reduced Growth and Seed Yield Together with Massively Altered Gene Expression. Plant Cell Physiol 2023; 64:1494-1510. [PMID: 37329302 DOI: 10.1093/pcp/pcad063] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/04/2023] [Accepted: 06/16/2023] [Indexed: 06/19/2023]
Abstract
Nucleotide limitation and imbalance is a well-described phenomenon in animal research but understudied in the plant field. A peculiarity of pyrimidine de novo synthesis in plants is the complex subcellular organization. Here, we studied two organellar localized enzymes in the pathway, with chloroplast aspartate transcarbamoylase (ATC) and mitochondrial dihydroorotate dehydrogenase (DHODH). ATC knock-downs were most severely affected, exhibiting low levels of pyrimidine nucleotides, a low energy state, reduced photosynthetic capacity and accumulation of reactive oxygen species. Furthermore, altered leaf morphology and chloroplast ultrastructure were observed in ATC mutants. Although less affected, DHODH knock-down mutants showed impaired seed germination and altered mitochondrial ultrastructure. Thus, DHODH might not only be regulated by respiration but also exert a regulatory function on this process. Transcriptome analysis of an ATC-amiRNA line revealed massive alterations in gene expression with central metabolic pathways being downregulated and stress response and RNA-related pathways being upregulated. In addition, genes involved in central carbon metabolism, intracellular transport and respiration were markedly downregulated in ATC mutants, being most likely responsible for the observed impaired growth. We conclude that impairment of the first committed step in pyrimidine metabolism, catalyzed by ATC, leads to nucleotide limitation and by this has far-reaching consequences on metabolism and gene expression. DHODH might closely interact with mitochondrial respiration, as seen in delayed germination, which is the reason for its localization in this organelle.
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Affiliation(s)
- Leo Bellin
- Pflanzenphysiologie, Fachbereich Biologie, Universität Kaiserslautern, Erwin-Schrödinger-Straße, Kaiserslautern D-67663, Germany
| | - Michael Melzer
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, Seeland, OT Gatersleben 06466, Germany
| | - Alexander Hilo
- Leibniz Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Corrensstrasse 3, Seeland, OT Gatersleben 06466, Germany
| | - Diana Laura Garza Amaya
- Pflanzenphysiologie, Fachbereich Biologie, Universität Kaiserslautern, Erwin-Schrödinger-Straße, Kaiserslautern D-67663, Germany
| | - Isabel Keller
- Pflanzenphysiologie, Fachbereich Biologie, Universität Kaiserslautern, Erwin-Schrödinger-Straße, Kaiserslautern D-67663, Germany
| | - Jörg Meurer
- Plant Sciences, Department Biology I, Ludwig-Maximilians-University Munich, Großhaderner Straße 2-4, Planegg-Martinsried 82152, Germany
| | - Torsten Möhlmann
- Pflanzenphysiologie, Fachbereich Biologie, Universität Kaiserslautern, Erwin-Schrödinger-Straße, Kaiserslautern D-67663, Germany
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Chen J, Yang S, Li Y, Ziwen X, Zhang P, Song Q, Yao Y, Pei H. De novo nucleotide biosynthetic pathway and cancer. Genes Dis 2023; 10:2331-2338. [PMID: 37554216 PMCID: PMC10404870 DOI: 10.1016/j.gendis.2022.04.018] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/18/2022] [Indexed: 11/27/2022] Open
Abstract
De novo nucleotide biosynthetic pathway is a highly conserved and essential biochemical pathway in almost all organisms. Both purine nucleotides and pyrimidine nucleotides are necessary for cell metabolism and proliferation. Thus, the dysregulation of the de novo nucleotide biosynthetic pathway contributes to the development of many human diseases, such as cancer. It has been shown that many enzymes in this pathway are overactivated in different cancers. In this review, we summarize and update the current knowledge on the de novo nucleotide biosynthetic pathway, regulatory mechanisms, its role in tumorigenesis, and potential targeting opportunities.
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Affiliation(s)
- Jie Chen
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430062, China
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D.C. 20057, USA
| | - Siqi Yang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430062, China
| | - Yingge Li
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430062, China
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D.C. 20057, USA
| | - Xu Ziwen
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D.C. 20057, USA
| | - Pingfeng Zhang
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430062, China
| | - Qibin Song
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430062, China
| | - Yi Yao
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan, Hubei 430062, China
| | - Huadong Pei
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, D.C. 20057, USA
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Sun Z, Sun Y, Shen J, Wang C, Wei Y. Simultaneous enrichment and sequential elution of cis-diol containing molecules and deoxyribo nucleotides with bifunctional boronate and titanium (Ⅳ) ion modified-magnetic nanoparticles prior to quantitation by high performance liquid chromatography. J Chromatogr A 2023; 1709:464386. [PMID: 37722178 DOI: 10.1016/j.chroma.2023.464386] [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: 07/10/2023] [Revised: 09/13/2023] [Accepted: 09/13/2023] [Indexed: 09/20/2023]
Abstract
Some diseases can cause abnormal concentrations of catecholamines (CAs), nucleosides (NSs) and nucleotides (NTs) in patients. Previous studies normally focused on the detection of the three types of substances separately. In this work, a bifunctional boronate and titanium (Ⅳ) ion affinity magnetic adsorbent with high-capacity was prepared. The adsorbent can simultaneously enrich CAs, NSs and NTs in a single extraction process, and the adsorbed analytes can be sequentially eluted by 1.0% trifluoroacetic acid and 20.0 mmol L-1 Na3PO4. An analytical method of the analytes has been established by coupling the adsorbent with RP-HPLC. The method has low detection limits (0.039-0.708 ng mL-1) and good reproducibility (inter- and intra-day of assay RSDs less than 15.0%). Serum sample from healthy volunteer was successfully quantified for two CAs, four NSs and five NTs. Compared with the reported methods, the proposed method is simpler to operate, consume less samples, and has enough accurate and sensitivity to obtain comprehensive information on the concentrations of analytes in a single extraction process.
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Affiliation(s)
- Zhian Sun
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China
| | - Yao Sun
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China
| | - Jiwei Shen
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China
| | - Chaozhan Wang
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China
| | - Yinmao Wei
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry & Materials Science, Northwest University, Xi'an, 710127, China.
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6
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Mahato RR, Juneja S, Maiti S. Benchmarking Cationic Monolayer Protected Nanoparticles and Micelles for Phosphate-Mediated and Nucleotide-Selective Proton Transfer Catalysis. Chem Asian J 2023; 18:e202300657. [PMID: 37639220 DOI: 10.1002/asia.202300657] [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: 07/29/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 08/29/2023]
Abstract
Both micelles and self-assembled monolayer (SAM)-protected nanoparticles are capable of efficiently hosting water-immiscible substrates to carry out organic reactions in aqueous media. Herein, we have analyzed the different catalytic effect of SAM-protected cationic nanoparticles and cationic surfactants of varying chain length towards base-catalyzed proton transfer mediated ring-opening reaction of 5-nitrobenzisoxazole (NBI) (also known as Kemp Elimination (KE) reaction). We use inorganic phosphate ion or different nucleotide (phosphate-ligated different nucleoside) as base to promote the reaction on micellar or nanoparticle interface. We find almost 2-3 orders of magnitude higher concentration of surfactants of comparable hydrophobicity required to reach the similar activity which attained by low cationic head group concentration bound on nanoparticle. Additionally, at low concentration of nanoparticle-bound surfactant or with high surfactant in micellar form, nucleotide-selectivity has been observed in activating KE reaction unlike free surfactant at low concentration. Finally, we showed enzyme-mediated nucleotide hydrolysis to generate phosphate ion which in situ upregulate the KE activity much more in GNP-based system compared to CTAB. Notably, we show a reasonable superiority of SAM-protected nanoparticles in activating chemical reaction in micromolar concentration of headgroup which certainly boost up application of SAM-based nanoparticles not only for selective recognition but also as eco-friendly catalyst.
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Affiliation(s)
- Rishi Ram Mahato
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Sakshi Juneja
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
| | - Subhabrata Maiti
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Manauli, 140306, India
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7
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Lo R, Gonçalves-Carneiro D. Sensing nucleotide composition in virus RNA. Biosci Rep 2023; 43:BSR20230372. [PMID: 37606964 PMCID: PMC10500230 DOI: 10.1042/bsr20230372] [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: 06/13/2023] [Revised: 08/10/2023] [Accepted: 08/22/2023] [Indexed: 08/23/2023] Open
Abstract
Nucleotide composition plays a crucial role in the structure, function and recognition of RNA molecules. During infection, virus RNA is exposed to multiple endogenous proteins that detect local or global compositional biases and interfere with virus replication. Recent advancements in RNA:protein mapping technologies have enabled the identification of general RNA-binding preferences in the human proteome at basal level and in the context of virus infection. In this review, we explore how cellular proteins recognise nucleotide composition in virus RNA and the impact these interactions have on virus replication. Protein-binding G-rich and C-rich sequences are common examples of how host factors detect and limit infection, and, in contrast, viruses may have evolved to purge their genomes from such motifs. We also give examples of how human RNA-binding proteins inhibit virus replication, not only by destabilising virus RNA, but also by interfering with viral protein translation and genome encapsidation. Understanding the interplay between cellular proteins and virus RNA composition can provide insights into host-virus interactions and uncover potential targets for antiviral strategies.
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Affiliation(s)
- Raymon Lo
- Imperial College London, Department of Infectious Disease, Imperial College London, London, U.K
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8
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Zolyan S. On the minimal elements of the genetic code and their semiotic functions (degeneracy, complementarity, wobbling). Biosystems 2023; 231:104962. [PMID: 37437772 DOI: 10.1016/j.biosystems.2023.104962] [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: 03/06/2023] [Revised: 06/17/2023] [Accepted: 06/19/2023] [Indexed: 07/14/2023]
Abstract
We address semiotic features of genetic coding, primarily the mechanisms for distinguishing between triplets. It implies that the minimal elements that allow codon recognition and amino acid coding should be identified. Half a century ago, linguist Roman Jakobson and microbiologist François Jacob revealed functional similarities between nucleotides in the genetic code and phonemes in natural language. Developing this analogy, we introduce the concept of a semiotic nucleotide. Unlike "material" nucleotides, its characteristics are limited to the function of differentiation within the processing of genetic information. We demonstrate that, similarly to phonemes, nucleotides are also non-elementary entities and can be represented as a set of two differential features: a) the number of rings and b) the number of hydrogen bonds. This makes it possible to convert semiotic nucleotides into double-byte units of digital information. Proceeding from this assumption, we suggest a new vision of such phenomena as the heterogeneity of the genetic code in terms of coding types, to reveal the code-distinguishing potential of positions within triplets, and represent wobbling as a specific reading regime. All these phenomena relate to the peculiarity of the triplet's third position, where complete or partial neutralization of distinguishing features is possible.
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Affiliation(s)
- Suren Zolyan
- Immanuel Kant Baltic Federal University, Kaliningrad, Russia; Institute of Scientific Information on Social Sciences of the Russian Academy of Sciences, Moscow, Russia.
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9
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Zhou Z, Liu H, Ye M. Research progress on the nucleoside/ nucleotide-loaded nanomedicines. Zhejiang Da Xue Xue Bao Yi Xue Ban 2023; 52:279-284. [PMID: 37476939 PMCID: PMC10409901 DOI: 10.3724/zdxbyxb-2022-0701] [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: 12/12/2022] [Accepted: 05/09/2023] [Indexed: 07/22/2023]
Abstract
Nucleoside drugs play an essential role in treating major diseases such as tumor and viral infections, and have been widely applied in clinics. However, the effectiveness and application of nucleoside drugs are significantly limited by their intrinsic properties such as low bioavailability, lack of targeting ability, and inability to enter the cells. Nanocarriers can improve the physiological properties of nucleoside drugs by improving drug delivery efficiency and availability, maintaining drug efficacy and system stability, adjusting the binding ability of the carrier and drug molecules, as well as modifying specific molecules to achieve active targeting. Starting from the design strategy of nucleoside drug nanodelivery systems, the design and therapeutic effect of these nanomedicines are described in this review, and the future development directions of nucleoside/nucleotide-loaded nanomedicines are also discussed.
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Affiliation(s)
- Zheng Zhou
- Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, Jiangsu Province, China.
- School of Nano-Technology and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China.
| | - Haifang Liu
- The Second Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Precision Diagnosis of Respiratory Infectious Diseases, Zhengzhou Key Laboratory of Precision Diagnosis of Respiratory Infectious Diseases, Zhengzhou 450000, China
| | - Mingzhou Ye
- Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, Jiangsu Province, China.
- School of Nano-Technology and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China.
