1
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van Breemen RB, Muchiri RN. Affinity selection-mass spectrometry in the discovery of anti-SARS-CoV-2 compounds. MASS SPECTROMETRY REVIEWS 2024; 43:39-46. [PMID: 35929396 PMCID: PMC9538385 DOI: 10.1002/mas.21800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Small molecule therapeutic agents are needed to treat or prevent infections by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which is the cause of the COVID-19 pandemic. To expedite the discovery of lead compounds for development, assays have been developed based on affinity selection-mass spectrometry (AS-MS), which enables the rapid screening of mixtures such as combinatorial libraries and extracts of botanicals or other sources of natural products. AS-MS assays have been used to find ligands to the SARS-CoV-2 spike protein for inhibition of cell entry as well as to the 3-chymotrypsin-like cysteine protease (3CLpro) and the RNA-dependent RNA polymerase complex constituent Nsp9, which are targets for inhibition of viral replication. The AS-MS approach of magnetic microbead affinity selection screening has been used to discover high-affinity peptide ligands to the spike protein as well as the hemp cannabinoids cannabidiolic acid and cannabigerolic acid, which can prevent cell infection by SARS-CoV-2. Another AS-MS method, native mass spectrometry, has been used to discover that the flavonoids baicalein, scutellarein, and ganhuangenin, can inhibit the SARS-CoV-2 protease 3CLpro. Native mass spectrometry has also been used to find an ent-kaurane natural product, oridonin, that can bind to the viral protein Nsp9 and interfere with RNA replication. These natural lead compounds are under investigation for the development of therapeutic agents to prevent or treat SARS-CoV-2 infection.
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Affiliation(s)
- Richard B. van Breemen
- Department of Pharmaceutical Sciences, Linus Pauling Institute, College of PharmacyOregon State UniversityCorvallisOregonUSA
| | - Ruth N. Muchiri
- Department of Pharmaceutical Sciences, Linus Pauling Institute, College of PharmacyOregon State UniversityCorvallisOregonUSA
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2
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Prudent R, Lemoine H, Walsh J, Roche D. Affinity selection mass spectrometry speeding drug discovery. Drug Discov Today 2023; 28:103760. [PMID: 37660985 DOI: 10.1016/j.drudis.2023.103760] [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: 03/23/2023] [Revised: 07/21/2023] [Accepted: 08/29/2023] [Indexed: 09/05/2023]
Abstract
Affinity selection mass spectrometry (AS-MS) has gained momentum in drug discovery. This review summarizes how this technology has slowly risen as a new paradigm in hit identification and its potential synergy with DNA encoded library technology. It presents an overview of the recent results on challenging targets and perspectives on new areas of research, such as RNA targeting with small molecules. The versatility of the approach is illustrated and strategic drivers discussed in terms of the experience of a small-medium CRO and a big pharma organization.
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Affiliation(s)
| | | | - Jarrod Walsh
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D Biopharmaceuticals, AstraZeneca, Alderley Park, UK
| | - Didier Roche
- Edelris, Bioparc, Bioserra 1 Building, Lyon, France.
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3
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Tsiara I, Riemer A, Correia MSP, Rodriguez-Mateos A, Globisch D. Immobilized Enzymes on Magnetic Beads for Separate Mass Spectrometric Investigation of Human Phase II Metabolite Classes. Anal Chem 2023; 95:12565-12571. [PMID: 37552796 PMCID: PMC10456218 DOI: 10.1021/acs.analchem.3c02988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023]
Abstract
The human body has evolved to remove xenobiotics through a multistep clearance process. Non-endogenous metabolites are converted through a series of phase I and different phase II enzymes into compounds with higher hydrophilicity. These compounds are important for diverse research fields such as toxicology, nutrition, biomarker discovery, doping control, and microbiome metabolism. One of the challenges in these research fields has been the investigation of the two major phase II modifications, sulfation and glucuronidation, and the corresponding unconjugated aglycon independently. We have now developed a new methodology utilizing an immobilized arylsulfatase and an immobilized β-glucuronidase to magnetic beads for treatment of human urine samples. The enzyme activities remained the same compared to the enzyme in solution. The separate mass spectrometric investigation of each metabolite class in a single sample was successfully applied to obtain the dietary glucuronidation and sulfation profile of 116 compounds. Our new chemical biology strategy provides a new tool for the investigation of metabolites in biological samples with the potential for broad-scale application in metabolomics, nutrition, and microbiome studies.
