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Global Pharmacopoeia Genome Database is an integrated and mineable genomic database for traditional medicines derived from eight international pharmacopoeias

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Science China(Life Sciences) 2022年第4期65卷 809-817页

作者： Baosheng Liao Haoyu Hu Shuiming Xiao Guanru Zhou Wei Sun Yang Chu Xiangxiao Meng Jianhe Wei Han Zhang Jiang Xu Shilin Chen institute of chinese Materia Medica China Academy of Chinese Medical SciencesBeijing100700China institute of Pharmacy Hubei University of Chinese MedicineWuhan430065China institute of Medicinal Plant Development Chinese Academy of Medical SciencesBeijing100193China Pharmacy College Chengdu University of Traditional Chinese MedicineChengdu611137China institute of Traditional chinese medicine Tianjin University of Traditional Chinese MedicineTianjin301617China

Genomic data have demonstrated considerable traction in accelerating contemporary studies in traditional medicine. However,the lack of a uniform format and dispersed storage limits the full potential of herb genomic data. In this study, we developed a Global Pharmacopoeia Genome Database(GPGD). The database contains 34,346 records for 903 herb species from eight global pharmacopoeias(Brazilian, Egyptian, European, Indian, Japanese, Korean, the Pharmacopoeia of the People’s Republic of China, and U.S. Pharmacopoeia’s herbal medicines Compendium). In particular, the GPGD contains 21,872 DNA barcodes from 867 species, 2,203 organelle genomes from 674 species, 55 whole genomes from 49 species, 534 genomic sequencing datasets from 366 species, and 9,682 transcriptome datasets from 350 species. Among the organelle genomes, 534 genomes from 366 species were newly generated in this study. Whole genomes, organelle genomes, genomic fragments, transcriptomes, and DNA barcodes were uniformly formatted and arranged by species. The GPGD is publicly accessible at http://*** and serves as an essential resource for species identification, decomposition of biosynthetic pathways, and molecular-assisted breeding analysis. Thus, the database is an invaluable resource for future studies on herbal medicine safety, drug discovery, and the protection and rational use of herbal resources.

关键词： Global Pharmacopoeia Genome Database herb traditional medicine genomics

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 medicine.In this article,we summarize recent progress in DNA bar-coding for herbal medicine to provide ideas for the further development and application of this tech-nology.Most importantly,the standard DNA barcode has been extended in two ways.First,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 levels.Second,mini-barcodes are attractive because they perform better in cases of degraded DNA from herbal materials.In 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 era.Furthermore,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 barcodes.In 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

Therapeutic effects of the extract of Sancao Formula, a chinese herbal compound, on imiquimod-induced psoriasis via cysteine-rich protein 61

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Journal of Integrative medicine 2022年第4期20卷 376-384页

作者： Wan-jun Guo Yi Wang Yu Deng Lin-yan Cheng Xin Liu Ruo-fan Xi Sheng-jie Zhu Xin-yi Feng Liang Hua Kan Ze Jian-yong Zhu Dong-jie Guo Fu-lun Li Department of Dermatology Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghai 200437China School of medicine Chengdu UniversityChengdu 610106Sichuan ProvinceChina institute of Cancer Biology and Drug Discovery Chengdu UniversityChengdu 610106Sichuan ProvinceChina Clinical Laboratory medicine Center Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghai 200437China

Objective: Psoriasis is a common chronic inflammatory skin disease that is prone to recurrence, and the proinflammatory factor, cysteine-rich protein 61(Cyr61), is important in its pathophysiology. Long-term clinical practice has shown that Sancao Formula(SC), a chinese herbal compound, is effective in the treatment of psoriasis, but the precise mechanism remains unknown. In this study, we investigate the mechanism by which SC extract alleviates imiquimod(IMQ)-induced psoriasis.Methods: The expression of Cyr61 in psoriatic lesions and normal healthy skin was detected using immunohistochemical analysis to investigate the biological role of Cyr61 in models of psoriatic inflammation. A psoriatic mouse model was established by topical application of IMQ, and the effect of topical application of SC extract was evaluated using the psoriasis area and severity index(PASI) score,hematoxylin-eosin staining, and histopathological features of the skin. Next, a HaCaT cell inflammation model was established using interferon-γ(IFN-γ), and the effect of SC extract on the mRNA and protein levels of Cyr61 and intercellular cell adhesion molecule-1(ICAM-1) was confirmed using Western blot and quantitative real-time polymerase chain reaction analyses.Results: Immunohistochemical staining showed that the expression of Cyr61 in psoriatic lesions was higher than that in normal skin samples(78.26% vs 41.18%, P < 0.05), and the number of Cyr61-positive cells in psoriatic lesions was also significantly higher than in normal skin(18.66 ± 2.51 vs4.33 ± 1.52, P < 0.05). Treatment in mice with IMQ-induced psoriasis showed that SC extract could significantly improve the inflammatory phenotype, PASI score(10.875 ± 0.744 vs 3.875 ± 0.582, P < 0.05),and pathological features compared with those in IMQ model group;SC treatment was also associated with decreased levels of Cyr61 and ICAM-1. In the IFN-γ-induced inflammatory cell model, the mRNA and protein levels of Cyr61 and ICAM-1 were upregulated, while the SC extract downregulated the levels of

