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De Soricellis G, Rinaldi F, Tengattini S, Temporini C, Negri S, Capelli D, Montanari R, Cena H, Salerno S, Massolini G, Guzzo F, Calleri E. Development of an analytical platform for the affinity screening of natural extracts by SEC-MS towards PPARα and PPARγ receptors. Anal Chim Acta 2024; 1309:342666. [PMID: 38772654 DOI: 10.1016/j.aca.2024.342666] [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: 02/15/2024] [Revised: 04/19/2024] [Accepted: 04/29/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND Peroxisome proliferator-activated receptors (PPARs) belong to the superfamily of nuclear receptors and represent the targets for the therapeutical treatment of type 2 diabetes, dyslipidemia and hyperglycemia associated with metabolic syndrome. Some medicinal plants have been traditionally used to treat this kind of metabolic diseases. Today only few drugs targeting PPARs have been approved and for this reason, the rapid identification of novel ligands and/or chemical scaffolds starting from natural extracts would benefit of a selective affinity ligand fishing assay. RESULTS In this paper we describe the development of a new ligand fishing assay based on size exclusion chromatography (SEC) coupled to LC-MS for the analysis of complex samples such as botanical extracts. The known PPARα and PPARγ ligands, WY-14643 and rosiglitazone respectively, were used for system development and evaluation. The system has found application on an Allium lusitanicum methanolic extract, containing saponins, a class of chemical compounds which have attracted interest as PPARs ligands because of their hypolipidemic and insulin-like properties. SIGNIFICANCE A new SEC-AS-MS method has been developed for the affinity screening of PPARα and PPARγ ligands. The system proved to be highly specific and will be used to improve the throughput for the identification of new selective metabolites from natural souces targeting PPARα and PPARγ.
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Affiliation(s)
- G De Soricellis
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, Pavia, 27100, Italy; National Biodiversity Future Center (NBFC), Palermo, 90133, Italy
| | - F Rinaldi
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, Pavia, 27100, Italy
| | - S Tengattini
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, Pavia, 27100, Italy
| | - C Temporini
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, Pavia, 27100, Italy
| | - S Negri
- National Biodiversity Future Center (NBFC), Palermo, 90133, Italy; Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - D Capelli
- Institute of Crystallography (IC), National Research Council (CNR), Via Salaria Km 29.300, Rome, 00016, Italy
| | - R Montanari
- Institute of Crystallography (IC), National Research Council (CNR), Via Salaria Km 29.300, Rome, 00016, Italy
| | - H Cena
- National Biodiversity Future Center (NBFC), Palermo, 90133, Italy; Laboratory of Dietetics and Clinical Nutrition, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Via Bassi 21, Pavia, 27100, Italy; Clinical Nutrition and Dietetics Service, Unit of Internal Medicine and Endocrinology, ICS Maugeri IRCCS, Pavia, 27100, Italy
| | - S Salerno
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, Pavia, 27100, Italy
| | - G Massolini
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, Pavia, 27100, Italy
| | - F Guzzo
- National Biodiversity Future Center (NBFC), Palermo, 90133, Italy; Department of Biotechnology, University of Verona, Verona, 37134, Italy
| | - E Calleri
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, Pavia, 27100, Italy; National Biodiversity Future Center (NBFC), Palermo, 90133, Italy.
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Jung S, Woo SY, Park MH, Kim DY, Lee SU, Oh SR, Kim MO, Lee J, Ryu HW. Potent inhibition of human tyrosinase inhibitor by verproside from the whole plant of Pseudolysimachion rotundum var. subintegrum. J Enzyme Inhib Med Chem 2023; 38:2252198. [PMID: 37649388 PMCID: PMC10472861 DOI: 10.1080/14756366.2023.2252198] [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: 05/18/2023] [Revised: 08/05/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
Affinity-based ultrafiltration-mass spectrometry coupled with ultraperformance liquid chromatography-quadrupole time-of-flight mass spectrometry was utilised for the structural identification of direct tyrosinase ligands from a crude Pseudolysimachion rotundum var. subintegrum extract. False positives were recognised by introducing time-dependent inhibition in the control for comparison. The P. rotundum extract contained nine main metabolites in the UPLC-QTOF-MS chromatogram. However, four metabolites were reduced after incubation with tyrosinase, indicating that these metabolites were bound to tyrosinase. The IC50 values of verproside (1) were 31.2 µM and 197.3 µM for mTyr and hTyr, respectively. Verproside showed 5.6-fold higher efficacy than that of its positive control (kojic acid in hTyr). The most potent tyrosinase inhibitor, verproside, features a 3,4-dihydroxybenzoic acid moiety on the iridoid glycoside and inhibits tyrosinase in a time-dependent and competitive manner. Among these three compounds, verproside is bound to the active site pocket with a docking energy of -6.9 kcal/mol and four hydrogen bonding interactions with HIS61 and HIS85.
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Affiliation(s)
- Sunin Jung
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
- Department of CBRN Medicine Research, center for Special Military Medicine, Armed Forces Medical Research Institute, Daejeon, South Korea
| | - So-Yeun Woo
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
| | - Mi Hyeon Park
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
| | - Doo-Young Kim
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
| | - Su Ui Lee
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
| | - Sei-Ryang Oh
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
| | - Mun-Ock Kim
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
| | - Jinhyuk Lee
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Hyung Won Ryu
- Korea Research Institute of Bioscience and Biotechnology, Cheong-ju si, Republic of Korea
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Dey AK, Banarjee R, Boroumand M, Rutherford DV, Strassheim Q, Nyunt T, Olinger B, Basisty N. Translating Senotherapeutic Interventions into the Clinic with Emerging Proteomic Technologies. BIOLOGY 2023; 12:1301. [PMID: 37887011 PMCID: PMC10604147 DOI: 10.3390/biology12101301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/25/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023]
Abstract
Cellular senescence is a state of irreversible growth arrest with profound phenotypic changes, including the senescence-associated secretory phenotype (SASP). Senescent cell accumulation contributes to aging and many pathologies including chronic inflammation, type 2 diabetes, cancer, and neurodegeneration. Targeted removal of senescent cells in preclinical models promotes health and longevity, suggesting that the selective elimination of senescent cells is a promising therapeutic approach for mitigating a myriad of age-related pathologies in humans. However, moving senescence-targeting drugs (senotherapeutics) into the clinic will require therapeutic targets and biomarkers, fueled by an improved understanding of the complex and dynamic biology of senescent cell populations and their molecular profiles, as well as the mechanisms underlying the emergence and maintenance of senescence cells and the SASP. Advances in mass spectrometry-based proteomic technologies and workflows have the potential to address these needs. Here, we review the state of translational senescence research and how proteomic approaches have added to our knowledge of senescence biology to date. Further, we lay out a roadmap from fundamental biological discovery to the clinical translation of senotherapeutic approaches through the development and application of emerging proteomic technologies, including targeted and untargeted proteomic approaches, bottom-up and top-down methods, stability proteomics, and surfaceomics. These technologies are integral for probing the cellular composition and dynamics of senescent cells and, ultimately, the development of senotype-specific biomarkers and senotherapeutics (senolytics and senomorphics). This review aims to highlight emerging areas and applications of proteomics that will aid in exploring new senescent cell biology and the future translation of senotherapeutics.
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Affiliation(s)
| | | | | | | | | | | | | | - Nathan Basisty
- Translational Geroproteomics Unit, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA; (A.K.D.); (R.B.); (M.B.); (D.V.R.); (Q.S.); (T.N.); (B.O.)
