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Gurard-Levin ZA, McMillan B, Whittington DA, Doyon B, Scholle MD, Ermolieff J, Bandi M, Liu MS, Amor A, Mallender WD. A duplexed high-throughput mass spectrometry assay for bifunctional POLB polymerase and lyase activity. SLAS Technol 2024; 29:100173. [PMID: 39094983 DOI: 10.1016/j.slast.2024.100173] [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: 06/15/2024] [Revised: 07/26/2024] [Accepted: 07/30/2024] [Indexed: 08/04/2024]
Abstract
Polymerase β (POLB), with dual functionality as a lyase and polymerase, plays a critical role in the base excision repair (BER) pathway to maintain genomic stability. POLB knockout and rescue studies in BRCA1/2-mutant cancer cell lines revealed that inhibition of lyase and polymerase activity is required for the synthetic lethal interaction observed with PARP inhibitors, highlighting POLB as a valuable therapeutic target. Traditional biochemical assays to screen for enzyme inhibitors focus on a single substrate to product relationship and limit the comprehensive analysis of enzymes such as POLB that utilize multiple substrates or catalyze a multi-step reaction. This report describes the first high-throughput mass spectrometry-based screen to measure the two distinct biochemical activities of POLB in a single assay using a duplexed self-assembled monolayer desorption ionization (SAMDI) mass spectrometry methodology. A multiplexed assay for POLB dual enzymatic activities was developed optimizing for kinetically balanced conditions and a collection of 200,000 diverse small molecules was screened in the duplexed format. Small molecule modulators identified in the screen were confirmed in a traditional fluorescence-based polymerase strand-displacement assay and an orthogonal label-free binding assay using SAMDI affinity selection mass spectrometry (ASMS). This work demonstrates the flexibility of high-throughput mass spectrometry approaches in drug discovery and highlights a novel application of SAMDI technology that opens new avenues for multiplexed high-throughput screening.
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Affiliation(s)
| | - Brian McMillan
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA; Jnana Therapeutics. One Design Center Place, Suite 19-400, Boston, MA, 02210, USA
| | | | - Brian Doyon
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA
| | | | - Jacques Ermolieff
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA; DICE Therapeutics/Lilly, 400 E Jamie CT, Third Floor, South San Francisco, CA, 94080, USA
| | - Madhavi Bandi
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA
| | - Mu-Sen Liu
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA
| | - Alvaro Amor
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA
| | - William D Mallender
- Tango Therapeutics Inc. 901 Brookline Avenue, Suite 901, Boston, MA, 02215, USA
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2
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Muller J, Marchisio L, Attia R, Zedet A, Maradan R, Vallet M, Aebischer A, Harakat D, Senejoux F, Ramseyer C, Foley S, Cardey B, Girard C, Pudlo M. A colorimetric assay adapted to fragment screening revealing aurones and chalcones as new arginase inhibitors. RSC Med Chem 2024; 15:1722-1730. [PMID: 38784454 PMCID: PMC11110760 DOI: 10.1039/d3md00713h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/23/2024] [Indexed: 05/25/2024] Open
Abstract
Arginase, a difficult-to-target metalloenzyme, is implicated in a wide range of diseases, including cancer, infectious, and cardiovascular diseases. Despite the medical need, existing inhibitors have limited structural diversity, consisting predominantly of amino acids and their derivatives. The search for innovative arginase inhibitors has now extended to screening approaches. Due to the small and narrow active site of arginase, screening must meet the criteria of fragment-based screening. However, the limited binding capacity of fragments requires working at high concentrations, which increases the risk of interference and false positives. In this study, we investigated three colorimetric assays and selected one based on interference for screening under these challenging conditions. The subsequent adaptation and application to the screening a library of metal chelator fragments resulted in the identification of four compounds with moderate activity. The synthesis and evaluation of a series of compounds from one of the hits led to compound 21a with an IC50 value of 91.1 μM close to the reference compound piceatannol. Finally, molecular modelling supports the potential binding of aurones and chalcones to the active site of arginase, suggesting them as new candidates for the development of novel arginase inhibitors.
