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Mistretta M, Cimino M, Campagne P, Volant S, Kornobis E, Hebert O, Rochais C, Dallemagne P, Lecoutey C, Tisnerat C, Lepailleur A, Ayotte Y, LaPlante SR, Gangneux N, Záhorszká M, Korduláková J, Vichier-Guerre S, Bonhomme F, Pokorny L, Albert M, Tinevez JY, Manina G. Dynamic microfluidic single-cell screening identifies pheno-tuning compounds to potentiate tuberculosis therapy. Nat Commun 2024; 15:4175. [PMID: 38755132 PMCID: PMC11099131 DOI: 10.1038/s41467-024-48269-2] [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: 03/13/2024] [Accepted: 04/25/2024] [Indexed: 05/18/2024] Open
Abstract
Drug-recalcitrant infections are a leading global-health concern. Bacterial cells benefit from phenotypic variation, which can suggest effective antimicrobial strategies. However, probing phenotypic variation entails spatiotemporal analysis of individual cells that is technically challenging, and hard to integrate into drug discovery. In this work, we develop a multi-condition microfluidic platform suitable for imaging two-dimensional growth of bacterial cells during transitions between separate environmental conditions. With this platform, we implement a dynamic single-cell screening for pheno-tuning compounds, which induce a phenotypic change and decrease cell-to-cell variation, aiming to undermine the entire bacterial population and make it more vulnerable to other drugs. We apply this strategy to mycobacteria, as tuberculosis poses a major public-health threat. Our lead compound impairs Mycobacterium tuberculosis via a peculiar mode of action and enhances other anti-tubercular drugs. This work proves that harnessing phenotypic variation represents a successful approach to tackle pathogens that are increasingly difficult to treat.
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Affiliation(s)
- Maxime Mistretta
- Institut Pasteur, Université Paris Cité, Microbial Individuality and Infection Laboratory, 75015, Paris, France
| | - Mena Cimino
- Institut Pasteur, Université Paris Cité, Microbial Individuality and Infection Laboratory, 75015, Paris, France
| | - Pascal Campagne
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015, Paris, France
| | - Stevenn Volant
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015, Paris, France
| | - Etienne Kornobis
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 75015, Paris, France
- Institut Pasteur, Université Paris Cité, Biomics Platform, 75015, Paris, France
| | | | | | | | | | | | | | - Yann Ayotte
- Institut National de la Recherche Scientifique-Armand-Frappier Santé Biotechnologie Research Centre, Laval, Quebec, H7V 1B7, Canada
| | - Steven R LaPlante
- Institut National de la Recherche Scientifique-Armand-Frappier Santé Biotechnologie Research Centre, Laval, Quebec, H7V 1B7, Canada
| | - Nicolas Gangneux
- Institut Pasteur, Université Paris Cité, Microbial Individuality and Infection Laboratory, 75015, Paris, France
| | - Monika Záhorszká
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15, Bratislava, Slovakia
| | - Jana Korduláková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 842 15, Bratislava, Slovakia
| | - Sophie Vichier-Guerre
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Epigenetic Chemical Biology Unit, 75015, Paris, France
| | - Frédéric Bonhomme
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Epigenetic Chemical Biology Unit, 75015, Paris, France
| | - Laura Pokorny
- Institut Pasteur, Université Paris Cité, Microbial Individuality and Infection Laboratory, 75015, Paris, France
| | - Marvin Albert
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, 75015, Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université Paris Cité, Image Analysis Hub, 75015, Paris, France
| | - Giulia Manina
- Institut Pasteur, Université Paris Cité, Microbial Individuality and Infection Laboratory, 75015, Paris, France.
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LaPlante SR, Coric P, Bouaziz S, França TCC. NMR spectroscopy can help accelerate antiviral drug discovery programs. Microbes Infect 2024:105297. [PMID: 38199267 DOI: 10.1016/j.micinf.2024.105297] [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: 07/04/2023] [Revised: 11/21/2023] [Accepted: 01/05/2024] [Indexed: 01/12/2024]
Abstract
Small molecule drugs have an important role to play in combating viral infections, and biophysics support has been central for contributing to the discovery and design of direct acting antivirals. Perhaps one of the most successful biophysical tools for this purpose is NMR spectroscopy when utilized strategically and pragmatically within team workflows and timelines. This report describes some clear examples of how NMR applications contributed to the design of antivirals when combined with medicinal chemistry, biochemistry, X-ray crystallography and computational chemistry. Overall, these multidisciplinary approaches allowed teams to reveal and expose compound physical properties from which design ideas were spawned and tested to achieve the desired successes. Examples are discussed for the discovery of antivirals that target HCV, HIV and SARS-CoV-2.
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Affiliation(s)
- Steven R LaPlante
- Pasteur Network, INRS-Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada; NMX Research and Solutions, Inc., 500 Boulevard Cartier Ouest, Laval, Québec, H7V 5B7, Canada; Université Paris Cité, CNRS, CiTCoM, F-75006, Paris, France.