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Affiliation(s)
- Ioanna Tsiara
- Department
of Chemistry - BMC, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Amelie Riemer
- Department
of Chemistry - BMC, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Mario S. P. Correia
- Department
of Chemistry - BMC, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
| | - Ana Rodriguez-Mateos
- Department
of Nutritional Sciences, School of Life Course and Population Sciences,
Faculty of Life Sciences and Medicine, King’s
College London, London SE1 9NH, UK
| | - Daniel Globisch
- Department
of Chemistry - BMC, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden
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4
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Kuang QX, Luo Y, Lei LR, Guo WX, Li XA, Wang YM, Huo XY, Liu MD, Zhang Q, Feng D, Huang LJ, Wang D, Gu YC, Deng Y, Guo DL. Hydroanthraquinones from Nigrospora sphaerica and Their Anti-inflammatory Activity Uncovered by Transcriptome Analysis. JOURNAL OF NATURAL PRODUCTS 2022; 85:1474-1485. [PMID: 35696541 DOI: 10.1021/acs.jnatprod.1c01141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Transcriptome analysis is shown to be an effective strategy to understand the potential function of natural products. Here, it is reported that 11 previously undescribed hydroanthraquinones [nigroquinones A-K (1-11)], along with eight known congeners, were isolated from Nigrospora sphaerica. Their structures were elucidated by interpreting spectroscopic and spectrometric data including high-resolution mass spectra and nuclear magnetic resonance. The absolute configurations of 1-11 were confirmed by electronic circular dichroism calculations. Transcriptome analysis revealed that 3 (isolated in the largest amount) might be anti-inflammatory. Assays based on LPS-induced RAW264.7 macrophages and zebrafish embryos confirmed that some of the isolated hydroanthraquinones attenuated the secretion of pro-inflammatory mediators in vitro and in vivo. Further Western blotting and immunofluorescence experiments indicated that 4 (which showed the most obvious nitric oxide inhibition) could suppress the expression of nuclear factor-kappa-B (NF-κB), phosphorylation of the inhibitor of NF-κB kinase and inhibit the transportation of NF-κB to the nucleus. Hence, the suppression of the NF-κB signaling pathway may be responsible for the anti-inflammatory effect. These results show that bioactivity evaluation on the basis of transcriptome analysis may be effective in the functional exploration of natural products.