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Xu LC, Ochetto A, Chen C, Sun D, Allcock HR, Siedlecki CA. Surfaces modified with small molecules that interfere with nucleotide signaling reduce Staphylococcus epidermidis biofilm and increase the efficacy of ciprofloxacin. Colloids Surf B Biointerfaces 2023; 227:113345. [PMID: 37196462 DOI: 10.1016/j.colsurfb.2023.113345] [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: 11/12/2022] [Revised: 03/30/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Staphylococcus epidermidis are common bacteria associated with biofilm related infections on implanted medical devices. Antibiotics are often used in combating such infections, but they may lose their efficacy in the presence of biofilms. Bacterial intracellular nucleotide second messenger signaling plays an important role in biofilm formation, and interference with the nucleotide signaling pathways provides a possible way to control biofilm formation and to increase biofilm susceptibility to antibiotic therapy. This study synthesized small molecule derivates of 4-arylazo-3,5-diamino-1 H-pyrazole (named as SP02 and SP03) and found these molecules inhibited S. epidermidis biofilm formation and induced biofilm dispersal. Analysis of bacterial nucleotide signaling molecules showed that both SP02 and SP03 significantly reduced cyclic dimeric adenosine monophosphate (c-di-AMP) levels in S. epidermidis at doses as low as 25 µM while having significant effects on multiple nucleotides signaling including cyclic dimeric guanosine monophosphate (c-di-GMP), c-di-AMP, and cyclic adenosine monophosphate (cAMP) at high doses (100 µM or greater). We then tethered these small molecules to polyurethane (PU) biomaterial surfaces and investigated biofilm formation on the modified surfaces. Results showed that the modified surfaces significantly inhibited biofilm formation during 24 h and 7-day incubations. The antibiotic ciprofloxacin was used to treat these biofilms and the efficacy of the antibiotic (2 µg/mL) was found to increase from 94.8% on unmodified PU surfaces to > 99.9% on both SP02 and SP03 modified surfaces (>3 log units). Results demonstrated the feasibility of tethering small molecules that interfere with nucleotide signaling onto polymeric biomaterial surfaces and in a way that interrupts biofilm formation and increases antibiotic efficacy for S. epidermidis infections.
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Affiliation(s)
- Li-Chong Xu
- Department of Surgery, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Alyssa Ochetto
- Department of Biological and Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA
| | - Chen Chen
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Dongxiao Sun
- Department of Pharmacology, Mass Spectrometry Core Facilities (RRID: SCR_017831), The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Harry R Allcock
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Christopher A Siedlecki
- Department of Surgery, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; Department of Biomedical Engineering, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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Zhou Q, Luo Y, Zhu Y, Chen Q, Qiu J, Cong F, Li Y, Zhang X. Nonsteroidal anti-inflammatory drugs (NSAIDs) and nucleotide analog GS-441524 conjugates with potent in vivo efficacy against coronaviruses. Eur J Med Chem 2023; 249:115113. [PMID: 36706621 PMCID: PMC9830933 DOI: 10.1016/j.ejmech.2023.115113] [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: 11/17/2022] [Revised: 12/25/2022] [Accepted: 01/09/2023] [Indexed: 01/11/2023]
Abstract
Coronaviruses (CoVs) infect a broad range of hosts, including humans and various animals, with a tendency to cross the species barrier, causing severe harm to human society and fostering the need for effective anti-coronaviral drugs. GS-441524 is a broad-spectrum antiviral nucleoside with potent anti-CoVs activities. However, its application is limited by poor oral bioavailability. Herein, we designed and synthesized several conjugates via covalently binding NSAIDs to 5'-OH of GS-441524 through ester bonds. The ibuprofen conjugate, ATV041, exhibited potent in vitro anti-coronaviral efficacy against four zoonotic coronaviruses in the alpha- and beta-genera. Oral-dosed ATV041 resulted in favorable bioavailability and rapid tissue distribution of GS-441524 and ibuprofen. In MHV-A59 infected mice, ATV041 dose-dependently decreased viral RNA replication and significantly reduced the proinflammatory cytokines in the liver and the lung at 3 dpi. As a result, the MHV-A59-induced lung and liver inflammatory injury was significantly alleviated. Taken together, this work provides a novel drug conjugate strategy to improve oral PK and offers a potent anti-coronaviral lead compound for further studies.
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Affiliation(s)
- Qifan Zhou
- Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies and Medi-X Pingshan, Southern University of Science and Technology, Shenzhen, Guangdong, 518000, China
| | - Yinzhu Luo
- Guangdong Province Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong, 510663, China
| | - Yujun Zhu
- Guangdong Province Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong, 510663, China
| | - Qishu Chen
- Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies and Medi-X Pingshan, Southern University of Science and Technology, Shenzhen, Guangdong, 518000, China
| | - Jingfei Qiu
- Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies and Medi-X Pingshan, Southern University of Science and Technology, Shenzhen, Guangdong, 518000, China
| | - Feng Cong
- Guangdong Province Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong, 510663, China.
| | - Yingjun Li
- Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies and Medi-X Pingshan, Southern University of Science and Technology, Shenzhen, Guangdong, 518000, China; State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Shenzhen, 518055, China.
| | - Xumu Zhang
- Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies and Medi-X Pingshan, Southern University of Science and Technology, Shenzhen, Guangdong, 518000, China.
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12
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Bonagurio LP, Murakami AE, Pereira-Maróstica HV, Almeida FLA, Santos TC, Pozza PC. Effects of different levels of inosine-5'-monophosphate (5'-IMP) supplementation on the growth performance and meat quality of finishing pigs (75 to 100 kg). Meat Sci 2023; 196:109016. [PMID: 36375320 DOI: 10.1016/j.meatsci.2022.109016] [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: 03/01/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/05/2022]
Abstract
This study aimed to assess the effects of dietary supplementation of inosine-5'-monophosphate (5'-IMP) on energy efficiency, growth performance, carcass characteristics, meat quality, oxidative status, and biochemical profile of blood plasma in finishing pigs. Fifty-four crossbred castrated male pigs were distributed in a randomized block design consisting of nine blocks, with six treatments per block and one animal per treatment per block. Experimental diets were as follows: positive control diet (PC, 3300 kcal ME/kg), negative control diet (NC, 3200 kcal ME/kg), and four diets prepared by supplementing the NC diet with 0.050%, 0.100%, 0.150%, or 0.200% 5'-IMP. Based on regression analysis, supplementation with 0.129% 5'-IMP increased average daily weight gain (1.30 kg). Backfat thickness, pH45minutes and redness of m. Longissimus Lumborum (LL) increased linearly with 5'-IMP supplementation level. Drip loss and pH at 24 h post-slaughter had a quadratic response to 5'-IMP supplementation. It is concluded that 5'-IMP supplementation positively influenced growth performance, carcass characteristics and LL meat quality in finishing barrows.
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Affiliation(s)
- Lucas P Bonagurio
- Department of Animal Sciences, State University of Maringá, Maringá, Brazil.
| | - Alice E Murakami
- Department of Animal Sciences, State University of Maringá, Maringá, Brazil
| | | | - Fernanda L A Almeida
- Department of Morphological Sciences, State University of Maringá, Maringá, Brazil
| | - Tatiana C Santos
- Department of Animal Sciences, State University of Maringá, Maringá, Brazil
| | - Paulo C Pozza
- Department of Animal Sciences, State University of Maringá, Maringá, Brazil
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Andy D, Gunaratne GS, Marchant JS, Walseth TF, Slama JT. Synthesis and biological evaluation of novel photo-clickable adenosine and cyclic ADP-ribose analogs: 8-N 3-2'-O-propargyladenosine and 8-N 3-2'-O-propargyl-cADPR. Bioorg Med Chem 2022; 76:117099. [PMID: 36446271 PMCID: PMC9842072 DOI: 10.1016/j.bmc.2022.117099] [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: 06/29/2022] [Revised: 11/03/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022]
Abstract
A photo-clickable analog of adenosine was devised and synthesized in which the photoactive functional group (8-azidoadenosine) and the click moiety (2'-O-propargyl-ether) were compactly combined within the structure of the adenosine nucleoside itself. We synthesized 8-N3-2'-O-propargyl adenosine in four steps starting from adenosine. This photo-clickable adenosine was 5'-phosphorylated and coupled to nicotinamide mononucleotide to form the NAD analog 8-N3-2'-O-propargyl-NAD. This NAD analog was recognized by Aplysia californica ADP-ribosyl cyclase and enzymatically cyclized producing 8-N3-2'-O-propargyl cyclic ADP-ribose. Photo-clickable cyclic-ADP-ribose analog was envisioned as a probe to label cyclic ADP-ribose binding proteins. The monofunctional 8-N3-cADPR has previously been shown to be an antagonist of cADPR-induced calcium release [T.F. Walseth et. al., J. Biol. Chem (1993) 268, 26686-26691]. 2'-O-propargyl-cADPR was recognized as an agonist which elicited Ca2+ release when added at low concentration to sea urchin egg homogenates. The bifunctional 8-N3-2'-O-propargyl cyclic ADP-ribose did not elicit Ca2+ release at low concentration or impact cyclic ADP-ribose mediated Ca2+ release either when added to sea urchin egg homogenates or when microinjected into cultured human U2OS cells. The photo-clickable adenosine will none-the-less be a useful scaffold for synthesizing photo-clickable probes for identifying proteins that interact with a variety of adenosine nucleotides.
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Affiliation(s)
- Divya Andy
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, 3000 Arlington Avenue, Toledo, OH 43614, USA
| | - Gihan S Gunaratne
- Department of Pharmacology, University of Minnesota Medical School, 312 Church St, Minneapolis, MN 55455-0217, USA
| | - Jonathan S Marchant
- Department of Cell Biology, Neurobiology & Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226-0509, USA
| | - Timothy F Walseth
- Department of Pharmacology, University of Minnesota Medical School, 312 Church St, Minneapolis, MN 55455-0217, USA
| | - James T Slama
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, 3000 Arlington Avenue, Toledo, OH 43614, USA.
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Yokoo H, Naganuma M, Oba M, Demizu Y. Recent Advances in PROTAC Technology toward New Therapeutic Modalities. Chem Biodivers 2022; 19:e202200828. [PMID: 36124821 DOI: 10.1002/cbdv.202200828] [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: 08/31/2022] [Accepted: 09/20/2022] [Indexed: 11/10/2022]
Abstract
PROTACs have emerged as a powerful technology for the degradation of disease-related proteins. A multitude of bifunctional PROTACs have been developed using small-molecule ligands; one ligand binds to the target protein of interest and one ligand binds to an E3 ligase. The characteristics of those PROTACs vary, including their reversible or irreversible covalent binding to the target protein, their binding to orthosteric and allosteric sites, their agonist or antagonist activity, and their use of multiple ligands. In addition, oligopeptides and nucleotides have recently been used as alternative targeting ligands. The properties of PROTACs, such as selectivity, delivery and sensitivity to drug resistance, can be improved through the use of a variety of targeting ligand modalities. This minireview introduces the mechanisms and behavior of small-molecule based PROTACs as well as targeted proteolysis techniques using peptides and nucleic acids as targeting ligands.
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Affiliation(s)
- Hidetomo Yokoo
- Kyoto Prefectural University of Medicine: Kyoto Furitsu Ika Daigaku, Medical Chemistry, -5 Shimogamo Hangicho, Sakyo-ku, Kyoto, JAPAN
| | - Miyako Naganuma
- NIHS: National Institute of Health Sciences, Divsion of Organic Chemistry, 3-25-26 Tonomachi, Kawasaki, JAPAN
| | - Makoto Oba
- Kyoto Prefectural University of Medicine: Kyoto Furitsu Ika Daigaku, Medical Chemistry, -5 Shimogamo Hangicho, Sakyo-ku, Kyoto, JAPAN
| | - Yosuke Demizu
- National Institute of Health Sciences, Division of Organic Chemistry, 1-18, Kamiyoga 1-chome, Setagaya-ku, 158-8501, Tokyo, JAPAN
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15
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Zegarra V, Bedrunka P, Bange G, Czech L. How to save a bacterial ribosome in times of stress. Semin Cell Dev Biol 2022:S1084-9521(22)00082-9. [PMID: 35331628 DOI: 10.1016/j.semcdb.2022.03.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 03/01/2022] [Accepted: 03/11/2022] [Indexed: 11/21/2022]
Abstract
Biogenesis of ribosomes is one of the most cost- and resource-intensive processes in all living cells. In bacteria, ribosome biogenesis is rate-limiting for growth and must be tightly coordinated to yield maximum fitness of the cells. Since bacteria are continuously facing environmental changes and stress conditions, they have developed sophisticated systems to sense and regulate their nutritional status. Amino acid starvation leads to the synthesis and accumulation of the nucleotide-based second messengers ppGpp and pppGpp [(p)ppGpp], which in turn function as central players of a pleiotropic metabolic adaptation mechanism named the stringent response. Here, we review our current knowledge on the multiple roles of (p)ppGpp in the stress-related modulation of the prokaryotic protein biosynthesis machinery with the ribosome as its core constituent. The alarmones ppGpp/pppGpp act as competitors of their GDP/GTP counterparts, to affect a multitude of ribosome-associated P-loop GTPases involved in the translation cycle, ribosome biogenesis and hibernation. A similar mode of inhibition has been found for the GTPases of the proteins involved in the SRP-dependent membrane-targeting machinery present in the periphery of the ribosome. In this sense, during stringent conditions, binding of (p)ppGpp restricts the membrane insertion and secretion of proteins. Altogether, we highlight the enormously resource-intensive stages of ribosome biogenesis as a critical regulatory hub of the stringent response that ultimately tunes the protein synthesis capacity and consequently the survival of the cell.
