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Gioiello A, Piccinno A, Lozza AM, Cerra B. The Medicinal Chemistry in the Era of Machines and Automation: Recent Advances in Continuous Flow Technology. J Med Chem 2020; 63:6624-6647. [PMID: 32049517 PMCID: PMC7997576 DOI: 10.1021/acs.jmedchem.9b01956] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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Medicinal
chemistry plays a fundamental and underlying role in
chemical biology, pharmacology, and medicine to discover safe and
efficacious drugs. Small molecule medicinal chemistry relies on iterative
learning cycles composed of compound design, synthesis, testing, and
data analysis to provide new chemical probes and lead compounds for
novel and druggable targets. Using traditional approaches, the time
from hypothesis to obtaining the results can be protracted, thus limiting
the number of compounds that can be advanced into clinical studies.
This challenge can be tackled with the recourse of enabling technologies
that are showing great potential in improving the drug discovery process.
In this Perspective, we highlight recent developments toward innovative
medicinal chemistry strategies based on continuous flow systems coupled
with automation and bioassays. After a discussion of the aims and
concepts, we describe equipment and representative examples of automated
flow systems and end-to-end prototypes realized to expedite medicinal
chemistry discovery cycles.
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Affiliation(s)
- Antimo Gioiello
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Alessandro Piccinno
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Anna Maria Lozza
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
| | - Bruno Cerra
- Laboratory of Medicinal and Advanced Synthetic Chemistry (Lab MASC), Department of Pharmaceutical Sciences, University of Perugia, Via del Liceo 1, 06123 Perugia, Italy
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Portychová L, Schug KA. Instrumentation and applications of electrochemistry coupled to mass spectrometry for studying xenobiotic metabolism: A review. Anal Chim Acta 2017; 993:1-21. [PMID: 29078951 DOI: 10.1016/j.aca.2017.08.050] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/21/2017] [Accepted: 08/26/2017] [Indexed: 01/03/2023]
Abstract
The knowledge of metabolic pathways and biotransformation of xenobiotics, artificial substances foreign to the entire biological system, is crucial for elucidation of degradation routes of potentially toxic substances. Nowadays, there are many methods to simulate xenobiotic metabolism in the human body in vitro. In this review, the metabolism of various substances in the human body is described, followed by a summary of methods used for prediction of metabolic pathways and biotransformation. Above all, focus is placed on the coupling of electrochemistry to mass spectrometry, which is still a relatively new technique. This promising tool can mimic both oxidative phase I and conjugative phase II metabolism. Different experimental arrangements, with or without a separation step, and various applications of this technique are illustrated and critically reviewed.
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Affiliation(s)
- Lenka Portychová
- Research Institute for Organic Synthesis, Inc., 533 54 Rybitví, Czech Republic; Department of Analytical Chemistry, Palacký University, 771 46 Olomouc, Czech Republic
| | - Kevin A Schug
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX 76019, USA.
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3
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Jamshidi-Aidji M, Morlock GE. From Bioprofiling and Characterization to Bioquantification of Natural Antibiotics by Direct Bioautography Linked to High-Resolution Mass Spectrometry: Exemplarily Shown for Salvia miltiorrhiza Root. Anal Chem 2016; 88:10979-10986. [DOI: 10.1021/acs.analchem.6b02648] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Maryam Jamshidi-Aidji
- Interdisciplinary Research
Center (IFZ) and Institute of Nutritional Science, Department of Food
Science, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Gertrud E. Morlock
- Interdisciplinary Research
Center (IFZ) and Institute of Nutritional Science, Department of Food
Science, Justus Liebig University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
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4
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Peng WB, Tan JL, Huang DD, Ding XP. On-Line HPLC with Biochemical Detection for Screening Bioactive Compounds in Complex Matrixes. Chromatographia 2015. [DOI: 10.1007/s10337-015-2982-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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5
