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Nai F, Flores Espinoza MP, Invernizzi A, Vargas-Rosales PA, Bobileva O, Herok M, Caflisch A. Small-Molecule Inhibitors of the m7G-RNA Writer METTL1. ACS Bio Med Chem Au 2024; 4:100-110. [PMID: 38645929 PMCID: PMC11027120 DOI: 10.1021/acsbiomedchemau.3c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/07/2023] [Accepted: 11/15/2023] [Indexed: 04/23/2024]
Abstract
We discovered the first inhibitors of the m7G-RNA writer METTL1 by high-throughput docking and an enzymatic assay based on luminescence. Eleven compounds, which belong to three different chemotypes, show inhibitory activity in the range 40-300 μM. Two adenine derivatives identified by docking have very favorable ligand efficiency of 0.34 and 0.31 kcal/mol per non-hydrogen atom, respectively. Molecular dynamics simulations provide evidence that the inhibitors compete with the binding of the cosubstrate S-adenosyl methionine to METTL1. We also present a soakable crystal form that was used to determine the structure of the complex of METTL1 with sinefungin at a resolution of 1.85 Å.
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Affiliation(s)
- Francesco Nai
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | | | - Annalisa Invernizzi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | | | - Olga Bobileva
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV-1006, Latvia
| | - Marcin Herok
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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Huseby DL, Cao S, Zamaratski E, Sooriyaarachchi S, Ahmad S, Bergfors T, Krasnova L, Pelss J, Ikaunieks M, Loza E, Katkevics M, Bobileva O, Cirule H, Gukalova B, Grinberga S, Backlund M, Simoff I, Leber AT, Berruga-Fernández T, Antonov D, Konda VR, Lindström S, Olanders G, Brandt P, Baranczewski P, Vingsbo Lundberg C, Liepinsh E, Suna E, Jones TA, Mowbray SL, Hughes D, Karlén A. Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria. Proc Natl Acad Sci U S A 2024; 121:e2317274121. [PMID: 38579010 PMCID: PMC11009625 DOI: 10.1073/pnas.2317274121] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/11/2023] [Accepted: 03/12/2024] [Indexed: 04/07/2024] Open
Abstract
Here, we describe the identification of an antibiotic class acting via LpxH, a clinically unexploited target in lipopolysaccharide synthesis. The lipopolysaccharide synthesis pathway is essential in most Gram-negative bacteria and there is no analogous pathway in humans. Based on a series of phenotypic screens, we identified a hit targeting this pathway that had activity on efflux-defective strains of Escherichia coli. We recognized common structural elements between this hit and a previously published inhibitor, also with activity against efflux-deficient bacteria. With the help of X-ray structures, this information was used to design inhibitors with activity on efflux-proficient, wild-type strains. Optimization of properties such as solubility, metabolic stability and serum protein binding resulted in compounds having potent in vivo efficacy against bloodstream infections caused by the critical Gram-negative pathogens E. coli and Klebsiella pneumoniae. Other favorable properties of the series include a lack of pre-existing resistance in clinical isolates, and no loss of activity against strains expressing extended-spectrum-β-lactamase, metallo-β-lactamase, or carbapenemase-resistance genes. Further development of this class of antibiotics could make an important contribution to the ongoing struggle against antibiotic resistance.
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Affiliation(s)
- Douglas L. Huseby
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Sha Cao
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Edouard Zamaratski
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | | | - Shabbir Ahmad
- Department of Cell and Molecular Biology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Terese Bergfors
- Department of Cell and Molecular Biology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Laura Krasnova
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | - Juris Pelss
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | | | - Einars Loza
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | | | - Olga Bobileva
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | - Helena Cirule
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | - Baiba Gukalova
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | | | - Maria Backlund
- Department of Pharmacy, Uppsala Drug Optimization and Pharmaceutical Profiling, Uppsala University, UppsalaSE-75123, Sweden
| | - Ivailo Simoff
- Department of Pharmacy, Uppsala Drug Optimization and Pharmaceutical Profiling, Uppsala University, UppsalaSE-75123, Sweden
| | - Anna T. Leber
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Talía Berruga-Fernández
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Dmitry Antonov
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Vivekananda R. Konda
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Stefan Lindström
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Gustav Olanders
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Peter Brandt
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Pawel Baranczewski
- Department of Pharmacy, SciLifeLab Drug Discovery and Development Platform, Uppsala University, UppsalaSE-75123, Sweden
| | | | | | - Edgars Suna
- Latvian Institute of Organic Synthesis, RigaLV-1006, Latvia
| | - T. Alwyn Jones
- Department of Cell and Molecular Biology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Sherry L. Mowbray
- Department of Cell and Molecular Biology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, BMC, Uppsala University, UppsalaSE-75123, Sweden
| | - Anders Karlén
- Department of Medicinal Chemistry, BMC, Uppsala University, UppsalaSE-75123, Sweden
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Bobileva O, Bobrovs R, Sirma EE, Kanepe I, Bula AL, Patetko L, Ramata-Stunda A, Grinberga S, Jirgensons A, Jaudzems K. 3-(Adenosylthio)benzoic Acid Derivatives as SARS-CoV-2 Nsp14 Methyltransferase Inhibitors. Molecules 2023; 28:molecules28020768. [PMID: 36677825 PMCID: PMC9862586 DOI: 10.3390/molecules28020768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 01/06/2023] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
SARS-CoV-2 nsp14 guanine-N7-methyltransferase plays an important role in the viral RNA translation process by catalyzing the transfer of a methyl group from S-adenosyl-methionine (SAM) to viral mRNA cap. We report a structure-guided design and synthesis of 3-(adenosylthio)benzoic acid derivatives as nsp14 methyltransferase inhibitors resulting in compound 5p with subnanomolar inhibitory activity and improved cell membrane permeability in comparison with the parent inhibitor. Compound 5p acts as a bisubstrate inhibitor targeting both SAM and mRNA-binding pockets of nsp14. While the selectivity of 3-(adenosylthio)benzoic acid derivatives against human glycine N-methyltransferase was not improved, the discovery of phenyl-substituted analogs 5p,t may contribute to further development of SARS-CoV-2 nsp14 bisubstrate inhibitors.
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Affiliation(s)
- Olga Bobileva
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
- Correspondence:
| | - Raitis Bobrovs
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | | | - Iveta Kanepe
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | - Anna L. Bula
- Latvian Institute of Organic Synthesis, LV-1006 Riga, Latvia
| | - Liene Patetko
- Faculty of Biology, University of Latvia, LV-1004 Riga, Latvia
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