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Tian Q, Jiang J, Yin H, Zhang Y, Li Y, Wu P, Peng C, Wang Z, Zhou J, Zeng H, Zhong D. Investigating the Metabolic Mechanisms of Butaselen, An Ebselen Analog. Curr Drug Metab 2022; 23:928-939. [PMID: 35619304 DOI: 10.2174/1389200223666220520115014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND Butaselen is an ebselen analog that is under clinical trials for treating hepatic and pulmonary fibrosis. Our previous studies showed that butaselen is mainly present in human plasma in the form of M2, a free Se-methylated metabolite. OBJECTIVE This study aimed to investigate the metabolic mechanisms of butaselen. METHODS AND RESULTS Butaselen was incubated with human plasma. Butaselen immediately disappeared, and the butaselen-HSA (human serum albumin) adduct was detected by HPLC-HRMS, showing that butaselen covalently binds to HSA. The butaselen-HSA adduct was precipitated using acetonitrile and then incubated with PBS, Cys, and GSH for 1 hour. The product was M1, a reduced form of butaselen. The results indicated that HSA, Cys, and GSH can reduce the butaselen-HSA covalent bond. The binding site for butaselen could be the cysteine-34 residue of HSA through pronase and trypsin hydrolysis. Incubating butaselen with cysteine, butaselen-Cys, butaselen-2Cys, and M1 were generated, indicating the covalent binding and reduction of butaselen by cysteine. We incubated liver microsomes and cytosol with butaselen, 6.22 and 246 nM M2 were generated, respectively. The results demonstrated that cytosolic enzymes are mainly involved in M2 production. The amount of M2 in the liver cytosol decreased from 246 nM to 2.21 nM when 10 mM m-anisic acid (a specific TPMT enzyme inhibitor) was added, showing that TPMT is responsible for M2 formation. CONCLUSION Butaselen was covalently bound to HSA, and the binding site was the cysteine-34 residue of HSA. The butaselen-HSA adduct was reduced by free thiol compounds to generate M1. M1 was further metabolized to M2 by cytosolic TPMT. This study provides a basis for studying the pharmacokinetics of selenium-containing drugs.
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Affiliation(s)
- Qianqian Tian
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Hanwei Yin
- Shanghai Yuanxi Medicine Corp, Shanghai 201203, China
| | - Yifan Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yilin Li
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Ping Wu
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Zhijie Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Jialan Zhou
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Huihui Zeng
- Shanghai Yuanxi Medicine Corp, Shanghai 201203, China
| | - Dafang Zhong
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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Zhu D, Su H, Ke C, Tang C, Witt M, Quinn RJ, Xu Y, Liu J, Ye Y. Efficient discovery of potential inhibitors for SARS-CoV-2 3C-like protease from herbal extracts using a native MS-based affinity-selection method. J Pharm Biomed Anal 2021; 209:114538. [PMID: 34929567 PMCID: PMC8670146 DOI: 10.1016/j.jpba.2021.114538] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/20/2022]
Abstract
The 3C-like protease (3CLpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential to the virus life cycle and is supposed to be a potential target for the treatment of coronaviral infection. Traditional Chinese medicines (TCMs) have played an impressive role in the treatment of COVID-19 in China. The effectiveness of TCM formulations prompts scientists to take continuous effort on searching for bioactive small molecules from the ancient resources. Herein, we developed a native mass spectrometry-based affinity-selection method for rapid screening of active small molecules from crude herbal extracts applied for COVID-19 therapy. Six common herbs named Lonicera japonica, Scutellaria baicalensis, Forsythia suspensa, Glycyrrhiza uralensis, Cirsium japonicum, and Andrographis paniculata were investigated. After preliminary separation of the crude extracts, the fractions were incubated with 3CLpro. A native MS-based affinity screening assay was then conducted to search for the protein-ligand complexes. A UHPLC-Q/TOF-MS with UNIFI data acquisition and data processing software was applied to identify the hit compounds. Standard compounds were used to verify the outcomes. Among the 16 hits, three flavonoids, baicalein, scutellarein and ganhuangenin, were identified as potential noncovalent inhibitors against 3CLpro with IC50 values of 0.94, 3.02, and 0.84 μM, respectively. Their binding affinities were further characterized by native MS, with Kd values being 1.43, 3.85, and 1.09 μM, respectively. Overall, we established an efficient native MS-based strategy for discovering 3CLpro ligands from crude mixtures, which supplies a potential strategy of small molecule lead discovery from TCMs.
