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Kamiyama H, Miyano M, Ito D, Kimura T, Hagiwara K, Kogai H, Kaburagi Y, Kotake Y, Takase Y. Identification of a novel ALDH1A3-selective inhibitor by a chemical probe with unrelated bioactivity: An approach to affinity-based drug target discovery. Chem Biol Drug Des 2023; 101:727-739. [PMID: 36334047 DOI: 10.1111/cbdd.14176] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/18/2022] [Accepted: 11/02/2022] [Indexed: 11/08/2022]
Abstract
The identification of biologically active target compounds and their binding proteins is important in mechanism-of-action studies for drug development. Additionally, the newly discovered binding proteins provide unforeseen ideas for novel drug discovery and for subsequent structural transformation to improve target specificity. Based on the lead and final candidate compounds related to the type 5 phosphodiesterase (PDE5) inhibitor E4021, we designed chemical probes and identified their target proteins by the affinity chromatography approach. Aldehyde dehydrogenase family 1 member A3 (ALDH1A3), currently reported as a cancer stem cell target, was clearly isolated as a binding protein of the lead 'immature' inhibitor probe against PDE5. In the early derivatization to the closely related structure, Compound 5 (ER-001135935) was found to significantly inhibit ALDH1A3 activity. The discovery process of a novel ALDH1A3-selective inhibitor with affinity-based binder identification is described, and the impact of this identification method on novel drug discovery is discussed.
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Affiliation(s)
| | - Masayuki Miyano
- Tsukuba Research Laboratories, Eisai Co., Ltd., Ibaraki, Japan
| | - Daisuke Ito
- Tsukuba Research Laboratories, Eisai Co., Ltd., Ibaraki, Japan
| | - Takayuki Kimura
- Tsukuba Research Laboratories, Eisai Co., Ltd., Ibaraki, Japan
| | - Koji Hagiwara
- Tsukuba Research Laboratories, Eisai Co., Ltd., Ibaraki, Japan
| | - Hiroyuki Kogai
- Tsukuba Research Laboratories, Eisai Co., Ltd., Ibaraki, Japan
| | - Yosuke Kaburagi
- Tsukuba Research Laboratories, Eisai Co., Ltd., Ibaraki, Japan
| | | | - Yasutaka Takase
- Tsukuba Research Laboratories, Eisai Co., Ltd., Ibaraki, Japan
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2
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Dueñas ME, Peltier‐Heap RE, Leveridge M, Annan RS, Büttner FH, Trost M. Advances in high-throughput mass spectrometry in drug discovery. EMBO Mol Med 2023; 15:e14850. [PMID: 36515561 PMCID: PMC9832828 DOI: 10.15252/emmm.202114850] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 12/15/2022] Open
Abstract
High-throughput (HT) screening drug discovery, during which thousands or millions of compounds are screened, remains the key methodology for identifying active chemical matter in early drug discovery pipelines. Recent technological developments in mass spectrometry (MS) and automation have revolutionized the application of MS for use in HT screens. These methods allow the targeting of unlabelled biomolecules in HT assays, thereby expanding the breadth of targets for which HT assays can be developed compared to traditional approaches. Moreover, these label-free MS assays are often cheaper, faster, and more physiologically relevant than competing assay technologies. In this review, we will describe current MS techniques used in drug discovery and explain their advantages and disadvantages. We will highlight the power of mass spectrometry in label-free in vitro assays, and its application for setting up multiplexed cellular phenotypic assays, providing an exciting new tool for screening compounds in cell lines, and even primary cells. Finally, we will give an outlook on how technological advances will increase the future use and the capabilities of mass spectrometry in drug discovery.
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Affiliation(s)
- Maria Emilia Dueñas
- Laboratory for Biomedical Mass Spectrometry, Biosciences InstituteNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Rachel E Peltier‐Heap
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Melanie Leveridge
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Roland S Annan
- Discovery Analytical, Screening Profiling and Mechanistic Biology, GSK R&DStevenageUK
| | - Frank H Büttner
- Drug Discovery Sciences, High Throughput BiologyBoehringer Ingelheim Pharma GmbH&CoKGBiberachGermany
| | - Matthias Trost
- Laboratory for Biomedical Mass Spectrometry, Biosciences InstituteNewcastle UniversityNewcastle‐upon‐TyneUK
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3
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Kushwaha N, Sahu A, Mishra J, Soni A, Dorwal D. An Insight on the Prospect of Quinazoline and Quinazolinone Derivatives as Anti-tubercular Agents. Curr Org Synth 2023; 20:838-869. [PMID: 36927421 DOI: 10.2174/1570179420666230316094435] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/22/2023] [Accepted: 01/27/2023] [Indexed: 03/18/2023]
Abstract
Multiple potential drugs have been developed based on the heterocyclic molecules for the treatment of different symptoms. Among the existing heterocyclic molecules, quinazoline and quinazolinone derivatives have been found to exhibit extensive pharmacological and biological characteristics. One significant property of these molecules is their potency as anti-tubercular agents. Thus, both quinazoline and quinazolinone derivatives are modified using different functional groups as substituents for investigating their anti-tubercular activities. We present a summary of the reported anti-tubercular drugs, designed using quinazoline and quinazolinone derivatives, in this review.
