51
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Sakamoto H, Nishikawa M, Yamada S. Development of tight junction-strengthening compounds using a high-throughput screening system to evaluate cell surface-localized claudin-1 in keratinocytes. Sci Rep 2024; 14:3312. [PMID: 38332234 PMCID: PMC10853544 DOI: 10.1038/s41598-024-53649-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/03/2024] [Indexed: 02/10/2024] Open
Abstract
Tight junctions (TJs) are important factors constituting the physical barriers of the skin, and their suppression has been described in various conditions, such as aged skin and atopic dermatitis lesions. However, the methods for improving skin TJ function remain insufficient. Therefore, to obtain compounds that can improve TJ function, we developed a novel high-throughput screening system termed live-cell immunostaining to evaluate cell surface-localized claudin-1 (CLDN1) with high selectivity using normal human epidermal keratinocytes (NHEKs). Heparinoid and phospho-pyridoxal (p-Pyr), a metabolite of pyridoxine, were identified as hit compounds. In addition, heparinoid was strongly suggested to increase CLDN1 expression by inhibiting epidermal growth factor receptor signaling. By contrast, p-Pyr did not enhance CLDN1 expression, but it accelerated the translocation of CLDN1 to the cell surface. Finally, we confirmed that heparinoid and p-Pyr improved barrier function in NHEKs in a transepithelial electrical resistance assay. In conclusion, heparinoid and p-Pyr could potentially ameliorate skin conditions by improving TJ function.
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Affiliation(s)
- Hiroki Sakamoto
- Research and Development Headquarters, Well-Being Research Laboratories, Lion Corporation, 100 Tajima, Odawara, Kanagawa, 256-0811, Japan
| | - Momoyo Nishikawa
- Research and Development Headquarters, Well-Being Research Laboratories, Lion Corporation, 100 Tajima, Odawara, Kanagawa, 256-0811, Japan
| | - Seigo Yamada
- Research and Development Headquarters, Well-Being Research Laboratories, Lion Corporation, 100 Tajima, Odawara, Kanagawa, 256-0811, Japan.
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52
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Keller WR, Picciano A, Wilson K, Xu J, Khasa H, Wendeler M. Rational downstream development for adeno-associated virus full/empty capsid separation - A streamlined methodology based on high-throughput screening and mechanistic modeling. J Chromatogr A 2024; 1716:464632. [PMID: 38219623 DOI: 10.1016/j.chroma.2024.464632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/16/2024]
Abstract
Recombinant adeno-associated virus (AAV) has emerged as one of the most promising systems for therapeutic gene delivery and has demonstrated clinical success in a wide range of genetic disorders. However, manufacturing of high-quality AAV in large amounts still remains a challenge. A significant difficulty for downstream processing is the need to remove empty capsids that are generated in all currently utilized expression systems and that represent product-related impurities that adversely affect safety and efficacy of AAV vectors. Empty and full capsids exhibit only subtle differences in surface charge and size, making chromatography-based separations highly challenging. Here, we present a rapid methodology for the systematic process development of the crucial AAV full/empty capsid separation on ion-exchange media based on high-throughput screening and mechanistic modeling. Two of the most commonly employed serotypes, AAV8 and AAV9, are used as case studies. First, high-throughput studies in filter-plate format are performed that allow the rapid and comprehensive study of binding and elution behavior of AAV on different resins, using different buffer systems, pH, salt conditions, and solution additives. Small amounts of separated empty and full AAV capsids are generated by iodixanol gradient centrifugation that allow studying the binding and elution behavior of the two vector species separately in miniaturized format. Process conditions that result in maximum differences in elution behavior between empty and full capsids are then transferred to benchtop chromatography systems that are used to generate calibration data for the estimation of steric mass-action isotherm and mass transport parameters for process simulation. The resulting column models are employed for in-silico process development that serves to enhance understanding of separation constraints and to identify optimized conditions for the removal of empty particles. Finally, optimized separation conditions are verified experimentally. The methodology presented in this work provides a systematic framework that affords mechanistic understanding of the crucial empty/full capsid separation and accelerates the development of a scalable AAV downstream process.
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Affiliation(s)
- William R Keller
- Purification Process Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, United States
| | - Angela Picciano
- Purification Process Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, United States
| | - Kelly Wilson
- Purification Process Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, United States
| | - Jin Xu
- Cell Culture and Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, United States
| | - Harshit Khasa
- Analytical Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, United States
| | - Michaela Wendeler
- Purification Process Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, United States.
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Brocklehurst CE, Altmann E, Bon C, Davis H, Dunstan D, Ertl P, Ginsburg-Moraff C, Grob J, Gosling DJ, Lapointe G, Marziale AN, Mues H, Palmieri M, Racine S, Robinson RI, Springer C, Tan K, Ulmer W, Wyler R. MicroCycle: An Integrated and Automated Platform to Accelerate Drug Discovery. J Med Chem 2024; 67:2118-2128. [PMID: 38270627 DOI: 10.1021/acs.jmedchem.3c02029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
We herein describe the development and application of a modular technology platform which incorporates recent advances in plate-based microscale chemistry, automated purification, in situ quantification, and robotic liquid handling to enable rapid access to high-quality chemical matter already formatted for assays. In using microscale chemistry and thus consuming minimal chemical matter, the platform is not only efficient but also follows green chemistry principles. By reorienting existing high-throughput assay technology, the platform can generate a full package of relevant data on each set of compounds in every learning cycle. The multiparameter exploration of chemical and property space is hereby driven by active learning models. The enhanced compound optimization process is generating knowledge for drug discovery projects in a time frame never before possible.
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Affiliation(s)
- Cara E Brocklehurst
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Eva Altmann
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Corentin Bon
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Holly Davis
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - David Dunstan
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Peter Ertl
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Carol Ginsburg-Moraff
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jonathan Grob
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Daniel J Gosling
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Guillaume Lapointe
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Alexander N Marziale
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Heinrich Mues
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Marco Palmieri
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Sophie Racine
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
| | - Richard I Robinson
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Clayton Springer
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Kian Tan
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - William Ulmer
- Global Discovery Chemistry, Novartis Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - René Wyler
- Global Discovery Chemistry, Novartis Biomedical Research, Novartis Pharma AG, Basel 4033, Switzerland
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54
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Wang S, Liu F, Li P, Wang JN, Mo Y, Lin B, Mei Y. Potent inhibitors targeting cyclin-dependent kinase 9 discovered via virtual high-throughput screening and absolute binding free energy calculations. Phys Chem Chem Phys 2024; 26:5377-5386. [PMID: 38269624 DOI: 10.1039/d3cp05582e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Due to the crucial regulatory mechanism of cyclin-dependent kinase 9 (CDK9) in mRNA transcription, the development of kinase inhibitors targeting CDK9 holds promise as a potential treatment strategy for cancer. A structure-based virtual screening approach has been employed for the discovery of potential novel CDK9 inhibitors. First, compounds with kinase inhibitor characteristics were identified from the ZINC15 database via virtual high-throughput screening. Next, the predicted binding modes were optimized by molecular dynamics simulations, followed by precise estimation of binding affinities using absolute binding free energy calculations based on the free energy perturbation scheme. The binding mode of molecule 006 underwent an inward-to-outward flipping, and the new binding mode exhibited binding affinity comparable to the small molecule T6Q in the crystal structure (PDB ID: 4BCF), highlighting the essential role of molecular dynamics simulation in capturing a plausible binding pose bridging docking and absolute binding free energy calculations. Finally, structural modifications based on these findings further enhanced the binding affinity with CDK9. The results revealed that enhancing the molecule's rigidity through ring formation, while maintaining the major interactions, reduced the entropy loss during the binding process and, thus, enhanced binding affinities.
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Affiliation(s)
- Shipeng Wang
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Fengjiao Liu
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai 201620, China.
| | - Pengfei Li
- Single Particle, LLC, 10531 4S Commons Dr 166-629, San Diego, CA 92127, USA
| | - Jia-Ning Wang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Yan Mo
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Bin Lin
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
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55
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Cao Y, Wu B, Xu Y, Wang M, Wu X, Liang X, Lin J, Li Z, Lin H, Luo C, Chen S. Discovery of GPX4 inhibitors through FP-based high-throughput screening. Eur J Med Chem 2024; 265:116044. [PMID: 38145603 DOI: 10.1016/j.ejmech.2023.116044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/03/2023] [Accepted: 12/09/2023] [Indexed: 12/27/2023]
Abstract
Ferroptosis is a form of non-apoptotic cell death, regulated by phospholipid hydroperoxide glutathione peroxidase 4 (GPX4), a selenoprotein with a selenocysteine residue (sec) in the active site. GPX4 is a promising target for cancer cells in therapy-resistant conditions via ferroptosis, which can reduce the level of lipid reactive oxygen species (ROS). So far, all existing GPX4 inhibitors covalently bind to GPX4 via a reactive alkyl chloride moiety or masked nitrile-oxide electrophiles with poor selectivity and pharmacokinetic properties and most were obtained by cell phenotype-based screening. Lacking of effective high-throughput screening methods for GPX4 protein limits the discovery of GPX4 inhibitors. Here, we report a fluorescence polarization (FP)-based high throughput screening (HTS) assay for GPX4-U46C-C10A-C66A in vitro, and found Metamizole sodium from our in-house compound library inhibits GPX4-U46C-C10A-C66A enzyme activity. Structure-activity relationships (SAR) demonstrated the importance of sulfonyl group on interaction between Metamizole sodium and GPX4-U46C-C10A-C66A. Our FP assay could be an effective tool for discovery of GPX4 inhibitors and Metamizole sodium was a potential inhibitor for GPX4 in vitro.
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Affiliation(s)
- Yu Cao
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Bin Wu
- School of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Ying Xu
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; China Pharmaceutical University, Nanjing, 210009, China
| | - Mingchen Wang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Xinyu Wu
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiaochen Liang
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; China Pharmaceutical University, Nanjing, 210009, China
| | - Jin Lin
- School of Pharmacy, Fujian Medical University, Fuzhou, 350122, China
| | - Zhihai Li
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
| | - Hua Lin
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; Key Laboratory of Microbial Pathogenesis and Interventions of Fujian Province University, The Key Laboratory of Innate Immune Biology of Fujian Province, Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528437, China.
| | - Cheng Luo
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China; Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528437, China.
| | - Shijie Chen
- The Center for Chemical Biology, Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.
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56
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Baybekov S, Llompart P, Marcou G, Gizzi P, Galzi JL, Ramos P, Saurel O, Bourban C, Minoletti C, Varnek A. Kinetic solubility: Experimental and machine-learning modeling perspectives. Mol Inform 2024; 43:e202300216. [PMID: 38149685 DOI: 10.1002/minf.202300216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/25/2023] [Accepted: 12/23/2023] [Indexed: 12/28/2023]
Abstract
Kinetic aqueous or buffer solubility is important parameter measuring suitability of compounds for high throughput assays in early drug discovery while thermodynamic solubility is reserved for later stages of drug discovery and development. Kinetic solubility is also considered to have low inter-laboratory reproducibility because of its sensitivity to protocol parameters [1]. Presumably, this is why little efforts have been put to build QSPR models for kinetic in comparison to thermodynamic aqueous solubility. Here, we investigate the reproducibility and modelability of kinetic solubility assays. We first analyzed the relationship between kinetic and thermodynamic solubility data, and then examined the consistency of data from different kinetic assays. In this contribution, we report differences between kinetic and thermodynamic solubility data that are consistent with those reported by others [1, 2] and good agreement between data from different kinetic solubility campaigns in contrast to general expectations. The latter is confirmed by achieving high performing QSPR models trained on merged kinetic solubility datasets. The poor performance of QSPR model trained on thermodynamic solubility when applied to kinetic solubility dataset reinforces the conclusion that kinetic and thermodynamic solubilities do not correlate: one cannot be used as an ersatz for the other. This encourages for building predictive models for kinetic solubility. The kinetic solubility QSPR model developed in this study is freely accessible through the Predictor web service of the Laboratory of Chemoinformatics (https://chematlas.chimie.unistra.fr/cgi-bin/predictor2.cgi).