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Affiliation(s)
- Dafu Zhu
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China; State Key Laboratory of Drug Research, and Natural Products Chemistry Department, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haixia Su
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Changqiang Ke
- State Key Laboratory of Drug Research, and Natural Products Chemistry Department, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Chunping Tang
- State Key Laboratory of Drug Research, and Natural Products Chemistry Department, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | | | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD 4111, Australia
| | - Yechun Xu
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310058, China.
| | - Jia Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310058, China.
| | - Yang Ye
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201203, China; State Key Laboratory of Drug Research, and Natural Products Chemistry Department, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Haniff HS, Knerr L, Chen JL, Disney MD, Lightfoot HL. Target-Directed Approaches for Screening Small Molecules against RNA Targets. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:869-894. [PMID: 32419578 PMCID: PMC7442623 DOI: 10.1177/2472555220922802] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
RNA molecules have a variety of cellular functions that can drive disease pathologies. They are without a doubt one of the most intriguing yet controversial small-molecule drug targets. The ability to widely target RNA with small molecules could be revolutionary, once the right tools, assays, and targets are selected, thereby defining which biomolecules are targetable and what constitutes drug-like small molecules. Indeed, approaches developed over the past 5-10 years have changed the face of small molecule-RNA targeting by addressing historic concerns regarding affinity, selectivity, and structural dynamics. Presently, selective RNA-protein complex stabilizing drugs such as branaplam and risdiplam are in clinical trials for the modulation of SMN2 splicing, compounds identified from phenotypic screens with serendipitous outcomes. Fully developing RNA as a druggable target will require a target engagement-driven approach, and evolving chemical collections will be important for the industrial development of this class of target. In this review we discuss target-directed approaches that can be used to identify RNA-binding compounds and the chemical knowledge we have today of small-molecule RNA binders.
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Affiliation(s)
- Hafeez S. Haniff
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Laurent Knerr
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jonathan L. Chen
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Matthew D. Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
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Liu T, Limpikirati P, Vachet RW. Synergistic Structural Information from Covalent Labeling and Hydrogen-Deuterium Exchange Mass Spectrometry for Protein-Ligand Interactions. Anal Chem 2019; 91:15248-15254. [PMID: 31664819 DOI: 10.1021/acs.analchem.9b04257] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hydrogen-deuterium exchange (HDX) mass spectrometry (MS) and covalent labeling (CL) MS are typically considered to be complementary methods for protein structural analysis, because one probes the protein backbone, while the other probes side chains. For protein-ligand interactions, we demonstrate in this work that the two labeling techniques can provide synergistic structural information about protein-ligand binding when reagents like diethylpyrocarbonate (DEPC) are used for CL because of the differences in the reaction rates of DEPC and HDX. Using three model protein-ligand systems, we show that the slower time scale for DEPC labeling makes it only sensitive to changes in solvent accessibility and insensitive to changes in protein structural fluctuations, whereas HDX is sensitive to changes in both solvent accessibility and structural fluctuations. When used together, the two methods more clearly reveal binding sites and ligand-induced changes to structural fluctuations that are distant from the binding site, which is more comprehensive information than either technique alone can provide. We predict that these two methods will find widespread usage together for more deeply understanding protein-ligand interactions.
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Affiliation(s)
- Tianying Liu
- Department of Chemistry , University of Massachusetts , Amherst , Massachusetts 01003 , United States
| | - Patanachai Limpikirati
- Department of Chemistry , University of Massachusetts , Amherst , Massachusetts 01003 , United States
| | - Richard W Vachet
- Department of Chemistry , University of Massachusetts , Amherst , Massachusetts 01003 , United States
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Orr A, Stotesbury T, Wilson P, Stock NL. The use of high-resolution mass spectrometry (HRMS) for the analysis of DNA and other macromolecules: A how-to guide for forensic chemistry. Forensic Chem 2019. [DOI: 10.1016/j.forc.2019.100169] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Kaltashov IA. Mass spectrometry-based methods to study macromolecular higher order structure and interactions. Methods 2018; 144:1-2. [DOI: 10.1016/j.ymeth.2018.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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