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Phenotype prediction of nonsynonymous single nucleotide polymorphisms in human phase II drug/xenobiotic metabolizing enzymes: perspectives on molecular evolution

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Science China(Life Sciences) 2010年第10期53卷 1252-1262页

作者： HAO Dacheng XIAO PeiGen chen shilin Laboratory of Biotechnology College of EnvironmentDalian Jiaotong UniversityDalian 116028China Institute of Medicinal Plant Development Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100193China

Nonsynonymous single nucleotide polymorphisms (nsSNPs) in coding regions can lead to amino acid changes that might alter the protein’s function and account for susceptibility to disease and altered drug/xenobiotic response. Many nsSNPs have been found in genes encoding human phase II metabolizing enzymes; however, there is little known about the relationship between the genotype and phenotype of nsSNPs in these enzymes. We have identified 923 validated nsSNPs in 104 human phase II enzyme genes from the Ensembl genome database and the NCBI SNP database. Using PolyPhen, Panther, and SNAP algorithms, 44%?59% of nsSNPs in phase II enzyme genes were predicted to have functional impacts on protein function. Predictions largely agree with the available experimental annotations. 68% of deleterious nsSNPs were correctly predicted as damaging. This study also identified many amino acids that are likely to be functionally critical, but have not yet been studied experimentally. There was significant concordance between the predicted results of Panther and PolyPhen, and between SNAP non-neutral predictions and PolyPhen scores. Evolutionarily non-neutral (destabilizing) amino acid substitutions are thought to be the pathogenetic basis for the alteration of phase II enzyme activity and to be associated with disease susceptibility and drug/xenobiotic toxicity. Furthermore, the molecular evolutionary patterns of phase II enzymes were characterized with regards to the predicted deleterious nsSNPs.

关键词： phenotype PolyPhen Panther SNAP SNP phase II drug/xenobiotic metabolizing enzyme

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Biosynthetic pathway of terpenoid indole alkaloids in Catharanthus roseus

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Frontiers of Medicine 2014年第3期8卷 285-293页

作者： Xiaoxuan Zhu Xinyi Zeng Chao Sun shilin chen Institute of Medicinal Plant Development China Academy of Medical Sciences & Peking Union Medical College Beijing 100193 China Institute of Chinese Materia Medica China Academy of-Chinese Medical Sciences Beijing 100700 China

Catharanthus roseus is one of the most extensively investigated medicinal plants, which can produce more than 130 alkaloids, including the powerful antitumor drugs vinblastine and vincristine. Here we review the recent advances in the biosynthetic pathway of terpenoid indole alkaloids （TIAs） in C. roseus, and the identification and characterization of the corresponding enzymes involved in this pathway. Strictosidine is the central intermediate in the biosynthesis of different TIAs, which is formed by the condensation of secologanin and tryptamine. Secologanin is derived from terpenoid （isoprenoid） biosynthetic pathway, while tryptamine is derived from indole biosynthetic pathway. Then various specific end products are produced by different routes during downstream process. Although many genes and corresponding enzymes have been characterized in this pathway, our knowledge on the whole TIA biosynthetic pathway still remains largely unknown up to date. Full elucidation of TIA biosynthetic pathway is an important prerequisite to understand the regulation of the TIA biosynthesis in the medicinal plant and to produce valuable TIAs by synthetic biological technology.

关键词： Catharanthus roseus terpenoidindole alkaloids biosynthetic pathway vinblastine vincristine

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Letter to the editor: Comment on the Regulatios of the Simplified Registration and Approval Management for Compound Recipe of Classical Prescription of Traditional Chinese Medicine

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Acta Pharmaceutica Sinica B 2018年第1期8卷 127-129页

作者： shilin chen Aihua Liang Boli Zhang China Academy of Chinese Medical Sciences

To the Editor:On Oct 9,2017,China Food and Drug Administration announced1~ the Regulations of the Simplified Registration and Approval Management for Compound Recipe of Classical Prescription of Traditional Chinese Medicine(Exposure Draft)which has been stirring up intense debate in the *** article China to Roll Back Regulations for Traditional Medicine Despite Safety Concerns lately

关键词： In Letter to the editor Comment on the Regulatios of the Simplified Registration and Approval Management for Compound Recipe of Classical Prescription of Traditional Chinese Medicine

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Editorial of Special Column “Research on Emerging COVID-19(Target, Mechanism, and Therapeutics)”

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Acta Pharmaceutica Sinica B 2020年第7期10卷 1146-1148页

作者： Hai-Bin Luo shilin chen Peiqing Liu School of Pharmaceutical Sciences Sun Yat-sen UniversityGuangzhou 510006China Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China Laboratory of Pharmacology&Toxicology and New Drug R&D Center School of Pharmaceutical SciencesSun Yat-Sen UniversityGuangzhou 510006China

Coronavirus disease 2019(COVID-19)pandemic caused by severe acute respiratory syndrome coronavirus 2(SARS-Co V-2)has become a global crisis1,*** from SARS-Co V-2 can result in severe lymphopenia,prolonged coagulation profiles,lethal acute respiratory distress syndrome(ARDS),watery diarrhea,cardiac disease,multiorgan dysfunction,and sudden death3,4.