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Affiliation(s)
- Shamkhal Baybekov
- Laboratoire de Chémoinformatique UMR 7140 CNRS, Institut Le Bel, University of Strasbourg, 4 Rue Blaise Pascal, 67081, Strasbourg, France
| | - Pierre Llompart
- Laboratoire de Chémoinformatique UMR 7140 CNRS, Institut Le Bel, University of Strasbourg, 4 Rue Blaise Pascal, 67081, Strasbourg, France
- IDD/CADD, Sanofi, Vitry-Sur-Seine, France
| | - Gilles Marcou
- Laboratoire de Chémoinformatique UMR 7140 CNRS, Institut Le Bel, University of Strasbourg, 4 Rue Blaise Pascal, 67081, Strasbourg, France
| | - Patrick Gizzi
- Plateforme de Chimie Biologique Intégrative de Strasbourg UAR 3286 CNRS, University of Strasbourg, 300 Boulevard Sébastien Brant, 67412, Illkirch, France
| | - Jean-Luc Galzi
- Biotechnologie et signalisation cellulaire UMR 7242 CNRS, École supérieure de biotechnologie de Strasbourg, University of Strasbourg, 300 Boulevard Sébastien Brant, 67412, Illkirch, France
- ChemBioFrance - Chimiothèque Nationale UAR 3035, ENSCM - 240, Avenue du Prof. E. Jeanbrau, CS 60297-34296, Montpellier Cedex 5, France
| | - Pascal Ramos
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Olivier Saurel
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Claire Bourban
- Plateforme de Chimie Biologique Intégrative de Strasbourg UAR 3286 CNRS, University of Strasbourg, 300 Boulevard Sébastien Brant, 67412, Illkirch, France
| | | | - Alexandre Varnek
- Laboratoire de Chémoinformatique UMR 7140 CNRS, Institut Le Bel, University of Strasbourg, 4 Rue Blaise Pascal, 67081, Strasbourg, France
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57
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Nippa DF, Atz K, Hohler R, Müller AT, Marx A, Bartelmus C, Wuitschik G, Marzuoli I, Jost V, Wolfard J, Binder M, Stepan AF, Konrad DB, Grether U, Martin RE, Schneider G. Enabling late-stage drug diversification by high-throughput experimentation with geometric deep learning. Nat Chem 2024; 16:239-248. [PMID: 37996732 PMCID: PMC10849962 DOI: 10.1038/s41557-023-01360-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 10/03/2023] [Indexed: 11/25/2023]
Abstract
Late-stage functionalization is an economical approach to optimize the properties of drug candidates. However, the chemical complexity of drug molecules often makes late-stage diversification challenging. To address this problem, a late-stage functionalization platform based on geometric deep learning and high-throughput reaction screening was developed. Considering borylation as a critical step in late-stage functionalization, the computational model predicted reaction yields for diverse reaction conditions with a mean absolute error margin of 4-5%, while the reactivity of novel reactions with known and unknown substrates was classified with a balanced accuracy of 92% and 67%, respectively. The regioselectivity of the major products was accurately captured with a classifier F-score of 67%. When applied to 23 diverse commercial drug molecules, the platform successfully identified numerous opportunities for structural diversification. The influence of steric and electronic information on model performance was quantified, and a comprehensive simple user-friendly reaction format was introduced that proved to be a key enabler for seamlessly integrating deep learning and high-throughput experimentation for late-stage functionalization.
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Affiliation(s)
- David F Nippa
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kenneth Atz
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland
| | - Remo Hohler
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Alex T Müller
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Andreas Marx
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Christian Bartelmus
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Georg Wuitschik
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Irene Marzuoli
- Process Chemistry and Catalysis (PCC), F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Vera Jost
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Jens Wolfard
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Martin Binder
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Antonia F Stepan
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland
| | - David B Konrad
- Department of Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Uwe Grether
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Rainer E Martin
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland.
| | - Gisbert Schneider
- Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland.
- ETH Singapore SEC Ltd, Singapore, Singapore.
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58
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Souza-Silva IM, Peluso AA, Mortensen C, Nazarova AL, Stage TB, Sumners C, Katritch V, Steckelings UM. Development of an automated, high-throughput assay to detect angiotensin AT 2-receptor agonistic compounds by nitric oxide measurements in vitro. Peptides 2024; 172:171137. [PMID: 38142816 DOI: 10.1016/j.peptides.2023.171137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 12/26/2023]
Abstract
Angiotensin AT2-receptor (AT2R) agonists have shown a wide range of protective effects in many preclinical disease models. However, the availability of AT2R-agonists is very limited due to the lack of high-throughput assays for AT2R-agonist identification. Therefore, we aimed to design and validate an assay for high-throughput screening of AT2R-agonist candidates. The assay is based on nitric oxide (NO) release measurements in primary human aortic endothelial cells (HAEC), in AT2R-transfected CHO cells (AT2R-CHO) or in non-transfected CHO cells (Flp-CHO) using the fluorescent probe DAF-FM diacetate. It is run in 96-well plates and fluorescence signals are semi-automatically quantified. The assay was tested for sensitivity (recognition of true positive results), selectivity (recognition of true negative results), and reliability (by calculating the repeatability coefficient (RC)). The high-throughput, semi-automated method was proven suitable, as the NO-releasing agents C21, CGP42112A, angiotensin-(1-7) and acetylcholine significantly increased NO release from HAEC. The assay is sensitive and selective, since the established AT2R-agonists C21, CGP42112A and angiotensin II significantly increased NO release from AT2R-CHO cells, while the non-AT2R-agonists angiotensin-(1-7) and acetylcholine had no effect. Assay reliability was shown by high-throughput screening of a library comprised of 40 potential AT2R-agonists, of which 39 met our requirements for reliability (RC ≤ 20% different from RC for C21). Our newly developed high-throughput method for detection of AT2R-agonistic activity was proven to be sensitive, selective, and reliable. This method is suitable for the screening of potential AT2R-agonists in future drug development programs.
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Affiliation(s)
- Igor Maciel Souza-Silva
- Institute for Molecular Medicine, Department of Cardiovascular and Renal Research, University of Southern Denmark, Odense, Denmark
| | - A Augusto Peluso
- Institute for Molecular Medicine, Department of Cardiovascular and Renal Research, University of Southern Denmark, Odense, Denmark; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Christina Mortensen
- Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Antonina L Nazarova
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA; Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA
| | | | - Colin Sumners
- Department of Physiology and Aging, University of Florida, Gainesville, USA
| | - Vsevolod Katritch
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA; Center for New Technologies in Drug Discovery and Development, Bridge Institute, Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA; Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - U Muscha Steckelings
- Institute for Molecular Medicine, Department of Cardiovascular and Renal Research, University of Southern Denmark, Odense, Denmark.
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59
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Brown SJ, Ryan TM, Drummond CJ, Greaves TL, Han Q. Lysozyme aggregation and unfolding in ionic liquid solvents: Insights from small angle X-ray scattering and high throughput screening. J Colloid Interface Sci 2024; 655:133-144. [PMID: 37931553 DOI: 10.1016/j.jcis.2023.10.139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/09/2023] [Accepted: 10/25/2023] [Indexed: 11/08/2023]
Abstract
Understanding protein behaviour is crucial for developing functional solvent systems. Ionic liquids (ILs) are designer salts with versatile ion combinations, where some suppress unfavourable protein behaviour. This work utilizes small angle X-ray scattering (SAXS) to investigate the size and shape changes of model protein hen egg white lysozyme (HEWL) in 137 IL and salt solutions. Guinier, Kratky, and pair distance distribution analysis were used to evaluate the protein size, shape, and aggregation changes in these solvents. At low IL and salt concentration (1 mol%), HEWL remained monodispersed and globular. Most ILs increased HEWL size compared to buffer, while the nitrate and mesylate anions induced the most significant size increases. IL cation branching, hydroxyl groups, and longer alkyl chains counteracted this size increase. Common salts exhibited specific ion effects, while the IL effect varied with concentration due to complex ion-pairing. Protein aggregation and unfolding occurred at 10 mol% IL, altering the protein shape, especially for ILs with multiple alkyl chains on the cation, or with a mesylate/nitrate anion. This study highlights the usefulness of adopting a high-throughput SAXS strategy for understanding IL effects on protein behaviour and provides insights on controlling protein aggregation and unfolding with ILs.
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Affiliation(s)
- Stuart J Brown
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Timothy M Ryan
- SAXS/WAXS Beamline, Australian Synchrotron, 800 Blackburn Rd, Clayton, VIC 3168, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
| | - Qi Han
- School of Science, STEM College, RMIT University, Melbourne, VIC 3000, Australia.
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Wei SY, Fu WS, Liu CH, Wang WL, Shih YT, Chien S, Chiu JJ. Identification of KU-55933 as an anti-atherosclerosis compound by using a hemodynamic-based high-throughput drug screening platform. Proc Natl Acad Sci U S A 2024; 121:e2318718121. [PMID: 38252820 PMCID: PMC10835076 DOI: 10.1073/pnas.2318718121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Several compounds have been used for atherosclerosis treatment, including clinical trials; however, no anti-atherosclerotic drugs based on hemodynamic force-mediated atherogenesis have been discovered. Our previous studies demonstrated that "small mothers against decapentaplegic homolog 1/5" (Smad1/5) is a convergent signaling molecule for chemical [e.g., bone morphogenetic proteins (BMPs)] and mechanical (e.g., disturbed flow) stimulations and hence may serve as a promising hemodynamic-based target for anti-atherosclerosis drug development. The goal of this study was to develop a high-throughput screening (HTS) platform to identify potential compounds that can inhibit disturbed flow- and BMP-induced Smad1/5 activation and atherosclerosis. Through HTS using a Smad1/5 downstream target inhibitor of DNA binding 1 (Id-1) as a luciferase reporter, we demonstrated that KU-55933 and Apicidin suppressed Id-1 expression in AD-293 cells. KU-55933 (10 μM), Apicidin (10 μM), and the combination of half doses of each [1/2(K + A)] inhibited disturbed flow- and BMP4-induced Smad1/5 activation in human vascular endothelial cells (ECs). KU-55933, Apicidin, and 1/2(K + A) treatments caused 50.6%, 47.4%, and 73.3% inhibitions of EC proliferation induced by disturbed flow, respectively, whereas EC inflammation was only suppressed by KU-55933 and 1/2(K + A), but not Apicidin alone. Administrations of KU-55933 and 1/2(K + A) to apolipoprotein E-deficient mice inhibited Smad1/5 activation in ECs in athero-susceptible regions, thereby suppressing endothelial proliferation and inflammation, with the attenuation of atherosclerotic lesions in these mice. A unique drug screening platform has been developed to demonstrate that KU-55933 and its combination with Apicidin are promising therapeutic compounds for atherosclerosis based on hemodynamic considerations.
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Affiliation(s)
- Shu-Yi Wei
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli350, Taiwan
| | - Wei-Shan Fu
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli350, Taiwan
| | - Chang-Hsuan Liu
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli350, Taiwan
| | - Wei-Li Wang
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli350, Taiwan
| | - Yu-Tsung Shih
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli350, Taiwan
- Department of Anatomy and Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei110, Taiwan
| | - Shu Chien
- Department of Bioengineering and Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA93093
- Department of Medicine, University of California, San Diego, La Jolla, CA93093
| | - Jeng-Jiann Chiu
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli350, Taiwan
- College of Medical Science and Technology, Taipei Medical University, Taipei110, Taiwan
- Taipei Heart Institute, Taipei Medical University, Taipei110, Taiwan
- Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu300, Taiwan
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61
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Guo J, Mi Y, Guo Y, Bai Y, Wang M, Wang W, Wang Y. Current Advances in Japanese Encephalitis Virus Drug Development. Viruses 2024; 16:202. [PMID: 38399978 PMCID: PMC10892782 DOI: 10.3390/v16020202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/14/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Japanese encephalitis virus (JEV) belongs to the Flaviviridae family and is a representative mosquito-borne flavivirus responsible for acute encephalitis and meningitis in humans. Despite the availability of vaccines, JEV remains a major public health threat with the potential to spread globally. According to the World Health Organization (WHO), there are an estimated 69,000 cases of JE each year, and this figure is probably an underestimate. The majority of JE victims are children in endemic areas, and almost half of the surviving patients have motor or cognitive sequelae. Thus, the absence of a clinically approved drug for the treatment of JE defines an urgent medical need. Recently, several promising and potential drug candidates were reported through drug repurposing studies, high-throughput drug library screening, and de novo design. This review focuses on the historical aspects of JEV, the biology of JEV replication, targets for therapeutic strategies, a target product profile, and drug development initiatives.