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Affiliation(s)
- Qi-Xuan Kuang
- State Key Laboratory of Characteristic Chinese Medicine Resources of Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Yan Luo
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Li-Rong Lei
- State Key Laboratory of Characteristic Chinese Medicine Resources of Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Wen-Xiu Guo
- State Key Laboratory of Characteristic Chinese Medicine Resources of Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Xin-Ai Li
- State Key Laboratory of Characteristic Chinese Medicine Resources of Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Yu-Mei Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Xue-Yan Huo
- State Key Laboratory of Characteristic Chinese Medicine Resources of Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Meng-Dan Liu
- State Key Laboratory of Characteristic Chinese Medicine Resources of Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Qi Zhang
- State Key Laboratory of Characteristic Chinese Medicine Resources of Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Dan Feng
- Department of Natural Medicinal Chemistry and Pharmacognosy, School of Pharmacy, Qingdao University, Qingdao 266021, People's Republic of China
| | - Li-Jun Huang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Dong Wang
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Yu-Cheng Gu
- Syngenta Jealott's Hill International Research Centre, Berkshire RG42 6EY, U.K
| | - Yun Deng
- State Key Laboratory of Characteristic Chinese Medicine Resources of Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Da-Le Guo
- State Key Laboratory of Characteristic Chinese Medicine Resources of Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
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5
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van Breemen RB, Muchiri RN, Bates TA, Weinstein JB, Leier HC, Farley S, Tafesse FG. Cannabinoids Block Cellular Entry of SARS-CoV-2 and the Emerging Variants. JOURNAL OF NATURAL PRODUCTS 2022; 85:176-184. [PMID: 35007072 PMCID: PMC8768006 DOI: 10.1021/acs.jnatprod.1c00946] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Indexed: 05/27/2023]
Abstract
As a complement to vaccines, small-molecule therapeutic agents are needed to treat or prevent infections by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and its variants, which cause COVID-19. Affinity selection-mass spectrometry was used for the discovery of botanical ligands to the SARS-CoV-2 spike protein. Cannabinoid acids from hemp (Cannabis sativa) were found to be allosteric as well as orthosteric ligands with micromolar affinity for the spike protein. In follow-up virus neutralization assays, cannabigerolic acid and cannabidiolic acid prevented infection of human epithelial cells by a pseudovirus expressing the SARS-CoV-2 spike protein and prevented entry of live SARS-CoV-2 into cells. Importantly, cannabigerolic acid and cannabidiolic acid were equally effective against the SARS-CoV-2 alpha variant B.1.1.7 and the beta variant B.1.351. Orally bioavailable and with a long history of safe human use, these cannabinoids, isolated or in hemp extracts, have the potential to prevent as well as treat infection by SARS-CoV-2.
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Affiliation(s)
- Richard B. van Breemen
- Linus
Pauling Institute, Department of Pharmaceutical Sciences, College
of Pharmacy, Oregon State University, 2900 SW Campus Way, Corvallis, Oregon 97331, United States
| | - Ruth N. Muchiri
- Linus
Pauling Institute, Department of Pharmaceutical Sciences, College
of Pharmacy, Oregon State University, 2900 SW Campus Way, Corvallis, Oregon 97331, United States
| | - Timothy A. Bates
- Molecular
Microbiology & Immunology, Oregon Health
& Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Jules B. Weinstein
- Molecular
Microbiology & Immunology, Oregon Health
& Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Hans C. Leier
- Molecular
Microbiology & Immunology, Oregon Health
& Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Scotland Farley
- Molecular
Microbiology & Immunology, Oregon Health
& Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
| | - Fikadu G. Tafesse
- Molecular
Microbiology & Immunology, Oregon Health
& Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, United States
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6
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Muchiri RN, Kibitel J, Redick MA, van Breemen RB. Advances in Magnetic Microbead Affinity Selection Screening: Discovery of Natural Ligands to the SARS-CoV-2 Spike Protein. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:181-188. [PMID: 34939787 PMCID: PMC9429804 DOI: 10.1021/jasms.1c00318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Affinity selection-mass spectrometry, which includes magnetic microbead affinity selection-screening (MagMASS), is ideal for the discovery of ligands in complex mixtures that bind to pharmacological targets. Therapeutic agents are needed to prevent or treat COVID-19, which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection of human cells by SARS-CoV-2 involves binding of the virus spike protein subunit 1 (S1) to the human cell receptor angiotensin converting enzyme-2 (ACE2). Like antibodies, small molecules have the potential to block the interaction of the viral S1 protein with human ACE2 and prevent SARS-CoV-2 infection. Therefore, a MagMASS assay was developed for the discovery of ligands to the S1 protein. Unlike previous MagMASS approaches, this new assay used robotics for 5-fold enhancement of throughput and sensitivity. The assay was validated using the SBP-1 peptide, which is identical to the ACE2 amino acid sequence recognized by the S1 protein, and then applied to the discovery of natural ligands from botanical extracts. Small molecule ligands to the S1 protein were discovered in extracts of the licorice species, Glycyrrhiza inflata. In particular, the licorice ligand licochalcone A was identified through dereplication and comparison with standards using HPLC with high-resolution tandem mass spectrometry.
