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Unmodified methodologies in target discovery for small molecule drugs:A rising star

Chinese Chemical Letters 2022年第12期33卷 4980-4988页

作者： Jiayue Tang Meng Ou Qiuling Zheng Ya Ding Key Laboratory of Drug Quality Control and Pharmacovigilance Ministry of EducationChina Pharmaceutical UniversityNanjing 210009China State Key Laboratory of Natural Medicines Department of Pharmaceutical AnalysisCollege of PharmacyChina Pharmaceutical UniversityNanjing 210009China

target discovery,involving target identification and validation,is the prerequisite for drug discovery and *** methodologies and technologies for the precise discovery and confirmation of drug targets are powerful tools in understanding the disease,looking for a drug and elucidating the mechanism of drug *** the common target identification and confirmation methods,the modified method is time-consuming and laborious,which may reduce or change the activity of natural *** unmodified methods developed in recent years without chemical modification have gradually become an important means of studying drug targets.A wide range of unmodified approaches have been reported,introducing and analyzing the recent emerging methodologies and *** review highlights the advantages and limitations of these methods for the application of drug target discovery and presents an overview of their contributions to the target discovery of small molecule *** application and future development trends of methodologies in target discovery are also prospected to provide a reference for drug target research.

关键词： target discovery target identification Small molecule drug Methodologies Unmodified

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The proteomic study and the target discovery of W026B, a new compound with brain protective effect

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Journal of Chinese Pharmaceutical Sciences 2019年第6期28卷 381-392页

作者： Siyu Zhao Xiaoyan Liu Yuanjun Zhu Ye Liu Yinye Wang Department of Molecular and Cellular Pharmacology School of Pharmaceutical SciencesPeking University Health ScienceCenterBeijing100191China Beijing Honghui New Medical Technology Co.Ltd. Beijing Daxing Biological Medicine Industry BaseBeijing102600China

W026B is a new compound that has a protective effect on cerebral ischemia reperfusion(I-R)injury in mice,while its specific mechanism is still *** this study,proteomics was used to observe the effect of W026B on protein expression in brain I-R tissue,and to reveal its potential target.A total of 42 significantly altered proteins were identified in both brain I-R model and W026B treatment from 4852 proteins detected by proteomics,and most of these proteins were related to immunity and inflammation,metabolism,neuroprotection as well as cell proliferation and cell *** blotting analysis showed that three out of five selected proteins showed consistent alteration with the *** of G protein signaling 17(RGS17)was selected for further study,and its knockdown by siRNA RGS17 aggravated brain injury and abolished the protective effect of W026B.W026B could bind with RGS17(KD:6.04×10–6 mol/L).The knockdown of RGS17 aggravated Neuro-2 a cell damage induced by group I metabotropic glutamate receptors(mGluRs)agonist,and abolished the protective effect of *** conclusion,W026B protected brain against I-R injury by affecting diverse ***17 might be one of its targets and a potential therapeutic target of brain I-R *** upstream receptor of G protein,which was regulated by RGS17 and affected by W026B,might be group I m *** study provided useful evidence for the further R&D and the potential clinical application of W026B.

关键词： Brain ischemia Reperfusion injury Proteomics target discovery W026B

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Artificial Intelligence in Pharmaceutical Sciences

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Engineering 2023年第8期27卷 37-69页

作者： Mingkun Lu Jiayi Yin Qi Zhu Gaole Lin Minjie Mou Fuyao Liu Ziqi Pan Nanxin You Xichen Lian Fengcheng Li Hongning Zhang Lingyan Zheng Wei Zhang Hanyu Zhang Zihao Shen Zhen Gu Honglin Li Feng Zhu College of Pharmaceutical Sciences&The Second Affiliated Hospital School of MedicineZhejiang UniversityHangzhou 310058China Shanghai Key Laboratory of New Drug Design East China University of Science and TechnologyShanghai 200237China Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University Alibaba-Zhejiang University Joint Research Center of Future Digital HealthcareHangzhou 330110China Innovation Center for AI and Drug discovery East China Normal UniversityShanghai 200062China Lingang Laboratory Shanghai 200031China

Drug discovery and development affects various aspects of human health and dramatically impacts the pharmaceutical ***,investments in a new drug often go unrewarded due to the long and complex process of drug research and development(R&D).With the advancement of experimental technology and computer hardware,artificial intelligence(AI)has recently emerged as a leading tool in analyzing abundant and high-dimensional *** growth in the size of biomedical data provides advantages in applying AI in all stages of drug R&*** by big data in biomedicine,AI has led to a revolution in drug R&D,due to its ability to discover new drugs more efficiently and at lower *** review begins with a brief overview of common AI models in the field of drug discovery;then,it summarizes and discusses in depth their specific applications in various stages of drug R&D,such as target discovery,drug discovery and design,preclinical research,automated drug synthesis,and influences in the pharmaceutical ***,the major limitations of AI in drug R&D are fully discussed and possible solutions are proposed.