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Wang Y, Chen XY, Yang L, Yao Q, Chen KP. Human SARS-CoV-2 has evolved to increase U content and reduce genome size. Int J Biol Macromol 2022; 204:356-363. [PMID: 35149094 PMCID: PMC8824384 DOI: 10.1016/j.ijbiomac.2022.02.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 11/08/2021] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 12/30/2022]
Abstract
Infections caused by SARS-CoV-2 have brought great harm to human health. After transmission for over two years, SARS-CoV-2 has diverged greatly and formed dozens of different lineages. Understanding the trend of its genome evolution could help foresee difficulties in controlling transmission of the virus. In this study, we conducted an extensive monthly survey and in-depth analysis on variations of nucleotide, amino acid and codon numbers in 311,260 virus samples collected till January 2022. The results demonstrate that the evolution of SARS-CoV-2 is toward increasing U-content and reducing genome-size. C, G and A to U mutations have all contributed to this U-content increase. Mutations of C, G and A at codon position 1, 2 or 3 have no significant difference in most SARS-CoV-2 lineages. Current viruses are more cryptic and more efficient in replication, and are thus less virulent yet more infectious. Delta and Omicron variants have high mutability over other lineages, bringing new threat to human health. This trend of genome evolution may provide a clue for tracing the origin of SARS-CoV-2, because ancestral viruses should have lower U-content and probably bigger genome-size.
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Affiliation(s)
- Yong Wang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
| | - Xin-Yu Chen
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Liu Yang
- School of Food and Biological Engineering, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China
| | - Qin Yao
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
| | - Ke-Ping Chen
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang 212013, China.
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Kumar Palli K, Ghosh P, Krishna Avula S, Sridhara Shanmukha Rao B, Patil AD, Ghosh S, Sudhakar G, Raji Reddy C, Mainkar PS, Chandrasekhar S. Total synthesis of remdesivir. Tetrahedron Lett 2022; 88:153590. [PMID: 34908617 PMCID: PMC8656175 DOI: 10.1016/j.tetlet.2021.153590] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/19/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 12/16/2022]
Abstract
Remdesivir, the first drug approved by the FDA to treat COVID-19, is in high demand for patients infected with the SARS-CoV-2 virus. Herein, we report a facile approach minimizing the protecting group manipulations to afford remdesivir in good overall yield.
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Affiliation(s)
- Kishore Kumar Palli
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Palash Ghosh
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shiva Krishna Avula
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - B. Sridhara Shanmukha Rao
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Amol D. Patil
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Subhash Ghosh
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gangarajula Sudhakar
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Chada Raji Reddy
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Prathama S. Mainkar
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Srivari Chandrasekhar
- Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India,Corresponding author at: Department of Organic Synthesis & Process Chemistry, CSIR-Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500007, India
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18
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Ullah MF, Alnour TMS, Elssaig EH, Ahmed-Abakur EH. Characterization of altered genomic landscape of SARS-CoV-2 variants isolated in Saudi Arabia in a comparative in silico study. Saudi J Biol Sci 2021; 28:6803-6807. [PMID: 34866979 PMCID: PMC8626222 DOI: 10.1016/j.sjbs.2021.07.054] [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: 05/10/2021] [Revised: 07/17/2021] [Accepted: 07/17/2021] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 has become one of the unprecedented global health challenge for human population. Genomic signature studies of SARS-CoV-2 reveals relation between geographical location of the isolates and genetic diversity. The present work is an in silico, cross sectional study aimed to determine the genetic heterogeneity of SARS-CoV-2 variants isolated in Saudi Arabia compared to the first isolated strain NC_045512 (reference sequence). Each sequence was aligned against the reference sequence using local alignment search tool (NCBI) Nucleotide-BLAST. A total of 58 SARS-CoV-2 genomes were isolated in KSA and retrieved from NCBI. Our study shows that KSA variants demonstrated homology ranging between 99.96 and 99.98 % compared to the reference strain. There are 89 nucleotide changes that have been identified among the KSA variants; the most common nucleotide change was C: T accounting for 50.6% (45/89). These nucleotides changes resulted in 53.9% (48/89) missense mutations and 42.7% (38/89) silent mutations; while the majority of mutations- 48.3% (43/89) occurred in ORF1ab gene. All structural genes displayed mutations; N gene harbored 16.9% (15/89) mutations, S gene displayed 15.7% (14/89) mutations, M gene exhibited 2.2% (2/89) mutations and E gene showed only 1 mutation which was silent. The most frequently changed nucleotide was C3037T (silent mutation) and A23403G (D614G), each of which occurred in 57 variants out of 58 followed by C14408T (P4715L) and C241T (5'UTR) which were found in 56 and 55 variants respectively. The Phylogenetic trees showed that SARS-CoV-2 variants isolated in Saudi Arabia clustered together closely.
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Affiliation(s)
- Mohammad Fahad Ullah
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.,Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia
| | - Tarig M S Alnour
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.,Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum North 11111, Sudan
| | - Elmutuz H Elssaig
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.,Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia
| | - Eltayib H Ahmed-Abakur
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.,Prince Fahad Research Chair, University of Tabuk, P.O. Box 741, Tabuk 71411, Saudi Arabia.,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum North 11111, Sudan
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19
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Xu X, Sun C, Liu B, Zhou Q, Xu P, Liu M, Wang A, Tian H, Luo W, Jiang Q. Flesh flavor of red swamp crayfish (Procambarus clarkii Girard, 1852) processing by GS-IMS and electronic tongue is changed by dietary animal and plant protein. Food Chem 2021; 373:131453. [PMID: 34731807 DOI: 10.1016/j.foodchem.2021.131453] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 10/04/2021] [Accepted: 10/20/2021] [Indexed: 11/20/2022]
Abstract
The aroma and taste of Procambarus clarkii (Girard, 1852) fed with different dietary protein were investigated by E-tongue and gas chromatography-ion migration spectrometry (GC-IMS) after cooking. The results showed that dietary protein sources had no significant growth performance. Nevertheless, significantly higher richness taste was observed in animal protein group. The inosine-5'-monophosphate content in animal protein group was significantly higher than that in plant protein group. Twelve aldehydes, eleven alcohols, six ketones, three esters, and two acids were identified in the muscle using GC-IMS. 2-Propanol (monomer), 3-octanol (monomer), 3-furanmethanol (dimer), 2-methyl-1-pentanol (monomer), heptanal (monomer), and allylacetic acid (monomer) changed significantly between dietary animal protein and plant protein. These results suggested that dietary plant and animal protein have a similar effect on the growth performance. For the flavor, the crayfish fed with animal protein had higher volatiles and IMP contents, which might contribute to higher richness.
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20
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Das JK, Roy S. Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns. Genomics 2021; 113:2177-2188. [PMID: 34019999 PMCID: PMC8131179 DOI: 10.1016/j.ygeno.2021.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 05/09/2021] [Accepted: 05/14/2021] [Indexed: 01/04/2023]
Abstract
The prevailing COVID-19 pandemic has drawn the attention of the scientific community to study the evolutionary origin of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). This study is a comprehensive quantitative analysis of the protein-coding sequences of seven human coronaviruses (HCoVs) to decipher the nucleotide sequence variability and codon usage patterns. It is essential to understand the survival ability of the viruses, their adaptation to hosts, and their evolution. The current analysis revealed a high abundance of the relative dinucleotide (odds ratio), GC and CT pairs in the first and last two codon positions, respectively, as well as a low abundance of the CG pair in the last two positions of the codon, which might be related to the evolution of the viruses. A remarkable level of variability of GC content in the third position of the codon among the seven coronaviruses was observed. Codons with high RSCU values are primarily from the aliphatic and hydroxyl amino acid groups, and codons with low RSCU values belong to the aliphatic, cyclic, positively charged, and sulfur-containing amino acid groups. In order to elucidate the evolutionary processes of the seven coronaviruses, a phylogenetic tree (dendrogram) was constructed based on the RSCU scores of the codons. The severe and mild categories CoVs were positioned in different clades. A comparative phylogenetic study with other coronaviruses depicted that SARS-CoV-2 is close to the CoV isolated from pangolins (Manis javanica, Pangolin-CoV) and cats (Felis catus, SARS(r)-CoV). Further analysis of the effective number of codon (ENC) usage bias showed a relatively higher bias for SARS-CoV and MERS-CoV compared to SARS-CoV-2. The ENC plot against GC3 suggested that the mutational bias might have a role in determining the codon usage variation among candidate viruses. A codon adaptability study on a few human host parasites (from different kingdoms), including CoVs, showed a diverse adaptability pattern. SARS-CoV-2 and SARS-CoV exhibit relatively lower but similar codon adaptability compared to MERS-CoV.
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Affiliation(s)
- Jayanta Kumar Das
- Department of Pediatrics, Johns Hopkins University School of Medicine, MD, USA.
| | - Swarup Roy
- Network Reconstruction & Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, Gangtok, India.
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21
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Gao L, Xie C, Liang X, Li Z, Li B, Wu X, Yin Y. Yeast-based nucleotide supplementation in mother sows modifies the intestinal barrier function and immune response of neonatal pigs. Anim Nutr 2021; 7:84-93. [PMID: 33997335 PMCID: PMC8110885 DOI: 10.1016/j.aninu.2020.06.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 05/16/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023]
Abstract
In the present study, we aimed to evaluate the effects of maternal yeast-based nucleotide (YN) supplementation on the intestinal immune response and barrier function in neonatal pigs, as well as the diarrhoea rate and growth performance in suckling piglets. Sixty-four late-gestation sows were assigned to the following groups: the CON (fed a basal diet) and YN groups (fed a basal diet with 4 g YN/kg diet). The experiment started on d 85 of gestation and ended on d 20 of lactation. Diarrhoea rate and average daily gain of the piglets were recorded, and samples of blood and intestines from neonatal piglets were collected before they consumed colostrum during farrowing. Compared with the CON group, maternal YN supplementation increased the weaning weight of litter and decreased the diarrhoea rate (P < 0.01). In addition, maternal YN supplementation promoted the ileal villus development in the neonates compared with that in the CON group (P < 0.01). Maternal YN supplementation also increased the ileal secretory immunoglobulin A (sIgA) level compared with that in the CON group (P < 0.05). The real-time PCR results showed that maternal dietary YN supplementation increased the jejunal and ileal expression of interleukin (IL)-17, IL-8, IL-1β, IL-10 and tumor necrosis factor (TNF)- α in the neonates compared with that in the CON group (P < 0.05). Overall, maternal nucleotide supplementation improved the villus development and innate immunity of neonatal piglets during late pregnancy. This may be associated with the decrease in diarrhoea and the increase in weaning weight of the litter of suckling piglets.