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Affiliation(s)
- Ruth N. Muchiri
- Linus Pauling Institute and College of Pharmacy, Oregon State University, Corvallis, OR 97331 USA
| | | | - Margaret A. Redick
- Linus Pauling Institute and College of Pharmacy, Oregon State University, Corvallis, OR 97331 USA
| | - Richard B. van Breemen
- Linus Pauling Institute and College of Pharmacy, Oregon State University, Corvallis, OR 97331 USA
- Corresponding author: 373 Linus Pauling Science Center, Corvallis, OR 97331 USA, TEL: 541-737-5080,
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7
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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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8
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Burton TC, Lankin DC, Nikolic D, Guo B, Ju J, Dietz BM, Che CT, Soejarto DD, van Breemen RB. Isolation and elucidation of two isoflavonoids from an American Indian plant, Amorpha canescens Pursh, using Magnetic Microbead Affinity Selection Screening (MagMASS) for estrogen receptor alpha ligands. PHYTOCHEMISTRY LETTERS 2021; 45:110-116. [PMID: 35465454 PMCID: PMC9032482 DOI: 10.1016/j.phytol.2021.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
A new isoflavonoid, xanthocerin J, along with previously described xanthocerin A, were isolated from a methanol extract of aerial parts of a traditional American Indian herb, Amorpha canescens Pursh (Asteraceae). The structures of these compounds were characterized using mass spectrometry and NMR based on an isolation protocol using magnetic microbead affinity selection screening (MagMASS) for ligands to the estrogen receptor alpha (ERα). These compounds bound to ERα from an active fraction that exhibited dose-dependent antiestrogenic activity in the in vitro Ishikawa assay. However, these compounds did not exhibit antiestrogenic activity in the cell-based Ishikawa assay. Xanthocerin A and J may exhibit synergistic or additive activity with other compounds found in A. canescens which needs further exploration. This work highlights the potential of A. canescens as a prospect for the future discovery of compounds for women's health related to estrogen pathways.
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Affiliation(s)
- Tristesse C.J. Burton
- Division of Academic Internal Medicine and Geriatrics, Department of Medicine, College of Medicine, University of Illinois at Chicago, 1747 W Roosevelt Road, Chicago, IL, 60608, USA
- Corresponding author at: Division of Academic Internal Medicine and Geriatrics, Department of Medicine, College of Medicine, University of Illinois at Chicago, 1747 W Roosevelt Road, Chicago, Illinois, 60608, USA. (T.C.J. Burton)
| | - David C. Lankin
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Dejan Nikolic
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
- UIC/NIH Center for Botanical Dietary Supplements Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Brian Guo
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Jianming Ju
- Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210028, China
| | - Birgit M. Dietz
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
- UIC/NIH Center for Botanical Dietary Supplements Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Chun-Tao Che
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Djaja Djendoel Soejarto
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, Illinois, 60605, USA
| | - Richard B. van Breemen
- UIC/NIH Center for Botanical Dietary Supplements Research, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
- Linus Pauling Institute, College of Pharmacy, Oregon State University, 305 Linus Pauling Science Center, Corvallis, Oregon, 97331, USA
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9
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Magnetic particles for enzyme immobilization: A versatile support for ligand screening. J Pharm Biomed Anal 2021; 204:114286. [PMID: 34358814 DOI: 10.1016/j.jpba.2021.114286] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/20/2021] [Accepted: 07/25/2021] [Indexed: 12/12/2022]
Abstract
Enzyme inhibitors represent a substantial fraction of all small molecules currently in clinical use. Therefore, the early stage of drug-discovery process and development efforts are focused on the identification of new enzyme inhibitors through screening assays. The use of immobilized enzymes on solid supports to probe ligand-enzyme interactions have been employed with success not only to identify and characterize but also to isolate new ligands from complex mixtures. Between the available solid supports, magnetic particles have emerged as a promising support for enzyme immobilization due to the high superficial area, easy separation from the reaction medium and versatility. Particularly, the ligand fishing assay has been employed as a very useful tool to rapidly isolate bioactive compounds from complex mixtures, and hence the use of magnetic particles for enzyme immobilization has been widespread. Thus, this review provides a critical overview of the screening assays using immobilized enzymes on magnetic particles between 2006 and 2021.