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Affiliation(s)
- Jiao Guo
- The Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, School of Basic Medicine, Xi’an Medical University, Xi’an 710021, China; (J.G.); (Y.M.); (Y.B.)
| | - Yunqi Mi
- The Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, School of Basic Medicine, Xi’an Medical University, Xi’an 710021, China; (J.G.); (Y.M.); (Y.B.)
| | - Yan Guo
- College of Animal Science and Technology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China;
| | - Yang Bai
- The Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, School of Basic Medicine, Xi’an Medical University, Xi’an 710021, China; (J.G.); (Y.M.); (Y.B.)
| | - Meihua Wang
- Faculty of Life Science and Medicine, University of Science and Technology of China, Hefei 230026, China;
| | - Wei Wang
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
| | - Yang Wang
- The Xi’an Key Laboratory of Pathogenic Microorganism and Tumor Immunity, School of Basic Medicine, Xi’an Medical University, Xi’an 710021, China; (J.G.); (Y.M.); (Y.B.)
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Bothe U, Günther J, Nubbemeyer R, Siebeneicher H, Ring S, Bömer U, Peters M, Rausch A, Denner K, Himmel H, Sutter A, Terebesi I, Lange M, Wengner AM, Guimond N, Thaler T, Platzek J, Eberspächer U, Schäfer M, Steuber H, Zollner TM, Steinmeyer A, Schmidt N. Discovery of IRAK4 Inhibitors BAY1834845 (Zabedosertib) and BAY1830839. J Med Chem 2024; 67:1225-1242. [PMID: 38228402 PMCID: PMC10823478 DOI: 10.1021/acs.jmedchem.3c01714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/18/2024]
Abstract
Interleukin-1 receptor-associated kinase 4 (IRAK4) plays a critical role in innate inflammatory processes. Here, we describe the discovery of two clinical candidate IRAK4 inhibitors, BAY1834845 (zabedosertib) and BAY1830839, starting from a high-throughput screening hit derived from Bayer's compound library. By exploiting binding site features distinct to IRAK4 using an in-house docking model, liabilities of the original hit could surprisingly be overcome to confer both candidates with a unique combination of good potency and selectivity. Favorable DMPK profiles and activity in animal inflammation models led to the selection of these two compounds for clinical development in patients.
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Affiliation(s)
- Ulrich Bothe
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Judith Günther
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | | | | | - Sven Ring
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | | | - Michaele Peters
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | | | - Karsten Denner
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Herbert Himmel
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Andreas Sutter
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Ildiko Terebesi
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | | | - Antje M. Wengner
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Nicolas Guimond
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Tobias Thaler
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Johannes Platzek
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Uwe Eberspächer
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | | | | | - Thomas M. Zollner
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Andreas Steinmeyer
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
| | - Nicole Schmidt
- Bayer AG, Research &
Development, Pharmaceuticals, 13353 Berlin, Germany
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63
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Alfatah M, Zhang Y, Naaz A, Cheng TYN, Eisenhaber F. PICLS with human cells is the first high throughput screening method for identifying novel compounds that extend lifespan. Biol Direct 2024; 19:8. [PMID: 38254217 PMCID: PMC10804585 DOI: 10.1186/s13062-024-00455-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024] Open
Abstract
Gerontology research on anti-aging interventions with drugs could be an answer to age-related diseases, aiming at closing the gap between lifespan and healthspan. Here, we present two methods for assaying chronological lifespan in human cells: (1) a version of the classical outgrowth assay with quantitative assessment of surviving cells and (2) a version of the PICLS method (propidium iodide fluorescent-based measurement of cell death). Both methods are fast, simple to conduct, cost-effective, produce quantitative data for further analysis and can be used with diverse human cell lines. Whereas the first method is ideal for validation and testing the post-intervention reproductive potential of surviving cells, the second method has true high-throughput screening potential. The new technologies were validated with known anti-aging compounds (2,5-anhydro-D-mannitol and rapamycin). Using the high-throughput screening method, we screened a library of 162 chemical entities and identified three compounds that extend the longevity of human cells.
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Affiliation(s)
- Mohammad Alfatah
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore.
| | - Yizhong Zhang
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore
| | - Arshia Naaz
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome #02-01, Singapore, 138672, Republic of Singapore
| | - Trishia Yi Ning Cheng
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore
| | - Frank Eisenhaber
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Republic of Singapore
- LASA - Lausitz Advanced Scientific Applications gGmbH, Straße der Einheit 2-24, 02943, Weißwasser, Federal Republic of Germany
- School of Biological Sciences (SBS), Nanyang Technological University (NTU), Singapore, 637551, Republic of Singapore
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64
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Meng Q, Wei L, Ma K, Shi M, Lin X, Ho JWK, Li Y, Zhang X. scDecouple: decoupling cellular response from infected proportion bias in scCRISPR-seq. Brief Bioinform 2024; 25:bbae011. [PMID: 38324621 PMCID: PMC10849189 DOI: 10.1093/bib/bbae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/18/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
Single-cell clustered regularly interspaced short palindromic repeats-sequencing (scCRISPR-seq) is an emerging high-throughput CRISPR screening technology where the true cellular response to perturbation is coupled with infected proportion bias of guide RNAs (gRNAs) across different cell clusters. The mixing of these effects introduces noise into scCRISPR-seq data analysis and thus obstacles to relevant studies. We developed scDecouple to decouple true cellular response of perturbation from the influence of infected proportion bias. scDecouple first models the distribution of gene expression profiles in perturbed cells and then iteratively finds the maximum likelihood of cell cluster proportions as well as the cellular response for each gRNA. We demonstrated its performance in a series of simulation experiments. By applying scDecouple to real scCRISPR-seq data, we found that scDecouple enhances the identification of biologically perturbation-related genes. scDecouple can benefit scCRISPR-seq data analysis, especially in the case of heterogeneous samples or complex gRNA libraries.
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Affiliation(s)
- Qiuchen Meng
- MOE Key Lab of Bioinformatics & Bioinformatics Division BRNIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Lei Wei
- MOE Key Lab of Bioinformatics & Bioinformatics Division BRNIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Kun Ma
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Ming Shi
- MOE Key Lab of Bioinformatics & Bioinformatics Division BRNIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xinyi Lin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Joshua W K Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
- Laboratory of Data Discovery for Health Limited (D24H), Hong Kong Science Park, Hong Kong SAR, China
| | - Yinqing Li
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- IDG-McGovern Institute for Brain Research, Center for Synthetic and Systems Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xuegong Zhang
- MOE Key Lab of Bioinformatics & Bioinformatics Division BRNIST, Department of Automation, Tsinghua University, Beijing 100084, China
- Center for Synthetic and Systems Biology, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China
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65
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Yoon S, Kilicarslan You D, Jeong U, Lee M, Kim E, Jeon TJ, Kim SM. Microfluidics in High-Throughput Drug Screening: Organ-on-a-Chip and C. elegans-Based Innovations. Biosensors (Basel) 2024; 14:55. [PMID: 38275308 PMCID: PMC10813408 DOI: 10.3390/bios14010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
The development of therapeutic interventions for diseases necessitates a crucial step known as drug screening, wherein potential substances with medicinal properties are rigorously evaluated. This process has undergone a transformative evolution, driven by the imperative need for more efficient, rapid, and high-throughput screening platforms. Among these, microfluidic systems have emerged as the epitome of efficiency, enabling the screening of drug candidates with unprecedented speed and minimal sample consumption. This review paper explores the cutting-edge landscape of microfluidic-based drug screening platforms, with a specific emphasis on two pioneering approaches: organ-on-a-chip and C. elegans-based chips. Organ-on-a-chip technology harnesses human-derived cells to recreate the physiological functions of human organs, offering an invaluable tool for assessing drug efficacy and toxicity. In parallel, C. elegans-based chips, boasting up to 60% genetic homology with humans and a remarkable affinity for microfluidic systems, have proven to be robust models for drug screening. Our comprehensive review endeavors to provide readers with a profound understanding of the fundamental principles, advantages, and challenges associated with these innovative drug screening platforms. We delve into the latest breakthroughs and practical applications in this burgeoning field, illuminating the pivotal role these platforms play in expediting drug discovery and development. Furthermore, we engage in a forward-looking discussion to delineate the future directions and untapped potential inherent in these transformative technologies. Through this review, we aim to contribute to the collective knowledge base in the realm of drug screening, providing valuable insights to researchers, clinicians, and stakeholders alike. We invite readers to embark on a journey into the realm of microfluidic-based drug screening platforms, fostering a deeper appreciation for their significance and promising avenues yet to be explored.
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Affiliation(s)
- Sunhee Yoon
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Dilara Kilicarslan You
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Uiechan Jeong
- Department of Mechanical Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Mina Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Eunhye Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
| | - Tae-Joon Jeon
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
- Department of Biological Engineering, Inha University, Incheon 22212, Republic of Korea
- Biohybrid Systems Research Center (BSRC), Inha University, Incheon 22212, Republic of Korea
| | - Sun Min Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea; (S.Y.); (D.K.Y.); (M.L.); (E.K.)
- Department of Mechanical Engineering, Inha University, Incheon 22212, Republic of Korea
- Biohybrid Systems Research Center (BSRC), Inha University, Incheon 22212, Republic of Korea
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66
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Kumar R, Gullapalli RR. High Throughput Screening Assessment of Reactive Oxygen Species (ROS) Generation using Dihydroethidium (DHE) Fluorescence Dye. J Vis Exp 2024. [PMID: 38314817 DOI: 10.3791/66238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024] Open
Abstract
Reactive oxygen species (ROS) play a key role in the regulation of cellular metabolism in physiological and pathological processes. Physiological ROS production plays a central role in the spatial and temporal modulation of normal cellular functions such as proliferation, signaling, apoptosis, and senescence. In contrast, chronic ROS overproduction is responsible for a wide spectrum of diseases, such as cancer, cardiovascular disease, and diabetes, among others. Quantifying ROS levels in an accurate and reproducible manner is thus essential to understanding normal cellular functionality. Fluorescence imaging-based methods to characterize intra-cellular ROS species is a common approach. Many of the imaging ROS protocols in the literature use 2'-7'-dichlorodihydrofluorescein diacetate (DCFH-DA) dye. However, this dye suffers from significant limitations in its usage and interpretability. The current protocol demonstrates the use of a dihydroethidium (DHE) fluorescent probe as an alternative method to quantify total ROS production in a high-throughput setting. The high throughput imaging platform, CX7 Cellomics, was used to measure and quantify the ROS production. This study was conducted in three hepatocellular cancer cell lines - HepG2, JHH4, and HUH-7. This protocol provides an in-depth description of the various procedures involved in the assessment of ROS within the cells, including - preparation of DHE solution, incubation of cells with DHE solution, and measurement of DHE intensity necessary to characterize the ROS production. This protocol demonstrates that DHE fluorescent dye is a robust and reproducible choice to characterize intracellular ROS production in a high-throughput manner. High throughput approaches to measure ROS production are likely to be helpful in a variety of studies, such as toxicology, drug screening, and cancer biology.
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Affiliation(s)
- Rahul Kumar
- Department of Pathology, University of New Mexico; Department of Chemical and Biological Engineering, University of New Mexico
| | - Rama R Gullapalli
- Department of Pathology, University of New Mexico; Department of Chemical and Biological Engineering, University of New Mexico;
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67
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Irvine EB, Reddy ST. Advancing Antibody Engineering through Synthetic Evolution and Machine Learning. J Immunol 2024; 212:235-243. [PMID: 38166249 DOI: 10.4049/jimmunol.2300492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/20/2023] [Indexed: 01/04/2024]
Abstract
Abs are versatile molecules with the potential to achieve exceptional binding to target Ags, while also possessing biophysical properties suitable for therapeutic drug development. Protein display and directed evolution systems have transformed synthetic Ab discovery, engineering, and optimization, vastly expanding the number of Ab clones able to be experimentally screened for binding. Moreover, the burgeoning integration of high-throughput screening, deep sequencing, and machine learning has further augmented in vitro Ab optimization, promising to accelerate the design process and massively expand the Ab sequence space interrogated. In this Brief Review, we discuss the experimental and computational tools employed in synthetic Ab engineering and optimization. We also explore the therapeutic challenges posed by developing Abs for infectious diseases, and the prospects for leveraging machine learning-guided protein engineering to prospectively design Abs resistant to viral escape.