关键词： Traditional chinese medicine Sancao Formula Psoriasis Plant extracts Cysteine-rich protein 61 Intercellular cell adhesion molecule-1

Improved stability and oral bioavailability of Ganneng dropping pills following transforming lignans of herpeto- spermum caudigerum into nanosuspensions

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chinese Journal of Natural medicines 2018年第1期16卷 70-80页

作者： LI Juan-Juan CHENG Ling SHEN Gang QIU Ling SHEN Cheng-Ying ZHENG Juan XU Rong YUAN Hai-Long Department of Pharmacy Air Force General Hospital of PLA Beijing 100142 China Department of Pharmacy Guangyuan Central Hospital Guanyuan 628000 China Department of Pharmacy Shuangliu District Maternal and Child Health Hospital Chengdu 610075 China Chengdu Institute of Chinese Herbal Medicine Chengdu 610045 China

The present study was designed to improve storage stability and oral bioavailability of Ganneng dropping pills(GNDP) by transforming lignans of Herpetospermum caudigerum(HL) composed of herpetrione(HPE) and herpetin(HPN) into nanosuspension(HL-NS), the main active ingredient of GNDP, HL-NS was prepared by high pressure homogenization and lyophilized to transform into solid nanoparticles(HL nanoparticles), and then the formulated HL nanoparticles were perfused into matrix to obtain NS-GNDP by melting method. For a period of 3 months, the content uniformity, storage stability and pharmacokinetics test in vivo of NS-GNDP were evaluated and compared with regular GNDP at room temperature. The results demonstrated that uniformity of dosage units of NS-GNDP was acceptable according to the criteria of chinese Pharmacopoeia 2015 J. Physical stability of NS-GNDP was investigated systemically using photon correlation spectroscopy(PCS), zeta potential measurement, and scanning electron microscopy(SEM). There was a slight increase in particles and PI of HL-NS re-dispersed from NS-GNDP after storage for 3 months, compared with new formulated NS-GNDP, which indicated a good redispersibility of the NS-GNDP containing HL-NS after storage. Besides, chemical stability of NS-GNDP was studied and the results revealed that HPE and HPN degradation was less when compared with that of GNDP, providing more than 99% of drug residue after storage for 3 months. In the dissolution test in vitro, NS-GNDP remarkably exhibited an increased dissolution velocity compared with GNDP and no distinct dissolution difference existed within 3 months. The pharmacokinetic study showed that HPE and HPN in NS-GNDP exhibited a significant increase in AUC0–t, Cmax and decrease in Tmax when compared with regular GNDP. These results indicated that NS-GNDP possessed superiority with improved storage stability and increased dissolution rate and oral bioavailability.

关键词： Ganneng dropping pills Lignans Herpetospermum caudigerum Nanosuspensions Stability Oral bioavailability

Novel wine in an old bottle:Preventive and therapeutic potentials of andrographolide in atherosclerotic cardiovascular diseases

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Journal of Pharmaceutical Analysis 2023年第6期13卷 563-589页

作者： Tingting Gou Minghao Hu Min Xu Yuchen Chen Rong Chen Tao Zhou Junjing Liu Li Guo Hui Ao Qiang Ye State Key Laboratory of Southwestern chinese medicine Resources Chengdu University of Traditional Chinese MedicineChengdu611137China School of Pharmacy Chengdu University of Traditional Chinese MedicineChengdu611137China Innovative institute of chinese medicine and Pharmacy Chengdu University of Traditional Chinese MedicineChengdu611137China