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10
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Ma H, Liang H, Cai S, O'Keefe BR, Mooberry SL, Cichewicz RH. An Integrated Strategy for the Detection, Dereplication, and Identification of DNA-Binding Biomolecules from Complex Natural Product Mixtures. JOURNAL OF NATURAL PRODUCTS 2021; 84:750-761. [PMID: 33226219 PMCID: PMC9229839 DOI: 10.1021/acs.jnatprod.0c00946] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A fundamental factor in natural product drug discovery programs is the necessity to identify the active component(s) from complex chemical mixtures. Whereas this has traditionally been accomplished using bioassay-guided fractionation, we questioned whether alternative techniques could supplement and, in some cases, even supplant this approach. We speculated that a combination of ligand-fishing methods and modern analytical tools (e.g., LC-MS and online natural product databases) offered a route to enhance natural product drug discovery. Herein, a candidate solution referred to as the lickety-split ligand-affinity-based molecular angling system (LLAMAS) is described. This approach utilizes an ultrafiltration-based LC-PDA-MS/MS-guided DNA-binding assay in combination with the (i) Global Natural Products Social Molecular Networking, (ii) Dictionary of Natural Products, and (iii) SciFinder platforms to identify DNA binders in complex chemical mixtures. LLAMAS was initially vetted in tests using known small-molecule DNA binders and then optimized to a 96-well plate-based format. A set of 332 plant samples used in traditional Chinese medicine was screened for DNA-binding activity with LLAMAS, resulting in the identification of seven DNA-binding molecules, including berberine (12), palmatine (13), coptisine (14), fangchinoline (15), tetrandrine (16), daurisoline (17), and dauricine (18). These results demonstrate that LLAMAS is an effective natural product discovery platform for the efficient identification and dereplication of DNA-binding molecules from complex mixtures.
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Affiliation(s)
- Hongyan Ma
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, and Natural Products Discovery Group and Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Huiyun Liang
- Department of Pharmacology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Shengxin Cai
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, and Natural Products Discovery Group and Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Barry R O'Keefe
- Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, and Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Susan L Mooberry
- Department of Pharmacology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, and Natural Products Discovery Group and Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma 73019, United States
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11
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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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12
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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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13
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Blay V, Otero-Muras I, Annis DA. Solving the Competitive Binding Equilibria between Many Ligands: Application to High-Throughput Screening and Affinity Optimization. Anal Chem 2020; 92:12630-12638. [PMID: 32812419 DOI: 10.1021/acs.analchem.0c02715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Modern small-molecule drug discovery relies on the selective targeting of biological macromolecules by low-molecular weight compounds. Therefore, the binding affinities of candidate drugs to their targets are key for pharmacological activity and clinical use. For drug discovery methods where multiple drug candidates can simultaneously bind to the same target, a competition is established, and the resulting equilibrium depends on the dissociation constants and concentration of all the species present. Such coupling between all equilibrium-governing parameters complicates analysis and development of improved mixture-based, high-throughput drug discovery techniques. In this work, we present an iterative computational algorithm to solve coupled equilibria between an arbitrary number of ligands and a biomolecular target that is efficient and robust. The algorithm does not require the estimation of initial values to rapidly converge to the solution of interest. We explored binding equilibria under ligand/receptor conditions used in mixture-based library screening by affinity selection-mass spectrometry (AS-MS). Our studies support a facile method for affinity-ranking hits. The ranking method involves varying the receptor-to-ligand concentration ratio in a pool of candidate ligands in two sequential AS-MS analyses. The ranking is based on the relative change in bound ligand concentration. The method proposed does not require a known reference ligand and produces a ranking that is insensitive to variations in the concentration of individual compounds, thereby enabling the use of unpurified compounds generated by mixture-based combinatorial synthesis techniques.
