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Zampaloni C, Mattei P, Bleicher K, Winther L, Thäte C, Bucher C, Adam JM, Alanine A, Amrein KE, Baidin V, Bieniossek C, Bissantz C, Boess F, Cantrill C, Clairfeuille T, Dey F, Di Giorgio P, du Castel P, Dylus D, Dzygiel P, Felici A, García-Alcalde F, Haldimann A, Leipner M, Leyn S, Louvel S, Misson P, Osterman A, Pahil K, Rigo S, Schäublin A, Scharf S, Schmitz P, Stoll T, Trauner A, Zoffmann S, Kahne D, Young JAT, Lobritz MA, Bradley KA. A novel antibiotic class targeting the lipopolysaccharide transporter. Nature 2024; 625:566-571. [PMID: 38172634 PMCID: PMC10794144 DOI: 10.1038/s41586-023-06873-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 12/20/2022] [Accepted: 11/16/2023] [Indexed: 01/05/2024]
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) has emerged as a major global pathogen with limited treatment options1. No new antibiotic chemical class with activity against A. baumannii has reached patients in over 50 years1. Here we report the identification and optimization of tethered macrocyclic peptide (MCP) antibiotics with potent antibacterial activity against CRAB. The mechanism of action of this molecule class involves blocking the transport of bacterial lipopolysaccharide from the inner membrane to its destination on the outer membrane, through inhibition of the LptB2FGC complex. A clinical candidate derived from the MCP class, zosurabalpin (RG6006), effectively treats highly drug-resistant contemporary isolates of CRAB both in vitro and in mouse models of infection, overcoming existing antibiotic resistance mechanisms. This chemical class represents a promising treatment paradigm for patients with invasive infections due to CRAB, for whom current treatment options are inadequate, and additionally identifies LptB2FGC as a tractable target for antimicrobial drug development.
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Affiliation(s)
- Claudia Zampaloni
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Patrizio Mattei
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Konrad Bleicher
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
- SixPeaks Bio, Basel, Switzerland
| | - Lotte Winther
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Claudia Thäte
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
- Preclinical Sciences and Translational Safety, Janssen Pharmaceutica, Beerse, Belgium
| | - Christian Bucher
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Jean-Michel Adam
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
- AutoChem R&D, Mettler-Toledo International, Greifensee, Switzerland
| | - Alexander Alanine
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
- Independent consultant, Cambridge, Great Britain
| | - Kurt E Amrein
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Vadim Baidin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Christoph Bieniossek
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Caterina Bissantz
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Franziska Boess
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Carina Cantrill
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Thomas Clairfeuille
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Fabian Dey
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Patrick Di Giorgio
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Pauline du Castel
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - David Dylus
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Pawel Dzygiel
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Antonio Felici
- Discovery Microbiology, Aptuit (Verona) Srl, an Evotec Company, Verona, Italy
| | - Fernando García-Alcalde
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Andreas Haldimann
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Matthew Leipner
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Semen Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Séverine Louvel
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Pauline Misson
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Andrei Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Karanbir Pahil
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Sébastien Rigo
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Adrian Schäublin
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
- SixPeaks Bio, Basel, Switzerland
| | - Sebastian Scharf
- Roche Pharma Research and Early Development, Informatics, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Petra Schmitz
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Theodor Stoll
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Andrej Trauner
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Sannah Zoffmann
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
- Therapeutics Discovery, Janssen Pharmaceutica, Beerse, Belgium
| | - Daniel Kahne
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - John A T Young
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland
| | - Michael A Lobritz
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland.
| | - Kenneth A Bradley
- Roche Pharma Research and Early Development, Immunology, Infectious Disease and Ophthalmology, Roche Innovation Center Basel, F. Hoffmann-La Roche, Basel, Switzerland.
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Mari SA, Pluhackova K, Pipercevic J, Leipner M, Hiller S, Engel A, Müller DJ. Gasdermin-A3 pore formation propagates along variable pathways. Nat Commun 2022; 13:2609. [PMID: 35545613 PMCID: PMC9095878 DOI: 10.1038/s41467-022-30232-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 04/22/2022] [Indexed: 12/31/2022] Open
Abstract
Gasdermins are main effectors of pyroptosis, an inflammatory form of cell death. Released by proteolysis, the N-terminal gasdermin domain assembles large oligomers to punch lytic pores into the cell membrane. While the endpoint of this reaction, the fully formed pore, has been well characterized, the assembly and pore-forming mechanisms remain largely unknown. To resolve these mechanisms, we characterize mouse gasdermin-A3 by high-resolution time-lapse atomic force microscopy. We find that gasdermin-A3 oligomers assemble on the membrane surface where they remain attached and mobile. Once inserted into the membrane gasdermin-A3 grows variable oligomeric stoichiometries and shapes, each able to open transmembrane pores. Molecular dynamics simulations resolve how the membrane-inserted amphiphilic β-hairpins and the structurally adapting hydrophilic head domains stabilize variable oligomeric conformations and open the pore. The results show that without a vertical collapse gasdermin pore formation propagates along a set of multiple parallel but connected reaction pathways to ensure a robust cellular response.
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Affiliation(s)
- Stefania A Mari
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
| | - Kristyna Pluhackova
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland.
| | | | - Matthew Leipner
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
| | | | - Andreas Engel
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zurich, 4058, Basel, Switzerland.
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