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Haupenthal J, Rafehi M, Kany AM, Lespine A, Stefan K, Hirsch AKH, Stefan SM. Target repurposing unravels avermectins and derivatives as novel antibiotics inhibiting energy-coupling factor transporters (ECFTs). Arch Pharm (Weinheim) 2024; 357:e2400267. [PMID: 38896404 DOI: 10.1002/ardp.202400267] [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: 04/10/2024] [Revised: 05/23/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024]
Abstract
Energy-coupling factor transporters (ECFTs) are membrane-bound ATP-binding cassette (ABC) transporters in prokaryotes that are found in pathogens against which novel antibiotics are urgently needed. To date, just 54 inhibitors of three molecular-structural classes with mostly weak inhibitory activity are known. Target repurposing is a strategy that transfers knowledge gained from a well-studied protein family to under-studied targets of phylogenetic relation. Forty-eight human ABC transporters are known that may harbor structural motifs similar to ECFTs to which particularly multitarget compounds may bind. We assessed 31 multitarget compounds which together target the entire druggable human ABC transporter proteome against ECFTs, of which nine showed inhibitory activity (hit rate 29.0%) and four demonstrated moderate to strong inhibition of an ECFT (IC50 values between 4.28 and 50.2 µM) as well as antibacterial activity against ECFT-expressing Streptococcus pneumoniae. Here, ivermectin was the most potent candidate (MIC95: 22.8 µM), and analysis of five ivermectin derivatives revealed moxidectin as one of the most potent ECFT-targeting antibacterial agents (IC50: 2.23 µM; MIC95: 2.91 µM). Distinct molecular-structural features of avermectins and derivatives as well as the differential biological response of the hit compounds in general provided first indications with respect to the structure-activity relationships and mode of action, respectively.
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Affiliation(s)
- Jörg Haupenthal
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University, Saarbrücken, Germany
| | - Muhammad Rafehi
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Göttingen, Germany
- Department of Medical Education Augsburg, Augsburg University Medicine, Augsburg, Germany
| | - Andreas M Kany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University, Saarbrücken, Germany
| | - Anne Lespine
- INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | - Katja Stefan
- Lübeck Institute of Experimental Dermatology, Medicinal Chemistry and Systems Polypharmacology, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Sven Marcel Stefan
- Lübeck Institute of Experimental Dermatology, Medicinal Chemistry and Systems Polypharmacology, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
- Department of Biopharmacy, Medical University of Lublin, Lublin, Poland
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2
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Rudzite M, O’Toole GA. An energy coupling factor transporter of Streptococcus sanguinis impacts antibiotic susceptibility as well as metal and membrane homeostasis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603315. [PMID: 39026867 PMCID: PMC11257530 DOI: 10.1101/2024.07.12.603315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Streptococcus sanguinis is a prevalent member of human microbiome capable of acting as a causative agent of oral and respiratory infections. S. sanguinis competitive success within the infection niche is dependent on acquisition of metal ions and vitamins. Among the systems that bacteria use for micronutrient uptake is the energy coupling factor (ECF) transporter system EcfAAT. Here we describe physiological changes arising from EcfAAT transporter disruption. We found that EcfAAT contributes to S. sanguinis antibiotic sensitivity as well as metal and membrane homeostasis. Specifically, our work found that disruption of EcfAAT results in increased polymyxin susceptibility. We performed assessment of cell-associated metal content and found depletion of iron, magnesium, and manganese. Furthermore, membrane composition analysis revealed significant enrichment in unsaturated fatty acid species resulting in increased membrane fluidity. Our results demonstrate how disruption of a single EcfAAT transporter can have broad consequences on bacterial cell homeostasis. ECF transporters are of interest within the context of infection biology in bacterial species other than streptococci, hence work described here will further the understanding of how micronutrient uptake systems contribute to bacterial pathogenesis.
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Affiliation(s)
- Marta Rudzite
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - G. A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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3
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Exapicheidou IA, Shams A, Ibrahim H, Tsarenko A, Backenköhler M, Hamed MM, Diamanti E, Volkamer A, Slotboom DJ, Hirsch AKH. Hit optimization by dynamic combinatorial chemistry on Streptococcus pneumoniae energy-coupling factor transporter ECF-PanT. Chem Commun (Camb) 2024; 60:870-873. [PMID: 38164786 DOI: 10.1039/d3cc04738e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Herein, we present the first application of target-directed dynamic combinatorial chemistry (tdDCC) to the whole complex of the highly dynamic transmembrane, energy-coupling factor (ECF) transporter ECF-PanT in Streptococcus pneumoniae. In addition, we successfully employed the tdDCC technique as a hit-identification and -optimization strategy that led to the identification of optimized ECF inhibitors with improved activity. We characterized the best compounds regarding cytotoxicity and performed computational modeling studies on the crystal structure of ECF-PanT to rationalize their binding mode. Notably, docking studies showed that the acylhydrazone linker is able to maintain the crucial interactions.