关键词： Artificial intelligence Machine learning Deep learning target identification target discovery Drug design Drug discovery

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“Omics” in pharmaceutical research: overview, applications, challenges, and future perspectives

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Chinese Journal of Natural Medicines 2015年第1期13卷 3-21页

作者： YAN Shi-Kai LIU Run-Hui JIN Hui-Zi LIU Xin-Ru YE Ji SHAN Lei ZHANG Wei-Dong School of Pharmacy Shanghai Jiao Tong University School of Pharmacy Second Military Medical University Shanghai Institute of Pharmaceutical Industry

In the post-genomic era, biological studies are characterized by the rapid development and wide application of a series of "omics" technologies, including genomics, proteomics, metabolomics, transcriptomics, lipidomics, cytomics, metallomics, ionomics, interactomics, and phenomics. These "omics" are often based on global analyses of biological samples using high through-put analytical approaches and bioinformatics and may provide new insights into biological phenomena. In this paper, the development and advances in these omics made in the past decades are reviewed, especially genomics, transcriptomics, proteomics and metabolomics; the applications of omics technologies in pharmaceutical research are then summarized in the fields of drug target discovery, toxicity evaluation, personalized medicine, and traditional Chinese medicine; and finally, the limitations of omics are discussed, along with the future challenges associated with the multi-omics data processing, dynamics omics analysis, and analytical approaches, as well as amenable solutions and future prospects.

关键词： Omics Genomics Transcriptomics Proteomics Metabolomics target discovery Toxicity Assessment PersonalizedMedicine Traditional Chinese Medicine

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Integrated chromatin and transcriptomic profiling of patient-derived colon cancer organoids identifies personalized drug targets to overcome oxaliplatin resistance

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Genes & Diseases 2021年第2期8卷 203-214页

作者： Kuei-Ling Tung Kai-Yuan Chen Marcos Negrete Tianyi Chen Alexias Safi Abed Alhalim Aljamal Lingyun Song Gregory E.Crawford Shengli Ding David S.Hsu Xiling Shen Department of Biological and Environmental Engineering Cornell UniversityIthacaNY14853USA Department of Biomedical Engineering Pratt School of EngineeringDuke UniversityDurhamNC27708USA Center for Genomics and Computational Biology Duke UniversityDurhamNC27708USA Department of Medical Oncology Duke University Medical CenterDurhamNC27708USA Department of Pediatrics Division of Medical GeneticsDuke UniversityDurhamNC27708USA Duke Cancer Institute Duke UniversityDurhamNC27708USA

Colorectal cancer is a leading cause of cancer *** colorectal cancer patients eventually develop chemoresistance to the current standard-of-care ***,we used patient-derived colorectal cancer organoids to demonstrate that resistant tumor cells undergo significant chromatin changes in response to oxaliplatin *** transcriptomic and chromatin accessibility analyses using ATAC-Seq and RNA-Seq identified a group of genes associated with significantly increased chromatin accessibility and upregulated gene ***/Cas9 silencing of fibroblast growth factor receptor 1(FGFR1)and oxytocin receptor(OXTR)helped overcome oxaliplatin ***,treatment with oxaliplatin in combination with an FGFR1 inhibitor(PD166866)or an antagonist of OXTR(L-368,899)suppressed chemoresistant ***,oxaliplatin treatment did not activate either FGFR1 or OXTR expression in another resistant organoid,suggesting that chromatin accessibility changes are *** use of patient-derived cancer organoids in combination with transcriptomic and chromatin profiling may lead to precision treatments to overcome chemoresistance in colorectal cancer.

关键词： Chromatin accessibility Drug screening Patient-derived organoids Personalized medicine target discovery

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Statistical considerations for high throughput screening data

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Frontiers in Biology 2010年第4期5卷 354-360页

作者： Xian-Jin XIE Division of Biostatistics Department of Clinical Sciences&Simmons Comprehensive Cancer CenterThe University of Texas Southwestern Medical CenterDallasTexas 75390USA

High throughput screening(HTS)is a widely used effective approach in genome-wide association and large scale protein expression studies,drug discovery,and biomedical imaging *** to accurately identify candidate‘targets’or biologically meaningful features with a high degree of confidence has led to extensive statistical research in an effort to minimize both false-positive and false-negative rates.A large body of literature on this topic with in-depth statistical contents is *** examine currently available statistical methods on HTS and aim to summarize some selected methods into a concise,easy-tofollow introduction for experimental biologists.

关键词： high throughput screen false-positive rate false-negative rate target discovery predictive modeling

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