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Affiliation(s)
| | - Adarsh Sahu
- Department of Pharmaceutical Sciences, Harisingh Gour Vishwavidyalaya, Sagar, MP, India
| | - Jyotika Mishra
- Department of Pharmaceutical Sciences, Harisingh Gour Vishwavidyalaya, Sagar, MP, India
| | - Ankit Soni
- Sri Aurobindo Institute of Pharmacy, Indore, MP, India
| | - Dhawal Dorwal
- Sri Aurobindo Institute of Pharmacy, Indore, MP, India
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4
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Muchiri RN, van Breemen RB. Drug discovery from natural products using affinity selection-mass spectrometry. DRUG DISCOVERY TODAY. TECHNOLOGIES 2021; 40:59-63. [PMID: 34916024 DOI: 10.1016/j.ddtec.2021.10.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 12/22/2022]
Abstract
As a starting point for drug discovery, affinity selection-mass spectrometry (AS-MS) is ideal for the discovery of lead compounds from chemically diverse sources such as botanical, fungal and microbial extracts. Based on binding interactions between macromolecular receptors and ligands of low molecular mass, AS-MS enables the rapid isolation of pharmacologically active small molecules from complex mixtures for mass spectrometric characterization and identification. Unlike conventional high-throughput screening, AS-MS requires no radiolabels, no UV or fluorescent chromophores, and is compatible with all classes of receptors, enzymes, incubation buffers, cofactors, and ligands. The most successful types of AS-MS include pulsed ultrafiltration (PUF) AS-MS, size exclusion chromatography (SEC) AS-MS, and magnetic microbead affinity selection screening (MagMASS), which differ in their approaches for separating the ligand-receptor complexes from the non-binding compounds in mixtures. After affinity isolation, the ligand(s) from the mixture are characterized using high resolution UHPLC-MS and tandem mass spectrometry. Based on these elemental composition and structural data, the identities of the lead compounds are determined by searching on-line databases for known natural products and by comparison with standards. The structures of novel natural products are determined using a combination of spectroscopic techniques including two-dimensional NMR and MS.
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Affiliation(s)
- Ruth N Muchiri
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, United States; College of Pharmacy, Oregon State University, Corvallis, OR 97331, United States
| | - Richard B van Breemen
- Linus Pauling Institute, Oregon State University, Corvallis, OR 97331, United States; College of Pharmacy, Oregon State University, Corvallis, OR 97331, United States
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5
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Yu W, Deng Y, Sloman D, Li D, Liu K, Fradera X, Lesburg CA, Martinot T, Doty A, Ferguson H, Richard Miller J, Knemeyer I, Otte K, Vincent S, Sciammetta N, Jonathan Bennett D, Han Y. Discovery of IDO1 inhibitors containing a decahydroquinoline, decahydro-1,6-naphthyridine, or octahydro-1H-pyrrolo[3,2-c]pyridine scaffold. Bioorg Med Chem Lett 2021; 49:128314. [PMID: 34391891 DOI: 10.1016/j.bmcl.2021.128314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/21/2021] [Accepted: 08/08/2021] [Indexed: 01/25/2023]
Abstract
A series of IDO1 inhibitors containing a decahydroquinoline, decahydro-1,6-naphthyridine, or octahydro-1H-pyrrolo[3,2-c]pyridine scaffold were identified with good cellular and human whole blood activity against IDO1. These inhibitors contain multiple chiral centers and all diastereomers were separated. The absolute stereochemistry of each isomers were not determined. Compounds 15 and 27 stood out as leads due to their good cellular as well as human whole blood IDO1 inhibition activity, low unbound clearance, and reasonable mean residence time in rat cassette PK studies.
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Affiliation(s)
- Wensheng Yu
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.
| | - Yongqi Deng
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - David Sloman
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Derun Li
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Kun Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Xavier Fradera
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | - Theo Martinot
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Amy Doty
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Heidi Ferguson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - J Richard Miller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ian Knemeyer
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Karin Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Stella Vincent
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | | | - Yongxin Han
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
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6
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Yu W, Deng Y, Hopkins B, Huang X, Sloman D, Zhang H, Li D, McGowan MA, White C, Pu Q, Liu K, Fradera X, Lesburg CA, Martinot T, Doty A, Ferguson H, Nickbarg EB, Cheng M, Geda P, Song X, Smotrov N, Abeywickrema P, Andrews C, Chamberlin C, Mabrouk O, Curran P, Richards M, Saradjian P, Miller JR, Knemeyer I, Otte K, Vincent S, Sciammetta N, Bennett DJ, Han Y. SAR towards indoline and 3-azaindoline classes of IDO1 inhibitors. Bioorg Med Chem Lett 2021; 47:128214. [PMID: 34166782 DOI: 10.1016/j.bmcl.2021.128214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/08/2021] [Accepted: 06/16/2021] [Indexed: 11/16/2022]
Abstract
A novel series of IDO1 inhibitors have been identified with good IDO1 Hela cell and human whole blood activity. These inhibitors contain an indoline or a 3-azaindoline scaffold. Their structure-activity-relationship studies have been explored. Compounds 37 and 41 stood out as leads due to their good potency in IDO1 Hela assay, good IDO1 unbound hWB IC50s, reasonable unbound clearance, and good MRT in rat and dog PK studies.
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Affiliation(s)
- Wensheng Yu
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA.