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Ripon Rouf ASM, Amin MA, Islam MK, Haque F, Ahmed KR, Rahman MA, Islam MZ, Kim B. Statistical Bioinformatics to Uncover the Underlying Biological Mechanisms That Linked Smoking with Type 2 Diabetes Patients Using Transcritpomic and GWAS Analysis. Molecules 2022; 27:molecules27144390. [PMID: 35889263 PMCID: PMC9323276 DOI: 10.3390/molecules27144390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 12/14/2022] Open
Abstract
Type 2 diabetes (T2D) is a chronic metabolic disease defined by insulin insensitivity corresponding to impaired insulin sensitivity, decreased insulin production, and eventually failure of beta cells in the pancreas. There is a 30–40 percent higher risk of developing T2D in active smokers. Moreover, T2D patients with active smoking may gradually develop many complications. However, there is still no significant research conducted to solve the issue. Hence, we have proposed a highthroughput network-based quantitative pipeline employing statistical methods. Transcriptomic and GWAS data were analysed and obtained from type 2 diabetes patients and active smokers. Differentially Expressed Genes (DEGs) resulted by comparing T2D patients’ and smokers’ tissue samples to those of healthy controls of gene expression transcriptomic datasets. We have found 55 dysregulated genes shared in people with type 2 diabetes and those who smoked, 27 of which were upregulated and 28 of which were downregulated. These identified DEGs were functionally annotated to reveal the involvement of cell-associated molecular pathways and GO terms. Moreover, protein–protein interaction analysis was conducted to discover hub proteins in the pathways. We have also identified transcriptional and post-transcriptional regulators associated with T2D and smoking. Moreover, we have analysed GWAS data and found 57 common biomarker genes between T2D and smokers. Then, Transcriptomic and GWAS analyses are compared for more robust outcomes and identified 1 significant common gene, 19 shared significant pathways and 12 shared significant GOs. Finally, we have discovered protein–drug interactions for our identified biomarkers.
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Affiliation(s)
| | - Md. Al Amin
- Department of Computer Science & Engineering, Prime University, Dhaka 1216, Bangladesh;
| | - Md. Khairul Islam
- Department of Information & Communication Technology, Islamic University, Kushtia 7003, Bangladesh;
| | - Farzana Haque
- Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia 7003, Bangladesh;
| | - Kazi Rejvee Ahmed
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 02447, Korea;
| | - Md. Ataur Rahman
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 02447, Korea;
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea
- Correspondence: (M.A.R.); (M.Z.I.); (B.K.)
| | - Md. Zahidul Islam
- Department of Information & Communication Technology, Islamic University, Kushtia 7003, Bangladesh;
- Correspondence: (M.A.R.); (M.Z.I.); (B.K.)
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 02447, Korea;
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea
- Correspondence: (M.A.R.); (M.Z.I.); (B.K.)
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Ambrose AJ, Pham NT, Sivinski J, Guimarães L, Mollasalehi N, Jimenez P, Abad MA, Jeyaprakash AA, Shave S, Costa-Lotufo LV, La Clair JJ, Auer M, Chapman E. A two-step resin based approach to reveal survivin-selective fluorescent probes. RSC Chem Biol 2021; 2:181-186. [PMID: 34458780 PMCID: PMC8342005 DOI: 10.1039/d0cb00122h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/07/2020] [Indexed: 01/24/2023] Open
Abstract
The identification of modulators for proteins without assayable biochemical activity remains a challenge in chemical biology. The presented approach adapts a high-throughput fluorescence binding assay and functional chromatography, two protein-resin technologies, enabling the discovery and isolation of fluorescent natural product probes that target proteins independently of biochemical function. The resulting probes also suggest targetable pockets for lead discovery. Using human survivin as a model, we demonstrate this method with the discovery of members of the prodiginine family as fluorescent probes to the cancer target survivin.
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Affiliation(s)
- Andrew J Ambrose
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
| | - Nhan T Pham
- School of Biological Sciences and Edinburgh Medical School, Biomedical Sciences, University of Edinburgh The King's Buildings CH Waddington Building 3.07 Max Born Crescent Edinburgh EH9 3BF UK
| | - Jared Sivinski
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
| | - Larissa Guimarães
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
- Departamento de Farmacologia, Universidade de São Paulo São Paulo SP 05508-900 Brazil
| | - Niloufar Mollasalehi
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
| | - Paula Jimenez
- Instituto do Mar, Universidade Federal de São Paulo Santos SP 11.070-100 Brazil
| | - Maria A Abad
- Wellcome Centre for Cell Biology, University of Edinburgh Edinburgh EH9 3BF UK
| | | | - Steven Shave
- School of Biological Sciences and Edinburgh Medical School, Biomedical Sciences, University of Edinburgh The King's Buildings CH Waddington Building 3.07 Max Born Crescent Edinburgh EH9 3BF UK
| | | | - James J La Clair
- Xenobe Research Institute P. O. Box 3052 San Diego CA 92163-1052 USA
| | - Manfred Auer
- School of Biological Sciences and Edinburgh Medical School, Biomedical Sciences, University of Edinburgh The King's Buildings CH Waddington Building 3.07 Max Born Crescent Edinburgh EH9 3BF UK
| | - Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona Tucson AZ 85721 USA
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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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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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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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Blay V, Tolani B, Ho SP, Arkin MR. High-Throughput Screening: today's biochemical and cell-based approaches. Drug Discov Today 2020; 25:1807-1821. [PMID: 32801051 DOI: 10.1016/j.drudis.2020.07.024] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/01/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022]
Abstract
High-throughput screening (HTS) provides starting chemical matter in the adventure of developing a new drug. In this review, we survey several HTS methods used today for hit identification, organized in two main flavors: biochemical and cell-based assays. Biochemical assays discussed include fluorescence polarization and anisotropy, FRET, TR-FRET, and fluorescence lifetime analysis. Binding-based methods are also surveyed, including NMR, SPR, mass spectrometry, and DSF. On the other hand, cell-based assays discussed include viability, reporter gene, second messenger, and high-throughput microscopy assays. We devote some emphasis to high-content screening, which is becoming very popular. An advisable stage after hit discovery using phenotypic screens is target deconvolution, and we provide an overview of current chemical proteomics, in silico, and chemical genetics tools. Emphasis is made on recent CRISPR/dCas-based screens. Lastly, we illustrate some of the considerations that inform the choice of HTS methods and point to some areas with potential interest for future research.
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Affiliation(s)
- Vincent Blay
- Division of Biomaterials and Bioengineering, School of Dentistry, University of California San Francisco, San Francisco, CA 94143, USA; Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Bhairavi Tolani
- Thoracic Oncology Program, Department of Surgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Sunita P Ho
- Division of Biomaterials and Bioengineering, School of Dentistry, University of California San Francisco, San Francisco, CA 94143, USA; Department of Urology, School of Medicine, University of California San Francisco, San Francisco, CA 94143, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and the Small Molecule Discovery Center, University of California, San Francisco, CA, USA.
