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Gao Y, Chen Y, Zhu F, Pan D, Huang J, Wu X. Revealing the biological significance of multiple metabolic pathways of chloramphenicol by Sphingobium sp. WTD-1. J Hazard Mater 2024; 469:134069. [PMID: 38518693 DOI: 10.1016/j.jhazmat.2024.134069] [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] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/10/2024] [Accepted: 03/16/2024] [Indexed: 03/24/2024]
Abstract
Chloramphenicol (CAP) is an antibiotic that commonly pollutes the environment, and microorganisms primarily drive its degradation and transformation. Although several pathways for CAP degradation have been documented in different bacteria, multiple metabolic pathways in the same strain and their potential biological significance have not been revealed. In this study, Sphingobium WTD-1, which was isolated from activated sludge, can completely degrade 100 mg/L CAP within 60 h as the sole energy source. UPLC-HRMS and HPLC analyses showed that three different pathways, including acetylation, hydroxyl oxidation, and oxidation (C1-C2 bond cleavage), are responsible for the metabolism of CAP. Importantly, acetylation and C3 hydroxyl oxidation reduced the cytotoxicity of the substrate to strain WTD-1, and the C1-C2 bond fracture of CAP generated the metabolite p-nitrobenzoic acid (PNBA) to provide energy for its growth. This indicated that the synergistic action of three metabolic pathways caused WTD-1 to be adaptable and able to degrade high concentrations of CAP in the environment. This study deepens our understanding of the microbial degradation pathway of CAP and highlights the biological significance of the synergistic metabolism of antibiotic pollutants by multiple pathways in the same strain.
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Affiliation(s)
- Yongsheng Gao
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Yao Chen
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Fang Zhu
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Dandan Pan
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China
| | - Junwei Huang
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Xiangwei Wu
- Anhui Provincial Key Laboratory of Hazardous Factors and Risk Control of Agri-food Quality Safety, College of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
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Chen S, Fu Z, Chen K, Zheng X, Fu Z. Decoding HiPSC-CM's Response to SARS-CoV-2: mapping the molecular landscape of cardiac injury. BMC Genomics 2024; 25:271. [PMID: 38475718 DOI: 10.1186/s12864-024-10194-5] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 03/06/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Acute cardiac injury caused by coronavirus disease 2019 (COVID-19) increases mortality. Acute cardiac injury caused by COVID-19 requires understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly infects cardiomyocytes. This study provides a solid foundation for related studies by using a model of SARS-CoV-2 infection in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) at the transcriptome level, highlighting the relevance of this study to related studies. SARS-CoV-2 infection in hiPSC-CMs has previously been studied by bioinformatics without presenting the full molecular biological process. We present a unique bioinformatics view of the complete molecular biological process of SARS-CoV-2 infection in hiPSC-CMs. METHODS To validate the RNA-seq datasets, we used GSE184715 and GSE150392 for the analytical studies, GSE193722 for validation at the cellular level, and GSE169241 for validation in heart tissue samples. GeneCards and MsigDB databases were used to find genes associated with the phenotype. In addition to differential expression analysis and principal component analysis (PCA), we also performed protein-protein interaction (PPI) analysis, functional enrichment analysis, hub gene analysis, upstream transcription factor prediction, and drug prediction. RESULTS Differentially expressed genes (DEGs) were classified into four categories: cardiomyocyte cytoskeletal protein inhibition, proto-oncogene activation and inflammation, mitochondrial dysfunction, and intracellular cytoplasmic physiological function. Each of the hub genes showed good diagnostic prediction, which was well validated in other datasets. Inhibited biological functions included cardiomyocyte cytoskeletal proteins, adenosine triphosphate (ATP) synthesis and electron transport chain (ETC), glucose metabolism, amino acid metabolism, fatty acid metabolism, pyruvate metabolism, citric acid cycle, nucleic acid metabolism, replication, transcription, translation, ubiquitination, autophagy, and cellular transport. Proto-oncogenes, inflammation, nuclear factor-kappaB (NF-κB) pathways, and interferon signaling were activated, as well as inflammatory factors. Viral infection activates multiple pathways, including the interferon pathway, proto-oncogenes and mitochondrial oxidative stress, while inhibiting cardiomyocyte backbone proteins and energy metabolism. Infection limits intracellular synthesis and metabolism, as well as the raw materials for mitochondrial energy synthesis. Mitochondrial dysfunction and energy abnormalities are ultimately caused by proto-oncogene activation and SARS-CoV-2 infection. Activation of the interferon pathway, proto-oncogene up-regulation, and mitochondrial oxidative stress cause the inflammatory response and lead to diminished cardiomyocyte contraction. Replication, transcription, translation, ubiquitination, autophagy, and cellular transport are among the functions that decline physiologically. CONCLUSION SARS-CoV-2 infection in hiPSC-CMs is fundamentally mediated via mitochondrial dysfunction. Therapeutic interventions targeting mitochondrial dysfunction may alleviate the cardiovascular complications associated with SARS-CoV-2 infection.
