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Valipour M, Zakeri Khatir Z, Abdollahi E, Ayati A. Recent Applications of Protoberberines as Privileged Starting Materials for the Development of Novel Broad-Spectrum Antiviral Agents: A Concise Review (2017-2023). ACS Pharmacol Transl Sci 2024; 7:48-71. [PMID: 38230282 PMCID: PMC10789142 DOI: 10.1021/acsptsci.3c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 01/18/2024]
Abstract
Berberine is a well-known phytochemical with significant antiviral activity against a wide range of viruses. Due to having a unique backbone consisting of four interconnected rings, it can be used as a platform for the design and development of novel semisynthetic antiviral agents. The question here is whether novel broad-spectrum antiviral drugs with enhanced activity and toxicity potential can be obtained by attempting to modify the structure of this privileged lead compound. The present study aims to review the results of recent studies in which berberine and its close analogues (protoberberine alkaloids) have been used as starting materials for the production of new semisynthetic antiviral structures. For this purpose, relevant studies published in high-quality journals indexed in databases such as Scopus, Web of Science, PubMed, etc. in the time frame of 2017 to 2023 were collected. Our selection criterion in the current review focuses on the studies in which protoberberines were used as starting materials for the production of semisynthetic agents with antiviral activity during the indicated time period. Correspondingly, studies were identified in which semisynthetic derivatives with significant inhibitory activity against a wide range of viruses including human immunodeficiency virus (HIV), enterovirus 71 (EV71), zika virus (ZIKV), influenza A/B, cytomegalovirus (CMV), respiratory syncytial virus (RSV), and coxsackieviruses were designed and synthesized. Our conclusion is that, despite the introduction of diverse semisynthetic derivatives of berberine with improved activity profiles compared to the parent natural leads, sufficient derivatization has not been done yet and more studies are needed.
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Affiliation(s)
- Mehdi Valipour
- Razi
Drug Research Center, Iran University of
Medical Sciences, Tehran 1449614535, Iran
| | - Zahra Zakeri Khatir
- Department
of Medicinal Chemistry, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari 6964114483, Iran
- Student
Research Committee, Mazandaran University
of Medical Sciences, Sari 6964114483, Iran
| | - Elaheh Abdollahi
- Department
of Pharmacology and Toxicology, School of Pharmacy, Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Adileh Ayati
- Department
of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences
Research Center, Tehran University of Medical
Sciences, Tehran 1416753955, Iran
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Selvakesavan RK, Nuc M, Kolarčik V, Krajewski P, Franklin G. Single molecule real-time sequencing data sets of Hypericum perforatum L. plantlets and cell suspension cultures. Sci Data 2024; 11:42. [PMID: 38184679 PMCID: PMC10771467 DOI: 10.1038/s41597-023-02878-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 12/18/2023] [Indexed: 01/08/2024] Open
Abstract
Hypericum is a large genus that includes more than 500 species of pharmacological, ecological and conservation value. Although latest advances in sequencing technologies were extremely exploited for generating and assembling genomes of many living organisms, annotated whole genome sequence data is not publicly available for any of the Hypericum species so far. Bioavailability of secondary metabolites varies for different tissues and the data derived from different cultures will be a valuable tool for comparative studies. Here, we report the single molecule real-time sequencing (SMRT) data sets of Hypericum perforatum L. plantlets and cell suspension cultures for the first time. Sequencing data from cell suspension cultures yielded more than 33,000 high-quality transcripts from 20 Gb of raw data, while more than 55,000 high-quality transcripts were obtained from 35 Gb of raw data from plantlets. This dataset is a valuable tool for comparative transcriptomic analysis and will help to understand the unknown biosynthetic pathways of high medicinal value in the Hypericum genus.
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Affiliation(s)
- Rajendran K Selvakesavan
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
- Department of Biotechnology, PSGR Krishnammal College for Women, Coimbatore, 641004, India
| | - Maria Nuc
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Vladislav Kolarčik
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Mánesova 23, SK-041 54, Košice, Slovakia
| | - Paweł Krajewski
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Gregory Franklin
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
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Singh D, Mittal N, Verma S, Singh A, Siddiqui MH. Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review. Mol Biol Rep 2023; 51:23. [PMID: 38117315 DOI: 10.1007/s11033-023-09057-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.