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Affiliation(s)
- Lumin Gao
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha, Hunan 410125, China
| | - Chunyan Xie
- Hunan Co-Innovation Center of Safety Animal Production, College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
| | - Xiaoxiao Liang
- Henan Zhongke Ground Food Co., Ltd, Zhengzhou 450001, China
| | - Zhihong Li
- The Hubei Provincial Key Laboratory of Yeast Function, Angel Yeast Co., Ltd, Yichang 443003, China
| | - Biao Li
- The Hubei Provincial Key Laboratory of Yeast Function, Angel Yeast Co., Ltd, Yichang 443003, China
| | - Xin Wu
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha, Hunan 410125, China
- Hunan Co-Innovation Center of Safety Animal Production, College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330096, China
| | - Yulong Yin
- Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Changsha, Hunan 410125, China
- Hunan Co-Innovation Center of Safety Animal Production, College of Resources and Environment, Hunan Agricultural University, Changsha 410128, China
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Jasmer KJ, Woods LT, Forti KM, Martin AL, Camden JM, Colonna M, Weisman GA. P2Y 2 receptor antagonism resolves sialadenitis and improves salivary flow in a Sjögren's syndrome mouse model. Arch Oral Biol 2021; 124:105067. [PMID: 33561807 DOI: 10.1016/j.archoralbio.2021.105067] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 01/15/2023]
Abstract
OBJECTIVE Sjögren's syndrome (SS) is a chronic autoimmune exocrinopathy characterized by lymphocytic infiltration of the salivary and lacrimal glands and decreased saliva and tear production. Previous studies indicate that the G protein-coupled P2Y2 nucleotide receptor (P2Y2R) is upregulated in numerous models of salivary gland inflammation (i.e., sialadenitis), where it has been implicated as a key mediator of chronic inflammation. Here, we evaluate both systemic and localized P2Y2R antagonism as a means to resolve sialadenitis in the NOD.H-2h4,IFNγ-/-,CD28-/- (NOD.H-2h4 DKO) mouse model of SS. DESIGN Female 4.5 month old NOD.H-2h4 DKO mice received daily intraperitoneal injections for 10 days of the selective P2Y2R antagonist, AR-C118925, or vehicle-only control. Single-dose localized intraglandular antagonist delivery into the Wharton's duct was also evaluated. Carbachol-induced saliva was measured and then submandibular glands (SMGs) were isolated and either fixed and paraffin-embedded for H&E staining, homogenized for RNA isolation or dissociated for flow cytometry analysis. RESULTS Intraperitoneal injection, but not localized intraglandular administration, of AR-C118925 significantly enhanced carbachol-induced salivation and reduced lymphocytic foci and immune cell markers in SMGs of 5 month old NOD.H-2h4 DKO mice, compared to vehicle-injected control mice. We found that B cells represent the primary immune cell population in inflamed SMGs of NOD.H-2h4 DKO mice that express elevated levels of P2Y2R compared to C57BL/6 control mice. We further demonstrate a role for P2Y2Rs in mediating B cell migration and the release of IgM. CONCLUSION Our findings suggest that the P2Y2R represents a novel therapeutic target for the treatment of Sjögren's syndrome.
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23
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Brandon HE, Wieden HJ. A Quick Primer in Fluorescence-Based Equilibrium and Pre-steady State Methods for Determining Protein- Nucleotide Affinities. Methods Mol Biol 2021; 2263:273-287. [PMID: 33877603 DOI: 10.1007/978-1-0716-1197-5_12] [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: 06/12/2023]
Abstract
Biomolecular interactions facilitate the biochemical processes that sustain life. Proteins, RNAs, and ribonucleoprotein complexes perform cellular functions that range from catalyzing the formation or cleavage of bonds to being structural building blocks, both of which are only possible through the interaction with their respective biomolecular partner(s). Having access to the parameters that describe these interactions is important for our understanding of the principles that underlie enzymatic and nonenzymatic processes. Here we describe two fluorescence-based approaches to determine two key parameters, the affinity and the rate of association/dissociation of a protein and a ligand. Considerations are provided to expand the described approach to other experimental systems.
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Affiliation(s)
- Harland E Brandon
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, AB, Canada
| | - Hans-Joachim Wieden
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute (ARRTI), University of Lethbridge, Lethbridge, AB, Canada.
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Tan C, Ji Y, Zhao X, Xin Z, Li J, Huang S, Cui Z, Wen L, Liu C, Kim SW, Deng J, Yin Y. Effects of dietary supplementation of nucleotides from late gestation to lactation on the performance and oxidative stress status of sows and their offspring. ACTA ACUST UNITED AC 2020; 7:111-118. [PMID: 33997338 PMCID: PMC8110849 DOI: 10.1016/j.aninu.2020.10.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 12/15/2022]
Abstract
Increased metabolic burdens in breeding sows, which are induced by elevated systemic oxidative stress, could increase the need for nucleotides to repair lymphocyte DNA damage; however, de novo synthesis of nucleotides may be insufficient to cover this increased need. This study investigated the effects of dietary nucleotides on milk composition, oxidative stress status, and the reproductive and lactational performance of sows. Forty multiparous sows were assigned to 2 dietary treatments (Control group, and 1 g/kg Nucleotides group) based on a randomized complete block design using their BW at 85 d of gestation as a block. Sows from 2 groups were fed a restricted diet during gestation and ad libitum during lactation. The experiment lasted from 85 d of gestation to 21 d of lactation. The reproductive performance of sows and the growth performance of suckling piglets were measured. Oxidative stress parameters and milk components were also analysed. Data were analyzed using contrasts in the MIXED procedure of SAS. Sows in the Nucleotides group consumed more feed during the first week (P < 0.01) and from 1 to 21 d (P < 0.05) of lactation than those in Control group. Correspondingly, the litter weight gain of piglets showed a tendency to increase from cross-fostering to 9 d (P = 0.09) and from cross-fostering to 20 d (P = 0.10) in the Nucleotides group relative to the Control group. Additionally, the Nucleotides group was higher (P < 0.01) than the Control group in the concentrations of uridine 5'monophosphate, guanosine 5'monophosphate, inosine 5'monophosphate, adenosine 5'monophosphate and total nucleotides in milk. Furthermore, the Nucleotides group was higher (P < 0.01) than the Control group in the serum levels of total antioxidant capacity (P < 0.01) for sows at 109 d of gestation and glutathione peroxidase for weaning piglets, but lower at the levels of thiobarbituric acid-reactive substances (P < 0.05) in serum of weaning piglets. This study indicated that maternal dietary nucleotides could promote piglet growth, probably due to the higher lactational feed intake and higher concentration of nucleotides in the milk of sows, and lower oxidative stress for both sows and piglets.
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Affiliation(s)
- Chengquan Tan
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yongcheng Ji
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xichen Zhao
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Zhongquan Xin
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Jiaying Li
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Shuangbo Huang
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Zhiying Cui
- Guangdong Hinabiotech Co., Ltd., Guangzhou, 510642, China
| | - Lijun Wen
- Guangdong Hinabiotech Co., Ltd., Guangzhou, 510642, China
| | - Caihua Liu
- Hubei Hiyee Biological Technology Co., Ltd., Xiangyang, 510642, China
| | - Sung Woo Kim
- Department of Animal Science North Carolina State University, Raleigh, NC, 27695, USA
| | - Jinping Deng
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
| | - Yulong Yin
- National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
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25
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Ghoteimi R, Braka A, Rodriguez C, Cros-Perrial E, Tai Nguyen V, Uttaro JP, Mathé C, Chaloin L, Ménétrier-Caux C, Jordheim LP, Peyrottes S. 4-Substituted-1,2,3-triazolo nucleotide analogues as CD73 inhibitors, their synthesis, in vitro screening, kinetic and in silico studies. Bioorg Chem 2020; 107:104577. [PMID: 33450542 DOI: 10.1016/j.bioorg.2020.104577] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/17/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022]
Abstract
Three series of nucleotide analogues were synthesized and evaluated as potential CD73 inhibitors. Nucleobase replacement consisted in connecting the appropriate aromatic or purine residues through a triazole moiety that is generated from 1,3-dipolar cycloaddition. The first series is related to 4-substituted-1,2,3-triazolo-β-hydroxyphosphonate ribonucleosides. Additional analogues were also obtained, in which the phosphonate group was replaced by a bisphosphonate pattern (P-C-P-C, series 2) or the ribose moiety was removed leading to acyclic derivatives (series 3). The β-hydroxyphosphonylphosphonate ribonucleosides (series 2) were found to be potent inhibitors of CD73 using both purified recombinant protein and cell-based assays. Two compounds (2a and 2b) that contained a bis(trifluoromethyl)phenyl or a naphthyl substituents proved to be the most potent inhibitors, with IC50 values of 4.8 ± 0.8 µM and 0.86 ± 0.2 µM, compared to the standard AOPCP (IC50 value of 3.8 ± 0.9 µM), and were able to reverse the adenosine-mediated immune suppression on human T cells. This series of compounds illustrates a new type of CD73 inhibitors.
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Affiliation(s)
- Rayane Ghoteimi
- Institut des Biomolécules Max Mousseron (IBMM), Univ. Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Abdennour Braka
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Univ. Montpellier, CNRS, 34293 Montpellier, France
| | - Céline Rodriguez
- Univ. Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Emeline Cros-Perrial
- Univ. Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Van Tai Nguyen
- Institut des Biomolécules Max Mousseron (IBMM), Univ. Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Jean-Pierre Uttaro
- Institut des Biomolécules Max Mousseron (IBMM), Univ. Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Christophe Mathé
- Institut des Biomolécules Max Mousseron (IBMM), Univ. Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Laurent Chaloin
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Univ. Montpellier, CNRS, 34293 Montpellier, France
| | - Christine Ménétrier-Caux
- Univ. Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Lars Petter Jordheim
- Univ. Lyon, Université Claude Bernard Lyon 1, INSERM U1052, CNRS 5286, Centre Léon Bérard, Centre de Recherche en Cancérologie de Lyon, 69008 Lyon, France
| | - Suzanne Peyrottes
- Institut des Biomolécules Max Mousseron (IBMM), Univ. Montpellier, CNRS, ENSCM, 34095 Montpellier, France.
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26
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Shoji S, Yamaji T, Makino H, Ishii J, Kondo A. Metabolic design for selective production of nicotinamide mono nucleotide from glucose and nicotinamide. Metab Eng 2020; 65:167-177. [PMID: 33220420 DOI: 10.1016/j.ymben.2020.11.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [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: 09/14/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/30/2022]
Abstract
β-Nicotinamide mononucleotide (NMN) is, one of the nucleotide compounds, a precursor of NAD+ and has recently attracted attention as a nutraceutical. Here, we develop a whole-cell biocatalyst using Escherichia coli, which enabled selective and effective high production of NMN from the inexpensive feedstock substrates glucose and nicotinamide (Nam). Notably, we identify two actively functional transporters (NiaP and PnuC) and a high-activity key enzyme (Nampt), permitting intracellular Nam uptake, efficient conversion of phosphoribosyl pyrophosphate (PRPP; supplied from glucose) and Nam to NMN, and NMN excretion extracellularly. Further, enhancement of the PRPP biosynthetic pathway and optimization of individual gene expression enable drastically higher NMN production than reported thus far. The strain extracellularly produces 6.79 g l-1 of NMN from glucose and Nam, and the reaction selectivity from Nam to NMN is 86%. Our approach will be promising for low-cost, high-quality industrial production of NMN and other nucleotide compounds using microorganisms.
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Affiliation(s)
- Shinichiro Shoji
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Taiki Yamaji
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Harumi Makino
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Jun Ishii
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan; Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan; Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, 230-0045, Japan
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27
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Zaparte A, Cappellari AR, Brandão CA, de Souza JB, Borges TJ, Kist LW, Bogo MR, Zerbini LF, Ribeiro Pinto LF, Glaser T, Gonçalves MCB, Naaldijk Y, Ulrich H, Morrone FB. P2Y 2 receptor activation promotes esophageal cancer cells proliferation via ERK1/2 pathway. Eur J Pharmacol 2020; 891:173687. [PMID: 33130276 DOI: 10.1016/j.ejphar.2020.173687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 02/08/2023]
Abstract
Esophageal cancer is a prominent worldwide illness that is divided into two main subtypes: esophageal squamous cell carcinoma and esophageal adenocarcinoma. Mortality rates are alarming, and the understanding of the mechanisms involved in esophageal cancer development, becomes essential. Purinergic signaling is related to many diseases and among these various types of tumors. Here we studied the effects of the P2Y2 receptor activation in different types of esophageal cancer. Esophageal tissue samples of healthy controls were used for P2Y2R expression quantification. Two human esophageal cancer cell lines Kyse-450 (squamous cell carcinoma) and OE-33 (adenocarcinoma) were used to perform in vitro analysis of cell proliferation, migration, adhesion, and the signaling pathways involved in P2Y2R activation. Data showed that P2Y2R was expressed in biopsies of patients with ESCC and adenocarcinoma, as well as in the two human esophageal cancer cell lines studied. The RT-qPCR analysis demonstrated that OE-33 cells have higher P2RY2 expression than Kyse-450 squamous cell line. Results showed that P2Y2R activation, induced by ATP or UTP, promoted esophageal cancer cells proliferation and colony formation. P2Y2R blockage with the selective antagonist, AR-C 118925XX, led to decreased proliferation, colony formation and adhesion. Treatments with ATP or UTP activated ERK 1/2 pathway in ESCC and ECA cells. The P2Y2R antagonism did not alter the migration of esophageal cancer cells. Interestingly, the esophageal cancer cell lines presented a distinct profile of nucleotide hydrolysis activity. The modulation of P2Y2 receptors may be a promising target for esophageal cancer treatment.