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Affiliation(s)
- Edward B Irvine
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
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68
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Zhao M, Fan W, Wang Y, Qiang P, Zheng Z, Shan H, Zhang M, Liu P, Wang Y, Li G, Li M, Hong L. M335, a novel small-molecule STING agonist activates the immune response and exerts antitumor effects. Eur J Med Chem 2024; 264:116018. [PMID: 38091891 DOI: 10.1016/j.ejmech.2023.116018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 12/30/2023]
Abstract
In the context of antitumor immune responses, the activation of the stimulator of interferon genes (STING) assumes a critical role and imparts enhanced immunogenicity. An effective strategy for exogenously activating the immune system involves the utilization of STING agonists, and prior investigations primarily concentrated on modifying endogenous cyclic dinucleotides (CDNs) to achieve this. Nevertheless, the practical utility of CDNs was restricted due to limitations associated with their physicochemical attributes and administration protocols. In this article, we present the discovery of a novel small-molecule agonist denoted as M335, identified through high-throughput screening using surface plasmon resonance (SPR). M335 demonstrates the ability to activate the TBK1-IRF3-IFN axis in a STING-dependent manner in vitro. Through experimentation on mouse models bearing tumors, we observed that the administration of M335 resulted in the activation of immune cells. Notably, significant antitumor effects were achieved with both intratumoral and intraperitoneal administration of M335. These findings suggest the potential of M335 as a promising agent for cancer immunotherapy, which will promote the development of STING agonists in anti-tumor applications.
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Affiliation(s)
- Man Zhao
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China; School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Weizhen Fan
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ying Wang
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Pengfei Qiang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhihua Zheng
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Hao Shan
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ming Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Pengyutian Liu
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Yao Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Guofeng Li
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China.
| | - Min Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Liang Hong
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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69
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Kim SH, Shin N, Jeon JM, Yoon JJ, Joo JC, Kim HT, Bhatia SK, Yang YH. Application of liquid-based colorimetric method for high throughput screening of bioplastic-degrading strains using esterase assay. Anal Biochem 2024; 685:115390. [PMID: 37951454 DOI: 10.1016/j.ab.2023.115390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
To alleviate environmental problems caused by using conventional plastics, bioplastics have garnered significant interest as alternatives to petroleum-based plastics. Despite possessing better degradability traits compared to traditional plastics, the degradation of bioplastics still demands a longer duration than initially anticipated. This necessitates the utilization of degradation strains or enzymes to enhance degradation efficiency, ensuring timely degradation. In this study, a novel screening method to identify bioplastic degraders faster was suggested to circumvent the time-consuming and laborious characteristics of solid-based plate assays. This liquid-based colorimetric method confirmed the extracellular esterase activity with p-nitrophenyl esters. It eliminated the needs to prepare plastic emulsion plates at the initial screening system, shortening the time for the overall screening process and providing more quantitative data. p-nitrophenyl hexanoate (C6) was considered the best substrate among the various p-nitrophenyl esters as substrates. The screening was performed in liquid-based 96-well plates, resulting in the discovery of a novel strain, Bacillus sp. SH09, with a similarity of 97.4% with Bacillus licheniformis. Furthermore, clear zone assays, degradation investigations, scanning electron microscopy, and gel permeation chromatography were conducted to characterize the biodegradation capabilities of the new strain, the liquid-based approach offered a swift and less labor-intensive option during the initial stages.
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Affiliation(s)
- Su Hyun Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Nara Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jong-Min Jeon
- Department of Green & Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Republic of Korea
| | - Jeong-Jun Yoon
- Department of Green & Sustainable Materials R&D Department, Research Institute of Clean Manufacturing System, Korea Institute of Industrial Technology (KITECH), Republic of Korea
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Republic of Korea
| | - Hee Taek Kim
- Department of Food Science and Technology, Chungnam National University, Chungchung nam-do, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul, Republic of Korea.
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70
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Wulandari DA, Tsuru K, Minamihata K, Wakabayashi R, Goto M, Kamiya N. A Functional Hydrogel Bead-Based High-Throughput Screening System for Mammalian Cells with Enhanced Secretion of Therapeutic Antibodies. ACS Biomater Sci Eng 2024; 10:628-636. [PMID: 38048166 DOI: 10.1021/acsbiomaterials.3c01386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Droplet-based high-throughput screening systems are an emerging technology that provides a quick test to screen millions of cells with distinctive characteristics. Biopharmaceuticals, specifically therapeutic proteins, are produced by culturing cells that secrete heterologous recombinant proteins with different populations and expression levels; therefore, a technology to discriminate cells that produce more target proteins is needed. Here, we present a droplet-based microfluidic strategy for encapsulating, screening, and selecting target cells with redox-responsive hydrogel beads (HBs). As a proof-of-concept study, we demonstrate the enrichment of hybridoma cells with enhanced capability of antibody secretion using horseradish peroxidase (HRP)-catalyzed hydrogelation of tetra-thiolate poly(ethylene glycol); hybridoma cells were encapsulated in disulfide-bonded HBs. Recombinant protein G or protein M with a C-terminal cysteine residue was installed in the HBs via disulfide bonding to capture antibodies secreted from the cells. HBs were fluorescently stained by adding the protein L-HRP conjugate using a tyramide signal amplification system. HBs were then separated by fluorescence-activated droplet sorting and degraded by reducing the disulfide bonds to recover the target cells. Finally, we succeeded in the selection of hybridoma cells with enhanced antibody secretion, indicating the potential of this system in the therapeutic protein production.
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Affiliation(s)
- Diah Anggraini Wulandari
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kyosuke Tsuru
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kosuke Minamihata
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Rie Wakabayashi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Masahiro Goto
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Division of Biotechnology, Centre for Future Chemistry, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Noriho Kamiya
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Division of Biotechnology, Centre for Future Chemistry, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka 819-0395, Japan
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71
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Tan L, Liu M, Wang L, Zhao G, Zhang Y. Flow cytometry-based high-throughput screening of synthetic peptides for palladium adsorption. J Hazard Mater 2024; 461:132656. [PMID: 37793255 DOI: 10.1016/j.jhazmat.2023.132656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 07/28/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023]
Abstract
Conventionally, the measurement of metal ion adsorption capacity in biosorbent relies on expensive and time-consuming ICP-OES technique. Herein, a semi-quantitative method to measure Pd(II) adsorption capacity of single cells has been presented by analyzing side scatter (SSC) intensity in flow cytometry. Within the sensitive range and applicable conditions, excellent linearity correlation (R2 ranges from 0.89 to 0.96) between the amount of Pd(II) absorbed on yeast and the fold increase in SSC intensity has been observed. Using this method, six strains with high Pd adsorption capacities have sorted from a yeast library with metal-binding peptides displayed (up to 107 strains) based on SSC signal intensity. The optimal peptide (EF1) displayed on yeast and E. coli surface demonstrated Pd adsorption improvements of ∼32% and ∼200%, respectively. In summary, our study proposes an alternative high-throughput method for analyzing the Pd(II) adsorption capacity of individual yeast cells, enabling the screening of specific peptides/proteins with high Pd(II) affinity from extensive libraries.
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Affiliation(s)
- Ling Tan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Meizi Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Lixian Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Key Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Guoping Zhao
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China; CAS-Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yanfei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China.
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72
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Qiu X, Hou X, Yang Y, Fang H, Cui F, Yang X. An in-line method for high-throughput screening of protein tyrosine phosphatase receptor type O inhibitors by capillary electrophoresis based on electrophoretically mediated microanalysis. J Chromatogr A 2024; 1713:464511. [PMID: 38007841 DOI: 10.1016/j.chroma.2023.464511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/28/2023]
Abstract
Protein tyrosine phosphatase receptor type O (PTPRO) plays an important role in inflammation-related pathways and has become an emerging drug target. In this study, we developed an in-line capillary electrophoresis (CE) method for the investigation of the enzymatic activity of PTPRO, which was based on electrophoretically mediated microanalysis (EMMA). After a thorough method validation of the optimized conditions, this protocol was successfully employed to determine the kinetics of PTPRO as well as the half-maximal inhibitory concentration (IC50) of two typical PTPRO inhibitors. The final results were consistent with the values obtained through classical ultraviolet-visible (UV-vis) spectrophotometry. Our new method exhibited improved accuracy and reduced consumption, avoiding the disadvantages of traditional methods. This work provides a new strategy for PTPRO enzyme kinetic studies as well as inhibitory activity determination through capillary electrophoresis for the first time.
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Affiliation(s)
- Xueting Qiu
- Department of Pharmaceutical Analysis and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Xuben Hou
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Yue Yang
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Hao Fang
- Department of Medicinal Chemistry and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Fei Cui
- Department of Pharmaceutical Analysis and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China
| | - Xinying Yang
- Department of Pharmaceutical Analysis and Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 250012 Jinan, Shandong, PR China.
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73
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Yang C, Lei Y, Ren T, Yao M. The Current Situation and Development Prospect of Whole-Genome Screening. Int J Mol Sci 2024; 25:658. [PMID: 38203828 PMCID: PMC10779205 DOI: 10.3390/ijms25010658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
High-throughput genetic screening is useful for discovering critical genes or gene sequences that trigger specific cell functions and/or phenotypes. Loss-of-function genetic screening is mainly achieved through RNA interference (RNAi), CRISPR knock-out (CRISPRko), and CRISPR interference (CRISPRi) technologies. Gain-of-function genetic screening mainly depends on the overexpression of a cDNA library and CRISPR activation (CRISPRa). Base editing can perform both gain- and loss-of-function genetic screening. This review discusses genetic screening techniques based on Cas9 nuclease, including Cas9-mediated genome knock-out and dCas9-based gene activation and interference. We compare these methods with previous genetic screening techniques based on RNAi and cDNA library overexpression and propose future prospects and applications for CRISPR screening.
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Affiliation(s)
| | | | | | - Mingze Yao
- Shanxi Provincial Key Laboratory for Medical Molecular Cell Biology, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education and Institute of Biomedical Sciences, Shanxi University, Taiyuan 030006, China; (C.Y.); (Y.L.); (T.R.)
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74
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Martin RL, Heifetz A, Bodkin MJ, Townsend-Nicholson A. High-Throughput Structure-Based Drug Design (HT-SBDD) Using Drug Docking, Fragment Molecular Orbital Calculations, and Molecular Dynamic Techniques. Methods Mol Biol 2024; 2716:293-306. [PMID: 37702945 DOI: 10.1007/978-1-0716-3449-3_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Structure-based drug design (SBDD) is rapidly evolving to be a fundamental tool for faster and more cost-effective methods of lead drug discovery. SBDD aims to offer a computational replacement to traditional high-throughput screening (HTS) methods of drug discovery. This "virtual screening" technique utilizes the structural data of a target protein in conjunction with large databases of potential drug candidates and then applies a range of different computational techniques to determine which potential candidates are likely to bind with high affinity and efficacy. It is proposed that high-throughput SBDD (HT-SBDD) will significantly enrich the success rate of HTS methods, which currently fluctuates around ~1%. In this chapter, we focus on the theory and utility of high-throughput drug docking, fragment molecular orbital calculations, and molecular dynamics techniques. We also offer a comparative review of the benefits and limitations of traditional methods against more recent SBDD advances. As HT-SBDD is computationally intensive, we will also cover the important role high-performance computing (HPC) clusters play in the future of computational drug discovery.
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Affiliation(s)
- Reuben L Martin
- Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London, UK.
- Evotec (UK) Ltd., Abingdon, Oxfordshire, UK.
| | | | | | - Andrea Townsend-Nicholson
- Research Department of Structural & Molecular Biology, Division of Biosciences, University College London, London, UK
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75
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Rostamighadi M, Kamelshahroudi A, Mehta V, Zeng FY, Pass I, Chung TDY, Salavati R. High-throughput screening of compounds targeting RNA editing in Trypanosoma brucei: Novel molecular scaffolds with broad trypanocidal effects. Biochem Pharmacol 2024; 219:115937. [PMID: 37995979 DOI: 10.1016/j.bcp.2023.115937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
Mitochondrial uridine insertion/deletion RNA editing, catalyzed by a multiprotein complex (editosome), is essential for gene expression in trypanosomes and Leishmania parasites. As this process is absent in the human host, a drug targeting this mechanism promises high selectivity and reduced toxicity. Here, we successfully miniaturized our FRET-based full-round RNA editing assay, which replicates the complete RNA editing process, adapting it into a 1536-well format. Leveraging this assay, we screened over 100,000 compounds against purified editosomes derived from Trypanosoma brucei, identifying seven confirmed primary hits. We sourced and evaluated various analogs to enhance the inhibitory and parasiticidal effects of these primary hits. In combination with secondary assays, our compounds marked inhibition of essential catalytic activities, including the RNA editing ligase and interactions of editosome proteins. Although the primary hits did not exhibit any growth inhibitory effect on parasites, we describe eight analog compounds capable of effectively killing T. brucei and/or Leishmania donovani parasites within a low micromolar concentration. Whether parasite killing is - at least in part - due to inhibition of RNA editing in vivo remains to be assessed. Our findings introduce novel molecular scaffolds with the potential for broad antitrypanosomal effects.