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Affiliation(s)
- Sicheng Chen
- Department of Cardiology, Shantou Central Hospital, Shantou, 515031, China
| | - Zhenquan Fu
- School of Information Engineering, Guangdong University of Technology, Guangzhou, 510006, China
| | - Kaitong Chen
- Department of Cardiology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, China
| | - Xinyao Zheng
- Shantou University Medical College, Shantou, 515041, China
- Department of Cardiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Zhenyang Fu
- Department of Cardiology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, 510080, China.
- Department of Cardiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China.
- Department of Cardiology, The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510630, China.
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Gareev I, Encarnacion Ramirez MDJ, Nurmukhametov R, Ivliev D, Shumadalova A, Ilyasova T, Beilerli A, Wang C. The role and clinical relevance of long non-coding RNAs in glioma. Noncoding RNA Res 2023; 8:562-570. [PMID: 37602320 PMCID: PMC10432901 DOI: 10.1016/j.ncrna.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 08/05/2023] [Accepted: 08/06/2023] [Indexed: 08/22/2023] Open
Abstract
Glioma represents a complex and heterogeneous disease, posing significant challenges to both clinicians and researchers. Despite notable advancements in glioma treatment, the overall survival rate for most glioma patients remains dishearteningly low. Hence, there is an urgent necessity to discover novel biomarkers and therapeutic targets specifically tailored for glioma. In recent years, long non-coding RNAs (lncRNAs) have emerged as pivotal regulators of gene expression and have garnered attention for their involvement in the development and progression of various cancers, including glioma. The dysregulation of lncRNAs plays a critical role in glioma pathogenesis and influences clinical outcomes. Consequently, there is growing interest in exploring the potential of lncRNAs as diagnostic and prognostic biomarkers, as well as therapeutic targets. By understanding the functions and dysregulation of lncRNAs in glioma, researchers aim to unlock new avenues for the development of innovative treatment strategies catered to glioma patients. The identification and thorough characterization of lncRNAs hold the promise of novel therapeutic approaches that could potentially improve patient outcomes and enhance the management of glioma, ultimately striving for better prospects and enhanced quality of life for those affected by this challenging disease. The primary objective of this paper is to comprehensively review the current state of knowledge regarding lncRNA biology and their intricate roles in glioma. It also delves into the potential of lncRNAs as valuable diagnostic and prognostic indicators and explores their feasibility as promising targets for therapeutic interventions.
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Affiliation(s)
- Ilgiz Gareev
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Manuel de Jesus Encarnacion Ramirez
- Department of Neurosurgery, Рeoples’ Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya Street, Moscow, 117198, Russian Federation
| | - Renat Nurmukhametov
- Division of Spine Surgery, Central Clinical Hospital of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Denis Ivliev
- Department of Neurosurgery, Smolensk State Medical University of the Ministry of Health of the Russian Federation, Smolensk, Russia
| | - Alina Shumadalova
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Tatiana Ilyasova
- Bashkir State Medical University, Ufa, Republic of Bashkortostan, 450008, Russia
| | - Aferin Beilerli
- Department of Obstetrics and Gynecology, Tyumen State Medical University, Tyumen, Russia
| | - Chunlei Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
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Khan SU, Khan MU, Kalsoom F, Khan MI, Gao S, Unar A, Zubair M, Bilal M. Mechanisms of gene regulation by histone degradation in adaptation of yeast: an overview of recent advances. Arch Microbiol 2022; 204:287. [PMID: 35482104 DOI: 10.1007/s00203-022-02897-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 12/29/2021] [Revised: 03/12/2022] [Accepted: 04/04/2022] [Indexed: 02/07/2023]
Abstract
Histones are important component of eukaryotic cells chromatin and consist of arginine and lysine residues. Histones play an important role in the protection of DNA. Their contents significantly affect high-level chromatin structure formation, gene expression, DNA replication, and other important life activities. Protein degradation is an important regulatory mechanism of histone content. Recent studies have revealed that modification of amino acid sequence is directly related to histone breakdown. In addition, histone degradation is closely related to covalent modifications, such as ubiquitination and acetylation, which are considered to be driving factors in gene regulation. Gene regulation is an important mechanism in adaptation to the environment and survival of species. With the introduction of highly efficient technology, various mutations in histones have been identified in yeast. In the field of epigenetics and the transmission of chromatin states, two widely used model organisms are the budding yeast Saccharomyces cerevisiae and Schizosaccharomyces pombe. Higher eukaryotes can use their silent loci to maintain their epigenetic states and providing the base to investigate mechanisms underlying development. Therfore, both species have contributed a plethora of information on these mechanisms in both yeast and higher eukaryotes. This study focuses on the role of histone modifications in controlling telomeric silencing in Saccharomyces cerevisiae and centromeric silencing in S. pombe as examples of genetic loci that demonstrate epigenetic inheritance. In view of recent advances, this review focuses on the post-translational modification of histone amino acid residues and reviews the relationship between histone degradation and amino acid residue modification.
