scholarly journals Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification

2019 ◽  
Author(s):  
Sherine E. Thomas ◽  
Andrew J. Whitehouse ◽  
Karen Brown ◽  
Juan M. Belardinelli ◽  
Ramanuj Lahiri ◽  
...  
Keyword(s):  
Bacterial Infections ◽  
Protein Translation ◽  
Mycobacterium Abscessus ◽  
Trna Modification ◽  
Macrophage Infection ◽  
Reading Frame ◽  
New Class ◽  
Translational Frameshift ◽  
Fragment Library

AbstractTranslational frameshift errors are often deleterious to the synthesis of functional proteins as they lead to the production of truncated or inactive proteins. TrmD (tRNA-(N(1)G37) methyltransferase) is an essential tRNA modification enzyme in bacteria that prevents +1 errors in the reading frame during protein translation and has been identified as a therapeutic target for several bacterial infections. Here we validate TrmD as a target inMycobacterium abscessusand describe the application of a structure-guided fragment-based drug discovery approach for the design of a new class of inhibitors against this enzyme. A fragment library screening followed by structure-guided chemical elaboration of hits led to the development of compounds with potentin vitroTrmD inhibitory activity. Several of these compounds exhibit activity against planktonicM. abscessus and Mycobacterium tuberculosis.The compounds were further active in macrophage infection models againstMycobacterium lepraeandM. abscessussuggesting the potential for novel broad-spectrum mycobacterial drugs.

scholarly journals Fragment-based discovery of a new class of inhibitors targeting mycobacterial tRNA modification

2020 ◽  
Vol 48 (14) ◽  
pp. 8099-8112 ◽  
Author(s):  
Sherine E Thomas ◽  
Andrew J Whitehouse ◽  
Karen Brown ◽  
Sophie Burbaud ◽  
Juan M Belardinelli ◽  
...  
Keyword(s):  
Rapid Development ◽  
Protein Translation ◽  
Mycobacterium Abscessus ◽  
Attractive Potential ◽  
Trna Modification ◽  
Reading Frame ◽  
New Class ◽  
Translational Frameshift ◽  
New Antibiotics

Abstract Translational frameshift errors are often deleterious to the synthesis of functional proteins and could therefore be promoted therapeutically to kill bacteria. TrmD (tRNA-(N(1)G37) methyltransferase) is an essential tRNA modification enzyme in bacteria that prevents +1 errors in the reading frame during protein translation and represents an attractive potential target for the development of new antibiotics. Here, we describe the application of a structure-guided fragment-based drug discovery approach to the design of a new class of inhibitors against TrmD in Mycobacterium abscessus. Fragment library screening, followed by structure-guided chemical elaboration of hits, led to the rapid development of drug-like molecules with potent in vitro TrmD inhibitory activity. Several of these compounds exhibit activity against planktonic M. abscessus and M. tuberculosis as well as against intracellular M. abscessus and M. leprae, indicating their potential as the basis for a novel class of broad-spectrum mycobacterial drugs.

scholarly journals Evolutionary repair reveals an unexpected role of the tRNA modification m1G37 in aminoacylation

2021 ◽  
Author(s):  
Ben E Clifton ◽  
Muhammad Aiman Fariz ◽  
Gen-Ichiro Uechi ◽  
Paola Laurino
Keyword(s):  
Experimental Evolution ◽  
Protein Translation ◽  
Trna Modification ◽  
E Coli ◽  
Growth Defects ◽  
Translational Accuracy ◽  
Translational Frameshift ◽  
Mutant Strains ◽  
Trna Methyltransferase

The tRNA modification m1G37, which is introduced by the tRNA methyltransferase TrmD, is thought to be essential for growth in bacteria due to its role in suppressing translational frameshift errors at proline codons. However, because bacteria can tolerate high levels of mistranslation, it is unclear why loss of m1G37 is not tolerated. Here, we addressed this question by performing experimental evolution of trmD mutant strains of E. coli. Surprisingly, trmD mutant strains were viable even if the m1G37 modification was completely abolished, and showed rapid recovery of growth rate, mainly via tandem duplication or coding mutations in the proline-tRNA ligase gene proS. Growth assays and in vitro aminoacylation assays showed that G37-unmodified tRNAPro is aminoacylated less efficiently than m1G37-modified tRNAPro, and that growth of trmD mutant strains can be largely restored by single mutations in proS that restore aminoacylation of G37-unmodified tRNAPro. These results show that inefficient aminoacylation of tRNAPro is the main reason for growth defects observed in trmD mutant strains and that the ProRS enzyme may act as a gatekeeper of translational accuracy, preventing the use of error-prone unmodified tRNAPro in protein translation. Our work shows the utility of experimental evolution for uncovering the hidden functions of essential genes and has implications for the development of antibiotics targeting TrmD.