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Affiliation(s)
- Mojtaba Rostamighadi
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada
| | - Arezou Kamelshahroudi
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada
| | - Vaibhav Mehta
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada; Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Fu-Yue Zeng
- Sanford Burnham Prebys Medical Discovery Institute, Conrad Prebys Center for Chemical Genomics, La Jolla, CA, USA
| | - Ian Pass
- Sanford Burnham Prebys Medical Discovery Institute, Conrad Prebys Center for Chemical Genomics, La Jolla, CA, USA
| | - Thomas D Y Chung
- Sanford Burnham Prebys Medical Discovery Institute, Conrad Prebys Center for Chemical Genomics, La Jolla, CA, USA
| | - Reza Salavati
- Institute of Parasitology, McGill University, Ste. Anne de Bellevue, Quebec H9X 3V9, Canada; Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada.
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76
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Silva Júnior JVJ, da Silva ANMR, da Silva Santos JJ, Gil LHVG. Reverse Genetics of Dengue Virus. Methods Mol Biol 2024; 2733:231-248. [PMID: 38064036 DOI: 10.1007/978-1-0716-3533-9_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Dengue virus (DENV) is one of the most important and widespread arthropod-borne viruses, causing millions of infections over the years. Considering its epidemiological importance, efforts have been directed towards understanding various aspects of DENV biology, which have been facilitated by the development of different molecular strategies for engineering viral genomes, such as reverse genetics approaches. Reverse genetic systems are a powerful tool for investigating virus-host interaction, for vaccine development, and for high-throughput screening of antiviral compounds. However, stable manipulation of DENV genomes is a major molecular challenge, especially when using conventional cloning systems. To circumvent this issue, we describe a simple and efficient yeast-based reverse genetics system to recover infectious DENV clones.
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Affiliation(s)
- José Valter Joaquim Silva Júnior
- Virology Sector, Department of Preventive Veterinary Medicine, Federal University of Santa Maria, Santa Maria, RS, Brazil
- Virology Sector, Laboratory of Immunopathology Keizo Asami, Federal University of Pernambuco, Recife, PE, Brazil
| | | | | | - Laura Helena Vega Gonzales Gil
- Laboratory of Virology and Experimental Therapy, Aggeu Magalhães Institute, Oswaldo Cruz Foundation, Recife, PE, Brazil.
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77
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Müller J, Hemphill A. In vitro screening technologies for the discovery and development of novel drugs against Toxoplasma gondii. Expert Opin Drug Discov 2024; 19:97-109. [PMID: 37921660 DOI: 10.1080/17460441.2023.2276349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 11/04/2023]
Abstract
INTRODUCTION Toxoplasmosis constitutes a challenge for public health, animal production and welfare. Since more than 60 years, only a limited panel of drugs has been in use for clinical applications. AREAS COVERED Herein, the authors describe the methodology and the results of library screening approaches to identify inhibitors of Toxoplasma gondii and related strains. The authors then provide the reader with their expert perspectives for the future. EXPERT OPINION Various library screening projects, in particular those using reporter strains, have led to the identification of numerous compounds with good efficacy and specificity in vitro. However, only few compounds are effective in suitable animal models such as rodents. Whereas no novel compound has cleared the hurdle to applications in humans, the few compounds with known indication and application profiles in human patients are of interest for further investigations. Taken together, drug repurposing as well as high-throughput screening of novel compound libraries may shorten the way to novel drugs against toxoplasmosis.
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Affiliation(s)
- Joachim Müller
- Institute of Parasitology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Andrew Hemphill
- Institute of Parasitology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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78
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Melis S, Batisti Biffignandi G, Olivieri E, Galon C, Vicari N, Prati P, Moutailler S, Sassera D, Castelli M. High-throughput screening of pathogens in Ixodes ricinus removed from hosts in Lombardy, northern Italy. Ticks Tick Borne Dis 2024; 15:102285. [PMID: 38035456 DOI: 10.1016/j.ttbdis.2023.102285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023]
Abstract
Ticks are important vectors of many pathogens in Europe, where the most impactful species is Ixodes ricinus. Recently, the geographical distribution of this tick species has been expanding, resulting in an increased risk of human exposure to tick bites. With the present study, we aimed to screen 350 I. ricinus specimens collected from humans and wild animals (mainly ungulates), to have a broader understanding of the tick-borne pathogens circulating in the Lombardy region, in northern Italy. To do so, we took advantage of a high-throughput real-time microfluidic PCR approach to screen ticks in a cost-effective and time-saving manner. Molecular analysis of the dataset revealed the presence of four genera of bacteria and two genera of protozoa: in ungulates, 77 % of collected ticks carried Anaplasma phagocytophilum, while the most common pathogen species in ticks removed from humans were those belonging to Borrelia burgdorferi sensu lato group (7.6 %). We also detected other pathogenic microorganisms, such as Rickettisa monacensis, Rickettsia helvetica, Neoehrlichia mikurensis, Babesia venatorum, and Hepatozoon martis. Besides, we also reported the presence of the pathogenic agent Borrelia miyamotoi in the area (1.4 % overall). The most common dual co-infection detected in the same tick individual involved A. phagocytophilum and Rickettsia spp. Our study provided evidence of the circulation of different tick-borne pathogens in a densely populated region in Italy.
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Affiliation(s)
- Sophie Melis
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | | | - Emanuela Olivieri
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Pavia, Italy
| | - Clémence Galon
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
| | - Nadia Vicari
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Pavia, Italy
| | - Paola Prati
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Pavia, Italy
| | - Sara Moutailler
- ANSES, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy; Fondazione IRCCS Policlinico San Matteo Pavia Italy
| | - Michele Castelli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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79
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Columbus J, Turbyville T. Studying RAS Interactions in Live Cells with BRET. Methods Mol Biol 2024; 2797:253-260. [PMID: 38570465 DOI: 10.1007/978-1-0716-3822-4_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
Bioluminescence resonance energy transfer (BRET) is a valuable technique for studying protein-protein interactions (PPIs) within live cells (Pfleger and Eidne, Nat Methods 3:165-174, 2006). Among the various BRET methodologies, a recent addition called NanoBRET has emerged, leveraging advancements in donor and acceptor technologies (Machleidt and Woodroofe, ACS Chem Biol 10:1797-1804, 2015). In this study, we present a developed methodology designed to measure PPIs involving the RAS protein family and their effectors and interactors at the plasma membrane. By utilizing the NanoLuc and HaloTag BRET pair, we provide evidence of a saturable interaction between KRAS4b-G12D and full-length RAF1. Conversely, the RAF1 R89L mutant, known to impede RAF1 binding to active RAS, exhibits nonspecific interactions. The assay exhibits remarkable signal-to-background ratios and is highly suitable for investigating the interactions of RAS with effectors, as well as for high-throughput screening assays.
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Affiliation(s)
- John Columbus
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Thomas Turbyville
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
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80
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Ma X, Wang M, Wang F, Li J, Zhang Z, Zhu J, Liu B. High resolution crystal structure of BRD4-BD1 in complex with a novel inhibitor precursor. Biochem Biophys Res Commun 2024; 690:149284. [PMID: 38006801 DOI: 10.1016/j.bbrc.2023.149284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/16/2023] [Accepted: 11/16/2023] [Indexed: 11/27/2023]
Abstract
The inhibition of BRD4 bromodomain is an effective therapeutic strategy for a variety of diseases in which BRD4 are implicated. Herein, we identified a small-molecule BRD4 inhibitor hit named compound 3 using high-throughput screening. The 1.6 Å resolution co-crystal structure confirmed that the compound occupies the KAc recognition pockets of BRD4 by forming key hydrogen bonds with Asn140 and engaging in hydrophobic interactions, thus impedes the binding of acetylated lysine to BRD4. These findings suggest compound 3 can be a lead compound to develop a structurally novel BRD4 inhibitors.
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Affiliation(s)
- Xiuxiu Ma
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China
| | - Meng Wang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China
| | - Fan Wang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China
| | - Jiao Li
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China
| | - Zhengguang Zhang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China
| | - Jiapeng Zhu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China; Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China; Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China.
| | - Bing Liu
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210023, China.
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81
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Dasgupta S, Simonich MT, Tanguay RL. Developmental Toxicity Assessment Using Zebrafish-Based High-Throughput Screening. Methods Mol Biol 2024; 2707:71-82. [PMID: 37668905 DOI: 10.1007/978-1-0716-3401-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Zebrafish-based high-throughput screening has been extensively used to study toxicological profiles of individual chemicals and mixtures, identify novel toxicants, and study modes of action to prioritize chemicals for further testing and policy decisions. Within this chapter, we describe a protocol for automated zebrafish developmental high-throughput screening in our laboratory, with emphasis on exposure setups, morphological and behavioral readouts, and quality control.
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Affiliation(s)
- Subham Dasgupta
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Michael T Simonich
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA
| | - Robyn L Tanguay
- Sinnhuber Aquatic Research Laboratory, Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, USA.
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82
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Lee H, Ibrahimi L, Han KY. Fluorescence-Based Peptidolytic Assay for High-Throughput Screening of MMP14 Inhibitors. Methods Mol Biol 2024; 2747:229-242. [PMID: 38038944 DOI: 10.1007/978-1-0716-3589-6_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
The membrane-bound matrix metalloproteinase 14 (MMP14, also known as MT1-MMP) plays important roles in the remodeling of the extracellular matrix during various cellular processes such as cancer metastasis, angiogenesis, and wound healing through its proteolytic activity. There are no known MMP14-specific inhibitors to date, and hence identification of MMP14-specific inhibitors will be beneficial for finding potential therapeutics for various diseases, including cancer and inflammation. High-throughput screening (HTS) assays have become a common way to search for new small compounds, peptides, and natural products. Enzymatic assays are highly amenable to HTS because most enzyme activities are quantifiable with the effect of many small molecules of interest on a specific target enzyme. Here, we describe a fluorescence-based enzymatic assay that can be applied as a large-scale HTS and a follow-up enzyme kinetics assay to find MMP14-specific inhibitors.
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Affiliation(s)
- Hyun Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
- Biophysics Core at the Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Lucas Ibrahimi
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Kyu-Yeon Han
- Department of Ophthalmology and Visual Sciences, Illinois Eye and Ear Infirmary, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA.
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83
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Wang X, Huang J, Li H, Li Y, Cai S, Xue B, Zhu Z, Zeng X, Zeng X. Establishment and application of high throughput screening cell model for nutrient regulation of embryonic development. J Nutr Biochem 2024; 123:109502. [PMID: 37890711 DOI: 10.1016/j.jnutbio.2023.109502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Embryo development exerts far-reaching influence on pregnancy outcome, postnatal development and lifelong health. Thereafter, to select functional nutrients to improve embryo development is of great importance. Herein, a stable porcine trophectoderm cell line expressing a luciferase reporter gene driven by a 1,009 bp PCNA gene promoter was constructed through lentiviral transduction and G418 selection. A high throughput screening assay was subsequently developed using the stable reporter cell line to screen a library of 225 nutrients. Seven nutrients with a minimum Z-score of 2.0 were initially identified to be capable of enhancing embryonic development. Among these nutrients, resveratrol, apigenin, and retinol palmitate were furtherly confirmed the beneficial effects for embryo development. Resveratrol significantly increased the expression of key genes involved in pTr cell proliferation and the number of S-phase cells. Resveratrol was furtherly confirmed to promote the expression of key genes in trophoblast development and increase embryo adhesion rate in vitro. Similarly, dietary 0.05% resveratrol supplementation significantly increased the number of embryo attachment and serum level of P4 and E2 in rats. Resveratrol could also improve maternal antioxidant levels and reduce intracellular ROS. Collectively, a high throughput screening cell model for nutrient regulation of embryonic development was established, which can be used to highly effectively select the potential candidates for embryo development. These findings have great implications for exploring optimal functional nutrients to improve embryo development, ultimately beneficial for pregnancy outcome, offspring postnatal development and lifelong health for human beings and mammalian animals.