| | - Pascale Coric
- Université Paris Cité, CNRS, CiTCoM, F-75006, Paris, France
| | - Serge Bouaziz
- Université Paris Cité, CNRS, CiTCoM, F-75006, Paris, France
| | - Tanos C C França
- Pasteur Network, INRS-Centre Armand-Frappier Santé Biotechnologie, 531 Boulevard des Prairies, Laval, Québec, H7V 1B7, Canada
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Sow AA, Pahmeier F, Ayotte Y, Anton A, Mazeaud C, Charpentier T, Angelo L, Woo S, Cerikan B, Falzarano D, Abrahamyan L, Lamarre A, Labonté P, Cortese M, Bartenschlager R, LaPlante SR, Chatel-Chaix L. N-Phenylpyridine-3-Carboxamide and 6-Acetyl-1H-Indazole Inhibit the RNA Replication Step of the Dengue Virus Life Cycle. Antimicrob Agents Chemother 2023; 67:e0133122. [PMID: 36700643 PMCID: PMC9933715 DOI: 10.1128/aac.01331-22] [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] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/26/2022] [Indexed: 01/27/2023] Open
Abstract
Dengue virus (DENV) is a Flavivirus that causes the most prevalent arthropod-borne viral disease. Clinical manifestation of DENV infection ranges from asymptomatic to severe symptoms that can lead to death. Unfortunately, no antiviral treatments against DENV are currently available. In order to identify novel DENV inhibitors, we screened a library of 1,604 chemically diversified fragment-based compounds using DENV reporter viruses that allowed quantification of viral replication in infected cells. Following a validation screening, the two best inhibitor candidates were N-phenylpyridine-3-carboxamide (NPP3C) and 6-acetyl-1H-indazole (6A1HI). The half maximal effective concentration of NPP3C and 6A1H1 against DENV were 7.1 μM and 6.5 μM, respectively. 6A1H1 decreased infectious DENV particle production up to 1,000-fold without any cytotoxicity at the used concentrations. While 6A1HI was DENV-specific, NPP3C also inhibited the replication of other flaviviruses such as West Nile virus and Zika virus. Structure-activity relationship (SAR) studies with 151 analogues revealed key structural elements of NPP3C and 6A1HI required for their antiviral activity. Time-of-drug-addition experiments identified a postentry step as a target of these compounds. Consistently, using a DENV subgenomic replicon, we demonstrated that these compounds specifically impede the viral RNA replication step and exhibit a high genetic barrier-to-resistance. In contrast, viral RNA translation and the de novo biogenesis of DENV replication organelles were not affected. Overall, our data unveil NPP3C and 6A1H1 as novel DENV inhibitors. The information revealed by our SAR studies will help chemically optimize NPP3C and 6A1H1 in order to improve their anti-flaviviral potency and to challenge them in in vivo models.
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Affiliation(s)
- Aïssatou Aïcha Sow
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Felix Pahmeier
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, Heidelberg, Germany
| | - Yann Ayotte
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Anaïs Anton
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Clément Mazeaud
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Tania Charpentier
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Léna Angelo
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Simon Woo
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Berati Cerikan
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, Heidelberg, Germany
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Levon Abrahamyan
- Faculty of Veterinary Medicine, University of Montreal, Saint-Hyacinthe, Quebec, Canada
| | - Alain Lamarre
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Patrick Labonté
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Mirko Cortese
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, Heidelberg, Germany
- Telethon Institute of Genetics and Medicine, Naples, Italy
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research (CIID), Heidelberg University, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, Heidelberg, Germany
| | - Steven R. LaPlante
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
| | - Laurent Chatel-Chaix
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, Laval, Quebec, Canada
- Center of Excellence in Orphan Diseases Research-Foundation Courtois, Quebec, Canada
- Réseau Intersectoriel de Recherche en Santé de l’Université du Québec, Quebec, Canada
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Fragment-Based Lead Discovery Strategies in Antimicrobial Drug Discovery. Antibiotics (Basel) 2023; 12:antibiotics12020315. [PMID: 36830226 PMCID: PMC9951956 DOI: 10.3390/antibiotics12020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Fragment-based lead discovery (FBLD) is a powerful application for developing ligands as modulators of disease targets. This approach strategy involves identification of interactions between low-molecular weight compounds (100-300 Da) and their putative targets, often with low affinity (KD ~0.1-1 mM) interactions. The focus of this screening methodology is to optimize and streamline identification of fragments with higher ligand efficiency (LE) than typical high-throughput screening. The focus of this review is on the last half decade of fragment-based drug discovery strategies that have been used for antimicrobial drug discovery.
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Togre NS, Vargas AM, Bhargavi G, Mallakuntla MK, Tiwari S. Fragment-Based Drug Discovery against Mycobacteria: The Success and Challenges. Int J Mol Sci 2022; 23:ijms231810669. [PMID: 36142582 PMCID: PMC9500838 DOI: 10.3390/ijms231810669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/29/2022] Open
Abstract
The emergence of drug-resistant mycobacteria, including Mycobacterium tuberculosis (Mtb) and non-tuberculous mycobacteria (NTM), poses an increasing global threat that urgently demands the development of new potent anti-mycobacterial drugs. One of the approaches toward the identification of new drugs is fragment-based drug discovery (FBDD), which is the most ingenious among other drug discovery models, such as structure-based drug design (SBDD) and high-throughput screening. Specialized techniques, such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and many others, are part of the drug discovery approach to combat the Mtb and NTM global menaces. Moreover, the primary drawbacks of traditional methods, such as the limited measurement of biomolecular toxicity and uncertain bioavailability evaluation, are successfully overcome by the FBDD approach. The current review focuses on the recognition of fragment-based drug discovery as a popular approach using virtual, computational, and biophysical methods to identify potent fragment molecules. FBDD focuses on designing optimal inhibitors against potential therapeutic targets of NTM and Mtb (PurC, ArgB, MmpL3, and TrmD). Additionally, we have elaborated on the challenges associated with the FBDD approach in the identification and development of novel compounds. Insights into the applications and overcoming the challenges of FBDD approaches will aid in the identification of potential therapeutic compounds to treat drug-sensitive and drug-resistant NTMs and Mtb infections.
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Phenotypic drug discovery: recent successes, lessons learned and new directions. Nat Rev Drug Discov 2022; 21:899-914. [DOI: 10.1038/s41573-022-00472-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2022] [Indexed: 12/29/2022]
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