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de Schepper JKH, Slootweg T, Behnisch P, Felzel E, Houtman CJ. Beyond the Drinking Water Directive: The use of reporter gene assays as an added tool for effect-based monitoring of polycyclic aromatic hydrocarbons and polychlorinated biphenyls in drinking water sources. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 941:173366. [PMID: 38796005 DOI: 10.1016/j.scitotenv.2024.173366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) are legacy organic micropollutants (OMPs) that are sporadically detected in drinking water (DW) sources. The European Drinking Water Directive requires EU member states to monitor 5 PAHs in DW and its sources. The Dutch national regulations require 6 additional PAHs to be monitored and 7 polychlorinated biphenyls (PCBs). These indicator compounds act as representatives for large compound classes. PCBs alone comprise 209 congeners, it is evident that conventional chemical target analysis (GC-tQ-MS) alone is not sufficient to monitor these entire compound classes. This study investigated the application of reporter gene assays as effect-based methods (EBMs) to monitor PAHs and PCBs in DW sources. Herein, it was assessed what added value the bioassays can bring compared to the current approach of chemical target analysis for PCBs and PAHs. Regulated and non-regulated PAHs and PCBs were tested in four bioassays to determine the relative potency factors (RPFs) for these compounds. Non-regulated congeners were found to be active in the PAH-CALUX and anti-AR CALUX. An assessment of surface water (SW) spiked with standard mixtures containing PAHs and PCBs confirmed the predictable behavior of the PAH-CALUX. Moreover, the bioassay was able to detect AhR-mediated activity caused by non-regulated PAHs and PCBs, whereas this would have been missed by conventional chemical target analysis. Last, a field study was conducted in Dutch DW sources at six sampling moments. The PAH-CALUX detected AhR-mediated activity at all sampling moments and an ecological effect-based trigger (EBT) value was exceeded on multiple accounts. Combined application of GC-tQ-MS and the PAH-CALUX ensures compliancy with monitoring legislation and provides additional insights into potential hazards to humans and the environment.
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Affiliation(s)
- J K H de Schepper
- Het Waterlaboratorium N.V. (HWL), 2031 BE Haarlem, the Netherlands; Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands.
| | - T Slootweg
- Het Waterlaboratorium N.V. (HWL), 2031 BE Haarlem, the Netherlands
| | - P Behnisch
- BioDetection Systems B.V. (BDS), 1098 XH Amsterdam, the Netherlands
| | - E Felzel
- BioDetection Systems B.V. (BDS), 1098 XH Amsterdam, the Netherlands
| | - C J Houtman
- Het Waterlaboratorium N.V. (HWL), 2031 BE Haarlem, the Netherlands; Amsterdam Institute for Life and Environment (A-LIFE), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, the Netherlands
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2
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Pahl A, Liu J, Patil S, Rezaei Adariani S, Schölermann B, Warmers J, Bonowski J, Koska S, Akbulut Y, Seitz C, Sievers S, Ziegler S, Waldmann H. Illuminating Dark Chemical Matter Using the Cell Painting Assay. J Med Chem 2024; 67:8862-8876. [PMID: 38687818 PMCID: PMC11181314 DOI: 10.1021/acs.jmedchem.4c00160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/02/2024]
Abstract
Screening for small-molecule modulators of disease-relevant targets and phenotypes is the first step on the way to new drugs. Large compound libraries have been synthesized by academia and, particularly, pharmaceutical companies to meet the need for novel chemical entities that are as diverse as possible. Screening of these compound libraries revealed a portion of small molecules that is inactive in more than 100 different assays and was therefore termed "dark chemical matter" (DCM). Deorphanization of DCM promises to yield very selective compounds as they are expected to have less off-target effects. We employed morphological profiling using the Cell Painting assay to detect bioactive DCM. Within the DCM collection, we identified bioactive compounds and confirmed several modulators of microtubules, DNA synthesis, and pyrimidine biosynthesis. Profiling approaches are, therefore, powerful tools to probe compound collections for bioactivity in an unbiased manner and are particularly suitable for deorphanization of DCM.