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10
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Identification of α-Glucosidase Inhibitors from Ipomoea alba by Affinity-Directed Fractionation-Mass Spectrometry. REVISTA BRASILEIRA DE FARMACOGNOSIA 2020. [DOI: 10.1007/s43450-020-00068-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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11
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Sázelová P, Koval D, Severa L, Teplý F, Vigh G, Kašička V. Determination of binding constants of multiple charged cyclodextrin complexes by ACE using uncorrected and ionic strength corrected actual mobilities of the species involved. Electrophoresis 2020; 41:523-535. [DOI: 10.1002/elps.201900352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/06/2019] [Accepted: 11/21/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Petra Sázelová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 Czechia
| | - Dušan Koval
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 Czechia
| | - Lukáš Severa
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 Czechia
| | - Filip Teplý
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 Czechia
| | - Gyula Vigh
- Texas A&M UniversityDepartment Chemistry College Station TX USA
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Prague 6 Czechia
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de Moraes MC, Cardoso CL, Cass QB. Solid-Supported Proteins in the Liquid Chromatography Domain to Probe Ligand-Target Interactions. Front Chem 2019; 7:752. [PMID: 31803714 PMCID: PMC6873629 DOI: 10.3389/fchem.2019.00752] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
Ligand-target interactions play a central role in drug discovery processes because these interactions are crucial in biological systems. Small molecules-proteins interactions can regulate and modulate protein function and activity through conformational changes. Therefore, bioanalytical tools to screen new ligands have focused mainly on probing ligand-target interactions. These interactions have been evaluated by using solid-supported proteins, which provide advantages like increased protein stability and easier protein extraction from the reaction medium, which enables protein reuse. In some specific approaches, precisely in the ligand fishing assay, the bioanalytical method allows the ligands to be directly isolated from complex mixtures, including combinatorial libraries and natural products extracts without prior purification or fractionation steps. Most of these screening assays are based on liquid chromatography separation, and the binding events can be monitored through on-line or off-line methods. In the on-line approaches, solid supports containing the immobilized biological target are used as chromatographic columns most of the time. Several terms have been used to refer to such approaches, such as weak affinity chromatography, high-performance affinity chromatography, on-flow activity assays, and high-performance liquid affinity chromatography. On the other hand, in the off-line approaches, the binding event occurs outside the liquid chromatography system and may encompass affinity and activity-based assays in which the biological target is immobilized on magnetic particles or monolithic silica, among others. After the incubation step, the supernatant or the eluate from the binding assay is analyzed by liquid chromatography coupled to various detectors. Regardless of the selected bioanalytical approach, the use of solid supported proteins has significantly contributed to the development of automated and reliable screening methods that enable ligands to be isolated and characterized in complex matrixes without purification, thereby reducing costs and avoiding time-laborious steps. This review provides a critical overview of recently developed assays.
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Affiliation(s)
- Marcela Cristina de Moraes
- Laboratório SINCROMA, Instituto de Química, Departamento de Química Orgânica, Universidade Federal Fluminense, Niterói, Brazil
| | - Carmen Lucia Cardoso
- Grupo de Cromatografia de Bioafinidade e Produtos Naturais, Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Quezia Bezerra Cass
- Separare, Departamento de Química, Universidade Federal de São Carlos, São Carlos, Brazil
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Igel-Egalon A, Laferrière F, Moudjou M, Bohl J, Mezache M, Knäpple T, Herzog L, Reine F, Jas-Duval C, Doumic M, Rezaei H, Béringue V. Early stage prion assembly involves two subpopulations with different quaternary structures and a secondary templating pathway. Commun Biol 2019; 2:363. [PMID: 31602412 PMCID: PMC6778151 DOI: 10.1038/s42003-019-0608-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
The dynamics of aggregation and structural diversification of misfolded, host-encoded proteins in neurodegenerative diseases are poorly understood. In many of these disorders, including Alzheimer's, Parkinson's and prion diseases, the misfolded proteins are self-organized into conformationally distinct assemblies or strains. The existence of intrastrain structural heterogeneity is increasingly recognized. However, the underlying processes of emergence and coevolution of structurally distinct assemblies are not mechanistically understood. Here, we show that early prion replication generates two subsets of structurally different assemblies by two sequential processes of formation, regardless of the strain considered. The first process corresponds to a quaternary structural convergence, by reducing the parental strain polydispersity to generate small oligomers. The second process transforms these oligomers into larger ones, by a secondary autocatalytic templating pathway requiring the prion protein. This pathway provides mechanistic insights into prion structural diversification, a key determinant for prion adaptation and toxicity.
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Affiliation(s)
| | - Florent Laferrière
- VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- Present Address: Institute of Neurodegenerative Diseases, CNRS UMR5293, University of Bordeaux, Bordeaux, France
| | | | - Jan Bohl
- VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- LCP, CNRS, Université Paris Sud, 91400 Orsay, France
| | - Mathieu Mezache
- VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- INRIA, MAMBA, Université Paris VI, 75005 Paris, France
| | - Tina Knäpple
- VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Laetitia Herzog
- VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Fabienne Reine
- VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Christelle Jas-Duval
- VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
- Pathogenesis and Control of Chronic Infections, EFS, INSERM, University of Montpellier, 34000 Montpellier, France
| | - Marie Doumic
- INRIA, MAMBA, Université Paris VI, 75005 Paris, France
| | - Human Rezaei
- VIM, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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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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15
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Affiliation(s)
- Kit S Lam
- Department of Biochemistry and Molecular Medicine, Division of Hematology & Oncology, School of Medicine, UC Davis NCI-designated Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA.
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16
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Zietek BM, Still KBM, Jaschusch K, Bruyneel B, Ariese F, Brouwer TJF, Luger M, Limburg RJ, Rosier JC, V Iperen DJ, Casewell NR, Somsen GW, Kool J. Bioactivity Profiling of Small-Volume Samples by Nano Liquid Chromatography Coupled to Microarray Bioassaying Using High-Resolution Fractionation. Anal Chem 2019; 91:10458-10466. [PMID: 31373797 PMCID: PMC6706796 DOI: 10.1021/acs.analchem.9b01261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
High-throughput
screening platforms for the identification of bioactive
compounds in mixtures have become important tools in the drug discovery
process. Miniaturization of such screening systems may overcome problems
associated with small sample volumes and enhance throughput and sensitivity.
Here we present a new screening platform, coined picofractionation
analytics, which encompasses microarray bioassays and mass spectrometry
(MS) of components from minute amounts of samples after their nano
liquid chromatographic (nanoLC) separation. Herein, nanoLC was coupled
to a low-volume liquid dispenser equipped with pressure-fed solenoid
valves, enabling 50-nL volumes of column effluent (300 nL/min) to
be discretely deposited on a glass slide. The resulting fractions
were dried and subsequently bioassayed by sequential printing of nL-volumes
of reagents on top of the spots. Unwanted evaporation of bioassay
liquids was circumvented by employing mineral oil droplets. A fluorescence
microscope was used for assay readout in kinetic mode. Bioassay data
were correlated to MS data obtained using the same nanoLC conditions
in order to assign bioactives. The platform provides the possibility
of freely choosing a wide diversity of bioassay formats, including
those requiring long incubation times. The new method was compared
to a standard bioassay approach, and its applicability was demonstrated
by screening plasmin inhibitors and fibrinolytic bioactives from mixtures
of standards and snake venoms, revealing active peptides and coagulopathic
proteases.