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Affiliation(s)
- Safir Ullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Munir Ullah Khan
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - Fadia Kalsoom
- Department of Microbiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Muhammad Imran Khan
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
- Hefei National Laboratory for Physical Sciences at Microscale and the Center for Biomedical Engineering, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
- Department of Pathology, District headquarters hospital, Jhang, 35200, Punjab Province, Islamic Republic of Pakistan.
| | - Shuang Gao
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Ahsanullah Unar
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Muhammad Zubair
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, People's Republic of China.
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Abstract
The magnitude of many biological traits relates strongly and regularly to body size. Consequently, a major goal of comparative biology is to understand and apply these 'size-scaling' relationships, traditionally quantified by using linear regression analyses based on log-transformed data. However, recently some investigators have questioned this traditional method, arguing that linear or non-linear regression based on untransformed arithmetic data may provide better statistical fits than log-linear analyses. Furthermore, they advocate the replacement of the traditional method by alternative specific methods on a case-by-case basis, based simply on best-fit criteria. Here, I argue that the use of logarithms in scaling analyses presents multiple valuable advantages, both statistical and conceptual. Most importantly, log-transformation allows biologically meaningful, properly scaled (scale-independent) comparisons of organisms of different size, whereas non-scaled (scale-dependent) analyses based on untransformed arithmetic data do not. Additionally, log-based analyses can readily reveal biologically and theoretically relevant discontinuities in scale invariance during developmental or evolutionary increases in body size that are not shown by linear or non-linear arithmetic analyses. In this way, log-transformation advances our understanding of biological scaling conceptually, not just statistically. I hope that my Commentary helps students, non-specialists and other interested readers to understand the general benefits of using log-transformed data in size-scaling analyses, and stimulates advocates of arithmetic analyses to show how they may improve our understanding of scaling conceptually, not just statistically.
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Affiliation(s)
- Douglas S Glazier
- Department of Biology, Juniata College, 1700 Moore Street, Huntingdon, PA 16652, USA
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Heinrich P, Hanslik L, Kämmer N, Braunbeck T. The tox is in the detail: technical fundamentals for designing, performing, and interpreting experiments on toxicity of microplastics and associated substances. Environ Sci Pollut Res Int 2020; 27:22292-22318. [PMID: 32335837 DOI: 10.1007/s11356-020-08859-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
Over the last 10 years, there has been a plethora of experimental studies estimating the potential of microplastic particles (MPs) to exert toxic effects in the environment, many specifically focusing on their postulated capacity to enhance the transfer of environmental pollutants into organisms after ingestion. Obviously, there is little to no consensus on appropriate experimental design, which is mainly owing to the novelty, the interdisciplinarity of the subject, and the complexity of parameters involved. This results in fundamental discrepancies regarding the materials applied, the approach for spiking MPs with pollutants, and the exact exposure scenario. Aiming for a non-chemist audience and providing illustrative, representative, and comparative examples, this review first outlines the theoretical essentials of processes involved in sorption. Also, it discusses the implications for designing experimental approaches using MPs and interpreting the results obtained under consideration of their relevance for environmental conditions. It may help to improve the interpretation of studies on MP toxicity already published, while also calling experimenters' attention to various aspects important to consider when designing and performing environmentally relevant experiments with MPs.
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Affiliation(s)
- Patrick Heinrich
- Aquatic Ecology and Toxicology Section, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 504, 69120, Heidelberg, Germany.