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Affiliation(s)
- Aline Zaparte
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Avenida Ipiranga, 6690. Partenon, 90619-900, Porto Alegre, RS, Brazil; Laboratório de Farmacologia Aplicada, Escola de Ciências da Saúde e da Vida, PUCRS, Avenida Ipiranga, 6681, Partenon, 90619-900, Porto Alegre, RS, Brazil
| | - Angélica R Cappellari
- Laboratório de Farmacologia Aplicada, Escola de Ciências da Saúde e da Vida, PUCRS, Avenida Ipiranga, 6681, Partenon, 90619-900, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Partenon, 90619-900, Porto Alegre, RS, Brazil
| | - Caroline A Brandão
- Laboratório de Farmacologia Aplicada, Escola de Ciências da Saúde e da Vida, PUCRS, Avenida Ipiranga, 6681, Partenon, 90619-900, Porto Alegre, RS, Brazil
| | - Júlia B de Souza
- Laboratório de Farmacologia Aplicada, Escola de Ciências da Saúde e da Vida, PUCRS, Avenida Ipiranga, 6681, Partenon, 90619-900, Porto Alegre, RS, Brazil
| | - Thiago J Borges
- Transplant Research Center, Renal Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Luíza W Kist
- Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Partenon, 90619-900, Porto Alegre, RS, Brazil
| | - Maurício R Bogo
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Avenida Ipiranga, 6690. Partenon, 90619-900, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Partenon, 90619-900, Porto Alegre, RS, Brazil
| | - Luiz F Zerbini
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Cancer Genomics Group, Cape Town, South Africa
| | - Luis Felipe Ribeiro Pinto
- Programa de Carcinogênese Molecular, Coordenação de Pesquisa, Instituto Nacional de Cancer, Rua Andre Cavalcante, 37, Centro, Rio de Janeiro, RJ, Brazil
| | - Talita Glaser
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Prof. Lineu Prestes, 748. Butantã, 05508-000, São Paulo, SP, Brazil
| | - Maria Carolina B Gonçalves
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Prof. Lineu Prestes, 748. Butantã, 05508-000, São Paulo, SP, Brazil
| | - Yahaira Naaldijk
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Prof. Lineu Prestes, 748. Butantã, 05508-000, São Paulo, SP, Brazil
| | - Henning Ulrich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Prof. Lineu Prestes, 748. Butantã, 05508-000, São Paulo, SP, Brazil
| | - Fernanda B Morrone
- Programa de Pós-Graduação em Medicina e Ciências da Saúde, PUCRS, Avenida Ipiranga, 6690. Partenon, 90619-900, Porto Alegre, RS, Brazil; Laboratório de Farmacologia Aplicada, Escola de Ciências da Saúde e da Vida, PUCRS, Avenida Ipiranga, 6681, Partenon, 90619-900, Porto Alegre, RS, Brazil; Programa de Pós-Graduação em Biologia Celular e Molecular, PUCRS, Avenida Ipiranga, 6681, Partenon, 90619-900, Porto Alegre, RS, Brazil.
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28
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Kitabatake K, Kaji T, Tsukimoto M. ATP and ADP enhance DNA damage repair in γ-irradiated BEAS-2B human bronchial epithelial cells through activation of P2X7 and P2Y12 receptors. Toxicol Appl Pharmacol 2020; 407:115240. [PMID: 32941855 DOI: 10.1016/j.taap.2020.115240] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/03/2020] [Accepted: 09/10/2020] [Indexed: 10/23/2022]
Abstract
Agents that promote DNA repair may be useful as radioprotectants to minimize side effects such as radiation pneumonia caused by damage to normal cells during radiation therapy to treat lung cancer. We have reported that extracellular nucleotides and nucleosides are involved in the P2 or P1 receptor-mediated DNA damage response (DDR) after γ-irradiation. Here, we investigated the effects of ATP, UTP, GTP, ITP and their metabolites on the γH2AX/53BP1 focus formation in nuclei (a measure of γ-irradiation-induced DDR) and the survival of γ-irradiated immortalized human bronchial epithelial (BEAS-2B) cells. Fluorescence immunostaining showed that ATP and ADP increase DDR and DNA repair, and exhibit radioprotective effects as evaluated by colony formation assay. These effects of ATP or ADP were blocked by inhibitors of P2X7 or P2Y12 receptor, respectively, and by ERK1/2 inhibitor. ATP and ADP enhanced phosphorylation of ERK1/2 by suppressing MKP-1 and MKP-3 expression after γ-irradiation. These results indicate that ATP and ADP exhibit radioprotective effects by phosphorylation of ERK1/2 via activation of P2X7 and P2Y12 receptors, respectively, to promote γ-irradiation-induced DDR and DNA repair. ATP and ADP appear to be candidates for radioprotectants to reduce damage to non-cancerous cells during lung cancer radiotherapy by promoting DDR and DNA repair.
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Affiliation(s)
- Kazuki Kitabatake
- Department of Radiation Biosciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-0022, Japan
| | - Toshiyuki Kaji
- Department of Environmental Health, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-0022, Japan
| | - Mitsutoshi Tsukimoto
- Department of Radiation Biosciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-0022, Japan.
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29
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Machon C, Catez F, Venezia ND, Vanhalle F, Guyot L, Vincent A, Garcia M, Roy B, Diaz JJ, Guitton J. Study of intracellular anabolism of 5-fluorouracil and incorporation in nucleic acids based on an LC-HRMS method. J Pharm Anal 2021; 11:77-87. [PMID: 33717614 DOI: 10.1016/j.jpha.2020.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
5-Fluorouracil (5-FU) is an anticancer drug extensively used for different cancers. Intracellular metabolic activation leads to several nucleoside and nucleotide metabolites essential to exert its cytotoxic activity on multiple cellular targets such as enzymes, DNA and RNA. In this paper, we describe the development of a method based on liquid chromatography coupled with high resolution mass spectrometry suitable for the simultaneous determination of the ten anabolic metabolites (nucleoside, nucleotide and sugar nucleotide) of 5-FU. The chromatographic separation was optimized on a porous graphitic carbon column allowing the analysis of the metabolites of 5-FU as well as endogenous nucleotides. The detection was performed on an Orbitrap® tandem mass spectrometer. Linearity of the method was verified in intracellular content and in RNA extracts. The limit of detection was equal to 12 pg injected on column for nucleoside metabolites of 5-FU and 150 pg injected on column for mono- and tri-phosphate nucleotide metabolites. Matrix effect was evaluated in cellular contents, DNA and RNA extracts for nucleoside and nucleotides metabolites. The method was successfully applied to i) measure the proportion of each anabolic metabolite of 5-FU in cellular contents, ii) follow the consequence of inhibition of enzymes on the endogenous nucleotide pools, iii) study the incorporation of metabolites of 5-FU into RNA and DNA, and iv) to determine the incorporation rate of 5-FUrd into 18 S and 28 S sub-units of rRNA. The LC-MS-HRMS method allows the analysis of the ten anabolic metabolites of 5-FU. The present method is useful to study the incorporation of 5-FU into RNA and DNA. Method to determine the incorporation rate of 5-FU into subunit of rRNA is innovative.
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30
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Chang J, Park H. Nucleotide and protein researches on anaerobic fungi during four decades. J Anim Sci Technol 2020; 62:121-140. [PMID: 32292921 PMCID: PMC7142291 DOI: 10.5187/jast.2020.62.2.121] [Citation(s) in RCA: 2] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/07/2020] [Accepted: 03/07/2020] [Indexed: 01/26/2023]
Abstract
Anaerobic fungi habitat in the gastrointestinal tract of foregut fermenters or
hindgut fermenters and degrade fibrous plant biomass through the hydrolysis
reactions with a wide variety of cellulolytic enzymes and physical penetration
through fiber matrix with their rhizoids. To date, seventeen genera have been
described in family Neocallimasticaceae, class
Neocallimastigomycetes, phylum
Neocallimastigomycota and one genus has been described in
phylum Neocallimastigomycota. In National Center for
Biotechnology Information (NCBI) database (DB), 23,830 nucleotide sequences and
59,512 protein sequences have been deposited and most of them were originated
from Piromyces, Neocallimastix and
Anaeromyces. Most of protein sequences (44,025) were
acquired with PacBio next generation sequencing system. The whole genome
sequences of Anaeromyces robustus, Neocallimastix
californiae, Pecoramyces ruminantium,
Piromyces finnis and Piromyces sp. E2 are
available in Joint Genome Institute (JGI) database. According to the results of
protein prediction, average Isoelectric points (pIs) were ranged from 5.88
(Anaeromyces) to 6.57 (Piromyces) and
average molecular weights were ranged from 38.7 kDa
(Orpinomyces) to 56.6 kDa (Piromyces). In
Carbohydrate-Active enZYmes (CAZY) database, glycoside hydrolases (36),
carbohydrate binding module (11), carbohydrate esterases (8),
glycosyltransferase (5) and polysaccharide lyases (3) from anaerobic fungi were
registered. During four decades, 1,031 research articles about anaerobic fungi
were published and 444 and 719 articles were available in PubMed (PM) and PubMed
Central (PMC) DB.
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Affiliation(s)
- Jongsoo Chang
- Department of Agricultural Sciences, Korea National Open University, Seoul 03087, Korea
| | - Hyunjin Park
- Department of Agricultural Sciences, Korea National Open University, Seoul 03087, Korea
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31
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Procházková E, Hřebabecký H, Dejmek M, Šála M, Šmídková M, Tloušťová E, Zborníková E, Eyer L, Růžek D, Nencka R. Could 5'-N and S ProTide analogues work as prodrugs of antiviral agents? Bioorg Med Chem Lett 2019; 30:126897. [PMID: 31882298 DOI: 10.1016/j.bmcl.2019.126897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 12/05/2019] [Accepted: 12/07/2019] [Indexed: 02/08/2023]
Abstract
The nucleoside/nucleotide derived antiviral agents have been the most important components of antiviral therapy used in clinics. Recently, the focus of the medicinal chemists within this exciting research field has been affected mainly by the lack of effective therapies for the Hepatitis C virus (HCV) infection and several other "neglected" diseases caused by viruses such as Zika or Dengue. 2'-Methyl modified nucleosides and their monophosphate prodrugs (ProTides) have revolutionized the therapies for HCV in the last few years and, according to the latest research efforts, have also brought a promise for treatment of diseases caused by other members of Flaviviridae family. Here, we report on the design and synthesis of 5'-N and S modified ProTides derived from 2'-methyladenosine. We studied potential applicability of these derivatives as prodrugs of this archetypal antiviral compound.
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Affiliation(s)
- Eliška Procházková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 116 10, Czech Republic
| | - Hubert Hřebabecký
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 116 10, Czech Republic
| | - Milan Dejmek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 116 10, Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 116 10, Czech Republic
| | - Markéta Šmídková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 116 10, Czech Republic
| | - Eva Tloušťová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 116 10, Czech Republic
| | - Eva Zborníková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 116 10, Czech Republic
| | - Luděk Eyer
- Department of Virology, Veterinary Research Institute, Brno 621 00, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice 370 05, Czech Republic
| | - Daniel Růžek
- Department of Virology, Veterinary Research Institute, Brno 621 00, Czech Republic; Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Ceske Budejovice 370 05, Czech Republic
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 116 10, Czech Republic
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32
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Attah IY, Neumann A, Al-Hroub H, Rafehi M, Baqi Y, Namasivayam V, Müller CE. Ligand binding and activation of UTP-activated G protein-coupled P2Y 2 and P2Y 4 receptors elucidated by mutagenesis, pharmacological and computational studies. Biochim Biophys Acta Gen Subj 2019; 1864:129501. [PMID: 31812541 DOI: 10.1016/j.bbagen.2019.129501] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/17/2019] [Accepted: 12/03/2019] [Indexed: 12/18/2022]
Abstract
The nucleotide receptors P2Y2 and P2Y4 are the most closely related G protein-coupled receptors (GPCRs) of the P2Y receptor (P2YR) family. Both subtypes couple to Gq proteins and are activated by the pyrimidine nucleotide UTP, but only P2Y2R is also activated by the purine nucleotide ATP. Agonists and antagonists of both receptor subtypes have potential as drugs e.g. for neurodegenerative and inflammatory diseases. So far, potent and selective, "drug-like" ligands for both receptors are scarce, but would be required for target validation and as lead structures for drug development. Structural information on the receptors is lacking since no X-ray structures or cryo-electron microscopy images are available. Thus, we performed receptor homology modeling and docking studies combined with mutagenesis experiments on both receptors to address the question how ligand binding selectivity for these closely related P2YR subtypes can be achieved. The orthosteric binding site of P2Y2R appeared to be more spacious than that of P2Y4R. Mutation of Y197 to alanine in P2Y4R resulted in a gain of ATP sensitivity. Anthraquinone-derived antagonists are likely to bind to the orthosteric or an allosteric site depending on their substitution pattern and the nature of the orthosteric binding site of the respective P2YR subtype. These insights into the architecture of P2Y2- and P2Y4Rs and their interactions with structurally diverse agonists and antagonist provide a solid basis for the future design of potent and selective ligands.