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Affiliation(s)
- Barbara M Zietek
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Kristina B M Still
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Kevin Jaschusch
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Ben Bruyneel
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Freek Ariese
- LaserLaB , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Tinco J F Brouwer
- Electronic Engineering , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Matthijs Luger
- Electronic Engineering , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Rob J Limburg
- Electronic Engineering , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Joost C Rosier
- Fine Mechanics and Engineering Beta-VU , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Dick J V Iperen
- Fine Mechanics and Engineering Beta-VU , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Nicholas R Casewell
- Centre for Snakebite Research & Interventions , Liverpool School of Tropical Medicine , Pembroke Place , Liverpool L3 5QA , U.K.,Centre for Drugs and Diagnostics , Liverpool School of Tropical Medicine , Pembroke Place , Liverpool L3 5QA , U.K
| | - Govert W Somsen
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
| | - Jeroen Kool
- Division of BioAnalytical Chemistry, Amsterdam Institute of Molecules, Medicines and Systems , Vrije Universiteit Amsterdam , Amsterdam 1081 HZ , The Netherlands
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17
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Liao S, Zhao M, Luo J, Luo K, Wu J, Liu R, Wang S, Jia P, Bai Y, Zheng X. The interaction mechanism between alkaloids and pepsin based on lum-AuNPs in the chemiluminescence analysis. RSC Adv 2019; 9:25569-25575. [PMID: 35530091 PMCID: PMC9070008 DOI: 10.1039/c9ra02978h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 07/20/2019] [Indexed: 12/14/2022] Open
Abstract
Herein, novel luminol functional gold nanoparticles (lum-AuNPs) were quickly prepared in an alkaline luminol solution with HAuCl4, which had the unique characteristics of uniform size and excellent luminescence properties. A self-made flow injection-chemiluminescence (FI-CL) system was established to study the interaction between pepsin (Pep) and five alkaloids (anisodamine, berberine, reserpine, jatrorrhizine and matrine) using lum-AuNPs as the CL probe. Based on the abovementioned home-made CL system, the possible interaction mechanisms of Pep with five alkaloids have been comprehensively discussed by molecular docking simulation, chemical thermodynamics and kinetic studies. The results indicated that there were obvious CL enhancement and inhibition effects on the lum-AuNPs CL system for the Pep and the complex of Pep/alkaloids, respectively. The possible mechanism for the interaction of Pep-five alkaloids was mainly mediated by the hydrophobic force. The binding constant K and binding site n for the Pep-alkaloid interaction are consistent with the list of Ber > Res > Ani, Jat > Mat, which is relative to the potential of groups of alkaloids interacting with the active site of Pep.
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Affiliation(s)
- Sha Liao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University Xi'an 710069 China
| | - Meimei Zhao
- School of Pharmacy, Shaanxi Institute of International Trade & Commerce Xi'an 712046 China
| | - Jing Luo
- Shaanxi Traditional Chinese Medicine Hospital Xi'an 710004 China
| | - Kai Luo
- Department of Chemistry, Fudan University Shanghai 200438 China
| | - Jingni Wu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University Xi'an 710069 China
| | - Ruimin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University Xi'an 710069 China
| | - Shixiang Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University Xi'an 710069 China
| | - Pu Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University Xi'an 710069 China
| | - Yajun Bai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University Xi'an 710069 China
| | - Xiaohui Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Northwest University Xi'an 710069 China
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18
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Šolínová V, Žáková L, Jiráček J, Kašička V. Pressure assisted partial filling affinity capillary electrophoresis employed for determination of binding constants of human insulin hexamer complexes with serotonin, dopamine, arginine, and phenol. Anal Chim Acta 2019; 1052:170-178. [DOI: 10.1016/j.aca.2018.11.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 11/10/2018] [Accepted: 11/12/2018] [Indexed: 11/30/2022]
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Otvos RA, Still KBM, Somsen GW, Smit AB, Kool J. Drug Discovery on Natural Products: From Ion Channels to nAChRs, from Nature to Libraries, from Analytics to Assays. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2019; 24:362-385. [PMID: 30682257 PMCID: PMC6484542 DOI: 10.1177/2472555218822098] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/16/2018] [Accepted: 12/07/2018] [Indexed: 12/21/2022]
Abstract
Natural extracts are complex mixtures that may be rich in useful bioactive compounds and therefore are attractive sources for new leads in drug discovery. This review describes drug discovery from natural products and in explaining this process puts the focus on ion-channel drug discovery. In particular, the identification of bioactives from natural products targeting nicotinic acetylcholine receptors (nAChRs) and serotonin type 3 receptors (5-HT3Rs) is discussed. The review is divided into three parts: "Targets," "Sources," and "Approaches." The "Targets" part will discuss the importance of ion-channel drug targets in general, and the α7-nAChR and 5-HT3Rs in particular. The "Sources" part will discuss the relevance for drug discovery of finding bioactive compounds from various natural sources such as venoms and plant extracts. The "Approaches" part will give an overview of classical and new analytical approaches that are used for the identification of new bioactive compounds with the focus on targeting ion channels. In addition, a selected overview is given of traditional venom-based drug discovery approaches and of diverse hyphenated analytical systems used for screening complex bioactive mixtures including venoms.
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Affiliation(s)
- Reka A. Otvos
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kristina B. M. Still
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Govert W. Somsen
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jeroen Kool
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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20
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Deng S, Xia L, Zhu X, Zhu J, Cai M, Wang X. Natural Alpha-Glucosidase Inhibitors Rapid Fishing from Cyperus Rotundus Using Immobilized Enzyme Affinity Screening Combined with UHPLC-QTOF MS. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2019; 18:1508-1515. [PMID: 32641959 PMCID: PMC6934975 DOI: 10.22037/ijpr.2019.1100753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
An efficient and rapid affinity-based screening method for directly fishing out natural alpha-glucosidase inhibitors from Cyperus rotundus extract by using immobilized enzyme technology combined with UHPLC-QTOF MS analysis was established. As a result without time-consuming and laborious isolation workload and false positive interference, five natural alpha-glucosidase inhibitors were successfully recognized and identified from only 400 uL of C. rotundus extracts within only a couple of hours, which suggested that the screening method was rapid, economical, sensitive and feasible. In addition, the captured compounds were isolated and characterized as stilbenoids oligomers, and were proved to be strong alpha-glucosidase inhibitors by inhibitory assay in-vitro. Among them, 3 stilbenoids trimers were reported to be potent α-glucosidase inhibitors for the first time. This method could be modified and have the potential for rapidly screening of active compounds extracts against some new targets by immobilizing some other biomacromolecules.
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21
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Cheignon C, Cordeau E, Prache N, Cantel S, Martinez J, Subra G, Arnaudguilhem C, Bouyssiere B, Enjalbal C. Receptor-Ligand Interaction Measured by Inductively Coupled Plasma Mass Spectrometry and Selenium Labeling. J Med Chem 2018; 61:10173-10184. [PMID: 30395477 DOI: 10.1021/acs.jmedchem.8b01320] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In the search for an alternative strategy to the radioactivity measurement conventionally performed to probe receptor-ligand interactions in pharmacological assays, we demonstrated that selenium labeling of the studied ligand combined with elemental mass spectrometry was as efficient and robust as the reference method but devoid of its environmental and health hazards. The proof-of-concept was illustrated on two GPCR receptors, vasopressin (V1A) and cholecystokinin B (CCK-B), involving peptides as endogenous ligands. We proposed several methodologies to produce selenium-labeled ligands according to peptide sequences along with binding affinity constraints. A selection of selenopeptides that kept high affinities toward the targeted receptor were engaged in saturation and competitive binding experiments with subsequent sensitive RP-LC-ICP-MS measurements. Experimental values of affinity constant ( Ki) were perfectly correlated to literature data, illustrating the general great potency of replacing radioactive iodine by selenium for ligand labeling to further undergo unaffected pharmacology experiments efficiently monitored by elemental mass spectrometry.