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6
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Oberacher H, Pitterl F, Erb R, Plattner S. Mass spectrometric methods for monitoring redox processes in electrochemical cells. MASS SPECTROMETRY REVIEWS 2015; 34:64-92. [PMID: 24338642 PMCID: PMC4286209 DOI: 10.1002/mas.21409] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 07/24/2013] [Accepted: 08/12/2013] [Indexed: 06/03/2023]
Abstract
Electrochemistry (EC) is a mature scientific discipline aimed to study the movement of electrons in an oxidation-reduction reaction. EC covers techniques that use a measurement of potential, charge, or current to determine the concentration or the chemical reactivity of analytes. The electrical signal is directly converted into chemical information. For in-depth characterization of complex electrochemical reactions involving the formation of diverse intermediates, products and byproducts, EC is usually combined with other analytical techniques, and particularly the hyphenation of EC with mass spectrometry (MS) has found broad applicability. The analysis of gases and volatile intermediates and products formed at electrode surfaces is enabled by differential electrochemical mass spectrometry (DEMS). In DEMS an electrochemical cell is sampled with a membrane interface for electron ionization (EI)-MS. The chemical space amenable to EC/MS (i.e., bioorganic molecules including proteins, peptides, nucleic acids, and drugs) was significantly increased by employing electrospray ionization (ESI)-MS. In the simplest setup, the EC of the ESI process is used to analytical advantage. A limitation of this approach is, however, its inability to precisely control the electrochemical potential at the emitter electrode. Thus, particularly for studying mechanistic aspects of electrochemical processes, the hyphenation of discrete electrochemical cells with ESI-MS was found to be more appropriate. The analytical power of EC/ESI-MS can further be increased by integrating liquid chromatography (LC) as an additional dimension of separation. Chromatographic separation was found to be particularly useful to reduce the complexity of the sample submitted either to the EC cell or to ESI-MS. Thus, both EC/LC/ESI-MS and LC/EC/ESI-MS are common.
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Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine and Core Facility Metabolomics, Innsbruck Medical UniversityInnsbruck, Austria
| | - Florian Pitterl
- Institute of Legal Medicine and Core Facility Metabolomics, Innsbruck Medical UniversityInnsbruck, Austria
| | - Robert Erb
- Institute of Legal Medicine and Core Facility Metabolomics, Innsbruck Medical UniversityInnsbruck, Austria
| | - Sabine Plattner
- Institute of Legal Medicine and Core Facility Metabolomics, Innsbruck Medical UniversityInnsbruck, Austria
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7
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Comparison of (bio-)transformation methods for the generation of metabolite-like compound libraries of p38α MAP kinase inhibitors using high-resolution screening. J Pharm Biomed Anal 2014; 88:235-44. [DOI: 10.1016/j.jpba.2013.08.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/26/2013] [Accepted: 08/27/2013] [Indexed: 11/17/2022]
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8
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Nicolardi S, Giera M, Kooijman P, Kraj A, Chervet JP, Deelder AM, van der Burgt YEM. On-line electrochemical reduction of disulfide bonds: improved FTICR-CID and -ETD coverage of oxytocin and hepcidin. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1980-7. [PMID: 24018861 PMCID: PMC3837188 DOI: 10.1007/s13361-013-0725-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 07/25/2013] [Accepted: 07/25/2013] [Indexed: 05/21/2023]
Abstract
Particularly in the field of middle- and top-down peptide and protein analysis, disulfide bridges can severely hinder fragmentation and thus impede sequence analysis (coverage). Here we present an on-line/electrochemistry/ESI-FTICR-MS approach, which was applied to the analysis of the primary structure of oxytocin, containing one disulfide bridge, and of hepcidin, containing four disulfide bridges. The presented workflow provided up to 80% (on-line) conversion of disulfide bonds in both peptides. With minimal sample preparation, such reduction resulted in a higher number of peptide backbone cleavages upon CID or ETD fragmentation, and thus yielded improved sequence coverage. The cycle times, including electrode recovery, were rapid and, therefore, might very well be coupled with liquid chromatography for protein or peptide separation, which has great potential for high-throughput analysis.