| | - Yongqi Deng
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Brett Hopkins
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Xianhai Huang
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ 07033, USA
| | - David Sloman
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Hongjun Zhang
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Derun Li
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | - Catherine White
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Qinglin Pu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Kun Liu
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Xavier Fradera
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | - Theo Martinot
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Amy Doty
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Heidi Ferguson
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | - Mangeng Cheng
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Prasanthi Geda
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Xuelei Song
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Nadya Smotrov
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | | | - Chad Chamberlin
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Omar Mabrouk
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Patrick Curran
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Matthew Richards
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Peter Saradjian
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - J Richard Miller
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Ian Knemeyer
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Karin Otte
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Stella Vincent
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
| | | | | | - Yongxin Han
- Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, MA 02115, USA
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7
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Motoyaji T. [High-throughput Screening Technology for Selective Inhibitors of Transporters and Its Application in Drug Discovery]. YAKUGAKU ZASSHI 2021; 141:511-515. [PMID: 33790118 DOI: 10.1248/yakushi.20-00204-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The first step in small-molecule drug discovery is the identification of hit compounds via high-throughput screening (HTS). In transporter drug discovery, most HTS assays are based on the uptake of labeled substrates, but such functional assays cannot be developed for many transporters, such as intracellular organelle transporters. These transporters remain unexplored in drug discovery despite their promise as drug targets. Affinity selection-mass spectrometry (AS-MS) is a label-free binding assay technology that has been developed as an HTS technology for analyzing interactions between targets and compounds. The use of AS-MS technology enables HTS against every type of drug target, in contrast to functional assays. AS-MS technology is usually used for soluble proteins, but we have developed this technology for application to membrane proteins as well. So far, we have used AS-MS for HTS of approximately 400000 compounds. In this review, the principles and application of AS-MS technology are introduced and an HTS campaign for solute carrier type 17A8 (SLC17A8) (vesicular glutamate transporter 3) is presented as an example.
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8
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McLaren DG, Shah V, Wisniewski T, Ghislain L, Liu C, Zhang H, Saldanha SA. High-Throughput Mass Spectrometry for Hit Identification: Current Landscape and Future Perspectives. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:168-191. [PMID: 33482074 DOI: 10.1177/2472555220980696] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
For nearly two decades mass spectrometry has been used as a label-free, direct-detection method for both functional and affinity-based screening of a wide range of therapeutically relevant target classes. Here, we present an overview of several established and emerging mass spectrometry platforms and summarize the unique strengths and performance characteristics of each as they apply to high-throughput screening. Multiple examples from the recent literature are highlighted in order to illustrate the power of each individual technique, with special emphasis given to cases where the use of mass spectrometry was found to be differentiating when compared with other detection formats. Indeed, as many of these examples will demonstrate, the inherent strengths of mass spectrometry-sensitivity, specificity, wide dynamic range, and amenability to complex matrices-can be leveraged to enhance the discriminating power and physiological relevance of assays included in screening cascades. It is our hope that this review will serve as a useful guide to readers of all backgrounds and experience levels on the applicability and benefits of mass spectrometry in the search for hits, leads, and, ultimately, drugs.
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9
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Yang D, Zhou Q, Labroska V, Qin S, Darbalaei S, Wu Y, Yuliantie E, Xie L, Tao H, Cheng J, Liu Q, Zhao S, Shui W, Jiang Y, Wang MW. G protein-coupled receptors: structure- and function-based drug discovery. Signal Transduct Target Ther 2021; 6:7. [PMID: 33414387 PMCID: PMC7790836 DOI: 10.1038/s41392-020-00435-w] [Citation(s) in RCA: 245] [Impact Index Per Article: 81.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/30/2020] [Accepted: 12/05/2020] [Indexed: 02/08/2023] Open
Abstract
As one of the most successful therapeutic target families, G protein-coupled receptors (GPCRs) have experienced a transformation from random ligand screening to knowledge-driven drug design. We are eye-witnessing tremendous progresses made recently in the understanding of their structure-function relationships that facilitated drug development at an unprecedented pace. This article intends to provide a comprehensive overview of this important field to a broader readership that shares some common interests in drug discovery.
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Affiliation(s)
- Dehua Yang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Qingtong Zhou
- School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China
| | - Viktorija Labroska
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Shanshan Qin
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Sanaz Darbalaei
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Elita Yuliantie
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Linshan Xie
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Houchao Tao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Jianjun Cheng
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China
| | - Qing Liu
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, 201210, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China.
| | - Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China.
| | - Ming-Wei Wang
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China. .,The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203, Shanghai, China. .,School of Basic Medical Sciences, Fudan University, 200032, Shanghai, China. .,University of Chinese Academy of Sciences, 100049, Beijing, China. .,School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China. .,School of Pharmacy, Fudan University, 201203, Shanghai, China.
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10
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Muchiri RN, van Breemen RB. Affinity selection-mass spectrometry for the discovery of pharmacologically active compounds from combinatorial libraries and natural products. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4647. [PMID: 32955158 DOI: 10.1002/jms.4647] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/15/2020] [Accepted: 08/11/2020] [Indexed: 05/12/2023]
Abstract
Invented to address the high-throughput screening (HTS) demands of combinatorial chemistry, affinity selection-mass spectrometry (AS-MS) utilizes binding interactions between ligands and receptors to isolate pharmacologically active compounds from mixtures of small molecules and then relies on the selectivity, sensitivity, and speed of mass spectrometry to identify them. No radiolabels, fluorophores, or chromophores are required. Although many variations of AS-MS have been devised, three approaches have emerged as the most flexible, productive, and popular, and they differ primarily in how ligand-receptor complexes are separated from nonbinding compounds in the mixture. These are pulsed ultrafiltration (PUF) AS-MS, size exclusion chromatography (SEC) AS-MS, and magnetic microbead affinity selection screening (MagMASS). PUF and SEC AS-MS are solution-phase screening approaches, and MagMASS uses receptors immobilized on magnetic microbeads. Because pools of compounds are screened using AS-MS, each containing hundreds to thousands of potential ligands, hundreds of thousands of compounds can be screened per day. AS-MS is also compatible with complex mixtures of chemically diverse natural products in extracts of botanicals and fungi and microbial cultures, which often contain fluorophores and chromophores that can interfere with convention HTS. Unlike conventional HTS, AS-MS may be used to discover ligands binding to allosteric as well as orthosteric receptor sites, and AS-MS has been useful for discovering ligands to targets that are not easily incorporated into conventional HTS such as membrane-bound receptors.
