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Narasimhan J, Letinski S, Jung SP, Gerasyuto A, Wang J, Arnold M, Chen G, Hedrick J, Dumble M, Ravichandran K, Levitz T, Cui C, Drennan CL, Stubbe J, Karp G, Branstrom A. Ribonucleotide reductase, a novel drug target for gonorrhea. eLife 2022; 11:e67447. [PMID: 35137690 PMCID: PMC8865847 DOI: 10.7554/elife.67447] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Antibiotic-resistant Neisseria gonorrhoeae (Ng) are an emerging public health threat due to increasing numbers of multidrug resistant (MDR) organisms. We identified two novel orally active inhibitors, PTC-847 and PTC-672, that exhibit a narrow spectrum of activity against Ng including MDR isolates. By selecting organisms resistant to the novel inhibitors and sequencing their genomes, we identified a new therapeutic target, the class Ia ribonucleotide reductase (RNR). Resistance mutations in Ng map to the N-terminal cone domain of the α subunit, which we show here is involved in forming an inhibited α4β4 state in the presence of the β subunit and allosteric effector dATP. Enzyme assays confirm that PTC-847 and PTC-672 inhibit Ng RNR and reveal that allosteric effector dATP potentiates the inhibitory effect. Oral administration of PTC-672 reduces Ng infection in a mouse model and may have therapeutic potential for treatment of Ng that is resistant to current drugs.
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Affiliation(s)
| | | | | | | | - Jiashi Wang
- PTC Therapeutics, IncSouth PlainfieldUnited States
| | | | | | - Jean Hedrick
- PTC Therapeutics, IncSouth PlainfieldUnited States
| | | | - Kanchana Ravichandran
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Talya Levitz
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Chang Cui
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Gary Karp
- PTC Therapeutics, IncSouth PlainfieldUnited States
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Thyer R, d'Oelsnitz S, Blevins MS, Klein DR, Brodbelt JS, Ellington AD. Directed Evolution of an Improved Aminoacyl‐tRNA Synthetase for Incorporation of L‐3,4‐Dihydroxyphenylalanine (L‐DOPA). Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100579] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ross Thyer
- Department of Molecular Biosciences The University of Texas at Austin Austin TX USA
- Department of Chemical and Biomolecular Engineering Rice University Houston TX USA
| | - Simon d'Oelsnitz
- Department of Molecular Biosciences The University of Texas at Austin Austin TX USA
| | - Molly S. Blevins
- Department of Chemistry The University of Texas at Austin Austin TX USA
| | - Dustin R. Klein
- Department of Chemistry The University of Texas at Austin Austin TX USA
| | | | - Andrew D. Ellington
- Department of Molecular Biosciences The University of Texas at Austin Austin TX USA
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3
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Thyer R, d'Oelsnitz S, Blevins MS, Klein DR, Brodbelt JS, Ellington AD. Directed Evolution of an Improved Aminoacyl-tRNA Synthetase for Incorporation of L-3,4-Dihydroxyphenylalanine (L-DOPA). Angew Chem Int Ed Engl 2021; 60:14811-14816. [PMID: 33871147 DOI: 10.1002/anie.202100579] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/24/2021] [Indexed: 11/07/2022]
Abstract
The catechol group of 3,4-dihydroxyphenylalanine (L-DOPA) derived from L-tyrosine oxidation is a key post-translational modification (PTM) in many protein biomaterials and has potential as a bioorthogonal handle for precision protein conjugation applications such as antibody-drug conjugates. Despite this potential, indiscriminate enzymatic modification of exposed tyrosine residues or complete replacement of tyrosine using auxotrophic hosts remains the preferred method of introducing the catechol moiety into proteins, which precludes many protein engineering applications. We have developed new orthogonal translation machinery to site-specifically incorporate L-DOPA into recombinant proteins and a new fluorescent biosensor to selectively monitor L-DOPA incorporation in vivo. We show simultaneous biosynthesis and incorporation of L-DOPA and apply this translation machinery to engineer a novel metalloprotein containing a DOPA-Fe chromophore.
