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Chen H, Sahu SK, Wang S, Liu J, Yang J, Cheng L, Chiu TY, Liu H. Chromosome-level Alstonia scholaris genome unveils evolutionary insights into biosynthesis of monoterpenoid indole alkaloids. iScience 2024; 27:109599. [PMID: 38646178 PMCID: PMC11033161 DOI: 10.1016/j.isci.2024.109599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Alstonia scholaris of the Apocynaceae family is a medicinal plant with a rich source of bioactive monoterpenoid indole alkaloids (MIAs), which possess anti-cancer activity like vinca alkaloids. To gain genomic insights into MIA biosynthesis, we assembled a high-quality chromosome-level genome for A. scholaris using nanopore and Hi-C data. The 444.95 Mb genome contained 35,488 protein-coding genes. A total of 20 chromosomes were assembled with a scaffold N50 of 21.75 Mb. The genome contained a cluster of strictosidine synthases and tryptophan decarboxylases with synteny to other species and a saccharide-terpene cluster involved in the monoterpenoid biosynthesis pathway of the MIA upstream pathway. The multi-omics data of A. scholaris provide a valuable resource for understanding the evolutionary origins of MIAs and for discovering biosynthetic pathways and synthetic biology efforts for producing pharmaceutically useful alkaloids.
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Affiliation(s)
- Haixia Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Shujie Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Jia Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jinlong Yang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Le Cheng
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Tsan-Yu Chiu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
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Chen L, Cui Y, Dean B, Liang X. Matrix effect in bioanalytical assay development using supercritical fluid chromatography-mass spectrometry. Biomed Chromatogr 2024; 38:e5759. [PMID: 37845809 DOI: 10.1002/bmc.5759] [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: 04/11/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/18/2023]
Abstract
Matrix effect (ME) is commonly caused by coelution of compounds with target analytes, resulting in either suppression or enhancement of analyte ionization. Thus, to achieve the desired accuracy, precision, and sensitivity, ME needs to be evaluated and controlled during bioanalytical method development. As the application of supercritical fluid chromatography-mass spectrometry (SFC-MS) for analysis of biological samples has increased, ME using SFC-MS has also been investigated with a focus on the difference in ME in SFC-MS compared to other chromatographic techniques used for achiral separation in biological samples. Here, we provide a summary of the status of ME evaluation and mitigation in SFC-MS methods. This review presents an overview of the phenomenon of ME and methods for evaluating ME in bioanalysis. Next, the factors that can impact ME in SFC-MS-based bioanalytical methods are discussed in detail with an emphasis on SFC. A literature review of the evaluation of ME in targeted bioanalytical methods using SFC-MS is included at the end. Robust instrumentation, effective sample preparation, and superb separation selectivity are the foundations of reliable analytical methods as well as the ability to mitigate detrimental ME in SFC-MS methods.
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Affiliation(s)
- Liuxi Chen
- Drug Metabolism and Pharmacokinetics, Genentech Inc, South San Francisco, California, USA
| | - Yuxiang Cui
- Drug Metabolism and Pharmacokinetics, Genentech Inc, South San Francisco, California, USA
| | - Brian Dean
- Drug Metabolism and Pharmacokinetics, Genentech Inc, South San Francisco, California, USA
| | - Xiaorong Liang
- Drug Metabolism and Pharmacokinetics, Genentech Inc, South San Francisco, California, USA
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Chen L, Dean B, Liang X. A technical overview of supercritical fluid chromatography-mass spectrometry (SFC-MS) and its recent applications in pharmaceutical research and development. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:69-75. [PMID: 34916026 DOI: 10.1016/j.ddtec.2021.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 09/28/2021] [Accepted: 10/05/2021] [Indexed: 06/14/2023]
Abstract
In this paper, we review the growing development and applications of supercritical fluid chromatography-mass spectrometry (SFC-MS) for the analysis of small molecular analytes and biomarkers in drug discovery. As an alternative chromatographic technique, SFC instrumentation and methodology have dramatically advanced over the last decade. Mass spectrometry (MS) provides the powerful detection capability as it couples with SFC. A growing number of SFC-MS/MS applications were reported over the last decade and the application areas of SFC-MS/MS is rapidly expanding. The first part of this review is devoted to the different aspects of SFC-MS development and recent technological advancements. In the second part of this review, we highlight the recent application areas in pharmaceutical research and development.