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Affiliation(s)
- Dhananjay Singh
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, 226026, India
| | - Nishu Mittal
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
| | - Swati Verma
- College of Horticulture and Forestry Thunag, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173230, India
| | - Anjali Singh
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
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Park NI, Roy NS, Park Y, Choi BS, Jeon MJ, Oh JY, Kim BY, Kim YD, Kim YI, Um T, Kwak HJ, Kim NS, Kim S, Choi IY. Isolation and Characterization of the Genes Involved in the Berberine Synthesis Pathway in Asian Blue Cohosh, Caulophyllum robustum. PLANTS (BASEL, SWITZERLAND) 2023; 12:1483. [PMID: 37050109 PMCID: PMC10096549 DOI: 10.3390/plants12071483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Caulophyllum robustum, commonly named Asian blue cohosh, is a perennial herb in the family Berberidaceae. It has traditionally been used for folk medicine in China. We isolated berberine from the leaves, stem, roots, and fruits of C. robustum, and this is the first report on berberine in this species. Transcriptome analysis was conducted for the characterization of berberine biosynthesis genes in C. robustum, in which, all the genes for berberine biosynthesis were identified. From 40,094 transcripts, using gene ontology (GO) analysis, 26,750 transcripts were assigned their functions in the categories of biological process, molecular function, and cellular component. In the analysis of genes expressed in different tissues, the numbers of genes in the categories of intrinsic component of membrane and transferase activity were up-regulated in leaves versus stem. The berberine synthesis genes in C. robustum were characterized by phylogenetic analysis with corresponding genes from other berberine-producing species. The co-existence of genes from different plant families in the deepest branch subclade implies that the differentiation of berberine synthesis genes occurred early in the evolution of berberine-producing plants. Furthermore, the copy number increment of the berberine synthesis genes was detected at the species level.
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Affiliation(s)
- Nam-Il Park
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Republic of Korea
| | - Neha Samir Roy
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Yeri Park
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Beom-Soon Choi
- Next Bio Information Technology, Bodeumkwan 504, Kangwon National University, Gangwondaehakgil-1, Chuncheon 24341, Republic of Korea
| | - Mi Jin Jeon
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Ji Yeon Oh
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Bo-Yun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Republic of Korea
| | - Young-Dong Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Yong-In Kim
- On Biological Resource Research Institute, Chuncheon 24239, Republic of Korea
| | - Taeyoung Um
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hwan Jong Kwak
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Nam-Soo Kim
- Next Bio Information Technology, Bodeumkwan 504, Kangwon National University, Gangwondaehakgil-1, Chuncheon 24341, Republic of Korea
| | - Soonok Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
| | - Ik-Young Choi
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
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Roy NS, Park NI, Kim NS, Park Y, Kim BY, Kim YD, Yu JK, Kim YI, Um T, Kim S, Choi IY. Comparative Transcriptomics for Genes Related to Berberine and Berbamine Biosynthesis in Berberidaceae. PLANTS (BASEL, SWITZERLAND) 2022; 11:2676. [PMID: 36297700 PMCID: PMC9610958 DOI: 10.3390/plants11202676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Berberine and berbamine are bioactive compounds of benzylisoquinoline alkaloids (BIAs) present in Berberis species. The contents of berbamine are 20 times higher than berberine in leaf tissues in three closely related species: Berberis koreana, B. thunbergii and B. amurensis. This is the first report on the quantification of berberine compared to the berbamine in the Berberis species. Comparative transcriptome analyses were carried out with mRNAs from the leaf tissues of the three-species. The comparison of the transcriptomes of B. thunbergii and B. amurensis to those of B. koreana, B. thunbergii showed a consistently higher number of differentially expressed genes than B. amurensis in KEGG and DEG analyses. All genes encoding enzymes involved in berberine synthesis were identified and their expressions were variable among the three species. There was a single copy of CYP80A/berbamunine synthase in B. koreana. Methyltransferases and cytochrome P450 mono-oxidases (CYPs) are key enzymes for BIA biosynthesis. The current report contains the copy numbers and other genomic characteristics of the methyltransferases and CYPs in Berberis species. Thus, the contents of the current research are valuable for molecular characterization for the medicinal utilization of the Berberis species.