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Affiliation(s)
- Clémence Cheignon
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Emmanuelle Cordeau
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Nolween Prache
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Sonia Cantel
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Jean Martinez
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Gilles Subra
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
| | - Carine Arnaudguilhem
- CNRS/Univ Pau & Pays Adour/E2S UPPA , Institut des Sciences Analytiques et de Physico-Chimie pour L'Environnement et les Matériaux, UMR 5254 , 64000 Pau , France
| | - Brice Bouyssiere
- CNRS/Univ Pau & Pays Adour/E2S UPPA , Institut des Sciences Analytiques et de Physico-Chimie pour L'Environnement et les Matériaux, UMR 5254 , 64000 Pau , France
| | - Christine Enjalbal
- IBMM, University of Montpellier, CNRS, ENSCM , 34095 Montpellier , France
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22
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Rapid ligand fishing for identification of acetylcholinesterase-binding peptides in snake venom reveals new properties of dendrotoxins. Toxicon 2018; 152:1-8. [DOI: 10.1016/j.toxicon.2018.06.080] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/16/2018] [Accepted: 06/25/2018] [Indexed: 11/23/2022]
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23
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Temporini C, Brusotti G, Pochetti G, Massolini G, Calleri E. Affinity-based separation methods for the study of biological interactions: The case of peroxisome proliferator-activated receptors in drug discovery. Methods 2018; 146:12-25. [DOI: 10.1016/j.ymeth.2018.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/30/2018] [Accepted: 02/05/2018] [Indexed: 10/18/2022] Open
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24
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MS methods to study macromolecule-ligand interaction: Applications in drug discovery. Methods 2018; 144:152-174. [PMID: 29890284 DOI: 10.1016/j.ymeth.2018.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/01/2018] [Accepted: 06/03/2018] [Indexed: 12/12/2022] Open
Abstract
The interaction of small compounds (i.e. ligands) with macromolecules or macromolecule assemblies (i.e. targets) is the mechanism of action of most of the drugs available today. Mass spectrometry is a popular technique for the interrogation of macromolecule-ligand interactions and therefore is also widely used in drug discovery and development. Thanks to its versatility, mass spectrometry is used for multiple purposes such as biomarker screening, identification of the mechanism of action, ligand structure optimization or toxicity assessment. The evolution and automation of the instruments now allows the development of high throughput methods with high sensitivity and a minimized false discovery rate. Herein, all these approaches are described with a focus on the methods for studying macromolecule-ligand interaction aimed at defining the structure-activity relationships of drug candidates, along with their mechanism of action, metabolism and toxicity.
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25
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Rossato M, Miralles G, M'Kadmi C, Maingot M, Amblard M, Mouillac B, Gagne D, Martinez J, Subra G, Enjalbal C, Cantel S. Quantitative MALDI-MS Binding Assays: An Alternative to Radiolabeling. ChemMedChem 2016; 11:2582-2587. [PMID: 27922213 DOI: 10.1002/cmdc.201600447] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/27/2016] [Indexed: 12/20/2022]
Abstract
Radiolabeling of ligands is still the gold standard in the study of high-affinity receptor-ligand interactions. In an effort toward safer and simpler alternatives to the use of radioisotopes, we developed a quantitative and highly sensitive matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) method that relies on the use of chemically tagged ligands designed to be specifically detectable when present as traces in complex biological mixtures such as cellular lysates. This innovative technology allows easy, sensitive detection and accurate quantification of analytes at the sub-nanomolar level. After statistical validation, we were able to perform pharmacological evaluations of G protein-coupled receptor (V1A-R)-ligand interactions. Both saturation and competitive binding assays were successfully processed.
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Affiliation(s)
- Maxime Rossato
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Guillaume Miralles
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Céline M'Kadmi
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Mathieu Maingot
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Muriel Amblard
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Bernard Mouillac
- Institut de Génomique Fonctionnelle (IGF), 141 Rue de la Cardonille, 34090, Montpellier, France
| | - Didier Gagne
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Gilles Subra
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Christine Enjalbal
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
| | - Sonia Cantel
- Institut des Biomolécules Max Mousseron (IBMM), UMR5247 CNRS, ENSCM, Université de Montpellier, Place E. Bataillon, 34095, Montpellier Cedex 5, France
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26
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Zhuo R, Liu H, Liu N, Wang Y. Ligand Fishing: A Remarkable Strategy for Discovering Bioactive Compounds from Complex Mixture of Natural Products. Molecules 2016; 21:molecules21111516. [PMID: 27845727 PMCID: PMC6274472 DOI: 10.3390/molecules21111516] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/01/2016] [Accepted: 11/06/2016] [Indexed: 12/16/2022] Open
Abstract
Identification of active compounds from natural products is a critical and challenging task in drug discovery pipelines. Besides commonly used bio-guided screening approaches, affinity selection strategy coupled with liquid chromatography or mass spectrometry, known as ligand fishing, has been gaining increasing interest from researchers. In this review, we summarized this emerging strategy and categorized those methods as off-line or on-line mode according to their features. The separation principles of ligand fishing were introduced based on distinct analytical techniques, including biochromatography, capillary electrophoresis, ultrafiltration, equilibrium dialysis, microdialysis, and magnetic beads. The applications of ligand fishing approaches in the discovery of lead compounds were reviewed. Most of ligand fishing methods display specificity, high efficiency, and require less sample pretreatment, which makes them especially suitable for screening active compounds from complex mixtures of natural products. We also summarized the applications of ligand fishing in the modernization of Traditional Chinese Medicine (TCM), and propose some perspectives of this remarkable technique.
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Affiliation(s)
- Rongjie Zhuo
- Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, China.
| | - Hao Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Ningning Liu
- TCM Research Center, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.
| | - Yi Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
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Imaduwage KP, Go EP, Zhu Z, Desaire H. HAMS: High-Affinity Mass Spectrometry Screening. A High-Throughput Screening Method for Identifying the Tightest-Binding Lead Compounds for Target Proteins with No False Positive Identifications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1870-1877. [PMID: 27600575 PMCID: PMC5501305 DOI: 10.1007/s13361-016-1472-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 07/21/2016] [Accepted: 07/23/2016] [Indexed: 06/06/2023]
Abstract
A major challenge in drug discovery is the identification of high affinity lead compounds that bind a particular target protein; these leads are typically identified by high throughput screens. Mass spectrometry has become a detection method of choice in drug screening assays because the target and the ligand need not be modified. Label-free assays are advantageous because they can be developed more rapidly than assays requiring labels, and they eliminate the risk of the label interfering with the binding event. However, in commonly used MS-based screening methods, detection of false positives is a major challenge. Here, we describe a detection strategy designed to eliminate false positives. In this approach, the protein and the ligands are incubated together, and the non-binders are separated for detection. Hits (protein binders) are not detectable by MS after incubation with the protein, but readily identifiable by MS when the target protein is not present in the incubation media. The assay was demonstrated using three different proteins and hundreds of non-inhibitors; no false positive hits were identified in any experiment. The assay can be tuned to select for ligands of a particular binding affinity by varying the quantity of protein used and the immobilization method. As examples, the method selectively detected inhibitors that have Ki values of 0.2 μM, 50 pM, and 700 pM. These findings demonstrate that the approach described here compares favorably with traditional MS-based screening methods. Graphical Abstract ᅟ.