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Affiliation(s)
- Isaac Y Attah
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Germany
| | - Alexander Neumann
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Germany
| | - Haneen Al-Hroub
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Germany
| | - Muhammad Rafehi
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Germany
| | - Younis Baqi
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Germany; Department of Chemistry, Faculty of Science, Sultan Qaboos University, PO Box 36, Postal Code 123 Muscat, Oman
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, Germany.
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Ye G, Ding D, Gao H, Chi Y, Chen J, Wu Z, Lin Y, Dong S. Comprehensive metabolic responses of HepG2 cells to fine particulate matter exposure: Insights from an untargeted metabolomics. Sci Total Environ 2019; 691:874-884. [PMID: 31326811 DOI: 10.1016/j.scitotenv.2019.07.192] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 03/29/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
Exposure to fine particulate matter (PM2.5) increases the risk of metabolic diseases, such as cancer and cardiovascular disease. Disturbed hepatocyte metabolism accelerates the incidence and progression of metabolic diseases. However, toxic effects of PM2.5 on hepatocyte metabolism remain unclear. Accordingly, an untargeted metabolomics approach based on liquid chromatography-mass spectrometry was used to characterize comprehensive metabolic responses of HepG2 cells to PM2.5 exposure and to discover potential therapeutic targets for PM2.5-induced metabolic dysregulation in metabolic diseases. Metabolomics revealed that exposure to liposoluble extracts of PM2.5 samples (LE) triggered substantial changes in 46 metabolic pathways, mainly involved in lipid, amino acid, nucleotide and carbohydrate metabolism, in HepG2 cells. Notably, LE exposure induced accumulation of FFAs and medium-chained acylcarnitines (6-12 carbons), but decreased levels of short-chained acylcarnitines (<5 carbons) in HepG2 cells. Meanwhile, levels of citrate/isocitrate and aconitate were decreased, while 2-hydroxyglutate and succinate accumulated in HepG2 cells treated with LE. Additionally, levels of adenosine triphosphate, guanosine triphosphate, uridine triphosphate and cytidine triphosphate were decreased; however, contents of adenosine monophosphate, guanosine monophosphate, purines and pyrimidines were increased in HepG2 cells treated with LE. Moreover, levels of glutathione, Glu-Cys, Cys-Gly, lipoic acid, methionine sulfoxide, methionine and S-adenosyl-L-methionine were increased, while those of most amino acids were decreased in HepG2 cells treated with LE. These data demonstrated that LE exposure triggered accumulation of FAAs and oncometabolites (2-hydroxyglutate and succinate), mitochondrial dysfunctions characterized by incomplete FFA oxidation and reduced energy supply from TCA cycle and oxidative phosphorylation, disturbances in methylation and redox homeostasis, and the inhibition of most amino acid metabolism in HepG2 cells. Above metabolic disorders indicates potential therapeutic targets for treating PM2.5-induced injury and diseases. To the best of our knowledge, this study provides the first evidence that LE exposure triggered accumulation of medium-chain acylcarnitines, oncometabolites, purines and pyrimidines in HepG2 cells.
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Affiliation(s)
- Guozhu Ye
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Dongxiao Ding
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Han Gao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yulang Chi
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Jinsheng Chen
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Zeming Wu
- iPhenome Biotechnology (Dalian) Inc., 300-8 Jinlongsi Road, Dalian 116063, China
| | - Yi Lin
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, Xiamen 361102, China.
| | - Sijun Dong
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
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Abstract
Productive HIV infection requires integration of viral genes into the host genome. But how viral DNA gets to the nucleus in the first place remains one of the most controversial yet deceptively simple questions in HIV post-entry biology. This is illustrated in cartoons of viral entry, which often depict the entry process as an 'explosion' of the HIV capsid in the cytosol and independent movement of viral DNA through nuclear pores and into the nucleus. HIV enters the cell cytosol with two encapsidated RNA strands and must undergo reverse transcription (RT) to synthesise DNA. Even here there is no consensus for where, when or how RT happens. HIV must get into the nucleus, which in a non-dividing cell requires transport through the nuclear pore. Finally, the virus must 'uncoat': shed its protein capsid to allow its DNA to be spliced with that of the host. Where the virus uncoats and whether this is a single or multi-step process are similarly hotly debated. Understanding these processes is further complicated by three broad factors. First, that there are inter-relationships between these processes that may ensure HIV undergoes the right step at the right place at the right time. Second, the host has cofactors which the virus is dependent upon and must recruit but also immune factors that can sense and inhibit virus and so must be avoided. Third, HIV post-entry biology is cell-type dependent-meaning that factors which are essential in one cell type can be redundant in another.
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Mehdinejad N, Imanpour MR, Jafari V. Combined or Individual Effects of Dietary Probiotic, Pediococcus acidilactici and Nucleotide on Reproductive Performance in Goldfish (Carassius auratus). Probiotics Antimicrob Proteins 2019; 11:233-238. [PMID: 29318466 DOI: 10.1007/s12602-017-9377-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This work evaluated the effect of dietary supplementation of probiotic, Pediococcus acidilactici and nucleotide (combined or individual) on reproductive performance including semen quality (motility and density) and egg indices (egg diameter, ovum diameter, absolute fecundity, relative fecundity, gonadosomatic index, hepatosomatic index, fertilization rate, and hatching rate) in goldfish (Carassius auratus). Fish (46.9 ± 2.15 g) were acclimatized and divided into eight experimental diets supplemented with P. acidilactici different concentrations (0.1, 0.2, and 0.3% diet) and nucleotides (0 and 0.5% diet) for 180 days. Female fish fed experimental diets showed significant differences in reproductive parameters as compared to control diet (P < 0.05). Combined diet (probiotic 0.2% and nucleotide) had the highest percentage and duration of sperm motility, absolute fecundity, and fertilization success as compared to other diets (P < 0.05). The significance of the results obtained herein underlines the importance of diet in the reproductive processes, supporting the hypothesis that feed additives could improve gamete quality.
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Affiliation(s)
- Nooshin Mehdinejad
- Department of Fisheries, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Mohammad Reza Imanpour
- Department of Fisheries, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.
| | - Valiollah Jafari
- Department of Fisheries, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
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Zborníková E, Knejzlík Z, Hauryliuk V, Krásný L, Rejman D. Analysis of nucleotide pools in bacteria using HPLC-MS in HILIC mode. Talanta 2019; 205:120161. [PMID: 31450400 DOI: 10.1016/j.talanta.2019.120161] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 01/25/2023]
Abstract
Nucleotides, nucleosides and their derivatives are present in all cells at varying concentrations that change with the nutritional, and energetic status of the cell. Precise measurement of the concentrations of these molecules is instrumental for understanding their regulatory effects. Such measurement is challenging due to the inherent instability of these molecules and, despite many decades of research, the reported values differ widely. Here, we present a comprehensive and easy-to-use approach for determination of the intracellular concentrations of >25 target molecular species. The approach uses rapid filtration and cold acidic extraction followed by high performance liquid chromatography (HPLC) in the hydrophilic interaction liquid chromatography (HILIC) mode using zwitterionic columns coupled with UV and MS detectors. The method reliably detects and quantifies all the analytes expected to be observed in the bacterial cell and paves the way for future studies correlating their concentrations with biological effects.
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Affiliation(s)
- Eva Zborníková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovonam. 2, CZ-166 10, Prague 6, Czech Republic; Charles University, Faculty of Science, Department of Analytical Chemistry, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Zdeněk Knejzlík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovonam. 2, CZ-166 10, Prague 6, Czech Republic
| | - Vasili Hauryliuk
- Department of Molecular Biology, Umeå University, Building 6K, 6L University Hospital Area, SE-901 87, Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Building 6K and 6L, University Hospital Area, 90187, Umeå, Sweden; University of Tartu, Institute of Technology, 50411, Tartu, Estonia
| | - Libor Krásný
- Institute of Microbiology, Czech Academy of Sciences v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
| | - Dominik Rejman
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, v.v.i., Flemingovonam. 2, CZ-166 10, Prague 6, Czech Republic.
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Wei Z, Wu Y, Feng K, Yang M, Zhang Y, Tu Q, Wang J, Deng Y. ARGA, a pipeline for primer evaluation on antibiotic resistance genes. Environ Int 2019; 128:137-145. [PMID: 31054477 DOI: 10.1016/j.envint.2019.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 02/03/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
Molecular biology techniques have assisted in the investigation of antibiotic resistance genes (ARGs) from various environments. However, their accuracy relies on primer quality and data interpretation, both of which require a full-coverage sequence database for ARGs. Here, based upon the abandoned Antibiotic Resistance Genes Database (ARDB), we created an updated sequence database of antibiotic resistance genes (SDARG). A total of 1,260,069 protein sequences and 1,164,479 nucleotide sequences, 56 times more sequences than ARDB, from 448 types of ARGs (enabling resistance to 18 categories of antibiotics) were collected and integrated with different hierarchical credibility and full-scale taxonomic information. Based on this comprehensive sequence database, an online pipeline - ARG analyzer (ARGA, http://mem.rcees.ac.cn:8083/) was developed to assess current ARGs primers, as well as annotate ARGs from environmental metagenomes. Thereafter, a list of 658 published primer pairs, targeting 173 ARGs, was evaluated using ARGA and integrated in ARGA as ARGs primer database. The results showed that 65.05% primers are of high specificity (≥90%), while only 29.79% primers cover >50% of targeted sequences, indicating a divergence in the quality of current ARG primers. Hence, primer assessment or redesign is highly recommended to improve the accuracy of ARGs studies. ARGs primer database was attached in ARGA to provide researchers alternatives to better survey ARGs in the environment.
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Affiliation(s)
- Ziyan Wei
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yueni Wu
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Feng
- Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Yang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Zhang
- State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qichao Tu
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Jun Wang
- College of Resources and Environment, Shandong Agricultural University, Taian 271018, China
| | - Ye Deng
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; Key Laboratory of Environmental Biotechnology of CAS, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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Pedro L, Cross M, Hofmann A, Mak T, Quinn RJ. Development of an HPLC-based guanosine monophosphate kinase assay and application to Plasmodium vivax guanylate kinase. Anal Biochem 2019; 575:63-69. [PMID: 30943378 PMCID: PMC6494078 DOI: 10.1016/j.ab.2019.03.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 12/23/2018] [Revised: 03/18/2019] [Accepted: 03/29/2019] [Indexed: 11/12/2022]
Abstract
The development of a high-performance liquid chromatography (HPLC)-based method, for guanosine monophosphate kinase activity assays, is presented. The method uses the intrinsic UV absorption (at 260 nm) of substrates and products of the enzymatic reaction (GMP, ATP, ADP and GDP) to unambiguously determine percent conversion of substrate into product. It uses a commercially available C18 column which can separate reaction samples by elution under isocratic conditions in 12 min per run. The kinetics of the forward reaction catalyzed by Plasmodium vivax guanylate kinase (PvGK), a potential drug target against malaria, was determined. The relative concentrations of the two substrates (GMP and ATP) have a distinct effect on reaction velocity. Kinetic analyses showed the PvGK-catalyzed reaction to be associated with atypical kinetics, where substrate inhibition kinetics and non-Michaelis-Menten (sigmoidal) kinetics were found with respect to GMP and ATP, respectively. Additionally, the method was used in inhibition assays to screen twenty fragment-like compounds. The assays were robust and reproducible, with a signal window of 3.8 and a Z’ factor of 0.6. For the best inhibitor, an IC50 curve was generated. Simple HPLC separation of nucleotides involved in the guanylate kinase reaction. Direct and unambiguous determination of percent conversion of substrate into product. Successful application to Plasmodium vivax guanylate kinase (PvGK) activity studies. Reaction catalyzed by PvGK found to be associated with atypical kinetics. Robust and reproducible inhibition assay for compound screening.
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Affiliation(s)
- Liliana Pedro
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Megan Cross
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Andreas Hofmann
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Tin Mak
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia.