关键词： acute respiratory distress

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Safety issues and new rapid detection methods in traditional Chinese medicinal materials

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Acta Pharmaceutica Sinica B 2015年第1期5卷 38-46页

作者： Lili Wang Weijun Kong Meihua Yang Jianping Han shilin chen Institute of Medicinal Plant Development Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Chinese Materia Medica China Academy of Chinese Medical Sciences

The safety of traditional Chinese medicine(TCM) is a major strategic issue that involves human health. With the continuous improvement in disease prevention and treatment, the export of TCM and its related products has increased dramatically in China. However, the frequent safety issues of Chinese medicine have become the ‘bottleneck' impeding the modernization of TCM. It was proved that mycotoxins seriously affect TCM safety; the pesticide residues of TCM are a key problem in TCM international trade; adulterants have also been detected, which is related to market circulation. These three factors have greatly affected TCM safety. In this study, fast, highly effective, economically-feasible and accurate detection methods concerning TCM safety issues were reviewed, especially on the authenticity, mycotoxins and pesticide residues of medicinal materials.

关键词： Traditional Chinese medicine Safety issue Rapid detection Mycotoxins Pesticide residues Authentication 2D DNA barcodes Traceability

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Progress and prediction of multicomponent quantification in complex systems with practical LC-UV methods

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Journal of Pharmaceutical Analysis 2023年第2期13卷 142-155页

作者： Xi chen Zhao Yang Yang Xu Zhe Liu Yanfang Liu Yuntao Dai shilin chen Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing100700China Key Lab of Separation Science for Analytical Chemistry Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalian116023China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu611137China

Complex systems exist widely,including medicines from natural products,functional foods,and biological *** biological activity of complex systems is often the result of the synergistic effect of multiple *** the quality evaluation of complex samples,multicomponent quantitative analysis(MCQA)is usually *** overcome the difficulty in obtaining standard products,scholars have proposed achieving MCQA through the“single standard to determine multiple components(SSDMC)”*** method has been used in the determination of multicomponent content in natural source drugs and the analysis of impurities in chemical drugs and has been included in the Chinese *** on a convenient(ultra)high-performance liquid chromatography method,how can the repeatability and robustness of the MCQA method be improved?How can the chromatography conditions be optimized to improve the number of quantitative components?How can computer software technology be introduced to improve the efficiency of multicomponent analysis(MCA)?These are the key problems that remain to be solved in practical ***,this review article summarizes the calculation methods of relative correction factors in the SSDMC approach in the past five years,as well as the method robustness and accuracy ***,it also summarizes methods to improve peak capacity and quantitative accuracy in MCA,including column selection and twodimensional chromatographic analysis ***,computer software technologies for predicting chromatographic conditions and analytical parameters are introduced,which provides an idea for intelligent method development in *** paper aims to provide methodological ideas for the improvement of complex system analysis,especially MCQA.

关键词： Multicomponent quantification analysis Single standard to determine multiple components Predictive software

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Rapid Authentication of the Poisonous Plant Gelsemium elegans by Combining Filter-Paper-Based DNA Extraction and RPA–LFD Detection

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Engineering 2021年第1期7卷 14-16页

作者： Xiasheng Zheng Wenli An Hui Yao Jiang Xu shilin chen National Engineering Research Center for Modernization of Traditional Chinese Medicine Mathematical Engineering Academy of Chinese MedicineGuangzhou University of Chinese MedicineGuangzhou 510006China Institute of Chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China Institute of Medicinal Plant Development Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100193China

Numerous plants and animals are edible and officinal,but some can be *** is sometimes confusion between poisonous and non-poisonous materials because of similarities in their ***,the unwitting intake of poisonous plant or animal material has resulted in poisoning cases and sometimes in death,especially for situation in the *** and accurate authentication of toxic species is essential for establishing and adopting optimal and urgent treatment for patients in such cases,and can be life-saving or can at least minimize the damage to ***,most of the current species authentication methods,including DNA barcoding,loop-mediated isothermal amplification(LAMP),chromatography technologies,and other methods,depend on professional equipment and a specialist laboratory,which are impracticable for real-time application in the *** is therefore crucial to develop a rapid,accurate,and specific authentication method for poisonous species that does not require any equipment.