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Affiliation(s)
- Ruth N Muchiri
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon, 97331, USA
| | - Richard B van Breemen
- Linus Pauling Institute, Oregon State University, Corvallis, Oregon, 97331, USA
- Department of Pharmaceutical Sciences, Oregon State University, Corvallis, Oregon, 97331, USA
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11
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Tao Y, Yan J, Cai B. LABEL-FREE BIO-AFFINITY MASS SPECTROMETRY FOR SCREENING AND LOCATING BIOACTIVE MOLECULES. MASS SPECTROMETRY REVIEWS 2021; 40:53-71. [PMID: 31755145 DOI: 10.1002/mas.21613] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 11/04/2019] [Indexed: 06/10/2023]
Abstract
Despite the recent increase in the development of bioactive molecules in the drug industry, the enormous chemical space and lack of productivity are still important issues. Additional alternative approaches to screen and locate bioactive molecules are urgently needed. Label-free bio-affinity mass spectrometry (BA-MS) provides opportunities for the discovery and development of innovative drugs. This review provides a comprehensive portrayal of BA-MS techniques and of their applications in screening and locating bioactive molecules. After introducing the basic principles, alongside some application notes, the current state-of-the-art of BA-MS-assisted drug discovery is discussed, including native MS, size-exclusion chromatography-MS, ultrafiltration-MS, solid-phase micro-extraction-MS, and cell membrane chromatography-MS. Finally, several challenges and limitations of the current methods are summarized, with a view to potential future directions for BA-MS-assisted drug discovery. © 2019 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Yi Tao
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Jizhong Yan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Baochang Cai
- Jiangsu Key Laboratory of Chinese Medicine Processing, Nanjing University of Chinese Medicine, Nanjing, 210023, PR China
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12
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Gabriel J, Höfner G, Wanner KT. Combination of MS Binding Assays and affinity selection mass spectrometry for screening of structurally homogenous libraries as exemplified for a focused oxime library addressing the neuronal GABA transporter 1. Eur J Med Chem 2020; 206:112598. [PMID: 32896797 DOI: 10.1016/j.ejmech.2020.112598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/09/2020] [Accepted: 06/16/2020] [Indexed: 11/30/2022]
Abstract
This study presents an efficient screening approach based on combination of mass spectrometry (MS) based binding assays (MS Binding Assays) and affinity selection mass spectrometry (ASMS) customized for screening of structurally homogeneous libraries sharing a common mass spectrometric fragmentation pattern. After reaction of a nipecotic acid derivative possessing a hydroxylamine functionality with aldehydes, the resulting oxime library was screened accordingly toward the GABA transporter subtype 1 (GAT1), a drug target for several neurological disorders. After assessing sublibraries' activities for inhibition of reporter ligand binding, hits in active ones were directly identified. This could be achieved by recording mass transitions for the reporter ligand as well as those predicted for the library components in a single LC-MS/MS run with a triple quadrupole mass spectrometer in the multiple reaction monitoring mode. Identification of hits with a predefined affinity could be reliably accomplished by calculation of IC50-values from specific binding concentrations of library constituents and reporter ligand. Application of this strategy revealed six hits, from which two of them were resynthesized for further biological evaluation. Thereby, the best one displayed a pKi of 7.38 in MS Binding Assays and a pIC50 of 6.82 in [3H]GABA uptake assays for GAT1.
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Affiliation(s)
- Jürgen Gabriel
- Faculty of Chemistry and Pharmacy, Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Georg Höfner
- Faculty of Chemistry and Pharmacy, Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Klaus T Wanner
- Faculty of Chemistry and Pharmacy, Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
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13
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Exploring new targets and chemical space with affinity selection-mass spectrometry. Nat Rev Chem 2020; 5:62-71. [PMID: 37118102 DOI: 10.1038/s41570-020-00229-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2020] [Indexed: 12/15/2022]
Abstract
Affinity selection-mass spectrometry (AS-MS) is a high-throughput screening (HTS) technique for drug discovery that enables rapid screening of large collections of compounds to identify ligands for a specific biomolecular target. AS-MS is a binding assay that is insensitive to the functional effects a ligand might have, which is important because it lets us identify novel ligands irrespective of their binding site. This approach is gaining popularity, notably due to its role in the emergence of useful agents for targeted protein degradation. This Perspective highlights the use of AS-MS techniques to explore broad chemical space and identify small-molecule ligands for biological targets that have proven challenging to address with other screening paradigms. We present chemical structures of reported AS-MS hits to illustrate the potential of this screening approach to deliver high-quality hits for further optimization. AS-MS has, thus, evolved from being an infrequent alternative to traditional HTS or DNA-encoded library strategies to now firmly establishing itself as a HTS approach for drug discovery.