| | - Lisa Hanslik
- Aquatic Ecology and Toxicology Section, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 504, 69120, Heidelberg, Germany
| | - Nadine Kämmer
- Aquatic Ecology and Toxicology Section, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 504, 69120, Heidelberg, Germany
| | - Thomas Braunbeck
- Aquatic Ecology and Toxicology Section, Centre for Organismal Studies, University of Heidelberg, Im Neuenheimer Feld 504, 69120, Heidelberg, Germany
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Sultana N. Microbial biotransformation of bioactive and clinically useful steroids and some salient features of steroids and biotransformation. Steroids 2018; 136:76-92. [PMID: 29360535 DOI: 10.1016/j.steroids.2018.01.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [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: 04/08/2017] [Revised: 12/16/2017] [Accepted: 01/16/2018] [Indexed: 01/11/2023]
Abstract
Steroids are perhaps one of the most widely used group of drugs in present day. Beside the established utilization as immunosuppressive, anti-inflammatory, anti-rheumatic, progestational, diuretic, sedative, anabolic and contraceptive agents, recent applications of steroid compounds include the treatment of some forms of cancer, osteoporosis, HIV infections and treatment of declared AIDS. Steroids isolated are often available in minute amounts. So biotransformation of natural products provides a powerful means in solving supply problems in clinical trials and marketing of the drug for obtaining natural products in bulk amounts. If the structure is complex, it is often an impossible task to isolate enough of the natural products for clinical trials. The microbial biotransformation of steroids yielded several novel metabolites, exhibiting different activities. The metabolites produced from pregnenolone acetate by Cunning hamella elegans and Rhizopus stolonifer were screened against tyrosinase and cholinesterase showed significant inhibitory activities than the parent compound. Diosgenin and its transformed sarsasapogenin were screened for their acetyl cholinesterase and butyryl cholinesterase inhibitory activities. Sarsasapogenin was screened for phytotoxicity, and was found to be more active than the parent compound. Diosgenin, prednisone and their derivatives were screened for their anti-leishmanial activity. All derivatives were found to be more active than the parent compound. The biotransformation of steroids have been reviewed to a little extent. This review focuses on the biotransformation and functions of selected steroids, the classification, advantages and agents of enzymatic biotransformation and examines the potential role of new enzymatically transformed steroids and their derivatives in the chemoprevention and treatment of other diseases. tyrosinase and cholinesterase inhibitory activities, severe asthma, rheumatic disorders, renal disorders and diseases of inflammatory bowel, skin, gastrointestinal tract.
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Affiliation(s)
- Nighat Sultana
- Pharmaceutical Research Center, PCSIR Laboratories Complex, Shahrah-e-Dr. Salimuzzaman Siddiqui, Off University Road, Karachi 75280, Pakistan.
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Urbanek A, Szadziewski R, Giłka W. Ultrastructure of mediodorsal setae in biting midge larvae of the genus Atrichopogon Kieffer with notes on their biological significance (Diptera: Ceratopogonidae). Arthropod Struct Dev 2015; 44:10-20. [PMID: 25449976 DOI: 10.1016/j.asd.2014.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 05/29/2014] [Revised: 10/01/2014] [Accepted: 10/19/2014] [Indexed: 06/04/2023]
Abstract
The ultrastructure of the strong mediodorsal setae in terrestrial stage IV larvae of Atrichopogon (Meloehelea) oedemerarum and A. (M.) meloesugans was examined using light, scanning and transmission electron microscopy. Serrated setae placed on prominent processes are distributed in pairs on all thoracic and abdominal segments. Setae are innervated by a single dendrite and their surface has no pores. The trichogen cell is not retracted from the setal lumen on completion of the hair-forming process but fills the mediodorsal seta also when the larval cuticle is fully sclerotised. Such a phenomenon was previously reported in terrestrial larvae of the genus Forcipomyia. We suggest that the mediodorsal setae described in Atrichopogon are plesiotypic mechanoreceptors for the subfamily Forcipomyiinae. They are preserved in the truly terrestrial larvae of Atrichopogon, but modified to secretory setae in the genus Forcipomyia. Both genera bearing distinct mediodorsal setae have developed functional tracheal gills, unknown in other biting midges.
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Affiliation(s)
- Aleksandra Urbanek
- Department of Invertebrate Zoology and Parasitology, University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland.
| | - Ryszard Szadziewski
- Department of Invertebrate Zoology and Parasitology, University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Wojciech Giłka
- Department of Invertebrate Zoology and Parasitology, University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
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Nevagi RJ, Dighe SN, Dighe SN. Biological and medicinal significance of benzofuran. Eur J Med Chem 2014; 97:561-81. [PMID: 26015069 DOI: 10.1016/j.ejmech.2014.10.085] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [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: 08/31/2014] [Revised: 10/15/2014] [Accepted: 10/31/2014] [Indexed: 11/29/2022]
Abstract
This article emphasizes on the importance of benzofuran as a biologically relevant heterocycle. It covers most of the physiologically as well as medicinally important compounds containing benzofuran rings. This article also covers clinically approved drugs containing benzofuran scaffold.
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Affiliation(s)
- Reshma J Nevagi
- Department of Pharmaceutical Chemistry, SMBT College of Pharmacy, Nandi Hills, Dhamangaon, Igatpuri, Nashik 422403, Maharashtra, India
| | - Santosh N Dighe
- Department of Chemistry, Sir Parshurambhau College, Pune 30, Maharashtra, India
| | - Satish N Dighe
- Department of Pharmaceutical Chemistry, Sinhgad College of Pharmacy, Vadgaon (BK), Pune, Maharashtra, India.
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