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Biswas R, Panja AS, Bandopadhyay R. Molecular Mechanism of Antibiotic Resistance: The Untouched Area of Future Hope. Indian J Microbiol 2019; 59:254-259. [PMID: 31031444 DOI: 10.1007/s12088-019-00781-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 09/10/2018] [Accepted: 01/12/2019] [Indexed: 11/25/2022] Open
Abstract
The treatment of bacterial infections is becoming increasingly ineffective due to rapid mutation which leads to antibiotic resistant and resistant bacteria become more prevalent. As a result the existing antibiotics are gradually obsolete and again new drugs are needed to be designed for the same threat. However, the prediction of evolutionary processes/antibiotic resistance is uncertain. Still, the understanding of mode of evolution of resistance in bacteria is a determining step in the preclinical development of new antibiotics, because drug developers assess the risk of resistance arising against a drug during preclinical development. Multidrug efflux pump systems play an important role for making multidrug resistance to a range of clinically important antibiotics in gram-negative bacteria like Pseudomonas aeruginosa, which lower the intracellular drug concentration by exporting incoming antibiotics across the membranes. We tried to show that the wild type susceptible bacteria P. aeruginosa modified its genetic makeup at mutational hotspots under stress. This strain may either become multidrug resistant or remain susceptible depending on position of amino acid changes in regulatory proteins of efflux pump. Multidrug resistant strain made significant changes at the amino acid positions, 103rd (G → A) and 126th (E → V) through the mutation on the nucleotide position of 308th (G → C); both 377th (A → T) and 378th (G → T), respectively in mexR, a repressor of mexAB-oprM efflux pump. This mutant protein showed low affinity with their operator. But the alteration at 103th position (G → A) in mexR may provide almost similar structural and functional stability as wild type. It was found that mutation was seemed to be well regulated within the limit and position specific under stress which might be back to its original form by supplying counter stress unless addition or deletion takes place.
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Affiliation(s)
- Raju Biswas
- 1Department of Botany, UGC-Center of Advanced Study, The University of Burdwan, Golapbag, Burdwan, West Bengal 713104 India
- Department of Botany, Syamsundar College, Shyamsundar, Burdwan, West Bengal 713424 India
| | - Anindya Sundar Panja
- 3Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal 721102 India
| | - Rajib Bandopadhyay
- 1Department of Botany, UGC-Center of Advanced Study, The University of Burdwan, Golapbag, Burdwan, West Bengal 713104 India
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Ye G, Gao H, Lin Y, Ding D, Liao X, Zhang H, Chi Y, Dong S. Peroxisome proliferator-activated receptor A/G reprogrammes metabolism associated with lipid accumulation in macrophages. Metabolomics 2019; 15:36. [PMID: 30830452 DOI: 10.1007/s11306-019-1485-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 01/31/2019] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Macrophage metabolism contributes to the progression of metabolic diseases, and peroxisome proliferator-activated receptors (PPARs) play vital roles in macrophage metabolism and the treatment of metabolic diseases. However, the role of PPARs in metabolic reprogramming related to lipid accumulation in macrophages, a key pathological event in metabolic diseases, remains unclear. OBJECTIVES We aimed to identify PPAR-mediated metabolic reprogramming and potential therapeutic targets associated with lipid accumulation in macrophages. METHODS Following treatment with oleate, oleate + WY-14643 and oleate + pioglitazone to induce alterations in PPAR signaling, lipids and relevant metabolism, macrophage samples were analyzed employing an untargeted metabolomics based on gas chromatography-mass spectrometry. RESULTS The metabolomics approach revealed that multiple metabolic pathways were altered during lipid accumulation in oleate-treated macrophages and responsive to WY-14643 and pioglitazone treatment. Notably, levels of most metabolites involved in amino acid metabolism and nucleotide metabolism were accumulated in oleate-treated macrophages, and these effects were alleviated or abolished by PPARA/G activation. Additionally, during oleate-induced lipid accumulation and lipid lowering with WY-14643 and pioglitazone in macrophages, levels of most amino acids were positively associated with neutral lipid, total cholesterol, cholesterol ester, total free fatty acid and triglyceride levels but negatively associated with expression of genes related to PPARA/G signaling. Furthermore, glycine was found to be a potential biomarker for assessing lipid accumulation and the lipid-lowering effects of PPARA/G in oleate-treated macrophages. CONCLUSION The results of this study revealed a high correlation of amino acid metabolism with lipid accumulation and the lipid-lowering effects of PPARA/G in macrophages.
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Affiliation(s)
- Guozhu Ye
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
| | - Han Gao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Yi Lin
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Dongxiao Ding
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Xu Liao
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Han Zhang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Yulang Chi
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China
| | - Sijun Dong
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
- Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, China.
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Mehdinejad N, Imanpour MR, Jafari V. Combined or Individual Effects of Dietary Probiotic Pedicoccus acidilactici and Nucleotide on Growth Performance, Intestinal Microbiota, Hemato-biochemical Parameters, and Innate Immune Response in Goldfish (Carassius auratus). Probiotics Antimicrob Proteins 2019. [PMID: 28639176 DOI: 10.1007/s12602-017-9297-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This study investigated the effect of dietary supplementation of probiotic Pedicoccus acidilactici and nucleotide (separately or combined) on growth performance, intestinal microbiota, hemato-immunological parameters, and immunity response in goldfish (Carassius auratus). Fish (average weight 5-6 g) were acclimatized and divided into eight experimental diets supplemented with P. acidilactici of different concentrations (0.1, 0.2, and 0.3% diet) and nucleotides (0 and 0.5% diet) for 6 months. Fish fed with experimental diets showed significant differences in terms of final weight, weight gain, feed conversion ratio, daily growth rate, and condition factor when compared to control diet (P < 0.05). Fish fed with probiotic (0.3%) separately and combined with nucleotide (0.5%) had highest RBC and WBC when compared to other diets (P < 0.05), while the highest values for Hb and Hct as well as total protein, glucose, albumin, and globulin were observed in probiotic (0.2%) and nucleotide (0.5%) combined diet. Serum lysozyme and anti-protease activities were significantly higher in probiotic (0.1 and 0.2%) and nucleotide (0.5%) combined diets. Similarly, these two diets combined showed the highest colonization of P. acidilactici when compared to other diets. In conclusion, combined dietary probiotic and nucleotide improve the growth performance, hemato-biochemical parameters, and intestine growth in C. auratus.
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Affiliation(s)
- Nooshin Mehdinejad
- Department of Fisheries, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.
| | - Mohammad Reza Imanpour
- Department of Fisheries, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Valiollah Jafari
- Department of Fisheries, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
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Vázquez N, López-Fernández H, Vieira CP, Fdez-Riverola F, Vieira J, Reboiro-Jato M. BDBM 1.0: A Desktop Application for Efficient Retrieval and Processing of High-Quality Sequence Data and Application to the Identification of the Putative Coffea S-Locus. Interdiscip Sci 2019; 11:57-67. [PMID: 30712176 DOI: 10.1007/s12539-019-00320-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 08/24/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 11/25/2022]
Abstract
Nowadays, bioinformatics is one of the most important areas in modern biology and the creation of high-quality scientific software supporting this recent research area is one of the core activities of many researchers. In this context, high-quality sequence datasets are needed to perform inferences on the evolution of species, genes, and gene families, or to get evidence for adaptive amino acid evolution, among others. Nevertheless, sequence data are very often spread over several databases, many useful genomes and transcriptomes are non-annotated, the available annotation is not for the desired coding sequence isoform, and/or is unlikely to be accurate. Moreover, although the FASTA text-based format is quite simple and usable by most software applications, there are a number of issues that may be critical depending on the software used to analyse such files. Therefore, researchers without training in informatics often use a fraction of all available data. The above issues can be addressed using already available software applications, but there is no easy-to-use single piece of software that allows performing all these tasks within the same graphical interface, such as the one here presented, named BDBM (Blast DataBase Manager). BDBM can be used to efficiently get gene sequences from annotated and non-annotated genomes and transcriptomes. Moreover, it can be used to look for alternatives to existing annotations and to easily create reliable custom databases. Such databases are essential to prepare high-quality datasets. The analyses that we have performed on the Coffea canephora genome using BDBM aimed at the identification of the S-locus region (that harbours the genes involved in gametophytic self-incompatibility) led to the conclusion that there are two likely regions, one on chromosome 2 (around region 6600000-6650000), and another on chromosome 5 (around 15830000-15930000). Such findings are discussed in the context of the Rubiaceae gametophytic self-incompatibility evolution.
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Affiliation(s)
- Noé Vázquez
- ESEI-Escuela Superior de Ingeniería Informática, Universidade de Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain
- CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
| | - Hugo López-Fernández
- ESEI-Escuela Superior de Ingeniería Informática, Universidade de Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain.
- CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain.
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain.
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.
| | - Cristina P Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Florentino Fdez-Riverola
- ESEI-Escuela Superior de Ingeniería Informática, Universidade de Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain
- CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
| | - Jorge Vieira
- Instituto de Biologia Molecular e Celular (IBMC), Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Miguel Reboiro-Jato
- ESEI-Escuela Superior de Ingeniería Informática, Universidade de Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain
- CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Vigo, Spain
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Kuskovsky R, Buj R, Xu P, Hofbauer S, Doan MT, Jiang H, Bostwick A, Mesaros C, Aird KM, Snyder NW. Simultaneous isotope dilution quantification and metabolic tracing of deoxyribo nucleotides by liquid chromatography high resolution mass spectrometry. Anal Biochem 2018; 568:65-72. [PMID: 30605633 DOI: 10.1016/j.ab.2018.12.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/26/2018] [Accepted: 12/29/2018] [Indexed: 12/21/2022]
Abstract
Quantification of cellular deoxyribonucleoside mono- (dNMP), di- (dNDP), triphosphates (dNTPs) and related nucleoside metabolites are difficult due to their physiochemical properties and widely varying abundance. Involvement of dNTP metabolism in cellular processes including senescence and pathophysiological processes including cancer and viral infection make dNTP metabolism an important bioanalytical target. We modified a previously developed ion pairing reversed phase chromatography-mass spectrometry method for the simultaneous quantification and 13C isotope tracing of dNTP metabolites. dNMPs, dNDPs, and dNTPs were chromatographically resolved to avoid mis-annotation of in-source fragmentation. We used commercially available 13C15N-stable isotope labeled analogs as internal standards and show that this isotope dilution approach improves analytical figures of merit. At sufficiently high mass resolution achievable on an Orbitrap mass analyzer, stable isotope resolved metabolomics allows simultaneous isotope dilution quantification and 13C isotope tracing from major substrates including 13C-glucose. As a proof of principle, we quantified dNMP, dNDP and dNTP pools from multiple cell lines. We also identified isotopologue enrichment from glucose corresponding to ribose from the pentose-phosphate pathway in dNTP metabolites.
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Affiliation(s)
- Rostislav Kuskovsky
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA
| | - Raquel Buj
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, USA
| | - Peining Xu
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA
| | - Samuel Hofbauer
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, Department of Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mary T Doan
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA
| | - Helen Jiang
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA
| | - Anna Bostwick
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA
| | - Clementina Mesaros
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, Department of Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Katherine M Aird
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, USA
| | - Nathaniel W Snyder
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA.
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Hayama T, Ohyama K. Recent development and trends in sample extraction and preparation for mass spectrometric analysis of nucleotides, nucleosides, and proteins. J Pharm Biomed Anal 2018; 161:51-60. [PMID: 30145449 DOI: 10.1016/j.jpba.2018.08.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/02/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022]
Abstract
This review describes the recent developments in sample extraction and preparation techniques for mass spectrometric analysis of nucleotides, nucleosides, and proteins. Unique materials and techniques have been developed for highly selective extraction of nucleotides and nucleosides by solid-phase extraction strategies using various affinities. However, for proteins, the analysis of small-scale sections of diseased tissues (formalin-fixed, paraffin-embedded tissues) and the direct analysis of an exact lesion on the surface of diseased tissues (liquid extraction surface analysis) have become important advances in this field. In this review, we focus on the latest developments of these techniques and strategies.
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Affiliation(s)
- Tadashi Hayama
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | - Kaname Ohyama
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto-machi, Nagasaki 852-8588, Japan.
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Al-Banna L, Sadder MT, Lafi HA, Dawabah AAM, Al-Nadhari SN. Bioinformatics analysis of ubiquitin expression protein gene from Heterodera latipons. Saudi J Biol Sci 2018; 26:1463-1467. [PMID: 31762610 PMCID: PMC6864184 DOI: 10.1016/j.sjbs.2018.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 06/01/2018] [Accepted: 06/26/2018] [Indexed: 11/28/2022] Open
Abstract
Ubiquitin expression protein DNA clone (Hl-UBI) was isolated from Heterodera latipons collected from North Jordan. Its sequence of 285 nucleotides was also determined and deposited in the GeneBank. The 285-bp open reading frame coded for 76-amino acid protein having two domains; the ubiquitin domain and the C terminal extension. The first 59 amino acids were predicted with the ubiquitin domain with identity percentages of 78% to ubiquitin of H. schachtii, 77% to polyubiquitin of Globodera pallida, 74% to ubiquitin of Globodera rostochiensis and 72% to ubiquitin of Heterodera glycines. The other domain at the C-terminus, containing 17 amino acids, showed no homology to any known protein. Sequence analysis showed a calculated encoding amino acids molecular weight of 8.77 kDa, theoretical isoelectric point = 4.76, negatively charged residues = 12, positively charged residues = 9, extinction coefficient = 1490, estimated half-life = 30 h, instability index = 32.51 and grand average of hydropathicity = -0.537. The demonstrated subcellular localization analysis of cytoplasm, cell nucleus, mitochondrion, cell skeleton and plasma membrane of Hl-UBI protein occupied about 52.20, 21.70, 17.40, 4.30 and 4.30%, respectively. Sequence, homology and structural analysis confirmed that Hl-UBI gene was highly conserved during evolution and belonged to ubiquitin gene family.