关键词： intake establishing Plant

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Herbgenomics: A stepping stone for research into herbal medicine

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Science China(Life Sciences) 2019年第7期62卷 913-920页

作者： Haoyu Hu Xiaofeng Shen Baosheng Liao Lu Luo Jiang Xu shilin chen Institute of Chinese Materia Medica China Academy of Chinese Medicinal Sciences

From the prehistoric era until the publishing of the Compendium of Materia Medica and the first scientific Nobel Prize in the Chinese mainland for Tu's discovery on anti-malarial tablets,each milestone and stepping stone in the developmental history of herbal medicine involved intrepid exploration,bold hypothesis formulation,and cautious *** thousands of years of discovery and development,herbal research has entered a new era—the era of *** combines herbal and genomic research,bridging the gap between traditional herbal medicine and cutting-edge omics ***,it provides a general picture of the genetic background of traditional herbs,enabling researchers to investigate the mechanisms underlying the prevention and treatment of human diseases from an omics perspective.

关键词： herbgenomics herbal medicines omics potential application

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Cannabis sativa: origin and history, glandular trichome development, and cannabinoid biosynthesis

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Horticulture Research 2023年第9期10卷 306-320页

作者： Ziyan Xie Yaolei Mi Lingzhe Kong Maolun Gao Shanshan chen Weiqiang chen Xiangxiao Meng Wei Sun shilin chen Zhichao Xu Key Laboratory of Saline-alkali Vegetation Ecology Restoration(Northeast Forestry University) Ministry of EducationHarbin 150040China College of Life Science Northeast Forestry UniversityHarbin 150040China Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine Institute of Chinese Materia MedicaChina Academy of Chinese Medical SciencesBeijing 100700China Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China

Is Cannabis a boon or bane?Cannabis sativa has long been a versatile crop for fiber extraction(industrial hemp),traditional Chinese medicine(hemp seeds),and recreational drugs(marijuana).Cannabis faced global prohibition in the twentieth century because of the psychoactive properties of △^(9)-tetrahydrocannabinol;however,recently,the perspective has changed with the recognition of additional therapeutic values,particularly the pharmacological potential of cannabidiol.A comprehensive understanding of the underlying mechanism of cannabinoid biosynthesis is necessary to cultivate and promote globally the medicinal application of Cannabis ***,we comprehensively review the historical usage of Cannabis,biosynthesis of trichome-specific cannabinoids,regulatory network of trichome development,and synthetic biology of *** review provides valuable insights into the efficient biosynthesis and green production of cannabinoids,and the development and utilization of novel Cannabis varieties.

关键词： comprehensive versatile globally

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DNA barcoding in herbal medicine: Retrospective and prospective

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Journal of Pharmaceutical Analysis 2023年第5期13卷 431-441页

作者： shilin chen Xianmei Yin Jianping Han Wei Sun Hui Yao Jingyuan Song Xiwen Li Institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu611137China Key Laboratoryof Beijing for Identification and Safety Evaluation of Chinese Medicine Instituteof Chinese Materia MedicaChina Academyof Chinese Medical SciencesBeijing100700China State Key Laboratory of Southwestern Chinese Medicine Resources Chengdu University of Traditional Chinese MedicineChengdu611137China Institute of Medicinal Plant Development Chinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing100193China

DNA barcoding has been widely used for herb identification in recent decades,enabling safety and innovation in the field of herbal *** this article,we summarize recent progress in DNA bar-coding for herbal medicine to provide ideas for the further development and application of this *** importantly,the standard DNA barcode has been extended in two ***,while conventional DNA barcodes have been widely promoted for their versatility in the identification of fresh or well-preserved samples,super-barcodes based on plastid genomes have rapidly developed and have shown advantages in species identification at low taxonomic ***,mini-barcodes are attractive because they perform better in cases of degraded DNA from herbal *** addition,some mo-lecular techniques,such as high-throughput sequencing and isothermal amplification,are combined with DNA barcodes for species identification,which has expanded the applications of herb identification based on DNA barcoding and brought about the post-DNA-barcoding ***,standard and high-species coverage DNA barcode reference libraries have been constructed to provide reference se-quences for species identification,which increases the accuracy and credibility of species discrimination based on DNA *** summary,DNA barcoding should play a key role in the quality control of traditional herbal medicine and in the international herb trade.

关键词： Herbal identification Super-barcode Mini-barcode Meta-barcoding Cutting-edgebarcoding

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