1. Microbiology and Infectious Disease

Ribonucleotide reductase, a novel drug target for gonorrhea

  1. Jana Narasimhan  Is a corresponding author
  2. Suzanne Letinski
  3. Stephen P Jung
  4. Aleksey Gerasyuto
  5. Jiashi Wang
  6. Michael Arnold
  7. Guangming Chen
  8. Jean Hedrick
  9. Melissa Dumble
  10. Kanchana Ravichandran
  11. Talya Levitz
  12. Cui Chang
  13. Catherine L Drennan
  14. JoAnne Stubbe  Is a corresponding author
  15. Gary Karp
  16. Arthur Branstrom  Is a corresponding author
  1. PTC Therapeutics, Inc., United States
  2. Bristol Myers Squibb, United States
  3. Schrödinger, Inc., United States
  4. PMV Pharmaceuticals, United States
  5. Massachusetts Institute of Technology, United States
  6. Howard Hughes Medical Institute, Massachusetts Institute of Technology, United States
  7. PTC Therapeutics Inc, United States
https://doi.org/10.7554/eLife.67447
Share this article
Cite this article
  1. Jana Narasimhan
  2. Suzanne Letinski
  3. Stephen P Jung
  4. Aleksey Gerasyuto
  5. Jiashi Wang
  6. Michael Arnold
  7. Guangming Chen
  8. Jean Hedrick
  9. Melissa Dumble
  10. Kanchana Ravichandran
  11. Talya Levitz
  12. Cui Chang
  13. Catherine L Drennan
  14. JoAnne Stubbe
  15. Gary Karp
  16. Arthur Branstrom
(2022)
Ribonucleotide reductase, a novel drug target for gonorrhea
eLife 11:e67447.
https://doi.org/10.7554/eLife.67447
  2. Download BibTeX
  3. Download .RIS

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 a4b4 state in the presence of the b 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.

Data availability

All data generated or analyzed during this study are included in the manuscript and supplemental section.

Article and author information

Author details

  1. Jana Narasimhan

    Pharmacology and Biomarkers, PTC Therapeutics, Inc., South Plainfield, United States
    For correspondence
    jnarasimhan@ptcbio.com
    Competing interests
    Jana Narasimhan, was employed by PTC Therapeutics when the work was performed and received salary and compensation during their tenure..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5621-8592

  2. Suzanne Letinski

    Analytical Development and Attribute Sciences, Bristol Myers Squibb, New Brunswick, United States
    Competing interests
    Suzanne Letinski, was employed by PTC Therapeutics when the work was performed and received salary and compensation during their tenure..

  3. Stephen P Jung

    Pharmacology and Biomarkers, PTC Therapeutics, Inc., South Plainfield, United States
    Competing interests
    Stephen P Jung, was employed by PTC Therapeutics when the work was performed and received salary and compensation during their tenure..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9276-175X

  4. Aleksey Gerasyuto

    Medicinal Chemistry, Schrödinger, Inc., New York, United States
    Competing interests
    Aleksey Gerasyuto, was employed by PTC Therapeutics when the work was performed and received salary and compensation during their tenure..

  5. Jiashi Wang

    Medicinal Chemistry, Schrödinger, Inc., New York, United States
    Competing interests
    Jiashi Wang, was employed by PTC Therapeutics when the work was performed and received salary and compensation during their tenure..

  6. Michael Arnold

    Chemistry, PTC Therapeutics, Inc., South Plainfield, United States
    Competing interests
    Michael Arnold, Arnold,were employed by PTC Therapeutics when the work wasperformed and received salary and compensation during their tenure.

  7. Guangming Chen

    Chemistry, PTC Therapeutics, Inc., South Plainfield, United States
    Competing interests
    Guangming Chen, was employed by PTC Therapeutics when the work was performed and received salary and compensation during their tenure..