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Affiliation(s)
- Axel Pahl
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Jie Liu
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sohan Patil
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Soheila Rezaei Adariani
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Technical
University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Beate Schölermann
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Jens Warmers
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Technical
University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
| | - Jana Bonowski
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sandra Koska
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Yasemin Akbulut
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Carina Seitz
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sonja Sievers
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Slava Ziegler
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Herbert Waldmann
- Max-Planck
Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Technical
University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, Dortmund 44227, Germany
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3
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Chen S, Liu Y, Wang Z, Qi C, Yu Y, Xu L, Hou T, Sheng R. Identification of 3-aryl-5-methyl-isoxazole-4-carboxamide derivatives and analogs as novel HIF-2α agonists through docking-based virtual screening and structural modification. Eur J Med Chem 2024; 268:116227. [PMID: 38387335 DOI: 10.1016/j.ejmech.2024.116227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/25/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Hypoxia-inducible factor-2 (HIF-2) serves as the pivotal transcription factor in cellular responses to low oxygen levels, particularly concerning the regulation of erythropoietin (EPO) production. A docking-based virtual screening on crystal structures of HIF-2α inhibitors unexpectedly identified 3-phenyl-5-methyl-isoxazole-4-carboxamide derivative v19 as a hit of HIF-2α agonist. Further structural optimizations of compound v19 led to the discovery of a series of HIF-2α agonists with novel scaffolds. The most promising compounds 12g and 14d exhibited potent HIF-2α agonistic activities in vitro with EC50 values of 2.29 μM and 1.78 μM, respectively. Molecular dynamics simulations have revealed their capacity to allosterically enhance HIF-2 dimerization, which shed light on their mechanism of action. Moreover, compound 14d demonstrated a favorable pharmacokinetic (PK) profile, boasting an impressive oral bioavailability value of 68.71 %. These findings strongly suggest that compound 14d is an auspicious lead compound for the treatment of renal anemia.
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Affiliation(s)
- Siyuan Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yao Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhe Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Chengcheng Qi
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yanzhen Yu
- 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.
| | - Rong Sheng
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; Jinhua Institute of Zhejiang University, Zhejiang University, Jinhua, 321036, China.
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Zhuang J, Shang Q, Rastinejad F, Wu D. Decoding Allosteric Control in Hypoxia-Inducible Factors. J Mol Biol 2024; 436:168352. [PMID: 37935255 DOI: 10.1016/j.jmb.2023.168352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/10/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
The mammalian family of basic helix-loop-helix-PER-ARNT-SIM (bHLH-PAS) transcription factors possess the ability to sense and respond to diverse environmental and physiological cues. These proteins all share a common structural framework, comprising a bHLH domain, two PAS domains, and transcriptional activation or repression domain. To function effectively as transcription factors, members of the family must form dimers, bringing together bHLH segments to create a functional unit that allows for DNA response element binding. The significance of bHLH-PAS family is underscored by their involvement in many major human diseases, offering potential avenues for therapeutic intervention. Notably, the clear identification of ligand-binding cavities within their PAS domains enables the development of targeted small molecules. Two examples are Belzutifan, targeting hypoxia-inducible factor (HIF)-2α, and Tapinarof, targeting the aryl hydrocarbon receptor (AHR), both of which have gained regulatory approval recently. Here, we focus on the HIF subfamily. The crystal structures of all three HIF-α proteins have been elucidated, revealing their bHLH and tandem PAS domains are used to engage their dimerization partner aryl hydrocarbon receptor nuclear translocator (ARNT, also called HIF-1β). A broad range of recent findings point to a shared allosteric modulation mechanism among these proteins, whereby small-molecules at the PAS-B domains exert direct influence over the HIF-α transcriptional functions. As our understanding of the architectural and allosteric mechanisms of bHLH-PAS proteins continues to advance, the possibility of discovering new therapeutic drugs becomes increasingly promising.
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Affiliation(s)
- Jingjing Zhuang
- Marine College, Shandong University, Weihai 264209, China; Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Qinghong Shang
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Fraydoon Rastinejad
- Target Discovery Institute, Nuffield Department of Medicine Research Building, University of Oxford, Old Road Campus, Oxford OX3 7FZ, UK.
| | - Dalei Wu
- Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.
