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Yin J, Chen Z, You N, Li F, Zhang H, Xue J, Ma H, Zhao Q, Yu L, Zeng S, Zhu F. VARIDT 3.0: the phenotypic and regulatory variability of drug transporter. Nucleic Acids Res 2024; 52:D1490-D1502. [PMID: 37819041 PMCID: PMC10767864 DOI: 10.1093/nar/gkad818] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/01/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
The phenotypic and regulatory variability of drug transporter (DT) are vital for the understanding of drug responses, drug-drug interactions, multidrug resistances, and so on. The ADME property of a drug is collectively determined by multiple types of variability, such as: microbiota influence (MBI), transcriptional regulation (TSR), epigenetics regulation (EGR), exogenous modulation (EGM) and post-translational modification (PTM). However, no database has yet been available to comprehensively describe these valuable variabilities of DTs. In this study, a major update of VARIDT was therefore conducted, which gave 2072 MBIs, 10 610 TSRs, 46 748 EGRs, 12 209 EGMs and 10 255 PTMs. These variability data were closely related to the transportation of 585 approved and 301 clinical trial drugs for treating 572 diseases. Moreover, the majority of the DTs in this database were found with multiple variabilities, which allowed a collective consideration in determining the ADME properties of a drug. All in all, VARIDT 3.0 is expected to be a popular data repository that could become an essential complement to existing pharmaceutical databases, and is freely accessible without any login requirement at: https://idrblab.org/varidt/.
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Affiliation(s)
- Jiayi Yin
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhen Chen
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Nanxin You
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
- The Children's Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310052, China
| | - Hanyu Zhang
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Jia Xue
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Hui Ma
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Qingwei Zhao
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Lushan Yu
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, National Key Laboratory of Advanced Drug Delivery and Release Systems, Zhejiang University, Hangzhou 310058, China
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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Song J, Ren T, Duan Y, Guo H, Wang G, Gan Y, Bai M, Dong X, Zhao Z, An J. Near-infrared fluorescence imaging of hepatocellular carcinoma cells regulated by β-catenin signaling pathway. Front Oncol 2023; 13:1140256. [PMID: 37064109 PMCID: PMC10090467 DOI: 10.3389/fonc.2023.1140256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
BackgroundNear-infrared fluorescence (NIRF) imaging has recently emerged as a promising tool for noninvasive cancer imaging. However, lack of tumor sensitivity and specificity restricts the application of NIRF dyes in surgical navigation.MethodsHerein, we investigated the imaging features of NIRF dye MHI-148 and indocyanine green (ICG) in live cell imaging and xenograft nude mice models. TCGA dataset analysis and immunohistochemistry were conducted to investigate the expression of OATPs or ABCGs in hepatocellular carcinoma (HCC) tissues. OATPs or ABCGs were knocked down and overexpressed in HCC cells using transient transfection by siRNA and plasmids or stable transfection by lentivirus. Further, qRT-PCR ,Western blotting and the use of agonists or inhibitors targeting β-catenin signaling pathway were applied to explore its important role in regulation of OATP2B1 and ABCG2 expression.ResultsHere we demonstrated that NIRF dye MHI-148 was biocompatible as indocyanine green (ICG) but with higher imaging intensity and preferential uptake and retention in hepatocellular carcinoma (HCC) cells and tissues. Moreover, our data indicated that membrane transporters OATP2B1 and ABCG2, which regulated by β-catenin signaling pathway, mediated tumor-specific accumulation and retention of MHI-148 in HCC cells. In addition, the treatment with β-catenin inhibitor significantly enhanced the accumulation of MHI-148 in HCC tissues and improved the efficacy of tumor imaging with MHI-148 in vivo.ConclusionsOur study uncovers a mechanism that links the distribution and expression of the membrane transporters OATP2B1 and ABCG2 to the tumor-specific accumulation of MHI-148, and provides evidence supporting a regulating role of the β-catenin signaling pathway in OATP2B1 and ABCG2- induced retention of MHI-148 inHCC tissues, and strategy targeting key components of MHI-148 transport machinery may be a potential approach to improve HCC imaging.