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Affiliation(s)
- Jason Muller
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Luca Marchisio
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Rym Attia
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Andy Zedet
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Robin Maradan
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Maxence Vallet
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Alison Aebischer
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Dominique Harakat
- URCATech, ICMR, CNRS UMR 7312 URCA Bât 18, BP 1039, Cedex 2 51687 Reims France
| | - François Senejoux
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Christophe Ramseyer
- Chrono-environnement UMR6249, CNRS Université de Franche-Comté F-25000 Besançon France
| | - Sarah Foley
- Chrono-environnement UMR6249, CNRS Université de Franche-Comté F-25000 Besançon France
| | - Bruno Cardey
- Chrono-environnement UMR6249, CNRS Université de Franche-Comté F-25000 Besançon France
| | - Corine Girard
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
| | - Marc Pudlo
- Université de Franche-Comté, EFS, INSERM, UMR RIGHT F-25000 Besançon France
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3
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Fernández De Santaella J, Ren J, Vanella R, Nash MA. Enzyme Cascade with Horseradish Peroxidase Readout for High-Throughput Screening and Engineering of Human Arginase-1. Anal Chem 2023; 95:7150-7157. [PMID: 37094096 DOI: 10.1021/acs.analchem.2c05429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
We report an enzyme cascade with horseradish peroxidase-based readout for screening human arginase-1 (hArg1) activity. We combined the four enzymes hArg1, ornithine decarboxylase, putrescine oxidase, and horseradish peroxidase in a reaction cascade that generated colorimetric or fluorescent signals in response to hArg1 activity and used this cascade to assay wild-type and variant hArg1 sequences as soluble enzymes and displayed on the surface of Escherichia coli. We screened a curated 13-member hArg1 library covering mutations that modified the electrostatic environment surrounding catalytic residues D128 and H141, and identified the R21E variant with a 13% enhanced catalytic turnover rate compared to wild type. Our scalable one-pot single-step arginase assay with continuous kinetic readout is amenable to high-throughput screening and directed evolution of arginase libraries and testing drug candidates for arginase inhibition.
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Affiliation(s)
- Jaime Fernández De Santaella
- Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- National Center for Competence in Research (NCCR), Molecular Systems Engineering, 4058 Basel, Switzerland
| | - Jin Ren
- Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Rosario Vanella
- Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
| | - Michael A Nash
- Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4058 Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, 4058 Basel, Switzerland
- National Center for Competence in Research (NCCR), Molecular Systems Engineering, 4058 Basel, Switzerland
- Swiss Nanoscience Institute, 4056 Basel, Switzerland
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4
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Winter M, Simon RP, Wang Y, Bretschneider T, Bauer M, Magarkar A, Reindl W, Fernández-Montalván A, Montel F, Büttner FH. Differential analyte derivatization enables unbiased MALDI-TOF-based high-throughput screening: A proof-of-concept study for the discovery of catechol-o-methyltransferase inhibitors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:287-297. [PMID: 35597517 DOI: 10.1016/j.slasd.2022.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Recent advances in label-free high-throughput screening via matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) offer unprecedented opportunities for the identification of novel chemical starting points in target-based drug discovery. A clear advantage of the technology is the possibility for label-free, direct quantification of analytes with high precision and robustness. Here we have expanded the range of analytes and biology that can be addressed via MALDI-TOF HTS, by developing a method based on post-reaction pyrylium-based derivatization to detect 3-methoxytyramine, the physiological enzyme product of the catechol-O-methyltransferase (COMT) enzyme. The introduction of pyrylium-type reagents as universal derivatization strategy under aqueous conditions for molecules containing primary amines represents a valuable addition to the toolbox of MALDI-TOF assay development. Characterization of COMT's enzymatic activity and inhibition by reference inhibitors, and comparison of the results obtained in our assay with data from previous mechanistic studies validated the performance of this new method. To address the problem of isobaric interference, a source of false results in MALDI-TOF assays measuring low molecular weight analytes, we devised a differential derivatization workflow which can potentially replace other counter- or orthogonal assays in future screening campaigns. Finally, we report on the first label-free HTS campaign for the identification of COMT inhibitors performed in miniaturized 1536-well microtiter plate format via MALDI-TOF MS analysis.