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Affiliation(s)
- Xinyu Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China; Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing, China
| | - Jun Huang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China; Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing, China
| | - Huan Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China; Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing, China
| | - Yanlong Li
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China; Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing, China
| | - Shuang Cai
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China; Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing, China
| | - Bangxin Xue
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China; Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing, China
| | - Zhekun Zhu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China; Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing, China
| | - Xiangzhou Zeng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China; Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing, China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China; Beijing Key Laboratory of Biofeed Additives, China Agricultural University, Beijing, China.
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84
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Martinez-Gzegozewska Y, Rasmussen L, McKellip S, Manuvakhova A, Nebane NM, Reece AJ, Ruiz P, Sosa M, Bostwick R, Vinson P. High-Throughput cell-based immunofluorescence assays against influenza. SLAS Discov 2024; 29:66-76. [PMID: 37925159 DOI: 10.1016/j.slasd.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
A rapid drug discovery response to influenza outbreaks with the potential to reach pandemic status could help minimize the virus's impact by reducing the time to identify anti-influenza drugs. Although several anti-influenza strategies have been considered in the search for new drugs, only a few therapeutic agents are approved for clinical use. The cytopathic effect induced by the influenza virus in Madin Darby canine kidney (MDCK) cells has been widely used for high-throughput anti-influenza drug screening, but the fact that the MDCK cells are not human cells constitutes a disadvantage when searching for new therapeutic agents for human use. We have developed a highly sensitive cell-based imaging assay for the identification of inhibitors of influenza A and B virus that is high-throughput compatible using the A549 human cell line. The assay has also been optimized for the assessment of the neutralizing effect of anti-influenza antibodies in the absence of trypsin, which allows testing of purified antibodies and serum samples. This assay platform can be applied to full high-throughput screening campaigns or later stages requiring quantitative potency determinations for structure-activity relationships.
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Affiliation(s)
- Yohanka Martinez-Gzegozewska
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States.
| | - Lynn Rasmussen
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Sara McKellip
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Anna Manuvakhova
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - N Miranda Nebane
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Andrew J Reece
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Pedro Ruiz
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Melinda Sosa
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Robert Bostwick
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
| | - Paige Vinson
- Scientific Platforms Division, Southern Research, High-Throughput Screening Center, Birmingham, Alabama, United States
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85
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Roth JR, Rush T, Thompson SJ, Aldaher AR, Dunn TB, Mesina JS, Cochran JN, Boyle NR, Dean HB, Yang Z, Pathak V, Ruiz P, Wu M, Day JJ, Bostwick JR, Suto MJ, Augelli-Szafran CE, Roberson ED. Development of small-molecule Tau-SH3 interaction inhibitors that prevent amyloid-β toxicity and network hyperexcitability. Neurotherapeutics 2024; 21:e00291. [PMID: 38241154 PMCID: PMC10903085 DOI: 10.1016/j.neurot.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 01/21/2024] Open
Abstract
Alzheimer's disease (AD) is the leading cause of dementia and lacks highly effective treatments. Tau-based therapies hold promise. Tau reduction prevents amyloid-β-induced dysfunction in preclinical models of AD and also prevents amyloid-β-independent dysfunction in diverse disease models, especially those with network hyperexcitability, suggesting that strategies exploiting the mechanisms underlying Tau reduction may extend beyond AD. Tau binds several SH3 domain-containing proteins implicated in AD via its central proline-rich domain. We previously used a peptide inhibitor to demonstrate that blocking Tau interactions with SH3 domain-containing proteins ameliorates amyloid-β-induced dysfunction. Here, we identify a top hit from high-throughput screening for small molecules that inhibit Tau-FynSH3 interactions and describe its optimization with medicinal chemistry. The resulting lead compound is a potent cell-permeable Tau-SH3 interaction inhibitor that binds Tau and prevents amyloid-β-induced dysfunction, including network hyperexcitability. These data support the potential of using small molecule Tau-SH3 interaction inhibitors as a novel therapeutic approach to AD.
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Affiliation(s)
- Jonathan R Roth
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Travis Rush
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Samantha J Thompson
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Adam R Aldaher
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Trae B Dunn
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jacob S Mesina
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - J Nicholas Cochran
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicholas R Boyle
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hunter B Dean
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Zhengrong Yang
- Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vibha Pathak
- Chemistry Department, Southern Research, Birmingham, AL, USA
| | - Pedro Ruiz
- Chemistry Department, Southern Research, Birmingham, AL, USA
| | - Mousheng Wu
- Chemistry Department, Southern Research, Birmingham, AL, USA
| | - Jeremy J Day
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Mark J Suto
- Chemistry Department, Southern Research, Birmingham, AL, USA
| | | | - Erik D Roberson
- Center for Neurodegeneration and Experimental Therapeutics, Alzheimer's Disease Center, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
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86
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Qu Z, Krabill AD, Zhang ZY. High-Throughput Discovery and Characterization of Covalent Inhibitors for Protein Tyrosine Phosphatases. Methods Mol Biol 2024; 2743:301-316. [PMID: 38147223 DOI: 10.1007/978-1-0716-3569-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Covalent inhibition has gained increasing interest in targeting the undruggable protein tyrosine phosphatases (PTPs). However, a systematic method for discovering and characterizing covalent PTP inhibitors has yet to be established. Here, we describe a workflow involving high-throughput screening of covalent fragment libraries and a novel biochemical assay that enables the acquisition of kinetics parameters of PTP inhibition by covalent inhibitors with higher throughput.
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Affiliation(s)
- Zihan Qu
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Aaron D Krabill
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA
| | - Zhong-Yin Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
- Institute for Cancer Research, Purdue University, West Lafayette, IN, USA.
- Institute for Drug Discovery, Purdue University, West Lafayette, IN, USA.
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87
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Lin L, Clevers H. Decoding endocrine cell differentiation: insights from high-throughput CRISPR screening in human gut organoids. Clin Transl Med 2024; 14:e1526. [PMID: 38279896 PMCID: PMC10819080 DOI: 10.1002/ctm2.1526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/29/2024] Open
Affiliation(s)
- Lin Lin
- Hubrecht InstituteRoyal Netherlands Academy of Arts and Sciences (KNAW) and UMC UtrechtUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
- Princess Maxima Center for Pediatric OncologyUtrechtThe Netherlands
| | - Hans Clevers
- Hubrecht InstituteRoyal Netherlands Academy of Arts and Sciences (KNAW) and UMC UtrechtUtrechtThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
- Princess Maxima Center for Pediatric OncologyUtrechtThe Netherlands
- Present address:
Pharma, Research and Early Development (pRED) of F. Hoffmann‐La Roche LtdBaselSwitzerland
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88
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Xin Q, Jia H, Wang B, Pan L. CRISPR-dCpf1 mediated whole genome crRNA inhibition library for high-throughput screening of growth characteristic genes in Bacillus amyloliquefaciens LB1ba02. Int J Biol Macromol 2023; 253:127179. [PMID: 37802457 DOI: 10.1016/j.ijbiomac.2023.127179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/06/2023] [Accepted: 09/23/2023] [Indexed: 10/10/2023]
Abstract
Bacillus amyloliquefaciens LB1ba02 is generally recognized as food safe (GRAS) microbial host and important enzyme-producing strain in the industry. However, autolysis affects the growth of bacteria, further affecting the yield of target products. Besides, the restriction-modification system, existed in B. amyloliquefaciens LB1ba02, results in a low transformation efficiency, which further leads to a lack of high-throughput screening tools. Here, we constructed a genome-wide crRNA inhibition library based on the CRISPR/dCpf1 system and high-throughput screening of related genes affecting the cell growth and autolysis using flow cytometry in B. amyloliquefaciens LB1ba02. The whole genome crRNA library was first validated for resistance to the toxic chemical 5-fluorouracil, and then used for validation of essential genes. In addition, seven gene loci (oppD, flil, tuaA, prmA, sigO, hslU, and GE03231) that affect the growth characteristics of LB1ba02 were screened. Among them, the Opp system had the greatest impact on growth. When the expression of operon oppA-oppB-oppC-oppD-oppF was inhibited, the cell growth difference was most significant. Inhibition of other sites could also promote rapid growth of bacteria to varying degrees; however, inhibition of GE03231 site accelerated cell autolysis. Therefore, the whole genome crRNA inhibition library is well suited for B. amyloliquefaciens LB1ba02 and can be further applied to high-throughput mining of other functional genes.
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Affiliation(s)
- Qinglong Xin
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Panyu District, Guangzhou 510006, Guangdong, PR China
| | - Hang Jia
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Panyu District, Guangzhou 510006, Guangdong, PR China
| | - Bin Wang
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Panyu District, Guangzhou 510006, Guangdong, PR China.
| | - Li Pan
- School of Biology and Biological Engineering, Guangzhou Higher Education Mega Centre, South China University of Technology, Panyu District, Guangzhou 510006, Guangdong, PR China.
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89
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Anantharajan J, Tan QW, Fulwood J, Sifang W, Huang Q, Ng HQ, Koh X, Xu W, Cherian J, Baburajendran N, Kang C, Ke Z. Identification and characterization of inhibitors covalently modifying catalytic cysteine of UBE2T and blocking ubiquitin transfer. Biochem Biophys Res Commun 2023; 689:149238. [PMID: 37979329 DOI: 10.1016/j.bbrc.2023.149238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023]
Abstract
UBE2T is an E2 ubiquitin ligase critical for ubiquitination of substrate and plays important roles in many diseases. Despite the important function, UBE2T is considered as an undruggable target due to lack of a pocket for binding to small molecules with satisfied properties for clinical applications. To develop potent and specific UBE2T inhibitors, we adopted a high-throughput screening assay and two compounds-ETC-6152 and ETC-9004 containing a sulfone tetrazole scaffold were identified. Solution NMR study demonstrated the direct interactions between UBE2T and compounds in solution. Further co-crystal structures reveal the binding modes of these compounds. Both compound hydrolysation and formation of a hydrogen bond with the thiol group of the catalytic cysteine were observed. The formation of covalent complex was confirmed with mass spectrometry. As these two compounds inhibit ubiquitin transfer, our study provides a strategy to develop potent inhibitors of UBE2T.
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Affiliation(s)
- Jothi Anantharajan
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Qian Wen Tan
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Justina Fulwood
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Wang Sifang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Qiwei Huang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Hui Qi Ng
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Xiaoying Koh
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Weijun Xu
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Joseph Cherian
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore
| | - Nithya Baburajendran
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore.
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore.
| | - Zhiyuan Ke
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, #5-01, 138670, Singapore.
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90
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SHAHRANI MESFERAL, GAHTANI REEM, ABOHASSAN MOHAMMAD, ALSHAHRANI MOHAMMAD, ALRAEY YASSER, DERA AYED, ASIRI MOHAMMADRAJEH, RAJAGOPALAN PRASANNA. High-throughput computational screening and in vitro evaluation identifies 5-(4-oxo-4H-3,1-benzoxazin-2-yl)-2-[3-(4-oxo-4H-3,1-benzoxazin-2-yl) phenyl]-1H-isoindole-1,3(2H)-dione (C3), as a novel EGFR-HER2 dual inhibitor in gastric tumors. Oncol Res 2023; 32:251-259. [PMID: 38186572 PMCID: PMC10765126 DOI: 10.32604/or.2023.043139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/11/2023] [Indexed: 01/09/2024] Open
Abstract
Gastric cancers are caused primarily due to the activation and amplification of the EGFR or HER2 kinases resulting in cell proliferation, adhesion, angiogenesis, and metastasis. Conventional therapies are ineffective due to the intra-tumoral heterogeneity and concomitant genetic mutations. Hence, dual inhibition strategies are recommended to increase potency and reduce cytotoxicity. In this study, we have conducted computational high-throughput screening of the ChemBridge library followed by in vitro assays and identified novel selective inhibitors that have a dual impediment of EGFR/HER2 kinase activities. Diversity-based High-throughput Virtual Screening (D-HTVS) was used to screen the whole ChemBridge small molecular library against EGFR and HER2. The atomistic molecular dynamic simulation was conducted to understand the dynamics and stability of the protein-ligand complexes. EGFR/HER2 kinase enzymes, KATOIII, and Snu-5 cells were used for in vitro validations. The atomistic Molecular Dynamics simulations followed by solvent-based Gibbs binding free energy calculation of top molecules, identified compound C3 (5-(4-oxo-4H-3,1-benzoxazin-2-yl)-2-[3-(4-oxo-4H-3,1-benzoxazin-2-yl) phenyl]-1H-isoindole-1,3(2H)-dione) to have a good affinity for both EGFR and HER2. The predicted compound, C3, was promising with better binding energy, good binding pose, and optimum interactions with the EGFR and HER2 residues. C3 inhibited EGFR and HER2 kinases with IC50 values of 37.24 and 45.83 nM, respectively. The GI50 values of C3 to inhibit KATOIII and Snu-5 cells were 84.76 and 48.26 nM, respectively. Based on these findings, we conclude that the identified compound C3 showed a conceivable dual inhibitory activity on EGFR/HER2 kinase, and therefore can be considered as a plausible lead-like molecule for treating gastric cancers with minimal side effects, though testing in higher models with pharmacokinetic approach is required.