scholarly journals Salmonella persisters undermine host immune defenses during antibiotic treatment

Science ◽  
2018 ◽  
Vol 362 (6419) ◽  
pp. 1156-1160 ◽  
Author(s):  
Daphne A. C. Stapels ◽  
Peter W. S. Hill ◽  
Alexander J. Westermann ◽  
Robert A. Fisher ◽  
Teresa L. Thurston ◽  
...  
Keyword(s):  
Bacterial Infections ◽  
Macrophage Polarization ◽  
Physiological State ◽  
Innate Immune Responses ◽  
Macrophage Infection ◽  
Immune Defenses ◽  
Type 3 Secretion System ◽  
Type 3 ◽  
Inflammatory Macrophage

Many bacterial infections are hard to treat and tend to relapse, possibly due to the presence of antibiotic-tolerant persisters. In vitro, persister cells appear to be dormant. After uptake of Salmonella species by macrophages, nongrowing persisters also occur, but their physiological state is poorly understood. In this work, we show that Salmonella persisters arising during macrophage infection maintain a metabolically active state. Persisters reprogram macrophages by means of effectors secreted by the Salmonella pathogenicity island 2 type 3 secretion system. These effectors dampened proinflammatory innate immune responses and induced anti-inflammatory macrophage polarization. Such reprogramming allowed nongrowing Salmonella cells to survive for extended periods in their host. Persisters undermining host immune defenses might confer an advantage to the pathogen during relapse once antibiotic pressure is relieved.

scholarly journals Curative Treatment of Severe Gram-Negative Bacterial Infections by a New Class of Antibiotics Targeting LpxC

mBio ◽  
2017 ◽  
Vol 8 (4) ◽  
Author(s):  
Nadine Lemaître ◽  
Xiaofei Liang ◽  
Javaria Najeeb ◽  
Chul-Jin Lee ◽  
Marie Titecat ◽  
...  
Keyword(s):  
Bacterial Infections ◽  
Biosynthetic Pathway ◽  
Lipid A ◽  
Multidrug Resistant ◽  
Gram Negative Bacteria ◽  
Drug Resistant ◽  
Bubonic Plague ◽  
Gram Negative ◽  
New Class

ABSTRACT The infectious diseases caused by multidrug-resistant bacteria pose serious threats to humankind. It has been suggested that an antibiotic targeting LpxC of the lipid A biosynthetic pathway in Gram-negative bacteria is a promising strategy for curing Gram-negative bacterial infections. However, experimental proof of this concept is lacking. Here, we describe our discovery and characterization of a biphenylacetylene-based inhibitor of LpxC, an essential enzyme in the biosynthesis of the lipid A component of the outer membrane of Gram-negative bacteria. The compound LPC-069 has no known adverse effects in mice and is effective in vitro against a broad panel of Gram-negative clinical isolates, including several multiresistant and extremely drug-resistant strains involved in nosocomial infections. Furthermore, LPC-069 is curative in a murine model of one of the most severe human diseases, bubonic plague, which is caused by the Gram-negative bacterium Yersinia pestis. Our results demonstrate the safety and efficacy of LpxC inhibitors as a new class of antibiotic against fatal infections caused by extremely virulent pathogens. The present findings also highlight the potential of LpxC inhibitors for clinical development as therapeutics for infections caused by multidrug-resistant bacteria. IMPORTANCE The rapid spread of antimicrobial resistance among Gram-negative bacilli highlights the urgent need for new antibiotics. Here, we describe a new class of antibiotics lacking cross-resistance with conventional antibiotics. The compounds inhibit LpxC, a key enzyme in the lipid A biosynthetic pathway in Gram-negative bacteria, and are active in vitro against a broad panel of clinical isolates of Gram-negative bacilli involved in nosocomial and community infections. The present study also constitutes the first demonstration of the curative treatment of bubonic plague by a novel, broad-spectrum antibiotic targeting LpxC. Hence, the data highlight the therapeutic potential of LpxC inhibitors against a wide variety of Gram-negative bacterial infections, including the most severe ones caused by Y. pestis and by multidrug-resistant and extensively drug-resistant carbapenemase-producing strains. IMPORTANCE The rapid spread of antimicrobial resistance among Gram-negative bacilli highlights the urgent need for new antibiotics. Here, we describe a new class of antibiotics lacking cross-resistance with conventional antibiotics. The compounds inhibit LpxC, a key enzyme in the lipid A biosynthetic pathway in Gram-negative bacteria, and are active in vitro against a broad panel of clinical isolates of Gram-negative bacilli involved in nosocomial and community infections. The present study also constitutes the first demonstration of the curative treatment of bubonic plague by a novel, broad-spectrum antibiotic targeting LpxC. Hence, the data highlight the therapeutic potential of LpxC inhibitors against a wide variety of Gram-negative bacterial infections, including the most severe ones caused by Y. pestis and by multidrug-resistant and extensively drug-resistant carbapenemase-producing strains.