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14
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Grant EK, Fallon DJ, Hann MM, Fantom KGM, Quinn C, Zappacosta F, Annan RS, Chung C, Bamborough P, Dixon DP, Stacey P, House D, Patel VK, Tomkinson NCO, Bush JT. A Photoaffinity‐Based Fragment‐Screening Platform for Efficient Identification of Protein Ligands. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008361] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Emma K. Grant
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
- Pure and Applied Chemistry University of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
| | - David J. Fallon
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
- Pure and Applied Chemistry University of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
| | - Michael M. Hann
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Ken G. M. Fantom
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Chad Quinn
- GlaxoSmithKline South Collegeville Road Collegeville PA 19426 USA
| | | | - Roland S. Annan
- GlaxoSmithKline South Collegeville Road Collegeville PA 19426 USA
| | - Chun‐wa Chung
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Paul Bamborough
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - David P. Dixon
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Peter Stacey
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - David House
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | | | | | - Jacob T. Bush
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
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15
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Grant EK, Fallon DJ, Hann MM, Fantom KGM, Quinn C, Zappacosta F, Annan RS, Chung C, Bamborough P, Dixon DP, Stacey P, House D, Patel VK, Tomkinson NCO, Bush JT. A Photoaffinity‐Based Fragment‐Screening Platform for Efficient Identification of Protein Ligands. Angew Chem Int Ed Engl 2020; 59:21096-21105. [DOI: 10.1002/anie.202008361] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Emma K. Grant
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
- Pure and Applied Chemistry University of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
| | - David J. Fallon
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
- Pure and Applied Chemistry University of Strathclyde 295 Cathedral Street Glasgow G1 1XL UK
| | - Michael M. Hann
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Ken G. M. Fantom
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Chad Quinn
- GlaxoSmithKline South Collegeville Road Collegeville PA 19426 USA
| | | | - Roland S. Annan
- GlaxoSmithKline South Collegeville Road Collegeville PA 19426 USA
| | - Chun‐wa Chung
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Paul Bamborough
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - David P. Dixon
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - Peter Stacey
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | - David House
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
| | | | | | - Jacob T. Bush
- GlaxoSmithKline Gunnels Wood Road Stevenage Hertfordshire SG1 2NY UK
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16
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White C, McGowan MA, Zhou H, Sciammetta N, Fradera X, Lim J, Joshi EM, Andrews C, Nickbarg EB, Cowley P, Trewick S, Augustin M, von Köenig K, Lesburg CA, Otte K, Knemeyer I, Woo H, Yu W, Cheng M, Spacciapoli P, Geda P, Song X, Smotrov N, Curran P, Heo MR, Abeywickrema P, Miller JR, Bennett DJ, Han Y. Strategic Incorporation of Polarity in Heme-Displacing Inhibitors of Indoleamine-2,3-dioxygenase-1 (IDO1). ACS Med Chem Lett 2020; 11:550-557. [PMID: 32292563 DOI: 10.1021/acsmedchemlett.0c00010] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/10/2020] [Indexed: 12/13/2022] Open
Abstract
Indoleamine-2,3-dioxygenase-1 (IDO1) has emerged as a target of significant interest to the field of cancer immunotherapy, as the upregulation of IDO1 in certain cancers has been linked to host immune evasion and poor prognosis for patients. In particular, IDO1 inhibition is of interest as a combination therapy with immune checkpoint inhibition. Through an Automated Ligand Identification System (ALIS) screen, a diamide class of compounds was identified as a promising lead for the inhibition of IDO1. While hit 1 possessed attractive cell-based potency, it suffered from a significant right-shift in a whole blood assay, poor solubility, and poor pharmacokinetic properties. Through a physicochemical property-based approach, including a focus on lowering AlogP98 via the strategic introduction of polar substitution, compound 13 was identified bearing a pyridyl oxetane core. Compound 13 demonstrated improved whole blood potency and solubility, and an improved pharmacokinetic profile resulting in a low predicted human dose.
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17
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Zhang B, Zhao S, Yang D, Wu Y, Xin Y, Cao H, Huang XP, Cai X, Sun W, Ye N, Xu Y, Peng Y, Zhao S, Liu ZJ, Zhong G, Wang MW, Shui W. A Novel G Protein-Biased and Subtype-Selective Agonist for a G Protein-Coupled Receptor Discovered from Screening Herbal Extracts. ACS CENTRAL SCIENCE 2020; 6:213-225. [PMID: 32123739 PMCID: PMC7047268 DOI: 10.1021/acscentsci.9b01125] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Indexed: 05/14/2023]
Abstract
Subtype selectivity and functional bias are vital in current drug discovery for G protein-coupled receptors (GPCRs) as selective and biased ligands are expected to yield drug leads with optimal on-target benefits and minimal side-effects. However, structure-based design and medicinal chemistry exploration remain challenging in part because of highly conserved binding pockets within subfamilies. Herein, we present an affinity mass spectrometry approach for screening herbal extracts to identify active ligands of a GPCR, the 5-HT2C receptor. Using this method, we discovered a naturally occurring aporphine 1857 that displayed strong selectivity for activating 5-HT2C without activating the 5-HT2A or 5-HT2B receptors. Remarkably, this novel ligand exhibited exclusive bias toward G protein signaling for which key residues were identified, and it showed comparable in vivo efficacy for food intake suppression and weight loss as the antiobesity drug, lorcaserin. Our study establishes an efficient approach to discovering novel GPCR ligands by exploring the largely untapped chemical space of natural products.