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Affiliation(s)
- Vincent Blay
- Division of Biomaterials and Bioengineering, University of California San Francisco, San Francisco, California 94143, United States
| | - Irene Otero-Muras
- BioProcess Engineering Group, IIM-CSIC, Spanish National Research Council, Vigo 36208, Spain
| | - David Allen Annis
- Aileron Therapeutics, Inc., 490 Arsenal Way, Watertown, Massachusetts 02472, United States
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de Lima JM, Furlani IL, da Silva LRG, Valverde AL, Cass QB. Micro- and nano-sized amine-terminated magnetic beads in a ligand fishing assay. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4116-4122. [PMID: 32766628 DOI: 10.1039/d0ay01269f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Functionalized micro- and nano-sized magnetic beads (MBs) have been widely used as versatile supports for proteins, enzymes, and drugs. Immobilized protein on MB surfaces has been successfully applied for ligand fishing assays allowing for direct identification of active ligands from complex mixtures, such as natural products and synthetic libraries. MBs with different properties such as different core compositions, sizes, coatings, and surface modifications are available commercially. Studies have been conducted to understand the role of these properties for ligand fishing assays. Here we evaluated, for the first time, the effect of MB size on the ligand fishing assay for acetylcholinesterase from Electrophorus electricus (AChE). For this purpose, four commercially available amine-terminated magnetic particles with diameters ranging from 4.5 nm to 106 μm were evaluated to fish out galantamine, a well-known AChE inhibitor, from an aqueous solution. All MBs were efficient at using glutaraldehyde to covalently immobilize AChE. The particles with diameters of about 1 μm (small microparticles) presented a higher protein mass capacity per milligram of particle than did those with diameters of about 4.5 nm (nanoparticles) and those with diameters of about 106 μm (large microparticles). The influence of these supports on the produced AChE-MBs with regards to hydrolysis turnover and ligand fishing was evaluated and is fully discussed.
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Affiliation(s)
- Juliana Maria de Lima
- Separare, Departamento de Química, Universidade Federal de São Carlos, São Carlos, Brazil.
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15
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Arai MA, Morita K, Kawano H, Makita Y, Hashimoto M, Suganami A, Tamura Y, Sadhu SK, Ahmed F, Ishibashi M. Target protein-oriented isolation of Hes1 dimer inhibitors using protein based methods. Sci Rep 2020; 10:1381. [PMID: 31992824 PMCID: PMC6987128 DOI: 10.1038/s41598-020-58451-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/15/2020] [Indexed: 12/14/2022] Open
Abstract
Natural products isolation using protein based methods is an attractive for obtaining bioactive compounds. To discover neural stem cell (NSC) differentiation activators, we isolated eight inhibitors of Hes1 dimer formation from Psidium guajava using the Hes1-Hes1 interaction fluorescent plate assay and one inhibitor from Terminalia chebula using the Hes1-immobilized beads method. Of the isolated compounds, gallic acid (8) and 4-O-(4”-O-galloyl-α-L-rhamnopyranosyl)ellagic acid (11) showed potent Hes1 dimer formation inhibitory activity, with IC50 values of 10.3 and 2.53 μM, respectively. Compound 11 accelerated the differentiation activity of C17.2 NSC cells dose dependently, increasing the number of neurons with a 125% increase (5 μM) compared to the control.
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Affiliation(s)
- Midori A Arai
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan.
| | - Kaori Morita
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Haruka Kawano
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Yuna Makita
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Manami Hashimoto
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan
| | - Akiko Suganami
- Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Yutaka Tamura
- Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Samir K Sadhu
- Pharmacy Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Firoj Ahmed
- Department of Pharmaceutical Chemistry, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Masami Ishibashi
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan.
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