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Affiliation(s)
- Martin Winter
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany.
| | - Roman P Simon
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Yuting Wang
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Tom Bretschneider
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Margit Bauer
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Aniket Magarkar
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Wolfgang Reindl
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | | | - Florian Montel
- Medicinal Chemistry, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany
| | - Frank H Büttner
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riß, Germany.
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Towards one sample per second for mass spectrometric screening of engineered microbial strains. Curr Opin Biotechnol 2022; 76:102725. [PMID: 35489307 DOI: 10.1016/j.copbio.2022.102725] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 03/03/2022] [Accepted: 03/20/2022] [Indexed: 12/11/2022]
Abstract
Microbial cell factories convert renewable feedstocks into desirable chemicals and materials. Due to the lack of predictive modeling, high-throughput screening remains essential for microbial strain engineering. Mass spectrometry (MS) is a label-free modality with superior sensitivity and chemical specificity. Critical advances in improving the throughput of MS assays on complex microbial samples include massively parallel cultivation, robotic sample preparation, and chromatography-free instrumentation. Here, we review the recent development and application of rapid MS assays in screening microbial libraries, achieving or approaching a rate of one sample per second. We conclude with unique challenges associated with MS screening of strain libraries and discuss future solutions.
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Label-free duplex SAMDI-MS screen reveals novel SARS-CoV-2 3CLpro inhibitors. Antiviral Res 2022; 200:105279. [PMID: 35278580 PMCID: PMC8906060 DOI: 10.1016/j.antiviral.2022.105279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/01/2022] [Accepted: 03/06/2022] [Indexed: 11/20/2022]
Abstract
The 3-chymotrypsin-like cysteine protease (3CLpro) of severe acute respiratory syndrome conoravirus 2 (SARS-CoV-2) remains a promising therapeutic target to combat COVID-19. Our group recently described a novel duplexed biochemical assay that combines self-assembled monolayers of alkanethiolates on gold with matrix assisted laser desorption ionization (MALDI) time of flight (TOF) mass spectrometry (MS) to simultaneously measure 3CLpro and human rhinovirus 3C protease activities. This study describes applying the assay for the completion of a high-throughput duplexed screen of 300,000 diverse, drug-like small molecules in 3 days. The hits were confirmed and evaluated in dose response analyses against recombinant 3CLpro, HRV3C, and the human Cathepsin L proteases. The 3CLpro specific inhibitors were further assessed for activity in cellular cytotoxicity and anti-viral assays. Structure activity relationship studies informed on structural features required for activity and selectivity to 3CLpro over HRV3C. These results will guide the optimization of 3CLpro selective inhibitors to combat COVID-19 along with antiviral compounds against coronaviruses and rhinoviruses.
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Muller J, Attia R, Zedet A, Girard C, Pudlo M. An Update on Arginase Inhibitors and Inhibitory Assays. Mini Rev Med Chem 2021; 22:1963-1976. [PMID: 34967285 DOI: 10.2174/1389557522666211229105703] [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: 09/20/2021] [Revised: 10/18/2021] [Accepted: 10/22/2021] [Indexed: 11/22/2022]
Abstract
Arginase, which converts arginine into ornithine and urea, is a promising therapeutic target. Arginase is involved in cardiovascular diseases, parasitic infections and, through a critical role in immunity, in some cancers. There is a need to develop effective arginase inhibitors and therefore efforts to identify and optimize new inhibitors are increasing. Several methods of evaluating arginase activity are available, but few directly measure the product. Radiometric assays need to separate urea and dying reactions require acidic conditions and sometimes heating. Hence, there are a variety of different approaches available, and each approach has its own limits and benefits. In this review, we provide an update on arginase inhibitors, followed by a discussion on available arginase assays and alternative methods, with a focus on the intrinsic biases and parameters that are likely to impact results.