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Affiliation(s)
- MESFER AL SHAHRANI
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - REEM GAHTANI
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - MOHAMMAD ABOHASSAN
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - MOHAMMAD ALSHAHRANI
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - YASSER ALRAEY
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - AYED DERA
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - MOHAMMAD RAJEH ASIRI
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - PRASANNA RAJAGOPALAN
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
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91
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Scherf J, Vogel D, Gul S, Reinshagen J, Gribbon P, Rosenthal M. Limited high-throughput screening compatibility of the phenuivirus cap-binding domain. Sci Rep 2023; 13:22820. [PMID: 38129678 PMCID: PMC10739838 DOI: 10.1038/s41598-023-50158-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
Bunyaviruses constitute a large and diverse group of viruses encompassing many emerging pathogens, such as Rift Valley fever virus (family Phenuiviridae), with public and veterinary health relevance but with very limited medical countermeasures are available. For the development of antiviral strategies, the identification and validation of virus-specific targets would be of high value. The cap-snatching mechanism is an essential process in the life cycle of bunyaviruses to produce capped mRNAs, which are then recognized and translated into viral proteins by the host cell translation machinery. Cap-snatching involves cap-binding as well as endonuclease functions and both activities have been demonstrated to be druggable in related influenza viruses. Here, we explore the suitability of the phenuivirus cap-binding function as a target in medium- and high-throughput drug discovery approaches. We developed a range of in vitro assays aiming to detect the interaction between the cap-binding domain (CBD) and the analogue of its natural cap-ligand m7GTP. However, constricted by its shallow binding pocket and low affinity for m7GTP, we conclude that the CBD has limited small molecule targeting potential using classical in vitro drug discovery approaches.
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Affiliation(s)
- Janna Scherf
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Dominik Vogel
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Sheraz Gul
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany.
- Fraunhofer Cluster of Excellence for Immune-Mediated Diseases (CIMD), Theodor Stern Kai 7, 60590, Frankfurt, Germany.
| | - Maria Rosenthal
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP), Discovery Research ScreeningPort, Hamburg, Germany.
- Center for Structural Systems Biology, Hamburg, Germany.
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92
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Xi C, Diao J, Moon TS. Advances in ligand-specific biosensing for structurally similar molecules. Cell Syst 2023; 14:1024-1043. [PMID: 38128482 PMCID: PMC10751988 DOI: 10.1016/j.cels.2023.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 08/23/2023] [Accepted: 10/19/2023] [Indexed: 12/23/2023]
Abstract
The specificity of biological systems makes it possible to develop biosensors targeting specific metabolites, toxins, and pollutants in complex medical or environmental samples without interference from structurally similar compounds. For the last two decades, great efforts have been devoted to creating proteins or nucleic acids with novel properties through synthetic biology strategies. Beyond augmenting biocatalytic activity, expanding target substrate scopes, and enhancing enzymes' enantioselectivity and stability, an increasing research area is the enhancement of molecular specificity for genetically encoded biosensors. Here, we summarize recent advances in the development of highly specific biosensor systems and their essential applications. First, we describe the rational design principles required to create libraries containing potential mutants with less promiscuity or better specificity. Next, we review the emerging high-throughput screening techniques to engineer biosensing specificity for the desired target. Finally, we examine the computer-aided evaluation and prediction methods to facilitate the construction of ligand-specific biosensors.
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Affiliation(s)
- Chenggang Xi
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Jinjin Diao
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO, USA; Division of Biology and Biomedical Sciences, Washington University in St. Louis, St. Louis, MO, USA.
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93
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Chen J, Zhou J, Li M, Zhang K, Dai J, Zhao Y. Systematic analysis of circadian disrupting substances with a high-throughput zebrafish circadian behavior screening approach. Sci Total Environ 2023; 904:167037. [PMID: 37709093 DOI: 10.1016/j.scitotenv.2023.167037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023]
Abstract
Circadian rhythm aligns numerous biological functions in majority of animals. Aside from well-known external factors such as the light-dark cycle and temperature, circadian rhythm can also be regulated by rarely explored factors such as synthetic substances. Here, we established a circadian behavior screening approach utilizing zebrafish larvae model, which integrated high-throughput capabilities with automated batch processing. With this approach, we systematically analyzed the circadian disruptive effects of >60 synthetic substances commonly detected in aquatic environment by assessing both the circadian period length and amplitude of circadian behavior, with an exposure concentration set at 100 μg/L. Among tested substances, a series of circadian disrupting compounds (circadian disruptors) were identified. Several categories of the hit compounds can be recognized, such as phthalate (diisopentyl phthalate (DIPP), with 10.1 % and 49.6 % increases for circadian period length and amplitude, respectively), neuroactive substance (mirtazapine, with 10.6 % and 63.1 % increases, respectively), and biocides (thiamethoxam, with 100.3 % increase for amplitude). Among these compounds, DIPP increased circadian period length and amplitude with a high degree. Aside from DIPP, we further examined eleven other phthalates and demonstrated that benzyl butyl phthalate, diisobutyl phthalate and diisohexyl phthalate could also significantly increase the zebrafish circadian period length by 7.9 %, 3.7 % and 8.5 %, respectively. Collectively, the present findings substantiated the feasibility of this high throughput screening strategy for circadian disruptor's discovery and provided novel insights into understanding of the potential risks of synthetic substances.
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Affiliation(s)
- Jierong Chen
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jie Zhou
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Minjia Li
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Kun Zhang
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jiayin Dai
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yanbin Zhao
- State Environmental Protection Key Laboratory of Environmental Health Impact Assessment of Emerging Contaminants, School of Environmental Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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94
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Li M, Yu H, Li Y, Li X, Huang S, Liu X, Weng G, Xu L, Hou T, Guo DS, Wang Y. Rational design of supramolecular self-assembly sensor for living cell imaging of HDAC1 and its application in high-throughput screening. Biosens Bioelectron 2023; 242:115716. [PMID: 37820557 DOI: 10.1016/j.bios.2023.115716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023]
Abstract
Supramolecular chemistry offers new insights in bioimaging, but specific tracking of enzyme in living cells via supramolecular host-guest reporter pair remains challenging, largely due to the interference caused by the complex cellular environment on the binding between analytes and hosts. Here, by exploiting the principle of supramolecular tandem assay (STA) and the classic host-guest reporter pair (p-sulfonatocalix[4]arene (SC4A) and lucigenin (LCG)) and rationally designing artificial peptide library to screen sequence with high affinity of the target enzyme, we developed a "turn-on" fluorescent sensing system for intracellular imaging of histone deacetylase 1 (HDAC1), which is a potential therapeutic target for various diseases, including cancer, neurological, and cardiovascular diseases. Based on computational simulations and experimental validations, we verified that the deacetylated peptide by HDAC1 competed LCG, freeing it from the SC4A causing fluorescence increase. Enzyme kinetics experiments were further conducted to prove that this assay could detect HDAC1 specifically with high sensitivity (the LOD value is 0.015 μg/mL, ten times lower than the published method). This system was further applied for high-throughput screening of HDAC1 inhibitors over a natural compound library containing 147 compounds, resulting in the identification of a novel HDAC1 down-regulator (Ginsenoside RK3). Our results demonstrated the sensitivity and robustness of the assay system towards HDAC1. It should serve as a valuable tool for biochemical studies and drug screening.
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Affiliation(s)
- Min Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huijuan Yu
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yiran Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xin Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shiqing Huang
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road 487372, Singapore
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road 487372, Singapore
| | - Gaoqi Weng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dong-Sheng Guo
- College of Chemistry, Key Laboratory of Functional Polymer Materials (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Nankai University, Tianjin 300071, China
| | - Yi Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Future Health Laboratory Innovation Center of Yangtze River Delta Zhejiang University, Jiaxing 314100, China.
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95
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Zhang JW, Guo C, Xuan CG, Gu JW, Cui ZN, Zhang J, Zhang L, Jiang W, Zhang LQ. High-Throughput, Quantitative Screening of Quorum-Sensing Inhibitors Based on a Bacterial Biosensor. ACS Chem Biol 2023; 18:2544-2554. [PMID: 37983266 DOI: 10.1021/acschembio.3c00537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Quorum sensing (QS) is a cell-cell communication mechanism by which bacteria synchronize social behaviors such as biofilm formation and virulence factor secretion by producing and sensing small molecular signals. Quorum quenching (QQ) by degrading signals or blocking signal transmissions has become a promising strategy for disrupting QS and preventing bacterial infection and biofilm formation. However, studies of high-throughput screening and identification approaches for quorum-sensing inhibitors (QSIs) are still inadequate. In this work, we developed a sensitive, high-throughput approach for screening QSIs based on the bacterial biosensor strain Agrobacterium tumefaciens N5 (pBA7P), which contains a traG gene promoter induced by QS signals fused with a promoterless β-lactamase gene reporter. Using this approach, we identified 31 QQ bacteria from ∼2000 soil bacterial isolates, some belonging to the genera Bosea, Cupriavidus, and Flavobacterium that have not been reported previously as QQ bacteria. We also identified four QS inhibitory compounds and one QS signal analogue from ∼5000 small-molecule compounds, which profoundly affected the expression of QS-regulated genes and phenotypes of the pathogenic bacteria. This high-throughput screening system is effective and sensitive for screening of both QQ microbes and small molecules, enabling the discovery of a wide variety of biocompatible compounds.
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Affiliation(s)
- Jun-Wei Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Cong Guo
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Chen-Guang Xuan
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Jing-Wen Gu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
| | - Zi-Ning Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou 510642, China
| | - Jing Zhang
- Institute of Functional Molecules, Shenyang University of Chemical Technology, Shenyang, Liaoning 110142, China
| | - Lixin Zhang
- Institute of Functional Molecules, Shenyang University of Chemical Technology, Shenyang, Liaoning 110142, China
| | - Wenjun Jiang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Li-Qun Zhang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
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96
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Jiang W, Wijerathne TD, Zhang H, Lin YC, Jo S, Im W, Lacroix JJ, Luo YL. Structural and thermodynamic framework for PIEZO1 modulation by small molecules. Proc Natl Acad Sci U S A 2023; 120:e2310933120. [PMID: 38060566 PMCID: PMC10723123 DOI: 10.1073/pnas.2310933120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/12/2023] [Indexed: 12/17/2023] Open
Abstract
Mechanosensitive PIEZO channels constitute potential pharmacological targets for multiple clinical conditions, spurring the search for potent chemical PIEZO modulators. Among them is Yoda1, a widely used synthetic small molecule PIEZO1 activator discovered through cell-based high-throughput screening. Yoda1 is thought to bind to PIEZO1's mechanosensory arm domain, sandwiched between two transmembrane regions near the channel pore. However, how the binding of Yoda1 to this region promotes channel activation remains elusive. Here, we first demonstrate that cross-linking PIEZO1 repeats A and B with disulfide bridges reduces the effects of Yoda1 in a redox-dependent manner, suggesting that Yoda1 acts by perturbing the contact between these repeats. Using molecular dynamics-based absolute binding free energy simulations, we next show that Yoda1 preferentially occupies a deeper, amphipathic binding site with higher affinity in PIEZO1 open state. Using Yoda1's binding poses in open and closed states, relative binding free energy simulations were conducted in the membrane environment, recapitulating structure-activity relationships of known Yoda1 analogs. Through virtual screening of an 8 million-compound library using computed fragment maps of the Yoda1 binding site, we subsequently identified two chemical scaffolds with agonist activity toward PIEZO1. This study supports a pharmacological model in which Yoda1 activates PIEZO1 by wedging repeats A and B, providing a structural and thermodynamic framework for the rational design of PIEZO1 modulators. Beyond PIEZO channels, the three orthogonal computational approaches employed here represent a promising path toward drug discovery in highly heterogeneous membrane protein systems.