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Affiliation(s)
- Liuxi Chen
- Drug Metabolism & Pharmacokinetics, 1 DNA way, Genentech Inc., South San Francisco, CA, USA.
| | - Brian Dean
- Drug Metabolism & Pharmacokinetics, 1 DNA way, Genentech Inc., South San Francisco, CA, USA
| | - Xiaorong Liang
- Drug Metabolism & Pharmacokinetics, 1 DNA way, Genentech Inc., South San Francisco, CA, USA
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Maldonado MM, Rosado-González G, Bloom J, Duconge J, Ruiz-Calderón JF, Hernández-O’Farrill E, Vlaar C, Rodríguez-Orengo JF, Dharmawardhane S. Pharmacokinetics of the Rac/Cdc42 Inhibitor MBQ-167 in Mice by Supercritical Fluid Chromatography-Tandem Mass Spectrometry. ACS OMEGA 2019; 4:17981-17989. [PMID: 31720502 PMCID: PMC6843717 DOI: 10.1021/acsomega.9b01641] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/24/2019] [Indexed: 06/02/2023]
Abstract
The Rho GTPases Rac and Cdc42 are potential targets against metastatic diseases. We characterized the small molecule MBQ-167 as an effective dual Rac/Cdc42 inhibitor that reduces HER2-type tumor growth and metastasis in mice by ∼90%. This study reports the pharmacokinetics and tissue distribution of MBQ-167 following intraperitoneal and oral single-dose administrations. We first developed and validated a bioanalytical method for the quantitation of MBQ-167 in mouse plasma and tissues by supercritical fluid chromatography coupled with electrospray ionization tandem mass spectrometry. MBQ-167 was rapidly distributed into the kidneys after intraperitoneal dosing, whereas oral administration resulted in higher distribution to lungs. The elimination half-lives were 2.17 and 2.6 h for the intraperitoneal and oral dosing, respectively. The relative bioavailability of MBQ-167 after oral administration was 35%. This investigation presents the first analysis of the pharmacokinetics of MBQ-167 and supports further preclinical evaluation of this drug as a potential anticancer therapeutic.
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Affiliation(s)
- María
del Mar Maldonado
- Department
of Biochemistry and Department of Pharmaceutical Sciences, School
of Pharmacy, University of Puerto Rico Medical
Sciences Campus, PO Box 365067, San Juan, Puerto Rico 00936-5067, United States
| | - Gabriela Rosado-González
- Department
of Biochemistry and Department of Pharmaceutical Sciences, School
of Pharmacy, University of Puerto Rico Medical
Sciences Campus, PO Box 365067, San Juan, Puerto Rico 00936-5067, United States
- Department
of Biology & Chemistry, University of
Puerto Rico Río Piedras, PO Box 23346, San Juan, Puerto Rico 00931-3346, United States
| | - Joseph Bloom
- Department
of Biochemistry and Department of Pharmaceutical Sciences, School
of Pharmacy, University of Puerto Rico Medical
Sciences Campus, PO Box 365067, San Juan, Puerto Rico 00936-5067, United States
| | - Jorge Duconge
- Department
of Biochemistry and Department of Pharmaceutical Sciences, School
of Pharmacy, University of Puerto Rico Medical
Sciences Campus, PO Box 365067, San Juan, Puerto Rico 00936-5067, United States
| | - Jean F. Ruiz-Calderón
- Department
of Biochemistry and Department of Pharmaceutical Sciences, School
of Pharmacy, University of Puerto Rico Medical
Sciences Campus, PO Box 365067, San Juan, Puerto Rico 00936-5067, United States
| | - Eliud Hernández-O’Farrill
- Department
of Biochemistry and Department of Pharmaceutical Sciences, School
of Pharmacy, University of Puerto Rico Medical
Sciences Campus, PO Box 365067, San Juan, Puerto Rico 00936-5067, United States
| | - Cornelis Vlaar
- Department
of Biochemistry and Department of Pharmaceutical Sciences, School
of Pharmacy, University of Puerto Rico Medical
Sciences Campus, PO Box 365067, San Juan, Puerto Rico 00936-5067, United States
| | - José F. Rodríguez-Orengo
- Department
of Biochemistry and Department of Pharmaceutical Sciences, School
of Pharmacy, University of Puerto Rico Medical
Sciences Campus, PO Box 365067, San Juan, Puerto Rico 00936-5067, United States
- FDI
Clinical Research, 998
Ave. Luis Muñoz Rivera, San Juan, Puerto Rico 00927, United States
| | - Suranganie Dharmawardhane
- Department
of Biochemistry and Department of Pharmaceutical Sciences, School
of Pharmacy, University of Puerto Rico Medical
Sciences Campus, PO Box 365067, San Juan, Puerto Rico 00936-5067, United States
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Li Y, Zhang X, Bai X, Li X, Jiang Q, Zhang T. A sensitive, high-throughput, and eco-friendly analysis of daidzein and its valine carbamate prodrug in rat plasma by supercritical fluid chromatography with tandem mass spectrometry. J Sep Sci 2018; 41:3250-3257. [DOI: 10.1002/jssc.201800430] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/28/2018] [Accepted: 07/03/2018] [Indexed: 12/23/2022]
Affiliation(s)
- Yingchao Li
- Department of Pharmaceutical Analysis, School of Pharmacy; Shenyang Pharmaceutical University; Shenyang P. R. China