Atherosclerotic cardiovascular disease(ASCVD)frequently results in sudden death and poses a serious threat to public health worldwide.The drugs approved for the prevention and treatment of ASCVD are usually used in combination but are inefficient owing to their side effects and single therapeutic targets.Therefore,the use of natural products in developing drugs for the prevention and treatment of ASCVD has received great scholarly attention.Andrographolide(AG)is a diterpenoid lactone compound extracted from Andrographis paniculata.In addition to its use in conditions such as sore throat,AG can be used to prevent and treat ASCVD.It is different from drugs that are commonly used in the prevention and treatment of ASCVD and can not only treat obesity,diabetes,hyperlipidaemia and ASCVD but also inhibit the pathological process of atherosclerosis(AS)including lipid accumulation,inflammation,oxidative stress and cellular abnormalities by regulating various targets and pathways.However,the pharmacological mechanisms of AG underlying the prevention and treatment of ASCVD have not been corroborated,which may hinder its clinical development and application.Therefore,this review summarizes the physiological and pathological mechanisms underlying the development of ASCVD and the in vivo and in vitro pharmacological effects of AG on the relative risk factors of AS and ASCVD.The findings support the use of the old pharmacological compound(‘old bottle’)as a novel drug(‘novel wine’)for the prevention and treatment of ASCVD.Additionally,this review summarizes studies on the availability as well as pharmaceutical and pharmacokinetic properties of AG,aiming to provide more information regarding the clinical application and further research and development of AG.

关键词： Andrographolide Atherosclerosis Atherosclerotic cardiovascular disease Pharmacological effects Pharmacokinetics properties Toxicity

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人工智能加速GPCR配体的发现

Engineering 2024年第1期32卷 18-28页

作者： Wei Chen Chi Song Liang Leng Sanyin Zhang Shilin Chen State Key Laboratory of Southwestem chinese medicine Resources Innovative Institute of Chinese Medicine and PharmacyChengdu University of Traditional Chinese MedicineChengdu 611137China institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China

G protein-coupled receptors(GPCRs)are crucial players in various physiological processes,making them attractive candidates for drug discovery.However,traditional approaches to GPCR ligand discovery are time-consuming and resource-intensive.The emergence of artificial intelligence(AI)methods has revo-lutionized the field of GPCR ligand discovery and has provided valuable tools for accelerating the identi-fication and optimization of GPCR ligands.In this study,we provide guidelines for effectively utilizing AI methods for GPCR ligand discovery,including data collation and representation,model selection,and specific applications.First,the online resources that are instrumental in GPCR ligand discovery were sum-marized,including databases and repositories that contain valuable GPCR-related information and ligand data.Next,GPCR and ligand representation schemes that can convert data into computer-readable for-mats were introduced.Subsequently,the key applications of Al methods in the different stages of GPCR drug discovery were discussed,ranging from GPCR function prediction to ligand design and agonist identification.Furthermore,an Al-driven multi-omics integration strategy for GPCR ligand discovery that combines information from various omics disciplines was proposed.Finally,the challenges and future directions of the application of Al in GPCR research were deliberated.In conclusion,continued advance-ments in Al techniques coupled with interdisciplinary collaborations will offer great potential for improv-ing the efficiency of GPCR ligand discovery.

关键词： G protein-coupled receptor Ligand Artificial intelligence Multi-omics Drug discovery

Characterization of Rheum palmatum mitochondrial genome and comparative analysis among Caryophyllales species

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Acupuncture and herbal medicine 2023年第4期3卷 323-332页

作者： Longlong Gao Lijun Hao Wenjie Xu Tianyi Xin Chi Song Yulin Lin Lingping Zhu Jingyuan Song Key Lab of chinese medicine Resources Conservation State Administration of Traditional Chinese Medicine of the People’s Republic of ChinaEngineering Research Center of Chinese Medicine Resource of Ministry of EducationInstitute of Medicinal Plant DevelopmentPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina institute of Herbgenomics State Key Laboratory of Southwest Chinese Medicine ResourcesPharmacy CollegeChengdu University of Traditional Chinese MedicineChengduChina

Objective:This work aimed to report the first complete mitochondrial genome(mitogenome)of Rheum palmatum,summarize the features of Caryophyllales mitogenomes,and to reveal the potential of utilizing the mitogenomes of R.palmatum and other Caryophyllales species for inferring phylogenetic relationships and species identification.Methods:Both Illumina short reads and PacBio HiFi reads were utilized to obtain a complete mitogenome of R.palmatum.A variety of bioinformatics tools were employed to characterize the R.palmatum mitogenome,compare the reported mitogenomes in Caryophyllales and conduct phylogenetic analysis.Results:The mitogenome of R.palmatum was assembled into a single master circle of 302,993 bp,encoding 35 known protein-coding genes,18 transfer RNA genes,and three ribosome RNA genes.A total of 249 long repeats and 49 simple sequence repeats were identified in this mitogenome.The sizes of mitogenomes in Caryophyllales varied from 253 kb to 11.3 Mb.Among them,23 mitogenomes were circular molecules,one was linear,and one consisted of relaxed circles,linear molecules,and supercoiled DNA.Out of the total mitogenomes,11 were single-chromosome structure,whereas the remaining 14 were multi-chromosomal organizations.The phylogenetic analysis is consistent with both the Engler system(1964)and the Angiosperm Phylogeny Group III system.Conclusions:We obtained the first mitogenome of R.palmatum,which consists of a master circle.Mitogenomes in Caryophyllales have variable genome sizes and structures even within the same species.Circular molecules are still the dominant pattern in Caryophyllales.Single-chromosome mitogenomes account for nearly a half of all the mitogenomes in Caryophyllales,in contrast to previous studies.It is feasible to utilize mitochondrial genomes for inferring phylogenetic relationships and conducting species identification.