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Affiliation(s)
- Neha Samir Roy
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea
| | - Nam-Il Park
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Korea
| | - Nam-Soo Kim
- NBIT, Kangwon National University, Gangwondaehakgil-1, Bodeumkwan 504, Chuncheon 24341, Korea
| | - Yeri Park
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Korea
| | - Bo-Yun Kim
- Plant Resources Division, National Institute of Biological Resources, Incheon 22689, Korea
| | - Young-Dong Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Korea
| | - Ju-Kyung Yu
- Syngenta Crop Protection LLC, 9 Davis Drive, Research Triangle Park, NC 27709, USA
| | - Yong-In Kim
- On Biological Resource Research Institute, Chuncheon 24239, Korea
| | - Taeyoung Um
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea
| | - Soonok Kim
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Korea
| | - Ik-Young Choi
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea
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Jeon MJ, Roy NS, Choi BS, Oh JY, Kim YI, Park HY, Um T, Kim NS, Kim S, Choi IY. Identifying Terpenoid Biosynthesis Genes in Euphorbia maculata via Full-Length cDNA Sequencing. Molecules 2022; 27:molecules27144591. [PMID: 35889464 PMCID: PMC9316252 DOI: 10.3390/molecules27144591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/18/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Abstract
The annual herb Euphorbia maculata L. produces anti-inflammatory and biologically active substances such as triterpenoids, tannins, and polyphenols, and it is used in traditional Chinese medicine. Of these bioactive compounds, terpenoids, also called isoprenoids, are major secondary metabolites in E. maculata. Full-length cDNA sequencing was carried out to characterize the transcripts of terpenoid biosynthesis reference genes and determine the copy numbers of their isoforms using PacBio SMRT sequencing technology. The Illumina short-read sequencing platform was also employed to identify differentially expressed genes (DEGs) in the secondary metabolite pathways from leaves, roots, and stems. PacBio generated 62 million polymerase reads, resulting in 81,433 high-quality reads. From these high-quality reads, we reconstructed a genome of 20,722 genes, in which 20,246 genes (97.8%) did not have paralogs. About 33% of the identified genes had two or more isoforms. DEG analysis revealed that the expression level differed among gene paralogs in the leaf, stem, and root. Whole sets of paralogs and isoforms were identified in the mevalonic acid (MVA), methylerythritol phosphate (MEP), and terpenoid biosynthesis pathways in the E. maculata L. The nucleotide information will be useful for identifying orthologous genes in other terpenoid-producing medicinal plants.
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Affiliation(s)
- Mi Jin Jeon
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Korea; (M.J.J.); (J.Y.O.)
| | - Neha Samir Roy
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea; (N.S.R.); (T.U.)
| | | | - Ji Yeon Oh
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Korea; (M.J.J.); (J.Y.O.)
| | - Yong-In Kim
- On Biological Resource Research Institute, Chuncheon 24239, Korea;
| | - Hye Yoon Park
- Biological Resources Assessment Division, National Institute of Biological Resources, Incheon 22689, Korea;
| | - Taeyoung Um
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea; (N.S.R.); (T.U.)
| | - Nam-Soo Kim
- BIT Institute, NBIT Co., Ltd., Chuncheon 24341, Korea;
- Correspondence: (N.-S.K.); (S.K.); (I.-Y.C.); Tel.: +82-10-5522-6472 (N.-S.K.); +82-32-590-7110 (S.K.); +82-33-250-7768 (I.-Y.C.)
| | - Soonok Kim
- Microorganism Resources Division, National Institute of Biological Resources, Incheon 22689, Korea; (M.J.J.); (J.Y.O.)
- Correspondence: (N.-S.K.); (S.K.); (I.-Y.C.); Tel.: +82-10-5522-6472 (N.-S.K.); +82-32-590-7110 (S.K.); +82-33-250-7768 (I.-Y.C.)
| | - Ik-Young Choi
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea; (N.S.R.); (T.U.)
- BIT Institute, NBIT Co., Ltd., Chuncheon 24341, Korea;
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: (N.-S.K.); (S.K.); (I.-Y.C.); Tel.: +82-10-5522-6472 (N.-S.K.); +82-32-590-7110 (S.K.); +82-33-250-7768 (I.-Y.C.)
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Liu X, Gong X, Liu Y, Liu J, Zhang H, Qiao S, Li G, Tang M. Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds. FRONTIERS IN PLANT SCIENCE 2022; 13:900035. [PMID: 35909744 PMCID: PMC9331165 DOI: 10.3389/fpls.2022.900035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/10/2022] [Indexed: 05/11/2023]
Abstract
The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gong
- Department of Rheumatology and Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Sen Qiao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Gang Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- Gang Li,
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- *Correspondence: Min Tang,
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