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Affiliation(s)
- Kasun P Imaduwage
- The Ralph N. Adams Institute for Bioanalytical Chemistry and Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Eden P Go
- The Ralph N. Adams Institute for Bioanalytical Chemistry and Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Zhikai Zhu
- The Ralph N. Adams Institute for Bioanalytical Chemistry and Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA
| | - Heather Desaire
- The Ralph N. Adams Institute for Bioanalytical Chemistry and Department of Chemistry, University of Kansas, 2030 Becker Drive, Lawrence, KS, 66047, USA.
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Wei H, Zhang X, Tian X, Wu G. Pharmaceutical applications of affinity-ultrafiltration mass spectrometry: Recent advances and future prospects. J Pharm Biomed Anal 2016; 131:444-453. [PMID: 27668554 DOI: 10.1016/j.jpba.2016.09.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/06/2016] [Accepted: 09/20/2016] [Indexed: 11/17/2022]
Abstract
The immunoaffinity of protein with ligand is broadly involved in many bioanalytical methods. Affinity-ultrafiltration mass spectrometry (AUF-MS), a platform based on interaction of protein-ligand affinity, has been developed to fish out interesting molecules from complex matrixes. Here we reviewed the basics of AUF-MS and its recent applications to pharmaceutical field, i.e. target-oriented discovery of lead compounds from combinatorial libraries and natural product extracts, and determination of free drug concentration in biosamples. Selected practical examples were highlighted to illustrate the advances of AUF-MS in pharmaceutical fields. The future prospects were also presented.
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Affiliation(s)
- Han Wei
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China.
| | - Xiaojian Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Xin Tian
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Guanghua Wu
- Department of Pharmacy, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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29
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The automatic use of capillary isoelectric focusing with whole column imaging detection for carbamazepine binding to human serum albumin. J Pharm Biomed Anal 2016; 127:9-17. [DOI: 10.1016/j.jpba.2016.01.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 12/01/2015] [Accepted: 01/10/2016] [Indexed: 12/23/2022]
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30
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Zhou Y, Liu Z, Rothschild KJ, Lim MJ. Proteome-wide drug screening using mass spectrometric imaging of bead-arrays. Sci Rep 2016; 6:26125. [PMID: 27194112 PMCID: PMC4872124 DOI: 10.1038/srep26125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/27/2016] [Indexed: 12/17/2022] Open
Abstract
A fundamental challenge in the drug discovery process is to develop compounds with high efficacy and minimal side-effects. We describe a new approach to proteome-wide drug screening for detection of on- and off-target binding which combines the advantages of mass spectrometry with microarray technology. The method involves matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) of agarose micro-beads randomly arrayed at high-density in custom micro-well plates. Each bead carries a unique protein target and a corresponding photocleavable mass-tag for coding (PC-Mass-Tag). Compounds bound to specific protein beads and a photo-released coding PC-Mass-Tag are detected simultaneously using MALDI-MSI. As an initial demonstration of this approach, two kinase-targeted drugs, Dasatinib and Brigatinib (AP26113), were simultaneously screened against a model 50-member kinase-bead library. A MALDI-MSI scan performed at the equivalent density of 495,000 beads in the footprint of a microscope slide yielded 100% sensitivity for detecting known strong interactions with no false positives.
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Affiliation(s)
- Ying Zhou
- AmberGen, Inc., 313 Pleasant Street, Watertown, MA 02472, United States
| | - Ziying Liu
- AmberGen, Inc., 313 Pleasant Street, Watertown, MA 02472, United States
| | - Kenneth J Rothschild
- AmberGen, Inc., 313 Pleasant Street, Watertown, MA 02472, United States.,Molecular Biophysics Laboratory, Department of Physics and Photonics Center, Boston University, Boston, MA 02215, United States
| | - Mark J Lim
- AmberGen, Inc., 313 Pleasant Street, Watertown, MA 02472, United States
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31
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De-qiang L, Zhao J, Wu D, Shao-ping L. Discovery of active components in herbs using chromatographic separation coupled with online bioassay. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:81-90. [DOI: 10.1016/j.jchromb.2016.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 01/19/2016] [Accepted: 02/03/2016] [Indexed: 11/30/2022]
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32
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Neaga I, Bodoki E, Hambye S, Blankert B, Oprean R. Study of nucleic acid–ligand interactions by capillary electrophoretic techniques: A review. Talanta 2016; 148:247-56. [DOI: 10.1016/j.talanta.2015.10.077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/21/2015] [Accepted: 10/25/2015] [Indexed: 10/22/2022]
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33
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Yao C, Wang T, Zhang B, He D, Na N, Ouyang J. Screening of the binding of small molecules to proteins by desorption electrospray ionization mass spectrometry combined with protein microarray. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1950-1958. [PMID: 26174365 DOI: 10.1007/s13361-015-1221-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 06/04/2023]
Abstract
The interaction between bioactive small molecule ligands and proteins is one of the important research areas in proteomics. Herein, a simple and rapid method is established to screen small ligands that bind to proteins. We designed an agarose slide to immobilize different proteins. The protein microarrays were allowed to interact with different small ligands, and after washing, the microarrays were screened by desorption electrospray ionization mass spectrometry (DESI MS). This method can be applied to screen specific protein binding ligands and was shown for seven proteins and 34 known ligands for these proteins. In addition, a high-throughput screening was achieved, with the analysis requiring approximately 4 s for one sample spot. We then applied this method to determine the binding between the important protein matrix metalloproteinase-9 (MMP-9) and 88 small compounds. The molecular docking results confirmed the MS results, demonstrating that this method is suitable for the rapid and accurate screening of ligands binding to proteins. Graphical Abstract ᅟ.
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Affiliation(s)
- Chenxi Yao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Tao Wang
- Department of Pharmacy, Changzhi Medical College, Changzhi, 046000, People's Republic of China
| | - Buqing Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Dacheng He
- Key Laboratory for Cell Proliferation and Regulation Biology, Ministry of Education Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Na Na
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China.
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34
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Zhang L, Huo W, Gao Y, Shi S, Gao Y. Determination of Affinity and Kinetic Constants of the Biotin-Streptavidin Complex Using Microfluidic GMR Biosensors. IEEE TRANSACTIONS ON MAGNETICS 2015; 51:1-4. [PMID: 0 DOI: 10.1109/tmag.2015.2443125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
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35
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Mladic M, Scholten DJ, Niessen WMA, Somsen GW, Smit MJ, Kool J. At-line coupling of LC-MS to bioaffinity and selectivity assessment for metabolic profiling of ligands towards chemokine receptors CXCR1 and CXCR2. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1002:42-53. [PMID: 26301479 DOI: 10.1016/j.jchromb.2015.08.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 08/03/2015] [Accepted: 08/04/2015] [Indexed: 11/28/2022]
Abstract
This study describes an analytical method for bioaffinity and selectivity assessment of CXCR2 antagonists and their metabolites. The method is based on liquid chromatographic separation (LC) of metabolic mixtures followed by parallel mass spectrometry (MS) identification and bioaffinity determination. The bioaffinity is assessed using radioligand binding assays in 96-well plates after at-line nanofractionation. The described method was optimized for chemokines and low-molecular weight CXCR2 ligands. The limits of detection (LODs; injected amounts) for MK-7123, a high affinity binder to both CXCR1 and CXCR2 receptors belonging to the diaminocyclobutendione chemical class, were 40pmol in CXCR1 binding and 8pmol in CXCR2 binding. For CXCL8, the LOD was 5pmol in both binding assays. A control compound was always taken along with each bioassay plate as triplicate dose-response curve. For MK-7123, the calculated IC50 values were 314±59nM (CXCR1 binding) and 38±11nM (CXCR2 binding). For CXCL8, the IC50 values were 6.9±1.4nM (CXCR1 binding) and 2.7±1.3nM (CXCR2 binding). After optimization, the method was applied to the analysis of metabolic mixtures of eight LMW CXCR2 antagonists generated by incubation with pig liver microsomes. Moreover, metabolic profiling of the MK-7123 compound was described using the developed method. Three bioactive metabolites were found, two of which were (partially) identified. This method is suitable for bioaffinity and selectivity assessment of mixtures targeting the CXCR2. In contrary to conventional LC-MS based metabolic profiling studies done at the early lead discovery stage, additional qualitative bioactivity information of drug metabolites is obtained with the method described.