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5
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Bonati L, Motta S, Callea L. The AhR Signaling Mechanism: A Structural Point of View. J Mol Biol 2024; 436:168296. [PMID: 37797832 DOI: 10.1016/j.jmb.2023.168296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 09/28/2023] [Indexed: 10/07/2023]
Abstract
The Aryl hydrocarbon Receptor (AhR) is a well-known sensor of xenobiotics; moreover, it is considered a promising drug target as it is involved in the regulation of many patho-physiological processes. For these reasons the study of its ligand-activated transcription mechanism has stimulated several studies for over twenty years. In this review we highlight the key role of molecular structural information in understanding the different steps of the signaling mechanism. The architecture of the AhR cytosolic complex, encompassing the hsp90 chaperone protein and the XAP2 and p23 co-chaperones, has become available in the last year thanks to Cryo-EM experiments. The structure of the AhR ligand-binding (PAS-B) domain has remained elusive for a long time; it has been predicted by homology modelling, based on known PAS systems, and its ligand-bound forms were modelled through ligand molecular docking. Although very recently some structural information on this domain has become available, considerable efforts are still needed to determine the binding geometries of the AhR key ligands by experimental high-resolution studies. On the other hand, the dimeric structure of AhR with the ARNT protein, bound to the specific DNA responsive element, was partially determined by X-ray crystallography and it was completed by homology modelling. On the whole the current structural knowledge of the main protein complexes that form over the AhR mechanism opens the way to confirm and further investigate the main steps of the proposed ligand-activated transcription mechanism of the AhR.
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Affiliation(s)
- Laura Bonati
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
| | - Lara Callea
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milan, Italy.
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Kwong HS, Paloni M, Grandvuillemin L, Sirounian S, Ancelin A, Lai-Kee-Him J, Grimaldi M, Carivenc C, Lancey C, Ragan TJ, Hesketh EL, Balaguer P, Barducci A, Gruszczyk J, Bourguet W. Structural Insights into the Activation of Human Aryl Hydrocarbon Receptor by the Environmental Contaminant Benzo[a]pyrene and Structurally Related Compounds. J Mol Biol 2024; 436:168411. [PMID: 38135181 DOI: 10.1016/j.jmb.2023.168411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/10/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor belonging to the bHLH/PAS protein family and responding to hundreds of natural and chemical substances. It is primarily involved in the defense against chemical insults and bacterial infections or in the adaptive immune response, but also in the development of pathological conditions ranging from inflammatory to neoplastic disorders. Despite its prominent roles in many (patho)physiological processes, the lack of high-resolution structural data has precluded for thirty years an in-depth understanding of the structural mechanisms underlying ligand-binding specificity, promiscuity and activation of AHR. We recently reported a cryogenic electron microscopy (cryo-EM) structure of human AHR bound to the natural ligand indirubin, the chaperone Hsp90 and the co-chaperone XAP2 that provided the first experimental visualization of its ligand-binding PAS-B domain. Here, we report a 2.75 Å resolution structure of the AHR complex bound to the environmental pollutant benzo[a]pyrene (B[a]P). The structure substantiates the existence of a bipartite PAS-B ligand-binding pocket with a geometrically constrained primary binding site controlling ligand binding specificity and affinity, and a secondary binding site contributing to the binding promiscuity of AHR. We also report a docking study of B[a]P congeners that validates the B[a]P-bound PAS-B structure as a suitable model for accurate computational ligand binding assessment. Finally, comparison of our agonist-bound complex with the recently reported structures of mouse and fruit fly AHR PAS-B in different activation states suggests a ligand-induced loop conformational change potentially involved in the regulation of AHR function.
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Affiliation(s)
- Hok-Sau Kwong
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Matteo Paloni
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Loïc Grandvuillemin
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Savannah Sirounian
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Aurélie Ancelin
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Josephine Lai-Kee-Him
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Marina Grimaldi
- IRCM (Institut de Recherche en Cancérologie de Montpellier), Univ Montpellier, Inserm, ICM, Montpellier, France
| | - Coralie Carivenc
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Claudia Lancey
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK
| | - Timothy J Ragan
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK
| | - Emma L Hesketh
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Lancaster Rd, Leicester LE1 7HB, UK
| | - Patrick Balaguer
- IRCM (Institut de Recherche en Cancérologie de Montpellier), Univ Montpellier, Inserm, ICM, Montpellier, France
| | - Alessandro Barducci
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France
| | - Jakub Gruszczyk
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France.
| | - William Bourguet
- CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, Inserm, Montpellier, France.