scholarly journals Activity of LCB01-0371, a Novel Oxazolidinone, against Mycobacterium abscessus

2017 ◽  
Vol 61 (9) ◽  
Author(s):  
Tae Sung Kim ◽  
Jin Ho Choe ◽  
Young Jae Kim ◽  
Chul-Su Yang ◽  
Hyun-Jin Kwon ◽  
...  
Keyword(s):  
Similar Efficacy ◽  
Mycobacterium Abscessus ◽  
Sequencing Analysis ◽  
Highly Pathogenic ◽  
Content Type ◽  
New Class ◽  
Nucleotide Insertion ◽  
Resistant Strains

ABSTRACT Mycobacterium abscessus is a highly pathogenic drug-resistant rapidly growing mycobacterium. In this study, we evaluated the in vitro, intracellular, and in vivo activities of LCB01-0371, a novel and safe oxazolidinone derivative, for the treatment of M. abscessus infection and compared its resistance to that of other oxazolidinone drugs. LCB01-0371 was effective against several M. abscessus strains in vitro and in a macrophage model of infection. In the murine model, a similar efficacy to linezolid was achieved, especially in the lungs. We induced laboratory-generated resistance to LCB01-0371; sequencing analysis revealed mutations in rplC of T424C and G419A and a nucleotide insertion at the 503 position. Furthermore, LCB01-0371 inhibited the growth of amikacin-, cefoxitin-, and clarithromycin-resistant strains. Collectively, our data indicate that LCB01-0371 might represent a promising new class of oxazolidinones with improved safety, which may replace linezolid for the treatment of M. abscessus.

scholarly journals High Levels of Intrinsic Tetracycline Resistance inMycobacterium abscessusAre Conferred by a Tetracycline-Modifying Monooxygenase

2018 ◽  
Vol 62 (6) ◽  
Author(s):  
Paulami Rudra ◽  
Kelley Hurst-Hess ◽  
Pascal Lappierre ◽  
Pallavi Ghosh
Keyword(s):  
Bacterial Infections ◽  
Efflux Pump ◽  
Tetracycline Resistance ◽  
Resistance Mechanisms ◽  
Mycobacterium Abscessus ◽  
Repeat Sequence ◽  
Content Type ◽  
High Level

ABSTRACTTetracyclines have been one of the most successful classes of antibiotics. However, its extensive use has led to the emergence of widespread drug resistance, resulting in discontinuation of use against several bacterial infections. Prominent resistance mechanisms include drug efflux and the use of ribosome protection proteins. Infrequently, tetracyclines can be inactivated by the TetX class of enzymes, also referred to as tetracycline destructases. Low levels of tolerance to tetracycline inMycobacterium smegmatisandMycobacterium tuberculosishave been previously attributed to the WhiB7-dependent TetV/Tap efflux pump. However,Mycobacterium abscessusis ∼500-fold more resistant to tetracycline thanM. smegmatisandM. tuberculosis. In this report, we show that this high level of resistance to tetracycline and doxycycline inM. abscessusis conferred by a WhiB7-independent tetracycline-inactivating monooxygenase, MabTetX (MAB_1496c). The presence of sublethal doses of tetracycline and doxycycline results in a >200-fold induction of MabTetX, and an isogenic deletion strain is highly sensitive to both antibiotics. Further, purified MabTetX can rapidly monooxygenate both antibiotics. We also demonstrate that expression of MabTetX is repressed by MabTetRx, by binding to an inverted repeat sequence upstream of MabTetRx; the presence of either antibiotic relieves this repression. Moreover, anhydrotetracycline (ATc) can effectively inhibit MabTetX activityin vitroand decreases the MICs of both tetracycline and doxycyclinein vivo. Finally, we show that tigecycline, a glycylcycline tetracycline, not only is a poor substrate of MabTetX but also is incapable of inducing the expression of MabTetX. This is therefore the first demonstration of a tetracycline-inactivating enzyme in mycobacteria. It (i) elucidates the mechanism of tetracycline resistance inM. abscessus, (ii) demonstrates the use of an inhibitor that can potentially reclaim the use of tetracycline and doxycycline, and (iii) identifies two sequential bottlenecks—MabTetX and MabTetRx—for acquiring resistance to tigecycline, thereby reiterating its use againstM. abscessus.

scholarly journals Epetraborole is Active against Mycobacterium abscessus

2021 ◽  
Author(s):  
Uday S. Ganapathy ◽  
Martin Gengenbacher ◽  
Thomas Dick
Keyword(s):  
Mouse Model ◽  
Lung Disease ◽  
Trna Synthetase ◽  
Mycobacterium Abscessus ◽  
Gram Negative ◽  
Lead Compounds ◽  
New Class ◽  
Mouse Model Of Infection ◽  
Clinical Candidate