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Affiliation(s)
- Luma Al-Banna
- Department of Plant Protection, Faculty of Agriculture, The University of Jordan, Amman, Jordan
| | - Monther T Sadder
- Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan, Amman, Jordan
| | - Hamzeh A Lafi
- Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ahmed A M Dawabah
- Nematode Diseases Research Department, Plant Pathology Research Institute, Agricultural Research Center, 9 Gamaa Street, Giza 12619, Egypt
| | - Saleh N Al-Nadhari
- Department of Plant Protection, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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Gampe C, White ACS, Siva S, Zécri F, Diener J. 3'-Modification stabilizes mRNA and increases translation in cells. Bioorg Med Chem Lett 2018; 28:2451-2453. [PMID: 29907393 DOI: 10.1016/j.bmcl.2018.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/01/2018] [Accepted: 06/02/2018] [Indexed: 01/19/2023]
Abstract
Successful implementation of mRNA gene therapy is facing many hurdles, for example poor expression levels of the exogenously delivered mRNA transcripts. Herein we describe the synthesis of various 3'-modified RNA oligonucleotides, and we show that 3'-modification drastically stabilizes these oligonucleotides in cell extracts. Modification of the 3'-terminus of gaussia luciferase mRNA results in 3-fold increased and extended (>48 h) translation of the mRNA. Our findings suggest 3'-modification of RNA-transcripts as a valid approach to increase expression levels for application in mRNA gene therapy.
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Affiliation(s)
- Christian Gampe
- Novartis Institutes for BioMedical Research, 181 Massachusetts Ave., Cambridge, MA 02139, USA.
| | - Amy C Seila White
- Novartis Institutes for BioMedical Research, 181 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Swetha Siva
- Novartis Institutes for BioMedical Research, 181 Massachusetts Ave., Cambridge, MA 02139, USA
| | - Frédéric Zécri
- Novartis Institutes for BioMedical Research, 181 Massachusetts Ave., Cambridge, MA 02139, USA
| | - John Diener
- Novartis Institutes for BioMedical Research, 181 Massachusetts Ave., Cambridge, MA 02139, USA
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Abstract
Eukaryotic protein kinases are an intensely investigated class of enzymes which have garnered attention due to their usefulness as drug targets. Determining the regulation of ATP binding to a protein kinase is not only critical for understanding function in a cellular context but also for designing kinase-specific molecular inhibitors. Here, we provide a general procedure for characterizing ATP binding to eukaryotic protein kinases. The protocol can be adapted to identify the conditions under which a particular kinase is activated. The approach is simple, requiring only a fluorescent ATP analog such as TNP-ATP or MANT-ATP and an instrument to monitor changes in fluorescence. Although the interaction kinetics between a kinase and a given ATP analog may differ from that of native ATP, this disadvantage is offset by the ease of performing and interpreting this assay. Importantly, it can be optimized to probe a large variety of conditions under which the kinase-nucleotide binding might be affected.
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Affiliation(s)
- Leslie E W LaConte
- Virginia Tech Carilion Research Institute, Roanoke, 2 Riverside Circle, Roanoke, VA, 24016, USA
| | - Sarika Srivastava
- Virginia Tech Carilion Research Institute, Roanoke, 2 Riverside Circle, Roanoke, VA, 24016, USA
| | - Konark Mukherjee
- Virginia Tech Carilion Research Institute, Roanoke, 2 Riverside Circle, Roanoke, VA, 24016, USA. .,Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24060, USA.
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48
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Garrett M, Sperry J, Braas D, Yan W, Le TM, Mottahedeh J, Ludwig K, Eskin A, Qin Y, Levy R, Breunig JJ, Pajonk F, Graeber TG, Radu CG, Christofk H, Prins RM, Lai A, Liau LM, Coppola G, Kornblum HI. Metabolic characterization of isocitrate dehydrogenase (IDH) mutant and IDH wildtype gliomaspheres uncovers cell type-specific vulnerabilities. Cancer Metab 2018; 6:4. [PMID: 29692895 PMCID: PMC5905129 DOI: 10.1186/s40170-018-0177-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [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: 12/18/2017] [Accepted: 02/21/2018] [Indexed: 11/10/2022] Open
Abstract
Background There is considerable interest in defining the metabolic abnormalities of IDH mutant tumors to exploit for therapy. While most studies have attempted to discern function by using cell lines transduced with exogenous IDH mutant enzyme, in this study, we perform unbiased metabolomics to discover metabolic differences between a cohort of patient-derived IDH1 mutant and IDH wildtype gliomaspheres. Methods Using both our own microarray and the TCGA datasets, we performed KEGG analysis to define pathways differentially enriched in IDH1 mutant and IDH wildtype cells and tumors. Liquid chromatography coupled to mass spectrometry analysis with labeled glucose and deoxycytidine tracers was used to determine differences in overall cellular metabolism and nucleotide synthesis. Radiation-induced DNA damage and repair capacity was assessed using a comet assay. Differences between endogenous IDH1 mutant metabolism and that of IDH wildtype cells transduced with the IDH1 (R132H) mutation were also investigated. Results Our KEGG analysis revealed that IDH wildtype cells were enriched for pathways involved in de novo nucleotide synthesis, while IDH1 mutant cells were enriched for pathways involved in DNA repair. LC-MS analysis with fully labeled 13C-glucose revealed distinct labeling patterns between IDH1 mutant and wildtype cells. Additional LC-MS tracing experiments confirmed increased de novo nucleotide synthesis in IDH wildtype cells relative to IDH1 mutant cells. Endogenous IDH1 mutant cultures incurred less DNA damage than IDH wildtype cultures and sustained better overall growth following X-ray radiation. Overexpression of mutant IDH1 in a wildtype line did not reproduce the range of metabolic differences observed in lines expressing endogenous mutations, but resulted in depletion of glutamine and TCA cycle intermediates, an increase in DNA damage following radiation, and a rise in intracellular ROS. Conclusions These results demonstrate that IDH1 mutant and IDH wildtype cells are easily distinguishable metabolically by analyzing expression profiles and glucose consumption. Our results also highlight important differences in nucleotide synthesis utilization and DNA repair capacity that could be exploited for therapy. Altogether, this study demonstrates that IDH1 mutant gliomas are a distinct subclass of glioma with a less malignant, but also therapy-resistant, metabolic profile that will likely require distinct modes of therapy.
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Affiliation(s)
- Matthew Garrett
- 1Department of Neurosurgery, and the Interdepartmental Program in the Neurosciences, University of California, Los Angeles, CA 90095 USA
| | - Jantzen Sperry
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Daniel Braas
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,3UCLA Metabolomics Center, UCLA, Los Angeles, USA
| | - Weihong Yan
- 4Department of Chemistry and Biochemistry, UCLA, Los Angeles, USA
| | - Thuc M Le
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,5Ahmanson Translational Imaging Division, UCLA, Los Angeles, USA
| | - Jack Mottahedeh
- 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Kirsten Ludwig
- 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Ascia Eskin
- 7Department of Human Genetics, UCLA, Los Angeles, USA
| | - Yue Qin
- 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Rachelle Levy
- 8Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA USA
| | - Joshua J Breunig
- 8Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, CA USA.,9Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA USA.,10Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA USA
| | - Frank Pajonk
- 11Department of Radiation Oncology, David Geffen School of Medicine at UCLA, Los Angeles, USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Thomas G Graeber
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,3UCLA Metabolomics Center, UCLA, Los Angeles, USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Caius G Radu
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,5Ahmanson Translational Imaging Division, UCLA, Los Angeles, USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Heather Christofk
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,3UCLA Metabolomics Center, UCLA, Los Angeles, USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,14Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Robert M Prins
- 1Department of Neurosurgery, and the Interdepartmental Program in the Neurosciences, University of California, Los Angeles, CA 90095 USA.,2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Albert Lai
- 12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,13Department of Neurology, UCLA, Los Angeles, USA
| | - Linda M Liau
- 1Department of Neurosurgery, and the Interdepartmental Program in the Neurosciences, University of California, Los Angeles, CA 90095 USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
| | - Giovanni Coppola
- 6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,13Department of Neurology, UCLA, Los Angeles, USA
| | - Harley I Kornblum
- 2Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,6Department of Psychiatry and Biobehavioral Sciences and Semel Institute for Neuroscience & Human Behavior, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,12Jonsson Comprehensive Cancer Center, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA.,14Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, UCLA, Room 379 Neuroscience Research Building, 635 Charles E. Young Dr. South, Los Angeles, CA 90095 USA
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Kiyokawa E, Hayama T, Yoshida H, Yamaguchi M, Nohta H. Fluorous-assisted metal chelate affinity extraction for nucleotides followed by HILIC-MS/MS analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1074-1075:86-90. [PMID: 29334633 DOI: 10.1016/j.jchromb.2017.12.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/26/2017] [Accepted: 12/29/2017] [Indexed: 11/26/2022]
Abstract
We herein developed a selective method for the determination of nucleotides by fluorous-assisted metal chelate affinity extraction followed by hydrophilic interaction liquid chromatography (HILIC) combined with tandem mass spectrometric (MS/MS) analysis. In this study, the nucleotides were selectively chelated by Fe(III)-immobilized perfluoroalkyliminodiacetic acid, and the resulting chelates were subsequently extracted into a fluorous solvent. The nucleotides present in the fluorous solvent were then back-extracted into a non-fluorous solution, such as a solution of ammonia in aqueous acetonitrile. The resulting non-fluorous solution containing the nucleotides was then directly injected into an amide-type HILIC column using a mixture of acetonitrile and aqueous ammonium bicarbonate as the mobile phase for gradient elution, and the nucleotides were detected using the negative electrospray ionization MS/MS mode. In this method, the extraction recoveries of the nucleotides ranged from 43.2 to 94.7% within a relative standard deviation of 17%. This method enabled the determination of intracellular concentrations of nucleotides.
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Affiliation(s)
- Ena Kiyokawa
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | - Tadashi Hayama
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | - Hideyuki Yoshida
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | - Masatoshi Yamaguchi
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | - Hitoshi Nohta
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan.
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50
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Grossman JD, Camire EJ, Perlstein DL. Approaches to Interrogate the Role of Nucleotide Hydrolysis by Metal Trafficking NTPases: The Nbp35-Cfd1 Iron-Sulfur Cluster Scaffold as a Case Study. Methods Enzymol 2018; 599:293-325. [PMID: 29746244 DOI: 10.1016/bs.mie.2017.11.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Nucleotide hydrolases play integral yet poorly understood roles in several metallocluster biosynthetic pathways. For example, the cytosolic iron-sulfur cluster assembly (CIA) is initiated by the CIA scaffold, an ATPase which builds new iron-sulfur clusters for proteins localized to the cytosol and the nucleus in eukaryotic organisms. While in vivo studies have demonstrated the scaffold's nucleotide hydrolase domain is vital for its function, in vitro approaches have not revealed tight allosteric coupling between the cluster scaffolding site and the ATPase site. Thus, the role of ATP hydrolysis has been hard to pinpoint. Herein, we describe methods to probe the nucleotide affinity and hydrolysis activity of the CIA scaffold from yeast, which is comprised of two homologous polypeptides called Nbp35 and Cfd1. In particular, we report two different equilibrium binding assays that make use of commercially available fluorescent nucleotide analogs. Importantly, these assays can be applied to probe nucleotide affinity of both the apo- and holo-forms of the CIA scaffold. Generally, these fluorescent nucleotide analogs have been underutilized to probe metal trafficking NTPase because one of the most commonly used probes, mantATP, which is labeled with the methylanthraniloyl probe via the 2' or 3' sugar hydroxyls, has an absorption which overlaps with the UV-Vis features of many metal-binding proteins. However, by exploiting analogs like BODIPY-FL and trinitrophenyl-labeled nucleotides which have better photophysical properties for metalloprotein applications, these approaches have the potential to reveal the mechanistic underpinnings of NTPases required for metallocluster biosynthesis.
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