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Affiliation(s)
- Bingjie Zhang
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Simeng Zhao
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Dehua Yang
- The
National Center for Drug Screening and the CAS Key Laboratory of Receptor
Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yiran Wu
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Ye Xin
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Haijie Cao
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Xi-Ping Huang
- Department
of Pharmacology, NIMH Psychoactive Drug Screening Program, School
of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | - Xiaoqing Cai
- The
National Center for Drug Screening and the CAS Key Laboratory of Receptor
Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wen Sun
- The
National Center for Drug Screening and the CAS Key Laboratory of Receptor
Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Ye
- Jiangsu
Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical
Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Yueming Xu
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Yao Peng
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
| | - Suwen Zhao
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of
Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
| | - Zhi-Jie Liu
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of
Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
| | - Guisheng Zhong
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of
Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- E-mail:
| | - Ming-Wei Wang
- The
National Center for Drug Screening and the CAS Key Laboratory of Receptor
Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School
of
Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- School
of Pharmacy, Fudan University, Shanghai 201203, China
- E-mail:
| | - Wenqing Shui
- iHuman
Institute, ShanghaiTech University, Shanghai 201210, China
- School
of
Life Science and Technology, ShanghaiTech
University, Shanghai 201210, China
- E-mail:
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18
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Rizvi NF, Santa Maria JP, Nahvi A, Klappenbach J, Klein DJ, Curran PJ, Richards MP, Chamberlin C, Saradjian P, Burchard J, Aguilar R, Lee JT, Dandliker PJ, Smith GF, Kutchukian P, Nickbarg EB. Targeting RNA with Small Molecules: Identification of Selective, RNA-Binding Small Molecules Occupying Drug-Like Chemical Space. SLAS DISCOVERY 2019; 25:384-396. [DOI: 10.1177/2472555219885373] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Although the potential value of RNA as a target for new small molecule therapeutics is becoming increasingly credible, the physicochemical properties required for small molecules to selectively bind to RNA remain relatively unexplored. To investigate the druggability of RNAs with small molecules, we have employed affinity mass spectrometry, using the Automated Ligand Identification System (ALIS), to screen 42 RNAs from a variety of RNA classes, each against an array of chemically diverse drug-like small molecules (~50,000 compounds) and functionally annotated tool compounds (~5100 compounds). The set of RNA–small molecule interactions that was generated was compared with that for protein–small molecule interactions, and naïve Bayesian models were constructed to determine the types of specific chemical properties that bias small molecules toward binding to RNA. This set of RNA-selective chemical features was then used to build an RNA-focused set of ~3800 small molecules that demonstrated increased propensity toward binding the RNA target set. In addition, the data provide an overview of the specific physicochemical properties that help to enable binding to potential RNA targets. This work has increased the understanding of the chemical properties that are involved in small molecule binding to RNA, and the methodology used here is generally applicable to RNA-focused drug discovery efforts.
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Affiliation(s)
| | | | - Ali Nahvi
- Merck & Co., Inc., West Point, PA, USA
| | | | | | | | | | | | | | | | - Rodrigo Aguilar
- Department of Molecular Biology, Massachusetts General Hospital; Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jeannie T. Lee
- Department of Molecular Biology, Massachusetts General Hospital; Department of Genetics, The Blavatnik Institute, Harvard Medical School, Boston, MA, USA
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19
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Gabriel J, Höfner G, Wanner KT. A Library Screening Strategy Combining the Concepts of MS Binding Assays and Affinity Selection Mass Spectrometry. Front Chem 2019; 7:665. [PMID: 31637233 PMCID: PMC6787468 DOI: 10.3389/fchem.2019.00665] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 09/18/2019] [Indexed: 01/16/2023] Open
Abstract
The primary objective of early drug development is to identify hits and leads for a target of interest. To achieve this aim, rapid, and reliable screening techniques for a huge number of compounds are needed. Mass spectrometry based binding assays (MS Binding Assays) represent a well-established technique for library screening based on competitive binding experiments revealing active sublibraries due to reduced binding of a reporter ligand and following hit identification for active libraries by deconvolution in further competitive binding experiments. In the present study, we combined the concepts of MS Binding Assays and affinity selection mass spectrometry (ASMS) to improve the efficiency of the hit identification step. In that case, only a single competitive binding experiment is performed that is in the first step analyzed for reduced binding of the reporter ligand and—only if a sublibrary is active—additionally for specific binding of individual library components. Subsequently, affinities of identified hits as well as activities of reduced sublibraries (i.e., all sublibrary components without hit) are assessed in additional competitive binding experiments. We exemplified this screening concept for the identification of ligands addressing the most widespread GABA transporter subtype in the brain (GAT1) studying in the beginning a library composed of 128 and further on a library of 1,280 well-characterized GAT1 inhibitors, drug substances, and pharmacological tool compounds. Determination of sublibraries' activities was done by quantification of bound NO711 as reporter ligand and hit identification for the active ones achieved in a further LC-ESI-MS/MS run in the multiple reaction monitoring mode enabling detection of all sublibrary components followed by hit verification and investigation of reduced sublibraries in further competitive binding experiments. In this way, we could demonstrate that all GAT1 inhibitors reducing reporter ligand binding below 50% at a concentration of 1 μM are detected reliably without generation of false positive or false negative hits. As the described strategy is apart from its reliability also highly efficient, it can be assumed to become a valuable tool in early drug research, especially for membrane integrated drug targets that are often posing problems in established screening techniques.
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Affiliation(s)
- Jürgen Gabriel
- Department of Pharmacy, Faculty of Chemistry and Pharmacy, Ludwig Maximilian University München, Munich, Germany
| | - Georg Höfner
- Department of Pharmacy, Faculty of Chemistry and Pharmacy, Ludwig Maximilian University München, Munich, Germany
| | - Klaus T Wanner
- Department of Pharmacy, Faculty of Chemistry and Pharmacy, Ludwig Maximilian University München, Munich, Germany
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20
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Lu Y, Qin S, Zhang B, Dai A, Cai X, Ma M, Gao ZG, Yang D, Stevens RC, Jacobson KA, Wang MW, Shui W. Accelerating the Throughput of Affinity Mass Spectrometry-Based Ligand Screening toward a G Protein-Coupled Receptor. Anal Chem 2019; 91:8162-8169. [PMID: 31094506 PMCID: PMC6669887 DOI: 10.1021/acs.analchem.9b00477] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Affinity mass spectrometry (MS) enables rapid screening of compound mixtures for ligands bound to a specific protein target, yet its current throughput is limited to individually assay pools of 400-2000 compounds. Typical affinity MS screens implemented in pharmaceutical industry laboratories identify putative ligands based on qualitative analysis of compound binding to the target whereas no quantitative information is acquired to discriminate high- and low-affinity ligands in the screening phase. Furthermore, these screens require purification of a stabilized form of the protein target, which poses a great challenge for membrane receptor targets. Here, we describe a new, potentially general affinity MS strategy that allows screening of 20,000 compounds in one pool for highly efficient ligand discovery toward a G protein-coupled receptor (GPCR) target. Quantitative measurement of compound binding to the receptor enables high-affinity ligand selection using both the purified receptor and receptor-embedded cell membranes. This high-throughput, label-free and quantitative affinity MS screen resulted in discovery of three new antagonists of the A2A adenosine receptor.