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Affiliation(s)
- Marija Mladic
- Amsterdam Institute for Molecules Medicines and Systems, Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands; Amsterdam Institute for Molecules Medicines and Systems, Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Danny J Scholten
- Amsterdam Institute for Molecules Medicines and Systems, Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Wilfried M A Niessen
- Amsterdam Institute for Molecules Medicines and Systems, Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands; hyphen MassSpec, de Wetstraat 8, 2332XT Leiden, The Netherlands
| | - Govert W Somsen
- Amsterdam Institute for Molecules Medicines and Systems, Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Martine J Smit
- Amsterdam Institute for Molecules Medicines and Systems, Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Jeroen Kool
- Amsterdam Institute for Molecules Medicines and Systems, Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands.
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36
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Štěpánová S, Kašička V. Capillary electrophoretic methods applied to the investigation of peptide complexes. J Sep Sci 2015; 38:2708-21. [DOI: 10.1002/jssc.201500399] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 05/01/2015] [Accepted: 05/01/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Sille Štěpánová
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Prague Czech Republic
| | - Václav Kašička
- Institute of Organic Chemistry and Biochemistry; Czech Academy of Sciences; Prague Czech Republic
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37
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Mass-spectrometry-based method for screening of new peptide ligands for G-protein-coupled receptors. Anal Bioanal Chem 2015; 407:5299-307. [DOI: 10.1007/s00216-015-8692-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 10/23/2022]
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38
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Li Q, Wang J, Yang L, Gao X, Chen H, Zhao X, Bian L, Zheng X. Estimation of interaction between oriented immobilized green fluorescent protein and its antibody by high performance affinity chromatography and molecular docking. J Mol Recognit 2015; 28:438-46. [DOI: 10.1002/jmr.2460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/17/2014] [Accepted: 12/17/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Qian Li
- College of Life Sciences; Northwest University; Xi'an 710069 China
| | - Jing Wang
- College of Life Sciences; Northwest University; Xi'an 710069 China
| | - Lingjian Yang
- College of Life Sciences; Northwest University; Xi'an 710069 China
| | - Xiaokang Gao
- College of Life Sciences; Northwest University; Xi'an 710069 China
| | - Hongwei Chen
- College of Life Sciences; Northwest University; Xi'an 710069 China
| | - Xinfeng Zhao
- College of Life Sciences; Northwest University; Xi'an 710069 China
| | - Liujiao Bian
- College of Life Sciences; Northwest University; Xi'an 710069 China
| | - Xiaohui Zheng
- College of Life Sciences; Northwest University; Xi'an 710069 China
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39
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Sun J, Zhang GL, Li S, Ivanov AR, Fenyo D, Lisacek F, Murthy SK, Karger BL, Brusic V. Pathway analysis and transcriptomics improve protein identification by shotgun proteomics from samples comprising small number of cells--a benchmarking study. BMC Genomics 2014; 15 Suppl 9:S1. [PMID: 25521637 PMCID: PMC4290587 DOI: 10.1186/1471-2164-15-s9-s1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Proteomics research is enabled with the high-throughput technologies, but our ability to identify expressed proteome is limited in small samples. The coverage and consistency of proteome expression are critical problems in proteomics. Here, we propose pathway analysis and combination of microproteomics and transcriptomics analyses to improve mass-spectrometry protein identification from small size samples. RESULTS Multiple proteomics runs using MCF-7 cell line detected 4,957 expressed proteins. About 80% of expressed proteins were present in MCF-7 transcripts data; highly expressed transcripts are more likely to have expressed proteins. Approximately 1,000 proteins were detected in each run of the small sample proteomics. These proteins were mapped to gene symbols and compared with gene sets representing canonical pathways, more than 4,000 genes were extracted from the enriched gene sets. The identified canonical pathways were largely overlapping between individual runs. Of identified pathways 182 were shared between three individual small sample runs. CONCLUSIONS Current technologies enable us to directly detect 10% of expressed proteomes from small sample comprising as few as 50 cells. We used knowledge-based approaches to elucidate the missing proteome that can be verified by targeted proteomics. This knowledge-based approach includes pathway analysis and combination of gene expression and protein expression data for target prioritization. Genes present in both the enriched gene sets (canonical pathways collection) and in small sample proteomics data correspond to approximately 50% of expressed proteomes in larger sample proteomics data. In addition, 90% of targets from canonical pathways were estimated to be expressed. The comparison of proteomics and transcriptomics data, suggests that highly expressed transcripts have high probability of protein expression. However, approximately 10% of expressed proteins could not be matched with the expressed transcripts.
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40
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Abstract
This paper discusses a novel, simple, and inexpensive micro-volume ultrafiltration technique for protein concentration, desalting, buffer exchange, and size-based protein purification. The technique is suitable for processing protein samples in a high-throughput mode. It utilizes a combination of capillary action, and osmosis for drawing water and other permeable species from a micro-volume sample droplet applied on the surface of an ultrafiltration membrane. A macromolecule coated on the permeate side of the membrane functions as the osmolyte. The action of the osmolyte could, if required, be augmented by adding a supersorbent polymer layer over the osmolyte. The mildly hydrophobic surface of the polymeric ultrafiltration membrane used in this study minimized sample droplet spreading, thus making it easy to recover the retained material after separation, without sample interference and cross-contamination. High protein recoveries were observed in the micro-volume ultrafiltration experiments described in the paper.
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Affiliation(s)
- Raja Ghosh
- Department of Chemical Engineering, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4L7, Canada.