| | - Xingxing Zhang
- Department of Pharmaceutical Analysis, School of Pharmacy; Shenyang Pharmaceutical University; Shenyang P. R. China
| | - Xiaochen Bai
- Department of Pharmaceutical Analysis, School of Pharmacy; Shenyang Pharmaceutical University; Shenyang P. R. China
| | - Xiaoting Li
- Department of Pharmaceutical Analysis, School of Pharmacy; Shenyang Pharmaceutical University; Shenyang P. R. China
| | - Qikun Jiang
- Wuya College of Innovation; Shenyang Pharmaceutical University; Shenyang P. R. China
| | - Tianhong Zhang
- Department of Pharmaceutical Analysis, School of Pharmacy; Shenyang Pharmaceutical University; Shenyang P. R. China
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Yang Y, Gao H, Hou S, Su R, Liu H, Sun J. A sensitive, high-throughput, and ecofriendly method for the determination of lumefantrine, artemether, and its active metabolite dihydroartemisinin by supercritical fluid chromatography and tandem mass spectrometry. J Sep Sci 2018; 41:2688-2696. [DOI: 10.1002/jssc.201800025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 03/21/2018] [Accepted: 03/29/2018] [Indexed: 01/31/2023]
Affiliation(s)
- Yinxian Yang
- Wuya College of Innovation; Shenyang Pharmaceutical University; Shenyang P. R. China
| | - Hailing Gao
- College of Pharmacy; Shenyang Pharmaceutical University; Shenyang P. R. China
| | - Shanshan Hou
- College of Pharmacy; Shenyang Pharmaceutical University; Shenyang P. R. China
| | - Ruijuan Su
- College of Pharmacy; Shenyang Pharmaceutical University; Shenyang P. R. China
| | - Hongzhuo Liu
- College of Pharmacy; Shenyang Pharmaceutical University; Shenyang P. R. China
| | - Jin Sun
- Wuya College of Innovation; Shenyang Pharmaceutical University; Shenyang P. R. China
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Supercritical fluid chromatography: a promising alternative to current bioanalytical techniques. Bioanalysis 2017; 10:107-124. [PMID: 29236519 DOI: 10.4155/bio-2017-0211] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
During the last years, chemistry was involved in the worldwide effort toward environmental problems leading to the birth of green chemistry. In this context, green analytical tools were developed as modern Supercritical Fluid Chromatography in the field of separative techniques. This chromatographic technique knew resurgence a few years ago, thanks to its high efficiency, fastness and robustness of new generation equipment. These advantages and its easy hyphenation to MS fulfill the requirements of bioanalysis regarding separation capacity and high throughput. In the present paper, the technical aspects focused on bioanalysis specifications will be detailed followed by a critical review of bioanalytical supercritical fluid chromatography methods published in the literature.
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Su C, Yang H, Meng X, Fawcett JP, Cao J, Yang Y, Gu J. Determination of rabeprazole enantiomers in dog plasma by supercritical fluid chromatography tandem mass spectrometry and its application to a pharmacokinetic study. J Sep Sci 2017; 40:1010-1016. [DOI: 10.1002/jssc.201601232] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 11/27/2016] [Accepted: 12/01/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Chong Su
- College of Life Science Jilin University Changchun P. R. China
| | - Hong Yang
- College of Life Science Jilin University Changchun P. R. China
| | - Xiangjun Meng
- College of Life Science Jilin University Changchun P. R. China
| | | | - Jianming Cao
- Department of Technology Waters Corporation Shanghai China
| | - Yan Yang
- College of Life Science Jilin University Changchun P. R. China
| | - Jingkai Gu
- College of Life Science Jilin University Changchun P. R. China
- Clinical Pharmacology Center Research Institute of Translational Medicine The First Hospital of Jilin University Changchun P. R. China
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Guo B, Pei Y, Li X, Zhu M, Zhao L, Zhang T. Supercritical fluid chromatography with tandem mass spectrometry combined with postcolumn compensation and one-step acetone protein precipitation to evaluate the bioavailability of probucol solid dispersion tablet. J Sep Sci 2016; 39:3677-3682. [DOI: 10.1002/jssc.201600595] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 07/21/2016] [Accepted: 07/27/2016] [Indexed: 11/05/2022]
Affiliation(s)
- Bei Guo
- School of Pharmacy; Shenyang Pharmaceutical University; Shenyang PR China
| | - Yuanyuan Pei
- School of Pharmacy; Shenyang Pharmaceutical University; Shenyang PR China
| | - Xiaoting Li
- School of Pharmacy; Shenyang Pharmaceutical University; Shenyang PR China
| | - Meng Zhu
- School of Pharmacy; Shenyang Pharmaceutical University; Shenyang PR China
| | - Longshan Zhao
- School of Pharmacy; Shenyang Pharmaceutical University; Shenyang PR China
| | - Tianhong Zhang
- School of Pharmacy; Shenyang Pharmaceutical University; Shenyang PR China
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