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Theuretzbacher U, Blasco B, Duffey M, Piddock LJV. Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections. Nat Rev Drug Discov 2023; 22:957-975. [PMID: 37833553 DOI: 10.1038/s41573-023-00791-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 10/15/2023]
Abstract
Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.
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Affiliation(s)
| | - Benjamin Blasco
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Maëlle Duffey
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland.
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2
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Wilkinson AJ, Ooi N, Finlayson J, Lee VE, Lyth D, Maskew KS, Newman R, Orr D, Ansell K, Birchall K, Canning P, Coombs P, Fusani L, McIver E, Pisco J, Ireland PM, Jenkins C, Norville IH, Southern SJ, Cowan R, Hall G, Kettleborough C, Savage VJ, Cooper IR. Evaluating the druggability of TrmD, a potential antibacterial target, through design and microbiological profiling of a series of potent TrmD inhibitors. Bioorg Med Chem Lett 2023; 90:129331. [PMID: 37187252 DOI: 10.1016/j.bmcl.2023.129331] [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: 04/03/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/17/2023]
Abstract
The post-transcriptional modifier tRNA-(N1G37) methyltransferase (TrmD) has been proposed to be essential for growth in many Gram-negative and Gram-positive pathogens, however previously reported inhibitors show only weak antibacterial activity. In this work, optimisation of fragment hits resulted in compounds with low nanomolar TrmD inhibition incorporating features designed to enhance bacterial permeability and covering a range of physicochemical space. The resulting lack of significant antibacterial activity suggests that whilst TrmD is highly ligandable, its essentiality and druggability are called into question.
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Affiliation(s)
- Andrew J Wilkinson
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK.
| | - Nicola Ooi
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Jonathan Finlayson
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Victoria E Lee
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - David Lyth
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Kathryn S Maskew
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Rebecca Newman
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - David Orr
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Keith Ansell
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Kristian Birchall
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Peter Canning
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Peter Coombs
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Lucia Fusani
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Ed McIver
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - João Pisco
- LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK
| | - Philip M Ireland
- CBR division, Dstl Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK
| | | | | | | | - Richard Cowan
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 7RH, UK
| | - Gareth Hall
- Leicester Institute of Structural and Chemical Biology and Department of Molecular and Cell Biology, Henry Wellcome Building, University of Leicester, Leicester, LE1 7RH, UK
| | | | - Victoria J Savage
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
| | - Ian R Cooper
- Infex Therapeutics Ltd, Mereside, Alderley Park, Macclesfield, SK10 4TG, UK
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3
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Bührmann M, Kallepu S, Warmuth JD, Wiese JN, Ehrt C, Vatheuer H, Hiller W, Seitz C, Levy L, Czodrowski P, Sievers S, Müller MP, Rauh D. Fragtory: Pharmacophore-Focused Design, Synthesis, and Evaluation of an sp 3-Enriched Fragment Library. J Med Chem 2023; 66:6297-6314. [PMID: 37130057 DOI: 10.1021/acs.jmedchem.3c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Fragment-based drug discovery has played an important role in medicinal chemistry and pharmaceutical research. Despite numerous demonstrated successes, the limited diversity and overrepresentation of planar, sp2-rich structures in commercial libraries often hamper the full potential of this approach. Hence, the thorough design of screening libraries inevitably determines the probability for meaningful hits and subsequent structural elaboration. Against this background, we present the generation of an exclusive fragment library based on iterative entry nomination by a specifically designed computational workflow: "Fragtory". Following a pharmacophore diversity-driven approach, we used Fragtory in an interdisciplinary academic setting to guide both tailored synthesis efforts and the implementation of in-house compounds to build a curated 288-member library of sp3-enriched fragments. Subsequent NMR screens against a model protein and hit validation by protein crystallography led to the identification of structurally novel ligands that were further characterized by isothermal titration calorimetry, demonstrating the applicability of our experimental approach.