  8. Jean Hedrick

    Pharmacology and Biomarkers, PTC Therapeutics, Inc., South Plainfield, United States
    Competing interests
    Jean Hedrick, was employed by PTC Therapeutics when the work was performed and received salary and compensation during their tenure..

  9. Melissa Dumble

    Preclinical Development and Translational Science, PMV Pharmaceuticals, Cranbury, United States
    Competing interests
    Melissa Dumble, was employed by PTC Therapeutics when the work was performed and received salary and compensation during their tenure..

  10. Kanchana Ravichandran

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    No competing interests declared.

  11. Talya Levitz

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    No competing interests declared.

  12. Cui Chang

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    No competing interests declared.

  13. Catherine L Drennan

    Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5486-2755

  14. JoAnne Stubbe

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
    For correspondence
    stubbe@mit.edu
    Competing interests
    No competing interests declared.

  15. Gary Karp

    Chemistry, PTC Therapeutics, Inc., South Plainfield, United States
    Competing interests
    Gary Karp, was employed by PTC Therapeutics when the work was performed and received salary and compensation during their tenure..

  16. Arthur Branstrom

    Biology, PTC Therapeutics Inc, South Plainfield, United States
    For correspondence
    abranstrom@ptcbio.com
    Competing interests
    Arthur Branstrom, was employed by PTC Therapeutics when the work was performed and received salary and compensation during their tenure.

Funding

Wellcome Trust (097753)

  • Arthur Branstrom

National Institutes of Health (GM126982)

  • Catherine L Drennan

National Institutes of Health (GM007287)

  • Talya Levitz

National Science Foundation (2017246757)

  • Talya Levitz

National Institutes of Health (GM29595)

  • JoAnne Stubbe

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: Animal studies were done according to procedures reviewed and approved by the Rutgers Institutional Animal Care and Use Committee (IACUC). The IACUC protocol ID used was I12-075-12

Copyright

© 2022, Narasimhan et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 1,385
    views
  • 231
    downloads
  • 8
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Jana Narasimhan
  2. Suzanne Letinski
  3. Stephen P Jung
  4. Aleksey Gerasyuto
  5. Jiashi Wang
  6. Michael Arnold
  7. Guangming Chen
  8. Jean Hedrick
  9. Melissa Dumble
  10. Kanchana Ravichandran
  11. Talya Levitz
  12. Cui Chang
  13. Catherine L Drennan
  14. JoAnne Stubbe
  15. Gary Karp
  16. Arthur Branstrom
(2022)
Ribonucleotide reductase, a novel drug target for gonorrhea
eLife 11:e67447.
https://doi.org/10.7554/eLife.67447

Share this article

https://doi.org/10.7554/eLife.67447

Categories and tags

Further reading

    1. Microbiology and Infectious Disease

    Machine learning approaches identify immunologic signatures of total and intact HIV DNA during long-term antiretroviral therapy

    Lesia Semenova, Yingfan Wang ... Edward P Browne
    Research Article

    Understanding the interplay between the HIV reservoir and the host immune system may yield insights into HIV persistence during antiretroviral therapy (ART) and inform strategies for a cure. Here, we applied machine learning (ML) approaches to cross-sectional high-parameter HIV reservoir and immunology data in order to characterize host–reservoir associations and generate new hypotheses about HIV reservoir biology. High-dimensional immunophenotyping, quantification of HIV-specific T cell responses, and measurement of genetically intact and total HIV proviral DNA frequencies were performed on peripheral blood samples from 115 people with HIV (PWH) on long-term ART. Analysis demonstrated that both intact and total proviral DNA frequencies were positively correlated with T cell activation and exhaustion. Years of ART and select bifunctional HIV-specific CD4 T cell responses were negatively correlated with the percentage of intact proviruses. A leave-one-covariate-out inference approach identified specific HIV reservoir and clinical–demographic parameters, such as age and biological sex, that were particularly important in predicting immunophenotypes. Overall, immune parameters were more strongly associated with total HIV proviral frequencies than intact proviral frequencies. Uniquely, however, expression of the IL-7 receptor alpha chain (CD127) on CD4 T cells was more strongly correlated with the intact reservoir. Unsupervised dimension reduction analysis identified two main clusters of PWH with distinct immune and reservoir characteristics. Using reservoir correlates identified in these initial analyses, decision tree methods were employed to visualize relationships among multiple immune and clinical–demographic parameters and the HIV reservoir. Finally, using random splits of our data as training-test sets, ML algorithms predicted with approximately 70% accuracy whether a given participant had qualitatively high or low levels of total or intact HIV DNA . The techniques described here may be useful for assessing global patterns within the increasingly high-dimensional data used in HIV reservoir and other studies of complex biology.