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Affiliation(s)
- Wenjuan Jiang
- Department of Biotechnology and Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA91766
| | - Tharaka D. Wijerathne
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA91766
| | - Han Zhang
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015
- Department of Chemistry, Lehigh University, Bethlehem, PA18015
- Department of Bioengineering, Lehigh University, Bethlehem, PA18015
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA18015
| | - Yi-Chun Lin
- Department of Biotechnology and Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA91766
| | - Sunhwan Jo
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, MD21201
| | - Wonpil Im
- Department of Biological Sciences, Lehigh University, Bethlehem, PA18015
- Department of Chemistry, Lehigh University, Bethlehem, PA18015
- Department of Bioengineering, Lehigh University, Bethlehem, PA18015
- Department of Computer Science and Engineering, Lehigh University, Bethlehem, PA18015
| | - Jerome J. Lacroix
- Department of Basic Medical Sciences, Western University of Health Sciences, Pomona, CA91766
| | - Yun L. Luo
- Department of Biotechnology and Pharmaceutical Sciences, Western University of Health Sciences, Pomona, CA91766
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97
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Dolan M, St. John N, Zaidi F, Doyle F, Fasullo M. High-throughput screening of the Saccharomyces cerevisiae genome for 2-amino-3-methylimidazo [4,5-f] quinoline resistance identifies colon cancer-associated genes. G3 (Bethesda) 2023; 13:jkad219. [PMID: 37738679 PMCID: PMC11025384 DOI: 10.1093/g3journal/jkad219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 10/25/2022] [Accepted: 09/15/2023] [Indexed: 09/24/2023]
Abstract
Heterocyclic aromatic amines (HAAs) are potent carcinogenic agents found in charred meats and cigarette smoke. However, few eukaryotic resistance genes have been identified. We used Saccharomyces cerevisiae (budding yeast) to identify genes that confer resistance to 2-amino-3-methylimidazo[4,5-f] quinoline (IQ). CYP1A2 and NAT2 activate IQ to become a mutagenic nitrenium compound. Deletion libraries expressing human CYP1A2 and NAT2 or no human genes were exposed to either 400 or 800 µM IQ for 5 or 10 generations. DNA barcodes were sequenced using the Illumina HiSeq 2500 platform and statistical significance was determined for exactly matched barcodes. We identified 424 ORFs, including 337 genes of known function, in duplicate screens of the "humanized" collection for IQ resistance; resistance was further validated for a select group of 51 genes by growth curves, competitive growth, or trypan blue assays. Screens of the library not expressing human genes identified 143 ORFs conferring resistance to IQ per se. Ribosomal protein and protein modification genes were identified as IQ resistance genes in both the original and "humanized" libraries, while nitrogen metabolism, DNA repair, and growth control genes were also prominent in the "humanized" library. Protein complexes identified included the casein kinase 2 (CK2) and histone chaperone (HIR) complex. Among DNA Repair and checkpoint genes, we identified those that function in postreplication repair (RAD18, UBC13, REV7), base excision repair (NTG1), and checkpoint signaling (CHK1, PSY2). These studies underscore the role of ribosomal protein genes in conferring IQ resistance, and illuminate DNA repair pathways for conferring resistance to activated IQ.
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Affiliation(s)
- Michael Dolan
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Nick St. John
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Faizan Zaidi
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Francis Doyle
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
| | - Michael Fasullo
- College of Nanotechnology, Science, and Engineering, State University of NewYork at Albany, Albany, NY 12203, USA
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98
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Penner-Goeke S, Bothe M, Rek N, Kreitmaier P, Pöhlchen D, Kühnel A, Glaser LV, Kaya E, Krontira AC, Röh S, Czamara D, Ködel M, Monteserin-Garcia J, Diener L, Wölfel B, Sauer S, Rummel C, Riesenberg S, Arloth-Knauer J, Ziller M, Labeur M, Meijsing S, Binder EB. High-throughput screening of glucocorticoid-induced enhancer activity reveals mechanisms of stress-related psychiatric disorders. Proc Natl Acad Sci U S A 2023; 120:e2305773120. [PMID: 38011552 DOI: 10.1073/pnas.2305773120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/01/2023] [Indexed: 11/29/2023] Open
Abstract
Exposure to stressful life events increases the risk for psychiatric disorders. Mechanistic insight into the genetic factors moderating the impact of stress can increase our understanding of disease processes. Here, we test 3,662 single nucleotide polymorphisms (SNPs) from preselected expression quantitative trait loci in massively parallel reporter assays to identify genetic variants that modulate the activity of regulatory elements sensitive to glucocorticoids, important mediators of the stress response. Of the tested SNP sequences, 547 were located in glucocorticoid-responsive regulatory elements of which 233 showed allele-dependent activity. Transcripts regulated by these functional variants were enriched for those differentially expressed in psychiatric disorders in the postmortem brain. Phenome-wide Mendelian randomization analysis in 4,439 phenotypes revealed potentially causal associations specifically in neurobehavioral traits, including major depression and other psychiatric disorders. Finally, a functional gene score derived from these variants was significantly associated with differences in the physiological stress response, suggesting that these variants may alter disease risk by moderating the individual set point of the stress response.
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Affiliation(s)
- Signe Penner-Goeke
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- Graduate School of Systemic Neurosciences, Ludwig Maximilian University of Munich, Planegg 82152, Germany
| | - Melissa Bothe
- Department of Computational Molecular Biology, Max Planck Institute of Molecular Genetics, Berlin 14195, Germany
| | - Nils Rek
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Peter Kreitmaier
- Institute of Translational Genomics, Helmholtz Munich, Neuherberg 85764, Germany
| | - Dorothee Pöhlchen
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Anne Kühnel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Laura V Glaser
- Department of Computational Molecular Biology, Max Planck Institute of Molecular Genetics, Berlin 14195, Germany
| | - Ezgi Kaya
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- Graduate School of Systemic Neurosciences, Ludwig Maximilian University of Munich, Planegg 82152, Germany
| | - Anthi C Krontira
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Simone Röh
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Maik Ködel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Jose Monteserin-Garcia
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Laura Diener
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Barbara Wölfel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Susann Sauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Christine Rummel
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Stephan Riesenberg
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Janine Arloth-Knauer
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Michael Ziller
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
- Department of Psychiatry, University of Muenster, Muenster 48149, Germany
| | - Marta Labeur
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - Sebastiaan Meijsing
- Department of Computational Molecular Biology, Max Planck Institute of Molecular Genetics, Berlin 14195, Germany
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
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99
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Murciano N, Rotordam MG, Becker N, Ludlow MJ, Parsonage G, Darras A, Kaestner L, Beech DJ, George M, Fertig N, Rapedius M, Brüggemann A. A high-throughput electrophysiology assay to study the response of PIEZO1 to mechanical stimulation. J Gen Physiol 2023; 155:e202213132. [PMID: 37801066 PMCID: PMC10558326 DOI: 10.1085/jgp.202213132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 07/17/2023] [Accepted: 09/17/2023] [Indexed: 10/07/2023] Open
Abstract
PIEZO1 channels are mechanically activated cation channels that play a pivotal role in sensing mechanical forces in various cell types. Their dysfunction has been associated with numerous pathophysiological states, including generalized lymphatic dysplasia, varicose vein disease, and hereditary xerocytosis. Given their physiological relevance, investigating PIEZO1 is crucial for the pharmaceutical industry, which requires scalable techniques to allow for drug discovery. In this regard, several studies have used high-throughput automated patch clamp (APC) combined with Yoda1, a specific gating modifier of PIEZO1 channels, to explore the function and properties of PIEZO1 in heterologous expression systems, as well as in primary cells. However, a combination of solely mechanical stimulation (M-Stim) and high-throughput APC has not yet been available for the study of PIEZO1 channels. Here, we show that optimization of pipetting parameters of the SyncroPatch 384 coupled with multihole NPC-384 chips enables M-Stim of PIEZO1 channels in high-throughput electrophysiology. We used this approach to explore differences between the response of mouse and human PIEZO1 channels to mechanical and/or chemical stimuli. Our results suggest that applying solutions on top of the cells at elevated pipetting flows is crucial for activating PIEZO1 channels by M-Stim on the SyncroPatch 384. The possibility of comparing and combining mechanical and chemical stimulation in a high-throughput patch clamp assay facilitates investigations on PIEZO1 channels and thereby provides an important experimental tool for drug development.
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Affiliation(s)
- Nicoletta Murciano
- Nanion Technologies GmbH, München, Germany
- Theoretical Medicine and Biosciences, Saarland University, Homburg, Germany
| | | | | | - Melanie J. Ludlow
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Gregory Parsonage
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
| | - Alexis Darras
- Experimental Physics, Saarland University, Saarbrücken, Germany
| | - Lars Kaestner
- Theoretical Medicine and Biosciences, Saarland University, Homburg, Germany
- Experimental Physics, Saarland University, Saarbrücken, Germany
| | - David J. Beech
- Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, UK
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100
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Kamal M, Mukherjee S, Joshi B, Sindhu ZUD, Wangchuk P, Haider S, Ahmed N, Talukder MH, Geary TG, Yadav AK. Model nematodes as a practical innovation to promote high throughput screening of natural products for anthelmintics discovery in South Asia: Current challenges, proposed practical and conceptual solutions. Mol Biochem Parasitol 2023; 256:111594. [PMID: 37730126 DOI: 10.1016/j.molbiopara.2023.111594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/27/2023] [Accepted: 09/12/2023] [Indexed: 09/22/2023]
Abstract
With the increasing prevalence of anthelmintic resistance in animals recorded globally, and the threat of resistance in human helminths, the need for novel anthelmintic drugs is greater than ever. Most research aimed at discovering novel anthelmintic leads relies on high throughput screening (HTS) of large libraries of synthetic small molecules in industrial and academic settings in developed countries, even though it is the tropical countries that are most plagued by helminth infections. Tropical countries, however, have the advantage of possessing a rich flora that may yield natural products (NP) with promising anthelmintic activity. Focusing on South Asia, which produces one of the world's highest research outputs in NP and NP-based anthelmintic discovery, we find that limited basic research and funding, a lack of awareness of the utility of model organisms, poor industry-academia partnerships and lack of technological innovations greatly limit anthelmintics research in the region. Here we propose that utilizing model organisms including the free-living nematode Caenorhabditis elegans, that can potentially allow rapid target identification of novel anthelmintics, and Oscheius tipulae, a closely related, free-living nematode which is found abundantly in soil in hotter temperatures, could be a much-needed innovation that can enable cost-effective and efficient HTS of NPs for discovering compounds with anthelmintic/antiparasitic potential in South Asia and other tropical regions that historically have devoted limited funding for such research. Additionally, increased collaborations at the national, regional and international level between parasitologists and pharmacologists/ethnobotanists, setting up government-industry-academia partnerships to fund academic research, creating a centralized, regional collection of plant extracts or purified NPs as a dereplication strategy and HTS library, and holding regional C. elegans/O. tipulae-based anthelmintics workshops and conferences to share knowledge and resources regarding model organisms may collectively promote and foster a NP-based anthelmintics landscape in South Asia and beyond.
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Affiliation(s)
- Muntasir Kamal
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.
| | - Suprabhat Mukherjee
- Department of Animal Science, Kazi Nazrul University, Asansol 713340, West Bengal, India
| | - Bishnu Joshi
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Zia-Ud-Din Sindhu
- Department of Parasitology, University of Agriculture Faisalabad, Pakistan
| | - Phurpa Wangchuk
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns Campus, QLD 4878, Australia
| | | | - Nurnabi Ahmed
- Department of Parasitology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | | | - Timothy G Geary
- Institute of Parasitology, McGill University, Montreal, Canada; School of Biological Sciences, Queen's University-Belfast, Belfast, NI, UK
| | - Arun K Yadav
- Department of Zoology, North-Eastern Hill University, Shillong 793022, India
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