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Affiliation(s)
- Mike Bührmann
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW), Dortmund 44227, Germany
| | - Shivakrishna Kallepu
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
| | - Jonas D Warmuth
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
| | - Jan N Wiese
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
| | - Christiane Ehrt
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
| | - Helge Vatheuer
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
| | - Wolf Hiller
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
| | - Carina Seitz
- Max Planck Institute of Molecular Physiology, Compound Management and Screening Center (COMAS), Otto-Hahn-Strasse 11/15, Dortmund 44227, Germany
| | - Laura Levy
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW), Dortmund 44227, Germany
- Taros Chemicals GmbH & Co. KG, Emil-Figge-Strasse 76a, Dortmund 44227, Germany
| | - Paul Czodrowski
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
| | - Sonja Sievers
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW), Dortmund 44227, Germany
- Max Planck Institute of Molecular Physiology, Compound Management and Screening Center (COMAS), Otto-Hahn-Strasse 11/15, Dortmund 44227, Germany
| | - Matthias P Müller
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
| | - Daniel Rauh
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, Dortmund 44227, Germany
- Drug Discovery Hub Dortmund (DDHD) am Zentrum für integrierte Wirkstoffforschung (ZIW), Dortmund 44227, Germany
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4
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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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Gupta P, Thomas SE, Zaidan SA, Pasillas MA, Cory-Wright J, Sebastián-Pérez V, Burgess A, Cattermole E, Meghir C, Abell C, Coyne AG, Jacobs WR, Blundell TL, Tiwari S, Mendes V. A fragment-based approach to assess the ligandability of ArgB, ArgC, ArgD and ArgF in the L-arginine biosynthetic pathway of Mycobacterium tuberculosis. Comput Struct Biotechnol J 2021; 19:3491-3506. [PMID: 34194673 PMCID: PMC8220418 DOI: 10.1016/j.csbj.2021.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 11/23/2022] Open
Abstract
The L-arginine biosynthesis pathway consists of eight enzymes that catalyse the conversion of L-glutamate to L-arginine. Arginine auxotrophs (argB/argF deletion mutants) of Mycobacterium tuberculosis are rapidly sterilised in mice, while inhibition of ArgJ with Pranlukast was found to clear chronic M. tuberculosis infection in a mouse model. Enzymes in the arginine biosynthetic pathway have therefore emerged as promising targets for anti-tuberculosis drug discovery. In this work, the ligandability of four enzymes of the pathway ArgB, ArgC, ArgD and ArgF is assessed using a fragment-based approach. We identify several hits against these enzymes validated with biochemical and biophysical assays, as well as X-ray crystallographic data, which in the case of ArgB were further confirmed to have on-target activity against M. tuberculosis. These results demonstrate the potential for more enzymes in this pathway to be targeted with dedicated drug discovery programmes.
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Affiliation(s)
- Pooja Gupta
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Sherine E. Thomas
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Shaymaa A. Zaidan
- Department of Biological Sciences & Border Biomedical Research Centre, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Maria A. Pasillas
- Department of Biological Sciences & Border Biomedical Research Centre, University of Texas at El Paso, El Paso, TX 79968, USA
| | - James Cory-Wright
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Víctor Sebastián-Pérez
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ailidh Burgess
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Emma Cattermole
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Clio Meghir
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Anthony G. Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Sangeeta Tiwari
- Department of Biological Sciences & Border Biomedical Research Centre, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Vítor Mendes
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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Singh N, Villoutreix BO. Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises. Comput Struct Biotechnol J 2021; 19:2537-2548. [PMID: 33936562 PMCID: PMC8074526 DOI: 10.1016/j.csbj.2021.04.059] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 12/11/2022] Open
Abstract
There is an urgent need to identify new therapies that prevent SARS-CoV-2 infection and improve the outcome of COVID-19 patients. This pandemic has thus spurred intensive research in most scientific areas and in a short period of time, several vaccines have been developed. But, while the race to find vaccines for COVID-19 has dominated the headlines, other types of therapeutic agents are being developed. In this mini-review, we report several databases and online tools that could assist the discovery of anti-SARS-CoV-2 small chemical compounds and peptides. We then give examples of studies that combined in silico and in vitro screening, either for drug repositioning purposes or to search for novel bioactive compounds. Finally, we question the overall lack of discussion and plan observed in academic research in many countries during this crisis and suggest that there is room for improvement.
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Affiliation(s)
- Natesh Singh
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
| | - Bruno O. Villoutreix
- Université de Paris, Inserm UMR 1141 NeuroDiderot, Robert-Debré Hospital, 75019 Paris, France
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