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Affiliation(s)
- Simone Nicolardi
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Martin Giera
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Pieter Kooijman
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | | | | | - André M. Deelder
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
| | - Yuri E. M. van der Burgt
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, 2300 RC Leiden, The Netherlands
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Falck D, Oosthoek-de Vries AJ, Kolkman A, Lingeman H, Honing M, Wijmenga SS, Kentgens APM, Niessen WMA. EC–SPE–stripline-NMR analysis of reactive products: a feasibility study. Anal Bioanal Chem 2013; 405:6711-20. [DOI: 10.1007/s00216-013-7158-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/15/2013] [Accepted: 06/18/2013] [Indexed: 01/19/2023]
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10
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Falck D, Kool J, Honing M, Niessen WMA. Tandem mass spectrometry study of p38α kinase inhibitors and related substances. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:718-731. [PMID: 23722963 DOI: 10.1002/jms.3219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 06/02/2023]
Abstract
The p38 mitogen-activated protein kinase α (p38α) is an important drug target widely investigated for therapy of chronic inflammatory diseases. Its inhibitors are rather lipophilic and as such not very favourable lead compounds in drug discovery. Therefore, we explored various approaches to access new chemical space, create diversity, and generate lead libraries with improved solubility and reduced lipophilicity, based on known p38α inhibitors, e.g., BIRB796 and TAK-715. Compound modification strategies include incubation with human liver microsomes and bacterial cytochrome P450 mutants from Bacillus megaterium and treatment by electrochemical oxidation, H2O2, and intense light irradiation. The MS/MS fragmentation pathways of p38α inhibitors and their conversion products have been studied in an ion-trap-time-of-flight MS(n) instrument. Interpretation of accurate mass MS(n) data for four sets of related compounds revealed unexpected and peculiar fragmentation pathways that are discussed in detail. Emphasis is put on the usefulness of HRMS(n)-based structure elucidation in a screening setting and on peculiarities of the fragmentation with regard to the analytes and the MS instrument. In one example, an intramolecular rearrangement reaction accompanied by the loss of a bulky group is observed. For BIRB796, the double-charge precursor ion is used in MS(2), providing a wider range of fragment ions in our instrument. For TAK-715, a number of related compounds could be produced in a large-scale incubation with a Bacillus megaterium mutant, thus enabling comparison of the structure elucidation by (1)H NMR and MS(n). A surprisingly large number of homolytic cleavages are observed. Competition between two fragmentation pathways involving either the loss of CH3(•) or OH(•) radicals was observed for SB203580 and its conversion products.
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Affiliation(s)
- D Falck
- AIMMS Division of BioMolecular Analysis, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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Potterat O, Hamburger M. Concepts and technologies for tracking bioactive compounds in natural product extracts: generation of libraries, and hyphenation of analytical processes with bioassays. Nat Prod Rep 2013; 30:546-64. [DOI: 10.1039/c3np20094a] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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12
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Falck D, Schebb NH, Prihatiningtyas S, Zhang J, Heus F, Morisseau C, Kool J, Hammock BD, Niessen WMA. Development of On-line Liquid Chromatography-Biochemical Detection for Soluble Epoxide Hydrolase Inhibitors in Mixtures. Chromatographia 2013; 76:13-21. [PMID: 23526703 DOI: 10.1007/s10337-012-2343-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In this study, an end-point-based fluorescence assay for soluble epoxide hydrolase (sEH) was transformed into an on-line continuous-flow format. The on-line biochemical detection system (BCD) was coupled on-line to liquid chromatography (LC) to allow mixture analysis. The on-line BCD was based on a flow system wherein sEH activity was detected by competition of analytes with the substrate hydrolysis. The reaction product was measured by fluorescence detection. In parallel to the BCD data, UV and MS data were obtained through post-column splitting of the LC effluent. The buffer system and reagent concentrations were optimized resulting in a stable on-line BCD with a good assay window and good sensitivity (S/N > 60). The potency of known sEH inhibitors (sEHis) obtained by LC-BCD correlates well with published values. The LC-BCD system was applied to test how oxidative microsomal metabolism affects the potency of three sEHis. After incubation with pig liver microsomes, several metabolites of sEHis were characterized by MS, while their individual potencies were measured by BCD. For all compounds tested, active metabolites were observed. The developed method allows for the first time the detection of sEHis in mixtures providing new opportunities in the development of drug candidates.
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Affiliation(s)
- David Falck
- Department of BioMolecular Analysis, VU University Amsterdam, Amsterdam, The Netherlands
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Jahn S, Karst U. Electrochemistry coupled to (liquid chromatography/) mass spectrometry—Current state and future perspectives. J Chromatogr A 2012; 1259:16-49. [DOI: 10.1016/j.chroma.2012.05.066] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/09/2012] [Accepted: 05/19/2012] [Indexed: 02/04/2023]
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