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Affiliation(s)
- Yan Lu
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Shanshan Qin
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
| | - Bingjie Zhang
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
| | - Antao Dai
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Xiaoqing Cai
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Mengna Ma
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Zhan-Guo Gao
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892 United States
| | - Dehua Yang
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
| | - Raymond C. Stevens
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
| | - Kenneth A. Jacobson
- National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, Bethesda, Maryland 20892 United States
| | - Ming-Wei Wang
- University of Chinese Academy of Sciences, 100049 Beijing, China
- The National Center for Drug Screening and the CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 201203 Shanghai, China
- School of Pharmacy, Fudan University, 201203 Shanghai, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, 201210 Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210 Shanghai, China
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21
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Flusberg DA, Rizvi NF, Kutilek V, Andrews C, Saradjian P, Chamberlin C, Curran P, Swalm B, Kattar S, Smith GF, Dandliker P, Nickbarg EB, O'Neil J. Identification of G-Quadruplex-Binding Inhibitors of Myc Expression through Affinity Selection-Mass Spectrometry. SLAS DISCOVERY 2018; 24:142-157. [PMID: 30204533 DOI: 10.1177/2472555218796656] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Myc oncogene is overexpressed in many cancers, yet targeting it for cancer therapy has remained elusive. One strategy for inhibition of Myc expression is through stabilization of the G-quadruplex (G4), a G-rich DNA secondary structure found within the Myc promoter; stabilization of G4s has been shown to halt transcription of downstream gene products. Here we used the Automated Ligand Identification System (ALIS), an affinity selection-mass spectrometry method, to identify compounds that bind to the Myc G4 out of a pool of compounds that had previously been shown to inhibit Myc expression in a reporter screen. Using an ALIS-based screen, we identified hits that bound to the Myc G4, a small subset of which bound preferentially relative to G4s from the promoters of five other genes. To determine functionality and specificity of the Myc G4-binding compounds in cell-based assays, we compared inhibition of Myc expression in cells with and without Myc G4 regulation. Several compounds inhibited Myc expression only in the Myc G4-containing line, and one compound was verified to function through Myc G4 binding. Our study demonstrates that ALIS can be used to identify selective nucleic acid-binding compounds from phenotypic screen hits, increasing the pool of drug targets beyond proteins.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Sam Kattar
- 3 Chemistry, Merck & Co., Inc., Boston, MA, USA
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22
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Comess KM, McLoughlin SM, Oyer JA, Richardson PL, Stöckmann H, Vasudevan A, Warder SE. Emerging Approaches for the Identification of Protein Targets of Small Molecules - A Practitioners’ Perspective. J Med Chem 2018; 61:8504-8535. [DOI: 10.1021/acs.jmedchem.7b01921] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Kenneth M. Comess
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Shaun M. McLoughlin
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Jon A. Oyer
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Paul L. Richardson
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Henning Stöckmann
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Anil Vasudevan
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
| | - Scott E. Warder
- AbbVie Inc., 1 Waukegan Road, North Chicago, Illinois 60064-1802, United States
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23
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Qin S, Meng M, Yang D, Bai W, Lu Y, Peng Y, Song G, Wu Y, Zhou Q, Zhao S, Huang X, McCorvy JD, Cai X, Dai A, Roth BL, Hanson MA, Liu ZJ, Wang MW, Stevens RC, Shui W. High-throughput identification of G protein-coupled receptor modulators through affinity mass spectrometry screening. Chem Sci 2018; 9:3192-3199. [PMID: 29732102 PMCID: PMC5916221 DOI: 10.1039/c7sc04698g] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/19/2018] [Indexed: 12/24/2022] Open
Abstract
High-throughput identification of GPCR modulators through affinity MS screening.
G protein-coupled receptors (GPCRs) represent the largest class of cell surface proteins and thus constitute an important family of therapeutic targets. Therefore, significant effort has been put towards the identification of novel ligands that can modulate the activity of a GPCR target with high efficacy and selectivity. However, due to limitations inherent to the most common techniques for GPCR ligand discovery, there is a pressing need for more efficient and effective ligand screening methods especially for the identification of potential allosteric modulators. Here we present a high-throughput, label-free and unbiased screening approach for the identification of small molecule ligands towards GPCR targets based on affinity mass spectrometry. This new approach features the usage of target-expressing cell membranes rather than purified proteins for ligand screening and allows the detection of both orthosteric and allosteric ligands targeting specific GPCRs. Screening a small compound library with this approach led to the rapid discovery of an antagonist for the 5-HT receptor and four positive allosteric modulators for GLP-1 receptor that were not previously reported.