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7
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Sitsel O, Wang Z, Janning P, Kroczek L, Wagner T, Raunser S. Yersinia entomophaga Tc toxin is released by T10SS-dependent lysis of specialized cell subpopulations. Nat Microbiol 2024; 9:390-404. [PMID: 38238469 PMCID: PMC10847048 DOI: 10.1038/s41564-023-01571-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/29/2023] [Indexed: 02/04/2024]
Abstract
Disease-causing bacteria secrete numerous toxins to invade and subjugate their hosts. Unlike many smaller toxins, the secretion machinery of most large toxins remains enigmatic. By combining genomic editing, proteomic profiling and cryo-electron tomography of the insect pathogen Yersinia entomophaga, we demonstrate that a specialized subset of these cells produces a complex toxin cocktail, including the nearly ribosome-sized Tc toxin YenTc, which is subsequently exported by controlled cell lysis using a transcriptionally coupled, pH-dependent type 10 secretion system (T10SS). Our results dissect the Tc toxin export process by a T10SS, identifying that T10SSs operate via a previously unknown lytic mode of action and establishing them as crucial players in the size-insensitive release of cytoplasmically folded toxins. With T10SSs directly embedded in Tc toxin operons of major pathogens, we anticipate that our findings may model an important aspect of pathogenesis in bacteria with substantial impact on agriculture and healthcare.
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Affiliation(s)
- Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Zhexin Wang
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Petra Janning
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Lara Kroczek
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Thorsten Wagner
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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8
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Rastinejad F. The protein architecture and allosteric landscape of HNF4α. Front Endocrinol (Lausanne) 2023; 14:1219092. [PMID: 37732120 PMCID: PMC10507258 DOI: 10.3389/fendo.2023.1219092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/01/2023] [Indexed: 09/22/2023] Open
Abstract
Hepatocyte nuclear factor 4 alpha (HNF4α) is a multi-faceted nuclear receptor responsible for governing the development and proper functioning of liver and pancreatic islet cells. Its transcriptional functions encompass the regulation of vital metabolic processes including cholesterol and fatty acid metabolism, and glucose sensing and control. Various genetic mutations and alterations in HNF4α are associated with diabetes, metabolic disorders, and cancers. From a structural perspective, HNF4α is one of the most comprehensively understood nuclear receptors due to its crystallographically observed architecture revealing interconnected DNA binding domains (DBDs) and ligand binding domains (LBDs). This review discusses key properties of HNF4α, including its mode of homodimerization, its binding to fatty acid ligands, the importance of post-translational modifications, and the mechanistic basis for allosteric functions. The surfaces linking HNF4α's DBDs and LBDs create a convergence zone that allows signals originating from any one domain to influence distant domains. The HNF4α-DNA complex serves as a prime illustration of how nuclear receptors utilize individual domains for specific functions, while also integrating these domains to create cohesive higher-order architectures that allow signal responsive functions.
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Affiliation(s)
- Fraydoon Rastinejad
- Nuffield Department of Medicine, Target Discovery Institute (NDMRB), University of Oxford, Oxford, United Kingdom
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9
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Pahl A, Schölermann B, Lampe P, Rusch M, Dow M, Hedberg C, Nelson A, Sievers S, Waldmann H, Ziegler S. Morphological subprofile analysis for bioactivity annotation of small molecules. Cell Chem Biol 2023:S2451-9456(23)00159-9. [PMID: 37385259 DOI: 10.1016/j.chembiol.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 03/21/2023] [Accepted: 06/02/2023] [Indexed: 07/01/2023]
Abstract
Fast prediction of the mode of action (MoA) for bioactive compounds would immensely foster bioactivity annotation in compound collections and may early on reveal off-targets in chemical biology research and drug discovery. Morphological profiling, e.g., using the Cell Painting assay, offers a fast, unbiased assessment of compound activity on various targets in one experiment. However, due to incomplete bioactivity annotation and unknown activities of reference compounds, prediction of bioactivity is not straightforward. Here we introduce the concept of subprofile analysis to map the MoA for both, reference and unexplored compounds. We defined MoA clusters and extracted cluster subprofiles that contain only a subset of morphological features. Subprofile analysis allows for the assignment of compounds to, currently, twelve targets or MoA. This approach enables rapid bioactivity annotation of compounds and will be extended to further clusters in the future.
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Affiliation(s)
- Axel Pahl
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
| | - Beate Schölermann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Philipp Lampe
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Marion Rusch
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Mark Dow
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Christian Hedberg
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Adam Nelson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Sonja Sievers
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Herbert Waldmann
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
| | - Slava Ziegler
- Max Planck Institute of Molecular Physiology, Department of Chemical Biology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.
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