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Affiliation(s)
- Jason Muller
- PEPITE EA4267, Université de Bourgogne Franche-Comté, F-25030 Besançon, France
| | - Rym Attia
- PEPITE EA4267, Université de Bourgogne Franche-Comté, F-25030 Besançon, France
| | - Andy Zedet
- PEPITE EA4267, Université de Bourgogne Franche-Comté, F-25030 Besançon, France
| | - Corine Girard
- PEPITE EA4267, Université de Bourgogne Franche-Comté, F-25030 Besançon, France
| | - Marc Pudlo
- PEPITE EA4267, Université de Bourgogne Franche-Comté, F-25030 Besançon, France
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Scholle MD, McLaughlin D, Gurard-Levin ZA. High-Throughput Affinity Selection Mass Spectrometry Using SAMDI-MS to Identify Small-Molecule Binders of the Human Rhinovirus 3C Protease. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:974-983. [PMID: 34151629 DOI: 10.1177/24725552211023211] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Affinity selection mass spectrometry (ASMS) has emerged as a powerful high-throughput screening tool used in drug discovery to identify novel ligands against therapeutic targets. This report describes the first high-throughput screen using a novel self-assembled monolayer desorption ionization (SAMDI)-ASMS methodology to reveal ligands for the human rhinovirus 3C (HRV3C) protease. The approach combines self-assembled monolayers of alkanethiolates on gold with matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectrometry (MS), a technique termed SAMDI-ASMS. The primary screen of more than 100,000 compounds in pools of 8 compounds per well was completed in less than 8 h, and informs on the binding potential and selectivity of each compound. Initial hits were confirmed in follow-up SAMDI-ASMS experiments in single-concentration and dose-response curves. The ligands identified by SAMDI-ASMS were further validated using differential scanning fluorimetry (DSF) and in functional protease assays against HRV3C and the related SARS-CoV-2 3CLpro enzyme. SAMDI-ASMS offers key benefits for drug discovery over traditional ASMS approaches, including the high-throughput workflow and readout, minimizing compound misbehavior by using smaller compound pools, and up to a 50-fold reduction in reagent consumption. The flexibility of this novel technology opens avenues for high-throughput ASMS assays of any target, thereby accelerating drug discovery for diverse diseases.
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Scholle MD, Liu C, Deval J, Gurard-Levin ZA. Label-Free Screening of SARS-CoV-2 NSP14 Exonuclease Activity Using SAMDI Mass Spectrometry. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:766-774. [PMID: 33870746 PMCID: PMC8053483 DOI: 10.1177/24725552211008854] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus responsible for the global COVID-19 pandemic. Nonstructural protein 14 (NSP14), which features exonuclease (ExoN) and guanine N7 methyltransferase activity, is a critical player in SARS-CoV-2 replication and fidelity and represents an attractive antiviral target. Initiating drug discovery efforts for nucleases such as NSP14 remains a challenge due to a lack of suitable high-throughput assay methodologies. This report describes the combination of self-assembled monolayers and matrix-assisted laser desorption ionization mass spectrometry to enable the first label-free and high-throughput assay for NSP14 ExoN activity. The assay was used to measure NSP14 activity and gain insight into substrate specificity and the reaction mechanism. Next, the assay was optimized for kinetically balanced conditions and miniaturized, while achieving a robust assay (Z factor > 0.8) and a significant assay window (signal-to-background ratio > 200). Screening 10,240 small molecules from a diverse library revealed candidate inhibitors, which were counterscreened for NSP14 selectivity and RNA intercalation. The assay methodology described here will enable, for the first time, a label-free and high-throughput assay for NSP14 ExoN activity to accelerate drug discovery efforts and, due to the assay flexibility, can be more broadly applicable for measuring other enzyme activities from other viruses or implicated in various pathologies.
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Affiliation(s)
| | - Cheng Liu
- Aligos Therapeutics, Inc., South San Francisco, CA, USA
| | - Jerome Deval
- Aligos Therapeutics, Inc., South San Francisco, CA, USA
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