    1. Microbiology and Infectious Disease

    Rifampicin tolerance and growth fitness among isoniazid-resistant clinical Mycobacterium tuberculosis isolates from a longitudinal study

    Srinivasan Vijay, Nguyen Le Hoai Bao ... Nguyen Thuy Thuong
    Research Article

    Antibiotic tolerance in Mycobacterium tuberculosis reduces bacterial killing, worsens treatment outcomes, and contributes to resistance. We studied rifampicin tolerance in isolates with or without isoniazid resistance (IR). Using a minimum duration of killing assay, we measured rifampicin survival in isoniazid-susceptible (IS, n=119) and resistant (IR, n=84) isolates, correlating tolerance with bacterial growth, rifampicin minimum inhibitory concentrations (MICs), and isoniazid-resistant mutations. Longitudinal IR isolates were analyzed for changes in rifampicin tolerance and genetic variant emergence. The median time for rifampicin to reduce the bacterial population by 90% (MDK90) increased from 1.23 days (IS) and 1.31 days (IR) to 2.55 days (IS) and 1.98 days (IR) over 15–60 days of incubation, indicating fast and slow-growing tolerant sub-populations. A 6 log10-fold survival fraction classified tolerance as low, medium, or high, showing that IR is linked to increased tolerance and faster growth (OR = 2.68 for low vs. medium, OR = 4.42 for low vs. high, p-trend = 0.0003). High tolerance in IR isolates was associated with rifampicin treatment in patients and genetic microvariants. These findings suggest that IR tuberculosis should be assessed for high rifampicin tolerance to optimize treatment and prevent the development of multi-drug-resistant tuberculosis.

    1. Evolutionary Biology
    2. Microbiology and Infectious Disease

    Recombinant origin and interspecies transmission of a HERV-K(HML-2)-related primate retrovirus with a novel RNA transport element

    Zachary H Williams, Alvaro Dafonte Imedio ... Welkin E Johnson
    Research Article Updated

    HERV-K(HML-2), the youngest clade of human endogenous retroviruses (HERVs), includes many intact or nearly intact proviruses, but no replication competent HML-2 proviruses have been identified in humans. HML-2-related proviruses are present in other primates, including rhesus macaques, but the extent and timing of HML-2 activity in macaques remains unclear. We have identified 145 HML-2-like proviruses in rhesus macaques, including a clade of young, rhesus-specific insertions. Age estimates, intact open reading frames, and insertional polymorphism of these insertions are consistent with recent or ongoing infectious activity in macaques. 106 of the proviruses form a clade characterized by an ~750 bp sequence between env and the 3′ long terminal repeat (LTR), derived from an ancient recombination with a HERV-K(HML-8)-related virus. This clade is found in Old World monkeys (OWM), but not great apes, suggesting it originated after the ape/OWM split. We identified similar proviruses in white-cheeked gibbons; the gibbon insertions cluster within the OWM recombinant clade, suggesting interspecies transmission from OWM to gibbons. The LTRs of the youngest proviruses have deletions in U3, which disrupt the Rec Response Element (RcRE), required for nuclear export of unspliced viral RNA. We show that the HML-8-derived region functions as a Rec-independent constitutive transport element (CTE), indicating the ancestral Rec–RcRE export system was replaced by a CTE mechanism.