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Affiliation(s)
- Shanshan Qin
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China .
| | - Mengmeng Meng
- College of Pharmacy , Nankai University , 300071 , Tianjin , China
| | - Dehua Yang
- The National Center for Drug Screening , The CAS Key Laboratory of Receptor Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 201203 , Shanghai , China .
| | - Wenwen Bai
- College of Pharmacy , Nankai University , 300071 , Tianjin , China
| | - Yan Lu
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China . .,School of Life Science and Technology , ShanghaiTech University , 201202 , Shanghai , China
| | - Yao Peng
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China .
| | - Gaojie Song
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China .
| | - Yiran Wu
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China .
| | - Qingtong Zhou
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China .
| | - Suwen Zhao
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China . .,School of Life Science and Technology , ShanghaiTech University , 201202 , Shanghai , China
| | - Xiping Huang
- Department of Pharmacology , Chapel Hill School of Medicine , University of North Carolina , NC 27599 Chapel Hill , USA
| | - John D McCorvy
- Department of Pharmacology , Chapel Hill School of Medicine , University of North Carolina , NC 27599 Chapel Hill , USA
| | - Xiaoqing Cai
- The National Center for Drug Screening , The CAS Key Laboratory of Receptor Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 201203 , Shanghai , China .
| | - Antao Dai
- The National Center for Drug Screening , The CAS Key Laboratory of Receptor Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 201203 , Shanghai , China .
| | - Bryan L Roth
- Department of Pharmacology , Chapel Hill School of Medicine , University of North Carolina , NC 27599 Chapel Hill , USA
| | | | - Zhi-Jie Liu
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China . .,School of Life Science and Technology , ShanghaiTech University , 201202 , Shanghai , China
| | - Ming-Wei Wang
- The National Center for Drug Screening , The CAS Key Laboratory of Receptor Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 201203 , Shanghai , China . .,School of Life Science and Technology , ShanghaiTech University , 201202 , Shanghai , China.,School of Pharmacy , Fudan University , 201203 , Shanghai , China
| | - Raymond C Stevens
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China . .,School of Life Science and Technology , ShanghaiTech University , 201202 , Shanghai , China
| | - Wenqing Shui
- iHuman Institute , ShanghaiTech University , 201210 , Shanghai , China . .,School of Life Science and Technology , ShanghaiTech University , 201202 , Shanghai , China
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24
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Santa Maria JP, Park Y, Yang L, Murgolo N, Altman MD, Zuck P, Adam G, Chamberlin C, Saradjian P, Dandliker P, Boshoff HIM, Barry CE, Garlisi C, Olsen DB, Young K, Glick M, Nickbarg E, Kutchukian PS. Linking High-Throughput Screens to Identify MoAs and Novel Inhibitors of Mycobacterium tuberculosis Dihydrofolate Reductase. ACS Chem Biol 2017; 12:2448-2456. [PMID: 28806050 DOI: 10.1021/acschembio.7b00468] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Though phenotypic and target-based high-throughput screening approaches have been employed to discover new antibiotics, the identification of promising therapeutic candidates remains challenging. Each approach provides different information, and understanding their results can provide hypotheses for a mechanism of action (MoA) and reveal actionable chemical matter. Here, we describe a framework for identifying efficacy targets of bioactive compounds. High throughput biophysical profiling against a broad range of targets coupled with machine learning was employed to identify chemical features with predicted efficacy targets for a given phenotypic screen. We validate the approach on data from a set of 55 000 compounds in 24 historical internal antibacterial phenotypic screens and 636 bacterial targets screened in high-throughput biophysical binding assays. Models were built to reveal the relationships between phenotype, target, and chemotype, which recapitulated mechanisms for known antibacterials. We also prospectively identified novel inhibitors of dihydrofolate reductase with nanomolar antibacterial efficacy against Mycobacterium tuberculosis. Molecular modeling provided structural insight into target-ligand interactions underlying selective killing activity toward mycobacteria over human cells.
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Affiliation(s)
- John P. Santa Maria
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Yumi Park
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Lihu Yang
- Department of Chemistry, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Nicholas Murgolo
- Department of Information & Analytics, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - Michael D. Altman
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Paul Zuck
- Research Science, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Greg Adam
- Department of Pharmacology, Merck Sharp & Dohme Corp., North Wales, Pennsylvania, United States
| | - Chad Chamberlin
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Saradjian
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter Dandliker
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Helena I. M. Boshoff
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Clifton E. Barry
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States
| | - Charles Garlisi
- Department of Pharmacology, Merck Sharp & Dohme Corp., Kenilworth, New Jersey, United States
| | - David B. Olsen
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Katherine Young
- Neglected Tropical Disease Discovery, Merck Sharp & Dohme Corp., West Point, Pennsylvania, United States
| | - Meir Glick
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
| | - Elliott Nickbarg
- Department of Pharmacology, Merck Sharp & Dohme Corp., Boston, Massachusetts, United States
| | - Peter S. Kutchukian
- Modeling & Informatics, Merck Research Laboratories, Boston, Massachusetts, United States
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25
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Prioritizing multiple therapeutic targets in parallel using automated DNA-encoded library screening. Nat Commun 2017; 8:16081. [PMID: 28714473 PMCID: PMC5520047 DOI: 10.1038/ncomms16081] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 05/24/2017] [Indexed: 12/18/2022] Open
Abstract
The identification and prioritization of chemically tractable therapeutic targets is a significant challenge in the discovery of new medicines. We have developed a novel method that rapidly screens multiple proteins in parallel using DNA-encoded library technology (ELT). Initial efforts were focused on the efficient discovery of antibacterial leads against 119 targets from Acinetobacter baumannii and Staphylococcus aureus. The success of this effort led to the hypothesis that the relative number of ELT binders alone could be used to assess the ligandability of large sets of proteins. This concept was further explored by screening 42 targets from Mycobacterium tuberculosis. Active chemical series for six targets from our initial effort as well as three chemotypes for DHFR from M. tuberculosis are reported. The findings demonstrate that parallel ELT selections can be used to assess ligandability and highlight opportunities for successful lead and tool discovery. Encoded Library Technology (ELT) has streamlined the identification of chemical ligands for protein targets in drug discovery. Here, the authors optimize the ELT approach to screen multiple proteins in parallel and identify promising targets and antibacterial compounds for S. aureus, A. baumannii and M. tuberculosis.
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