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Affiliation(s)
- Jian Song
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Tingting Ren
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi’an, China
- *Correspondence: Jiaze An, ; Tingting Ren, ; Zheng Zhao,
| | - Yanheng Duan
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Haitao Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi’an, China
| | - Gang Wang
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi’an, China
| | - Yu Gan
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Mengcai Bai
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, Xi’an, China
| | - Xiaotian Dong
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
| | - Zheng Zhao
- Third Department of Medical Oncology, Shaanxi Provincial Cancer Hospital, Xi’an, China
- *Correspondence: Jiaze An, ; Tingting Ren, ; Zheng Zhao,
| | - Jiaze An
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi’an, China
- *Correspondence: Jiaze An, ; Tingting Ren, ; Zheng Zhao,
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Li F, Yin J, Lu M, Mou M, Li Z, Zeng Z, Tan Y, Wang S, Chu X, Dai H, Hou T, Zeng S, Chen Y, Zhu F. DrugMAP: molecular atlas and pharma-information of all drugs. Nucleic Acids Res 2022; 51:D1288-D1299. [PMID: 36243961 PMCID: PMC9825453 DOI: 10.1093/nar/gkac813] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/30/2022] [Accepted: 10/12/2022] [Indexed: 02/06/2023] Open
Abstract
The efficacy and safety of drugs are widely known to be determined by their interactions with multiple molecules of pharmacological importance, and it is therefore essential to systematically depict the molecular atlas and pharma-information of studied drugs. However, our understanding of such information is neither comprehensive nor precise, which necessitates the construction of a new database providing a network containing a large number of drugs and their interacting molecules. Here, a new database describing the molecular atlas and pharma-information of drugs (DrugMAP) was therefore constructed. It provides a comprehensive list of interacting molecules for >30 000 drugs/drug candidates, gives the differential expression patterns for >5000 interacting molecules among different disease sites, ADME (absorption, distribution, metabolism and excretion)-relevant organs and physiological tissues, and weaves a comprehensive and precise network containing >200 000 interactions among drugs and molecules. With the great efforts made to clarify the complex mechanism underlying drug pharmacokinetics and pharmacodynamics and rapidly emerging interests in artificial intelligence (AI)-based network analyses, DrugMAP is expected to become an indispensable supplement to existing databases to facilitate drug discovery. It is now fully and freely accessible at: https://idrblab.org/drugmap/.
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Affiliation(s)
| | | | - Mingkun Lu
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba–Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Zhenyu Zeng
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba–Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
| | - Ying Tan
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Shanshan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Xinyi Chu
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Haibin Dai
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Su Zeng
- Correspondence may also be addressed to Su Zeng.
| | - Yuzong Chen
- Correspondence may also be addressed to Yuzong Chen.
| | - Feng Zhu
- To whom correspondence should be addressed.
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Nian YL, You CG. Susceptibility genes of hyperuricemia and gout. Hereditas 2022; 159:30. [PMID: 35922835 PMCID: PMC9351246 DOI: 10.1186/s41065-022-00243-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 07/03/2022] [Indexed: 11/10/2022] Open
Abstract
Gout is a chronic metabolic disease that seriously affects human health. It is also a major challenge facing the world, which has brought a heavy burden to patients and society. Hyperuricemia (HUA) is the most important risk factor for gout. In recent years, with the improvement of living standards and the change of dietary habits, the incidence of gout in the world has increased dramatically, and gradually tends to be younger. An increasing number of studies have shown that gene mutations may play an important role in the development of HUA and gout. Therefore, we reviewed the existing literature and summarized the susceptibility genes and research status of HUA and gout, in order to provide reference for the early diagnosis, individualized treatment and the development of new targeted drugs of HUA and gout.
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Affiliation(s)
- Yue-Li Nian
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou, 730030, China
| | - Chong-Ge You
- Laboratory Medicine Center, Lanzhou University Second Hospital, Lanzhou, 730030, China.
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Fu T, Li F, Zhang Y, Yin J, Qiu W, Li X, Liu X, Xin W, Wang C, Yu L, Gao J, Zheng Q, Zeng S, Zhu F. VARIDT 2.0: structural variability of drug transporter. Nucleic Acids Res 2021; 50:D1417-D1431. [PMID: 34747471 PMCID: PMC8728241 DOI: 10.1093/nar/gkab1013] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 10/08/2021] [Accepted: 11/04/2021] [Indexed: 12/20/2022] Open
Abstract
The structural variability data of drug transporter (DT) are key for research on precision medicine and rational drug use. However, these valuable data are not sufficiently covered by the available databases. In this study, a major update of VARIDT (a database previously constructed to provide DTs' variability data) was thus described. First, the experimentally resolved structures of all DTs reported in the original VARIDT were discovered from PubMed and Protein Data Bank. Second, the structural variability data of each DT were collected by literature review, which included: (a) mutation-induced spatial variations in folded state, (b) difference among DT structures of human and model organisms, (c) outward/inward-facing DT conformations and (d) xenobiotics-driven alterations in the 3D complexes. Third, for those DTs without experimentally resolved structural variabilities, homology modeling was further applied as well-established protocol to enrich such valuable data. As a result, 145 mutation-induced spatial variations of 42 DTs, 1622 inter-species structures originating from 292 DTs, 118 outward/inward-facing conformations belonging to 59 DTs, and 822 xenobiotics-regulated structures in complex with 57 DTs were updated to VARIDT (https://idrblab.org/varidt/ and http://varidt.idrblab.net/). All in all, the newly collected structural variabilities will be indispensable for explaining drug sensitivity/selectivity, bridging preclinical research with clinical trial, revealing the mechanism underlying drug-drug interaction, and so on.
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Affiliation(s)
- Tingting Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Fengcheng Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yang Zhang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Jiayi Yin
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenqi Qiu
- Department of Surgery, HKU-SZH & Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xuedong Li
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Xingang Liu
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Wenwen Xin
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Chengzhao Wang
- Department of Pharmacology, Hebei Medical University, Shijiazhuang 050017, China
| | - Lushan Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, China
| | - Su Zeng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 330110, China
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