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Affiliation(s)
- Ioulia Antonia Exapicheidou
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
- Saarland University, Department of Pharmacy, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Atanaz Shams
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
- Saarland University, Department of Pharmacy, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Hamza Ibrahim
- Data Driven Drug Design Group, Center for Bioinformatics, Saarland Informatics Campus E2.1, Saarland University, Saarbrücken 66123, Germany
| | - Aleksei Tsarenko
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Michael Backenköhler
- Data Driven Drug Design Group, Center for Bioinformatics, Saarland Informatics Campus E2.1, Saarland University, Saarbrücken 66123, Germany
| | - Mostafa M Hamed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
| | - Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
| | - Andrea Volkamer
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
- Data Driven Drug Design Group, Center for Bioinformatics, Saarland Informatics Campus E2.1, Saarland University, Saarbrücken 66123, Germany
| | - Dirk J Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
- Saarland University, Department of Pharmacy, Campus Building E8.1, 66123, Saarbrücken, Germany
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Diamanti E, Souza PCT, Setyawati I, Bousis S, Monjas L, Swier LJYM, Shams A, Tsarenko A, Stanek WK, Jäger M, Marrink SJ, Slotboom DJ, Hirsch AKH. Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Commun Biol 2023; 6:1182. [PMID: 37985798 PMCID: PMC10662466 DOI: 10.1038/s42003-023-05555-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/08/2023] [Indexed: 11/22/2023] Open
Abstract
The energy-coupling factor (ECF) transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. The central role of vitamin transport in the metabolism of bacteria and absence from humans make the ECF transporters an attractive target for inhibition with selective chemical probes. Here, we report on the identification of a promising class of inhibitors of the ECF transporters. We used coarse-grained molecular dynamics simulations on Lactobacillus delbrueckii ECF-FolT2 and ECF-PanT to profile the binding mode and mechanism of inhibition of this novel chemotype. The results corroborate the postulated mechanism of transport and pave the way for further drug-discovery efforts.
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Affiliation(s)
- Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon, France
- Laboratoire de Biologie et Modélisation de la Cellule (UMR 5239, Inserm, U1293) and Centre Blaise Pascal, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1 and CNRS, 46 Allée d'Italie, 69007, Lyon, France
| | - Inda Setyawati
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
- Department of Biochemistry, Bogor Agricultural University, Dramaga, 16680, Bogor, Indonesia
| | - Spyridon Bousis
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747, AG Groningen, the Netherlands
| | - Leticia Monjas
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Lotteke J Y M Swier
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Atanaz Shams
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany
| | - Aleksei Tsarenko
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Weronika K Stanek
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Manuel Jäger
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747, AG Groningen, the Netherlands
| | - Siewert J Marrink
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Dirk J Slotboom
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany.
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747, AG Groningen, the Netherlands.
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5
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O’Boyle NM, Helesbeux JJ, Meegan MJ, Sasse A, O’Shaughnessy E, Qaisar A, Clancy A, McCarthy F, Marchand P. 30th Annual GP2A Medicinal Chemistry Conference. Pharmaceuticals (Basel) 2023; 16:ph16030432. [PMID: 36986531 PMCID: PMC10056312 DOI: 10.3390/ph16030432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/16/2023] [Indexed: 03/14/2023] Open
Abstract
The Group for the Promotion of Pharmaceutical Chemistry in Academia (GP2A) held their 30th annual conference in August 2022 in Trinity College Dublin, Ireland. There were 9 keynote presentations, 10 early career researcher presentations and 41 poster presentations.
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Affiliation(s)
- Niamh M. O’Boyle
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
- Correspondence: ; Tel.: +353-1896-2524
| | | | - Mary J. Meegan
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Astrid Sasse
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Elizabeth O’Shaughnessy
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Alina Qaisar
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Aoife Clancy
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute and Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Florence McCarthy
- School of Chemistry and ABCRF, University College Cork, T12 K8AF Cork, Ireland
| | - Pascal Marchand
- Cibles et Médicaments des Infections et de l’Immunité, IICiMed, Nantes Université, UR 1155, F-44000 Nantes, France
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