Benzoxaboroles are a new class of leucyl-tRNA synthetase inhibitors. We recently reported that the antitubercular 4-halogenated benzoxaboroles are active against Mycobacterium abscessus . Here, we find that the non-halogenated benzoxaborole epetraborole, a clinical candidate developed for Gram negative infections, is also active against M. abscessus in vitro and in a mouse model of infection. This expands the repertoire of advanced lead compounds for the discovery of a benzoxaborole-based candidate to treat M. abscessus lung disease.

scholarly journals Lessons Learned From the First 10 Consecutive Cases of Intravenous Bacteriophage Therapy to Treat Multidrug-Resistant Bacterial Infections at a Single Center in the United States

2020 ◽  
Vol 7 (9) ◽  
Author(s):  
Saima Aslam ◽  
Elizabeth Lampley ◽  
Darcy Wooten ◽  
Maile Karris ◽  
Constance Benson ◽  
...  
Keyword(s):  
United States ◽  
Bacterial Infections ◽  
The United States ◽  
Multidrug Resistant ◽  
Mycobacterium Abscessus ◽  
Lessons Learned ◽  
Successful Outcome ◽  
Bacteriophage Therapy ◽  
Successful Case

Abstract Background Due to increasing multidrug-resistant (MDR) infections, there is an interest in assessing the use of bacteriophage therapy (BT) as an antibiotic alternative. After the first successful case of intravenous BT to treat a systemic MDR infection at our institution in 2017, the Center for Innovative Phage Applications and Therapeutics (IPATH) was created at the University of California, San Diego, in June 2018. Methods We reviewed IPATH consult requests from June 1, 2018, to April 30, 2020, and reviewed the regulatory process of initiating BT on a compassionate basis in the United States. We also reviewed outcomes of the first 10 cases at our center treated with intravenous BT (from April 1, 2017, onwards). Results Among 785 BT requests to IPATH, BT was administered to 17 of 119 patients in whom it was recommended. One-third of requests were for Pseudomonas aeruginosa, Staphylococcus aureus, and Mycobacterium abscessus. Intravenous BT was safe with a successful outcome in 7/10 antibiotic-recalcitrant infections at our center (6 were before IPATH). BT may be safely self-administered by outpatients, used for infection suppression/prophylaxis, and combined successfully with antibiotics despite antibiotic resistance, and phage resistance may be overcome with new phage(s). Failure occurred in 2 cases despite in vitro phage susceptibility. Conclusions We demonstrate the safety and feasibility of intravenous BT for a variety of infections and discuss practical considerations that will be critical for informing future clinical trials.

scholarly journals Genome-Wide Analysis of Cellular Response to Bacterial Genotoxin CdtB in Yeast

2007 ◽  
Vol 75 (3) ◽  
pp. 1393-1402 ◽  
Author(s):  
Takao Kitagawa ◽  
Hisashi Hoshida ◽  
Rinji Akada
Keyword(s):  
Cellular Response ◽  
Protein Translation ◽  
Strand Break ◽  
Dna Lesions ◽  
Yeast Cells ◽  
Reading Frame ◽  
Vesicular Traffic ◽  
Genome Wide ◽  
Repair Mechanisms

ABSTRACT The cytolethal distending toxins (CDTs) are secreted virulence proteins produced by several bacterial pathogens, and the subunit CdtB has the ability to create DNA lesions, primarily DNA single-strand breaks (SSBs) in vitro, and cause cell cycle arrest, cellular distension, and cell death in both mammalian and yeast cells. To elucidate the components of the mechanisms underlying the response to CdtB-induced DNA lesions, a CdtB expression plasmid was transformed into a series of diploid yeast strains harboring deletions in 4,708 nonessential genes. A total of 4,706 of these clones were successfully transformed, which we have now designated as a systematic transformation array (STA), and were subsequently screened. We identified 61 sensitive strains from the STA whose deleted genes can be categorized into a number of groups, including DNA metabolism, chromosome segregation, vesicular traffic, RNA catabolism, protein translation, morphogenesis, and nuclear transport, as well as one unknown open reading frame. However, only 28 of these strains were found to be sensitive to HO endonuclease, which is known to create a DNA double-strand break (DSB), suggesting that CdtB-induced DNA lesion is not similar to the direct DSB. Amazingly, CdtB expression elicits severe growth defects in haploid yeast cells, but only marginal defects in diploid yeast cells. The presence and absence of genes known to be involved in DNA repair in these genome-wide data reveal that CdtB-induced DNA damage is specifically repaired well in the diploid by homologous recombination but not by other repair mechanisms. Our present results provide insights into how CdtB pathogenesis is linked to eukaryotic cellular functions.

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