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Affiliation(s)
- Ross Thyer
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Simon d'Oelsnitz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Molly S Blevins
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Dustin R Klein
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | | | - Andrew D Ellington
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
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4
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Greene BL, Kang G, Cui C, Bennati M, Nocera DG, Drennan CL, Stubbe J. Ribonucleotide Reductases: Structure, Chemistry, and Metabolism Suggest New Therapeutic Targets. Annu Rev Biochem 2020; 89:45-75. [PMID: 32569524 PMCID: PMC7316142 DOI: 10.1146/annurev-biochem-013118-111843] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the de novo conversion of nucleotides to deoxynucleotides in all organisms, controlling their relative ratios and abundance. In doing so, they play an important role in fidelity of DNA replication and repair. RNRs' central role in nucleic acid metabolism has resulted in five therapeutics that inhibit human RNRs. In this review, we discuss the structural, dynamic, and mechanistic aspects of RNR activity and regulation, primarily for the human and Escherichia coli class Ia enzymes. The unusual radical-based organic chemistry of nucleotide reduction, the inorganic chemistry of the essential metallo-cofactor biosynthesis/maintenance, the transport of a radical over a long distance, and the dynamics of subunit interactions all present distinct entry points toward RNR inhibition that are relevant for drug discovery. We describe the current mechanistic understanding of small molecules that target different elements of RNR function, including downstream pathways that lead to cell cytotoxicity. We conclude by summarizing novel and emergent RNR targeting motifs for cancer and antibiotic therapeutics.
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Affiliation(s)
- Brandon L Greene
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Gyunghoon Kang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Chang Cui
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
- Department of Chemistry, University of Göttingen, 37073 Göttingen, Germany
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Reichl E, Ertl M, Knör G. Multielectron Redox Catalysis with Efficient Tyrosinase Activity Based on a Visible-Light Controlled Artificial Photoenzyme. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eva Reichl
- Institute of Inorganic Chemistry; Johannes Kepler University Linz; Altenberger Strasse 69 4040 Linz Austria
| | - Martin Ertl
- Institute of Inorganic Chemistry; Johannes Kepler University Linz; Altenberger Strasse 69 4040 Linz Austria
- Linz School of Education; Altenberger Strasse 69 4040 Linz Austria
| | - Günther Knör
- Institute of Inorganic Chemistry; Johannes Kepler University Linz; Altenberger Strasse 69 4040 Linz Austria
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Berggren G, Sahlin M, Crona M, Tholander F, Sjöberg BM. Compounds with capacity to quench the tyrosyl radical in Pseudomonas aeruginosa ribonucleotide reductase. J Biol Inorg Chem 2019; 24:841-848. [PMID: 31218442 PMCID: PMC6754346 DOI: 10.1007/s00775-019-01679-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/12/2019] [Indexed: 11/02/2022]
Abstract
Ribonucleotide reductase (RNR) has been extensively probed as a target enzyme in the search for selective antibiotics. Here we report on the mechanism of inhibition of nine compounds, serving as representative examples of three different inhibitor classes previously identified by us to efficiently inhibit RNR. The interaction between the inhibitors and Pseudomonas aeruginosa RNR was elucidated using a combination of electron paramagnetic resonance spectroscopy and thermal shift analysis. All nine inhibitors were found to efficiently quench the tyrosyl radical present in RNR, required for catalysis. Three different mechanisms of radical quenching were identified, and shown to depend on reduction potential of the assay solution and quaternary structure of the protein complex. These results form a good foundation for further development of P. aeruginosa selective antibiotics. Moreover, this study underscores the complex nature of RNR inhibition and the need for detailed spectroscopic studies to unravel the mechanism of RNR inhibitors.
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Affiliation(s)
- Gustav Berggren
- Department of Chemistry, Ångström Laboratory, Uppsala University, Uppsala, Sweden.
| | - Margareta Sahlin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Mikael Crona
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Swedish Orphan Biovitrum AB, Stockholm, Sweden
| | - Fredrik Tholander
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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