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41
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Development and validation of an LC-ESI-MS/MS method for the triple reuptake inhibitor indatraline enabling its quantification in MS Binding Assays. Anal Bioanal Chem 2014; 407:471-85. [DOI: 10.1007/s00216-014-8312-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 10/29/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022]
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42
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Zheng X, Li Z, Beeram S, Podariu M, Matsuda R, Pfaunmiller EL, White CJ, Carter N, Hage DS. Analysis of biomolecular interactions using affinity microcolumns: a review. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 968:49-63. [PMID: 24572459 PMCID: PMC4112177 DOI: 10.1016/j.jchromb.2014.01.026] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 01/16/2014] [Accepted: 01/19/2014] [Indexed: 12/15/2022]
Abstract
Affinity chromatography has become an important tool for characterizing biomolecular interactions. The use of affinity microcolumns, which contain immobilized binding agents and have volumes in the mid-to-low microliter range, has received particular attention in recent years. Potential advantages of affinity microcolumns include the many analysis and detection formats that can be used with these columns, as well as the need for only small amounts of supports and immobilized binding agents. This review examines how affinity microcolumns have been used to examine biomolecular interactions. Both capillary-based microcolumns and short microcolumns are considered. The use of affinity microcolumns with zonal elution and frontal analysis methods are discussed. The techniques of peak decay analysis, ultrafast affinity extraction, split-peak analysis, and band-broadening studies are also explored. The principles of these methods are examined and various applications are provided to illustrate the use of these methods with affinity microcolumns. It is shown how these techniques can be utilized to provide information on the binding strength and kinetics of an interaction, as well as on the number and types of binding sites. It is further demonstrated how information on competition or displacement effects can be obtained by these methods.
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Affiliation(s)
- Xiwei Zheng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Zhao Li
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Sandya Beeram
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Maria Podariu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Ryan Matsuda
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Erika L Pfaunmiller
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - Christopher J White
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - NaTasha Carter
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA
| | - David S Hage
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588-0304, USA.
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43
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Affinity selection-based two-dimensional chromatography coupled with high-performance liquid chromatography-mass spectrometry for discovering xanthine oxidase inhibitors from Radix Salviae Miltiorrhizae. Anal Bioanal Chem 2014; 406:4987-95. [DOI: 10.1007/s00216-014-7902-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 05/12/2014] [Accepted: 05/14/2014] [Indexed: 01/03/2023]
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44
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Exploring drug–protein interactions using the relationship between injection volume and capacity factor. J Chromatogr A 2014; 1339:137-44. [DOI: 10.1016/j.chroma.2014.03.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 11/15/2022]
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45
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Orwig SD, Chi PV, Du Y, Hill SE, Cavitt MA, Suntharalingam A, Turnage KC, Dickey CA, France S, Fu H, Lieberman RL. Ligands for glaucoma-associated myocilin discovered by a generic binding assay. ACS Chem Biol 2014; 9:517-25. [PMID: 24279319 DOI: 10.1021/cb4007776] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mutations in the olfactomedin domain of myocilin (myoc-OLF) are the strongest link to inherited primary open angle glaucoma. In this recently identified protein misfolding disorder, aggregation-prone disease variants of myocilin hasten glaucoma-associated elevation of intraocular pressure, leading to vision loss. Despite its well-documented pathogenic role, myocilin remains a domain of unknown structure or function. Here we report the first small-molecule ligands that bind to the native state of myoc-OLF. To discover these molecules, we designed a general label-free, mix-and-measure, high throughput chemical assay for restabilization (CARS), which is likely readily adaptable to discover ligands for other proteins. Of the 14 hit molecules identified from screening myoc-OLF against the Sigma-Aldrich Library of Pharmacologically Active Compounds using CARS, surface plasmon resonance binding studies reveal three are stoichiometric ligand scaffolds with low micromolar affinity. Two compounds, GW5074 and apigenin, inhibit myoc-OLF amyloid formation in vitro. Structure-activity relationship-based soluble derivatives reduce aggregation in vitro as well as enhance secretion of full-length mutant myocilin in a cell culture model. Our compounds set the stage for a new chemical probe approach to clarify the biological function of wild-type myocilin and represent lead therapeutic compounds for diminishing intracellular sequestration of toxic mutant myocilin.
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Affiliation(s)
- Susan D. Orwig
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
| | - Pamela V. Chi
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
| | - Yuhong Du
- Department
of Pharmacology, Emory University School of Medicine, 1510 Clifton
Road, Atlanta, Georgia 30322, United States
| | - Shannon E. Hill
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
| | - Marchello A. Cavitt
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
| | - Amrithaa Suntharalingam
- Department
of Molecular Medicine and Byrd Alzheimer’s Research Institute, University of South Florida, 4001 E. Fletcher Ave. Tampa, Florida 33613, United States
| | - Katherine C. Turnage
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
| | - Chad A. Dickey
- Department
of Molecular Medicine and Byrd Alzheimer’s Research Institute, University of South Florida, 4001 E. Fletcher Ave. Tampa, Florida 33613, United States
| | - Stefan France
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
| | - Haian Fu
- Department
of Pharmacology, Emory University School of Medicine, 1510 Clifton
Road, Atlanta, Georgia 30322, United States
| | - Raquel L. Lieberman
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, Georgia 30332-0400, United States
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46
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Discovery of xanthine oxidase inhibitors from a complex mixture using an online, restricted-access material coupled with column-switching liquid chromatography with a diode-array detection system. Anal Bioanal Chem 2014; 406:1975-84. [DOI: 10.1007/s00216-013-7612-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Revised: 12/25/2013] [Accepted: 12/30/2013] [Indexed: 10/25/2022]
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47
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Deng S, Xia L, Xiao H. Screening of α-glucosidase inhibitors from green tea extracts using immobilized enzymes affinity capture combined with UHPLC-QTOF MS analysis. Chem Commun (Camb) 2014; 50:2582-4. [DOI: 10.1039/c3cc49681c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Huang S, Lyu Y, Qing X, Wang W, Tang L, Cheng K, Wang W. Autoprocessing: an essential step for expression and purification of enterovirus 71 3C(pro) in Escherichia coli. Biotechnol Lett 2013; 35:1845-52. [PMID: 23881322 DOI: 10.1007/s10529-013-1284-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 06/20/2013] [Indexed: 12/18/2022]
Abstract
A gene encoding the 3BC of human enterovirus 71 (EV71) was cloned and inserted into a derivative of plasmid pET-32a(+) driven by T7 promoter. The expressed 3C protease (3C(pro)) autocatalytically cleaved itself from the recombinant protein Trx-3BC and the mature 3C(pro) partitioned in the soluble fraction of bacterial lysate. The 13-amino-acid peptide substrates with the junction of 3B/3C were used to verify the proteolysis activity of the purified 3C(pro). The EV71 3C(pro) had a Km value of 63 μM (measured by a continuous fluorescence assay). The other solid-phase activity assay of the EV71 3C(pro) was developed using HPLC to analyze the proteolytic products. The combination of two activity assays contributes to promote the identification of the specific inhibitors targeted to the EV71 3C(pro).
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Affiliation(s)
- Shuqiong Huang
- Key Laboratory of Biosynthesis of Natural Products, State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Ministry of Health of PRC, Beijing, 100050, China,
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Honarparvar B, Govender T, Maguire GEM, Soliman MES, Kruger HG. Integrated Approach to Structure-Based Enzymatic Drug Design: Molecular Modeling, Spectroscopy, and Experimental Bioactivity. Chem Rev 2013; 114:493-537. [DOI: 10.1021/cr300314q] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Bahareh Honarparvar
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Thavendran Govender
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Glenn E. M. Maguire
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Mahmoud E. S. Soliman
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
| | - Hendrik G. Kruger
- Catalysis
and Peptide Research Unit and ‡School of Health Sciences, University of KwaZulu Natal, Durban 4001, South Africa
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50
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Bioactivity fingerprint analysis of cyclooxygenase-2 ligands from radix Aconiti by ultrafiltration–UPLC–MSn. Anal Bioanal Chem 2013; 405:7437-45. [DOI: 10.1007/s00216-013-7153-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 06/15/2013] [Accepted: 06/17/2013] [Indexed: 01/08/2023]
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