关键词： Caryophyllales Mitochondrial genome Molecular identification Phylogenetic analysis Rheum palmatum

Whole-genome sequencing in medicinal plants:current progress and prospect

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Science China(Life Sciences) 2024年第2期67卷 258-273页

作者： Yifei Pei Liang Leng Wei Sun Baocai Liu Xue Feng Xiwen Li Shilin Chen institute of chinese Materia Medica China Academy of Chinese Medical SciencesBeijing 100700China institute of Herbgenomics Chengdu University of Traditional Chinese MedicineChengdu 611137China Innovative institute of chinese medicine and Pharmacy Chengdu University of Traditional Chinese MedicineChengdu 611137China institute of Agricultural Bioresource Fujian Academy of Agricultural SciencesFuzhou 350003China

Advancements in genomics have dramatically accelerated the research on medicinal plants,and the development of herbgenomics has promoted the“Project of 1K Medicinal Plant Genome”to decipher their genetic code.However,it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity.Whole genomes of 123 medicinal plants were published until September 2022.These published genome sequences were investigated in this review,covering their classification,research teams,ploidy,medicinal functions,and sequencing strategies.More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes.Diploid species account for a majority of sequenced medicinal plants.The whole genomes of plants in the Poaceae family are the most studied.Almost 40%of the published papers studied species with tonifying,replenishing,and heat-cleaning medicinal effects.Medicinal plants are still in the process of domestication as compared with crops,thereby resulting in unclear genetic backgrounds and the lack of pure lines,thus making their genomes more difficult to complete.In addition,there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome.Herein,a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants.Moreover,whole genome-based biological studies of medicinal plants,including breeding and biosynthesis,were reviewed.We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.

关键词： herbgenomics whole genome high throughput sequencing research strategy model species application

Establishment of one-step approach to detoxification of hypertoxic aconite based on the evaluation of alkaloids contents and quality

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chinese Journal of Natural medicines 2017年第1期15卷 49-61页

作者： ZHANG Ding-Kun HAN Xue TAN Peng LI Rui-Yu NIU Ming ZHANG Cong-En WANG Jia-Bo YANG Ming XIAO Xiao-He Provincial and State Key Laboratory Breeding Base of System Research Development and Utilization of Chinese Herbal Medicine Resources Chengdu University of Traditional Chinese Medicine Chengdu 610075 China China Military institute of chinese medicine 302 Military Hospital Beijing 100039 China Key Laboratory of Modern Preparation of TCM Jiangxi University of Traditional Chinese Medicine Nanchang 330004 China Integrative Medical Center 302 Military Hospital Beijing 100039 China Sichuan Good Doctor Panxi Pharmaceutical Co. Ltd. Xichang 610031 China

Aconite is a valuable drug and also a toxic material, which can be used only after detoxification processing. Although traditional processing methods can achieve detoxification effect as desired, there are some obvious drawbacks, including a significant loss of alkaloids and poor quality consistency. It is thus necessary to develop a new detoxification approach. In the present study, we designed a novel one-step detoxification approach by quickly drying fresh-cut aconite particles. In order to evaluate the technical advantages, the contents of mesaconitine, aconitine, hypaconitine, benzoylmesaconine, benzoylaconine, benzoylhypaconine, neoline, fuziline, songorine, and talatisamine were determined using HPLC and UHPLC/Q-TOF-MS. Multivariate analysis methods, such as Clustering analysis and Principle component analysis, were applied to determine the quality differences between samples. Our results showed that traditional processes could reduce toxicity as desired, but also led to more than 85.2% alkaloids loss. However, our novel one-step method was capable of achieving virtually the same detoxification effect, with only an approximately 30% alkaloids loss. Cluster analysis and Principal component analysis analyses suggested that Shengfupian and the novel products were significantly different from various traditional products. Acute toxicity testing showed that the novel products achieved a good detoxification effect, with its maximum tolerated dose being equivalent to 20 times of adult dosage. And cardiac effect testing also showed that the activity of the novel products was stronger than that of traditional products. Moreover, particles specification greatly improved the quality consistency of the novel products, which was immensely superior to the traditional products. These results would help guide the rational optimization of aconite processing technologies, providing better drugs for clinical treatment.

关键词：乌头属植物解毒方法量的决心心脏的效果优秀一致性